@article {pmid33452897, year = {2021}, author = {Dahl, MB and Peršoh, D and Jentsch, A and Kreyling, J}, title = {Root-Associated Mycobiomes of Common Temperate Plants (Calluna vulgaris and Holcus lanatus) Are Strongly Affected by Winter Climate Conditions.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33452897}, issn = {1432-184X}, support = {DFG JE 282/5-1//Deutsche Forschungsgemeinschaft/ ; RTG 2010//Deutsche Forschungsgemeinschaft/ ; }, abstract = {Winter temperatures are projected to increase in Central Europe. Subsequently, snow cover will decrease, leading to increased soil temperature variability, with potentially different consequences for soil frost depending on e.g. altitude. Here, we experimentally evaluated the effects of increased winter soil temperature variability on the root associated mycobiome of two plant species (Calluna vulgaris and Holcus lanatus) at two sites in Germany; a colder and wetter upland site with high snow accumulation and a warmer and drier lowland site, with low snow accumulation. Mesocosm monocultures were set-up in spring 2010 at both sites (with soil and plants originating from the lowland site). In the following winter, an experimental warming pulse treatment was initiated by overhead infrared heaters and warming wires at the soil surface for half of the mesocosms at both sites. At the lowland site, the warming treatment resulted in a reduced number of days with soil frost as well as increased the average daily temperature amplitude. Contrary, the treatment caused no changes in these parameters at the upland site, which was in general a much more frost affected site. Soil and plant roots were sampled before and after the following growing season (spring and autumn 2011). High-throughput sequencing was used for profiling of the root-associated fungal (ITS marker) community (mycobiome). Site was found to have a profound effect on the composition of the mycobiome, which at the upland site was dominated by fast growing saprotrophs (Mortierellomycota), and at the lowland site by plant species-specific symbionts (e.g. Rhizoscyphus ericae and Microdochium bolleyi for C. vulgaris and H. lanatus respectively). The transplantation to the colder upland site and the temperature treatment at the warmer lowland site had comparable consequences for the mycobiome, implying that winter climate change resulting in higher temperature variability has large consequences for mycobiome structures regardless of absolute temperature of a given site.}, }
@article {pmid33452896, year = {2021}, author = {Bergo, NM and Bendia, AG and Ferreira, JCN and Murton, BJ and Brandini, FP and Pellizari, VH}, title = {Microbial Diversity of Deep-Sea Ferromanganese Crust Field in the Rio Grande Rise, Southwestern Atlantic Ocean.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33452896}, issn = {1432-184X}, support = {14/50820-7//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; }, abstract = {Seamounts are often covered with Fe and Mn oxides, known as ferromanganese (Fe-Mn) crusts. Future mining of these crusts is predicted to have significant effects on biodiversity in mined areas. Although microorganisms have been reported on Fe-Mn crusts, little is known about the role of crusts in shaping microbial communities. Here, we investigated microbial communities based on 16S rRNA gene sequences retrieved from Fe-Mn crusts, coral skeleton, calcarenite, and biofilm at crusts of the Rio Grande Rise (RGR). RGR is a prominent topographic feature in the deep southwestern Atlantic Ocean with Fe-Mn crusts. Our results revealed that crust field of the RGR harbors a usual deep-sea microbiome. No differences were observed on microbial community diversity among Fe-Mn substrates. Bacterial and archaeal groups related to oxidation of nitrogen compounds, such as Nitrospirae, Nitrospinae phyla, Candidatus Nitrosopumilus within Thaumarchaeota group, were present on those substrates. Additionally, we detected abundant assemblages belonging to methane oxidation, i.e., Methylomirabilales (NC10) and SAR324 (Deltaproteobacteria). The chemolithoautotrophs associated with ammonia-oxidizing archaea and nitrite-oxidizing bacteria potentially play an important role as primary producers in the Fe-Mn substrates from RGR. These results provide the first insights into the microbial diversity and potential ecological processes in Fe-Mn substrates from the Atlantic Ocean. This may also support draft regulations for deep-sea mining in the region.}, }
@article {pmid33452613, year = {2021}, author = {Vingiani, GM and Gasulla, F and Barón-Sola, Á and Sobrino-Plata, J and Henández, LE and Casano, LM}, title = {Physiological and Molecular Alterations of Phycobionts of Genus Trebouxia and Coccomyxa Exposed to Cadmium.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33452613}, issn = {1432-184X}, support = {CGL2016- 80259-P//Ministerio de Ciencia, Innovación y Universidades/ ; AGL2014-53771-R//Ministerio de Ciencia, Innovación y Universidades/ ; AGL2017-87591-R//Ministerio de Ciencia, Innovación y Universidades/ ; }, abstract = {Several studies on aeroterrestrial microalgae are unravelling their resistance mechanisms to different abiotic stressors, including hazardous metals, pointing to their future role as bioremediation microorganisms. In the present study, physiological and molecular alterations of four phycobionts of genus Trebouxia (T. TR1 and T. TR9) and Coccomyxa (C. subellipsoidea and C. simplex) exposed to Cd were studied. Cd accumulation and subcellular distribution, cell wall structure, production of biothiols (GSH and phytochelatins), reactive oxygen species (ROS) formation, expression of key antioxidant genes and ROS-related enzymes were evaluated to determine the physiological differences among the four microalgae, with the aim to identify the most suitable microorganism for further biotechnological applications. After 7 days of Cd exposure, Coccomyxa algae showed higher capacity of Cd intake than Trebouxia species, with C. subellipsoidea being the highest Cd accumulator at both intracellular and, especially, cell wall level. Cd induced ROS formation in the four microalgae, but to a greater extent in both Coccomyxa algae. Trebouxia TR9 showed the lowest Cd-dependent oxidative stress probably due to glutathione reductase induction. All microalgae synthetized phytochelatins in response to Cd but in a species-specific and a dose-dependent manner. Results from this study agree with the notion that each microalga has evolved a distinct strategy to detoxify hazardous metals like Cd and to cope with oxidative stress associated with them. Coccomyxa subellipsoidea and Trebouxia TR9 appear as the most interesting candidates for further applications.}, }
@article {pmid33218996, year = {2021}, author = {Hansen, ML and He, Z and Wibowo, M and Jelsbak, L}, title = {A Whole-Cell Biosensor for Detection of 2,4-Diacetylphloroglucinol (DAPG)-Producing Bacteria from Grassland Soil.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {3}, pages = {}, pmid = {33218996}, issn = {1098-5336}, abstract = {Fluorescent Pseudomonas spp. producing the antibiotic 2,4-diacetylphloroglucinol (DAPG) are ecologically important in the rhizosphere, as they can control phytopathogens and contribute to disease suppression. DAPG can also trigger a systemic resistance response in plants and stimulate root exudation and branching as well as induce plant-beneficial activities in other rhizobacteria. While studies of DAPG-producing Pseudomonas have predominantly focused on rhizosphere niches, the ecological role of DAPG as well as the distribution and dynamics of DAPG-producing bacteria remains less well understood for other environments, such as bulk soil and grassland, where the level of DAPG producers are predicted to be low. In this study, we constructed a whole-cell biosensor for detection of DAPG and DAPG-producing bacteria from environmental samples. The constructed biosensor contains a phlF response module and either lacZ or lux genes as output modules assembled on a pSEVA plasmid backbone for easy transfer to different host species and to enable easy future genetic modifications. We show that the sensor is highly specific toward DAPG, with a sensitivity in the low nanomolar range (>20 nM). This sensitivity is comparable to the DAPG levels identified in rhizosphere samples by chemical analysis. The biosensor enables guided isolation of DAPG-producing Pseudomonas Using the biosensor, we probed the same grassland soil sampling site to isolate genetically related DAPG-producing Pseudomonas kilonensis strains over a period of 12 months. Next, we used the biosensor to determine the frequency of DAPG-producing pseudomonads within three different grassland soil sites and showed that DAPG producers can constitute part of the Pseudomonas population in the range of 0.35 to 17% at these sites. Finally, we showed that the biosensor enables detection of DAPG produced by non-Pseudomonas species. Our study shows that a whole-cell biosensor for DAPG detection can facilitate isolation of bacteria that produce this important secondary metabolite and provide insight into the population dynamics of DAPG producers in natural grassland soil.IMPORTANCE The interest in bacterial biocontrol agents as biosustainable alternatives to pesticides to increase crop yields has grown. To date, we have a broad knowledge of antimicrobial compounds, such as DAPG, produced by bacteria growing in the rhizosphere surrounding plant roots. However, compared to the rhizosphere niches, the ecological role of DAPG as well as the distribution and dynamics of DAPG-producing bacteria remains less well understood for other environments, such as bulk and grassland soil. Currently, we are restricted to chemical methods with detection limits and time-consuming PCR-based and probe hybridization approaches to detect DAPG and its respective producer. In this study, we developed a whole-cell biosensor, which can circumvent the labor-intensive screening process as well as increase the sensitivity at which DAPG can be detected. This enables quantification of relative amounts of DAPG producers, which, in turn, increases our understanding of the dynamics and ecology of these producers in natural soil environments.}, }
@article {pmid33188000, year = {2021}, author = {Coe, GL and Pinkham, NV and Celis, AI and Johnson, C and DuBois, JL and Walk, ST}, title = {Dynamic Gut Microbiome Changes in Response to Low-Iron Challenge.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {3}, pages = {}, pmid = {33188000}, issn = {1098-5336}, support = {R01 GM086755/GM/NIGMS NIH HHS/United States ; R21 DK114607/DK/NIDDK NIH HHS/United States ; R35 GM136390/GM/NIGMS NIH HHS/United States ; }, abstract = {Iron is an essential micronutrient for life. In mammals, dietary iron is absorbed primarily in the small intestine. Currently, the impacts of dietary iron on the taxonomic structure and function of the gut microbiome and reciprocal effects on the animal host are not well understood. Here, we establish a mouse model of low-iron challenge in which intestinal biomarkers and reduced fecal iron reveal iron stress while serum iron and mouse behavioral markers indicate maintenance of iron homeostasis. We show that the diversity of the gut microbiome in conventional C57BL/6 mice changes dramatically during 2 weeks on a low-iron diet. We also show the effects of a low-iron diet on microbiome diversity are long lasting and not easily recovered when iron is returned to the diet. Finally, after optimizing taxon association methods, we show that some bacteria are unable to fully recover after the low-iron challenge and appear to be extirpated from the gut entirely. In particular, operational taxonomic units (OTUs) from the Prevotellaceae and Porphyromonadaceae families and Bacteroidales order are highly sensitive to low-iron conditions, while other seemingly insensitive OTUs recover. These results provide new insights into the iron requirements of gut microbiome members and add to the growing understanding of mammalian iron cycling.IMPORTANCE All cells need iron. Both too much and too little iron lead to diseases and unwanted outcomes. Although the impact of dietary iron on human cells and tissues has been well studied, there is currently a lack of understanding about how different levels of iron influence the abundant and diverse members of the human microbiome. This study develops a well-characterized mouse model for studying low-iron levels and identifies key groups of bacteria that are most affected. We found that the microbiome undergoes large changes when iron is removed from the diet but that many individual bacteria are able to rebound when iron levels are changed back to normal. That said, a select few members, referred to as iron-sensitive bacteria, seem to be lost. This study begins to identify individual members of the mammalian microbiome most affected by changes in dietary iron levels.}, }
@article {pmid33449130, year = {2021}, author = {Zai, X and Luo, W and Bai, W and Li, Y and Xiao, X and Gao, X and Wang, E and Wei, G and Chen, W}, title = {Effect of Root Diameter on the Selection and Network Interactions of Root-Associated Bacterial Microbiomes in Robinia pseudoacacia L.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33449130}, issn = {1432-184X}, support = {31870476//the National Natural Science Foundation of China/ ; 41830755//the National Natural Science Foundation of China/ ; }, abstract = {The high plasticity of root morphology, physiology, and function influences root-associated microbiomes. However, the variation in root-associated microbiome diversity and structures in response to root diameter at different root depths remains poorly understood. Here, we selected black locust (Robinia pseudoacacia L.) as a model plant to investigate the selection and network interactions of rhizospheric and root endophytic bacterial microbiomes associated with roots of different diameters (1, 1-2, and > 2 mm) among root depths of 0-100 cm via the Illumina sequencing of the 16S rRNA gene. The results showed that the alpha diversity of the root-associated bacterial communities decreased with increasing root diameters among different root depths; fewer orders with higher relative abundance, especially in the endosphere, were enriched in association with coarse roots (> 2 mm) than fine roots among root depths. Furthermore, the variation in the enriched bacterial orders associated with different root diameters was explained by bulk soil properties. Higher co-occurrence network complexity and stability emerged in the rhizosphere microbiomes of fine roots than those of coarse roots, in contrast to the situation in the endosphere microbiomes. In particular, the endosphere of roots with a diameter of 1-2 mm exhibited the lowest network complexity and stability and a high proportion of keystone taxa (e.g., Cytophagia, Flavobacteriia, Sphingobacteriia, β-Proteobacteria, and γ-Proteobacteria), suggesting a keystone taxon-reliant strategy in this transitional stage. In summary, this study indicated that root diameter at different root depths differentially affects rhizospheric and endophytic bacterial communities, which implies a close relationship between the bacterial microbiome, root function, and soil properties.}, }
@article {pmid33448446, year = {2020}, author = {Moraes, LC and Lang, PM and Arcanjo, RA and Rampelotto, PH and Fatturi-Parolo, CC and Ferreira, MBC and Montagner, F}, title = {Microbial ecology and predicted metabolic pathways in various oral environments from patients with acute endodontic infections.}, journal = {International endodontic journal}, volume = {53}, number = {12}, pages = {1603-1617}, doi = {10.1111/iej.13389}, pmid = {33448446}, issn = {1365-2591}, support = {//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; //Fundação de Amparo à Pesquisa do Estado do Rio Grande do Sul/ ; }, abstract = {AIM: To assess in a cross-sectional clinical study the effect of antibiotics on the diversity, structure and metabolic pathways of bacterial communities in various oral environments in patients with acute primary infections.<br><br>METHODOLOGY: Samples of saliva (SA), supragingival biofilm (SB) and from the pulp cavity (PC) were collected from teeth with acute primary infections and then grouped according to previous use of antibiotics (NoAtb = no antibiotics [n = 6]; Atb = antibiotics [n = 6]). DNA sequencing was conducted using MiSeq (Illumina, San Diego, CA, USA). The V1-V3 hyper-variable region of the 16S rRNA gene was amplified. A custom Mothur pipeline was used for 16S rRNA processing. Subsequent analyses of the sequence dataset were performed in R (using vegan, phyloseq and ggplot2 packages) or QIIME.<br><br>RESULTS: Twelve patients aged from 22 to 56 years were recruited. Participants in the Atb group had taken the beta-lactamics amoxicillin (5/6) or cephalexin (1/6) for 2-3 days. A total of 332 bacterial taxa (OTUs) were identified, belonging to 120 genera, 60 families and nine phyla. Firmicutes (41%) and Bacteroidetes (38%) were the most abundant phyla in all samples. Taxa clustered significantly by oral site (PCoA analysis; P < 0.05, ANOSIM). Use of antibiotics had little effect on this clustering. However, SA, SB and PC had different degrees of richness, diversity and evenness. The greatest diversity was observed in SB samples and the least diversity was observed in PC samples. Metabolic prediction identified 163 pathways and previous use of antibiotics had a major effect on the estimated functional clustering in SA and PC samples.<br><br>CONCLUSION: The ecological niche had a strong influence on the bacterial content of samples from various oral sites. Previous exposure to antibiotics may exert an effect on the phylogenetic composition of SA. Metabolic pathways appear to be modulated by antimicrobial agents in SA and PC samples. The dynamics of host/microbial interactions in the apical region and the functional ecology of the infected pulp cavity should be revisited.}, }
@article {pmid33447808, year = {2020}, author = {Lories, B and Belpaire, TER and Yssel, A and Ramon, H and Steenackers, HP}, title = {Agaric acid reduces Salmonella biofilm formation by inhibiting flagellar motility.}, journal = {Biofilm}, volume = {2}, number = {}, pages = {100022}, doi = {10.1016/j.bioflm.2020.100022}, pmid = {33447808}, issn = {2590-2075}, abstract = {Salmonella biofilms are a common cause of contaminations in the food or feed industry. In a screening for novel compounds to combat biofilm-associated foodborne outbreaks, we identified agaric acid as a Salmonella Typhimurium biofilm inhibitor that does not affect planktonic growth. Importantly, the remaining biofilm cells after preventive treatment with agaric acid were significantly more sensitive to the common disinfectant hydrogen peroxide. Screening of a GFP-promoter fusion library of biofilm related genes revealed that agaric acid downregulates the transcription of genes responsible for flagellar motility. Concurrently, swimming motility was completely abrogated in the presence of agaric acid, indicating that biofilm inhibition occurs via interference with the motility phenotype. Moreover, agaric acid also reduced biofilm formation of Pseudomonas aeruginosa, Staphylococcus aureus and Escherichia coli. Agaric acid thus shows potential as an anti-virulence compound that inhibits both motility and biofilm formation.}, }
@article {pmid33447802, year = {2020}, author = {Payne, AT and Davidson, AJ and Kan, J and Peipoch, M and Bier, R and Williamson, K}, title = {Widespread cryptic viral infections in lotic biofilms.}, journal = {Biofilm}, volume = {2}, number = {}, pages = {100016}, doi = {10.1016/j.bioflm.2019.100016}, pmid = {33447802}, issn = {2590-2075}, abstract = {Viruses have important impacts on aquatic microbial ecology and have been studied at length in the global ocean. However, the roles of bacteriophages in lotic ecosystems, particularly in benthic biofilms, have been largely under-studied. The main goals of this work were to determine whether viruses are consistent members of natural benthic biofilm communities of freshwater streams; whether temperate phages are present and active in such biofilms; and whether community profiling approaches like RAPD-PCR can be adapted to characterize biofilm virus communities. Results from both field and laboratory experiments suggest that viruses are consistent members of lotic biofilm communities. Interestingly, prophage induction was statistically significant but only a small percentage of the total bacterial population appeared to harbor prophage or engaged in induction. Finally, while the use of RAPD-PCR for the community level profiling of biofilm viral communities suggests temporal change in response to biofilm maturity, further refinements are required for broad-scale quantitative application.}, }
@article {pmid33446998, year = {2020}, author = {Li, M and Shao, D and Zhou, J and Gu, J and Qin, J and Chen, W and Wei, W}, title = {Signatures within esophageal microbiota with progression of esophageal squamous cell carcinoma.}, journal = {Chinese journal of cancer research = Chung-kuo yen cheng yen chiu}, volume = {32}, number = {6}, pages = {755-767}, doi = {10.21147/j.issn.1000-9604.2020.06.09}, pmid = {33446998}, issn = {1000-9604}, abstract = {Objective: Esophageal squamous cell carcinoma (ESCC) is one of the dominant malignances worldwide, but currently there is less focus on the microbiota with ESCC and its precancerous lesions.<br><br>Methods: Paired esophageal biopsy and swab specimens were obtained from 236 participants in Linzhou, China. Data from 16S ribosomal RNA gene sequencing were processed using quantitative insights into microbial ecology (QIIME2) and R Studio to evaluate differences. The Wilcoxon rank sum test and Kruskal-Wallis rank sum test were used to compare diversity and characteristic genera by specimens and participant groups. Ordinal logistic regression model was used to build microbiol prediction model.<br><br>Results: Microbial diversity was similar between biopsy and swab specimens, including operational taxonomic unit (OTU) numbers and Shannon index. There were variations and similarities of esophageal microbiota among different pathological characteristics of ESCC. Top 10 relative abundance genera in all groups include Streptococcus, Prevotella, Veillonella, Actinobacillus, Haemophilus, Neisseria, Alloprevotella, Rothia, Gemella and Porphyromonas. Genus Streptococcus, Haemophilus, Neisseria and Porphyromonas showed significantly difference in disease groups when compared to normal control, whereas Streptococcus showed an increasing tendency with the progression of ESCC and others showed a decreasing tendency. About models based on all combinations of characteristic genera, only taken Streptococcus and Neisseria into model, the prediction performance was the ideal one, of which the area under the curve (AUC) was 0.738.<br><br>Conclusions: Esophageal biopsy and swab specimens could yield similar microbial characterization. The combination of Streptococcus and Neisseria has the potential to predict the progression of ESCC, which is needed to confirm by large-scale, prospective cohort studies.}, }
@article {pmid33446818, year = {2021}, author = {McGill, SL and Yung, Y and Hunt, KA and Henson, MA and Hanley, L and Carlson, RP}, title = {Pseudomonas aeruginosa reverse diauxie is a multidimensional, optimized, resource utilization strategy.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {1457}, pmid = {33446818}, issn = {2045-2322}, support = {U01EB019416/NH/NIH HHS/United States ; W911NF-16-1-0463//Army Research Office/ ; }, abstract = {Pseudomonas aeruginosa is a globally-distributed bacterium often found in medical infections. The opportunistic pathogen uses a different, carbon catabolite repression (CCR) strategy than many, model microorganisms. It does not utilize a classic diauxie phenotype, nor does it follow common systems biology assumptions including preferential consumption of glucose with an 'overflow' metabolism. Despite these contradictions, P. aeruginosa is competitive in many, disparate environments underscoring knowledge gaps in microbial ecology and systems biology. Physiological, omics, and in silico analyses were used to quantify the P. aeruginosa CCR strategy known as 'reverse diauxie'. An ecological basis of reverse diauxie was identified using a genome-scale, metabolic model interrogated with in vitro omics data. Reverse diauxie preference for lower energy, nonfermentable carbon sources, such as acetate or succinate over glucose, was predicted using a multidimensional strategy which minimized resource investment into central metabolism while completely oxidizing substrates. Application of a common, in silico optimization criterion, which maximizes growth rate, did not predict the reverse diauxie phenotypes. This study quantifies P. aeruginosa metabolic strategies foundational to its wide distribution and virulence including its potentially, mutualistic interactions with microorganisms found commonly in the environment and in medical infections.}, }
@article {pmid33446769, year = {2021}, author = {Berger, C and Rückert, C and Blom, J and Rabaey, K and Kalinowski, J and Rosenbaum, MA}, title = {Estimation of pathogenic potential of an environmental Pseudomonas aeruginosa isolate using comparative genomics.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {1370}, pmid = {33446769}, issn = {2045-2322}, support = {AG156/1-1//Deutsche Forschungsgemeinschaft/ ; AG156/1-1//Deutsche Forschungsgemeinschaft/ ; }, abstract = {The isolation and sequencing of new strains of Pseudomonas aeruginosa created an extensive dataset of closed genomes. Many of the publicly available genomes are only used in their original publication while additional in silico information, based on comparison to previously published genomes, is not being explored. In this study, we defined and investigated the genome of the environmental isolate P. aeruginosa KRP1 and compared it to more than 100 publicly available closed P. aeruginosa genomes. By using different genomic island prediction programs, we could identify a total of 17 genomic islands and 8 genomic islets, marking the majority of the accessory genome that covers ~ 12% of the total genome. Based on intra-strain comparisons, we are able to predict the pathogenic potential of this environmental isolate. It shares a substantial amount of genomic information with the highly virulent PSE9 and LESB58 strains. For both of these, the increased virulence has been directly linked to their accessory genome before. Hence, the integrated use of previously published data can help to minimize expensive and time consuming wetlab work to determine the pathogenetic potential.}, }
@article {pmid33445025, year = {2021}, author = {González-Martínez, A and Muñoz-Palazon, B and Kruglova, A and Vilpanen, M and Kuokkanen, A and Mikola, A and Heinonen, M}, title = {Performance and microbial community structure of a full-scale ANITATMMox bioreactor for treating reject water located in Finland.}, journal = {Chemosphere}, volume = {271}, number = {}, pages = {129526}, doi = {10.1016/j.chemosphere.2020.129526}, pmid = {33445025}, issn = {1879-1298}, abstract = {The aim of this work was to study the operational performance and the microbial community dynamics during the start-up of ANITATMMox technology implemented at full-scale wastewater treatment plant in Finland to treat reject water from anaerobic digesters. The average ammonium removal in the studied setup reached around 90%, withstanding ammonium loads up to 0.13 g N m-2h-1. The nitrite concentration in the effluent did not exceed 10 mg L-1, and there was a slight accumulation of NO3--N during the operation which was controlled. Thus, the result showed a robust success to high ammonium loading in presence of organic matter. The sequencing showed a heterogeneous microbial population where Methanosaeta, WCHA1-57 genus, Sphingobacteriia, Chlorobia and diverse unknown fungi were found as dominant phylotypes. Moreover, members of the Brocadiaceae family were dominant in the adhered biomass, mostly represented by Candidatus Scalindua, rarely reported in WWTPs. Overall, the results demonstrated a drastic effect of region-specific operational conditions on carrier biofilm microbial communities as it was demonstrated by the microbial studies.}, }
@article {pmid33444853, year = {2020}, author = {Yang, Y and Herbold, CW and Jung, MY and Qin, W and Cai, M and Du, H and Lin, JG and Li, X and Li, M and Gu, JD}, title = {Survival strategies of ammonia-oxidizing archaea (AOA) in a full-scale WWTP treating mixed landfill leachate containing copper ions and operating at low-intensity of aeration.}, journal = {Water research}, volume = {191}, number = {}, pages = {116798}, doi = {10.1016/j.watres.2020.116798}, pmid = {33444853}, issn = {1879-2448}, abstract = {Recent studies indicate that ammonia-oxidizing archaea (AOA) may play an important role in nitrogen removal by wastewater treatment plants (WWTPs). However, our knowledge of the mechanisms employed by AOA for growth and survival in full-scale WWTPs is still limited. Here, metagenomic and metatranscriptomic analyses combined with a laboratory cultivation experiment revealed that three active AOAs (WS9, WS192, and WS208) belonging to family Nitrososphaeraceae were active in the deep oxidation ditch (DOD) of a full-scale WWTP treating landfill leachate, which is configured with three continuous aerobic-anoxic (OA) modules with low-intensity aeration (≤ 1.5 mg/L). AOA coexisted with AOB and complete ammonia oxidizers (Comammox), while the ammonia-oxidizing microbial (AOM) community was unexpectedly dominated by the novel AOA strain WS9. The low aeration, long retention time, and relatively high inputs of ammonium and copper might be responsible for the survival of AOA over AOB and Comammox, while the dominance of WS9, specifically may be enhanced by substrate preference and uniquely encoded retention strategies. The urease-negative WS9 is specifically adapted for ammonia acquisition as evidenced by the high expression of an ammonium transporter, whereas two metabolically versatile urease-positive AOA strains (WS192 and WS208) can likely supplement ammonia needs with urea. This study provides important information for the survival and application of the eutrophic Nitrososphaeraceae AOA and advances our understanding of archaea-dominated ammonia oxidation in a full-scale wastewater treatment system.}, }
@article {pmid33444433, year = {2021}, author = {Kerkhof, LJ}, title = {Is oxford nanopore sequencing ready for analyzing complex microbiomes?.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiab001}, pmid = {33444433}, issn = {1574-6941}, abstract = {This minireview will discuss the improvements in Oxford Nanopore sequencing technology which make the MinION a viable platform for microbial ecology studies. Specific issues being addressed are the increase in sequence accuracy from 65-96.5% during the last 5 years, the ability to obtain a quantifiable/predictive signal from the MinION with respect to target molecule abundance, simple-to-use GUI-based pathways for data analysis, and the modest additional equipment needs for sequencing in the field. Coupling these recent improvements with the low capital costs for equipment and the reasonable per sample cost makes MinION sequencing an attractive option for virtually any laboratory.}, }
@article {pmid33443587, year = {2021}, author = {Hugoni, M and Nunan, N and Thioulouse, J and Dubost, A and Abrouk, D and Martins, JMF and Goffner, D and Prigent-Combaret, C and Grundmann, G}, title = {Small-Scale Variability in Bacterial Community Structure in Different Soil Types.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33443587}, issn = {1432-184X}, support = {779949//EC2CO MicrobiEn/ ; ANR-11-LABX-0010//LabEx Chimie des Systèmes Complexes (FR)/ ; }, abstract = {Microbial spatial distribution has mostly been studied at field to global scales (i.e., ecosystem scales). However, the spatial organization at small scales (i.e., centimeter to millimeter scales), which can help improve our understanding of the impacts of spatial communities structure on microbial functioning, has received comparatively little attention. Previous work has shown that small-scale spatial structure exists in soil microbial communities, but these studies have not compared soils from geographically distant locations, nor have they utilized community ecology approaches, such as the core and satellite hypothesis and/or abundance-occupancy relationships, often used in macro-ecology, to improve the description of the spatial organization of communities. In the present work, we focused on bacterial diversity (i.e., 16S rRNA gene sequencing) occurring in micro-samples from a variety of locations with different pedo-climatic histories (i.e., from semi-arid, alpine, and temperate climates) and physicochemical properties. The forms of ecological spatial relationships in bacterial communities (i.e., occupancy-frequency and abundance-occupancy) and taxa distributions (i.e., habitat generalists and specialists) were investigated. The results showed that bacterial composition differed in the four soils at the small scale. Moreover, one soil presented a satellite mode distribution, whereas the three others presented bimodal distributions. Interestingly, numerous core taxa were present in the four soils among which 8 OTUs were common to the four sites. These results confirm that analyses of the small-scale spatial distribution are necessary to understand consequent functional processes taking place in soils, affecting thus ecosystem functioning.}, }
@article {pmid33442763, year = {2021}, author = {Mutnale, MC and Reddy, GS and Vasudevan, K}, title = {Bacterial Community in the Skin Microbiome of Frogs in a Coldspot of Chytridiomycosis Infection.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33442763}, issn = {1432-184X}, support = {BSC0207//Council of Scientific and Industrial Research, India/ ; }, abstract = {Chytridiomycosis is a fungal disease caused by the pathogens, Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal), which has caused declines in amphibian populations worldwide. Asia is considered as a coldspot of infection, since adult frogs are less susceptible to Bd-induced mortality or morbidity. Using the next-generation sequencing approach, we assessed the cutaneous bacterial community composition and presence of anti-Bd bacteria in six frog species from India using DNA isolated from skin swabs. All the six frog species sampled were tested using nested PCR and found Bd negative. We found a total of 551 OTUs on frog skin, of which the bacterial phyla such as Proteobacteria (56.15% average relative abundance) was dominated followed by Actinobacteria (21.98% average relative abundance) and Firmicutes (13.7% average relative abundance). The contribution of Proteobacteria in the anti-Bd community was highest and represented by 175 OTUs. Overall, the anti-Bd bacterial community dominated (51.7% anti-Bd OTUs) the skin microbiome of the frogs. The study highlights the putative role of frog skin microbiome in affording resistance to Bd infections in coldspots of infection.}, }
@article {pmid33442762, year = {2021}, author = {Qin, Y and Puppe, D and Zhang, L and Sun, R and Li, P and Xie, S}, title = {How Does Sphagnum Growing Affect Testate Amoeba Communities and Corresponding Protozoic Si Pools? Results from Field Analyses in SW China.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33442762}, issn = {1432-184X}, abstract = {The policy and practice of ecological restoration and conservation in China obtained some remarkable results. For example, Sphagnum moss growing on abandoned farmland, which was peatland before agricultural use, has rapidly expanded the wetland area in SW China. Microorganisms such as testate amoebae are sensitive to environmental change and thus have been widely used as ecological indicators in various habitats. We analyzed differently aged Sphagnum growing plots on a Sphagnum growing farmland and natural Sphagnum plots in SW China to examine how Sphagnum-dwelling testate amoeba communities and corresponding protozoic silicon (Si) pools respond to ecological restoration practice. We found that abundance, taxon richness, and diversity of testate amoebae were higher in Sphagnum growing farmland plots compared to natural Sphagnum plots. Protozoic Si pools showed an increase with Sphagnum growing time representing increased Si accumulation by idiosomic testate amoeba shells. However, protozoic Si pools were negatively correlated with taxon richness and diversity of testate amoebae. Our results showed that (i) natural Sphagnum plots were not characterized by the expected higher biodiversity of testate amoebae compared to Sphagnum growing plots and (ii) consequently protozoic Si pool quantity in natural Sphagnum plots was less driven by biodiversity of testate amoebae than expected. We concluded our results to underline the value of (i) environmental restoration policy in general and (ii) testate amoeba communities and corresponding protozoic Si pools for Si cycling in restoration areas of peatlands in particular. Based on our results, we recommend a sustainable cultivation of Sphagnum moss and an additional establishment of protected areas, where no Sphagnum harvesting occurs. These protected Sphagnum areas might represent hot spots of undisturbed testate amoeba communities and corresponding protozoic Si pools and thus of microbial Si cycling.}, }
@article {pmid33441489, year = {2021}, author = {Fritts, RK and McCully, AL and McKinlay, JB}, title = {Extracellular Metabolism Sets the Table for Microbial Cross-Feeding.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {85}, number = {1}, pages = {}, pmid = {33441489}, issn = {1098-5557}, abstract = {SUMMARYThe transfer of nutrients between cells, or cross-feeding, is a ubiquitous feature of microbial communities with emergent properties that influence our health and orchestrate global biogeochemical cycles. Cross-feeding inevitably involves the externalization of molecules. Some of these molecules directly serve as cross-fed nutrients, while others can facilitate cross-feeding. Altogether, externalized molecules that promote cross-feeding are diverse in structure, ranging from small molecules to macromolecules. The functions of these molecules are equally diverse, encompassing waste products, enzymes, toxins, signaling molecules, biofilm components, and nutrients of high value to most microbes, including the producer cell. As diverse as the externalized and transferred molecules are the cross-feeding relationships that can be derived from them. Many cross-feeding relationships can be summarized as cooperative but are also subject to exploitation. Even those relationships that appear to be cooperative exhibit some level of competition between partners. In this review, we summarize the major types of actively secreted, passively excreted, and directly transferred molecules that either form the basis of cross-feeding relationships or facilitate them. Drawing on examples from both natural and synthetic communities, we explore how the interplay between microbial physiology, environmental parameters, and the diverse functional attributes of extracellular molecules can influence cross-feeding dynamics. Though microbial cross-feeding interactions represent a burgeoning field of interest, we may have only begun to scratch the surface.}, }
@article {pmid33441406, year = {2021}, author = {Hu, J and Jin, VL and Konkel, JYM and Schaeffer, SM and Schneider, LG and DeBruyn, JM}, title = {Soil Health Management Enhances Microbial Nitrogen Cycling Capacity and Activity.}, journal = {mSphere}, volume = {6}, number = {1}, pages = {}, pmid = {33441406}, issn = {2379-5042}, abstract = {Soil microbial transformations of nitrogen (N) can be affected by soil health management practices. Here, we report in situ seasonal dynamics of the population size (gene copy abundances) and functional activity (transcript copy abundances) of five bacterial genes involved in soil N cycling (ammonia-oxidizing bacteria [AOB] amoA, nifH, nirK, nirS, and nosZ) in a long-term continuous cotton production system under different management practices (cover crops, tillage, and inorganic N fertilization). Hairy vetch (Vicia villosa Roth), a leguminous cover crop, most effectively promoted the expression of N cycle genes, which persisted after cover crop termination throughout the growing season. Moreover, we observed similarly high or even higher N cycle gene transcript abundances under vetch with no fertilizer as no cover crop with N fertilization throughout the cover crop peak and cotton growing seasons (April, May, and October). Further, both the gene and transcript abundances of amoA and nosZ were positively correlated to soil nitrous oxide (N2O) emissions. We also found that the abundances of amoA genes and transcripts both positively correlated to field and incubated net nitrification rates. Together, our results revealed relationships between microbial functional capacity and activity and in situ soil N transformations under different agricultural seasons and soil management practices.IMPORTANCE Conservation agriculture practices that promote soil health have distinct and lasting effects on microbial populations involved with soil nitrogen (N) cycling. In particular, using a leguminous winter cover crop (hairy vetch) promoted the expression of key functional genes involved in soil N cycling, equaling or exceeding the effects of inorganic N fertilizer. Hairy vetch also left a legacy on soil nutrient capacity by promoting the continued activity of N cycling microbes after cover crop termination and into the main growing season. By examining both genes and transcripts involved in soil N cycling, we showed different responses of functional capacity (i.e., gene abundances) and functional activity (i.e., transcript abundances) to agricultural seasons and management practices, adding to our understanding of the effects of soil health management practices on microbial ecology.}, }
@article {pmid33440279, year = {2021}, author = {Zhong, Q and Cruz-Paredes, C and Zhang, S and Rousk, J}, title = {Can heavy metal pollution induce bacterial resistance to heavy metals and antibiotics in soils from an ancient land-mine?.}, journal = {Journal of hazardous materials}, volume = {411}, number = {}, pages = {124962}, doi = {10.1016/j.jhazmat.2020.124962}, pmid = {33440279}, issn = {1873-3336}, abstract = {Microbial resistance to antibiotics is a growing challenge to human health. Recent evidence has indicated that antibiotic resistance can be co-selected for by exposure to heavy metals in agricultural soils. It remains unknown if this is a concern in other environments contaminated by metals. We here investigated soil microbial activities, composition and tolerance to heavy metals and antibiotics in a mining soil survey. We found that microbial respiration, growth, and biomass were affected by available metal concentrations. Most of the variation in microbial PLFA composition was explained by differences in heavy metal and pH. Additionally, pollution-induced bacterial community tolerance to toxicants including Cu, Pb, Zn, tetracycline and vancomycin was determined. Although only bacterial tolerance to Pb increased with higher levels of metals, the links between bacterial metal tolerance and soil metal concentrations were clear when considered together with previously published reports, suggesting that bacterial metal tolerance were universally elevated in the surveyed soils. The induced levels of heavy metal tolerance coincided with elevated levels of tolerance to vancomycin, but not to tetracycline. Our study showed that heavy metals can co-select for resistance to clinically important antibiotics also in ecosystems without manure input or antibiotic pollution.}, }
@article {pmid33438074, year = {2021}, author = {Shen, J and Wyness, AJ and Claire, MW and Zerkle, AL}, title = {Spatial Variability of Microbial Communities and Salt Distributions Across a Latitudinal Aridity Gradient in the Atacama Desert.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33438074}, issn = {1432-184X}, support = {678812//H2020 European Research Council/ ; 60501//John Templeton Foundation/ ; 201708060070//Chinese Scholarship Council/ ; }, abstract = {Over the past 150 million years, the Chilean Atacama Desert has been transformed into one of the most inhospitable landscapes by geophysical changes, which makes it an ideal Mars analog that has been explored for decades. However, a heavy rainfall that occurred in the Atacama in 2017 provides a unique opportunity to study the response of resident extremophiles to rapid environmental change associated with excessive water and salt shock. Here we combine mineral/salt composition measurements, amendment cell culture experiments, and next-generation sequencing analyses to study the variations in salts and microbial communities along a latitudinal aridity gradient of the Atacama Desert. In addition, we examine the reshuffling of Atacama microbiomes after the rainfall event. Analysis of microbial community composition revealed that soils within the southern arid desert were consistently dominated by Actinobacteria, Chloroflexi, Proteobacteria, Firmicutes, Bacteroidetes, Gemmatimonadetes, Planctomycetes, and Acidobacteria, and Verrucomicrobia. Intriguingly, the hyperarid microbial consortia exhibited a similar pattern to the more southern desert. Salts at the shallow subsurface were dissolved and leached down to a deeper layer, challenging indigenous microorganisms with the increasing osmotic stress. Microbial viability was found to change with aridity and rainfall events. This study sheds light on the structure of xerotolerant, halotolerant, and radioresistant microbiomes from the hyperarid northern desert to the less arid southern transition region, as well as their response to changes in water availability.}, }
@article {pmid33437426, year = {2021}, author = {Petrén, H and Gloder, G and Posledovich, D and Wiklund, C and Friberg, M}, title = {Innate preference hierarchies coupled with adult experience, rather than larval imprinting or transgenerational acclimation, determine host plant use in Pieris rapae.}, journal = {Ecology and evolution}, volume = {11}, number = {1}, pages = {242-251}, doi = {10.1002/ece3.7018}, pmid = {33437426}, issn = {2045-7758}, abstract = {The evolution of host range drives diversification in phytophagous insects, and understanding the female oviposition choices is pivotal for understanding host specialization. One controversial mechanism for female host choice is Hopkins' host selection principle, where females are predicted to increase their preference for the host species they were feeding upon as larvae. A recent hypothesis posits that such larval imprinting is especially adaptive in combination with anticipatory transgenerational acclimation, so that females both allocate and adapt their offspring to their future host. We study the butterfly Pieris rapae, for which previous evidence suggests that females prefer to oviposit on host individuals of similar nitrogen content as the plant they were feeding upon as larvae, and where the offspring show higher performance on the mother's host type. We test the hypothesis that larval experience and anticipatory transgenerational effects influence female host plant acceptance (no-choice) and preference (choice) of two host plant species (Barbarea vulgaris and Berteroa incana) of varying nitrogen content. We then test the offspring performance on these hosts. We found no evidence of larval imprinting affecting female decision-making during oviposition, but that an adult female experience of egg laying in no-choice trials on the less-preferred host Be. incana slightly increased the P. rapae propensity to oviposit on Be. incana in subsequent choice trials. We found no transgenerational effects on female host acceptance or preference, but negative transgenerational effects on larval performance, because the offspring of P. rapae females that had developed on Be. incana as larvae grew slower on both hosts, and especially on Be. incana. Our results suggest that among host species, preferences are guided by hard-wired preference hierarchies linked to species-specific host traits and less affected by larval experience or transgenerational effects, which may be more important for females evaluating different host individuals of the same species.}, }
@article {pmid33436516, year = {2021}, author = {Fu, S and Wang, Q and Zhang, Y and Yang, Q and Hao, J and Liu, Y and Pang, B}, title = {Dynamics and Microevolution of Vibrio parahaemolyticus Populations in Shellfish Farms.}, journal = {mSystems}, volume = {6}, number = {1}, pages = {}, pmid = {33436516}, issn = {2379-5077}, abstract = {Vibrio parahaemolyticus is becoming the leading cause of acute bacterial gastroenteritis, but its population dynamics in aquafarms have received limited attention. To address this research gap, we selected three shellfish farms to examine the impacts of ocean currents and the transport of live aquatic animals on the transmission and microevolution of V. parahaemolyticus by using multilocus sequence typing (MLST) and whole-genome sequencing. MLST and genomic analysis revealed that the community structure of V. parahaemolyticus in Dalian and Donggang was relatively stable in the presence of ocean currents; however, horizontal gene transfer of mobile genetic elements (MGEs) between Dalian and Donggang was very common. Further analysis indicated that the transport of live aquatic animals from Dalian to Xiamen not only introduced new V. parahaemolyticus populations but also allowed the exchange of genetic material between the two sites. More interestingly, Dalian-originated strain ST722 was introduced to Xiamen farms, resulting in one MLST allele change and the acquisition of two genomic islands from indigenous isolates in Xiamen within 8 months; such alterations are thought to promote the adaptation of V. parahaemolyticus These results provide direct observations of how ocean currents and the transport of live aquatic animals contribute to the dissemination and genetic mixture of V. parahaemolyticus, which provides insights into the dynamics and microevolution of V. parahaemolyticus in aquacultural environments.IMPORTANCE Globally, V. parahaemolyticus-related gastroenteritis outbreaks caused by seafood consumption represent an increasing threat to human health. Despite advances in our understanding of the global epidemiology of pandemic V. parahaemolyticus, fundamental questions about the key driving forces for the spread of V. parahaemolyticus at regional and national scales remain unanswered. This study revealed that the transregional transport of aquatic animals and the movement of ocean currents both contributed to the mixing of V. parahaemolyticus populations. More importantly, this study demonstrated how genetic mixture occurred between introduced and endemic V. parahaemolyticus populations via the transport of aquatic animals, which accelerated bacterial adaptation by transferring ecologically important functions. These results suggest that human activities entail a risk of the emergence of new virulent populations for both aquatic animals and humans by horizontal gene transfer and provide important insights into the microevolution and population mixing of V. parahaemolyticus.}, }
@article {pmid33436509, year = {2021}, author = {Meier, DV and Imminger, S and Gillor, O and Woebken, D}, title = {Distribution of Mixotrophy and Desiccation Survival Mechanisms across Microbial Genomes in an Arid Biological Soil Crust Community.}, journal = {mSystems}, volume = {6}, number = {1}, pages = {}, pmid = {33436509}, issn = {2379-5077}, abstract = {Desert surface soils devoid of plant cover are populated by a variety of microorganisms, many with yet unresolved physiologies and lifestyles. Nevertheless, a common feature vital for these microorganisms inhabiting arid soils is their ability to survive long drought periods and reactivate rapidly in rare incidents of rain. Chemolithotrophic processes such as oxidation of atmospheric hydrogen and carbon monoxide are suggested to be a widespread energy source to support dormancy and resuscitation in desert soil microorganisms. Here, we assessed the distribution of chemolithotrophic, phototrophic, and desiccation-related metabolic potential among microbial populations in arid biological soil crusts (BSCs) from the Negev Desert, Israel, via population-resolved metagenomic analysis. While the potential to utilize light and atmospheric hydrogen as additional energy sources was widespread, carbon monoxide oxidation was less common than expected. The ability to utilize continuously available energy sources might decrease the dependency of mixotrophic populations on organic storage compounds and carbon provided by the BSC-founding cyanobacteria. Several populations from five different phyla besides the cyanobacteria encoded CO2 fixation potential, indicating further potential independence from photoautotrophs. However, we also found population genomes with a strictly heterotrophic genetic repertoire. The highly abundant Rubrobacteraceae (Actinobacteriota) genomes showed particular specialization for this extreme habitat, different from their closest cultured relatives. Besides the ability to use light and hydrogen as energy sources, they encoded extensive O2 stress protection and unique DNA repair potential. The uncovered differences in metabolic potential between individual, co-occurring microbial populations enable predictions of their ecological niches and generation of hypotheses on the dynamics and interactions among them.IMPORTANCE This study represents a comprehensive community-wide genome-centered metagenome analysis of biological soil crust (BSC) communities in arid environments, providing insights into the distribution of genes encoding different energy generation mechanisms, as well as survival strategies, among populations in an arid soil ecosystem. It reveals the metabolic potential of several uncultured and previously unsequenced microbial genera, families, and orders, as well as differences in the metabolic potential between the most abundant BSC populations and their cultured relatives, highlighting once more the danger of inferring function on the basis of taxonomy. Assigning functional potential to individual populations allows for the generation of hypotheses on trophic interactions and activity patterns in arid soil microbial communities and represents the basis for future resuscitation and activity studies of the system, e.g., involving metatranscriptomics.}, }
@article {pmid33436507, year = {2021}, author = {Wang, H and Beier, N and Boedeker, C and Sztajer, H and Henke, P and Neumann-Schaal, M and Mansky, J and Rohde, M and Overmann, J and Petersen, J and Klawonn, F and Kucklick, M and Engelmann, S and Tomasch, J and Wagner-Döbler, I}, title = {Dinoroseobacter shibae Outer Membrane Vesicles Are Enriched for the Chromosome Dimer Resolution Site dif.}, journal = {mSystems}, volume = {6}, number = {1}, pages = {}, pmid = {33436507}, issn = {2379-5077}, abstract = {Outer membrane vesicles (OMVs) are universally produced by prokaryotes and play important roles in symbiotic and pathogenic interactions. They often contain DNA, but a mechanism for its incorporation is lacking. Here, we show that Dinoroseobacter shibae, a dinoflagellate symbiont, constitutively secretes OMVs containing DNA. Time-lapse microscopy captured instances of multiple OMV production at the septum during cell division. DNA from the vesicle lumen was up to 22-fold enriched for the region around the terminus of replication (ter). The peak of coverage was located at dif, a conserved 28-bp palindromic sequence required for binding of the site-specific tyrosine recombinases XerC/XerD. These enzymes are activated at the last stage of cell division immediately prior to septum formation when they are bound by the divisome protein FtsK. We suggest that overreplicated regions around the terminus have been repaired by the FtsK-dif-XerC/XerD molecular machinery. The vesicle proteome was clearly dominated by outer membrane and periplasmic proteins. Some of the most abundant vesicle membrane proteins were predicted to be required for direct interaction with peptidoglycan during cell division (LysM, Tol-Pal, Spol, lytic murein transglycosylase). OMVs were 15-fold enriched for the saturated fatty acid 16:00. We hypothesize that constitutive OMV secretion in D. shibae is coupled to cell division. The footprint of the FtsK-dif-XerC/XerD molecular machinery suggests a novel potentially highly conserved route for incorporation of DNA into OMVs. Clearing the division site from small DNA fragments might be an important function of vesicles produced during exponential growth under optimal conditions.IMPORTANCE Gram-negative bacteria continually form vesicles from their outer membrane (outer membrane vesicles [OMVs]) during normal growth. OMVs frequently contain DNA, and it is unclear how DNA can be shuffled from the cytoplasm to the OMVs. We studied OMV cargo in Dinoroseobacter shibae, a symbiont of dinoflagellates, using microscopy and a multi-omics approach. We found that vesicles formed during undisturbed exponential growth contain DNA which is enriched for genes around the replication terminus, specifically, the binding site for an enzyme complex that is activated at the last stage of cell division. We suggest that the enriched genes are the result of overreplication which is repaired by their excision and excretion via membrane vesicles to clear the divisome from waste DNA.}, }
@article {pmid33435231, year = {2021}, author = {Cohen Kadosh, K and Muhardi, L and Parikh, P and Basso, M and Jan Mohamed, HJ and Prawitasari, T and Samuel, F and Ma, G and Geurts, JM}, title = {Nutritional Support of Neurodevelopment and Cognitive Function in Infants and Young Children-An Update and Novel Insights.}, journal = {Nutrients}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/nu13010199}, pmid = {33435231}, issn = {2072-6643}, abstract = {Proper nutrition is crucial for normal brain and neurocognitive development. Failure to optimize neurodevelopment early in life can have profound long-term implications for both mental health and quality of life. Although the first 1000 days of life represent the most critical period of neurodevelopment, the central and peripheral nervous systems continue to develop and change throughout life. All this time, development and functioning depend on many factors, including adequate nutrition. In this review, we outline the role of nutrients in cognitive, emotional, and neural development in infants and young children with special attention to the emerging roles of polar lipids and high quality (available) protein. Furthermore, we discuss the dynamic nature of the gut-brain axis and the importance of microbial diversity in relation to a variety of outcomes, including brain maturation/function and behavior are discussed. Finally, the promising therapeutic potential of psychobiotics to modify gut microbial ecology in order to improve mental well-being is presented. Here, we show that the individual contribution of nutrients, their interaction with other micro- and macronutrients and the way in which they are organized in the food matrix are of crucial importance for normal neurocognitive development.}, }
@article {pmid33432372, year = {2021}, author = {Nguyen, TTT and Foysal, MJ and Fotedar, R and Gupta, SK and Siddik, MAB and Tay, CY}, title = {The Effect of Two Dietary Protein Sources on Water Quality and the Aquatic Microbial Communities in Marron (Cherax cainii) Culture.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33432372}, issn = {1432-184X}, support = {CIPRS) (No. 18508848 - Curtin)//Curtin University of Technology/ ; }, abstract = {Feeding freshwater crayfish species with different diets not only affects the water quality but also induces the abundance of various microbial communities in their digestive tracts. In this context, very limited research has been undertaken to understand the impacts of various protein incorporated aqua-diets on the characteristics of water and its microbial communities. In this study, we have critically analysed the water quality parameters including pH, dissolved oxygen, nitrate, nitrite, ammonia and phosphorus, as well as bacterial communities under marron (Cherax cainii) aquaculture, fed fishmeal (FM) and poultry by-product meal (PBM)-based diets for 60 days. The results unveiled that over the time, feeding has significant impacts on organic waste accumulation, especially ammonia, nitrate, nitrite and phosphate, while no effects were observed on pH and dissolved oxygen. Analysis of 16S rRNA sequence data of water sample indicated significant (P < 0.05) shift of microbial abundance in post-fed FM and PBM water with the evidence of microbial transmission from the gut of marron. Post-fed marron resulted in a significant correlation of Hafnia, Enterobacter, Candidatus Bacilloplasma and Aquitella with the quality and microbial population of water. The results of this study generated valuable knowledge database of microbes-water relationship for better health management practices and production of marron aquaculture fed with FM and PBM diets in under restricted feeding regime with the feeding ratios provided.}, }
@article {pmid33331146, year = {2020}, author = {Rozman, V and Accetto, T and Duncan, SH and Flint, HJ and Vodovnik, M}, title = {Type IV pili are widespread among non-pathogenic Gram-positive gut bacteria with diverse carbohydrate utilization patterns.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.15362}, pmid = {33331146}, issn = {1462-2920}, support = {P4-0097C//Gut Microbial Ecology/ ; P4-0097//Nutrition and Microbial Ecology of Gastrointestinal Tract/ ; }, abstract = {Type IV pili (T4P) are bacterial surface-exposed appendages that have been extensively studied in Gram-negative pathogenic bacteria. Despite recent sequencing efforts, little is known regarding these structures in non-pathogenic anaerobic Gram-positive species, particularly commensals of the mammalian gut. Early studies revealed that T4P in two ruminal Gram-positive species are associated with growth on cellulose, suggesting possible associations of T4P with substrate utilization patterns. In the present study, genome sequences of 118 taxonomically diverse, mainly Gram-positive, bacterial strains isolated from anaerobic (gastrointestinal) environments, have been analysed. The genes likely to be associated with T4P biogenesis were analysed and grouped according to T4P genetic organization. In parallel, consortia of Carbohydrate Active enZYmes (CAZymes) were also analysed and used to predict carbohydrate utilization abilities of selected strains. The predictive power of this approach was additionally confirmed by experimental assessment of substrate-related growth patterns of selected strains. Our analysis revealed that T4P systems with diverse genetic organization are widespread among Gram-positive anaerobic non-pathogenic bacteria isolated from different environments, belonging to two phylogenetically distantly related phyla: Firmicutes and Actinobacteria.}, }
@article {pmid33429312, year = {2021}, author = {Fu, Y and Wang, F and Sheng, H and Hu, F and Wang, Z and Xu, M and Bian, Y and Jiang, X and Tiedje, JM}, title = {Removal of extracellular antibiotic resistance genes using magnetic biochar/quaternary phosphonium salt in aquatic environments: A mechanistic study.}, journal = {Journal of hazardous materials}, volume = {411}, number = {}, pages = {125048}, doi = {10.1016/j.jhazmat.2021.125048}, pmid = {33429312}, issn = {1873-3336}, abstract = {The proliferation and spread of antibiotic resistance genes (ARGs) is becoming a worldwide crisis. Extracellular DNA encoding ARGs (eARGs) in aquatic environment plays a critical role in the dispersion of antimicrobial resistance genes. Strategies to control the dissemination of eARGs are urgently required for ecological safety and human health. Towards this goal, magnetic biochar/quaternary phosphonium salt (MBQ), was used to investigate the efficiency and removal mechanism for eARGs. Magnetic biochar modified by quaternary phosphonium salt enhanced the adsorption capacity of extracellular DNA to approximately 9 folds, compared to that of the unmodified. DNA adsorption by MBQ was mainly dominated by chemisorption in heterogeneous systems and was promoted in acidic and low-salt environment. The generation of •OH and MBQ colloid jointly cleaved DNA into fragments, facilitating the adsorption of the phosphate backbone of DNA onto MBQ through electrostatic force as well as the conformational transition of DNA. Furthermore, quantification of extracellular DNA after MBQ was applied in water demonstrated that over 92.7% of resistance genes were removed, indicating a significantly reduced risk of propagation of antimicrobial resistance in aquatic environments. These findings have a practical significance in the application of MBQ in mitigating the spread of ARGs in aquatic environment.}, }
@article {pmid33429117, year = {2021}, author = {Forés, E and Bofill-Mas, S and Itarte, M and Martínez-Puchol, S and Hundesa, A and Calvo, M and Borrego, CM and Corominas, LL and Girones, R and Rusiñol, M}, title = {Evaluation of two rapid ultrafiltration-based methods for SARS-CoV-2 concentration from wastewater.}, journal = {The Science of the total environment}, volume = {768}, number = {}, pages = {144786}, doi = {10.1016/j.scitotenv.2020.144786}, pmid = {33429117}, issn = {1879-1026}, abstract = {Quantitative measurements of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in raw wastewater have been implemented worldwide since the beginning of the pandemic. Recent efforts are being made to evaluate different viral concentration methodologies to overcome supplier shortages during lockdowns. A set of 22-wastewater samples seeded with murine hepatitis virus (MHV), a member of the Coronaviridae family, and the bacteriophage MS2, were used to characterize and compare two ultrafiltration-based methods: a centrifugal ultrafiltration device (Centricon® Plus-70) and the automated concentrating pipette CP-Select™. Based on the recovery efficiencies, significant differences were observed for MHV, with Centricon® Plus-70 (24%) being the most efficient method. Nevertheless, concentrations of naturally occurring SARS-CoV-2, Human adenoviruses and JC polyomaviruses in these samples did not result in significant differences between methods suggesting that testing naturally occurring viruses may complement the evaluation of viral concentration methodologies. Based on the virus adsorption to solids and the necessity of a pre-centrifugation step to remove larger particles and avoid clogging when using ultrafiltration methods, we assessed the percentage of viruses not quantified after ultrafiltration. Around 23% of the detected SARS-CoV-2 would be discarded during the debris removal step. The CP-Select™ provided the highest concentration factor (up to 333×) and the lowest LoD (6.19 × 103 GC/l) for MHV and proved to be fast, automatic, highly reproducible and suitable to work under BSL-2 measures.}, }
@article {pmid33428723, year = {2021}, author = {Laursen, MF and Bahl, MI and Licht, TR}, title = {Settlers of our inner surface - Factors shaping the gut microbiota from birth to toddlerhood.}, journal = {FEMS microbiology reviews}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsre/fuab001}, pmid = {33428723}, issn = {1574-6976}, abstract = {During the first three years of life, the microbial ecosystem within the human gut undergoes a process that is unlike what happens in this ecosystem at any other time of our life. This period in time is considered a highly important developmental window, where the gut microbiota is much less resilient and much more responsive to external and environmental factors than seen in the adult gut. While advanced bioinformatics and clinical correlation studies have received extensive focus within studies of the human microbiome, basic microbial growth physiology has attracted much less attention, although it plays a pivotal role to understand the developing gut microbiota during early life. In this review, we will thus take a microbial ecology perspective on the analysis of factors that influence the temporal development of the infant gut microbiota. Such factors include sources of microbes that seed the intestinal environment, physico-chemical (abiotic) conditions influencing microbial growth, and the availability of nutrients needed by the intestinal microbes.}, }
@article {pmid33424787, year = {2020}, author = {Figueroa-Gonzalez, PA and Bornemann, TLV and Adam, PS and Plewka, J and Révész, F and von Hagen, CA and Táncsics, A and Probst, AJ}, title = {Saccharibacteria as Organic Carbon Sinks in Hydrocarbon-Fueled Communities.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {587782}, doi = {10.3389/fmicb.2020.587782}, pmid = {33424787}, issn = {1664-302X}, abstract = {Organisms of the candidate phylum Saccharibacteria have frequently been detected as active members of hydrocarbon degrading communities, yet their actual role in hydrocarbon degradation remained unclear. Here, we analyzed three enrichment cultures of hydrocarbon-amended groundwater samples using genome-resolved metagenomics to unravel the metabolic potential of indigenous Saccharibacteria. Community profiling based on ribosomal proteins revealed high variation in the enrichment cultures suggesting little reproducibility although identical cultivation conditions were applied. Only 17.5 and 12.5% of the community members were shared between the three enrichment cultures based on ribosomal protein clustering and read mapping of reconstructed genomes, respectively. In one enrichment, two Saccharibacteria strains dominated the community with 16.6% in relative abundance and we were able to recover near-complete genomes for each of them. A detailed analysis of their limited metabolism revealed the capacity for peptide degradation, lactate fermentation from various hexoses, and suggests a scavenging lifestyle with external retrieval of molecular building blocks. In contrast to previous studies suggesting that Saccharibacteria are directly involved in hydrocarbon degradation, our analyses provide evidence that these organisms can be highly abundant scavengers acting rather as organic carbon sinks than hydrocarbon degraders in these communities.}, }
@article {pmid33422757, year = {2020}, author = {Vázquez-Blanco, R and Arias-Estévez, M and Bååth, E and Fernández-Calviño, D}, title = {Comparing the effect of Cu-based fungicides and pure Cu salts on microbial biomass, microbial community structure and bacterial community tolerance to Cu.}, journal = {Journal of hazardous materials}, volume = {409}, number = {}, pages = {124960}, doi = {10.1016/j.jhazmat.2020.124960}, pmid = {33422757}, issn = {1873-3336}, abstract = {The effect of Cu on three different microbial endpoints was studied using different Cu sources, in order to check the usefulness of pure Cu salts to estimate the toxicity of commercial Cu fungicides on soil microbes. Cu additions caused similar dose-response curves of substrate induced respiration (SIR) decreases regardless of Cu source, i.e. the use of pure Cu salts to estimate the effect of Cu fungicides on microbial biomass using SIR may be useful. Phospholipid fatty acid (PLFA) analysis showed that the Cu source was more important for the microbial community structure than Cu concentration. Thus, the use of Cu salts to infer the effects of Cu fungicides on microbial community structure using PLFA analysis is not recommended, since effects of Cu concentration will be confounded with Cu source. Analyzing pollution induced community tolerance (PICT) to Cu showed that the use of pure Cu salts may overestimate Cu effects if Cu salt additions modified the soil pH. The highest doses of Cu salts increased bacterial community tolerance to Cu between 300 and 600 times, while commercial Cu fungicide increases were between 20 and 160 times. Therefore, the use of pure Cu salts to estimate the Cu fungicides effects on soil microbes is not recommended for PLFAs analyses, not suitable for PICT at high Cu concentrations, while useful for SIR.}, }
@article {pmid33420911, year = {2021}, author = {Doliwa, A and Dunthorn, M and Rassoshanska, E and Mahé, F and Bass, D and Duarte Ritter, C}, title = {Identifying Potential Hosts of Short-Branch Microsporidia.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33420911}, issn = {1432-184X}, support = {#DU1319/5-1//Deutsche Forschungsgemeinschaft/ ; }, abstract = {Microsporidia are obligate parasites that are closely related to Fungi. While the widely known &quot;long-branch&quot; Microsporidia infect mostly metazoans, the hosts of &quot;short-branch&quot; Microsporidia are only partially characterized or not known at all. Here, we used network analyses from Neotropical rainforest soil metabarcoding data, to infer co-occurrences between environmental lineages of short-branch microsporidians and their potential hosts. We found significant co-occurrences with several taxa, especially with Apicomplexa, Cercozoa, and Fungi, as well as some Metazoa. Our results are the first step to identify potential hosts of the environmental lineages of short-branch microsporidians, which can be targeted in future molecular and microscopic studies.}, }
@article {pmid33420910, year = {2021}, author = {García Hernández, E and Berg, MP and Van Oosten, AR and Smit, C and Falcão Salles, J}, title = {Linking Bacterial Communities Associated with the Environment and the Ecosystem Engineer Orchestia gammarellus at Contrasting Salt Marsh Elevations.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33420910}, issn = {1432-184X}, support = {484425//Consejo Nacional de Ciencia y Tecnología/ ; ALWOP.219.00179028//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; }, abstract = {The digestive tract of animals harbors microbiota important for the host's fitness and performance. The interaction between digestive tract bacteria and soil animal hosts is still poorly explored despite the importance of soil fauna for ecosystem processes. In this study, we investigated the interactions between the bacterial communities from the digestive tract of the litter-feeding, semi-terrestrial crustacean Orchestia gammarellus and those obtained from the environment; these organisms thrive in, i.e., soil and plant litter from salt marshes. We hypothesized that elevation is an important driver of soil and litter bacterial communities, which indirectly (via ingested soil and litter bacteria) influences the bacterial communities in the digestive tract of O. gammarellus. Indeed, our results revealed that elevation modulated soil and litter bacterial community composition along with soil organic matter content and the C:N ratio. Soil and plant litter differed in alpha diversity indexes (richness and diversity), and in the case of plant litter, both indexes increased with elevation. In contrast, elevation did not affect the composition of bacterial communities associated with O. gammarellus' digestive tract, suggesting selection by the host, despite the fact that a large component of the bacterial community was also detected in external sources. Importantly, Ca. Bacilloplasma and Vibrio were highly prevalent and abundant in the host. The taxonomic comparison of Ca. Bacilloplasma amplicon sequence variants across the host at different elevations suggested a phylogenetic divergence due to host habitat (i.e., marine or semi-terrestrial), thus supporting their potential functional role in the animal physiology. Our study sheds light on the influence of the environment on soil animal-bacteria interactions and provides insights into the resilience of the O. gammarellus-associated bacteria to increased flooding frequency.}, }
@article {pmid33420625, year = {2021}, author = {Win, PM and Matsumura, E and Fukuda, K}, title = {Effects of Pesticides on the Diversity of Endophytic Fungi in Tea Plants.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33420625}, issn = {1432-184X}, abstract = {We examined the effects of agrochemicals on the endophytic fungal community associated with tea plants. Endophytic fungi were isolated from four different tea plant tissues (bark, xylem, old leaves, new leaves) collected from pesticide-treated and untreated plots. In pesticide-treated plot, the acaricides, fungicides, and insecticides are typically applied 3 times each year. The infection rate was slightly lower in the pesticide-treated plot, but the difference between plots was not statistically significant. Colletotrichum camelliae, Phyllosticta capitalensis, and Pleosporales sp. were common endophytes in both plots. Among a total of 41 fungal species, only 21 were considered common endophytes. Colletotrichum pseudomajus was the predominant endophyte in the bark tissue in the untreated plot, whereas C. camelliae was predominant in the pesticide-treated plot. Paraphaeosphaeria neglecta and Phoma bellendis were predominant in the xylem tissues of samples from the untreated and treated plots, respectively. Colletotrichum camelliae was the most commonly found species in leaf tissues in both plots, but the colonization frequency was significantly lower in the pesticide-treated plot. Species richness was not affected by pesticide treatment. The community structure of endophytic fungi in stem tissues (bark and xylem) differed significantly between plots, but leaf tissue endophytic fungal community structure was not significantly influenced by pesticide treatment.}, }
@article {pmid33420624, year = {2021}, author = {Eraqi, WA and ElRakaiby, MT and Megahed, SA and Yousef, NH and Elshahed, MS and Yassin, AS}, title = {Spatiotemporal Analysis of the Water and Sediment Nile Microbial Community Along an Urban Metropolis.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33420624}, issn = {1432-184X}, support = {2016423//National Science Foundation/ ; 3046//Academy of Scientific Research and Technology/ ; }, abstract = {Assessing microbial identity, diversity, and community structure could be a valuable tool for monitoring the impact of xenobiotics and anthropogenic inputs in rivers, especially in urban and industrial settings. Here, we characterize the Nile River microbial community in water and sediments in summer and winter at five locations that span its natural flow through the Cairo metropolis. 16S rRNA gene datasets were analyzed to identify the role played by sample type (sediment versus water), season, and location in shaping the community, as well as to predict functional potential of the Nile River microbiome. Microbial communities were mostly influenced by sampling type (sediments versus water), while seasonal effects were only observed in water samples. Spatial differences did not represent a significant factor in shaping the community in either summer or winter seasons. Proteobacteria was the most abundant phylum in both water and sediment samples, with the order Betaproteobacteriales being the abundant one. Chloroflexi and Bacteroidetes were also prevalent in sediment samples, while Cyanobacteria and Actinobacteria were abundant in water samples. The linear discriminative analysis effect size (LEfSe) identified the cyanobacterial genus Cyanobium PCC-6307 as the main variable between summer and winter water. Sequences representing human and animal potential pathogens, as well as toxin-producing Cyanobacteria, were identified in low abundance within the Nile microbiome. Functionally predicted metabolic pathways predicted the presence of antibiotic biosynthesis, as well as aerobic xenobiotic degradation pathways in the river microbiome.}, }
@article {pmid33417698, year = {2021}, author = {Moossavi, S and Fontes, ME and Rossi, L and Fusch, G and Surette, MG and Azad, MB}, title = {Capturing the diversity of the human milk microbiota through culture-enriched molecular profiling: a feasibility study.}, journal = {FEMS microbiology letters}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsle/fnab001}, pmid = {33417698}, issn = {1574-6968}, abstract = {Previous human milk studies have confirmed the existence of a highly diverse bacterial community using culture-independent and targeted culture-dependent techniques. However, culture-enriched molecular profiling of milk microbiota has not been done. Additionally, the impact of storage conditions and milk fractionation on microbiota composition is not understood. In this feasibility study, we optimised and applied culture-enriched molecular profiling to study culturable milk microbiota in eight milk samples collected from mothers of infants admitted to a neonatal intensive care unit. Fresh samples were immediately plated or stored at -80°C for two weeks (short-term frozen). Long-term samples were stored at -20°C for more than six months. Samples were cultured using 10 different culture media and incubated both aerobically and anaerobically. We successfully isolated major milk bacteria including Streptococcus, Staphylococcus, and Bifidobacterium from fresh milk samples, but were unable to culture any bacteria from the long-term frozen samples. Short-term freezing shifted the composition of viable milk bacteria from the original composition in fresh samples. Nevertheless, the inter-individual variability of milk microbiota composition was observed even after short-term storage. There was no major difference in the overall milk microbiota composition between milk fractions in this feasibility study. This is among the first studies on culture-enriched molecular profiling of the milk microbiota demonstrating the effect of storage and fractionation on milk microbiota composition.}, }
@article {pmid33415825, year = {2021}, author = {Rogiers, T and Claesen, J and Gompel, AV and Vanhoudt, N and Mysara, M and Williamson, A and Leys, N and Van Houdt, R and Boon, N and Mijnendonckx, K}, title = {Soil microbial community structure and functionality changes in response to long-term metal and radionuclide pollution.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.15394}, pmid = {33415825}, issn = {1462-2920}, abstract = {Microbial communities are essential for a healthy soil ecosystem. Metals and radionuclides can exert a persistent pressure on the soil microbial community. However, little is known on the effect of long-term co-contamination of metals and radionuclides on the microbial community structure and functionality. We investigated the impact of historical discharges of the phosphate and nuclear industry on the microbial community in the Grote Nete river basin in Belgium. Eight locations were sampled along a transect to the river edge and one location further in the field. Chemical analysis demonstrated a metal and radionuclide contamination gradient and revealed a distinct clustering of the locations based on all metadata. Moreover, a relation between the chemical parameters and the bacterial community structure was demonstrated. Although no difference in biomass was observed between locations, cultivation-dependent experiments showed that communities from contaminated locations survived better on singular metals than communities from control locations. Furthermore, nitrification, a key soil ecosystem process seemed affected in contaminated locations when combining metadata with microbial profiling. These results indicate that long-term metal and radionuclide pollution impacts the microbial community structure and functionality and provides important fundamental insights into microbial community dynamics in co-metal-radionuclide contaminated sites. This article is protected by copyright. All rights reserved.}, }
@article {pmid33415385, year = {2021}, author = {Colin, Y and Berthe, T and Molbert, N and Guigon, E and Vivant, AL and Alliot, F and Collin, S and Goutte, A and Petit, F}, title = {Urbanization Constrains Skin Bacterial Phylogenetic Diversity in Wild Fish Populations and Correlates with the Proliferation of Aeromonads.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33415385}, issn = {1432-184X}, abstract = {Changes in the state of rivers resulting from the activity and expansion of urban areas are likely to affect aquatic populations by increasing stress and disease, with the microbiota playing a potentially important intermediary role. Unraveling the dynamics of microbial flora is therefore essential to better apprehend the impact of anthropogenic disturbances on the health of host populations and the ecological integrity of hydrosystems. In this context, the present study simultaneously examined changes in the microbial communities associated with mucosal skin and gut tissues of eight fish species along an urbanization gradient in the Orge River (France). 16S rRNA gene metabarcoding revealed that the structure and composition of the skin microbiota varied substantially along the disturbance gradient and to a lesser extent according to fish taxonomy. Sequences affiliated with the Gammaproteobacteria, in particular the genus Aeromonas, prevailed on fish caught in the most urbanized areas, whereas they were nearly absent upstream. This rise of opportunistic taxa was concomitant with a decline in phylogenetic diversity, suggesting more constraining environmental pressures. In comparison, fish gut microbiota varied much more moderately with the degree of urbanization, possibly because this niche might be less directly exposed to environmental stressors. Co-occurrence networks further identified pairs of associated bacterial taxa, co-existing more or less often than expected at random. Few correlations could be identified between skin and gut bacterial taxa, supporting the assumption that these two microbial niches are disconnected and do not suffer from the same vulnerability to anthropic pressures.}, }
@article {pmid33415384, year = {2021}, author = {Shi, Y and Yang, H and Chu, M and Niu, X and Huo, X and Gao, Y and Zeng, J and Lin, Q and Lou, K}, title = {Diversity and Spatiotemporal Dynamics of Fungal Communities in the Rhizosphere Soil of Cotton in the Arid Region of Northwest China.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33415384}, issn = {1432-184X}, support = {41471220//the National Natural Science Foundation of China/ ; 31860024//National Natural Science Foundation of China/ ; 2017YFD0200608-05//Nation Key Research Program of China/ ; 2018D01A44//National Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2016M602953XB//China Postdoctoral Science Foundation Funded the Sixtieth Batch/ ; qn2005yx023//Xinjiang Uygur Autonomous Region Outstanding Young Talent Training Program/ ; }, abstract = {This study aimed to investigate the fungal diversity and its temporal and spatial dynamics in the rhizosphere soil of healthy cotton by high-throughput sequencing. We studied species richness, composition, and distribution of cotton rhizosphere fungal community with respect to location (Alaer, Kuerle, Tumushuke, Hami, Shihezi, Wusu, and Jinghe) and plant growth period (seedling stage, bud stage, flowering stage, and boll-opening stage) using the methods of PCR-based high-throughput sequencing and real-time quantitative PCR. A total of 1,838,454 fungal nuclear ribosomal internal transcribed spacer region sequences (rRNA ITS) were obtained from all cotton plants sampled at different growth stages in the seven locations in Xinjiang. The most abundant fungal group in the cotton rhizosphere was the Ascomycota (78.72%), followed by the Zygomycota (9.56%) and Basidiomycota (2.77%). These sequences revealed an enormous number of operational taxonomic units (OTUs) in cotton (1802 unique OTUs), with 67-464 OTUs in a single cotton sample, at a 3% threshold and a sequencing depth of 30,000 sequences. We identified 33 classes and 389 genera from the resulting 1,800,714 sequences. Sordariomycetes was the most frequent class in all samples, followed by Leotiomycetes and Eurotiomycetes. There were some differences in OTUs among different growth stages, but the differences were not significant, with 382 OTUs (14.66%) being common to each of the stages. A marked difference in the diversity of fungi in the rhizosphere soil of cotton was evident among the different locations, with the highest number of OTUs being detected in Jinghe (1084 OTUs) and clusters of OTUs representative of northern and eastern Xinjiang being detected. There were significantly more tags of Mortierella in Jinghe and Wusu than in the other sampling sites. The dynamics of the rhizosphere fungal communities were influenced by sampling sites. To the best of our knowledge, the current study is the first application of PCR-based Illumina to characterize and compare the fungal biodiversity in multiple rhizosphere soil samples from cotton.}, }
@article {pmid33414351, year = {2021}, author = {Verdera, AB and Montecillo, AD and Obusan, MCM}, title = {Draft Genome Sequence of Streptomyces sp. Isolate H28 from the Meycauayan River, Philippines.}, journal = {Microbiology resource announcements}, volume = {10}, number = {1}, pages = {}, pmid = {33414351}, issn = {2576-098X}, abstract = {In this paper, we report the draft genome sequence of Streptomyces sp. isolate H28, isolated from sediments of the Meycauayan River in the Philippines. This species exhibits production of melanin as well as the ability to utilize and degrade both high-density polyethylene (HDPE) and low-density polyethylene (LDPE).}, }
@article {pmid33414343, year = {2021}, author = {Mori, JF and Kanaly, RA}, title = {Complete Genome Sequence of Sphingobium barthaii KK22, a High-Molecular-Weight Polycyclic Aromatic Hydrocarbon-Degrading Soil Bacterium.}, journal = {Microbiology resource announcements}, volume = {10}, number = {1}, pages = {}, pmid = {33414343}, issn = {2576-098X}, abstract = {Sphingobium barthaii KK22T is a high-molecular-weight polycyclic aromatic hydrocarbon-degrading soil bacterium that has been investigated in biotransformation, microbial ecology, and DNA damage studies. The complete genome sequence of S. barthaii revealed four closed circular sequences, including two chromosomes, a megaplasmid, and a smaller plasmid, by hybrid assembly using short- and long-read sequencing technologies.}, }
@article {pmid33414017, year = {2021}, author = {Riber, L and Hansen, LH}, title = {Epigenetic Memories: The Hidden Drivers of Bacterial Persistence?.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2020.12.005}, pmid = {33414017}, issn = {1878-4380}, abstract = {Epigenetic modifications, including DNA methylation, stably alter gene expression without modifying genomic sequences. Recent evidence suggests that epigenetic regulation coupled with a long-term 'memory' effect plays a major role within bacterial persistence formation. Today, emerging high-resolution, single-molecule sequencing technologies allow an increased focus on DNA modifications as regulatory epigenetic marks, which presents a unique opportunity to identify possible epigenetic drivers of bacterial persistence.}, }
@article {pmid33412651, year = {2014}, author = {Clodoveo, ML and Hbaieb, RH and Kotti, F and Mugnozza, GS and Gargouri, M}, title = {Mechanical Strategies to Increase Nutritional and Sensory Quality of Virgin Olive Oil by Modulating the Endogenous Enzyme Activities.}, journal = {Comprehensive reviews in food science and food safety}, volume = {13}, number = {2}, pages = {135-154}, doi = {10.1111/1541-4337.12054}, pmid = {33412651}, issn = {1541-4337}, abstract = {This monograph is a critical review of the biological activities that occur during virgin olive oil (VOO) extraction process. Strategic choices of plant engineering systems and of processing technologies should be made to condition the enzymatic activities, in order to modulate the nutritional and the sensory quality of the product toward the consumer expectations. &quot;Modulation&quot; of the product quality properties has the main aim to predetermine the quantity and the quality of 2 classes of substances: polyphenols and volatile compounds responsible of VOO nutritional and sensory characteristics. In the 1st section, a systematic analysis of the literature has been carried out to investigate the main olive enzymatic activities involved in the complex biotransformation that occurs during the mechanical extraction process. In the 2nd section, a critical and interpretative discussion of the influence of each step of the extraction process on the polyphenols and the volatile compounds has been performed. The effect of the different mechanical devices that are part of the extraction process is analyzed and recommendations, strategies, and possible avenues for future researches are suggested.}, }
@article {pmid33412377, year = {2020}, author = {Wang, B and Ma, J and Zhang, L and Su, Y and Xie, Y and Ahmad, Z and Xie, B}, title = {The synergistic strategy and microbial ecology of the anaerobic co-digestion of food waste under the regulation of domestic garbage classification in China.}, journal = {The Science of the total environment}, volume = {765}, number = {}, pages = {144632}, doi = {10.1016/j.scitotenv.2020.144632}, pmid = {33412377}, issn = {1879-1026}, abstract = {With the implementation of new domestic garbage classification policy in China, attention is growing to improve the treatment efficiency of municipal 'wet' waste. Combing with the new regulation, the synergistic strategy and the microbial ecology of the anaerobic co-digestion (AcoD) of cooked food waste (CFW), uncooked food waste (UCFW) and rice straw (RS) were analyzed in current study. Results showed that the maximum cumulative methane yield (CMY) and synergic index were obtained when CFW and UCFW were mixed at the ratio of 1:1 (based on volatile solid content). The highest CMY 452.94 ± 0.99 mL/g-VS was obtained when the ratio of CFW, UCFW and RS was 0.81:0.09:0.10, which was 16.29%, 36.20% and 121.84% higher than their mono-digestion, respectively. The AcoD promoted the methane potential by prolonging the release time of organic matter and slowing down the hydrolysis rate. Furthermore, the AcoD increased the species diversification and relative abundance of fermentation bacteria in digesters, and Methanosaeta predominated the methanogen communities. This study demonstrated a clean and sustainable AcoD strategy for safe disposal of urban food waste and revealed the variation of microbial community, which can provide a base for efficient bioenergy recovery from urban domestic garbage.}, }
@article {pmid33411249, year = {2021}, author = {Chakraborty, P and Paul, P and Kumari, M and Bhattacharjee, S and Singh, M and Maiti, D and Dastidar, DG and Akhter, Y and Kundu, T and Das, A and Tribedi, P}, title = {Attenuation of Pseudomonas aeruginosa biofilm by thymoquinone: an individual and combinatorial study with tetrazine-capped silver nanoparticles and tryptophan.}, journal = {Folia microbiologica}, volume = {}, number = {}, pages = {}, pmid = {33411249}, issn = {1874-9356}, abstract = {Microbial biofilm indicates a cluster of microorganisms having the capability to display drug resistance property, thereby increasing its proficiency in spreading diseases. In the present study, the antibiofilm potential of thymoquinone, a black seed-producing natural molecule, was contemplated against the biofilm formation by Pseudomonas aeruginosa. Substantial antimicrobial activity was exhibited by thymoquinone against the test organism wherein the minimum inhibitory concentration of the compound was found to be 20 μg/mL. Thereafter, an array of experiments (crystal violet staining, protein count, and microscopic observation, etc.) were carried out by considering the sub-MIC doses of thymoquinone (5 and 10 μg/mL), each of which confirmed the biofilm attenuating capacity of thymoquinone. However, these concentrations did not show any antimicrobial activity. Further explorations on understanding the underlying mechanism of the same revealed that thymoquinone accumulated reactive oxygen species (ROS) and also inhibited the expression of the quorum sensing gene (lasI) in Pseudomonas aeruginosa. Furthermore, by taking up a combinatorial approach with two other reported antibiofilm agents (tetrazine-capped silver nanoparticles and tryptophan), the antibiofilm efficiency of thymoquinone was expanded. In this regard, the highest antibiofilm activity was observed when thymoquinone, tryptophan, and tetrazine-capped silver nanoparticles were applied together against Pseudomonas aeruginosa. These combinatorial applications of antibiofilm molecules were found to accumulate ROS in cells that resulted in the inhibition of biofilm formation. Thus, the combinatorial study of these antibiofilm molecules could be applied to control biofilm threats as the tested antibiofilm molecules alone or in combinations showed negligible or very little cytotoxicity.}, }
@article {pmid33410938, year = {2021}, author = {Oita, S and Carey, J and Kline, I and Ibáñez, A and Yang, N and Hom, EFY and Carbone, I and U'Ren, JM and Arnold, AE}, title = {Methodological Approaches Frame Insights into Endophyte Richness and Community Composition.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33410938}, issn = {1432-184X}, abstract = {Isolating microbes is vital to study microbiomes, but insights into microbial diversity and ecology can be constrained by recalcitrant or unculturable strains. Culture-free methods (e.g., next-generation sequencing, NGS) have become popular in part because they detect greater richness than culturing alone. Both approaches are used widely to characterize microfungi within healthy leaves (foliar endophytes), but methodological differences among studies can constrain large-scale insights into endophyte ecology. We examined endophytes in a temperate plant community to quantify how certain methodological factors, such as the choice of cultivation media for culturing and storage period after leaf collection, affect inferences regarding endophyte communities; how such effects vary among plant taxa; and how complementary culturing and NGS can be when subsets of the same plant tissue are used for each. We found that endophyte richness and composition from culturing were consistent across five media types. Insights from culturing and NGS were largely robust to differences in storage period (1, 5, and 10 days). Although endophyte richness, composition, and taxonomic diversity identified via culturing vs. NGS differed markedly, both methods revealed host-structured communities. Studies differing only in cultivation media or storage period thus can be compared to estimate endophyte richness, composition, and turnover at scales larger than those of individual studies alone. Our data show that it is likely more important to sample more host species, rather than sampling fewer species more intensively, to quantify endophyte diversity in given locations, with the richest insights into endophyte ecology emerging when culturing and NGS are paired.}, }
@article {pmid33410937, year = {2021}, author = {Rodrigues, LA and da Silva, DKA and Yano-Melo, AM}, title = {Arbuscular Mycorrhizal Fungal Assemblages in Conservation Unit of Atlantic Forest Areas Under Native Vegetation and Natural Regeneration.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33410937}, issn = {1432-184X}, support = {CNPq 421241 / 2017-9//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 131015/2018-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; APQ-0003- 2.03/18//Fundação de Amparo à Ciência e Tecnologia do Estado de Pernambuco/ ; }, abstract = {Arbuscular mycorrhizal fungi (AMF) play an important role in the dynamic of plant community in the south American Atlantic Rainforest biome. Even in protected areas, this biome is under several anthropic impacts, which can cause shifts in the soil microbiota, including AMF. This study aimed to determine the structure and composition of AMF community in areas of native Atlantic Forest and in natural regeneration and to identify which abiotic factors are influencing this community in these areas. Soil samples were collected at Monte Pascoal National and Historical Park, in Southern Bahia, in native and natural regeneration areas of Atlantic Forest in two seasons (rainy and dry). Greater number of glomerospores and richness and diversity of AMF were found in the area under regeneration, with differences between seasons being observed only for the number of glomerospores. Seventy-seven species of AMF were recorded, considering all areas and seasons, with Acaulospora and Glomus being the most representative genera. Greater abundance of species of the genera Acaulospora, Claroideoglomus, and Septoglomus was found in the regeneration area. The AMF community differed between the study areas, but not between seasons, with soil attributes (pH, K, Al, Mg, m, and clay) structuring factors for this difference in the AMF community. Atlantic Forest areas in natural regeneration and the soil edaphic factors provide changes in the structure and composition of the AMF community, increasing the richness and diversity of these fungi in conservation units.}, }
@article {pmid33410936, year = {2021}, author = {St James, AR and Lin, J and Richardson, RE}, title = {Relationship Between Peat Type and Microbial Ecology in Sphagnum-Containing Peatlands of the Adirondack Mountains, NY, USA.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33410936}, issn = {1432-184X}, abstract = {Peatland microbial community composition varies with respect to a range of biological and physicochemical variables. While the extent of peat degradation (humification) has been linked to microbial community composition along vertical stratification gradients within peatland sites, across-site variations have been relatively unexplored. In this study, we compared microbial communities across ten pristine Sphagnum-containing peatlands in the Adirondack Mountains, NY, which represented three different peat types-humic fen peat, humic bog peat, and fibric bog peat. Using 16S amplicon sequencing and network correlation analysis, we demonstrate that microbial community composition is primarily linked to peat type, and that distinct taxa networks distinguish microbial communities in each type. Shotgun metagenomic sequencing of the active water table region (mesotelm) from two Sphagnum-dominated bogs-one with fibric peat and one with humic peat-revealed differences in primary carbon degradation pathways, with the fibric peat being dominated by carbohydrate metabolism and hydrogenotrophic methanogenesis, and the humic peat being dominated by aliphatic carbon metabolism and aceticlastic methanogenesis. Our results suggest that peat humification is a major factor driving microbial community dynamics across peatland ecosystems.}, }
@article {pmid33410935, year = {2021}, author = {Li, W and Nelson, KE}, title = {Microbial Species that Initially Colonize the Human Gut at Birth or in Early Childhood Can Stay in Human Body for Lifetime.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33410935}, issn = {1432-184X}, abstract = {In recent years, many studies have described the composition and function of the human microbiome at different body sites and suggested a role for the microbiome in various diseases and health conditions. Some studies, using longitudinal samples, have also suggested how the microbiome changes over time due to disease, diet, development, travel, and other environmental factors. However, to date, no study has demonstrated whether the microorganisms established at birth or in early childhood, either transmitted from parents or obtained from the environment, can stay in the human body until adult or senior age. To directly answer this question is difficult, because microbiome samples at childhood and at later adulthood for the same individual will need to be compared and the field is not old enough to have allowed for that type of sample collection. Here, using a metagenomic approach, we analyzed 1004 gut microbiome samples from senior adults (65 ± 7.8 years) from the TwinsUK cohort. Our data indicate that many species in the human gut acquired in early childhood can stay for a lifetime until senior ages. We identified the rare genomic variants (single nucleotide variation and indels) for 27 prevalent species with enough sequencing coverage for confident genomic variant identification. We found that for some species, twin pairs, including both monozygotic (MZ) and dizygotic (DZ) twins, share significantly more rare variants than unrelated subject pairs. But no significant difference is found between MZ and DZ twin pairs. These observations strongly suggest that these species acquired in early childhood remained in these persons until senior adulthood.}, }
@article {pmid33410934, year = {2021}, author = {Tan, MH and Loke, S and Croft, LJ and Gleason, FH and Lange, L and Pilgaard, B and Trevathan-Tackett, SM}, title = {First Genome of Labyrinthula sp., an Opportunistic Seagrass Pathogen, Reveals Novel Insight into Marine Protist Phylogeny, Ecology and CAZyme Cell-Wall Degradation.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33410934}, issn = {1432-184X}, support = {ADPRF//Deakin University/ ; }, abstract = {Labyrinthula spp. are saprobic, marine protists that also act as opportunistic pathogens and are the causative agents of seagrass wasting disease (SWD). Despite the threat of local- and large-scale SWD outbreaks, there are currently gaps in our understanding of the drivers of SWD, particularly surrounding Labyrinthula spp. virulence and ecology. Given these uncertainties, we investigated the Labyrinthula genus from a novel genomic perspective by presenting the first draft genome and predicted proteome of a pathogenic isolate Labyrinthula SR_Ha_C, generated from a hybrid assembly of Nanopore and Illumina sequences. Phylogenetic and cross-phyla comparisons revealed insights into the evolutionary history of Stramenopiles. Genome annotation showed evidence of glideosome-type machinery and an apicoplast protein typically found in protist pathogens and parasites. Proteins involved in Labyrinthula SR_Ha_C's actin-myosin mode of transport, as well as carbohydrate degradation were also prevalent. Further, CAZyme functional predictions revealed a repertoire of enzymes involved in breakdown of cell-wall and carbohydrate storage compounds common to seagrasses. The relatively low number of CAZymes annotated from the genome of Labyrinthula SR_Ha_C compared to other Labyrinthulea species may reflect the conservative annotation parameters, a specialized substrate affinity and the scarcity of characterized protist enzymes. Inherently, there is high probability for finding both unique and novel enzymes from Labyrinthula spp. This study provides resources for further exploration of Labyrinthula spp. ecology and evolution, and will hopefully be the catalyst for new hypothesis-driven SWD research revealing more details of molecular interactions between the Labyrinthula genus and its host substrate.}, }
@article {pmid33410933, year = {2021}, author = {Luo, Y and Wang, H and Liang, J and Qian, H and Ye, J and Chen, L and Yang, X and Chen, Z and Wang, F and Octavia, S and Payne, M and Song, X and Jiang, J and Jin, D and Lan, R}, title = {Population Structure and Multidrug Resistance of Non-O1/Non-O139 Vibrio cholerae in Freshwater Rivers in Zhejiang, China.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33410933}, issn = {1432-184X}, support = {2019JZZY011018//Key Technology Research and Development Program of Shandong/ ; }, abstract = {To understand the environmental reservoirs of Vibrio cholerae and their public health significance, we surveyed freshwater samples from rivers in two cities (Jiaxing [JX] and Jiande [JD]) in Zhejiang, China. A total of 26 sampling locations were selected, and river water was sampled 456 times from 2015 to 2016 yielding 200 V. cholerae isolates, all of which were non-O1/non-O139. The average isolation rate was 47.3% and 39.1% in JX and JD, respectively. Antibiotic resistance profiles of the V. cholerae isolates were examined with nonsusceptibility to cefazolin (68.70%, 79/115) being most common, followed by ampicillin (47.83%, 55/115) and imipenem (27.83%, 32/115). Forty-two isolates (36.52%, 42/115) were defined as multidrug resistant (MDR). The presence of virulence genes was also determined, and the majority of the isolates were positive for toxR (198/200, 99%) and hlyA (196/200, 98%) with few other virulence genes observed. The population structure of the V. cholerae non-O1/non-O139 sampled was examined using multilocus sequence typing (MLST) with 200 isolates assigned to 128 STs and 6 subpopulations. The non-O1/non-O139 V. cholerae population in JX was more varied than in JD. By clonal complexes (CCs), 31 CCs that contained isolates from this study were shared with other parts of China and/or other countries, suggesting widespread presence of some non-O1/non-O139 clones. Drug resistance profiles differed between subpopulations. The findings suggest that non-O1/non-O139 V. cholerae in the freshwater environment is a potential source of human infections. Routine surveillance of non-O1/non-O139 V. cholerae in freshwater rivers will be of importance to public health.}, }
@article {pmid33410932, year = {2021}, author = {Hutchinson, MI and Bell, TAS and Gallegos-Graves, V and Dunbar, J and Albright, M}, title = {Merging Fungal and Bacterial Community Profiles via an Internal Control.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33410932}, issn = {1432-184X}, support = {F255LANL2018//Office of Science/ ; }, abstract = {Integrated measurements of fungi and bacteria are critical to understand how interactions between these taxa drive key processes in ecosystems ranging from soils to animal guts. High-throughput amplicon sequencing is commonly used to census microbiomes, but the genetic markers targeted for fungi and bacteria (typically ribosomal regions) are domain-specific so profiling must be performed separately, obscuring relationships between these groups. To solve this problem, we developed a spike-in method with an internal control (IC) construct containing primer sites commonly used for bacterial and fungal taxonomic profiling. The internal control offers several advantages: estimation of absolute abundances, estimation of fungal to bacterial ratios (F:B), integration of bacterial and fungal profiles for holistic community analysis, and lower costs compared to other quantitation methods. To validate the IC as a scaling method, we compared IC-derived measures of F:B to measures from quantitative PCR (qPCR) using a commercial mock community (the ZymoBiomic Microbial Community DNA Standard II, containing two fungi and eight bacteria) and complex environmental samples. For both the mock community and the environmental samples, the IC produced F:B values that were statistically consistent with qPCR. Merging the environmental fungal and bacterial profiles based on the IC-derived F:B values revealed new relationships among samples in terms of community similarity. This IC method is the first spike-in method to employ a single construct for cross-domain amplicon sequencing, offering more reliable measurements.}, }
@article {pmid33410931, year = {2021}, author = {Gomez, JA and Primm, TP}, title = {A Slimy Business: the Future of Fish Skin Microbiome Studies.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33410931}, issn = {1432-184X}, abstract = {Fish skin contains a mucosal microbiome for the largest and oldest group of vertebrates, a location ideal for microbial community ecology and practical applications in agriculture and veterinary medicine. These selective microbiomes are dominated by Proteobacteria, with compositions different from the surrounding water. Core taxa are a small percentage of those present and are currently functionally uncharacterized. Methods for skin sampling, DNA extraction and amplification, and sequence data processing are highly varied across the field, and reanalysis of recent studies using a consistent pipeline revealed that some conclusions did change in statistical significance. Further, the 16S gene sequencing approaches lack quantitation of microbes and copy number adjustment. Thus, consistency in the field is a serious limitation in comparing across studies. The most significant area for future study, requiring metagenomic and metabolomics data, is the biochemical pathways and functions within the microbiome community, the interactions between members, and the resulting effects on fish host health being linked to specific nutrients and microbial species. Genes linked to skin colonization, such as those for attachment or mucin degradation, need to be uncovered and explored. Skin immunity factors need to be directly linked to microbiome composition and individual taxa. The basic foundation has been laid, and many exciting future discoveries remain.}, }
@article {pmid33408702, year = {2020}, author = {Riva, A and Kolimár, D and Spittler, A and Wisgrill, L and Herbold, CW and Abrankó, L and Berry, D}, title = {Conversion of Rutin, a Prevalent Dietary Flavonol, by the Human Gut Microbiota.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {585428}, doi = {10.3389/fmicb.2020.585428}, pmid = {33408702}, issn = {1664-302X}, abstract = {The gut microbiota plays a pivotal role in the conversion of dietary flavonoids, which can affect their bioavailability and bioactivity and thereby their health-promoting properties. The ability of flavonoids to metabolically-activate the microbiota has, however, not been systematically evaluated. In the present study, we used a fluorescence-based single-cell activity measure [biorthogonal non-canonical ammino acid-tagging (BONCAT)] combined with fluorescence activated cell sorting (FACS) to determine which microorganisms are metabolically-active after amendment of the flavonoid rutin. We performed anaerobic incubations of human fecal microbiota amended with rutin and in the presence of the cellular activity marker L-azidohomoalanine (AHA) to detect metabolically-active cells. We found that 7.3% of cells in the gut microbiota were active after a 6 h incubation and 26.9% after 24 h. We then sorted BONCAT-positive cells and observed an enrichment of Lachnospiraceae (Lachnoclostridium and Eisenbergiella), Enterobacteriaceae, Tannerellaceae, and Erysipelotrichaceae species in the rutin-responsive fraction of the microbiota. There was marked inter-individual variability in the appearance of rutin conversion products after incubation with rutin. Consistent with this, there was substantial variability in the abundance of rutin-responsive microbiota among different individuals. Specifically, we observed that Enterobacteriaceae were associated with conversion of rutin into quercetin-3-glucoside (Q-glc) and Lachnospiraceae were associated with quercetin (Q) production. This suggests that individual microbiotas differ in their ability to metabolize rutin and utilize different conversion pathways.}, }
@article {pmid33408369, year = {2021}, author = {Meisner, A and Snoek, BL and Nesme, J and Dent, E and Jacquiod, S and Classen, AT and Priemé, A}, title = {Soil microbial legacies differ following drying-rewetting and freezing-thawing cycles.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {33408369}, issn = {1751-7370}, support = {330-2014-6430//Vetenskapsrådet (Swedish Research Council)/ ; Cofund Project INCA600398//EC | EC Seventh Framework Programm | FP7 People: Marie-Curie Actions (FP7-PEOPLE - Specific Programme &quot;People&quot; Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))/ ; }, abstract = {Climate change alters frequencies and intensities of soil drying-rewetting and freezing-thawing cycles. These fluctuations affect soil water availability, a crucial driver of soil microbial activity. While these fluctuations are leaving imprints on soil microbiome structures, the question remains if the legacy of one type of weather fluctuation (e.g., drying-rewetting) affects the community response to the other (e.g., freezing-thawing). As both phenomenons give similar water availability fluctuations, we hypothesized that freezing-thawing and drying-rewetting cycles have similar effects on the soil microbiome. We tested this hypothesis by establishing targeted microcosm experiments. We created a legacy by exposing soil samples to a freezing-thawing or drying-rewetting cycle (phase 1), followed by an additional drying-rewetting or freezing-thawing cycle (phase 2). We measured soil respiration and analyzed soil microbiome structures. Across experiments, larger CO2 pulses and changes in microbiome structures were observed after rewetting than thawing. Drying-rewetting legacy affected the microbiome and CO2 emissions upon the following freezing-thawing cycle. Conversely, freezing-thawing legacy did not affect the microbial response to the drying-rewetting cycle. Our results suggest that drying-rewetting cycles have stronger effects on soil microbial communities and CO2 production than freezing-thawing cycles and that this pattern is mediated by sustained changes in soil microbiome structures.}, }
@article {pmid33406784, year = {2021}, author = {Mayta-Apaza, AC and García-Cano, I and Dabrowski, K and Jiménez-Flores, R}, title = {Bacterial Diversity Analysis and Evaluation Proteins Hydrolysis During the Acid Whey and Fish Waste Fermentation.}, journal = {Microorganisms}, volume = {9}, number = {1}, pages = {}, doi = {10.3390/microorganisms9010100}, pmid = {33406784}, issn = {2076-2607}, abstract = {The disposal of acid whey (Aw), a by-product from fermented products, is a problem for the dairy industry. The fishery industry faces a similar dilemma, disposing of nearly 50% of fish processed for human consumption. Economically feasible and science-based alternatives are needed to overcome this problem. One possible solution is to add value to the remaining nutrients from these by-products. This study focuses on the breakdown of nutrients in controlled fermentations of Aw, fish waste (F), molasses (M), and a lactic acid bacteria (LAB) strain (Lr). The aim was to assess the dynamic variations in microbial diversity and the biochemical changes that occur during fermentation. Four treatments were compared (AwF, AwFM, AwFLr, and AwFMLr), and the fermentation lasted 14 days at 22.5 °C. Samples were taken every other day. Colorimetric tests for peptide concentrations, pH, and microbial ecology by 16S-v4 rRNA amplicon using Illumina MiSeq were conducted. The results of the microbial ecology showed elevated levels of alpha and beta diversity in the samples at day zero. By day 2 of fermentation, pH dropped, and the availability of a different set of nutrients was reflected in the microbial diversity. The fermentation started to stabilize and was driven by the Firmicutes phylum, which dominated the microbial community by day 14. Moreover, there was a significant increase (3.6 times) in peptides when comparing day 0 with day 14, making this treatment practical and feasible for protein hydrolysis. This study valorizes two nutrient-dense by-products and provides an alternative to the current handling of these materials.}, }
@article {pmid33406135, year = {2021}, author = {Kanzaki, N and Ekino, T and Hamaguchi, K and Takeuchi-Kaneko, Y}, title = {Three Seinura species from Japan with a description of S. shigaensis n. sp. (Tylenchomorpha: Aphelenchoididae).}, journal = {PloS one}, volume = {16}, number = {1}, pages = {e0244653}, doi = {10.1371/journal.pone.0244653}, pmid = {33406135}, issn = {1932-6203}, abstract = {A preliminary survey of Seinura spp. was conducted in the Kyoto area, Western Japan. The survey yielded four new strains of Seinura spp., including two strains of S. caverna, a strain of S. italiensis, and a strain of an undescribed species. Molecularly, the two strains of S. caverna were nearly identical to the type strain but showed some minor variations, particularly in the mitochondrial cytochrome oxidase subunit I gene. The small subunit and D2-D3 large subunit sequences of the Japanese strain of S. italiensis were nearly identical and identical to its original description, respectively, and the difference in the small subunit was due to mis-reading of the sequences. The new species, S. shigaensis n. sp., was phylogenetically close to S. caverna and S. persica, although these three species were clearly different phylogenetically. The new species was typologically similar or nearly identical to several other Seinura spp., including S. chertkovi, S. christiei, S. italiensis, S. steineri, and S. tenuicaudata, but it can be distinguished from those species by the morphometric values. Because the new species is phylogenetically very close to S. caverna, it could be a good comparative system for S. caverna as a potential satellite model for the predatory nematode.}, }
@article {pmid33404822, year = {2021}, author = {Álvarez-Pérez, S and Tsuji, K and Donald, M and Van Assche, A and Vannette, RL and Herrera, CM and Jacquemyn, H and Fukami, T and Lievens, B}, title = {Nitrogen Assimilation Varies Among Clades of Nectar- and Insect-Associated Acinetobacters.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33404822}, issn = {1432-184X}, support = {742964//H2020 Marie Skłodowska-Curie Actions/ ; DEB 1737758//National Science Foundation/ ; RYC2018-023847-I//Secretaría de Estado de Investigación, Desarrollo e Innovación/ ; }, abstract = {Floral nectar is commonly colonized by yeasts and bacteria, whose growth largely depends on their capacity to assimilate nutrient resources, withstand high osmotic pressures, and cope with unbalanced carbon-to-nitrogen ratios. Although the basis of the ecological success of these microbes in the harsh environment of nectar is still poorly understood, it is reasonable to assume that they are efficient nitrogen scavengers that can consume a wide range of nitrogen sources in nectar. Furthermore, it can be hypothesized that phylogenetically closely related strains have more similar phenotypic characteristics than distant relatives. We tested these hypotheses by investigating the growth performance on different nitrogen-rich substrates of a collection of 82 acinetobacters isolated from nectar and honeybees, representing members of five species (Acinetobacter nectaris, A. boissieri, A. apis, and the recently described taxa A. bareti and A. pollinis). We also analyzed possible links between growth performance and phylogenetic affiliation of the isolates, while taking into account their geographical origin. Results demonstrated that the studied isolates could utilize a wide variety of nitrogen sources, including common metabolic by-products of yeasts (e.g., ammonium and urea), and that phylogenetic relatedness was associated with the variation in nitrogen assimilation among the studied acinetobacters. Finally, nutrient source and the origin (sample type and country) of isolates also predicted the ability of the acinetobacters to assimilate nitrogen-rich compounds. Overall, these results demonstrate inter-clade variation in the potential of the acinetobacters as nitrogen scavengers and suggest that nutritional dependences might influence interactions between bacteria and yeasts in floral nectar.}, }
@article {pmid33404821, year = {2021}, author = {Shar, S and Reith, F and Ball, AS and Shahsavari, E}, title = {Long-term Impact of Gold and Platinum on Microbial Diversity in Australian Soils.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33404821}, issn = {1432-184X}, support = {ARC-FT100150200//Australian Research Council/ ; }, abstract = {The effects of platinum (Pt) and gold (Au) and on the soil bacterial community was evaluated in four different Australian soil types (acidic Burn Grounds (BGR), organic matter-rich Fox Lane, high silt/metal Pinpinio (PPN), and alkali Minnipa (MNP) spiked with either Pt or Au at 1, 25, and 100 mg kg-1 using a next-generation sequencing approach (amplicon-based, MiSeq). Soil type and metal concentrations were observed to be key drivers of Pt and Au effects on soil microbial community structure. Different trends were therefore observed in the response of the bacterial community to Pt and Au amendments; however in each soil type, Pt and Au amendment caused a detectable shift in community structure that in most samples was positively correlated with increasing metal concentrations. New dominant groups were only observed in BGR and PPN soils at 100 mg kg-1 (Kazan-3B-28 and Verrucomicrobia groups (BGR, Pt) and Firmicutes and Caldithrix groups (PPN, Pt) and WS2 (BGR, Au). The effects of Pt on soil microbial diversity were largely adverse at 100 mg kg-1 and were pronounced in acidic, basic, and metal/silt-rich soils. However, this effect was concentration-related; Au appeared to be more toxic to soil bacterial communities than Pt at 25 mg kg-1 but Pt was more toxic at 100 mg kg-1. More bacterial groups such as those belonging to Burkholderiales/Burkholderiaceae, Alicyclobacillaceae, Rubrobacteraceae, Cytophagaceae, Oxalobacteraceae were selectively enriched by Pt compared to Au (Sphingomonadaceae and Rhodospirillaceae) amendments irrespective of soil type. The research outcomes have important implications in the management (remediation) of Pt- and Au-contaminated environments.}, }
@article {pmid33404820, year = {2021}, author = {Leiva, D and Fernández-Mendoza, F and Acevedo, J and Carú, M and Grube, M and Orlando, J}, title = {The Bacterial Community of the Foliose Macro-lichen Peltigera frigida Is More than a Mere Extension of the Microbiota of the Subjacent Substrate.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33404820}, issn = {1432-184X}, support = {1181510//Fondo Nacional de Desarrollo Científico y Tecnológico/ ; }, abstract = {Lichens host highly diverse microbial communities, with bacteria being one of the most explored groups in terms of their diversity and functioning. These bacteria could partly originate from symbiotic propagules developed by many lichens and, perhaps more commonly and depending on environmental conditions, from different sources of the surroundings. Using the narrowly distributed species Peltigera frigida as an object of study, we propose that bacterial communities in these lichens are different from those in their subjacent substrates, even if some taxa might be shared. Ten terricolous P. frigida lichens and their substrates were sampled from forested sites in the Coyhaique National Reserve, located in an understudied region in Chile. The mycobiont identity was confirmed using partial 28S and ITS sequences. Besides, 16S fragments revealed that mycobionts were associated with the same cyanobacterial haplotype. From both lichens and substrates, Illumina 16S amplicon sequencing was performed using primers that exclude cyanobacteria. In lichens, Proteobacteria was the most abundant phylum (37%), whereas soil substrates were dominated by Acidobacteriota (39%). At lower taxonomic levels, several bacterial groups differed in relative abundance among P. frigida lichens and their substrates, some of them being highly abundant in lichens but almost absent in substrates, like Sphingomonas (8% vs 0.2%), and others enriched in lichens, as an unassigned genus of Chitinophagaceae (10% vs 2%). These results reinforce the idea that lichens would carry some components of their microbiome when propagating, but they also could acquire part of their bacterial community from the substrates.}, }
@article {pmid33404819, year = {2021}, author = {Ogaki, MB and Pinto, OHB and Vieira, R and Neto, AA and Convey, P and Carvalho-Silva, M and Rosa, CA and Câmara, PEAS and Rosa, LH}, title = {Fungi Present in Antarctic Deep-Sea Sediments Assessed Using DNA Metabarcoding.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33404819}, issn = {1432-184X}, abstract = {We assessed fungal diversity in deep-sea sediments obtained from different depths in the Southern Ocean using the internal transcribed spacer 2 (ITS2) region of nuclear ribosomal DNA by metabarcoding through high-throughput sequencing (HTS). We detected 655,991 DNA reads representing 263 fungal amplicon sequence variants (ASVs), dominated by Ascomycota, Basidiomycota, Mortierellomycota, Mucoromycota, Chytridiomycota and Rozellomycota, confirming that deep-sea sediments can represent a hotspot of fungal diversity in Antarctica. The community diversity detected included 17 dominant fungal ASVs, 62 intermediate and 213 rare. The dominant fungi included taxa of Mortierella, Penicillium, Cladosporium, Pseudogymnoascus, Phaeosphaeria and Torula. Despite the extreme conditions of the Southern Ocean benthos, the total fungal community detected in these marine sediments displayed high indices of diversity and richness, and moderate dominance, which varied between the different depths sampled. The highest diversity indices were obtained in sediments from 550 m and 250 m depths. Only 49 ASVs (18.63%) were detected at all the depths sampled, while 16 ASVs were detected only in the deepest sediment sampled at 1463 m. Based on sequence identities, the fungal community included some globally distributed taxa, primarily recorded otherwise from terrestrial environments, suggesting transport from these to deep marine sediments. The assigned taxa included symbionts, decomposers and plant-, animal- and human-pathogenic fungi, suggesting that deep-sea sediments host a complex fungal diversity, although metabarcoding does not itself confirm that living or viable organisms are present.}, }
@article {pmid33404818, year = {2021}, author = {Liu, Y and Anastacio, GR and Ishangulyyeva, G and Rodriguez-Ramos, JC and Erbilgin, N}, title = {Mutualistic Ophiostomatoid Fungi Equally Benefit from Both a Bark Beetle Pheromone and Host Tree Volatiles as Nutrient Sources.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33404818}, issn = {1432-184X}, abstract = {Interactions between mutualistic bark beetles and ophiostomatoid fungi have received considerable attention in recent years. Studies have shown how volatile organic compounds emitted from mutualist fungi affect the behaviors of several bark beetle species. However, we currently lack sufficient knowledge regarding whether bark beetle pheromones can influence mutualist fungi. Here, we measured growth and biomass of two mutualistic fungi of the mountain pine beetle in response to headspace of a beetle pheromone (trans-verbenol), a blend of host tree volatiles, the combination of both, or control (no volatile source) in vitro experiments consisting of a nitrogen-based medium. The surface area and ergosterol content of the mycelia were used as surrogates for fungal growth and biomass respectively. We found that both growth and biomass of Grosmannia clavigera and Ophiostoma montium were greater in medium exposed to any type of volatile sources than the control. While growth and ergosterol content of G. clavigera were highest in the combination treatment, there were no differences in growth or biomass among the types of volatiles introduced for O. montium. These results suggest that both mutualistic fungi can utilize both bark beetle pheromone and host tree volatiles as nutrient sources. Overall, these results support the on-going studies on the role of volatile organic compounds mediating mutualistic bark beetle-fungi interactions.}, }
@article {pmid33401417, year = {2021}, author = {Savadova-Ratkus, K and Mazur-Marzec, H and Karosienė, J and Kasperovičienė, J and Paškauskas, R and Vitonytė, I and Koreivienė, J}, title = {Interplay of Nutrients, Temperature, and Competition of Native and Alien Cyanobacteria Species Growth and Cyanotoxin Production in Temperate Lakes.}, journal = {Toxins}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/toxins13010023}, pmid = {33401417}, issn = {2072-6651}, support = {European Network for Algal Bioproducts (EUALGAE).//European Cooperation in Science and Technology (COST) Action ES1408/ ; }, abstract = {Global warming and eutrophication contribute to formation of HABs and distribution of alien cyanobacteria northward. The current study assessed how alien to Europe Sphaerospermopsis aphanizomenoides and Chrysosporum bergii will co-occur with dominant native Planktothrix agardhii and Aphanizomenon gracile species under changing conditions in temperate freshwaters. The experiments were carried out to examine the effect of nutrients and temperature on the growth rate of cyanobacteria, production of cyanotoxins, and interspecies competition. The highest growth rate was determined for A. gracile (0.43 day-1) and S. aphanizomenoides (0.40 day-1) strains at all the tested nutrient concentrations (IP and IN were significant factors). S. aphanizomenoides adapted to the wide range of nutrient concentrations and temperature due to high species ecological plasticity; however, A. gracile was able to suppress its dominance under changing conditions. Regularity between tested variables and STX concentration in A. gracile was not found, but IP concentration negatively correlated with the amount of dmMC-RR and other non-ribosomal peptides (NRPs) in P. agardhii strains. The relative concentration of NRPs in nontoxic P. agardhii strain was up to 3-fold higher than in MC-producing strain. Our study indicated that nutrients, temperature, and species had significant effects on interspecies competition. A. gracile had a negative effect on biomass of both alien species and P. agardhii.}, }
@article {pmid33399932, year = {2021}, author = {Aguero, CM and Eyer, PA and Crippen, TL and Vargo, EL}, title = {Reduced Environmental Microbial Diversity on the Cuticle and in the Galleries of a Subterranean Termite Compared to Surrounding Soil.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33399932}, issn = {1432-184X}, abstract = {Termites are intimately tied to the microbial world, as they utilize their gut microbiome for the conversion of plant cellulose into necessary nutrients. Subterranean termites must also protect themselves from the vast diversity of harmful microbes found in soil. However, not all soil microbes are harmful, such as Streptomyces and methanotrophic bacteria that some species of termites harbor in complex nest structures made of fecal material. The eastern subterranean termite, Reticulitermes flavipes, has a simple nest structure consisting of fecal lined galleries. We tested the hypothesis that R. flavipes maintains a select microbial community in its nests to limit the penetration of harmful soilborne pathogens and favor the growth of beneficial microbes. Using Illumina sequencing, we characterized the bacterial and fungal communities in the surrounding soil, in the nest galleries, and on the cuticle of workers. We found that the galleries provide a more beneficial microbial community than the surrounding soil. Bacterial and fungal diversity was highest in the soil, lower in the galleries, and least on the cuticle. Bacterial communities clustered together according to the substrate from which they were sampled, but this clustering was less clear in fungal communities. Most of the identified bacterial and fungal taxa were unique to one substrate, but the soil and gallery communities had very similar phylum-level taxonomic profiles. Notably, the galleries of R. flavipes also harbored both the potentially beneficial Streptomyces and the methanotrophic Methylacidiphilales, indicating that these microbial associations in fecal material pre-date the emergence of complex fecal nest structures. Surprisingly, several pathogenic groups were relatively abundant in the galleries and on the cuticle, suggesting that pathogens may accumulate within termite nests over time while putatively remaining at enzootic level during the lifetime of the colony.}, }
@article {pmid33399931, year = {2021}, author = {Shih, CM and Ophine, L and Chao, LL}, title = {Molecular Detection and Genetic Identification of Wolbachia Endosymbiont in Wild-Caught Culex quinquefasciatus (Diptera: Culicidae) Mosquitoes from Sumatera Utara, Indonesia.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33399931}, issn = {1432-184X}, support = {MOST 109-2314-B-037-077//Ministry of Science and Technology, Taiwan/ ; }, abstract = {The genetic identity of Wolbachia endosymbiont in wild-caught Culex quinquefasciatus was determined for the first time in Indonesia. A total of 314 Cx. quinquefasciatus were examined for Wolbachia by PCR assay targeting the Wolbachia surface protein (wsp) gene. The prevalence of Wolbachia infection was detected in 29.94% of Cx. specimens (45.86% female and 8.27% male). The group-specific infection was detected with an infection rate of 0.32%, 28.98%, and 0.64% in groups A, B, and A&amp;B, respectively. Phylogenetic analysis revealed all Wolbachia strains from Indonesia were genetically affiliated to the supergroup A and B with the high sequence similarity of 97.9-100% and 99.7-100%, respectively. Phylogenetic relationships can be easily distinguished by neighbor-joining analysis and were congruent by maximum likelihood method. The genetic distance (GD) values of intra- and inter-group analysis indicated a lower level (GD < 0.007 for group A and GD < 0.003 for group B) within the Indonesia strains and a higher level (GD > 1.125 for group A and GD > 1.129 for group B) as compared with other Wolbachia strains. Our results provide the first genetic identification of Wolbachia endosymbiont in Cx. quinquefasciatus collected from Indonesia, and the phylogenetic analysis revealed a new discovery of group A Wolbachia in wild-caught Cx. quinquefasciatus mosquitoes.}, }
@article {pmid33399896, year = {2021}, author = {Asha, K and Bhadury, P}, title = {Myceligenerans indicum sp. nov., an actinobacterium isolated from mangrove sediment of Sundarbans, India.}, journal = {Archives of microbiology}, volume = {}, number = {}, pages = {}, pmid = {33399896}, issn = {1432-072X}, abstract = {A new actinobacterial species of the genus Myceligenerans has been isolated from the intertidal sediment of Indian Sundarbans mangrove ecosystem. The isolate has been characterized based on polyphasic approaches. The isolate exhibit well-developed substrate mycelia along with the presence of cocci- and rod-shaped elements. The organism can grow across a wide range of temperature, salinity, and pH as well as on different carbon sources. Phylogenetic analyses based on 16S rRNA showed that this isolate is closely related to Myceligenerans salitolerans XHU 5031 (99% identity; 100% coverage). Presence of ketosynthase domain representing polyketide synthases in the isolate provides evidence of its potential ability to produce secondary metabolites. Multigene phylogeny based on atpD and rpoB gene sequences confirmed it as a new species within the family Promicromonosporaceae (Phylum Actinobacteria). The DNA G + C content of the isolate has been determined as 72 mol%. The peptidoglycan type was A4α and the whole-cell hydrolysates contained glucose, galactose, and mannose. The polar lipids were represented by diphosphatidylglycerol, one unknown phospholipid and one unknown glycolipid. Major fatty acids present in the isolate are anteiso-C15, iso-C15, iso-C16, and anteiso-C17. Whole-genome sequence indicates the size of genome is ~ 5 Mbp. GGDC (%), orthoANIu (%), and AAI of I2 genome indicated 28.9%, 77.44% and 0.859 identity with the genome of Myceligenerans xiligouense strain DSM 15,700. The isolate I2 has been proposed as a new species, Myceligenerans indicum sp. nov. The genome sequence has been deposited to GenBank/ENA/DDBJ under the accession number JABBYC000000000.}, }
@article {pmid33398112, year = {2021}, author = {Marco, ML and Sanders, ME and Gänzle, M and Arrieta, MC and Cotter, PD and De Vuyst, L and Hill, C and Holzapfel, W and Lebeer, S and Merenstein, D and Reid, G and Wolfe, BE and Hutkins, R}, title = {The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on fermented foods.}, journal = {Nature reviews. Gastroenterology &amp; hepatology}, volume = {}, number = {}, pages = {}, pmid = {33398112}, issn = {1759-5053}, abstract = {An expert panel was convened in September 2019 by The International Scientific Association for Probiotics and Prebiotics (ISAPP) to develop a definition for fermented foods and to describe their role in the human diet. Although these foods have been consumed for thousands of years, they are receiving increased attention among biologists, nutritionists, technologists, clinicians and consumers. Despite this interest, inconsistencies related to the use of the term 'fermented' led the panel to define fermented foods and beverages as &quot;foods made through desired microbial growth and enzymatic conversions of food components&quot;. This definition, encompassing the many varieties of fermented foods, is intended to clarify what is (and is not) a fermented food. The distinction between fermented foods and probiotics is further clarified. The panel also addressed the current state of knowledge on the safety, risks and health benefits, including an assessment of the nutritional attributes and a mechanistic rationale for how fermented foods could improve gastrointestinal and general health. The latest advancements in our understanding of the microbial ecology and systems biology of these foods were discussed. Finally, the panel reviewed how fermented foods are regulated and discussed efforts to include them as a separate category in national dietary guidelines.}, }
@article {pmid33396683, year = {2020}, author = {Kuramae, EE and Dimitrov, MR and da Silva, GHR and Lucheta, AR and Mendes, LW and Luz, RL and Vet, LEM and Fernandes, TV}, title = {On-Site Blackwater Treatment Fosters Microbial Groups and Functions to Efficiently and Robustly Recover Carbon and Nutrients.}, journal = {Microorganisms}, volume = {9}, number = {1}, pages = {}, doi = {10.3390/microorganisms9010075}, pmid = {33396683}, issn = {2076-2607}, support = {729.004.003//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 2013/50351-4//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 206884/2014-1//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 99999.008090/2015-07;0622/2014//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; }, abstract = {Wastewater is considered a renewable resource water and energy. An advantage of decentralized sanitation systems is the separation of the blackwater (BW) stream, contaminated with human pathogens, from the remaining household water. However, the composition and functions of the microbial community in BW are not known. In this study, we used shotgun metagenomics to assess the dynamics of microbial community structure and function throughout a new BW anaerobic digestion system installed at The Netherlands Institute of Ecology. Samples from the influent (BW), primary effluent (anaerobic digested BW), sludge and final effluent of the pilot upflow anaerobic sludge blanket (UASB) reactor and microalgae pilot tubular photobioreactor (PBR) were analyzed. Our results showed a decrease in microbial richness and diversity followed by a decrease in functional complexity and co-occurrence along the different modules of the bioreactor. The microbial diversity and function decrease were reflected both changes in substrate composition and wash conditions. Our wastewater treatment system also decreased microbial functions related to pathogenesis. In summary, the new sanitation system studied here fosters microbial groups and functions that allow the system to efficiently and robustly recover carbon and nutrients while reducing pathogenic groups, ultimately generating a final effluent safe for discharge and reuse.}, }
@article {pmid33392630, year = {2021}, author = {Oliveira, MM and Proenca, AM and Moreira-Silva, E and de Castro, AM and Dos Santos, FM and Marconatto, L and Medina-Silva, R}, title = {Biofilms of Pseudomonas and Lysinibacillus Marine Strains on High-Density Polyethylene.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33392630}, issn = {1432-184X}, support = {001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 0050.0096017.15.9//Petrobras/ ; }, abstract = {Environmental pollution by plastic debris is estimated on a scale of 100 million metric tons, a portion of which is fragmented into micro- and nanoplastics. These fragments are often colonized by bacterial species in marine environments, possibly contributing to the biodegradation of such materials. However, further investigations are necessary to determine the impact of abiotic polymer weathering on biofilm adhesion, as well as the specific biofilm formation strategies employed by marine isolates. Here, we evaluate deep-sea sediment bacterial isolates for biofilm adhesion, extracellular matrix production, and polymer degradation ability. Our study focuses on high-density polyethylene (HDPE) fragments for their high durability and environmental persistence, subjecting fragments to abiotic weathering prior to bacterial colonization. Marine isolates identified as Pseudomonas sp. and Lysinibacillus sp. exhibited decreasing biofilm formation on weathered HDPE, especially over the first 24 h of incubation. This effect was countered by increased extracellular matrix production, likely improving cell adhesion to surfaces roughened by abiotic degradation. These adhesion strategies were contrasted with a reference Pseudomonas aeruginosa strain, which displayed high levels of biofilm formation on non-weathered HDPE and lower extracellular matrix production over the first 24 h of incubation. Furthermore, our results suggest that an increase in biofilm biomass correlated with changes to HDPE structure, indicating that these strains have a potential for biodegradation of plastic fragments. Therefore, this work provides a detailed account of biofilm formation strategies and bacteria-plastic interactions that represent crucial steps in the biodegradation of plastic fragments in marine environments.}, }
@article {pmid33392629, year = {2021}, author = {do Carmo Linhares, D and Saia, FT and Duarte, RTD and Nakayama, CR and de Melo, IS and Pellizari, VH}, title = {Methanotrophic Community Detected by DNA-SIP at Bertioga's Mangrove Area, Southeast Brazil.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33392629}, issn = {1432-184X}, support = {04/13910-6//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2009/06601-0//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; }, abstract = {Methanotrophic bacteria can use methane as sole carbon and energy source. Its importance in the environment is related to the mitigation of methane emissions from soil and water to the atmosphere. Brazilian mangroves are highly productive, have potential to methane production, and it is inferred that methanotrophic community is of great importance for this ecosystem. The scope of this study was to investigate the functional and taxonomic diversity of methanotrophic bacteria present in the anthropogenic impacted sediments from Bertioga´s mangrove (SP, Brazil). Sediment sample was cultivated with methane and the microbiota actively involved in methane oxidation was identified by DNA-based stable isotope probing (DNA-SIP) using methane as a labeled substrate. After 4 days (96 h) of incubation and consumption of 0.7 mmol of methane, the most active microorganisms were related to methanotrophs Methylomonas and Methylobacter as well as to methylotrophic Methylotenera, indicating a possible association of these bacterial groups within a methane-derived food chain in the Bertioga mangrove. The abundance of genera Methylomonas, able to couple methane oxidation to nitrate reduction, may indicate that under low dissolved oxygen tensions, some aerobic methanotrophs could shift to intraerobic methane oxidation to avoid oxygen starvation.}, }
@article {pmid33392628, year = {2021}, author = {Vega, L and Jaimes, J and Morales, D and Martínez, D and Cruz-Saavedra, L and Muñoz, M and Ramírez, JD}, title = {Microbial Communities' Characterization in Urban Recreational Surface Waters Using Next Generation Sequencing.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33392628}, issn = {1432-184X}, support = {Dirección de Investigación e Innovación//Universidad del Rosario/ ; }, abstract = {Microbial communities in surface waters used for recreational purposes are indicators of contamination and risk of contact with human pathogens. Hence, monitoring microbial communities in recreational waters is important for potential public health threats to humans. Such monitoring is rare in Colombia, even in its capital, Bogotá, the most populous city in the country. This city encompasses metropolitan and linear parks with recreational water bodies that are used frequently by the public, and the presence of pathogens can compromise the health of the citizens. Therefore, we examined the bacterial, and eukaryotic communities in urban recreational lakes (URL) in four metropolitan parks in Bogotá, Colombia. Samples from four metropolitan parks (Los Novios, Simon Bolivar, El Tunal, and Timiza) and one stream contaminated with sewage from a linear park (El Virrey) were collected. We used amplicon next-generation sequencing of the 16S-rRNA gene and 18S-rRNA gene to characterize microbial communities followed by bioinformatics analyses. In addition, general water quality parameters-pH, hardness, acidity, alkalinity, dissolved oxygen, and nitrites-were recorded using a commercial kit. Genera of pathogens, including Legionella, Pseudomonas, Mycobacterium, Candida, and Naegleria, were found in lake waters. The stream El Virrey was, however, the only surface water that showed an abundance of fecal bacteria, often associated with low oxygen concentrations. All water bodies showed a predominance of fungal phyla, except for the lake at Timiza. This lake showed the highest pH, and its ecological dynamics are likely different from other water bodies. Likewise, some URLs displayed a greater abundance of cyanobacteria, including toxin-producing species. Algal genera associated with eutrophication were predominant among primary producing microorganisms. This study shows for the first time the description of the bacterial and eukaryotic communities of some URLs and a stream in Bogotá. The URLs and the stream harbored various pathogens that might pose a risk to the citizen's health.}, }
@article {pmid33392158, year = {2020}, author = {Cerruti, M and Stevens, B and Ebrahimi, S and Alloul, A and Vlaeminck, SE and Weissbrodt, DG}, title = {Enrichment and Aggregation of Purple Non-sulfur Bacteria in a Mixed-Culture Sequencing-Batch Photobioreactor for Biological Nutrient Removal From Wastewater.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {8}, number = {}, pages = {557234}, doi = {10.3389/fbioe.2020.557234}, pmid = {33392158}, issn = {2296-4185}, abstract = {Mixed-culture biotechnologies are widely used to capture nutrients from wastewater. Purple non-sulfur bacteria (PNSB), a guild of anoxygenic photomixotrophic organisms, rise interest for their ability to directly assimilate nutrients in the biomass. One challenge targets the aggregation and accumulation of PNSB biomass to separate it from the treated water. Our aim was to enrich and produce a concentrated, fast-settling PNSB biomass with high nutrient removal capacity in a 1.5-L, stirred-tank, anaerobic sequencing-batch photobioreactor (SBR). PNSB were rapidly enriched after inoculation with activated sludge at 0.1 gVSS L-1 in a first batch of 24 h under continuous irradiance of infrared (IR) light (>700 nm) at 375 W m-2, with Rhodobacter reaching 54% of amplicon sequencing read counts. SBR operations with decreasing hydraulic retention times (48 to 16 h, i.e., 1-3 cycles d-1) and increasing volumetric organic loading rates (0.2-1.3 kg COD d-1 m-3) stimulated biomass aggregation, settling, and accumulation in the system, reaching as high as 3.8 g VSS L-1. The sludge retention time (SRT) increased freely from 2.5 to 11 days. Acetate, ammonium, and orthophosphate were removed up to 96% at a rate of 1.1 kg COD d-1 m-3, 77% at 113 g N d-1 m-3, and 73% at 15 g P d-1 m-3, respectively, with COD:N:P assimilation ratio of 100:6.7:0.9 m/m/m. SBR regime shifts sequentially selected for Rhodobacter (90%) under shorter SRT and non-limiting concentration of acetate during reaction phases, for Rhodopseudomonas (70%) under longer SRT and acetate limitation during reaction, and Blastochloris (10%) under higher biomass concentrations, underlying competition for substrate and photons in the PNSB guild. With SBR operations we produced a fast-settling biomass, highly (>90%) enriched in PNSB. A high nutrient removal was achieved by biomass assimilation, reaching the European nutrient discharge limits. We opened further insights on the microbial ecology of PNSB-based processes for water resource recovery.}, }
@article {pmid33391698, year = {2020}, author = {Kroetsch, SA and Kidd, KA and Monk, WA and Culp, JM and Compson, ZG and Pavey, SA}, title = {The effects of taxonomy, diet, and ecology on the microbiota of riverine macroinvertebrates.}, journal = {Ecology and evolution}, volume = {10}, number = {24}, pages = {14000-14019}, doi = {10.1002/ece3.6993}, pmid = {33391698}, issn = {2045-7758}, abstract = {Freshwater macroinvertebrates play key ecological roles in riverine food webs, such as the transfer of nutrients to consumers and decomposition of organic matter. Although local habitat quality drives macroinvertebrate diversity and abundance, little is known about their microbiota. In most animals, the microbiota provides benefits, such as increasing the rate at which nutrients are metabolized, facilitating immune system development, and defending against pathogenic attack. Our objectives were to identify the bacteria within aquatic invertebrates and determine whether their composition varied with taxonomy, habitat, diet, and time of sample collection. In 2016 and 2017, we collected 264 aquatic invertebrates from the mainstem Saint John (Wolastoq) River in New Brunswick, Canada, representing 15 orders. We then amplified the V3-V4 hypervariable region of the 16S rRNA gene within each individual, which revealed nearly 20,000 bacterial operational taxonomic units (OTUs). The microbiota across all aquatic invertebrates were dominated by Proteobacteria (69.25% of the total sequence reads), but they differed significantly in beta diversity, both among host invertebrate taxa (genus-, family-, and order-levels) and temporally. In contrast to previous work, we observed no microbiota differences among functional feeding groups or traditional feeding habits, and neither water velocity nor microhabitat type structured microbiota variability. Our findings suggest that host invertebrate taxonomy was the most important factor in modulating the composition of the microbiota, likely through a combination of vertical and horizontal bacterial transmission, and evolutionary processes. This is one of the most comprehensive studies of freshwater invertebrate microbiota to date, and it underscores the need for future studies of invertebrate microbiota evolution and linkages to environmental bacteria and physico-chemical conditions.}, }
@article {pmid32941745, year = {2020}, author = {Fu, S and Ni, P and Yang, Q and Hu, H and Wang, Q and Ye, S and Liu, Y}, title = {Delineating the key virulence factors and intraspecies divergence of Vibrio harveyi via whole-genome sequencing.}, journal = {Canadian journal of microbiology}, volume = {}, number = {}, pages = {1-18}, doi = {10.1139/cjm-2020-0079}, pmid = {32941745}, issn = {1480-3275}, abstract = {Vibrio harveyi is one of the major pathogens in aquaculture. To identify the key virulence factors affecting pathogenesis of V. harveyi towards fish, we conducted a field investigation for three representative fish farms infected with V. harveyi. Multilocus sequence typing (MLST) and whole-genome sequencing were conducted to delineate the phylogenetic relationship and genetic divergence of V. harveyi. A total of 25 V. harveyi strains were isolated from the diseased fish and groundwater and were subtyped into 12 sequence types by MLST. Five virulence genes, mshB, pilA, hutR, ureB, and ureG, were variably presented in the sequenced strains. The virulence gene profiles strongly correlated with the distinct pathogenicity of V. harveyi strains, with a strain harboring all five genes exhibiting the highest virulence towards fish. Phenotype assay confirmed that reduced virulence correlated with decreased motility and biofilm formation ability. Additionally, three types of type VI secretion system, namely T6SS1, T6SS2, and T6SS3, were identified in V. harveyi strains, which can be classified into six, four, and 12 subtypes, respectively. In conclusion, the results indicated that the virulence level of V. harveyi is mainly determined by the above virulence genes, which may play vital roles in environmental adaptation for V. harveyi.}, }
@article {pmid33388944, year = {2021}, author = {Saona, LA and Soria, M and Durán-Toro, V and Wörmer, L and Milucka, J and Castro-Nallar, E and Meneses, C and Contreras, M and Farías, ME}, title = {Phosphate-Arsenic Interactions in Halophilic Microorganisms of the Microbial Mat from Laguna Tebenquiche: from the Microenvironment to the Genomes.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33388944}, issn = {1432-184X}, support = {1200834//ANID-FONDECYT/ ; ACT192057//ANID-PIA-Anillo INACH/ ; PICT 3825//Consejo Nacional de Investigaciones Científicas y Técnicas/ ; }, abstract = {Arsenic (As) is a metalloid present in the earth's crust and widely distributed in the environment. Due to its high concentrations in the Andean valleys and its chemical similarity with phosphorus (P), its biological role in Andean Microbial Ecosystems (AMEs) has begun to be studied. The AMEs are home to extremophilic microbial communities that form microbial mats, evaporites, and microbialites inhabiting Andean lakes, puquios, or salt flats. In this work, we characterize the biological role of As and the effect of phosphate in AMEs from the Laguna Tebenquiche (Atacama Desert, Chile). Using micro X-ray fluorescence, the distribution of As in microbial mat samples was mapped. Taxonomic and inferred functional profiles were obtained from enriched cultures of microbial mats incubated under As stress and different phosphate conditions. Additionally, representative microorganisms highly resistant to As and able to grow under low phosphate concentration were isolated and studied physiologically. Finally, the genomes of the isolated Salicola sp. and Halorubrum sp. were sequenced to analyze genes related to both phosphate metabolism and As resistance. The results revealed As as a key component of the microbial mat ecosystem: (i) As was distributed across all sections of the microbial mat and represented a significant weight percentage of the mat (0.17 %) in comparison with P (0.40%); (ii) Low phosphate concentration drastically changed the microbial community in microbial mat samples incubated under high salinity and high As concentrations; (iii) Archaea and Bacteria isolated from the microbial mat were highly resistant to arsenate (up to 500 mM), even under low phosphate concentration; (iv) The genomes of the two isolates were predicted to contain key genes in As metabolism (aioAB and arsC/acr3) and the genes predicted to encode the phosphate-specific transport operon (pstSCAB-phoU) are next to the arsC gene, suggesting a functional relationship between these two elements.}, }
@article {pmid33387813, year = {2020}, author = {Bossaert, S and Winne, V and Van Opstaele, F and Buyse, J and Verreth, C and Herrera-Malaver, B and Van Geel, M and Verstrepen, KJ and Crauwels, S and De Rouck, G and Lievens, B}, title = {Description of the temporal dynamics in microbial community composition and beer chemistry in sour beer production via barrel ageing of finished beers.}, journal = {International journal of food microbiology}, volume = {339}, number = {}, pages = {109030}, doi = {10.1016/j.ijfoodmicro.2020.109030}, pmid = {33387813}, issn = {1879-3460}, abstract = {Currently, there is a strong interest in barrel ageing of finished, conventionally fermented beers, as a novel way to produce sour beers with a rich and complex flavour profile. The production process, however, remains largely a process of trial and error, often resulting in profit losses and inconsistency in quality. To improve product quality and consistency, a better understanding of the interactions between microorganisms, wood and maturing beer is needed. The aim of this study was to describe the temporal dynamics in microbial community composition, beer chemistry and sensory characteristics during barrel ageing of three conventionally fermented beers that differed in parameters like alcohol content and bitterness. Beers were matured for 38 weeks in new (two types of wood) and used (one type of wood) oak barrels. Beer samples were taken at the start of the maturation and after 2, 12 and 38 weeks. Microbial community composition, determined using amplicon sequencing of the V4 region of the bacterial 16S rRNA gene and the fungal ITS1 region, beer chemistry and sensory characteristics substantially changed throughout the maturation process. Likewise, total bacterial and fungal population densities generally increased during maturation. PerMANOVA revealed significant differences in the bacterial and fungal community composition of the three beers and across time points, but not between the different wood types. By contrast, significant differences in beer chemistry were found across the different beers, wood types and sampling points. Results also indicated that the outcome of the maturation process likely depends on the initial beer properties. Specifically, results suggested that beer bitterness may restrain the bacterial community composition, thereby having an impact on beer souring. While the bacterial community composition of moderately-hopped beers shifted to a dominance of lactic acid bacteria, the bacterial community of the high-bitterness beer remained fairly constant, with low population densities. Bacterial community composition of the moderate-bitterness beers also resembled those of traditional sours like lambic beers, hosting typical lambic brewing species like Pediococcus damnosus, Lactobacillus brevis and Acetobacter sp. Furthermore, results suggested that alcohol level may have affected the fungal community composition and extraction of wood compounds. More specifically, the concentration of wood compounds like cis-3-methyl-4-octanolide, trans-3-methyl-4-octanolide, eugenol and total polyphenols was higher in beers with a high alcohol content. Altogether, our results provide novel insights into the barrel ageing process of beer, and may pave the way for a new generation of sour beers.}, }
@article {pmid33385649, year = {2020}, author = {Park, Y and Yu, J and Nguyen, VK and Park, S and Kim, J and Lee, T}, title = {Understanding complete ammonium removal mechanism in single-chamber microbial fuel cells based on microbial ecology.}, journal = {The Science of the total environment}, volume = {764}, number = {}, pages = {144231}, doi = {10.1016/j.scitotenv.2020.144231}, pmid = {33385649}, issn = {1879-1026}, abstract = {The removal of organics and ammonium from domestic wastewater was successfully achieved by a flat-panel air-cathode microbial fuel cell (FA-MFC). To elucidate the reason for complete ammonium removal in the single-chamber MFCs, microbial communities were analyzed in biofilms on the surface of each anode, separator, and cathode of separator-electrode assemblies (SEAs). The spatial distribution of bacterial families related to the nitrogen cycle varied based on local conditions. Since oxygen diffusing from the air-cathode created a locally aerobic condition, ammonia-oxidizing bacteria (AOB) Nitrosomonadacea and nitrite-oxidizing bacteria (NOB) Nitrospiraceae were present near the cathode. NOB (~12.1%) was more abundant than AOB (~4.4%), suggesting that the nitrate produced by NOB may be reduced back to nitrite by heterotrophic denitrifiers such as Rhodocyclaceae (~21.7%) and Comamonadaceae (~5%) in the anoxic zone close to the NOB layer. Near that zone, the &quot;nitrite loop&quot; also substantially enriched two nitrite-reducing bacterial families: Ignavibacteriaceae (~18.1%), facultative heterotrophs, and Brocadiaceae (~11.2%), anaerobic ammonium oxidizing autotrophs. A larger inner area of biofilm contained abundant heterotrophic denitrifiers and fermentation bacteria. These results indicate that the large-surface SEA of FA-MFC allows counter-diffusion between substrates and oxygen, resulting in interactions of bacteria involved in the nitrogen cycle for complete ammonium removal.}, }
@article {pmid33384680, year = {2020}, author = {Amacker, N and Gao, Z and Agaras, BC and Latz, E and Kowalchuk, GA and Valverde, CF and Jousset, A and Weidner, S}, title = {Biocontrol Traits Correlate With Resistance to Predation by Protists in Soil Pseudomonads.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {614194}, pmid = {33384680}, issn = {1664-302X}, abstract = {Root-colonizing bacteria can support plant growth and help fend off pathogens. It is clear that such bacteria benefit from plant-derived carbon, but it remains ambiguous why they invest in plant-beneficial traits. We suggest that selection via protist predation contributes to recruitment of plant-beneficial traits in rhizosphere bacteria. To this end, we examined the extent to which bacterial traits associated with pathogen inhibition coincide with resistance to protist predation. We investigated the resistance to predation of a collection of Pseudomonas spp. against a range of representative soil protists covering three eukaryotic supergroups. We then examined whether patterns of resistance to predation could be explained by functional traits related to plant growth promotion, disease suppression and root colonization success. We observed a strong correlation between resistance to predation and phytopathogen inhibition. In addition, our analysis highlighted an important contribution of lytic enzymes and motility traits to resist predation by protists. We conclude that the widespread occurrence of plant-protective traits in the rhizosphere microbiome may be driven by the evolutionary pressure for resistance against predation by protists. Protists may therefore act as microbiome regulators promoting native bacteria involved in plant protection against diseases.}, }
@article {pmid33384676, year = {2020}, author = {Assis, JM and Abreu, F and Villela, HMD and Barno, A and Valle, RF and Vieira, R and Taveira, I and Duarte, G and Bourne, DG and Høj, L and Peixoto, RS}, title = {Delivering Beneficial Microorganisms for Corals: Rotifers as Carriers of Probiotic Bacteria.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {608506}, pmid = {33384676}, issn = {1664-302X}, abstract = {The use of Beneficial Microorganisms for Corals (BMCs) to increase the resistance of corals to environmental stress has proven to be effective in laboratory trials. Because direct inoculation of BMCs in larger tanks or in the field can be challenging, a delivery mechanism is needed for efficient transmission of the BMC consortium. Packaged delivery mechanisms have been successfully used to transmit probiotics to other organisms, including humans, lobsters, and fish. Here, we tested a method for utilizing rotifers of the species Brachionus plicatilis for delivery of BMCs to corals of the species Pocillopora damicornis. Epifluorescence microscopy combined with a live/dead cell staining assay was used to evaluate the viability of the BMCs and monitor their in vivo uptake by the rotifers. The rotifers efficiently ingested BMCs, which accumulated in the digestive system and on the body surface after 10 min of interaction. Scanning electron microscopy confirmed the adherence of BMCs to the rotifer surfaces. BMC-enriched rotifers were actively ingested by P. damicornis corals, indicating that this is a promising technique for administering coral probiotics in situ. Studies to track the delivery of probiotics through carriers such as B. plicatilis, and the provision or establishment of beneficial traits in corals are the next proof-of-concept research priorities.}, }
@article {pmid33382858, year = {2020}, author = {Lequime, S and Dehecq, JS and Matheus, S and de Laval, F and Almeras, L and Briolant, S and Fontaine, A}, title = {Modeling intra-mosquito dynamics of Zika virus and its dose-dependence confirms the low epidemic potential of Aedes albopictus.}, journal = {PLoS pathogens}, volume = {16}, number = {12}, pages = {e1009068}, doi = {10.1371/journal.ppat.1009068}, pmid = {33382858}, issn = {1553-7374}, abstract = {Originating from African forests, Zika virus (ZIKV) has now emerged worldwide in urbanized areas, mainly transmitted by Aedes aegypti mosquitoes. Although Aedes albopictus can transmit ZIKV experimentally and was suspected to be a ZIKV vector in Central Africa, the potential of this species to sustain virus transmission was yet to be uncovered until the end of 2019, when several autochthonous transmissions of the virus vectored by Ae. albopictus occurred in France. Aside from these few locally acquired ZIKV infections, most territories colonized by Ae. albopictus have been spared so far. The risk level of ZIKV emergence in these areas remains however an open question. To assess Ae. albopictus' vector potential for ZIKV and identify key virus outbreak predictors, we built a complete framework using the complementary combination of (i) dose-dependent experimental Ae. albopictus exposure to ZIKV followed by time-dependent assessment of infection and systemic infection rates, (ii) modeling of intra-human ZIKV viremia dynamics, and (iii) in silico epidemiological simulations using an Agent-Based Model. The highest risk of transmission occurred during the pre-symptomatic stage of the disease, at the peak of viremia. At this dose, mosquito infection probability was estimated to be 20%, and 21 days were required to reach the median systemic infection rates. Mosquito population origin, either temperate or tropical, had no impact on infection rates or intra-host virus dynamic. Despite these unfavorable characteristics for transmission, Ae. albopictus was still able to trigger and yield large outbreaks in a simulated environment in the presence of sufficiently high mosquito biting rates. Our results reveal a low but existing epidemic potential of Ae. albopictus for ZIKV, that might explain the absence of large scale ZIKV epidemics so far in territories occupied only by Ae. albopictus. They nevertheless support active surveillance and eradication programs in these territories to maintain the risk of emergence to a low level.}, }
@article {pmid33382250, year = {2020}, author = {Kirchner, N and Cano-Prieto, C and Schulz-Fincke, AC and Gütschow, M and Ortlieb, N and Moschny, J and Niedermeyer, THJ and Horak, J and Lämmerhofer, M and van der Voort, M and Raaijmakers, JM and Gross, H}, title = {Discovery of Thanafactin A, a Linear, Proline-Containing Octalipopeptide from Pseudomonas sp. SH-C52, Motivated by Genome Mining.}, journal = {Journal of natural products}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jnatprod.0c01174}, pmid = {33382250}, issn = {1520-6025}, abstract = {Genome mining of the bacterial strains Pseudomonas sp. SH-C52 and Pseudomonas fluorescens DSM 11579 showed that both strains contained a highly similar gene cluster encoding an octamodular nonribosomal peptide synthetase (NRPS) system which was not associated with a known secondary metabolite. Insertional mutagenesis of an NRPS component followed by comparative profiling led to the discovery of the corresponding novel linear octalipopeptide thanafactin A, which was subsequently isolated and its structure determined by two-dimensional NMR and further spectroscopic and chromatographic methods. In bioassays, thanafactin A exhibited weak protease inhibitory activity and was found to modulate swarming motility in a strain-specific manner.}, }
@article {pmid33381966, year = {2020}, author = {Yu, Z and Schwarz, C and Zhu, L and Chen, L and Shen, Y and Yu, P}, title = {Hitchhiking Behavior in Bacteriophages Facilitates Phage Infection and Enhances Carrier Bacteria Colonization.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.0c06969}, pmid = {33381966}, issn = {1520-5851}, abstract = {Interactions between bacteriophages (phages) and biofilms remain poorly understood despite the broad implications for microbial ecology, water quality, and microbiome engineering. Here, we demonstrate that lytic coliphage PHH01 can hitchhike on carrier bacteria Bacillus cereus to facilitate its infection of host bacteria, Escherichia coli, in biofilms. Specifically, PHH01 could adsorb onto the flagella of B. cereus, and thus phage motility was increased, resulting in 4.36-fold more effective infection of E. coli in biofilm relative to free PHH01 alone. Moreover, phage infection mitigated interspecies competition and enhanced B. cereus colonization; the fraction of B. cereus in the final biofilm increased from 9% without phages to 43% with phages. The mutualistic relationship between the coliphage and carrier bacteria was substantiated by migration tests on an E. coli lawn: the conjugation of PHH01 and B. cereus enhanced B. cereus colonization by 6.54-fold compared to B. cereus alone (6.15 vs 0.94 cm2 in 24 h) and PHH01 migration by 5.15-fold compared to PHH01 alone (10.3 vs 2.0 mm in 24 h). Metagenomic and electron microscopic analysis revealed that the phages of diverse taxonomies and different morphologies could be adsorbed by the flagella of B. cereus, suggesting hitchhiking on flagellated bacteria might be a widespread strategy in aquatic phage populations. Overall, our study highlights that hitchhiking behavior in phages can facilitate phage infection of biofilm bacteria, promote carrier bacteria colonization, and thus significantly influence biofilm composition, which holds promise for mediating biofilm functions and moderating associated risks.}, }
@article {pmid33378450, year = {2020}, author = {Metze, D and Popp, D and Schwab, L and Keller, NS and da Rocha, UN and Richnow, HH and Vogt, C}, title = {Temperature management potentially affects carbon mineralization capacity and microbial community composition of a shallow aquifer.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaa261}, pmid = {33378450}, issn = {1574-6941}, abstract = {High-temperature aquifer thermal energy storage (HT-ATES) is a promising technique to reduce the CO2 footprint of heat supply in the frame of transitioning to renewable energies. However, HT-ATES causes temperature fluctuations in groundwater ecosystems potentially affecting important microbial-mediated ecosystem services. Hence, assessing the impact of increasing temperatures on the structure and functioning of aquifer microbiomes is crucial to evaluate potential environmental risks associated with HT-ATES. In this study, we investigated the effects of temperature variations (12-80°C) on microbial communities and their capacity to mineralize acetate in aerobically incubated sediments sampled from a pristine aquifer. Compared to natural conditions (12°C), increased acetate mineralization rates were observed at 25°C, 37°C and 45°C, whereas mineralization was decelerated at 60°C and absent at 80°C. Sequencing of 16S rRNA genes revealed that the bacterial diversity in acetate-amended and non-acetate-amended sediments decreased with rising temperatures. Distinct communities dominated by bacterial groups affiliated with meso- and thermophilic bacteria established at 45°C and 60°C, respectively, while the number of archaeal phylotypes decreased. The changes in microbial diversity observed at 45°C and 60°C indicate an increasing loss of ecosystem functioning, functional redundancy, and resilience, at higher temperatures, whereas 80°C results in a collapse of the ecosystem integrity.}, }
@article {pmid33378284, year = {2020}, author = {Afolayan, AO and Ayeni, FA}, title = {Metagenomic Analysis of Bacterial Communities in Water and Soil of the Fulani and non-Fulani in Nigeria.}, journal = {Journal of infection in developing countries}, volume = {14}, number = {12}, pages = {}, doi = {10.3855/jidc.12975}, pmid = {33378284}, issn = {1972-2680}, abstract = {INTRODUCTION: Interactions between environmental factors (water and soil) and humans are inevitable, particularly in rural and semi-urbanized regions. As such, knowledge on the microbial constituents of these environmental factors is key to understanding potential risk to public health. However, the microbial profile of soil and water present in vulnerable human communities in Nigeria is currently unknown. This study sought to investigate the composition of soil and water microbiota in the environment inhabited by recently studied human communities (the Fulani nomadic group and the urbanized Jarawa ethnic group) and estimate the contribution of these environmental factors to the microbiome of the aforementioned human communities.<br><br>METHODOLOGY: Soil and water samples were collected from the Fulani and non-Fulani community in Jengre (Plateau State, Nigeria) and Jos (Plateau State, Nigeria), respectively. Genomic DNA was extracted from these environmental samples, followed by Illumina sequencing of the V4 region of the 16S rRNA gene and bioinformatics analysis via Quantitative Insights into Microbial Ecology QIIME.<br><br>RESULTS: There is abundance of Proteobacteria (43%) signature members in soil samples obtained from both human communities. Analysis of the water samples revealed the abundance of Proteobacteria, particularly in water sourced from the borehole (Fulani). Pseudomonas (30%) had higher relative abundance in the drinking water of the Fulani.<br><br>CONCLUSIONS: The drinking water of the Fulani could be a potential health risk to the studied Fulani community. Factors that increase the abundance of public health threats and health risk, such as hygiene practices, soil and water quality need to be studied further for the improvement of health in vulnerable populations.}, }
@article {pmid33375064, year = {2020}, author = {Duranti, S and Longhi, G and Ventura, M and van Sinderen, D and Turroni, F}, title = {Exploring the Ecology of Bifidobacteria and Their Genetic Adaptation to the Mammalian Gut.}, journal = {Microorganisms}, volume = {9}, number = {1}, pages = {}, doi = {10.3390/microorganisms9010008}, pmid = {33375064}, issn = {2076-2607}, support = {SFI/12/RC/2273-P2/SFI_/Science Foundation Ireland/Ireland ; SFI/12/RC/2273-P1/SFI_/Science Foundation Ireland/Ireland ; }, abstract = {The mammalian gut is densely inhabited by microorganisms that have coevolved with their host. Amongst these latter microorganisms, bifidobacteria represent a key model to study host-microbe interaction within the mammalian gut. Remarkably, bifidobacteria naturally occur in a range of ecological niches that are either directly or indirectly connected to the animal gastrointestinal tract. They constitute one of the dominant bacterial members of the intestinal microbiota and are among the first colonizers of the mammalian gut. Notably, the presence of bifidobacteria in the gut has been associated with several health-promoting activities. In this review, we aim to provide an overview of current knowledge on the genetic diversity and ecology of bifidobacteria. Furthermore, we will discuss how this important group of gut bacteria is able to colonize and survive in the mammalian gut, so as to facilitate host interactions.}, }
@article {pmid33375046, year = {2020}, author = {Khomutovska, N and de Los Ríos, A and Jasser, I}, title = {Diversity and Colonization Strategies of Endolithic Cyanobacteria in the Cold Mountain Desert of Pamir.}, journal = {Microorganisms}, volume = {9}, number = {1}, pages = {}, doi = {10.3390/microorganisms9010006}, pmid = {33375046}, issn = {2076-2607}, abstract = {Microorganisms can survive in extreme environments and oligotrophic habitats thanks to their specific adaptive capacity. Due to its severe and contrasting climate conditions, the cold mountain desert in Eastern Pamir provides a unique environment for analyzing microbial adaptation mechanisms occurring within colonization of endolithic habitats. This study aims to investigate the composition and structure of endolithic microbial communities and analyze the interactions between microorganisms and colonized lithic substrates. Endolithic biofilms were examined using scanning electron microscopy in backscattered electron mode (SEM-BSE) and next-generation sequencing (NGS) applying amplicon sequence variants (ASVs) approach. The investigation of the V3-V4 region of 16S rRNA gene revealed that endolithic communities are dominated by Actinobacteria (26%), Proteobacteria (23%), and Cyanobacteria (11.4%). Cyanobacteria were represented by Oxyphotobacteria with a predominance of subclasses of Oscillatoriophycidae, Synechococcophycideae, and Nostocophycidae as well as the rarely occurring Sericytochromatia. The positive correlation between the contribution of the orders Synechococcales and Rhizobiales to community structure suggests that some functionally closed taxa of Cyanobacteria and Proteobacteria can complement each other, for example, in nitrogen fixation in endolithic communities. The endolithic communities occurring in Eastern Pamir were identified as complex systems whose composition and structure seem to be influenced by the architecture of microhabitats and related microenvironmental conditions.}, }
@article {pmid33374976, year = {2020}, author = {Rughöft, S and Jehmlich, N and Gutierrez, T and Kleindienst, S}, title = {Comparative Proteomics of Marinobacter sp. TT1 Reveals Corexit Impacts on Hydrocarbon Metabolism, Chemotactic Motility, and Biofilm Formation.}, journal = {Microorganisms}, volume = {9}, number = {1}, pages = {}, doi = {10.3390/microorganisms9010003}, pmid = {33374976}, issn = {2076-2607}, support = {Elite Program for Postdocs//Baden-Württemberg Stiftung/ ; 326028733//Deutsche Forschungsgemeinschaft/ ; }, abstract = {The application of chemical dispersants during marine oil spills can affect the community composition and activity of marine microorganisms. Several studies have indicated that certain marine hydrocarbon-degrading bacteria, such as Marinobacter spp., can be inhibited by chemical dispersants, resulting in lower abundances and/or reduced biodegradation rates. However, a major knowledge gap exists regarding the mechanisms underlying these physiological effects. Here, we performed comparative proteomics of the Deepwater Horizon isolate Marinobacter sp. TT1 grown under different conditions. Strain TT1 received different carbon sources (pyruvate vs. n-hexadecane) with and without added dispersant (Corexit EC9500A). Additional treatments contained crude oil in the form of a water-accommodated fraction (WAF) or chemically-enhanced WAF (CEWAF; with Corexit). For the first time, we identified the proteins associated with alkane metabolism and alginate biosynthesis in strain TT1, report on its potential for aromatic hydrocarbon biodegradation and present a protein-based proposed metabolism of Corexit components as carbon substrates. Our findings revealed that Corexit exposure affects hydrocarbon metabolism, chemotactic motility, biofilm formation, and induces solvent tolerance mechanisms, like efflux pumps, in strain TT1. This study provides novel insights into dispersant impacts on microbial hydrocarbon degraders that should be taken into consideration for future oil spill response actions.}, }
@article {pmid33374225, year = {2020}, author = {Shah, F and Gressler, M and Nehzati, S and Op De Beeck, M and Gentile, L and Hoffmeister, D and Persson, P and Tunlid, A}, title = {Secretion of Iron(III)-Reducing Metabolites during Protein Acquisition by the Ectomycorrhizal Fungus Paxillus involutus.}, journal = {Microorganisms}, volume = {9}, number = {1}, pages = {}, doi = {10.3390/microorganisms9010035}, pmid = {33374225}, issn = {2076-2607}, support = {2013.0073//Knut and Alice Wallenberg Foundation/ ; 2016-04561 and 2017-04261//Swedish Research Council/ ; }, abstract = {The ectomycorrhizal fungus Paxillus involutus decomposes proteins using a two-step mechanism, including oxidation and proteolysis. Oxidation involves the action of extracellular hydroxyl radicals (•OH) generated by the Fenton reaction. This reaction requires the presence of iron(II). Here, we monitored the speciation of extracellular iron and the secretion of iron(III)-reducing metabolites during the decomposition of proteins by P. involutus. X-ray absorption spectroscopy showed that extracellular iron was mainly present as solid iron(III) phosphates and oxides. Within 1 to 2 days, these compounds were reductively dissolved, and iron(II) complexes were formed, which remained in the medium throughout the incubation. HPLC and mass spectrometry detected five extracellular iron(III)-reducing metabolites. Four of them were also secreted when the fungus grew on a medium containing ammonium as the sole nitrogen source. NMR identified the unique iron(III)-reductant as the diarylcyclopentenone involutin. Involutin was produced from day 2, just before the elevated •OH production, preceding the oxidation of BSA. The other, not yet fully characterized iron(III)-reductants likely participate in the rapid reduction and dissolution of solid iron(III) complexes observed on day one. The production of these metabolites is induced by other environmental cues than for involutin, suggesting that they play a role beyond the Fenton chemistry associated with protein oxidation.}, }
@article {pmid33374112, year = {2020}, author = {LeBrun, ES and Nighot, M and Dharmaprakash, V and Kumar, A and Lo, CC and Chain, PSG and Ma, TY}, title = {The Gut Microbiome and Alcoholic Liver Disease: Ethanol Consumption Drives Consistent and Reproducible Alteration in Gut Microbiota in Mice.}, journal = {Life (Basel, Switzerland)}, volume = {11}, number = {1}, pages = {}, doi = {10.3390/life11010007}, pmid = {33374112}, issn = {2075-1729}, support = {R01Dk121073/NH/NIH HHS/United States ; R01DK106072/NH/NIH HHS/United States ; J. Lloyd Huck Chair in Medicine//Penn State College of Medicine/ ; }, abstract = {Phenotypic health effects, both positive and negative, have been well studied in association with the consumption of alcohol in humans as well as several other mammals including mice. Many studies have also associated these same health effects and phenotypes to specific members of gut microbiome communities. Here we utilized a chronic plus binge ethanol feed model (Gao-binge model) to explore microbiome community changes across three independent experiments performed in mice. We found significant and reproducible differences in microbiome community assemblies between ethanol-treated mice and control mice on the same diet absent of ethanol. We also identified significant differences in gut microbiota occurring temporally with ethanol treatment. Peak shift in communities was observed 4 days after the start of daily alcohol consumption. We quantitatively identified many of the bacterial genera indicative of these ethanol-induced shifts including 20 significant genera when comparing ethanol treatments with controls and 14 significant genera based on temporal investigation. Including overlap of treatment with temporal shifts, we identified 25 specific genera of interest in ethanol treatment microbiome shifts. Shifts coincide with observed presentation of fatty deposits in the liver tissue, i.e., Alcoholic Liver Disease-associated phenotype. The evidence presented herein, derived from three independent experiments, points to the existence of a common, reproducible, and characterizable &quot;mouse ethanol gut microbiome&quot;.}, }
@article {pmid33370423, year = {2020}, author = {Parks, M and Kedy, C and Skalla, C}, title = {Consistent patterns in 16S and 18S microbial diversity from the shells of the common and widespread red-eared slider turtle (Trachemys scripta).}, journal = {PloS one}, volume = {15}, number = {12}, pages = {e0244489}, doi = {10.1371/journal.pone.0244489}, pmid = {33370423}, issn = {1932-6203}, abstract = {Microbial communities associated with freshwater aquatic habitats and resident species are both critical to and indicative of ecosystem status and organismal health. External surfaces of turtle shells readily accumulate microbial growth and could carry representation of habitat-wide microbial diversity, since they are in regular contact with multiple elements of freshwater environments. Yet, microbial diversity residing on freshwater turtle shells is poorly understood. We applied 16S and 18S metabarcoding to characterize microbiota associated with external shell surfaces of 20 red-eared slider (Trachemys scripta) turtles collected from varied habitats in central and western Oklahoma, and ranging to southeast Iowa. Shell-associated microbial communities were highly diverse, with samples dominated by Bacteroidia and alpha-/gamma-proteobacteria, and ciliophoran alveolates. Alpha diversity was lower on turtle shells compared to shallow-water-associated environmental samples, likely resulting from basking-drying behavior and seasonal scute shedding, while alpha diversity was higher on carapace than plastron surfaces. Beta diversity of turtle shells was similarly differentiated from environmental samples, although sampling site was consistently a significant factor. Deinococcus-Thermus bacteria and ciliophoran alveolates were recovered with significantly higher abundance on turtle shells versus environmental samples, while bacterial taxa known to include human-pathogenic species were variably more abundant between shell and environmental samples. Microbial communities from a single, shared-site collection of the ecologically similar river cooter (P. concinna) largely overlapped with those of T. scripta. These data add to a foundation for further characterization of turtle shell microbial communities across species and habitats, with implications for freshwater habitat assessment, microbial ecology and wildlife conservation efforts.}, }
@article {pmid33363527, year = {2020}, author = {Smith, PE and Waters, SM and Gómez Expósito, R and Smidt, H and Carberry, CA and McCabe, MS}, title = {Synthetic Sequencing Standards: A Guide to Database Choice for Rumen Microbiota Amplicon Sequencing Analysis.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {606825}, pmid = {33363527}, issn = {1664-302X}, abstract = {Our understanding of complex microbial communities, such as those residing in the rumen, has drastically advanced through the use of high throughput sequencing (HTS) technologies. Indeed, with the use of barcoded amplicon sequencing, it is now cost effective and computationally feasible to identify individual rumen microbial genera associated with ruminant livestock nutrition, genetics, performance and greenhouse gas production. However, across all disciplines of microbial ecology, there is currently little reporting of the use of internal controls for validating HTS results. Furthermore, there is little consensus of the most appropriate reference database for analyzing rumen microbiota amplicon sequencing data. Therefore, in this study, a synthetic rumen-specific sequencing standard was used to assess the effects of database choice on results obtained from rumen microbial amplicon sequencing. Four DADA2 reference training sets (RDP, SILVA, GTDB, and RefSeq + RDP) were compared to assess their ability to correctly classify sequences included in the rumen-specific sequencing standard. In addition, two thresholds of phylogenetic bootstrapping, 50 and 80, were applied to investigate the effect of increasing stringency. Sequence classification differences were apparent amongst the databases. For example the classification of Clostridium differed between all databases, thus highlighting the need for a consistent approach to nomenclature amongst different reference databases. It is hoped the effect of database on taxonomic classification observed in this study, will encourage research groups across various microbial disciplines to develop and routinely use their own microbiome-specific reference standard to validate analysis pipelines and database choice.}, }
@article {pmid33362871, year = {2020}, author = {Setubal, JC and Stoye, J and Dutilh, BE}, title = {Editorial: Computational Methods for Microbiome Analysis.}, journal = {Frontiers in genetics}, volume = {11}, number = {}, pages = {623897}, doi = {10.3389/fgene.2020.623897}, pmid = {33362871}, issn = {1664-8021}, }
@article {pmid33361365, year = {2020}, author = {Van Holm, W and Ghesquière, J and Boon, N and Verspecht, T and Bernaerts, K and Zayed, N and Chatzigiannidou, I and Teughels, W}, title = {A viability qPCR dilemma: Are longer amplicons better?.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.02653-20}, pmid = {33361365}, issn = {1098-5336}, abstract = {The development of viability qPCR (v-qPCR) has allowed for a more accurate assessment of the viability of a microbial sample by limiting the amplification of DNA from dead cells. Although valuable, v-qPCR is not infallible. One of the most limiting factors for accurate live/dead distinction is the length of the qPCR amplicon used. However, no consensus or guidelines exist for selecting and designing amplicon lengths for optimal results. In this study, a wide range of incrementally increasing amplicon lengths (68-906 bp) was used on live and killed cells of nine bacterial species treated with viability dye (PMA). Increasing amplicon lengths up to approximately 200 bp resulted in increasing quantification cycle (Cq) differences between live and killed cells, while maintaining a good qPCR efficiency. Longer amplicon lengths, up to approximately 400 bp, further increased Cq difference, but at the cost of qPCR efficiency. Above 400 bp, no valuable increase in Cq differences was observed.ImportanceViability qPCR (v-qPCR) has evolved to a valuable, mainstream technique for determining the number of viable micro-organisms in samples by qPCR. Amplicon length is known to be positively correlated with the ability to distinguish between live and dead bacteria but is negatively correlated with qPCR efficiency. This trade-off is often not taken into account and might have an impact on the accuracy of v-qPCR data. Currently there is no consensus on the optimal amplicon length. This paper provides methods to determine the optimal amplicon length and suggests an amplicon length range for optimal v-qPCR, taking into consideration the trade-off between qPCR efficiency and live-dead distinction.}, }
@article {pmid33360128, year = {2020}, author = {Yuan, W and Wei, Y and Zhang, Y and Riaz, L and Yang, Q and Wang, Q and Wang, R}, title = {Resistance of multidrug resistant Escherichia coli to environmental nanoscale TiO2 and ZnO.}, journal = {The Science of the total environment}, volume = {761}, number = {}, pages = {144303}, doi = {10.1016/j.scitotenv.2020.144303}, pmid = {33360128}, issn = {1879-1026}, abstract = {Excessive production and utilization of nanoparticles (NPs) at industrial and household levels releases substantial quantities of NPs into the environment. These can be harmful to different types of organisms and cause adverse effects on ecosystems. Purchased TiO2 and ZnO NPs were characterized via XRD, XPS, FESEM, and Zeta potential. This study elucidates how multidrug resistant Escherichia coli LM13, which was recovered from livestock manure, counteracts the antibacterial activities of TiO2 and ZnO NPs to survive in the environment. E. coli ATCC25922, which is susceptible to antibiotics, was used as control. A dose-response experiment showed that the antibacterial activity of TiO2 was lower than that of ZnO NPs and, LM13 was more resistant to NPs than ATCC25922. An AcrAB-TolC efflux pump along with its regulation genes helped LM13 to minimize NP toxicity. Flow cytometry findings also indicated that the intensity of the side-scatter light parameter increased with TiO2 and ZnO NPs in a dose dependent manner, suggesting NP uptake by the both strains. The generation of reactive oxygen species in LM13 was several-fold lower than in ATCC25922, suggesting that reactive oxygen species mainly contribute to the toxicity mechanism. These results illustrate the necessity to evaluate the impacts of NPs on the survival capacity of bacteria and on the resistance genes in bacteria with higher NP resistance than NP susceptible bacteria.}, }
@article {pmid33360101, year = {2020}, author = {Ngo, KN and Van Winckel, T and Massoudieh, A and Wett, B and Al-Omari, A and Murthy, S and Takács, I and De Clippeleir, H}, title = {Towards more predictive clarification models via experimental determination of flocculent settling coefficient value.}, journal = {Water research}, volume = {190}, number = {}, pages = {116294}, doi = {10.1016/j.watres.2020.116294}, pmid = {33360101}, issn = {1879-2448}, abstract = {Improved settleability has become an essential feature of new wastewater treatment innovations. To accelerate adoption of such new technologies, improved clarifier models are needed to help with designing and predicting improvement in settleability. In general, the level of mathematics of settling clarifier models has gone far beyond the level of existing experimental methods available to support these models. To date, even for simple one-dimensional (1D) clarifier models, no experimental method has been described for flocculent settling coefficient (rp). As a consequence, rp cannot be considered as a sludge characteristic and is used as a calibration parameter to achieve observed effluent quality. In this study, we focused on the development of an empirical function based on a simple and practical experimental approach for the calculation of the rp value from sludge characteristics. This approach provided a similar approach as currently taken for hindered settling coefficient calculations (Veslind equation) and allowed for the model to predict effluent quality, thus increasing the power of the 1D model. The threshold of flocculation (TOF), which describes the collision efficiency of particles, directly correlated with the effluent quality of the five tested activated sludge systems and was selected as experimental method. The proposed empirical function between TOF and rp was validated for four years of validating data with five different sludge types operated under different operational conditions and configurations. The good effluent quality prediction with this approach brings us one step closer in making the clarification models more predictive towards effluent quality and clarifier performance.}, }
@article {pmid33360100, year = {2020}, author = {Ceballos-Escalera, A and Pous, N and Chiluiza-Ramos, P and Korth, B and Harnisch, F and Bañeras, L and Balaguer, MD and Puig, S}, title = {Electro-bioremediation of nitrate and arsenite polluted groundwater.}, journal = {Water research}, volume = {190}, number = {}, pages = {116748}, doi = {10.1016/j.watres.2020.116748}, pmid = {33360100}, issn = {1879-2448}, abstract = {The coexistence of different pollutants in groundwater is a common threat. Sustainable and resilient technologies are required for their treatment. The present study aims to evaluate microbial electrochemical technologies (METs) for treating groundwater contaminated with nitrate (NO3-) while containing arsenic (in form of arsenite (As(III)) as a co-contaminant. The treatment was based on the combination of nitrate reduction to dinitrogen gas and arsenite oxidation to arsenate (exhibiting less toxicity, solubility, and mobility), which can be removed more easily in further post-treatment. We operated a bioelectrochemical reactor at continuous-flow mode with synthetic contaminated groundwater (33 mg N-NO3- L-1 and 5 mg As(III) L-1) identifying the key operational conditions. Different hydraulic retention times (HRT) were evaluated, reaching a maximum nitrate reduction rate of 519 g N-NO3- m3Net Cathodic Compartment d-1 at HRT of 2.3 h with a cathodic coulombic efficiency of around 100 %. Simultaneously, arsenic oxidation was complete at all HRT tested down to 1.6 h reaching an oxidation rate of up to 90 g As(III) m-3Net Reactor Volume d -1. Electrochemical and microbiological characterization of single granules suggested that arsenite at 5 mg L-1 did not have an inhibitory effect on a denitrifying biocathode mainly represented by Sideroxydans sp. Although the coexistence of abiotic and biotic arsenic oxidation pathways was shown to be likely, microbial arsenite oxidation linked to denitrification by Achromobacter sp. was the most probable pathway. This research paves the ground towards a real application for treating groundwater with widespread pollutants.}, }
@article {pmid33355923, year = {2020}, author = {Lofgren, LA and Nguyen, NH and Vilgalys, R and Ruytinx, J and Liao, HL and Branco, S and Kuo, A and LaButti, K and Lipzen, A and Andreopoulos, W and Pangilinan, J and Riley, R and Hundley, H and Na, H and Barry, K and Grigoriev, IV and Stajich, JE and Kennedy, PG}, title = {Comparative genomics reveals dynamic genome evolution in host specialist ectomycorrhizal fungi.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.17160}, pmid = {33355923}, issn = {1469-8137}, abstract = {While there has been significant progress characterizing the 'symbiotic tool kit' of ectomycorrhizal (ECM) fungi, how host specificity may be encoded into ECM fungal genomes remains poorly understood. We conducted a comparative genomic analysis of ECM fungal host specialists and generalists, focusing on the specialist genus Suillus. Global analyses of genome dynamics across 46 species were assessed, along with targeted analyses of three classes of molecules previously identified as important determinants of host specificity: small secreted proteins (SSPs), secondary metabolites (SMs), and G-protein coupled receptors (GPCRs). Relative to other ECM fungi, including other host specialists, Suillus had highly dynamic genomes including numerous rapidly evolving gene families and many domain expansions and contractions. Targeted analyses supported a role for SMs but not SSPs or GPCRs in Suillus host specificity. Phylogenomic-based ancestral state reconstruction identified Larix as the ancestral host of Suillus, with multiple independent switches between white and red pine hosts. These results suggest that like other defining characteristics of the ECM lifestyle, host specificity is a dynamic process at the genome level. In the case of Suillus, both SMs and pathways involved in the deactivation of reactive oxygen species appear to be strongly associated with enhanced host specificity.}, }
@article {pmid33354438, year = {2018}, author = {Reyes, VC and Merino, N and Gedalanga, PB and Van Nostrand, JD and Keely, SP and De Long, SK and Zhou, J and Mahendra, S}, title = {Differential Sensitivity of Wetland-Derived Nitrogen Cycling Microorganisms to Copper Nanoparticles.}, journal = {ACS sustainable chemistry &amp; engineering}, volume = {6}, number = {9}, pages = {11642-11652}, pmid = {33354438}, issn = {2168-0485}, support = {EPA999999/ImEPA/Intramural EPA/United States ; }, abstract = {Metallic nanoparticles (NPs), the most abundant nanomaterials in consumer and industrial products, are the most probable class to enter the environment. In this study, wetland-derived microcosms were incubated with copper nanoparticles (Cu-NP) and ionic CuCl2 to investigate acute (10 days) and chronic (100 days) exposure towards nitrogen cycling microorganisms. The microbial ecology of wetlands play a crucial role in balancing nitrogen in pristine environments as well as in areas impacted by high nutrient loads (e.g., at wastewater effluent discharges). Gene abundance and expression changes were monitored using the GeoChip 5.0 high throughput functional gene microarray and metatranscriptomic shotgun sequencing (RNA-seq), respectively. After 10 days, the Cu-NP impacted microbial communities experienced structural shifts within microorganisms associated with dissimilatory nitrogen reduction accompanied by lower nitrate removal as compared to the unexposed controls. By day 100, these differences were largely resolved and nitrate removal was similar to the unexposed control. Furthermore, the Cu-NP exposed microcosms tolerated copper and were more resilient and adaptive than the unexposed controls based on the abundance and expression of other functions, including electron transfer, metal homeostasis, and stress response. These findings suggest sudden influxes of Cu-NPs into wetland systems may impair nitrogen removal initially, but long-term microbial shifts and functional redundancy would promote the net flux of total nitrogen out of the wetlands.}, }
@article {pmid33351643, year = {2020}, author = {Oesterle, I and Braun, D and Berry, D and Wisgrill, L and Rompel, A and Warth, B}, title = {Polyphenol Exposure, Metabolism, and Analysis: A Global Exposomics Perspective.}, journal = {Annual review of food science and technology}, volume = {}, number = {}, pages = {}, doi = {10.1146/annurev-food-062220-090807}, pmid = {33351643}, issn = {1941-1421}, abstract = {Polyphenols are generally known for their health benefits and estimating actual exposure levels in health-related studies can be improved by human biomonitoring. Here, the application of newly available exposomic and metabolomic technology, notably high-resolution mass spectrometry, in the context of polyphenols and their biotransformation products, is reviewed. Comprehensive workflows for investigating these important bioactives in biological fluids or microbiome-related experiments are scarce. Consequently, this new era of nontargeted analysis and omic-scale exposure assessment offers a unique chance for better assessing exposure to, as well as metabolism of, polyphenols. In clinical and nutritional trials, polyphenols can be investigated simultaneously with the plethora of other chemicals to which we are exposed, i.e., the exposome, which may interact abundantly and modulate bioactivity. This research direction aims at ultimately eluting into a true systems biology/toxicology evaluation of health effects associated with polyphenol exposure, especially during early life, to unravel their potential for preventing chronic diseases. Expected final online publication date for the Annual Review of Food Science and Technology, Volume 12 is March 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.}, }
@article {pmid33350826, year = {2020}, author = {Kosgey, K and Chandran, K and Gokal, J and Kiambi, SL and Bux, F and Kumari, S}, title = {Critical Analysis of Biomass Retention Strategies in Mainstream and Sidestream ANAMMOX-Mediated Nitrogen Removal Systems.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.0c00276}, pmid = {33350826}, issn = {1520-5851}, abstract = {ANAMMOX (anaerobic ammonium oxidation) represents an energy-efficient process for biological nitrogen removal, particularly from wastewater streams with low chemical oxygen demand (COD) to nitrogen (C/N) ratios. Its widespread application, however, is still hampered by a lack of access to biomass-enriched with ANAMMOX bacteria (AMX), slow growth rates of AMX, and their sensitivity to inhibition. Although the coupling of ANAMMOX processes with partial nitrification is already widespread, especially for sidestream treatment, maintaining a functional population density of AMX remains a challenge in these systems. Therefore, strategies that maximize retention of AMX-rich biomass are essential to promote process stability. This paper reviews existing methods of biomass retention in ANAMMOX-mediated systems, focusing on (i) granulation; (ii) biofilm formation on carrier materials; (iii) gel entrapment; and (iv) membrane technology in mainstream and sidestream systems. In addition, the microbial ecology of different ANAMMOX-mediated systems is reviewed.}, }
@article {pmid33349634, year = {2020}, author = {Molinaro, A and Bel Lassen, P and Henricsson, M and Wu, H and Adriouch, S and Belda, E and Chakaroun, R and Nielsen, T and Bergh, PO and Rouault, C and André, S and Marquet, F and Andreelli, F and Salem, JE and Assmann, K and Bastard, JP and Forslund, S and Le Chatelier, E and Falony, G and Pons, N and Prifti, E and Quinquis, B and Roume, H and Vieira-Silva, S and Hansen, TH and Pedersen, HK and Lewinter, C and Sønderskov, NB and ,  and Køber, L and Vestergaard, H and Hansen, T and Zucker, JD and Galan, P and Dumas, ME and Raes, J and Oppert, JM and Letunic, I and Nielsen, J and Bork, P and Ehrlich, SD and Stumvoll, M and Pedersen, O and Aron-Wisnewsky, J and Clément, K and Bäckhed, F}, title = {Author Correction: Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {6448}, doi = {10.1038/s41467-020-20412-9}, pmid = {33349634}, issn = {2041-1723}, }
@article {pmid33348645, year = {2020}, author = {Álvarez-Mena, A and Cámara-Almirón, J and de Vicente, A and Romero, D}, title = {Multifunctional Amyloids in the Biology of Gram-Positive Bacteria.}, journal = {Microorganisms}, volume = {8}, number = {12}, pages = {}, pmid = {33348645}, issn = {2076-2607}, support = {BacBio 637971//H2020 European Research Council/ ; AGL2016-78662-R//Ministerio de Ciencia, Innovación y Universidades/ ; PID2019-107724GB-I00//Ministerio de Ciencia, Innovación y Universidades/ ; }, abstract = {Since they were discovered, amyloids have proven to be versatile proteins able to participate in a variety of cellular functions across all kingdoms of life. This multitask trait seems to reside in their ability to coexist as monomers, aggregates or fibrillar entities, with morphological and biochemical peculiarities. It is precisely this common molecular behaviour that allows amyloids to cross react with one another, triggering heterologous aggregation. In bacteria, many of these functional amyloids are devoted to the assembly of biofilms by organizing the matrix scaffold that keeps cells together. However, consistent with their notion of multifunctional proteins, functional amyloids participate in other biological roles within the same organisms, and emerging unprecedented functions are being discovered. In this review, we focus on functional amyloids reported in gram-positive bacteria, which are diverse in their assembly mechanisms and remarkably specific in their biological functions that they perform. Finally, we consider cross-seeding between functional amyloids as an emerging theme in interspecies interactions that contributes to the diversification of bacterial biology.}, }
@article {pmid33341792, year = {2020}, author = {ElNaker, NA and Sallam, AM and El-Sayed, EM and El Ghandoor, H and Talaat, MS and Yousef, AF and Hasan, SW}, title = {A conceptual framework modeling of functional microbial communities in wastewater treatment electro-bioreactors.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {82}, number = {12}, pages = {3047-3061}, doi = {10.2166/wst.2020.553}, pmid = {33341792}, issn = {0273-1223}, mesh = {Bioreactors ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Waste Disposal, Fluid ; Waste Water ; *Water Purification ; }, abstract = {Understanding the microbial ecology of a system allows linking members of the community and their metabolic functions to the performance of the wastewater bioreactor. This study provided a comprehensive conceptual framework for microbial communities in wastewater treatment electro-bioreactors (EBRs). The model was based on data acquired from monitoring the effect of altering different bioreactor operational parameters, such as current density and hydraulic retention time, on the microbial communities of an EBR and its nutrient removal efficiency. The model was also based on the 16S rRNA gene high-throughput sequencing data analysis and bioreactor efficiency data. The collective data clearly demonstrated that applying various electric currents affected the microbial community composition and stability and the reactor efficiency in terms of chemical oxygen demand, N and P removals. Moreover, a schematic that recommends operating conditions that are tailored to the type of wastewater that needs to be treated based on the functional microbial communities enriched at specific operating conditions was suggested. In this study, a conceptual model as a simplified representation of the behavior of microbial communities in EBRs was developed. The proposed conceptual model can be used to predict how biological treatment of wastewater in EBRs can be improved by varying several operating conditions.}, }
@article {pmid33339826, year = {2019}, author = {Pareek, S and Kurakawa, T and Das, B and Motooka, D and Nakaya, S and Rongsen-Chandola, T and Goyal, N and Kayama, H and Dodd, D and Okumura, R and Maeda, Y and Fujimoto, K and Nii, T and Ogawa, T and Iida, T and Bhandari, N and Kida, T and Nakamura, S and Nair, GB and Takeda, K}, title = {Comparison of Japanese and Indian intestinal microbiota shows diet-dependent interaction between bacteria and fungi.}, journal = {NPJ biofilms and microbiomes}, volume = {5}, number = {1}, pages = {37}, pmid = {33339826}, issn = {2055-5008}, support = {JP15H02511//Ministry of Education, Culture, Sports, Science and Technology (MEXT)/ ; JP15J06509//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; }, abstract = {The bacterial species living in the gut mediate many aspects of biological processes such as nutrition and activation of adaptive immunity. In addition, commensal fungi residing in the intestine also influence host health. Although the interaction of bacterium and fungus has been shown, its precise mechanism during colonization of the human intestine remains largely unknown. Here, we show interaction between bacterial and fungal species for utilization of dietary components driving their efficient growth in the intestine. Next generation sequencing of fecal samples from Japanese and Indian adults revealed differential patterns of bacterial and fungal composition. In particular, Indians, who consume more plant polysaccharides than Japanese, harbored increased numbers of Prevotella and Candida. Candida spp. showed strong growth responses to the plant polysaccharide arabinoxylan in vitro. Furthermore, the culture supernatants of Candida spp. grown with arabinoxylan promoted rapid proliferation of Prevotella copri. Arabinose was identified as a potential growth-inducing factor in the Candida culture supernatants. Candida spp. exhibited a growth response to xylose, but not to arabinose, whereas P. copri proliferated in response to both xylose and arabinose. Candida spp., but not P. copri, colonized the intestine of germ-free mice. However, P. copri successfully colonized mouse intestine already harboring Candida. These findings demonstrate a proof of concept that fungal members of gut microbiota can facilitate a colonization of the intestine by their bacterial counterparts, potentially mediated by a dietary metabolite.}, }
@article {pmid33332530, year = {2020}, author = {Liu, C and Cui, Y and Li, X and Yao, M}, title = {microeco: An R package for data mining in microbial community ecology.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaa255}, pmid = {33332530}, issn = {1574-6941}, abstract = {A large amount of sequencing data is produced in microbial community ecology studies using the high-throughput sequencing technique, especially amplicon-sequencing-based community data. After conducting the initial bioinformatic analysis of amplicon sequencing data, performing the subsequent statistics and data mining based on the operational taxonomic unit and taxonomic assignment tables is still complicated and time-consuming. To address this problem, we present an integrated R package-'microeco' as an analysis pipeline for treating microbial community and environmental data. This package was developed based on the R6 class system and combines a series of commonly used and advanced approaches in microbial community ecology research. The package includes classes for data preprocessing, taxa abundance plotting, venn diagram, alpha diversity analysis, beta diversity analysis, differential abundance test and indicator taxon analysis, environmental data analysis, null model analysis, network analysis and functional analysis. Each class is designed to provide a set of approaches that can be easily accessible to users. Compared with other R packages in the microbial ecology field, the microeco package is fast, flexible and modularized to use, and provides powerful and convenient tools for researchers. The microeco package can be installed from CRAN (The Comprehensive R Archive Network) or github (https://github.com/ChiLiubio/microeco).}, }
@article {pmid33329631, year = {2020}, author = {Robles-Aguilar, AA and Grunert, O and Hernandez-Sanabria, E and Mysara, M and Meers, E and Boon, N and Jablonowski, ND}, title = {Effect of Applying Struvite and Organic N as Recovered Fertilizers on the Rhizosphere Dynamics and Cultivation of Lupine (Lupinus angustifolius).}, journal = {Frontiers in plant science}, volume = {11}, number = {}, pages = {572741}, pmid = {33329631}, issn = {1664-462X}, abstract = {Intensive agriculture and horticulture heavily rely on the input of fertilizers to sustain food (and feed) production. However, high carbon footprint and pollution are associated with the mining processes of P and K, and the artificial nitrogen fixation for the production of synthetic fertilizers. Organic fertilizers or recovered nutrients from different waste sources can be used to reduce the environmental impact of fertilizers. We tested two recovered nutrients with slow-release patterns as promising alternatives for synthetic fertilizers: struvite and a commercially available organic fertilizer. Using these fertilizers as a nitrogen source, we conducted a rhizotron experiment to test their effect on plant performance and nutrient recovery in lupine plants. Plant performance was not affected by the fertilizer applied; however, N recovery was higher from the organic fertilizer than from struvite. As root architecture is fundamental for plant productivity, variations in root structure and length as a result of soil nutrient availability driven by plant-bacteria interactions were compared showing also no differences between fertilizers. However, fertilized plants were considerably different in the root length and morphology compared with the no fertilized plants. Since the microbial community influences plant nitrogen availability, we characterized the root-associated microbial community structure and functionality. Analyses revealed that the fertilizer applied had a significant impact on the associations and functionality of the bacteria inhabiting the growing medium used. The type of fertilizer significantly influenced the interindividual dissimilarities in the most abundant genera between treatments. This means that different plant species have a distinct effect on modulating the associated microbial community, but in the case of lupine, the fertilizer had a bigger effect than the plant itself. These novel insights on interactions between recovered fertilizers, plant, and associated microbes can contribute to developing sustainable crop production systems.}, }
@article {pmid33329472, year = {2020}, author = {Kohler, TJ and Peter, H and Fodelianakis, S and Pramateftaki, P and Styllas, M and Tolosano, M and de Staercke, V and Schön, M and Busi, SB and Wilmes, P and Washburne, A and Battin, TJ}, title = {Patterns and Drivers of Extracellular Enzyme Activity in New Zealand Glacier-Fed Streams.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {591465}, pmid = {33329472}, issn = {1664-302X}, abstract = {Glacier-fed streams (GFSs) exhibit near-freezing temperatures, variable flows, and often high turbidities. Currently, the rapid shrinkage of mountain glaciers is altering the delivery of meltwater, solutes, and particulate matter to GFSs, with unknown consequences for their ecology. Benthic biofilms dominate microbial life in GFSs, and play a major role in their biogeochemical cycling. Mineralization is likely an important process for microbes to meet elemental budgets in these systems due to commonly oligotrophic conditions, and extracellular enzymes retained within the biofilm enable the degradation of organic matter and acquisition of carbon (C), nitrogen (N), and phosphorus (P). The measurement and comparison of these extracellular enzyme activities (EEA) can in turn provide insight into microbial elemental acquisition effort relative to environmental availability. To better understand how benthic biofilm communities meet resource demands, and how this might shift as glaciers vanish under climate change, we investigated biofilm EEA in 20 GFSs varying in glacier influence from New Zealand's Southern Alps. Using turbidity and distance to the glacier snout normalized for glacier size as proxies for glacier influence, we found that bacterial abundance (BA), chlorophyll a (Chl a), extracellular polymeric substances (EPS), and total EEA per gram of sediment increased with decreasing glacier influence. Yet, when normalized by BA, EPS decreased with decreasing glacier influence, Chl a still increased, and there was no relationship with total EEA. Based on EEA ratios, we found that the majority of GFS microbial communities were N-limited, with a few streams of different underlying bedrock geology exhibiting P-limitation. Cell-specific C-acquiring EEA was positively related to the ratio of Chl a to BA, presumably reflecting the utilization of algal exudates. Meanwhile, cell-specific N-acquiring EEA were positively correlated with the concentration of dissolved inorganic nitrogen (DIN), and both N- and P-acquiring EEA increased with greater cell-specific EPS. Overall, our results reveal greater glacier influence to be negatively related to GFS biofilm biomass parameters, and generally associated with greater microbial N demand. These results help to illuminate the ecology of GFS biofilms, along with their biogeochemical response to a shifting habitat template with ongoing climate change.}, }
@article {pmid33329469, year = {2020}, author = {Shintani, M and Nour, E and Elsayed, T and Blau, K and Wall, I and Jechalke, S and Spröer, C and Bunk, B and Overmann, J and Smalla, K}, title = {Plant Species-Dependent Increased Abundance and Diversity of IncP-1 Plasmids in the Rhizosphere: New Insights Into Their Role and Ecology.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {590776}, pmid = {33329469}, issn = {1664-302X}, abstract = {IncP-1 plasmids, first isolated from clinical specimens (R751, RP4), are recognized as important vectors spreading antibiotic resistance genes. The abundance of IncP-1 plasmids in the environment, previously reported, suggested a correlation with anthropogenic pollution. Unexpectedly, qPCR-based detection of IncP-1 plasmids revealed also an increased relative abundance of IncP-1 plasmids in total community DNA from the rhizosphere of lettuce and tomato plants grown in non-polluted soil along with plant age. Here we report the successful isolation of IncP-1 plasmids by exploiting their ability to mobilize plasmid pSM1890. IncP-1 plasmids were captured from the rhizosphere but not from bulk soil, and a high diversity was revealed by sequencing 14 different plasmids that were assigned to IncP-1β, δ, and ε subgroups. Although backbone genes were highly conserved and mobile elements or remnants as Tn501, IS1071, Tn402, or class 1 integron were carried by 13 of the sequenced IncP-1 plasmids, no antibiotic resistance genes were found. Instead, seven plasmids had a mer operon with Tn501-like transposon and five plasmids contained putative metabolic gene clusters linked to these mobile elements. In-depth sequence comparisons with previously known plasmids indicate that the IncP-1 plasmids captured from the rhizosphere are archetypes of those found in clinical isolates. Our findings that IncP-1 plasmids do not always carry accessory genes in unpolluted rhizospheres are important to understand the ecology and role of the IncP-1 plasmids in the natural environment.}, }
@article {pmid33329459, year = {2020}, author = {Ruiz-Lopez, S and Foster, L and Boothman, C and Cole, N and Morris, K and Lloyd, JR}, title = {Identification of a Stable Hydrogen-Driven Microbiome in a Highly Radioactive Storage Facility on the Sellafield Site.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {587556}, pmid = {33329459}, issn = {1664-302X}, abstract = {The use of nuclear power has been a significant part of the United Kingdom's energy portfolio with the Sellafield site being used for power production and more recently reprocessing and decommissioning of spent nuclear fuel activities. Before being reprocessed, spent nuclear fuel is stored in water ponds with significant levels of background radioactivity and in high alkalinity (to minimize fuel corrosion). Despite these challenging conditions, the presence of microbial communities has been detected. To gain further insight into the microbial communities present in extreme environments, an indoor, hyper-alkaline, oligotrophic, and radioactive spent fuel storage pond (INP) located on the Sellafield site was analyzed. Water samples were collected from sample points within the INP complex, and also the purge water feeding tank (FT) that supplies water to the pond, and were screened for the presence of the 16S and 18S rRNA genes to inform sequencing requirements over a period of 30 months. Only 16S rRNA genes were successfully amplified for sequencing, suggesting that the microbial communities in the INP were dominated by prokaryotes. Quantitative Polymerase Chain Reaction (qPCR) analysis targeting 16S rRNA genes suggested that bacterial cells in the order of 104-106 mL-1 were present in the samples, with loadings rising with time. Next generation Illumina MiSeq sequencing was performed to identify the dominant microorganisms at eight sampling times. The 16S rRNA gene sequence analysis suggested that 70% and 91% from of the OTUs samples, from the FT and INP respectively, belonged to the phylum Proteobacteria, mainly from the alpha and beta subclasses. The remaining OTUs were assigned primarily to the phyla Acidobacteria, Bacteroidetes, and, Cyanobacteria. Overall the most abundant genera identified were Hydrogenophaga, Curvibacter, Porphyrobacter, Rhodoferax, Polaromonas, Sediminibacterium, Roseococcus, and Sphingomonas. The presence of organisms most closely related to Hydrogenophaga species in the INP areas, suggests the metabolism of hydrogen as an energy source, most likely linked to hydrolysis of water caused by the stored fuel. Isolation of axenic cultures using a range of minimal and rich media was also attempted, but only relatively minor components (from the phylum Bacteroidetes) of the pond water communities were obtained, emphasizing the importance of DNA-based, not culture-dependent techniques, for assessing the microbiome of nuclear facilities.}, }
@article {pmid33329422, year = {2020}, author = {Mony, C and Vandenkoornhuyse, P and Bohannan, BJM and Peay, K and Leibold, MA}, title = {A Landscape of Opportunities for Microbial Ecology Research.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {561427}, pmid = {33329422}, issn = {1664-302X}, abstract = {Microbes encompass tremendous biodiversity, provide support to all living forms, including humans, and play an important role in many ecosystem services. The rules that govern microorganism community assembly are increasingly revealed due to key advances in molecular and analytical methods but their understanding remain a key challenge in microbial ecology. The existence of biogeographic patterns within microbial communities has been established and explained in relation to landscape-scale processes, including selection, drift, dispersal and mutation. The effect of habitat patchiness on microorganisms' assembly rules remains though incompletely understood. Here, we review how landscape ecology principles can be adapted to explore new perspectives on the mechanisms that determine microbial community structure. To provide a general overview, we characterize microbial landscapes, the spatial and temporal scales of the mechanisms that drive microbial assembly and the feedback between microorganisms and landscape structure. We provide evidence for the effects of landscape heterogeneity, landscape fragmentation and landscape dynamics on microbial community structure, and show that predictions made for macro-organisms at least partly also apply to microorganisms. We explain why emerging metacommunity approaches in microbial ecology should include explicit characterization of landscape structure in their development and interpretation. We also explain how biotic interactions, such as competition, prey-predator or mutualist relations may influence the microbial landscape and may be involved in the above-mentioned feedback process. However, we argue that the application of landscape ecology to the microbial world cannot simply involve transposing existing theoretical frameworks. This is due to the particularity of these organisms, in terms of size, generation time, and for some of them, tight interaction with hosts. These characteristics imply dealing with unusual and dependent space and time scales of effect. Evolutionary processes have also a strong importance in microorganisms' response to their landscapes. Lastly, microorganisms' activity and distribution induce feedback effects on the landscape that have to be taken into account. The transposition of the landscape ecology framework to microorganisms provides many challenging research directions for microbial ecology.}, }
@article {pmid33329414, year = {2020}, author = {Mullin, SW and Wanger, G and Kruger, BR and Sackett, JD and Hamilton-Brehm, SD and Bhartia, R and Amend, JP and Moser, DP and Orphan, VJ}, title = {Patterns of in situ Mineral Colonization by Microorganisms in a ~60°C Deep Continental Subsurface Aquifer.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {536535}, pmid = {33329414}, issn = {1664-302X}, abstract = {The microbial ecology of the deep biosphere is difficult to characterize, owing in part to sampling challenges and poorly understood response mechanisms to environmental change. Pre-drilled wells, including oil wells or boreholes, offer convenient access, but sampling is frequently limited to the water alone, which may provide only a partial view of the native diversity. Mineral heterogeneity demonstrably affects colonization by deep biosphere microorganisms, but the connections between the mineral-associated and planktonic communities remain unclear. To understand the substrate effects on microbial colonization and the community response to changes in organic carbon, we conducted an 18-month series of in situ experiments in a warm (57°C), anoxic, fractured carbonate aquifer at 752 m depth using replicate open, screened cartridges containing different solid substrates, with a proteinaceous organic matter perturbation halfway through this series. Samples from these cartridges were analyzed microscopically and by Illumina (iTag) 16S rRNA gene libraries to characterize changes in mineralogy and the diversity of the colonizing microbial community. The substrate-attached and planktonic communities were significantly different in our data, with some taxa (e.g., Candidate Division KB-1) rare or undetectable in the first fraction and abundant in the other. The substrate-attached community composition also varied significantly with mineralogy, such as with two Rhodocyclaceae OTUs, one of which was abundant on carbonate minerals and the other on silicic substrates. Secondary sulfide mineral formation, including iron sulfide framboids, was observed on two sets of incubated carbonates. Notably, microorganisms were attached to the framboids, which were correlated with abundant Sulfurovum and Desulfotomaculum sp. sequences in our analysis. Upon organic matter perturbation, mineral-associated microbial diversity differences were temporarily masked by the dominance of putative heterotrophic taxa in all samples, including OTUs identified as Caulobacter, Methyloversatilis, and Pseudomonas. Subsequent experimental deployments included a methanogen-dominated stage (Methanobacteriales and Methanomicrobiales) 6 months after the perturbation and a return to an assemblage similar to the pre-perturbation community after 9 months. Substrate-associated community differences were again significant within these subsequent phases, however, demonstrating the value of in situ time course experiments to capture a fraction of the microbial assemblage that is frequently difficult to observe in pre-drilled wells.}, }
@article {pmid33323508, year = {2020}, author = {Brooks, CN and Field, EK}, title = {Iron Flocs and the Three Domains: Microbial Interactions in Freshwater Iron Mats.}, journal = {mBio}, volume = {11}, number = {6}, pages = {}, pmid = {33323508}, issn = {2150-7511}, abstract = {Freshwater iron mats are dynamic geochemical environments with broad ecological diversity, primarily formed by the iron-oxidizing bacteria. The community features functional groups involved in biogeochemical cycles for iron, sulfur, carbon, and nitrogen. Despite this complexity, iron mat communities provide an excellent model system for exploring microbial ecological interactions and ecological theories in situ Syntrophies and competition between the functional groups in iron mats, how they connect cycles, and the maintenance of these communities by taxons outside bacteria (the eukaryota, archaea, and viruses) have been largely unstudied. Here, we review what is currently known about freshwater iron mat communities, the taxa that reside there, and the interactions between these organisms, and we propose ways in which future studies may uncover exciting new discoveries. For example, the archaea in these mats may play a greater role than previously thought as they are diverse and widespread in iron mats based on 16S rRNA genes and include methanogenic taxa. Studies with a holistic view of the iron mat community members focusing on their diverse interactions will expand our understanding of community functions, such as those involved in pollution removal. To begin addressing questions regarding the fundamental interactions and to identify the conditions in which they occur, more laboratory culturing techniques and coculture studies, more network and keystone species analyses, and the expansion of studies to more freshwater iron mat systems are necessary. Increasingly accessible bioinformatic, geochemical, and culturing tools now open avenues to address the questions that we pose herein.}, }
@article {pmid33319645, year = {2020}, author = {Christensen, L and Sørensen, CV and Wøhlk, FU and Kjølbæk, L and Astrup, A and Sanz, Y and Hjorth, MF and Benítez-Páez, A}, title = {Microbial enterotypes beyond genus level: Bacteroides species as a predictive biomarker for weight change upon controlled intervention with arabinoxylan oligosaccharides in overweight subjects.}, journal = {Gut microbes}, volume = {12}, number = {1}, pages = {1847627}, doi = {10.1080/19490976.2020.1847627}, pmid = {33319645}, issn = {1949-0984}, abstract = {Recent studies indicate that microbial enterotypes may influence the beneficial effects of wholegrain enriched diets including bodyweight regulation. In a 4-week intervention trial, overweight subjects were randomized to consume either arabinoxylan-oligosaccharides (AXOS) (10.4 g/d) from wheat bran or polyunsaturated fatty acids (PUFA) (3.6 g/d). In the present study, we have stratified the subjects participating in the intervention (n = 29) according to the baseline Prevotella-to-Bacteroides (P/B) ratios through a post-hoc analysis and applied a linear mixed model analysis to identify the influence of this P/B ratio on the differences in weight changes in the intervention arms. Following AXOS consumption (n = 15), the high P/B group showed no bodyweight changes [-0.14 kg (95% CI: -0.67; 0.38, p = .59)], while the low P/B group gained 0.65 kg (95% CI: 0.16; 1.14, p = .009). Consequently, a difference of -0.79 kg was found between P/B groups (95% CI: -1.51; -0.08, p = .030). No differences were found between P/B groups following PUFA consumption (0.61 kg, 95% CI: -0.13; 1.35, p = .10). Among the Bacteroides species, B. cellulosilyticus relative abundance exhibited the highest positive rank correlation (Kendall's tau = 0.51, FDR p = .070) with 4-week weight change on AXOS, and such association was further supported by using supervised classification methods (Random Forest). We outlined several carbohydrate-active enzyme (CAZy) genes involved in xylan-binding and degradation to be enriched in B. cellulosilyticus genomes, as well as multiple accessory genes, suggesting a supreme AXOS-derived glycan scavenging role of such species. This post-hoc analysis, ensuring species and strain demarcation at the human gut microbiota, permitted to uncover the predictive role of Bacteroides species over P/B enterotype in weight gain during a fiber-based intervention. The results of this pilot trial pave the way for future assessments on fiber fermentation outputs from Bacteroides species affecting lipid metabolism in the host and with direct impact on adiposity, thus helping to design personalized interventions.}, }
@article {pmid33315910, year = {2020}, author = {Oyuela Aguilar, M and Gobbi, A and Browne, PD and Ellegaard-Jensen, L and Hansen, LH and Semorile, L and Pistorio, M}, title = {Influence of vintage, geographic location and cultivar on the structure of microbial communities associated with the grapevine rhizosphere in vineyards of San Juan Province, Argentina.}, journal = {PloS one}, volume = {15}, number = {12}, pages = {e0243848}, pmid = {33315910}, issn = {1932-6203}, abstract = {Soil microbiomes, as a primary reservoir for plant colonizing fungi and bacteria, play a major role in determining plant productivity and preventing invasion by pathogenic microorganisms. The use of 16S rRNA and ITS high-throughput amplicon sequencing for analysis of complex microbial communities have increased dramatically in recent years, establishing links between wine specificity and, environmental and viticultural factors, which are framed into the elusive terroir concept. Given the diverse and complex role these factors play on microbial soil structuring of agricultural crops, the main aim of this study is to evaluate how external factors, such as vintage, vineyard location, cultivar and soil characteristics, may affect the diversity of the microbial communities present. Additionally, we aim to compare the influence these factors have on the structuring of bacterial and fungal populations associated with Malbec grapevine rhizosphere with that of the more widespread Cabernet Sauvignon grapevine cultivar. Samples were taken from Malbec and Cabernet Sauvignon cultivars from two different vineyards in the San Juan Province of Argentina. Total DNA extracts from the rhizosphere soil samples were sequenced using Illumina's Miseq technology, targeting the V3-V4 hypervariable 16S rRNA region in prokaryotes and the ITS1 region in yeasts. The major bacterial taxa identified were Proteobacteria, Bacteroidetes and Firmicutes, while the major fungal taxa were Ascomycetes, Basidiomycetes, Mortierellomycetes and a low percentage of Glomeromycetes. Significant differences in microbial community composition were found between vintages and vineyard locations, whose soils showed variances in pH, organic matter, and content of carbon, nitrogen, and absorbable phosphorus.}, }
@article {pmid33311714, year = {2020}, author = {Lee, KS and Pereira, FC and Palatinszky, M and Behrendt, L and Alcolombri, U and Berry, D and Wagner, M and Stocker, R}, title = {Optofluidic Raman-activated cell sorting for targeted genome retrieval or cultivation of microbial cells with specific functions.}, journal = {Nature protocols}, volume = {}, number = {}, pages = {}, pmid = {33311714}, issn = {1750-2799}, support = {GBMF3783//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; GBMF9197//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 542395//Simons Foundation/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; P26127-B20//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; P27831-B28//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; P26127-B20//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; P27831-B28//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; 2019-04401//Vetenskapsrådet (Swedish Research Council)/ ; }, abstract = {Stable isotope labeling of microbial taxa of interest and their sorting provide an efficient and direct way to answer the question &quot;who does what?&quot; in complex microbial communities when coupled with fluorescence in situ hybridization or downstream 'omics' analyses. We have developed a platform for automated Raman-based sorting in which optical tweezers and microfluidics are used to sort individual cells of interest from microbial communities on the basis of their Raman spectra. This sorting of cells and their downstream DNA analysis, such as by mini-metagenomics or single-cell genomics, or cultivation permits a direct link to be made between the metabolic roles and the genomes of microbial cells within complex microbial communities, as well as targeted isolation of novel microbes with a specific physiology of interest. We describe a protocol from sample preparation through Raman-activated live cell sorting. Subsequent cultivation of sorted cells is described, whereas downstream DNA analysis involves well-established approaches with abundant methods available in the literature. Compared with manual sorting, this technique provides a substantially higher throughput (up to 500 cells per h). Furthermore, the platform has very high sorting accuracy (98.3 ± 1.7%) and is fully automated, thus avoiding user biases that might accompany manual sorting. We anticipate that this protocol will empower in particular environmental and host-associated microbiome research with a versatile tool to elucidate the metabolic contributions of microbial taxa within their complex communities. After a 1-d preparation of cells, sorting takes on the order of 4 h, depending on the number of cells required.}, }
@article {pmid33310220, year = {2021}, author = {Thwaites, BJ and Stuetz, R and Short, M and Reeve, P and Alvarez-Gaitan, JP and Dinesh, N and Philips, R and van den Akker, B}, title = {Analysis of nitrous oxide emissions from aerobic granular sludge treating high saline municipal wastewater.}, journal = {The Science of the total environment}, volume = {756}, number = {}, pages = {143653}, doi = {10.1016/j.scitotenv.2020.143653}, pmid = {33310220}, issn = {1879-1026}, mesh = {Bioreactors ; Denitrification ; Nitrification ; Nitrogen/analysis ; Nitrous Oxide/analysis ; *Sewage ; Waste Disposal, Fluid ; *Waste Water ; }, abstract = {Conventional activated sludge (CAS)-based wastewater treatment processes have the potential to emit high concentrations of nitrous oxide (N2O) during nitrification and denitrification, which can significantly impact the environmental performance and carbon footprint of wastewater treatment operations. While N2O emissions from CAS have been extensively studied, there is little knowledge of N2O emissions from aerobic granular sludge (AGS) which is now an increasingly popular secondary treatment alternative. The N2O emissions performance of AGS needs to be investigated to ensure that the positive benefits of AGS, such as increased capacity and stable nutrient removal, are not offset by higher emissions. This study quantified N2O emissions from a pilot-scale AGS reactor operated under a range of organic loading rates. A second CAS pilot plant was operated in parallel and under identical loading rates to allow for side-by-side comparison of N2O emissions from floc-based activated sludge. Under low loadings of <0.6 kg COD/m3/d the N2O emission factor from AGS and CAS were similar, at around 1.46 ± 0.1% g N2Oemitted/g ammonium loaded. A step increase in the organic loading rate increased N2O emissions from AGS more so than CAS which appeared to be attributed to the reactor feeding strategy that was required for AGS formation. The use of a separate anaerobic feeding phase which was followed by the aeration phase, resulted in extended periods of low dissolved oxygen (DO) concentrations combined with an initial high biomass ammonium loading rate, which favours N2O production and was exacerbated at higher organic loads. Conversely, the combined feeding plus aeration operation (aerobic feed) employed by the CAS system enabled a more even biomass ammonium loading rate and DO supply. This work has shown that while AGS has many operational benefits, the impacts that aeration profile, loading rate and feeding strategy have on N2O emissions must be considered.}, }
@article {pmid33308279, year = {2020}, author = {Yulandi, A and Suwanto, A and Waturangi, DE and Wahyudi, AT}, title = {Shotgun metagenomic analysis reveals new insights into bacterial community profiles in tempeh.}, journal = {BMC research notes}, volume = {13}, number = {1}, pages = {562}, pmid = {33308279}, issn = {1756-0500}, abstract = {OBJECTIVE: Amplicon sequencing targeting 16S ribosomal RNA (rRNA) has been widely used to profile the microbial community from fermented food samples. However, polymerase chain reaction (PCR) steps on amplicon sequencing analysis and intragenomic heterogeneity within 16S rRNA are believed to contribute to bias in estimating microbial community composition. As potential paraprobiotics sources, a comprehensive profiling study of tempeh microbial ecology could contribute to tempeh product development. This study employed a shotgun metagenomic approach, where metagenome fragments from tempeh samples were sequenced directly for taxonomic and functional profiling analysis.<br><br>RESULTS: Taxonomic profiling showed that Proteobacteria, Firmicutes, and Bacteroidetes were the dominant phyla from the shotgun metagenomic analysis in all tempeh samples. In terms of composition, this shotgun metagenomic study revealed that Proteobacteria was the most abundant phylum. Functional profiling showed that iron complex outer-membrane recepter protein (KEGG ID: K02014) was the most transcribed gene based on this metagenomic analysis. The metagenome-assembled genomes (MAGs) results from the binning pipeline could reveal almost complete whole genome sequence of Lactobacillus fermentum, Enterococcus cecorum, Escherichia coli, Klebsiella pneumoniae, and Acinetobacter baumannii.}, }
@article {pmid33305821, year = {2020}, author = {Leininger, A and Yates, MD and Ramirez, M and Kjellerup, B}, title = {Biofilm structure, dynamics, and ecology of an upscaled biocathode wastewater microbial fuel cell.}, journal = {Biotechnology and bioengineering}, volume = {}, number = {}, pages = {}, doi = {10.1002/bit.27653}, pmid = {33305821}, issn = {1097-0290}, support = {MFC2016-18//Blue Plains Advanced Wastewater treatment Plant/ ; }, abstract = {A microbial fuel cell (MFC) system containing modular half-submerged biocathode was operated for 6 months in an 800 L flow-through system with domestic wastewater. For the first time, spatial and temporal differences in biofilm communities were examined on large three-dimensional electrodes in a wastewater MFC. Biocathode microbial community analysis showed a specialized biofilm community with electrogenic and electrotrophic taxa forming during operation, suggesting potentially opposing electrode reactions. The anodic community structure shifted during operation, but no spatial differences were observed along the length of the electrode. Power output from the system was most strongly influenced by pH. Higher power densities were associated with the use of solids-dewatering filtrate with increased organic matter, conductivity, and pH. The results show that the biocathode was the rate-limiting step and that future MFC design should consider the effect of size, shape, and orientation of biocathodes on their community assembly and electrotrophic ability.}, }
@article {pmid33305411, year = {2020}, author = {Cheng, J and Yang, Y and Yuan, MM and Gao, Q and Wu, L and Qin, Z and Shi, ZJ and Schuur, EAG and Cole, JR and Tiedje, JM and Zhou, J}, title = {Winter warming rapidly increases carbon degradation capacities of fungal communities in tundra soil: Potential consequences on carbon stability.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.15773}, pmid = {33305411}, issn = {1365-294X}, support = {2019QZKK0503//the Second Tibetan Plateau Scientific Expedition and Research (STEP) programme/ ; 41877048//the National Science Foundation of China/ ; 41825016//the National Science Foundation of China/ ; DE-SC0004601//the US Department of Energy, Office of Science, Genomic Science Program/ ; DE-SC0010715//the US Department of Energy, Office of Science, Genomic Science Program/ ; }, abstract = {High-latitude tundra ecosystems are increasingly affected by climate warming. As an important fraction of soil microorganisms, fungi play essential roles in carbon degradation, especially the old, chemically recalcitrant carbon. However, it remains obscure how fungi respond to climate warming and whether fungi, in turn, affect carbon stability of tundra. In a 2-year winter soil warming experiment of 2°C by snow fences, we investigated responses of fungal communities to warming in the active layer of an Alaskan tundra. Although fungal community composition, revealed by the 28S rRNA gene amplicon sequencing, remained unchanged (p > .05), fungal functional gene composition, revealed by a microarray named GeoChip, was altered (p < .05). Changes in functional gene composition were linked to winter soil temperature, thaw depth, soil moisture, and gross primary productivity (canonical correlation analysis, p < .05). Specifically, relative abundances of fungal genes encoding invertase, xylose reductase and vanillin dehydrogenase significantly increased (p < .05), indicating higher carbon degradation capacities of fungal communities under warming. Accordingly, we detected changes in fungal gene networks under warming, including higher average path distance, lower average clustering coefficient and lower percentage of negative links, indicating that warming potentially changed fungal interactions. Together, our study reveals higher carbon degradation capacities of fungal communities under short-term warming and highlights the potential impacts of fungal communities on tundra ecosystem respiration, and consequently future carbon stability of high-latitude tundra.}, }
@article {pmid33304469, year = {2020}, author = {Bassani, I and Larousse, M and Tran, QD and Attard, A and Galiana, E}, title = {Phytophthora zoospores: From perception of environmental signals to inoculum formation on the host-root surface.}, journal = {Computational and structural biotechnology journal}, volume = {18}, number = {}, pages = {3766-3773}, pmid = {33304469}, issn = {2001-0370}, abstract = {To explore moist soils and to target host plants, phytopathogenic Phytophthora species utilize the sensory and propulsion capabilities of the biflagellate unicellular zoospores they produce. Zoospore motion and interactions with the microenvironment are of primary importance for Phytophthora physiology. These are also of critical significance for plant pathology in early infection sequential events and their regulation: the directed zoospore migration toward the host, the local aggregation and adhesion at the host penetration site. In the soil, these early events preceding the root colonization are orchestrated by guidance factors, released from the soil particles in water films, or emitted within microbiota and by host plants. This signaling network is perceived by zoospores and results in coordinated behavior and preferential localization in the rhizosphere. Recent computational and structural studies suggest that rhizospheric ion and plant metabolite sensing is a key determinant in driving zoospore motion, orientation and aggregation. To reach their target, zoospores respond to various molecular, chemical and electrical stimuli. However, it is not yet clear how these signals are generated in local soil niches and which gene functions govern the sensing and subsequent responses of zoospores. Here we review studies on the soil, microbial and host-plant factors that drive zoospore motion, as well as the adaptations governing zoospore behavior. We propose several research directions that could be explored to characterize the role of zoospore microbial ecology in disease.}, }
@article {pmid33303324, year = {2021}, author = {Molderez, TR and Prévoteau, A and Ceyssens, F and Verhelst, M and Rabaey, K}, title = {A chip-based 128-channel potentiostat for high-throughput studies of bioelectrochemical systems: Optimal electrode potentials for anodic biofilms.}, journal = {Biosensors &amp; bioelectronics}, volume = {174}, number = {}, pages = {112813}, doi = {10.1016/j.bios.2020.112813}, pmid = {33303324}, issn = {1873-4235}, abstract = {The presence of microorganisms performing extracellular electron transfer has been established in many environments. Research to determine their role is moving slowly due to the high cost of potentiostats and the variance of data with small number of replicates. Here, we present a 128-channel potentiostat, connected to a 128 gold electrode array. Whereas the system is able to perform simultaneously 128 (bio)electrochemical measurements with an independent electrical signal input, the present manufacturing of the array limited the number of effective channels for this study to 77. We assessed the impact of 11 electrode potentials ranging from -0.45V to +0.2V vs. Ag/AgCl (7 replicates per potential) on the growth and electrochemical characteristics of anodic electroactive biofilms (EABs) formed by acetate-fed microbial communities. After 7 days of growth, maximum current was reached for electrodes poised at -0.3V, closely followed by -0.25V and -0.1V to +0.1V, a range well-fitting the midpoint potential of minerals naturally reduced by electroactive bacteria such as Geobacter Sulfurreducens. There was no significant difference in apparent midpoint potential of the EABs (-0.35V), suggesting that the mechanism of heterogeneous electron transfer was not affected by the electrode potential. The EABs poised below current plateau potential (≤-0.3V) exhibited slower growth but higher charge transfer parameters. The high-throughput and high reproducibility provided by the array may have a major facilitating impact on the field of electromicrobiology. Key aspects to improve are data processing algorithms to deal with the vast amount of generated data, and manufacturing of the electrode array itself.}, }
@article {pmid33297305, year = {2020}, author = {Nikolausz, M and Kretzschmar, J}, title = {Anaerobic Digestion in the 21st Century.}, journal = {Bioengineering (Basel, Switzerland)}, volume = {7}, number = {4}, pages = {}, pmid = {33297305}, issn = {2306-5354}, abstract = {Despite being a mature biotechnological process, anaerobic digestion is still attracting considerable research attention, mainly due to its versatility both in substrate and product spectra, as well as being a perfect test system for the microbial ecology of anaerobes [...].}, }
@article {pmid33297216, year = {2021}, author = {Vaezzadeh, V and Thomes, MW and Kunisue, T and Tue, NM and Zhang, G and Zakaria, MP and Affendi, YA and Yap, FC and Chew, LL and Teoh, HW and Lee, CW and Bong, CW}, title = {Examination of barnacles' potential to be used as bioindicators of persistent organic pollutants in coastal ecosystem: A Malaysia case study.}, journal = {Chemosphere}, volume = {263}, number = {}, pages = {128272}, doi = {10.1016/j.chemosphere.2020.128272}, pmid = {33297216}, issn = {1879-1298}, mesh = {Animals ; Ecosystem ; Environmental Biomarkers ; Environmental Monitoring ; Halogenated Diphenyl Ethers/analysis ; *Hydrocarbons, Chlorinated/analysis ; Malaysia ; Persistent Organic Pollutants ; *Pesticides/analysis ; *Polychlorinated Biphenyls/analysis ; *Thoracica ; }, abstract = {Barnacles are ubiquitous in coastal ecosystems of different geographical regions worldwide. This is the first study attempting to assess the suitability of barnacles as bioindicators of persistent organic pollutants (POPs) in coastal environments. Barnacles were collected from the coasts around Peninsular Malaysia and analyzed for POPs including polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs) and organochlorine pesticides (OCPs). Among POPs, PCBs showed the highest concentrations with elevated contributions of CB28 and CB153. As for PBDEs, BDE47 was the most frequently detected congener, while BDE209 was detected in barnacles from two stations in Port Klang and the levels reached up to >70% of total PBDE concentrations. Concentrations of OCPs detected in barnacles were in the order of CHLs > DDTs > HCHs > HCB and 4,4'-DDE and cis- and trans-chlordane were the predominant OCP compounds. A comparison with previous studies in Malaysia showed consistent levels of POPs. Green mussels collected from selected barnacles' habitats, for the sake of a comparison, showed almost similar profiles but lower concentrations of POPs. The spatial distribution of POPs observed in barnacles and comparison of POP levels and profiles with mussels indicated that barnacles can be useful bioindicators for monitoring POPs contamination in the coastal ecosystems.}, }
@article {pmid33296424, year = {2020}, author = {Fiedler, S and Wünnemann, H and Hofmann, I and Theobalt, N and Feuchtinger, A and Walch, A and Schwaiger, J and Wanke, R and Blutke, A}, title = {A practical guide to unbiased quantitative morphological analyses of the gills of rainbow trout (Oncorhynchus mykiss) in ecotoxicological studies.}, journal = {PloS one}, volume = {15}, number = {12}, pages = {e0243462}, pmid = {33296424}, issn = {1932-6203}, abstract = {Rainbow trout (Oncorhynchus mykiss) are frequently used as experimental animals in ecotoxicological studies, in which they are experimentally exposed to defined concentrations of test substances, such as heavy metals, pesticides, or pharmaceuticals. Following exposure to a broad variety of aquatic pollutants, early morphologically detectable toxic effects often manifest in alterations of the gills. Suitable methods for an accurate and unbiased quantitative characterization of the type and the extent of morphological gill alterations are therefore essential prerequisites for recognition, objective evaluation and comparison of the severity of gill lesions. The aim of the present guidelines is to provide practicable, standardized and detailed protocols for the application of unbiased quantitative stereological analyses of relevant morphological parameters of the gills of rainbow trout. These gill parameters inter alia include the total volume of the primary and secondary gill lamellae, the surface area of the secondary gill lamellae epithelium (i.e., the respiratory surface) and the thickness of the diffusion barrier. The featured protocols are adapted to fish of frequently used body size classes (300-2000 g). They include well-established, conventional sampling methods, probes and test systems for unbiased quantitative stereological analyses of light- and electron microscopic 2-D gill sections, as well as the application of modern 3-D light sheet fluorescence microscopy (LSFM) of optically cleared gill samples as an innovative, fast and efficient quantitative morphological analysis approach. The methods shown here provide a basis for standardized and representative state-of-the-art quantitative morphological analyses of trout gills, ensuring the unbiasedness and reproducibility, as well as the intra- and inter-study comparability of analyses results. Their broad implementation will therefore significantly contribute to the reliable identification of no observed effect concentration (NOEC) limits in ecotoxicological studies and, moreover, to limit the number of experimental animals by reduction of unnecessary repetition of experiments.}, }
@article {pmid33295059, year = {2020}, author = {Li, J and Bååth, E and Pei, J and Fang, C and Nie, M}, title = {Temperature adaptation of soil microbial respiration in alpine, boreal and tropical soils: An application of the square root (Ratkowsky) model.}, journal = {Global change biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/gcb.15476}, pmid = {33295059}, issn = {1365-2486}, support = {2020M670975//The Postdoctoral Science Foundation of China/ ; 31830009//The National Science Foundation of China/ ; 32030067//The National Science Foundation of China/ ; 91951112//The National Science Foundation of China/ ; 2020PJD003//The Shanghai Pujiang Program/ ; }, abstract = {Warming is expected to stimulate soil microbial respiration triggering a positive soil carbon-climate feedback loop while a consensus remains elusive regarding the magnitude of this feedback. This is partly due to our limited understanding of the temperature-adaptive response of soil microbial respiration, especially over broad climatic scales. We used the square root (Ratkowsky) model to calculate the minimum temperature for soil microbial respiration (Tmin , which describes the temperature adaptation of soil microbial respiration) of 298 soil samples from alpine grasslands on the Tibetan Plateau and forest ecosystems across China with a mean annual temperature (MAT) range from -6°C to +25°C. The instantaneous soil microbial respiration was determined between 4°C and 28°C. The square root model could well fit the temperature effect on soil microbial respiration for each individual soil, with R2 higher than 0.98 for all soils. Tmin ranged from -8.1°C to -0.1°C and increased linearly with increasing MAT (R2 = 0.68). MAT dominantly regulated Tmin variation when accounting simultaneously for multiple other drivers (mean annual precipitation, soil pH and carbon quality); an independent experiment showed that carbon availability had no significant effect on Tmin . Using the relationship between Tmin and MAT, soil microbial respiration after an increased MAT could be estimated, resulting in a relative increase in respiration with decreasing MAT. Thus, soil microbial respiration responses are adapted to long-term temperature differences in MAT. We suggest that Tmin = -5 + 0.2 × MAT, that is, every 1°C rise in MAT is estimated to increase Tmin of respiration by approximately 0.2°C, could be used as a first approximation to incorporate temperature adaptation of soil microbial respiration in model predictions. Our results can be used to predict future changes in the response of soil microbial respiration to temperature over different levels of warming and across broad geographic scales with different MAT.}, }
@article {pmid33294135, year = {2020}, author = {Tobias, NJ and Eberhard, FE and Guarneri, AA}, title = {Enzymatic biosynthesis of B-complex vitamins is supplied by diverse microbiota in the Rhodnius prolixus anterior midgut following Trypanosoma cruzi infection.}, journal = {Computational and structural biotechnology journal}, volume = {18}, number = {}, pages = {3395-3401}, pmid = {33294135}, issn = {2001-0370}, abstract = {Trypanosoma cruzi, the causative agent of Chagas disease, colonizes the gut of triatomine insects, including Rhodnius prolixus. It is believed that this colonization upsets the microbiota that are normally present, presumably switching the environment to one more favorable for parasite survival. It was previously thought that one particular bacterium, Rhodococcus rhodnii, was essential for insect survival due to its ability to produce vital B-complex vitamins. However, these bacteria are not always identified in great abundance in studies on R. prolixus microbiota. Here we sequenced the microbiota of the insect anterior midgut using shotgun metagenomic sequencing in order to obtain a high-resolution snapshot of the microbes inside at two different time points and under two conditions; in the presence or absence of parasite and immediately following infection, or three days post-infection. We identify a total of 217 metagenomic bins, and recovered one metagenome-assembled genome, which we placed in the genus Dickeya. We show that, despite Rhodococcus being present, it is not the only microbe capable of synthesizing B-complex vitamins, with the genes required for biosynthesis present in a number of different microbes. This work helps to gain a new insight into the microbial ecology of R. prolixus.}, }
@article {pmid33292591, year = {2020}, author = {Zhang, W and Bao, C and Wang, J and Zang, J and Cao, Y}, title = {Administration of Saccharomyces boulardii mafic-1701 improves feed conversion ratio, promotes antioxidant capacity, alleviates intestinal inflammation and modulates gut microbiota in weaned piglets.}, journal = {Journal of animal science and biotechnology}, volume = {11}, number = {1}, pages = {112}, pmid = {33292591}, issn = {1674-9782}, abstract = {BACKGROUND: Probiotics are used as a means to improve animal health and intestinal development. Saccharomyces boulardii is a well-known probiotic; however, few studies have examined the effects of S. boulardii on weaned piglet performance. Therefore, this 28-day study compared the effects of S. boulardii mafic-1701 and aureomycin in diets for weaned piglets on growth performance, antioxidant parameters, inflammation and intestinal microbiota. One hundred and eight piglets, weaned at 28 d of age (8.5 ± 1.1 kg), were randomly divided into the three dietary treatment groups with six pens and six piglets per pen (half male and half female). The dietary treatment groups were as follows: 1) basal diet (CON); 2) basal diet supplemented with 75 mg/kg aureomycin (ANT); 3) basal diet supplemented with 1 × 108 CFU/kg S. boulardii mafic-1701 (SB).<br><br>RESULTS: Compared to CON group, SB group had higher feed efficiency (P < 0.05) in the last 14 d and lower diarrhea rate (P < 0.05) over the entire 28 d. Total superoxide dismutase in serum was markedly increased in SB group (P < 0.05). Moreover, compared with CON group, SB group decreased the levels of pro-inflammatory cytokines interleukin-6 (P < 0.01) and Tumor necrosis factor-α (P < 0.05) in jejunum. Supplementation of S. boulardii mafic-1701 increased the abundance of Ruminococcaceae_UCG_009 and Turicibacter (P < 0.05), whereas the abundance of unclassified_Clostridiaceae_4 was decreased (P < 0.05). Furthermore, S. boulardii mafic-1701 administration increased cecal concentration of microbial metabolites, isobutyrate and valerate (P < 0.05).<br><br>CONCLUSIONS: The improvement in feed conversion ratio, reduction in diarrhea rate in weaned piglets provided diets supplemented with S. boulardii mafic-1701 may be associated with enhanced antioxidant activity, anti-inflammatory responses and improved intestinal microbial ecology.}, }
@article {pmid33290744, year = {2020}, author = {Songailiene, I and Juozapaitis, J and Tamulaitiene, G and Ruksenaite, A and Šulčius, S and Sasnauskas, G and Venclovas, Č and Siksnys, V}, title = {HEPN-MNT Toxin-Antitoxin System: The HEPN Ribonuclease Is Neutralized by OligoAMPylation.}, journal = {Molecular cell}, volume = {80}, number = {6}, pages = {955-970.e7}, doi = {10.1016/j.molcel.2020.11.034}, pmid = {33290744}, issn = {1097-4164}, abstract = {Prokaryotic toxin-antitoxin (TA) systems are composed of a toxin capable of interfering with key cellular processes and its neutralizing antidote, the antitoxin. Here, we focus on the HEPN-MNT TA system encoded in the vicinity of a subtype I-D CRISPR-Cas system in the cyanobacterium Aphanizomenon flos-aquae. We show that HEPN acts as a toxic RNase, which cleaves off 4 nt from the 3' end in a subset of tRNAs, thereby interfering with translation. Surprisingly, we find that the MNT (minimal nucleotidyltransferase) antitoxin inhibits HEPN RNase through covalent di-AMPylation (diadenylylation) of a conserved tyrosine residue, Y109, in the active site loop. Furthermore, we present crystallographic snapshots of the di-AMPylation reaction at different stages that explain the mechanism of HEPN RNase inactivation. Finally, we propose that the HEPN-MNT system functions as a cellular ATP sensor that monitors ATP homeostasis and, at low ATP levels, releases active HEPN toxin.}, }
@article {pmid33289627, year = {2020}, author = {Hofmann, K and Woller, A and Huptas, C and Wenning, M and Scherer, S and Doll, EV}, title = {Pseudomonas cremoris sp. nov., a novel proteolytic species isolated from cream.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1099/ijsem.0.004597}, pmid = {33289627}, issn = {1466-5034}, abstract = {During a study investigating the microbiota of raw milk and its semi-finished products, strains WS 5106T and WS 5096 were isolated from cream and skimmed milk concentrate. They could be assigned to the genus Pseudomonas by their 16S rRNA sequences, but not to any validly named species. In this work, a polyphasic approach was used to characterize the novel strains and to investigate their taxonomic status. Examinations based on the topology of core genome phylogenomy as well as average nucleotide identity (ANIm) comparisons suggested a novel Pseudomonas species within the Pseudomonas fluorescens subgroup. With pairwise ANIm values of 90.1 and 89.8 %, WS 5106T was most closely related to Pseudomonas nabeulensis CECT 9765T and Pseudomonas kairouanensis CECT 9766T. The G+C content of strain WS 5106T was 60.1 mol%. Morphologic analyses revealed Gram-stain-negative, aerobic, catalase and oxidase positive, rod-shaped and motile cells. Proteolysis on skimmed milk agar as well as lipolysis on tributyrin agar occurred at both 28 and 6 °C. Tolerated growth conditions were temperatures between 4 and 34 °C, pH values between 6.0 and 8.0, and salt concentrations of up to 5 %. Fatty acid profiles showed a pattern typical for Pseudomonas, with C16 : 0 as the dominant component. The major cellular polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol and the dominating quinone was Q-9. Based on these results, it is proposed to classify the strains as a novel species, Pseudomonas cremoris sp. nov., with WS 5106T (=DSM 111143T=LMG 31863T) as type strain and WS 5096 (=DSM 111129=LMG 31864) as an additional strain.}, }
@article {pmid33289410, year = {2020}, author = {Zhu, M and Ji, J and Duan, X and Li, Y}, title = {First Report of Golovinomyces cichoracearum Causing Powdery Mildew on Zinnia elegans in China.}, journal = {Plant disease}, volume = {}, number = {}, pages = {}, doi = {10.1094/PDIS-11-20-2333-PDN}, pmid = {33289410}, issn = {0191-2917}, abstract = {Zinnia elegans, common zinnia, is an annual plant with highly ornamental values. It is widely planted in many nurseries, city parks, universities and home gardens in China. From August to October 2020, powdery mildew-like signs and symptoms were observed on leaves of Z. elegans growing on the campus of Henan Normal University, Henan Province, China. White powdery colonies in circular- or irregularly shaped-lesions were abundant on both surfaces of leaves and covered up to 95 % of the leaf area. Any infected leaves were chlorotic, deformed or senescence. More than 70 % of the monitored Z. elegans plants showed these signs and symptoms. Conidiophores (n = 20) were 100 to 200 × 9 to 13 μm and composed of foot cells, followed by straight cells and conidia. Mycelial appressoria were single and nipple-shaped. The oval-shaped conidia (n = 30) were 22 to 36 × 12 to 18 μm, with a length/width ratio of 1.4 to 2.7, and produced germ tubes from the polar ends of the spore. No chasmothecia were found. Based on these morphological characteristics, the pathogen was initially identified morphologically as Golovinomyces cichoracearum (Braun and Cook 2012). Structures of the pathogen were scraped from infected leaves and total genomic DNA was isolated using the method previously described by Zhu et al. (2019). The internal transcribed spacer (ITS) region of rDNA was amplified by PCR using the primers ITS1/ITS4 (White et al. 1990) and the amplicon was sequenced by Invitrogen (Shanghai, China). The sequence for the fungus was deposited into GenBank under Accession No. MW029904 and was 99.83 % identical (595/596 bp) to G. cichoracearum on Symphyotrichum novi-belgii (HM769725)(Mørk et al. 2011). To perform pathogenicity analysis, leaf surfaces of five healthy plants were fixed in a settling tower and then inoculated by blowing fungal conidia from mildew-infested leaves using pressurized air. Five non-inoculated plants served as a control. The inoculated and non-inoculated plants were separately maintained in two growth chambers (humidity, 60 %; light/dark, 16 h/8 h; temperature, 18 ℃). Eleven- to twelve-days post-inoculation, powdery mildew signs were conspicuous on inoculated plants, while control plants remained healthy. Similar results were obtained by conducting two repeated pathogenicity assays. Thus, based on the morphological characteristics and molecular analysis, the pathogen was identified and confirmed as G. cichoracearum. This pathogen has been reported on Z. elegans in India, Israel, Jordan, Korea, Nepal, Sri Lanka, Switzerland, and Turkey (Farr and Rossman 2020). To our best knowledge, this is the first report of G. cichoracearum on Z. elegans in China. The sudden outbreak of powdery mildew caused by G. cichoracearum on Z. elegans may adversely impact the plant health and ornamental value in China. Therefore, the confirmation of G. cichoracearum infecting Z. elegans expands the understanding of this pathogen and provides the fundamental knowledge for future powdery mildew control.}, }
@article {pmid33288837, year = {2020}, author = {Busti, S and Rossi, B and Volpe, E and Ciulli, S and Piva, A and D'Amico, F and Soverini, M and Candela, M and Gatta, PP and Bonaldo, A and Grilli, E and Parma, L}, title = {Effects of dietary organic acids and nature identical compounds on growth, immune parameters and gut microbiota of European sea bass.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {21321}, pmid = {33288837}, issn = {2045-2322}, abstract = {A 71-day study was conducted to explore the effect of increasing dietary levels (0, 250, 500, 1000 mg kg feed-1; D0, D250, D500 and D1000, respectively) of a blend of microencapsulated organic acids (OA, specifically citric and sorbic acid) and nature identical compounds (NIC, specifically thymol and vanillin), on growth, intestinal immune parameters and gut microbiota (GM) of European sea bass juveniles reared under normal and subsequently suboptimal environmental conditions (high temperature, 30.0 ± 0.4 °C and low oxygen, 4.6 ± 0.6 mg L-1). OA and NIC did not promote growth, feed utilisation and feed intake at the inclusion tested but induced a significantly upregulation of IL-8, IL-10 and TGFβ. GM analyzed by next-generation sequencing showed that OA and NIC were able to exert prebiotic properties stimulating the development of beneficial bacteria taxa such as Lactobacillus, Leuconostoc, and Bacillus sp. Picrust analyses displayed a significant potential functional reconfiguration of GM promoting a decrease in inflammation-promoting and homeostatic functions at increasing OA and NIC administration. For the first time on this species the exposure to suboptimal rearing conditions was able to modify GM structure reducing LAB and increasing Proteobacteria, findings which were consistent with the inflammatory process observed at mRNA level.}, }
@article {pmid33282266, year = {2020}, author = {Zhao, L and Li, X and Yang, Q and Zhuang, D and Pan, X and Li, L}, title = {Adsorption kinetics and mechanism of di-n-butyl phthalate by Leuconostoc mesenteroides.}, journal = {Food science &amp; nutrition}, volume = {8}, number = {11}, pages = {6153-6163}, pmid = {33282266}, issn = {2048-7177}, abstract = {Di-n-butyl phthalate (DBP) poses a risk to humans as a ubiquitous environmental contaminant. A strain of Leuconostoc mesenteroides DM12 was chosen from lactic acid bacteria strains to study the DBP binding mechanisms. Adsorption of DBP by strain DM12 reached the highest binding rate of 87% after 11 hr of incubation, which could be explained by pseudo-second-order kinetics. The adsorption isotherm coincided with the model of Langmuir-Freundlich, indicating physical and chemical adsorption processes involved. Further, NaIO4 and TCA treatments were used to analyze the DBP binding mechanism of strain DM12, which indicated that peptidoglycan on the bacterial cell wall was involved in the process. The O-H, C-O, and N-H bonds were possibly involved in the binding process as the main functional groups.}, }
@article {pmid33281127, year = {2020}, author = {Nakajima, Y and Kojima, K and Kashiyama, Y and Doi, S and Nakai, R and Sudo, Y and Kogure, K and Yoshizawa, S}, title = {Bacterium Lacking a Known Gene for Retinal Biosynthesis Constructs Functional Rhodopsins.}, journal = {Microbes and environments}, volume = {35}, number = {4}, pages = {}, pmid = {33281127}, issn = {1347-4405}, abstract = {Microbial rhodopsins, comprising a protein moiety (rhodopsin apoprotein) bound to the light-absorbing chromophore retinal, function as ion pumps, ion channels, or light sensors. However, recent genomic and metagenomic surveys showed that some rhodopsin-possessing prokaryotes lack the known genes for retinal biosynthesis. Since rhodopsin apoproteins cannot absorb light energy, rhodopsins produced by prokaryotic strains lacking genes for retinal biosynthesis are hypothesized to be non-functional in cells. In the present study, we investigated whether Aurantimicrobium minutum KNCT, which is widely distributed in terrestrial environments and lacks any previously identified retinal biosynthesis genes, possesses functional rhodopsin. We initially measured ion transport activity in cultured cells. A light-induced pH change in a cell suspension of rhodopsin-possessing bacteria was detected in the absence of exogenous retinal. Furthermore, spectroscopic analyses of the cell lysate and HPLC-MS/MS analyses revealed that this strain contained an endogenous retinal. These results confirmed that A. minutum KNCT possesses functional rhodopsin and, hence, produces retinal via an unknown biosynthetic pathway. These results suggest that rhodopsin-possessing prokaryotes lacking known retinal biosynthesis genes also have functional rhodopsins.}, }
@article {pmid33279744, year = {2020}, author = {Agrawal, S and Weissbrodt, DG and Annavajhala, M and Jensen, MM and Arroyo, JMC and Wells, G and Chandran, K and Vlaeminck, SE and Terada, A and Smets, BF and Lackner, S}, title = {Time to act-assessing variations in qPCR analyses in biological nitrogen removal with examples from partial nitritation/anammox systems.}, journal = {Water research}, volume = {190}, number = {}, pages = {116604}, doi = {10.1016/j.watres.2020.116604}, pmid = {33279744}, issn = {1879-2448}, abstract = {Quantitative PCR (qPCR) is broadly used as the gold standard to quantify microbial community fractions in environmental microbiology and biotechnology. Benchmarking efforts to ensure the comparability of qPCR data for environmental bioprocesses are still scarce. Also, for partial nitritation/anammox (PN/A) systems systematic investigations are still missing, rendering meta-analysis of reported trends and generic insights potentially precarious. We report a baseline investigation of the variability of qPCR-based analyses for microbial communities applied to PN/A systems. Round-robin testing was performed for three PN/A biomass samples in six laboratories, using the respective in-house DNA extraction and qPCR protocols. The concentration of extracted DNA was significantly different between labs, ranged between 2.7 and 328 ng mg-1 wet biomass. The variability among the qPCR abundance data of different labs was very high (1-7 log fold) but differed for different target microbial guilds. DNA extraction caused maximum variation (3-7 log fold), followed by the primers (1-3 log fold). These insights will guide environmental scientists and engineers as well as treatment plant operators in the interpretation of qPCR data.}, }
@article {pmid33279588, year = {2021}, author = {Huang, L and Duan, C and Xia, X and Wang, H and Wang, Y and Zhong, Z and Wang, B and Ding, W and Yang, Y}, title = {Commensal microbe-derived propionic acid mediates juvenile social isolation-induced social deficits and anxiety-like behaviors.}, journal = {Brain research bulletin}, volume = {166}, number = {}, pages = {161-171}, doi = {10.1016/j.brainresbull.2020.12.001}, pmid = {33279588}, issn = {1873-2747}, abstract = {Social experiences during early life are thought to be critical for proper social and emotional development. Conversely, social insults during development causes long-lasting behavioral abnormalities later in life. However, how juvenile social deprivation influences social and emotional behaviors remains poorly understood. Here, we show that juvenile social isolation induces a shift in microbial ecology that negatively impacts social and emotional behaviors in adulthood. These behavioral changes, which occur during this critical period are transferable to antibiotic pre-treated mice by fecal microbiota transplant. In addition, juvenile social isolation decreases the expression of oxytocin receptor (OXTR) in the medial prefrontal cortex (mPFC), and increases the amounts of fecal propionic acid (PA), a short-chain fatty acid derived from gut micobiota. Accordingly, infusion with an OXTR antagonist (OXTR-A, l-368,899) specifically in the mPFC or supplementation of PA both can cause social deficits and anxiety-like behaviors in group housed mice. Collectively, our findings reveal that juvenile social experience regulates prefrontal cortical OXTR expression through gut microbiota-produced PA and that is essential for normal social and emotional behaviors, thus providing a cellular and molecular context to understand the consequences of juvenile social deprivation.}, }
@article {pmid33279067, year = {2021}, author = {Kim, E and Cho, EJ and Yang, SM and Kim, MJ and Kim, HY}, title = {Novel approaches for the identification of microbial communities in kimchi: MALDI-TOF MS analysis and high-throughput sequencing.}, journal = {Food microbiology}, volume = {94}, number = {}, pages = {103641}, doi = {10.1016/j.fm.2020.103641}, pmid = {33279067}, issn = {1095-9998}, abstract = {Complex interactions occur within microbial communities during the fermentation process of kimchi. Identification of these microorganisms provides the essential information required to improve food quality and to understand their role in this process. This was the first study to compare two methods for accuracy in the identification of microbial community changes during the fermentation of kimchi by comparing a culture-dependent (MALDI-TOF MS analysis) and a culture-independent method (high-throughput sequencing) of 16S rRNA gene fragment). Members of the Lactobacillus-related genera, Leuconostoc, and Weissella were identified as the predominant microorganisms by both methods. The culture-independent method was able to additionally identify non-lactic acid bacteria and yeasts, such as Kazachstania in kimchi. However, high-throughput sequencing failed to accurately recognize Latilactobacillus sakei, Latilactobacillus curvatus, Lactiplantibacillus plantarum, and W. cibaria, which played an important role in kimchi fermentation, as this method only allowed for identification at the genus level. Conversely, MALDI-TOF MS analysis could identify the isolates at the species level. Also, culture-dependent method could identify predominant species in viable cell communities. The culture-dependent method and culture-independent method provided complementary information by producing a more comprehensive view of the microbial ecology in fermented kimchi.}, }
@article {pmid33277271, year = {2020}, author = {Van Herreweghen, F and De Paepe, K and Marzorati, M and Van de Wiele, T}, title = {Mucin as a Functional Niche is a More Important Driver of in Vitro Gut Microbiota Composition and Functionality than Supplementation of Akkermansia muciniphila.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.02647-20}, pmid = {33277271}, issn = {1098-5336}, abstract = {IMPORTANCE SECTION Research into identification of biomarkers for gut health and ways to modulate the microbiota composition and activity to improve health, has put Akkermansia muciniphila in the spotlight. As a mucin degrader, A. muciniphila colonizes the interesting but not-fully described host-glycan degradation niche., . Plenty of research concerning A. muciniphila has been done, but little is known about its behavior in the complex microbial ecosystem in the colon, about the potential role of mucins to influence A. muciniphila behavior and the impact of its probiotic administration on the microbial ecosystem.This study aimed at investigating the impact of A. muciniphila administration on the endogenous community while also taking into account its nutritional specificity. As such, the effect of A.mucinihpila administration was investigated with and without addition of mucin. This allowed us to elucidate the importance of mucin presence to modulate the efficiency of the probiotic supplementation with A. muciniphilaAkkermansia muciniphila is an abundantly present commensal mucin degrading gut bacterium (1 - 4%) , widely distributed among healthy individuals. It has been positioned as a health biomarker and is currently explored as a biotherapeutic agent and next generation probiotic. Preliminary and ongoing research is mostly based on in vivo mouse models and human intervention trials. While these allow the assessment of physiologically relevant endpoints, the analysis of fecal samples presents limitations with respect to the in-depth mechanistic characterization of Akkermansia effects at the level of the microbiome. We aimed to evaluate the effect of A. muciniphila treatment on the endogenous community from four different donors in a validated, controlled in vitro model of the gut microbial ecosystem (SHIME). Taking into account the nutritional specificity of A. muciniphila, and the prebiotic-like action of mucins in the colon environment, the interplay between mucin, A. muciniphila and the endogenous community was investigated. The effects on the microbial community composition and functionality of A. muciniphila supplementation without mucin were limited, whereas mucin addition successfully induced compositional and metabolic changes in the gut microbiota. Indeed, mucin addition resulted in significantly higher acetate, propionate and butyrate production for all four donors, and the increase of several species, including A. muciniphila, Ruminococcus, Clostridium cluster XIVa, and Lachnospiraceae This study revealed that the supplementation of A. muciniphila together with mucin limited the observed prebiotic-like effect of mucin in inducing compositional changes.}, }
@article {pmid33274397, year = {2020}, author = {Bien, T and Hambleton, EA and Dreisewerd, K and Soltwisch, J}, title = {Molecular insights into symbiosis-mapping sterols in a marine flatworm-algae-system using high spatial resolution MALDI-2-MS imaging with ion mobility separation.}, journal = {Analytical and bioanalytical chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00216-020-03070-0}, pmid = {33274397}, issn = {1618-2650}, support = {Drei2/018/17//Interdisciplinary Center for Clinical Research, Münster, Germany/ ; SO976/5-1, project number 400912714//Deutsche Forschungsgemeinschaft/ ; }, abstract = {Waminoa sp. acoel flatworms hosting Symbiodiniaceae and the related Amphidinium dinoflagellate algae are an interesting model system for symbiosis in marine environments. While the host provides a microhabitat and safety, the algae power the system by photosynthesis and supply the worm with nutrients. Among these nutrients are sterols, including cholesterol and numerous phytosterols. While it is widely accepted that these compounds are produced by the symbiotic dinoflagellates, their transfer to and fate within the sterol-auxotrophic Waminoa worm host as well as their role in its metabolism are unknown. Here we used matrix-assisted laser desorption ionization (MALDI) mass spectrometry imaging combined with laser-induced post-ionization and trapped ion mobility spectrometry (MALDI-2-TIMS-MSI) to map the spatial distribution of over 30 different sterol species in sections of the symbiotic system. The use of laser post-ionization crucially increased ion yields and allowed the recording of images with a pixel size of 5 μm. Trapped ion mobility spectrometry (TIMS) helped with the tentative assignment of over 30 sterol species. Correlation with anatomical features of the worm, revealed by host-derived phospholipid signals, and the location of the dinoflagellates, revealed by chlorophyll a signal, disclosed peculiar differences in the distribution of different sterol species (e.g. of cholesterol versus stigmasterol) within the receiving host. These findings point to sterol species-specific roles in the metabolism of Waminoa beyond a mere source of energy. They also underline the value of the MALDI-2-TIMS-MSI method to future research in the spatially resolved analysis of sterols.}, }
@article {pmid33272988, year = {2020}, author = {Singh, RP and Johri, AK and Dua, M}, title = {Metagenomic Analysis of Microbial Diversity in Cotton Rhizosphere Soil in Alwar, India.}, journal = {Microbiology resource announcements}, volume = {9}, number = {49}, pages = {}, pmid = {33272988}, issn = {2576-098X}, abstract = {Cotton is an important cash crop for both the Indian economy and rural livelihoods. In the present study, metagenomic analysis is used to characterize microbial diversity in cotton rhizosphere soil from the Alwar district, located in the semiarid northeast region of the state of Rajasthan in India.}, }
@article {pmid33266447, year = {2020}, author = {Martucci, M and Conte, M and Bucci, L and Giampieri, E and Fabbri, C and Palmas, MG and Izzi, M and Salvioli, S and Zambrini, AV and Orsi, C and Brigidi, P and Santoro, A and Capri, M and Monti, D and Franceschi, C}, title = {Twelve-Week Daily Consumption of ad hoc Fortified Milk with ω-3, D, and Group B Vitamins Has a Positive Impact on Inflammaging Parameters: A Randomized Cross-Over Trial.}, journal = {Nutrients}, volume = {12}, number = {11}, pages = {}, pmid = {33266447}, issn = {2072-6643}, support = {00088MI01//Italian Ministry of Agriculture/ ; }, abstract = {BACKGROUND AND AIM: A state of chronic, subclinical inflammation known as inflammaging is present in elderly people and represents a risk factor for all age-related diseases. Dietary supplementation with ad hoc fortified foods seems an appealing strategy to counteract inflammaging. The purpose of this study was to test the efficacy of elderly-tailored fortified milk on inflammaging and different health parameters.<br><br>METHODS: A double-blind randomized cross-over study was performed on forty-eight volunteers aged 63-80 years. The fortified milk was enriched with ω-3 polyunsaturated fatty acids (eicosapentaenoic acid, EPA; docosahexaenoic acid, DHA), vitamins (25-hydroxyvitamin D, E, C, B6, B9, B12), and trace elements (zinc, selenium). The two intervention periods lasted for 12 weeks, with a 16-week washout intermission.<br><br>RESULTS: Compared to placebo, the consumption of fortified milk increased the circulating levels of different micronutrients, including vitamins and the ω-3 index of erythrocyte membranes. Conversely, it reduced the amount of arachidonic acid, homocysteine, and ω-6/ω-3 ratio.<br><br>CONCLUSION: Twelve-week daily consumption of adhoc fortified milk has an overall positive impact on different health parameters related to inflammaging in the elderly.}, }
@article {pmid33264963, year = {2021}, author = {Rai, PK and Lee, J and Brown, RJC and Kim, KH}, title = {Environmental fate, ecotoxicity biomarkers, and potential health effects of micro- and nano-scale plastic contamination.}, journal = {Journal of hazardous materials}, volume = {403}, number = {}, pages = {123910}, doi = {10.1016/j.jhazmat.2020.123910}, pmid = {33264963}, issn = {1873-3336}, abstract = {In recent decades, the quantity of plastic waste products has increased tremendously. As plastic wastes are released into the environment, they exert harmful effects on biota and human health. In this work, a comprehensive review is offered to describe the physical and chemical characteristics of microplastics and nanoplastics in relation to their fate, microbial ecology, transport, and ecotoxic behavior. Present discussion is expanded further to cover the biochemical, physiological, and molecular mechanisms controlling the environmental fate, ecotoxicity, and human health hazards of micro- and nanoplastics. The risks of their exposure to microbes, plants, animals, and human health are also reviewed with special emphasis. Finally, a direction for future interdisciplinary research in materials and polymer science is also discussed to help control the pollution caused by micro- and nanoplastics.}, }
@article {pmid33264923, year = {2021}, author = {Williamson, AJ and Verbruggen, F and Chavez Rico, VS and Bergmans, J and Spooren, J and Yurramendi, L and Laing, GD and Boon, N and Hennebel, T}, title = {Selective leaching of copper and zinc from primary ores and secondary mineral residues using biogenic ammonia.}, journal = {Journal of hazardous materials}, volume = {403}, number = {}, pages = {123842}, doi = {10.1016/j.jhazmat.2020.123842}, pmid = {33264923}, issn = {1873-3336}, abstract = {With the number of easily accessible ores depleting, alternate primary and secondary sources are required to meet the increasing demand of economically important metals. Whilst highly abundant, these materials are of lower grade with respect to traditional ores, thus highly selective and sustainable metal extraction technologies are needed to reduce processing costs. Here, we investigated the metal leaching potential of biogenic ammonia produced by a ureolytic strain of Lysinibacillus sphaericus on eight primary and secondary materials, comprised of mining and metallurgical residues, sludges and automotive shredder residues (ASR). For the majority of materials, moderate to high yields (30-70%) and very high selectivity (>97% against iron) of copper and zinc were obtained with 1 mol L-1 total ammonia. Optimal leaching was achieved and further refined for the ASR in a two-step indirect leaching system with biogenic ammonia. Copper leaching was the result of local corrosion and differences in leaching against the synthetic (NH4)2CO3 control could be accounted for by pH shifts from microbial metabolism, subsequently altering free NH3 required for coordination. These results provide important findings for future sustainable metal recovery technologies from secondary materials.}, }
@article {pmid33264383, year = {2020}, author = {Ghuneim, LJ and Distaso, MA and Chernikova, TN and Bargiela, R and Lunev, EA and Korzhenkov, AA and Toshchakov, SV and Rojo, D and Barbas, C and Ferrer, M and Golyshina, OV and Golyshin, PN and Jones, DL}, title = {Utilization of low molecular weight organic compounds by the filterable fraction of a lotic microbiome.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaa244}, pmid = {33264383}, issn = {1574-6941}, abstract = {Filterable microorganisms participate in dissolved organic carbon (DOC) cycling in freshwater systems, however their exact functional role remains unknown. We determined taxonomic identity and community dynamics of prokaryotic microbiomes in the 0.22 µm-filtered fraction and unfiltered freshwater from the Conwy River (North Wales, UK) in microcosms and, using targeted metabolomics and 14C-labelling, examined their role in utilization of amino acids, organic acids, and sugars spiked at environmentally-relevant (nanomolar) concentrations. To identify changes in community structure, we used 16S rRNA amplicon and shotgun sequencing. Unlike the unfiltered water samples where the consumption of DOC was rapid, the filtered fraction showed a 3-days lag phase before the consumption started. Analysis of functional categories of clusters of orthologous groups of proteins (COGs) showed COGs associated with energy production increased in numbers in both fractions with substrate addition. The filtered fraction utilized low-molecular-weight (LMW) DOC at much slower rates than the whole community. Addition of nanomolar concentrations of LMW DOC did not measurably influence the composition of the microbial community nor the rate of consumption across all substrate types in either fraction. We conclude that due to their low activity, filterable microorganisms play a minor role in LMW DOC processing within short residence time of lotic freshwater systems.}, }
@article {pmid33262758, year = {2020}, author = {Batista, MA and Calvo-Fortes, F and Silveira-Nunes, G and Camatta, GC and Speziali, E and Turroni, S and Teixeira-Carvalho, A and Martins-Filho, OA and Neretti, N and Maioli, TU and Santos, RR and Brigidi, P and Franceschi, C and Faria, AMC}, title = {Inflammaging in Endemic Areas for Infectious Diseases.}, journal = {Frontiers in immunology}, volume = {11}, number = {}, pages = {579972}, pmid = {33262758}, issn = {1664-3224}, abstract = {Immunosenescence is marked by a systemic process named inflammaging along with a series of defects in the immunological activity that results in poor responses to infectious agents and to vaccination. Inflammaging, a state of low-grade chronic inflammation, usually leads to chronic inflammatory diseases and frailty in the elderly. However, some elderly escape from frailty and reach advanced age free of the consequences of inflammaging. This process has been called immunological remodeling, and it is the hallmark of healthy aging as described in the studies of centenarians in Italy. The biological markers of healthy aging are still a matter of debate, and the studies on the topic have focused on inflammatory versus remodeling processes and molecules. The sub-clinical inflammatory status associated with aging might be a deleterious event for populations living in countries where chronic infectious diseases are not prevalent. Nevertheless, in other parts of the world where they are, two possibilities may occur. Inflammatory responses may have a protective effect against these infectious agents. At the same time, the long-term consequences of protective immune responses during chronic infections may result in accelerated immunosenescence in these individuals. Therefore, the biological markers of healthy aging can vary according to environmental, cultural, and geographical settings that reflect worldwide, and in a non-biased, non-westernized perspective, the changes that we experience regarding our contacts with microorganisms and the outcomes of such contacts.}, }
@article {pmid33262754, year = {2020}, author = {Baksi, KD and Kuntal, BK and Mande, SS}, title = {Corrigendum: 'TIME': A Web Application for Obtaining Insights into Microbial Ecology Using Longitudinal Microbiome Data.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {605295}, doi = {10.3389/fmicb.2020.605295}, pmid = {33262754}, issn = {1664-302X}, abstract = {[This corrects the article DOI: 10.3389/fmicb.2018.00036.].}, }
@article {pmid33262240, year = {2020}, author = {Khanolkar, RA and Clark, ST and Wang, PW and Hwang, DM and Yau, YCW and Waters, VJ and Guttman, DS}, title = {Ecological Succession of Polymicrobial Communities in the Cystic Fibrosis Airways.}, journal = {mSystems}, volume = {5}, number = {6}, pages = {}, pmid = {33262240}, issn = {2379-5077}, abstract = {Antimicrobial therapies against cystic fibrosis (CF) lung infections are largely aimed at the traditional, well-studied CF pathogens such as Pseudomonas aeruginosa and Burkholderia cepacia complex, despite the fact that the CF lung harbors a complex and dynamic polymicrobial community. A clinical focus on the dominant pathogens ignores potentially important community-level interactions in disease pathology, perhaps explaining why these treatments are often less effective than predicted based on in vitro testing. A better understanding of the ecological dynamics of this ecosystem may enable clinicians to harness these interactions and thereby improve treatment outcomes. Like all ecosystems, the CF lung microbial community develops through a series of stages, each of which may present with distinct microbial communities that generate unique host-microbe and microbe-microbe interactions, metabolic profiles, and clinical phenotypes. While insightful models have been developed to explain some of these stages and interactions, there is no unifying model to describe how these infections develop and persist. Here, we review current perspectives on the ecology of the CF airway and present the CF Ecological Succession (CFES) model that aims to capture the spatial and temporal complexity of CF lung infection, address current challenges in disease management, and inform the development of ecologically driven therapeutic strategies.}, }
@article {pmid33261862, year = {2020}, author = {Liu, D and Legras, JL and Zhang, P and Chen, D and Howell, K}, title = {Diversity and dynamics of fungi during spontaneous fermentations and association with unique aroma profiles in wine.}, journal = {International journal of food microbiology}, volume = {}, number = {}, pages = {108983}, doi = {10.1016/j.ijfoodmicro.2020.108983}, pmid = {33261862}, issn = {1879-3460}, abstract = {Microbial ecology is an integral part of an agricultural ecosystem and influences the quality of agricultural commodities. Microbial activity influences grapevine health and crop production, conversion of sugar to ethanol during fermentation, thus forming wine aroma and flavour. There are regionally differentiated microbial patterns in grapevines and must but how microbial patterns contribute to wine regional distinctiveness (terroir) at small scale (<100 km) is not well defined. Here we characterise fungal communities, yeast populations, and Saccharomyces cerevisiae populations during spontaneous fermentation using metagenomics and population genetics to investigate microbial distribution and fungal contributions to the resultant wine. We found differentiation of fungi, yeasts, and S. cerevisiae between geographic origins (estate/vineyard), with influences from the grape variety. Growth and dominance of S. cerevisiae during fermentation reshaped the fungal community and showed geographic structure at the strain level. Associations between fungal microbiota diversity and wine chemicals suggest that S. cerevisiae plays a primary role in determining wine aroma profiles at a sub-regional scale. The geographic distribution at scales of less than 12 km supports that differential microbial communities, including the dominant fermentative yeast S. cerevisiae can be distinct in a local setting. These findings provide further evidence for microbial contributions to wine terroir, and perspectives for sustainable agricultural practices to maintain microbial diversity and optimise fermentation function to craft beverage quality.}, }
@article {pmid33258525, year = {2020}, author = {Gweon, HS and Bowes, MJ and Moorhouse, HL and Oliver, AE and Bailey, MJ and Acreman, MC and Read, DS}, title = {Contrasting community assembly processes structure lotic bacteria metacommunities along the river continuum.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.15337}, pmid = {33258525}, issn = {1462-2920}, support = {NE/N018125/1//Natural Environment Research Council/ ; NE/R016429/1//Natural Environment Research Council/ ; }, abstract = {The heterogeneous nature of lotic habitats plays an important role in the complex ecological and evolutionary processes that structure the microbial communities within them. Due to such complexity, our understanding of lotic microbial ecology still lacks conceptual frameworks for the ecological processes that shape these communities. We explored how bacterial community composition and underlying ecological assembly processes differ between lotic habitats by examining community composition and inferring community assembly processes across four major habitat types (free-living, particle-associated, biofilm on benthic stones and rocks, and sediment). This was conducted at 12 river sites from headwater streams to the main river in the River Thames, UK. Our results indicate that there are distinct differences in the bacterial communities between four major habitat types, with contrasting ecological processes shaping their community assembly processes. While the mobile free-living and particle-associated communities were consistently less diverse than the fixed sediment and biofilm communities, the latter two communities displayed higher homogeneity across the sampling sites. This indicates that the relative influence of deterministic environmental filtering is elevated in sediment and biofilm communities compared with free-living and particle-associated communities, where stochastic processes play a larger role.}, }
@article {pmid33257312, year = {2020}, author = {Barbosa, RG and van Veelen, HPJ and Pinheiro, V and Sleutels, T and Verstraete, W and Boon, N}, title = {Enrichment of Hydrogen Oxidizing Bacteria from High Temperature and Salinity Environments.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.02439-20}, pmid = {33257312}, issn = {1098-5336}, abstract = {There is an urgent need for sustainable protein supply routes with low environmental footprint. Recently, the use of hydrogen oxidizing bacteria (HOB) as a platform for high quality microbial protein (MP) production has regained interest. This study aims to investigate the added value of using conditions such as salt and temperature to steer HOB communities to lower diversities, while maintaining a high protein content and a high quality amino acid profile. Pressure drop and hydrogen consumption were measured for 56 days to evaluate autotrophy of a total of six communities in serum flasks. Of the six communities, four were enriched under saline (0.0, 0.25, 0.5 and 1.0 mol NaCl l-1) and two under thermophilic conditions (65°C). Five communities enriched for HOB were subsequently cultivated in continuously stirred reactors under the same conditions to evaluate their potential as microbial protein producers. The protein percentages ranged from 41 to 80%. The highest protein content was obtained for the thermophilic enrichments. Amino acid profiles were comparable to protein sources commonly used for feed purposes. Members of the genus Achromobacter were found to dominate the saline enrichments while members of the genus Hydrogenibacillus were found to dominate the thermophilic enrichments. Here we show that enriching for HOB while steering the community toward low diversity and maintaining a high quality protein content can be successfully achieved, both in saline and thermophilic conditions.IMPORTANCE Alternative feed and food supply chains are required to decrease water and land use. HOB offer a promising substitute for traditional agricultural practice to produce microbial protein (MP) from residual materials and renewable energy. To safeguard product stability, the composition of the HOB community should be controlled. Defining strategies to maintain the stability of the communities is therefore key for optimization purposes. In this study, we use salt and temperature as independent conditions to stabilize the composition of the HOB communities. Based on the results presented, we conclude that HOB communities can be steered to have low diversity using the presented conditions while producing a desirable protein content with a valuable amino acid profile.}, }
@article {pmid33257152, year = {2020}, author = {Abel, SM and Primpke, S and Int-Veen, I and Brandt, A and Gerdts, G}, title = {Systematic identification of microplastics in abyssal and hadal sediments of the Kuril Kamchatka trench.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {116095}, doi = {10.1016/j.envpol.2020.116095}, pmid = {33257152}, issn = {1873-6424}, abstract = {The occurrence of microplastics throughout marine environments worldwide, from pelagic to benthic habitats, has become serious cause for concern. Hadal zones were recently described as the &quot;trash bins of the oceans&quot; and ultimate sink for marine plastic debris. The Kuril region covers a substantial area of the North Pacific Ocean and is characterised by high biological productivity, intense marine traffic through the Kuril straits, and anthropogenic activity. Moreover, strong tidal currents and eddy activity, as well as the influence of Pacific currents, have the potential for long distance transport and retention of microplastics in this area. To verify the hypothesis that the underlying Kuril Kamchatka Trench might accumulate microplastics from the surrounding environments and act as the final sink for high quantities of microplastics, we analysed eight sediment samples collected in the Kuril Kamchatka Trench at a depth range of 5143-8250 m during the Kuril Kamchatka Biodiversity Studies II (KuramBio II) expedition in summer 2016. Microplastics were characterised via Micro Fourier Transform Infrared spectroscopy. All samples were analysed in their entirety to avoid inaccuracies due to extrapolations of microplastic concentrations and polymer diversities, which would otherwise be based on commonly applied representative aliquots. The number of microplastic particles detected ranged from 14 to 209 kg-1 sediment (dry weight) with a total of 15 different plastic polymers detected. Polypropylene accounted for the largest proportion (33.2%), followed by acrylates/polyurethane/varnish (19%) and oxidized polypropylene (17.4%). By comparing extrapolated sample aliquots with in toto results, it was shown that aliquot-based extrapolations lead to severe under- or overestimations of microplastic concentrations, and an underestimation of polymer diversity.}, }
@article {pmid33256756, year = {2020}, author = {Gao, S and Kong, Y and Yu, J and Miao, L and Ji, L and Song, L and Zeng, C}, title = {Isolation of axenic cyanobacterium and the promoting effect of associated bacterium on axenic cyanobacterium.}, journal = {BMC biotechnology}, volume = {20}, number = {1}, pages = {61}, pmid = {33256756}, issn = {1472-6750}, support = {No.2013AA102805-04//National High-tech Research and Development Program/ ; No. 2019EC61-15//Key Project of Jingzhou Science and Technology/ ; No. 2016M591832//Postdoctoral Research Foundation of China/ ; No. BK20150165//Natural Science Foundation of Jiangsu Province/ ; No. KJ15ZB01//General Administration of Quality Supervision, Inspection and Quarantine of the People's Republic of China (CN)/ ; No. 2018ZJSHKF06//Key Laboratory of Water Pollution Control and Environmental Safety of Zhejiang Province/ ; }, abstract = {BACKGROUND: Harmful cyanobacterial blooms have attracted wide attention all over the world as they cause water quality deterioration and ecosystem health issues. Microcystis aeruginosa associated with a large number of bacteria is one of the most common and widespread bloom-forming cyanobacteria that secret toxins. These associated bacteria are considered to benefit from organic substrates released by the cyanobacterium. In order to avoid the influence of associated heterotrophic bacteria on the target cyanobacteria for physiological and molecular studies, it is urgent to obtain an axenic M. aeruginosa culture and further investigate the specific interaction between the heterotroph and the cyanobacterium.<br><br>RESULTS: A traditional and reliable method based on solid-liquid alternate cultivation was carried out to purify the xenic cyanobacterium M. aeruginosa FACHB-905. On the basis of 16S rDNA gene sequences, two associated bacteria named strain B905-1 and strain B905-2, were identified as Pannonibacter sp. and Chryseobacterium sp. with a 99 and 97% similarity value, respectively. The axenic M. aeruginosa FACHB-905A (Microcystis 905A) was not able to form colonies on BG11 agar medium without the addition of strain B905-1, while it grew well in BG11 liquid medium. Although the presence of B905-1 was not indispensable for the growth of Microcystis 905A, B905-1 had a positive effect on promoting the growth of Microcystis 905A.<br><br>CONCLUSIONS: The associated bacteria were eliminated by solid-liquid alternate cultivation method and the axenic Microcystis 905A was successfully purified. The associated bacterium B905-1 has the potentiality to promote the growth of Microcystis 905A. Moreover, the purification technique for cyanobacteria described in this study is potentially applicable to a wider range of unicellular cyanobacteria.}, }
@article {pmid33256601, year = {2020}, author = {Wagner, E and Zaiser, A and Leitner, R and Quijada, NM and Pracser, N and Pietzka, A and Ruppitsch, W and Schmitz-Esser, S and Wagner, M and Rychli, K}, title = {Virulence characterization and comparative genomics of Listeria monocytogenes sequence type 155 strains.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {847}, pmid = {33256601}, issn = {1471-2164}, support = {P27920-B22//Austrian Science Fund/ ; n.a.//Bundesministerium für Verkehr, Innovation und Technologie/ ; }, abstract = {BACKGROUND: Listeria (L.) monocytogenes strains show a high diversity regarding stress tolerance and virulence potential. Genome studies have mainly focused on specific sequence types (STs) predominantly associated with either food or human listeriosis. This study focused on the prevalent ST155, showing equal distribution among clinical and food isolates. We evaluated the virulence potential of 20 ST155 strains and performed comparative genomic analysis of 130 ST155 strains isolated from food, food processing environments and human listeriosis cases in different countries and years.<br><br>RESULTS: The in vitro virulence assays using human intestinal epithelial Caco2 and hepatocytic HEPG2 cells showed an impaired virulence phenotype for six of the 20 selected ST155 strains. Genome analysis revealed no distinct clustering of strains from the same source category (food, food processing environment, and clinical isolates). All strains harbored an intact inlA and inlB locus, except four strains, which had an internal deletion in the inlA gene. All strains harbored LIPI-1, but prfA was present in a longer variant in six strains, all showing impaired virulence. The longer PrfA variant resulted in lower expression of inlA, inlB, and prfA, and no expression of hly and actA. Regarding stress-related gene content, SSI-1 was present, whereas qacH was absent in all strains. 34.6% of the strains harbored a plasmid. All but one ST155 plasmids showed high conservation and harbored cadA2, bcrABC, and a triphenylmethane reductase.<br><br>CONCLUSIONS: This study contributes to an enhanced understanding of L. monocytogenes ST155 strains, being equally distributed among isolates from humans, food, and food processing environments. The conservation of the present genetic traits and the absence of unique inherent genetic features makes these types of STs especially interesting since they are apparently equally adapted to the conditions in food processing environments, as well as in food as to the human host environment. However, a ST155-specific mutation resulting in a longer PrfA variant impaired the virulence potential of several ST155 strains.}, }
@article {pmid33254950, year = {2021}, author = {Del Olmo, G and Husband, S and Sánchez Briones, C and Soriano, A and Calero Preciado, C and Macian, J and Douterelo, I}, title = {The microbial ecology of a Mediterranean chlorinated drinking water distribution systems in the city of Valencia (Spain).}, journal = {The Science of the total environment}, volume = {754}, number = {}, pages = {142016}, doi = {10.1016/j.scitotenv.2020.142016}, pmid = {33254950}, issn = {1879-1026}, mesh = {Animals ; Biofilms ; *Cyprinodontiformes ; *Drinking Water ; *Mycobiome ; Spain ; Water Microbiology ; Water Quality ; Water Supply ; }, abstract = {Drinking water distribution systems host extensive microbiomes with diverse biofilm communities regardless of treatment, disinfection, or operational practices. In Mediterranean countries higher temperatures can accelerate reactions and microbial growth that may increase aesthetic water quality issues, particularly where material deposits can develop as a result of net zero flows within looped urban networks. This study investigated the use of flow and turbidity monitoring to hydraulically manage mobilisation of pipe wall biofilms and associated material from the Mediterranean city of Valencia (Spain). Pipe sections of different properties were subjected to controlled incremental flushing with monitoring and sample collection for physico-chemical and DNA analysis with Illumina sequencing of bacterial and fungal communities. A core microbial community was detected throughout the network with microorganisms like Pseudomonas, Aspergillus or Alternaria increasing during flushing, indicating greater abundance in underlying and more consolidated material layers. Bacterial and fungal communities were found to be highly correlated, with bacteria more diverse and dynamic during flushing whilst fungi were more dominant and less variable between sampling sites. Results highlight that water quality management can be achieved through hydraulic strategies yet understanding community dynamics, including the fungal component, will be key to maintaining safe and ultimately beneficial microbiomes in drinking water distribution systems.}, }
@article {pmid33254908, year = {2021}, author = {Dong, J and Hunt, J and Delhaize, E and Zheng, SJ and Jin, CW and Tang, C}, title = {Impacts of elevated CO2 on plant resistance to nutrient deficiency and toxic ions via root exudates: A review.}, journal = {The Science of the total environment}, volume = {754}, number = {}, pages = {142434}, doi = {10.1016/j.scitotenv.2020.142434}, pmid = {33254908}, issn = {1879-1026}, mesh = {Biological Transport ; Biomass ; *Carbon Dioxide/toxicity ; Ions ; *Nutrients ; Plant Exudates ; Plant Roots ; }, abstract = {Elevated atmospheric CO2 (eCO2) concentration can increase root exudation into soils, which improves plant tolerance to abiotic stresses. This review used a meta-analysis to assess effect sizes of eCO2 on both efflux rates and total amounts of some specific root exudates, and dissected whether eCO2 enhances plant's resistance to nutrient deficiency and ion toxicity via root exudates. Elevated CO2 did not affect efflux rates of total dissolved organic carbon, a measure of combined root exudates per unit of root biomass or length, but increased the efflux amount of root systems per plant by 31% which is likely attributed to increased root biomass (29%). Elevated CO2 increased efflux rates of soluble-sugars, carboxylates, and citrate by 47%, 111%, and 16%, respectively, but did not affect those of amino acids and malate. The increased carbon allocation to roots, increased plant requirements of mineral nutrients, and heightened detoxification responses to toxic ions under eCO2 collectively contribute to the increased efflux rates despite lacking molecular evidence. The increased efflux rates of root exudates under eCO2 were closely associated with improved nutrient uptake whilst less studies have validated the associations between root exudates and resistance to toxic ions of plants when grown under eCO2. Future studies are required to reveal how climate change (eCO2) affect the efflux of specific root exudates, particularly organic anions, the corresponding nutrient uptake and toxic ion resistance from plant molecular biology and soil microbial ecology perspectives.}, }
@article {pmid33254807, year = {2021}, author = {Yuan, W and Zhang, Y and Riaz, L and Yang, Q and Du, B and Wang, R}, title = {Multiple antibiotic resistance and DNA methylation in Enterobacteriaceae isolates from different environments.}, journal = {Journal of hazardous materials}, volume = {402}, number = {}, pages = {123822}, doi = {10.1016/j.jhazmat.2020.123822}, pmid = {33254807}, issn = {1873-3336}, abstract = {Antibiotic resistant bacteria with diverse resistance phenotypes and genotypes are ubiquitous in the environments that have become a global health concern. The role of DNA methylation in the dissemination of antibiotic resistance among different environments is currently unclear. We recovered 646 Enterobacteriaceae (Eb) isolates from hospital, livestock manure, municipal wastewater-treatment plants, river sediment and soil for comprehensive analysis of resistance phenotypes, β-lactamase genes, integrons, integron-associated gene cassettes and the levels of DNA methylation. Antibiotic susceptibility testing revealed that approximately 87.31 % isolates were multidrug resistant Eb. The β-lactamase genes were positively detected in 473 isolates with greater diversity in human or animal sourced Eb, while its prevalence was found to be highest in the Eb isolates from the natural environments. Forty-three gene cassettes (28 different types mediated by intI1) were detected in 53 (19.63 %) isolates, with greater diversity in Eb isolates from hospital and livestock manure. The multiple antibiotic resistance index of single strain was positively correlated with the 5-methylcytosine and showed a negative correlation with 6-methylademine. We conclude that the development of antibiotic resistance could possibly be coupled with DNA methylation, which might enhance the antimicrobial resistance and survival capacity of Eb.}, }
@article {pmid33254460, year = {2021}, author = {Ghysels, S and Buffel, S and Rabaey, K and Ronsse, F and Ganigué, R}, title = {Biochar and activated carbon enhance ethanol conversion and selectivity to caproic acid by Clostridium kluyveri.}, journal = {Bioresource technology}, volume = {319}, number = {}, pages = {124236}, doi = {10.1016/j.biortech.2020.124236}, pmid = {33254460}, issn = {1873-2976}, mesh = {Caproates ; Charcoal ; *Clostridium kluyveri ; Ethanol ; }, abstract = {Syngas from biomass or steel mills can be fermented into a dilute stream of ethanol and acetic acid, which requires energy intensive distillation for product recovery. This can be circumvented by selective secondary fermentation of the syngas fermentation effluent to caproic acid as easier recoverable platform chemical with Clostridium kluyveri. Here, we explore the impact of biochar and activated carbon on this process. Changes during the fermentation with biochar or activated carbon were monitored, different doses were tested and the recyclability of biochar and activated carbon was assessed. Biochar decreased the lag phase and increased the caproic acid production rate (up to 0.50 g·L-1·h-1). Upon recycling for subsequent fermentation, biochar retained this property largely. Activated carbon addition, especially at high dose, could potentially increase the conversion and selectivity towards caproic acid to 14.15 g·L-1 (control: 11.01 g·L-1) and 92% (control: 84%), respectively.}, }
@article {pmid33253458, year = {2020}, author = {Ndhlovu, A and Durand, PM and Ramsey, G}, title = {Programmed cell death as a black queen in microbial communities.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.15757}, pmid = {33253458}, issn = {1365-294X}, abstract = {Programmed cell death (PCD) in unicellular organisms is in some instances an altruistic trait. When the beneficiaries are clones or close kin, kin selection theory may be used to explain the evolution of the trait, and when the trait evolves in groups of distantly related individuals, group or multilevel selection theory is invoked. In mixed microbial communities, the benefits are also available to unrelated taxa. But the evolutionary ecology of PCD in communities is poorly understood. Few hypotheses have been offered concerning the community role of PCD despite its far-reaching effects. The hypothesis we consider here is that PCD is a black queen. The Black Queen Hypothesis (BQH) outlines how public goods arising from a leaky function are exploited by other taxa in the community. Black Queen (BQ) traits are essential for community survival, but only some members bear the cost of possessing them, while others lose the trait In addition, BQ traits have been defined in terms of adaptive gene loss, and it is unknown whether this has occurred for PCD. Our conclusion is that PCD fulfils the two most important criteria of a BQ (leakiness and costliness), but that more empirical data are needed for assessing the remaining two criteria. In addition, we hold that for viewing PCD as a BQ, the original BQH needs to include social traits. Thus, despite some empirical and conceptual shortcomings, the BQH provides a helpful avenue for investigating PCD in microbial communities.}, }
@article {pmid33252774, year = {2020}, author = {Lee, JC and Whang, KS}, title = {Altererythrobacter segetis sp. nov., Isolated from Farmland Soil.}, journal = {Current microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00284-020-02294-8}, pmid = {33252774}, issn = {1432-0991}, abstract = {A Gram-stain-negative bacterium, designated YJ20T, was isolated from rhizosphere soil of a spinach farmland at Shinan in Korea. Strain YJ20T was found to be aerobic, non-motile rods which can grow at 10-33 °C (optimum, 28 °C), at pH 6.5-8.5 (optimum, pH 6.5-7.5) and in the absence of NaCl. The 16S rRNA gene sequence analysis showed that strain YJ20T belongs to the genus Altererythrobacter with moderate sequence similarities to Altererythrobacter dongtanensis KCTC 22672T (96.8%), Altererythrobacter soli MN-1T (96.6%) and Altererythrobacter xinjiangensis S3-63T (96.5%). The phylogenomic analysis based on the whole-genome sequence demonstrated that strain YJ20T formed a distinct phyletic line with Altererythrobacter soli MN-1T and Altererythrobacter salegens XY-R17T showing average nucleotide identity (ANI) values of 79.4 and 77.5%, respectively. The predominant ubiquinone was identified as Q-10, and the major fatty acids were C17:1 ω6c, C18:1 ω7c and C15:0 2-OH. The major polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidycholin, sphingoglycolipid, an unidentified glycolipid, an unidentified phospholipid and an unidentified lipid. The G+C content of the genome was determined to be 66.3 mol%. On the basis of phenotypic, chemotaxonomic properties and phylogenetic and phylogenomic analyses in this study, strain YJ20T is considered to represent a novel species in the genus Altererythrobacter, for which the name Altererythrobacter segetis sp. nov. is proposed. The type strain is YJ20T (= KACC 19554T = NBRC 113199T).}, }
@article {pmid33252655, year = {2020}, author = {Weißbecker, C and Schnabel, B and Heintz-Buschart, A}, title = {Dadasnake, a Snakemake implementation of DADA2 to process amplicon sequencing data for microbial ecology.}, journal = {GigaScience}, volume = {9}, number = {12}, pages = {}, pmid = {33252655}, issn = {2047-217X}, abstract = {BACKGROUND: Amplicon sequencing of phylogenetic marker genes, e.g., 16S, 18S, or ITS ribosomal RNA sequences, is still the most commonly used method to determine the composition of microbial communities. Microbial ecologists often have expert knowledge on their biological question and data analysis in general, and most research institutes have computational infrastructures to use the bioinformatics command line tools and workflows for amplicon sequencing analysis, but requirements of bioinformatics skills often limit the efficient and up-to-date use of computational resources.<br><br>RESULTS: We present dadasnake, a user-friendly, 1-command Snakemake pipeline that wraps the preprocessing of sequencing reads and the delineation of exact sequence variants by using the favorably benchmarked and widely used DADA2 algorithm with a taxonomic classification and the post-processing of the resultant tables, including hand-off in standard formats. The suitability of the provided default configurations is demonstrated using mock community data from bacteria and archaea, as well as fungi.<br><br>CONCLUSIONS: By use of Snakemake, dadasnake makes efficient use of high-performance computing infrastructures. Easy user configuration guarantees flexibility of all steps, including the processing of data from multiple sequencing platforms. It is easy to install dadasnake via conda environments. dadasnake is available at https://github.com/a-h-b/dadasnake.}, }
@article {pmid33250870, year = {2020}, author = {Miclotte, L and De Paepe, K and Rymenans, L and Callewaert, C and Raes, J and Rajkovic, A and Van Camp, J and Van de Wiele, T}, title = {Dietary Emulsifiers Alter Composition and Activity of the Human Gut Microbiota in vitro, Irrespective of Chemical or Natural Emulsifier Origin.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {577474}, pmid = {33250870}, issn = {1664-302X}, abstract = {The use of additives in food products has become an important public health concern. In recent reports, dietary emulsifiers have been shown to affect the gut microbiota, contributing to a pro-inflammatory phenotype and metabolic syndrome. So far, it is not yet known whether similar microbiome shifts are observable for a more diverse set of emulsifier types and to what extent these effects vary with the unique features of an individual's microbiome. To bridge this gap, we investigated the effect of five dietary emulsifiers on the fecal microbiota from 10 human individuals upon a 48 h exposure. Community structure was assessed with quantitative microbial profiling, functionality was evaluated by measuring fermentation metabolites, and pro-inflammatory properties were assessed with the phylogenetic prediction algorithm PICRUSt, together with a TLR5 reporter cell assay for flagellin. A comparison was made between two mainstream chemical emulsifiers (carboxymethylcellulose and P80), a natural extract (soy lecithin), and biotechnological emulsifiers (sophorolipids and rhamnolipids). While fecal microbiota responded in a donor-dependent manner to the different emulsifiers, profound differences between emulsifiers were observed. Rhamnolipids, sophorolipids, and soy lecithin eliminated 91 ± 0, 89 ± 1, and 87 ± 1% of the viable bacterial population after 48 h, yet they all selectively increased the proportional abundance of putative pathogens. Moreover, profound shifts in butyrate (-96 ± 6, -73 ± 24, and -34 ± 25%) and propionate (+13 ± 24, +88 ± 50, and +29 ± 16%) production were observed for these emulsifiers. Phylogenetic prediction indicated higher motility, which was, however, not confirmed by increased flagellin levels using the TLR5 reporter cell assay. We conclude that dietary emulsifiers can severely impact the gut microbiota, and this seems to be proportional to their emulsifying strength, rather than emulsifier type or origin. As biotechnological emulsifiers were especially more impactful than chemical emulsifiers, caution is warranted when considering them as more natural alternatives for clean label strategies.}, }
@article {pmid33250307, year = {2020}, author = {Ostermeyer, P and Bonin, L and Folens, K and Verbruggen, F and García-Timermans, C and Verbeken, K and Rabaey, K and Hennebel, T}, title = {Effect of speciation and composition on the kinetics and precipitation of arsenic sulfide from industrial metallurgical wastewater.}, journal = {Journal of hazardous materials}, volume = {}, number = {}, pages = {124418}, doi = {10.1016/j.jhazmat.2020.124418}, pmid = {33250307}, issn = {1873-3336}, abstract = {Precipitation of arsenic as As2S3 produces little waste sludge, has the potential for low chemical consumption and for selective metal(loid) removal. In this study, arsenic removal from acidic (pH 2), metallurgical wastewater was tested in industrially relevant conditions. Sulfides added at a S:As molar ratio of 2.5 and 5 resulted in removal of 99% and 84% of As(III) and As(V). Precipitation of As2S3 from the As(III) and industrial wastewater containing 17% As(V) was nearly instantaneous. For the synthetic As(V) solution, reduction to As(III) was the rate limiting step. At a S:As ratio of 20 and an observed removal rate (k2 = 4.8 (mol L-1) h-1), two hours were required to remove of 93% of arsenic from a 1 g As L-1 solution. In the case of As(V) in industrial samples this time lag was not observed, showing that components in the industrial wastewater affected the removal and reduction of arsenate. Speciation also affected flocculation and coagulation characteristics of As2S3 particles: As(V) reduction resulted in poor coagulation and flocculation. Selective precipitation of arsenic was possible, but depended on speciation, S:As ratio and other metals present.}, }
@article {pmid33247364, year = {2020}, author = {Burtseva, O and Baulina, O and Zaytseva, A and Fedorenko, T and Chekanov, K and Lobakova, E}, title = {In vitro Biofilm Formation by Bioluminescent Bacteria Isolated from the Marine Fish Gut.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01652-0}, pmid = {33247364}, issn = {1432-184X}, abstract = {The internal surface of the animal gastrointestinal tract is covered by microbial biofilms. They play an important role in the development and functioning of the host organism and protect it against pathogens. Microbial communities of gastrointestinal biofilms are less elucidated than luminal microbiota. Therefore, the studies of biofilm formation by gastrointestinal microorganisms are a topical issue. For the first time, we report the formation of a biofilm in vitro by the strains of bioluminescent bacteria isolated from the intestines of marine fish. These bacteria exhibit co-aggregation and tend to attach to solid surfaces. The attachment of cells is accompanied by appearance of the pili. Then, we observed the formation of microcolonies and the production of extracellular polymer substances (EPSs) connecting bacterial cells into an integrated system. The presence of acidic polysaccharides is shown in the EPS when using the ruthenium red staining. Acidic polysaccharides in this matrix is a biochemical evidence of microbial biofilms. On the fibers of the polymer matrix, these bacteria form the &quot;mushroom body&quot;-type structures. Matured biofilms exhibit a specific three-dimensional architecture with pores and channels formed by cells and EPS. We also demonstrated the formation of a biofilm by binary culture of the luminous enterobacterium Kosakonia cowanii and a Gram-positive Macrococcus sp. The data obtained help to understand the role of these bacteria in the intestines of fish. They lead to a new study in the field of investigation of the intestinal microbiome of fish.}, }
@article {pmid33244619, year = {2020}, author = {Mathai, PP and Bertram, JH and Padhi, SK and Singh, V and Tolo, IE and Primus, A and Mor, SK and Phelps, NBD and Sadowsky, MJ}, title = {Influence of Environmental Stressors on the Microbiota of Zebra Mussels (Dreissena polymorpha).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01642-2}, pmid = {33244619}, issn = {1432-184X}, support = {Minnesota Agricultural Experiment Station.//Minnesota Agricultural Experiment Station./ ; }, abstract = {Host-associated microbiota play a critical role in host fitness by providing nutrition, enhancing digestion capabilities, and by providing protection from pathogens. Here, we investigated the effects of two environmental stressors, temperature, and salinity, on the microbiota associated with zebra mussels (ZMs), a highly invasive bivalve in North America. To examine this in detail, lake-collected ZMs were acclimated to laboratory conditions, and subjected to temperature and salinity stress conditions. The impact of these stressors on the diversity, composition, and dynamics of ZM-associated microbiota were assessed by using amplicon- and shotgun-based sequencing, and qPCR-based approaches. Elevated temperature was found to be the primary driver of ZM mortality, although salinity alone also increased its likelihood. Stressor-induced ZM mortality, which ranged between 53 and 100%, was concomitant with significant increases in the relative abundance of several genera of putative opportunistic pathogens including Aeromonas. These genera were only present in low relative abundance in ZMs obtained from the control tank with 0% mortality. Shotgun sequencing and qPCR analyses indicated that the relative and absolute abundances of pathogenic Aeromonas species (particularly A. veronii) were significantly greater in temperature-induced dead ZMs. Taken together, our results show that environmental stress, especially elevated temperature (> 25 °C), is associated with the rapid mortality of ZMs as well as the proliferation of putative opportunistic bacterial pathogens.}, }
@article {pmid33244064, year = {2020}, author = {Shilts, MH and Rosas-Salazar, C and Lynch, CE and Tovchigrechko, A and Boone, HH and Russell, PB and Connolly, AS and Costello, KM and McCollum, MD and Mai, A and Wiggins, DA and Rajagopala, SV and Yooseph, S and Peebles, RS and Hartert, TV and Das, SR}, title = {Evaluation of the upper airway microbiome and immune response with nasal epithelial lining fluid absorption and nasal washes.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {20618}, pmid = {33244064}, issn = {2045-2322}, support = {K24AI77930//National Institute of Allergy and Infectious Diseases/International ; HHSN272200900007C/AI/NIAID NIH HHS/United States ; K12HD087023//Eunice Kennedy Shriver National Institute of Child Health and Human Development/International ; U19AI095227//NIAID, NIH/International ; U2CDK059637/DK/NIDDK NIH HHS/United States ; P30DK020593/DK/NIDDK NIH HHS/United States ; R21 AI149262/AI/NIAID NIH HHS/United States ; R21 AI154016/AI/NIAID NIH HHS/United States ; U19 AI110819/AI/NIAID NIH HHS/United States ; UL1 TR000445/TR/NCATS NIH HHS/United States ; UL1 RR024975/RR/NCRR NIH HHS/United States ; P30 CA068485/CA/NCI NIH HHS/United States ; P30 EY008126/EY/NEI NIH HHS/United States ; G20 RR030956/RR/NCRR NIH HHS/United States ; }, abstract = {Despite being commonly used to collect upper airway epithelial lining fluid, nasal washes are poorly reproducible, not suitable for serial sampling, and limited by a dilution effect. In contrast, nasal filters lack these limitations and are an attractive alternative. To examine whether nasal filters are superior to nasal washes as a sampling method for the characterization of the upper airway microbiome and immune response, we collected paired nasal filters and washes from a group of 40 healthy children and adults. To characterize the upper airway microbiome, we used 16S ribosomal RNA and shotgun metagenomic sequencing. To characterize the immune response, we measured total protein using a BCA assay and 53 immune mediators using multiplex magnetic bead-based assays. We conducted statistical analyses to compare common microbial ecology indices and immune-mediator median fluorescence intensities (MFIs) between sample types. In general, nasal filters were more likely to pass quality control in both children and adults. There were no significant differences in microbiome community richness, α-diversity, or structure between pediatric samples types; however, these were all highly dissimilar between adult sample types. In addition, there were significant differences in the abundance of amplicon sequence variants between sample types in children and adults. In adults, total proteins were significantly higher in nasal filters than nasal washes; consequently, the immune-mediator MFIs were not well detected in nasal washes. Based on better quality control sequencing metrics and higher immunoassay sensitivity, our results suggest that nasal filters are a superior sampling method to characterize the upper airway microbiome and immune response in both children and adults.}, }
@article {pmid33243511, year = {2020}, author = {Xu, M and Wang, F and Sheng, H and Stedtfeld, RD and Li, Z and Hashsham, SA and Jiang, X and Tiedje, JM}, title = {Does anaerobic condition play a more positive role in dissipation of antibiotic resistance genes in soil?.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {143737}, doi = {10.1016/j.scitotenv.2020.143737}, pmid = {33243511}, issn = {1879-1026}, abstract = {The persistence of antibiotic resistance genes (ARGs) under the aerobic vs. anaerobic conditions is unknown, especially under different fertilization. Towards this goal, a microcosm experiment was carried out with chemical fertilized and manured soil under aerobic and anaerobic conditions. High throughput qPCR was used to analyze ARGs with 144 primer sets and sequencing for microorganisms. Completely different dynamics of ARGs were observed in soil under aerobic and anaerobic conditions, regardless of the fertilization type. ARGs had different half-lives, even though they confer resistance to the same type of antibiotics. Aminoglycoside, chloramphenicol, macrolide - lincosamide - streptogramin B (MLSB) and tetracycline resistance genes were significantly accumulated in the aerobic soils. Anaerobic soil possessed a higher harboring capacity for exogenous microorganisms and ARGs than aerobic soil. The interaction between ARGs and mobile genetic elements (MGEs) in manured soil under aerobic condition was more pronounced than the anaerobic condition. These findings unveil that anaerobic soil could play a more positive role in reducing potential risk of ARGs in the farmland environment.}, }
@article {pmid33242583, year = {2021}, author = {Garrido-Benavent, I and Pérez-Ortega, S and de Los Ríos, A and Mayrhofer, H and Fernández-Mendoza, F}, title = {Neogene speciation and Pleistocene expansion of the genus Pseudephebe (Parmeliaceae, lichenized fungi) involving multiple colonizations of Antarctica.}, journal = {Molecular phylogenetics and evolution}, volume = {155}, number = {}, pages = {107020}, doi = {10.1016/j.ympev.2020.107020}, pmid = {33242583}, issn = {1095-9513}, abstract = {Widespread geographic distributions in lichens have been usually explained by the high dispersal capacity of their tiny diaspores. However, recent phylogenetic surveys have challenged this assumption and provided compelling evidence for cryptic speciation and more restricted distribution ranges in diverse lineages of lichen-forming fungi. To evaluate these scenarios, we focus on the fungal genus Pseudephebe (Parmeliaceae) which includes amphitropical species, a distribution pattern whose origin has been a matter of debate since first recognized in the nineteenth century. In our study, a six-locus dataset and a broad specimen sampling covering almost all Earth's continents is used to investigate species delimitation in Pseudephebe. Population structure, gene flow and dating analyses, as well as genealogical reconstruction methods, are employed to disentangle the most plausible transcontinental migration routes, and estimate the timing of the origin of the amphitropical distribution and the Antarctic populations. Our results demonstrate the existence of three partly admixed phylogenetic species that diverged between the Miocene and Pliocene, and whose Quaternary distribution has been strongly driven by glacial cycles. Pseudephebe minuscula is the only species showing an amphitropical distribution, with populations in Antarctica, whereas the restricted distribution of P. pubescens and an undescribed Alaskan species might reflect the survival of these species in European and North American refugia. Our microevolutionary analyses suggest a Northern Hemisphere origin for P. minuscula, which could have dispersed into the Southern Hemisphere directly and/or through &quot;mountain-hopping&quot; during the Pleistocene. The Antarctic populations of this species are sorted into two genetic clusters: populations of the Antarctic Peninsula were grouped together with South American ones, and the Antarctic Continental populations formed a second cluster with Bolivian and Svalbard populations. Therefore, our data strongly suggest that the current distribution of P. minuscula in Antarctica is the outcome of multiple, recent colonizations. In conclusion, our results stress the need for integrating species delimitation and population analyses to properly approach historical biogeography in lichen-forming fungi.}, }
@article {pmid33242086, year = {2020}, author = {Yue, L and Kong, W and Li, C and Zhu, G and Zhu, L and Makhalanyane, TP and Cowan, DA}, title = {Dissolved inorganic carbon determines the abundance of microbial primary producers and primary production in Tibetan Plateau lakes.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaa242}, pmid = {33242086}, issn = {1574-6941}, abstract = {Climate change globally accelerates the shrinkage of inland lakes, resulting in increases in both water salinity and dissolved inorganic carbon (DIC). The increases of salinity and DIC generate contrasting effects on microbial primary producers and primary production, however, their combined effects remain unclear in aquatic ecosystems. We hypothesized that increased DIC mitigates the constraints of enhanced salinity on microbial primary producers and primary production. To test this, we employed isotope labeling and molecular methods to explore primary production and four dominant types of microbial primary producers (form IA, IB, IC and ID) in lakes on the Tibetan Plateau. Results exhibited that DIC positively correlated with abundance of microbial primary producers and primary production (all P < 0.001) and offset salinity constraints. Structural equation models elucidated that DIC substantially enhanced primary production by stimulating the abundance of form ID microbial primary producers. The abundance of form ID primary producers explained more variations (14.6%) of primary production than form IAB (6%) and physicochemical factors (6.8%). Diatoms (form ID) played a determinant role in primary production in the lakes, by adapting to high DIC and high salinity. Our findings suggest that inland lakes may support higher primary productivity in future climate change scenarios.}, }
@article {pmid33242082, year = {2020}, author = {Stahl, LM and Olson, JB}, title = {Environmental abiotic and biotic factors affecting the distribution and abundance of Naegleria fowleri.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {1}, pages = {}, doi = {10.1093/femsec/fiaa238}, pmid = {33242082}, issn = {1574-6941}, abstract = {Naegleria fowleri is a free-living protozoan that resides in soil and freshwater. Human intranasal amoebae exposure through water or potentially dust particles can culminate in primary amoebic meningoencephalitis, which generally causes death. While many questions remain regarding pathogenesis, the microbial ecology of N. fowleri is even less understood. This review outlines current knowledge of the environmental abiotic and biotic factors that affect the distribution and abundance of N. fowleri. Although the impacts of some abiotic factors remain poorly investigated or inconclusive, N. fowleri appears to have a wide pH range, low salinity tolerance and thermophilic preference. From what is known about biotic factors, the amoebae preferentially feed upon bacteria and are preyed upon by other free-living amoebae. Additional laboratory and environmental studies are needed to fill in knowledge gaps, which are crucial for surveillance and management of N. fowleri in freshwaters. As surface water temperatures increase with climate change, it is likely that this amoeba will pose a greater threat to human health, suggesting that identifying its abiotic and biotic preferences is critical to mitigating this risk.}, }
@article {pmid33240229, year = {2020}, author = {Shaw, C and Brooke, C and Hawley, E and Connolly, MP and Garcia, JA and Harmon-Smith, M and Shapiro, N and Barton, M and Tringe, SG and Glavina Del Rio, T and Culley, DE and Castenholz, R and Hess, M}, title = {Phototrophic Co-cultures From Extreme Environments: Community Structure and Potential Value for Fundamental and Applied Research.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {572131}, pmid = {33240229}, issn = {1664-302X}, abstract = {Cyanobacteria are found in most illuminated environments and are key players in global carbon and nitrogen cycling. Although significant efforts have been made to advance our understanding of this important phylum, still little is known about how members of the cyanobacteria affect and respond to changes in complex biological systems. This lack of knowledge is in part due to our dependence on pure cultures when determining the metabolism and function of a microorganism. We took advantage of the Culture Collection of Microorganisms from Extreme Environments (CCMEE), a collection of more than 1,000 publicly available photosynthetic co-cultures maintained at the Pacific Northwest National Laboratory, and assessed via 16S rRNA amplicon sequencing if samples readily available from public culture collection could be used in the future to generate new insights into the role of microbial communities in global and local carbon and nitrogen cycling. Results from this work support the existing notion that culture depositories in general hold the potential to advance fundamental and applied research. Although it remains to be seen if co-cultures can be used at large scale to infer roles of individual organisms, samples that are publicly available from existing co-cultures depositories, such as the CCMEE, might be an economical starting point for such studies. Access to archived biological samples, without the need for costly field work, might in some circumstances be one of the few remaining ways to advance the field and to generate new insights into the biology of ecosystems that are not easily accessible. The current COVID-19 pandemic, which makes sampling expeditions almost impossible without putting the health of the participating scientists on the line, is a very timely example.}, }
@article {pmid33239370, year = {2020}, author = {Props, R and Monsieurs, P and Vandamme, P and Leys, N and Denef, VJ and Boon, N}, title = {Correction for Props et al., &quot;Gene Expansion and Positive Selection as Bacterial Adaptations to Oligotrophic Conditions&quot;.}, journal = {mSphere}, volume = {5}, number = {6}, pages = {}, doi = {10.1128/mSphere.01143-20}, pmid = {33239370}, issn = {2379-5042}, }
@article {pmid33238123, year = {2020}, author = {Zhang, H and Madi, A and Yosef, N and Chihara, N and Awasthi, A and Pot, C and Lambden, C and Srivastava, A and Burkett, PR and Nyman, J and Christian, E and Etminan, Y and Lee, A and Stroh, H and Xia, J and Karwacz, K and Thakore, PI and Acharya, N and Schnell, A and Wang, C and Apetoh, L and Rozenblatt-Rosen, O and Anderson, AC and Regev, A and Kuchroo, VK}, title = {An IL-27-Driven Transcriptional Network Identifies Regulators of IL-10 Expression across T Helper Cell Subsets.}, journal = {Cell reports}, volume = {33}, number = {8}, pages = {108433}, pmid = {33238123}, issn = {2211-1247}, support = {R01 NS030843/NS/NINDS NIH HHS/United States ; P01 AI129880/AI/NIAID NIH HHS/United States ; P01 AI056299/AI/NIAID NIH HHS/United States ; R01 CA229400/CA/NCI NIH HHS/United States ; P01 AI039671/AI/NIAID NIH HHS/United States ; R01 AI144166/AI/NIAID NIH HHS/United States ; P01 AI073748/AI/NIAID NIH HHS/United States ; }, abstract = {Interleukin-27 (IL-27) is an immunoregulatory cytokine that suppresses inflammation through multiple mechanisms, including induction of IL-10, but the transcriptional network mediating its diverse functions remains unclear. Combining temporal RNA profiling with computational algorithms, we predict 79 transcription factors induced by IL-27 in T cells. We validate 11 known and discover 5 positive (Cebpb, Fosl2, Tbx21, Hlx, and Atf3) and 2 negative (Irf9 and Irf8) Il10 regulators, generating an experimentally refined regulatory network for Il10. We report two central regulators, Prdm1 and Maf, that cooperatively drive the expression of signature genes induced by IL-27 in type 1 regulatory T cells, mediate IL-10 expression in all T helper cells, and determine the regulatory phenotype of colonic Foxp3+ regulatory T cells. Prdm1/Maf double-knockout mice develop spontaneous colitis, phenocopying ll10-deficient mice. Our work provides insights into IL-27-driven transcriptional networks and identifies two shared Il10 regulators that orchestrate immunoregulatory programs across T helper cell subsets.}, }
@article {pmid33237956, year = {2020}, author = {Buranarom, N and Komin, O and Matangkasombut, O}, title = {Hyposalivation, oral health, and Candida colonization in independent dentate elders.}, journal = {PloS one}, volume = {15}, number = {11}, pages = {e0242832}, pmid = {33237956}, issn = {1932-6203}, abstract = {Hyposalivation is an important problem in elders and could interfere with several oral functions and microbial ecology. While the number of independent elders who retain more natural teeth increases worldwide, few studies examined hyposalivation in this population. Thus, this study aims to examine relationships between hyposalivation, oral health conditions and oral Candida colonization in independent dentate elders and evaluate factors associated with salivary flow and Candida carriage. We conducted a cross-sectional study in fifty-three dentate elders (≥65 years old with at least 4 pairs of posterior occlusal contacts) with no, or well-controlled, systemic conditions. Participants were interviewed for medical history, subjective dry mouth symptoms, oral hygiene practices and denture information. Unstimulated and stimulated salivary flow rates, objective dry mouth signs, gingival, tongue-coating, and root-caries indices were recorded. Stimulated saliva was cultured on Sabouraud-dextrose agar for Candida counts. Candida species were identified using chromogenic Candida agar and polymerase chain reaction. Statistical significance level was set at p<0.05. The results showed that hyposalivation was associated with higher gingival and tongue-coating indices (p = 0.003 and 0.015, respectively), but not root-caries index. Hyposalivation was also associated with higher prevalence of oral Candida colonization (p = 0.010; adjusted OR = 4.36, 95% confidence interval = 1.29-14.72). These two indices and Candida load were negatively correlated with unstimulated and stimulated salivary flow rates. Interestingly, non-albicans Candida species were more prevalent in denture wearers (p = 0.017). Hence, hyposalivation is a risk factor for poorer oral health and oral Candida colonization in independent dentate elders. Because of its potential adverse effects on oral and systemic health, hyposalivation should be carefully monitored in elders.}, }
@article {pmid33236218, year = {2020}, author = {Saxena, S and Strobel, GA}, title = {Marvellous Muscodor spp.: Update on Their Biology and Applications.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33236218}, issn = {1432-184X}, abstract = {Nearly 20 years ago, the first report appeared on the discovery of a novel genus-Muscodor. This organism was isolated as an endophyte from a cinnamon tree that had been introduced to Honduras from Sri Lanka in the early part of the last century. Characteristically, the original Muscodor albus, and all of its species isolated since that time are non-spore producers and each one exudes a characteristic spectrum of volatile bioactive compounds. The majority have a whitish mycelium, which is sometimes coiling, intertwined and decorated with variously shaped structures. Presently, there are at least 22 type species known/documented and each has been described as an endophyte from various plant families with widely varying habitats. An enormous variety of volatile organic compounds (VOCs) are produced by Muscodor spp. and some of these include esters, acids, aldehydes, ketones, aromatics, alkanes, alcohols, nitrosamides and terpenoids. The VOCs are both inhibitory and lethal to a wide variety of fungi and bacteria including some major pathogens of plants and humans. Interestingly, in almost all cases studied, no one compound by itself can mimic the bioactivity of the complete gas mixture, suggesting that the volatiles are acting in a synergistic manner and this has been tested with individual as well as the VOCs in various mixtures and concentrations. This review will discuss some of the recent findings in all aspects of this unique fungal genus whilst at the same time pointing out some of the major questions that remain about its biology, ecology and its applications in agriculture, medicine and other sectors. Most importantly, the authors provide arguments supporting the claim that Muscodor is taxonomically distinct from Induratia, a recently proposed change to its nomenclature.}, }
@article {pmid33233106, year = {2020}, author = {Lianou, A and Nychas, GE and Koutsoumanis, KP}, title = {Strain variability in biofilm formation: A food safety and quality perspective.}, journal = {Food research international (Ottawa, Ont.)}, volume = {137}, number = {}, pages = {109424}, doi = {10.1016/j.foodres.2020.109424}, pmid = {33233106}, issn = {1873-7145}, abstract = {The inherent differences in microbial behavior among identically treated strains of the same microbial species, referred to as &quot;strain variability&quot;, are regarded as an important source of variability in microbiological studies. Biofilms are defined as the structured multicellular communities with complex architecture that enable microorganisms to grow adhered to abiotic or living surfaces and constitute a fundamental aspect of microbial ecology. The research studies assessing the strain variability in biofilm formation are relatively few compared to the ones evaluating other aspects of microbial behavior such as virulence, growth and stress resistance. Among the available research data on intra-species variability in biofilm formation, compiled and discussed in the present review, most of them refer to foodborne pathogens as compared to spoilage microorganisms. Molecular and physiological aspects of biofilm formation potentially related to strain-specific responses, as well as information on the characterization and quantitative description of this type of biological variability are presented and discussed. Despite the considerable amount of available information on the strain variability in biofilm formation, there are certain data gaps and still-existing challenges that future research should cover and address. Current and future advances in systems biology and omics technologies are expected to aid significantly in the explanation of phenotypic strain variability, including biofilm formation variability, allowing for its integration in microbiological risk assessment.}, }
@article {pmid33232448, year = {2020}, author = {d'Enfert, C and Kaune, AK and Alaban, LR and Chakraborty, S and Cole, N and Delavy, M and Kosmala, D and Marsaux, B and Fróis-Martins, R and Morelli, M and Rosati, D and Valentine, M and Xie, Z and Emritloll, Y and Warn, PA and Bequet, F and Bougnoux, ME and Bornes, S and Gresnigt, MS and Hube, B and Jacobsen, ID and Legrand, M and Leibundgut-Landmann, S and Manichanh, C and Munro, CA and Netea, MG and Queiroz, K and Roget, K and Thomas, V and Thoral, C and Van den Abbeele, P and Walker, AW and Brown, AJP}, title = {The impact of the Fungus-Host-Microbiota interplay upon Candida albicans infections: current knowledge and new perspectives.}, journal = {FEMS microbiology reviews}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsre/fuaa060}, pmid = {33232448}, issn = {1574-6976}, abstract = {Candida albicans is a major fungal pathogen of humans. It exists as a commensal in the oral cavity, gut or genital tract of most individuals, constrained by the local microbiota, epithelial barriers and immune defences. Their perturbation can lead to fungal outgrowth and the development of mucosal infections such as oropharyngeal or vulvovaginal candidiasis, and patients with compromised immunity are susceptible to life-threatening systemic infections. The importance of the interplay between fungus, host and microbiota in driving the transition from C. albicans commensalism to pathogenicity is widely appreciated. However, the complexity of these interactions, and the significant impact of fungal, host and microbiota variability upon disease severity and outcome, are less well understood. Therefore, we summarise the features of the fungus that promote infection, and how genetic variation between clinical isolates influences pathogenicity. We discuss antifungal immunity, how this differs between mucosae, and how individual variation influences a person's susceptibility to infection. Also, we describe factors that influence the composition of gut, oral and vaginal microbiotas, and how these affect fungal colonisation and antifungal immunity. We argue that a detailed understanding of these variables, which underlie fungal-host-microbiota interactions, will present opportunities for directed antifungal therapies that benefit vulnerable patients.}, }
@article {pmid33232202, year = {2020}, author = {Coleine, C and Stajich, JE and de Los Ríos, A and Selbmann, L}, title = {Beyond the extremes: Rocks as ultimate refuge for fungi in drylands.}, journal = {Mycologia}, volume = {}, number = {}, pages = {1-26}, doi = {10.1080/00275514.2020.1816761}, pmid = {33232202}, issn = {1557-2536}, abstract = {In an era of rapid climate change and expansion of desertification, the extremely harsh conditions of drylands are a true challenge for microbial life. Under drought conditions, where most life forms cannot survive, rocks represent the main refuge for life. Indeed, the endolithic habitat provides thermal buffering, physical stability, and protection against incident ultraviolet (UV) radiation and solar radiation and, to some extent, ensures water retention to microorganisms. The study of these highly specialized extreme-tolerant and extremophiles may provide tools for understanding microbial interactions and processes that allow them to keep their metabolic machinery active under conditions of dryness and oligotrophy that are typically incompatible with active life, up to the dry limits for life. Despite lithobiontic communities being studied all over the world, a comprehensive understanding of their ecology, evolution, and adaptation is still nascent. Herein, we survey the fungal component of these microbial ecosystems. We first provide an overview of the main defined groups (i.e., lichen-forming fungi, black fungi, and yeasts) of the most known and studied Antarctic endolithic communities that are almost the only life forms ensuring ecosystem functionality in the ice-free areas of the continent. For each group, we discuss their main traits and their diversity. Then, we focus on the fungal taxonomy and ecology of other worldwide endolithic communities. Finally, we highlight the utmost importance of a global rock survey in order to have a comprehensive view of the diversity, distribution, and functionality of these fungi in drylands, to obtain tools in desert area management, and as early alarm systems to climate change.}, }
@article {pmid33231332, year = {2020}, author = {Stothart, MR and Greuel, RJ and Gavriliuc, S and Henry, A and Wilson, AJ and McLoughlin, PD and Poissant, J}, title = {Bacterial dispersal and drift drive microbiome diversity patterns within a population of feral hindgut fermenters.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.15747}, pmid = {33231332}, issn = {1365-294X}, support = {25046//Canada Foundation for Innovation/ ; 2016-06459//Natural Sciences and Engineering Research Council of Canada/ ; 2019-04388//Natural Sciences and Engineering Research Council of Canada/ ; }, abstract = {Studies of microbiome variation in wildlife often emphasize host physiology and diet as proximate selective pressures acting on host-associated microbiota. In contrast, microbial dispersal and ecological drift are more rarely considered. Using amplicon sequencing, we characterized the bacterial microbiome of adult female (n = 86) Sable Island horses (Nova Scotia, Canada) as part of a detailed individual-based study of this feral population. Using data on sampling date, horse location, age, parental status, and local habitat variables, we contrasted the ability of spatiotemporal, life history, and environmental factors to explain microbiome diversity among Sable Island horses. We extended inferences made from these analyses with both phylogeny-informed and phylogeny-independent null modelling approaches to identify deviations from stochastic expectations. Phylogeny-informed diversity measures were correlated with spatial and local habitat variables, but null modelling results suggested that heterogeneity in ecological drift, rather than differential selective pressures acting on the microbiome, was responsible for these correlations. Conversely, phylogeny-independent diversity measures were best explained by host spatial and social structure, suggesting that taxonomic composition of the microbiome was shaped most strongly by bacterial dispersal. Parental status was important but correlated with measures of β-dispersion rather than β-diversity (mares without foals had lower alpha diversity and more variable microbiomes than mares with foals). Our results suggest that between host microbiome variation within the Sable Island horse population is driven more strongly by bacterial dispersal and ecological drift than by differential selective pressures. These results emphasize the need to consider alternative ecological processes in the study of microbiomes.}, }
@article {pmid33230594, year = {2020}, author = {Paul, P and Chakraborty, P and Chatterjee, A and Sarker, RK and Dastidar, DG and Kundu, T and Sarkar, N and Das, A and Tribedi, P}, title = {1,4-Naphthoquinone accumulates reactive oxygen species in Staphylococcus aureus: a promising approach towards effective management of biofilm threat.}, journal = {Archives of microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00203-020-02117-1}, pmid = {33230594}, issn = {1432-072X}, abstract = {Staphylococcus aureus, a Gram-positive opportunistic microorganism, promotes pathogenicity in the human host through biofilm formation. Microorganisms associated with biofilm often exhibit drug-resistance property that poses a major threat to public healthcare. Thus, the exploration of new therapeutic approaches is the need of the hour to manage biofilm-borne infections. In the present study, efforts are put together to test the antimicrobial as well as antibiofilm activity of 1,4-naphthoquinone against Staphylococcus aureus. The result showed that the minimum bactericidal concentration (MBC) of this compound was found to be 100 µg/mL against Staphylococcus aureus. In this regard, an array of experiments (crystal violet, biofilm protein measurement, and microscopic analysis) related to biofilm assay were conducted with the sub-MBC concentrations (1/20 and 1/10 MBC) of 1,4-naphthoquinone. All the results of biofilm assay demonstrated that these tested concentrations (1/20 and 1/10 MBC) of the compound (1,4-naphthoquinone) showed a significant reduction in biofilm development by Staphylococcus aureus. Moreover, the tested concentrations (1/20 and 1/10 MBC) of the compound (1,4-naphthoquinone) were able to reduce the microbial motility of Staphylococcus aureus that might affect the development of biofilm. Further studies revealed that the treatment of 1,4-naphthoquinone to the organism was found to increase the cellular accumulation of reactive oxygen species (ROS) that resulted in the inhibition of biofilm formation by Staphylococcus aureus. Hence, it can be concluded that 1,4-naphthoquinone might be considered as a promising compound towards biofilm inhibition caused by Staphylococcus aureus.}, }
@article {pmid33228011, year = {2020}, author = {Cano-Ortiz, A and Laborda-Illanes, A and Plaza-Andrades, I and Membrillo Del Pozo, A and Villarrubia Cuadrado, A and Rodríguez Calvo de Mora, M and Leiva-Gea, I and Sanchez-Alcoholado, L and Queipo-Ortuño, MI}, title = {Connection between the Gut Microbiome, Systemic Inflammation, Gut Permeability and FOXP3 Expression in Patients with Primary Sjögren's Syndrome.}, journal = {International journal of molecular sciences}, volume = {21}, number = {22}, pages = {}, pmid = {33228011}, issn = {1422-0067}, support = {CPI13/00003//Miguel Servet Type II&quot; program, ISCIII, Spain/ ; C-0030-2018//&quot;Nicolas Monardes&quot; research program of the Consejería de Salud (C-0030-2018, Junta de Andalucía, Spain/ ; PE-0106-2019//Predoctoral grant from Consejería de Salud y Familia, Andalucia, Spain/ ; FI19-00112//predoctoral grant PFIS-ISCIII, Madrid, Spain/ ; }, abstract = {The aims of this study were to explore intestinal microbial composition and functionality in primary Sjögren's syndrome (pSS) and to relate these findings to inflammation, permeability and the transcription factor Forkhead box protein P3 (FOXP3) gene expression in peripheral blood. The study included 19 pSS patients and 19 healthy controls matched for age, sex, and body mass index. Fecal bacterial DNA was extracted and analyzed by 16S rRNA sequencing using an Ion S5 platform followed by a bioinformatics analysis using Quantitative Insights into Microbial Ecology (QIIME II) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). Our data suggest that the gut microbiota of pSS patients differs at both the taxonomic and functional levels with respect to healthy controls. The gut microbiota profile of our pSS patients was characterized by a lower diversity and richness and with Bacteroidetes dominating at the phylum level. The pSS patients had less beneficial or commensal butyrate-producing bacteria and a higher proportion of opportunistic pathogens with proinflammatory activity, which may impair intestinal barrier function and therefore contribute to inflammatory processes associated with pSS by increasing the production of proinflammatory cytokines and decreasing the release of the anti-inflammatory cytokine IL-10 and the peripheral FOXP3 mRNA expression, implicated in the development and function of regulatory T cells (Treg) cells. Further studies are needed to better understand the real impact of dysbiosis on the course of pSS and to conceive preventive or therapeutic strategies to counteract microbiome-driven inflammation.}, }
@article {pmid33226191, year = {2020}, author = {Gonçalves E Silva, F and Dos Santos, HF and de Assis Leite, DC and Lutfi, DS and Vianna, M and Rosado, AS}, title = {Skin and stinger bacterial communities in two critically endangered rays from the South Atlantic in natural and aquarium settings.}, journal = {MicrobiologyOpen}, volume = {9}, number = {12}, pages = {e1141}, pmid = {33226191}, issn = {2045-8827}, support = {//National Council for Scientific and Technological Development (CNPq)/ ; //Coordination for the Improvement of Higher Education Personnel (CAPES)/ ; //Carlos Chagas Filho Foundation for Research Support of Rio de Janeiro State (FAPERJ)/ ; }, abstract = {Bacterial communities of two critically endangered rays from the South Atlantic, the butterfly ray (Gymnura altavela) and the groovebelly ray (Dasyatis hypostigma), were described using 16S rRNA gene metabarcoding. The study characterized the bacterial communities associated with (i) G. altavela in natural (in situ) and aquarium (ex situ) settings, (ii) skin and stinger of G. altavela, and D. hypostigma in aquaria, and (iii) newborns and adults of D. hypostigma. The results revealed potentially antibiotic-producing bacterial groups on the skin of rays from the natural environment, and some taxa with the potential to benefit ray health, mainly in rays from the natural environment, as well as possible pathogens to other animals, including fish and humans. Differences were observed between the G. altavela and D. hypostigma bacteria composition, as well as between the skin and stinger bacterial composition. The bacterial community associated with D. hypostigma changed with the age of the ray. The aquarium environment severely impacted the G. altavela bacteria composition, which changed from a complex bacterial community to one dominated almost exclusively by two taxa, Oceanimonas sp. and Sediminibacterium sp. on the skin and stinger, respectively.}, }
@article {pmid33225409, year = {2020}, author = {Labrador, MDM and Doña, J and Serrano, D and Jovani, R}, title = {Quantitative Interspecific Approach to the Stylosphere: Patterns of Bacteria and Fungi Abundance on Passerine Bird Feathers.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01634-2}, pmid = {33225409}, issn = {1432-184X}, abstract = {Feathers are the habitat of a myriad of organisms, from fungi and bacteria to lice and mites. Although most studies focus on specific taxa and their interaction with the bird host, anecdotal data glimpse feathers as holders of a system with its own ecology, what we call here the stylosphere. A major gap in our knowledge of the stylosphere is the ecology of the total abundance of microorganisms, being also rare to find studies that analyze abundance of more than one group of microorganisms at the bird interspecific level. Here, we quantified bacterial and fungi abundances through qPCR on the wing feathers of 144 birds from 24 passerine and one non-passerine bird species from three localities in Southern Spain. Bacteria and fungi abundances spanned three orders of magnitude among individual birds, but were consistent when comparing the right and the left wing feathers of individuals. Sampling locality explained ca. 14% of the variation in both bacteria and fungi abundances. Even when statistically controlling for sampling locality, microbial abundances consistently differed between birds from different species, but these differences were not explained by bird phylogeny. Finally, bird individuals and species having more bacteria also tended to held larger abundances of fungi. Our results suggest a quite complex explanation for stylosphere microorganisms' abundance, being shaped by bird individual and species traits, as well as environmental factors, and likely bacteria-fungi interactions.}, }
@article {pmid33220680, year = {2020}, author = {Hall, MA and Brettell, LE and Liu, H and Nacko, S and Spooner-Hart, R and Riegler, M and Cook, JM}, title = {Temporal changes in the microbiome of stingless bee foragers following colony relocation.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {1}, pages = {}, doi = {10.1093/femsec/fiaa236}, pmid = {33220680}, issn = {1574-6941}, abstract = {Maintaining beneficial interactions with microbial symbionts is vital for animal health. Yet, for social insects, the stability of microbial associations within and between cohorts is largely unknown. We investigated temporal changes in the microbiomes of nine stingless bee (Tetragonula carbonaria) colonies at seven timepoints across a 10-month period when moved between two climatically and florally different sites. Bacterial 16S rRNA gene and fungal ITS amplicon sequencing confirmed that microbiomes varied considerably between colonies initially at site one. However, following relocation, considerable changes occurred in bacterial community composition within each colony, and the microbiome composition became more similar across colonies. Notably, Snodgrassella disappeared and Zymobacter appeared as relatively abundant taxa. Remarkably, bacterial communities within colonies continued to shift over time but remained similar across colonies, becoming dominated by Acinetobacter six months after returning to the original site. Our results indicate that the stingless bee microbiome can undergo major changes in response to the environment, and that these changes can be long-lasting. Such legacy effects have not been reported for corbiculate bees. Further understanding the microbial ecology of stingless bees will aid future management of colonies used in agricultural production.}, }
@article {pmid33220679, year = {2020}, author = {Nilsson, JF and Castellani, LG and Draghi, WO and Mogro, EG and Wibberg, D and Winkler, A and Hansen, LH and Schlüter, A and Pühler, A and Kalinowski, J and Torres Tejerizo, GA and Pistorio, M}, title = {Global transcriptome analysis of Rhizobium favelukesii LPU83 in response to acid stress.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {1}, pages = {}, doi = {10.1093/femsec/fiaa235}, pmid = {33220679}, issn = {1574-6941}, abstract = {Acidic environments naturally occur worldwide and inappropriate agricultural management may also cause acidification of soils. Low soil pH values are an important barrier in the plant-rhizobia interaction. Acidic conditions disturb the establishment of the efficient rhizobia usually used as biofertilizer. This negative effect on the rhizobia-legume symbiosis is mainly due to the low acid tolerance of the bacteria. Here, we describe the identification of relevant factors in the acid tolerance of Rhizobium favelukesii using transcriptome sequencing. A total of 1924 genes were differentially expressed under acidic conditions, with ∼60% underexpressed. Rhizobium favelukesii acid response mainly includes changes in the energy metabolism and protein turnover, as well as a combination of mechanisms that may contribute to this phenotype, including GABA and histidine metabolism, cell envelope modifications and reverse proton efflux. We confirmed the acid-sensitive phenotype of a mutant in the braD gene, which showed higher expression under acid stress. Remarkably, 60% of the coding sequences encoded in the symbiotic plasmid were underexpressed and we evidenced that a strain cured for this plasmid featured an improved performance under acidic conditions. Hence, this work provides relevant information in the characterization of genes associated with tolerance or adaptation to acidic stress of R. favelukesii.}, }
@article {pmid33219851, year = {2020}, author = {Sun, M and Li, T and Li, D and Zhao, Y and Gao, F and Sun, L and Li, X}, title = {Conversion of Land Use from Upland to Paddy Field Changes Soil Bacterial Community Structure in Mollisols of Northeast China.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01632-4}, pmid = {33219851}, issn = {1432-184X}, support = {41701289//National Natural Science Foundation of China/ ; 2018M640287//China Postdoctoral Science Foundation/ ; }, abstract = {Mollisols are extremely important soil resource for crop and forage production. In northeast China, it is a major land use management practice from dry land crops to irrigated rice. However, there is few data regarding soil quality and microbial composition in Mollisols during land use transition. Here, we analyzed the upper 30 cm of soil from land with more than 30 years of paddy use and from adjacent areas with upland crops. Our results showed that land use and soil depth had a significant effect on soil properties and enzyme activities. Soil moisture (SM) and soil organic carbon (SOC) contents were substantially higher in paddy fields than in upland crop lands, while nitrogen-related enzyme activities were lower. Following the land use change, bacterial diversity was increased and bacterial community composition changed. Taxonomic analyses showed that Proteobacteria, Chloroflexi, Firmicutes, and Bacteroidetes were the dominant phyla present. At family level, Gemmatimonadaceae decreased with land use change, while Syntrophorhabdaceae and Syntrophacea that play a part in methane cycling and nitrifying bacteria such as Nitrospiraceae increased, indicating that the structure and composition of the bacterial community might be a promising indicator of Mollisol health. Redundancy analysis indicated that land use type had a stronger effect on the soil bacterial community composition than soil depth. Additionally, bacterial community composition was closely associated with soil parameters such as soil moisture, pH, SOC, NO3--N, and NH4+-N. Overall, land use change affects the physical and chemical properties of the soil, resulting in changes in the composition of the soil bacterial community and flora. These changes could provide a view of the bacterial community assembly and functional shifts following land use change.}, }
@article {pmid33219400, year = {2020}, author = {Torralba, MG and Aleti, G and Li, W and Moncera, KJ and Lin, YH and Yu, Y and Masternak, MM and Golusinski, W and Golusinski, P and Lamperska, K and Edlund, A and Freire, M and Nelson, KE}, title = {Correction to: Oral Microbial Species and Virulence Factors Associated with Oral Squamous Cell Carcinoma.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01641-3}, pmid = {33219400}, issn = {1432-184X}, abstract = {The original article contained mistakes in the authors' affiliations.}, }
@article {pmid33219399, year = {2020}, author = {Khan, S and Vancuren, SJ and Hill, JE}, title = {A Generalist Lifestyle Allows Rare Gardnerella spp. to Persist at Low Levels in the Vaginal Microbiome.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33219399}, issn = {1432-184X}, abstract = {Gardnerella spp. are considered a hallmark of bacterial vaginosis, a dysbiosis of the vaginal microbiome. There are four cpn60 sequence-based subgroups within the genus (A, B, C and D), and thirteen genome species have been defined recently. Gardnerella spp. co-occur in the vaginal microbiome with varying abundance, and these patterns are shaped by a resource-dependent, exploitative competition, which affects the growth rate of subgroups A, B and C negatively. The growth rate of rarely abundant subgroup D, however, increases with the increasing number of competitors, negatively affecting the growth rate of others. We hypothesized that a nutritional generalist lifestyle and minimal niche overlap with the other more abundant Gardnerella spp. facilitate the maintenance of subgroup D in the vaginal microbiome through negative frequency-dependent selection. Using 40 whole-genome sequences from isolates representing all four subgroups, we found that they could be distinguished based on the content of their predicted proteomes. Proteins associated with carbohydrate and amino acid uptake and metabolism were significant contributors to the separation of subgroups. Subgroup D isolates had significantly more of their proteins assigned to amino acid metabolism than the other subgroups. Subgroup D isolates were also significantly different from others in terms of number and type of carbon sources utilized in a phenotypic assay, while the other three could not be distinguished. Overall, the results suggest that a generalist lifestyle and lack of niche overlap with other Gardnerella spp. leads to subgroup D being favoured by negative frequency-dependent selection in the vaginal microbiome.}, }
@article {pmid33218113, year = {2020}, author = {Sperling, JLH and Fitzgerald, D and Sperling, FAH and Magor, KE}, title = {Microbiome Composition and Borrelia Detection in Ixodes scapularis Ticks at the Northwestern Edge of Their Range.}, journal = {Tropical medicine and infectious disease}, volume = {5}, number = {4}, pages = {}, pmid = {33218113}, issn = {2414-6366}, support = {RGPIN-2015-05045//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN-2020-04668//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN-2018-04920//Natural Sciences and Engineering Research Council of Canada/ ; Grant in Biodiversity to J. Sperling//Alberta Conservation Association/ ; scholarship to J. Sperling//Alberta Innovates - Technology Futures/ ; }, abstract = {Lyme disease-causing Borrelia burgdorferi has been reported in 10-19% of Ixodes ticks from Alberta, Canada, where the tick vector Ixodes scapularis is at the northwestern edge of its range. However, the presence of Borrelia has not been verified independently, and the bacterial microbiome of these ticks has not been described. We performed 16S rRNA bacterial surveys on female I. scapularis from Alberta that were previously qPCR-tested in a Lyme disease surveillance program. Both 16S and qPCR methods were concordant for the presence of Borrelia. The 16S studies also provided a profile of associated bacteria that showed the microbiome of I. scapularis in Alberta was similar to other areas of North America. Ticks that were qPCR-positive for Borrelia had significantly greater bacterial diversity than Borrelia-negative ticks, on the basis of generalized linear model testing. This study adds value to ongoing tick surveillance and is a foundation for deeper understanding of tick microbial ecology and disease transmission in a region where I. scapularis range expansion, induced by climate and land use changes, is likely to have increasing public health implications.}, }
@article {pmid33218015, year = {2020}, author = {Koller, G and Foschi, F and Mitchell, P and Witherden, E and Bruce, K and Mannocci, F}, title = {Amoebae in Chronic, Polymicrobial Endodontic Infections Are Associated with Altered Microbial Communities of Increased Virulence.}, journal = {Journal of clinical medicine}, volume = {9}, number = {11}, pages = {}, pmid = {33218015}, issn = {2077-0383}, abstract = {BACKGROUND: Infections of the root canal space involve polymicrobial biofilms and lead to chronic, low grade inflammatory responses arising from the seeding of microbes and by-products. Acute exacerbation and/or disseminating infections occur when established microbial communities undergo sudden changes in phenotypic behaviour.<br><br>METHODS: Within clinical endodontic infections, we assessedcategorical determinants comprising, and changing microbial composition of, chronic polymicrobial infections and their association with amoebae. After standardised assessment, primary or secondary infections underwent sampling and DNA processing, targeting bacteria, fungi and amoebae, including 16S high-throughput sequencing. After taxonomic assignment, community composition was correlated with clinical signs and symptoms. Diversity and abundance analyses were carried out in relation to the presence of non-bacterial amplicons.<br><br>RESULTS: Clinical specimens revealed two distinct community clusters, where specific changes correlated with clinical signs. An association between the compositions of microbiomes was found between these groups and the presence of Entamoeba gingivalis in 44% of cases. When amoebae were present in endodontic infections, we demonstrate changes in microbial community structure that mirror those observed in treatment-resistant or recurrent infections.<br><br>CONCLUSIONS: Amoeba are present in endodontic infections at a high prevalence, and may promote increased virulence by enrichment for phagocytosis-resistant bacteria.}, }
@article {pmid33217780, year = {2020}, author = {Ontiveros, VJ and Capitan, JA and Casamayor, EO and Alonso, D}, title = {The characteristic time of ecological communities.}, journal = {Ecology}, volume = {}, number = {}, pages = {e03247}, doi = {10.1002/ecy.3247}, pmid = {33217780}, issn = {1939-9170}, abstract = {A simple description of temporal dynamics of ecological communities may help us understand how community assembly proceeds, predict ecological responses to environmental disturbances, and improve the performance of biological conservation actions. Although community changes take place at multiple temporal scales, the variation of species composition and richness over time across communities and habitats shows general patterns that may potentially reveal the main drivers of community dynamics. We used the simplest stochastic model of Island Biogeography to propose two quantities to characterize community dynamics: the community characteristic time, as a measure of the typical time scale of species richness change, and (ii) the characteristic Jaccard index, as a measure of temporal β diversity, i.e., the variation of community composition over time. In addition, the community characteristic time, which sets the temporal scale at which null, non-interacting species assemblages operate, allowed us to define a relative sampling frequency (to the characteristic time). Here we estimate these quantities across microbial and macroscopic species assemblages to highlight two related results. First, we illustrated both characteristic time and Jaccard index and their relation with classic time-series in ecology, and found that the most thoroughly sampled communities, relative to their characteristic time, presented the largest similarity between consecutive samples. Second, our analysis across a variety of habitats and taxa show that communities span a large range of species turnover, from potentially very fast (short characteristic times) to rather slow (long characteristic times) communities. This was in agreement with previous knowledge, but indicated that some habitats may have been sampled less frequently than required. Our work provides new perspectives to explore the temporal component in ecological studies and highlights the usefulness of simple approximations to the complex dynamics of ecological communities.}, }
@article {pmid33215610, year = {2020}, author = {Madi, N and Vos, M and Murall, CL and Legendre, P and Shapiro, BJ}, title = {Does diversity beget diversity in microbiomes?.}, journal = {eLife}, volume = {9}, number = {}, pages = {}, doi = {10.7554/eLife.58999}, pmid = {33215610}, issn = {2050-084X}, abstract = {Microbes are embedded in complex communities where they engage in a wide array of intra- and inter-specific interactions. The extent to which these interactions drive or impede microbiome diversity is not well understood. Historically, two contrasting hypotheses have been suggested to explain how species interactions could influence diversity. 'Ecological Controls' (EC) predicts a negative relationship, where the evolution or migration of novel types is constrained as niches become filled. In contrast, 'Diversity Begets Diversity' (DBD) predicts a positive relationship, with existing diversity promoting the accumulation of further diversity via niche construction and other interactions. Using high-throughput amplicon sequencing data from the Earth Microbiome Project, we provide evidence that DBD is strongest in low-diversity biomes, but weaker in more diverse biomes, consistent with biotic interactions initially favouring the accumulation of diversity (as predicted by DBD). However, as niches become increasingly filled, diversity hits a plateau (as predicted by EC).}, }
@article {pmid33213979, year = {2020}, author = {Glodowska, M and Stopelli, E and Straub, D and Vu Thi, D and Trang, PTK and Viet, PH and AdvectAs Team Members,  and Berg, M and Kappler, A and Kleindienst, S}, title = {Arsenic behavior in groundwater in Hanoi (Vietnam) influenced by a complex biogeochemical network of iron, methane, and sulfur cycling.}, journal = {Journal of hazardous materials}, volume = {}, number = {}, pages = {124398}, doi = {10.1016/j.jhazmat.2020.124398}, pmid = {33213979}, issn = {1873-3336}, abstract = {The fate of arsenic (As) in groundwater is determined by multiple interrelated microbial and abiotic processes that contribute to As (im)mobilization. Most studies to date have investigated individual processes related to As (im)mobilization rather than the complex networks present in situ. In this study, we used RNA-based microbial community analysis in combination with groundwater hydrogeochemical measurements to elucidate the behavior of As along a 2 km transect near Hanoi, Vietnam. The transect stretches from the riverbank across a strongly reducing and As-contaminated Holocene aquifer, followed by a redox transition zone (RTZ) and a Pleistocene aquifer, at which As concentrations are low. Our analyses revealed fermentation and methanogenesis as important processes providing electron donors, fueling the microbially mediated reductive dissolution of As-bearing Fe(III) minerals and ultimately promoting As mobilization. As a consequence of high CH4 concentrations, methanotrophs thrive across the Holocene aquifer and the redox transition zone. Finally, our results underline the role of SO42--reducing and putative Fe(II)-/As(III)-oxidizing bacteria as a sink for As, particularly at the RTZ. Overall, our results suggest that a complex network of microbial and biogeochemical processes has to be considered to better understand the biogeochemical behavior of As in groundwater.}, }
@article {pmid33213887, year = {2021}, author = {Sutherland, WJ and Atkinson, PW and Broad, S and Brown, S and Clout, M and Dias, MP and Dicks, LV and Doran, H and Fleishman, E and Garratt, EL and Gaston, KJ and Hughes, AC and Le Roux, X and Lickorish, FA and Maggs, L and Palardy, JE and Peck, LS and Pettorelli, N and Pretty, J and Spalding, MD and Tonneijck, FH and Walpole, M and Watson, JEM and Wentworth, J and Thornton, A}, title = {A 2021 Horizon Scan of Emerging Global Biological Conservation Issues.}, journal = {Trends in ecology &amp; evolution}, volume = {36}, number = {1}, pages = {87-97}, doi = {10.1016/j.tree.2020.10.014}, pmid = {33213887}, issn = {1872-8383}, abstract = {We present the results from our 12th annual horizon scan of issues likely to impact biological conservation in the future. From a list of 97 topics, our global panel of 25 scientists and practitioners identified the top 15 issues that we believe society may urgently need to address. These issues are either novel in the biological conservation sector or represent a substantial positive or negative step-change in impact at global or regional level. Six issues, such as coral reef deoxygenation and changes in polar coastal productivity, affect marine or coastal ecosystems and seven relate to human and ecosystem-level responses to climate change. Identification of potential forthcoming issues for biological conservation may enable increased preparedness by researchers, practitioners, and decision-makers.}, }
@article {pmid33208892, year = {2020}, author = {Pelikan, C and Wasmund, K and Glombitza, C and Hausmann, B and Herbold, CW and Flieder, M and Loy, A}, title = {Anaerobic bacterial degradation of protein and lipid macromolecules in subarctic marine sediment.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-020-00817-6}, pmid = {33208892}, issn = {1751-7370}, support = {P29426//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; P25111-B22//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; }, abstract = {Microorganisms in marine sediments play major roles in marine biogeochemical cycles by mineralizing substantial quantities of organic matter from decaying cells. Proteins and lipids are abundant components of necromass, yet the taxonomic identities of microorganisms that actively degrade them remain poorly resolved. Here, we revealed identities, trophic interactions, and genomic features of bacteria that degraded 13C-labeled proteins and lipids in cold anoxic microcosms containing sulfidic subarctic marine sediment. Supplemented proteins and lipids were rapidly fermented to various volatile fatty acids within 5 days. DNA-stable isotope probing (SIP) suggested Psychrilyobacter atlanticus was an important primary degrader of proteins, and Psychromonas members were important primary degraders of both proteins and lipids. Closely related Psychromonas populations, as represented by distinct 16S rRNA gene variants, differentially utilized either proteins or lipids. DNA-SIP also showed 13C-labeling of various Deltaproteobacteria within 10 days, indicating trophic transfer of carbon to putative sulfate-reducers. Metagenome-assembled genomes revealed the primary hydrolyzers encoded secreted peptidases or lipases, and enzymes for catabolism of protein or lipid degradation products. Psychromonas species are prevalent in diverse marine sediments, suggesting they are important players in organic carbon processing in situ. Together, this study provides new insights into the identities, functions, and genomes of bacteria that actively degrade abundant necromass macromolecules in the seafloor.}, }
@article {pmid33208748, year = {2020}, author = {Molinaro, A and Bel Lassen, P and Henricsson, M and Wu, H and Adriouch, S and Belda, E and Chakaroun, R and Nielsen, T and Bergh, PO and Rouault, C and André, S and Marquet, F and Andreelli, F and Salem, JE and Assmann, K and Bastard, JP and Forslund, S and Le Chatelier, E and Falony, G and Pons, N and Prifti, E and Quinquis, B and Roume, H and Vieira-Silva, S and Hansen, TH and Pedersen, HK and Lewinter, C and Sønderskov, NB and ,  and Køber, L and Vestergaard, H and Hansen, T and Zucker, JD and Galan, P and Dumas, ME and Raes, J and Oppert, JM and Letunic, I and Nielsen, J and Bork, P and Ehrlich, SD and Stumvoll, M and Pedersen, O and Aron-Wisnewsky, J and Clément, K and Bäckhed, F}, title = {Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {5881}, pmid = {33208748}, issn = {2041-1723}, support = {/DH_/Department of Health/United Kingdom ; }, mesh = {Adult ; Aged ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Cohort Studies ; Diabetes Mellitus, Type 2/blood/metabolism/*microbiology ; Female ; *Gastrointestinal Microbiome ; Histidine/metabolism ; Humans ; Imidazoles/*blood ; Male ; Middle Aged ; }, abstract = {Microbiota-host-diet interactions contribute to the development of metabolic diseases. Imidazole propionate is a novel microbially produced metabolite from histidine, which impairs glucose metabolism. Here, we show that subjects with prediabetes and diabetes in the MetaCardis cohort from three European countries have elevated serum imidazole propionate levels. Furthermore, imidazole propionate levels were increased in subjects with low bacterial gene richness and Bacteroides 2 enterotype, which have previously been associated with obesity. The Bacteroides 2 enterotype was also associated with increased abundance of the genes involved in imidazole propionate biosynthesis from dietary histidine. Since patients and controls did not differ in their histidine dietary intake, the elevated levels of imidazole propionate in type 2 diabetes likely reflects altered microbial metabolism of histidine, rather than histidine intake per se. Thus the microbiota may contribute to type 2 diabetes by generating imidazole propionate that can modulate host inflammation and metabolism.}, }
@article {pmid33207956, year = {2020}, author = {de Melo Pereira, GV and de Carvalho Neto, DP and Maske, BL and De Dea Lindner, J and Vale, AS and Favero, GR and Viesser, J and de Carvalho, JC and Góes-Neto, A and Soccol, CR}, title = {An updated review on bacterial community composition of traditional fermented milk products: what next-generation sequencing has revealed so far?.}, journal = {Critical reviews in food science and nutrition}, volume = {}, number = {}, pages = {1-20}, doi = {10.1080/10408398.2020.1848787}, pmid = {33207956}, issn = {1549-7852}, abstract = {The emergence of next-generation sequencing (NGS) technologies has revolutionized the way to investigate the microbial diversity in traditional fermentations. In the field of food microbial ecology, different NGS platforms have been used for community analysis, including 454 pyrosequencing from Roche, Illumina's instruments and Thermo Fisher's SOLiD/Ion Torrent sequencers. These recent platforms generate information about millions of rDNA amplicons in a single running, enabling accurate phylogenetic resolution of microbial taxa. This review provides a comprehensive overview of the application of NGS for microbiome analysis of traditional fermented milk products worldwide. Fermented milk products covered in this review include kefir, buttermilk, koumiss, dahi, kurut, airag, tarag, khoormog, lait caillé, and suero costeño. Lactobacillus-mainly represented by Lb. helveticus, Lb. kefiranofaciens, and Lb. delbrueckii-is the most important and frequent genus with 51 reported species. In general, dominant species detected by culturing were also identified by NGS. However, NGS studies have revealed a more complex bacterial diversity, with estimated 400-600 operational taxonomic units, comprising uncultivable microorganisms, sub-dominant populations, and late-growing species. This review explores the importance of these discoveries and address related topics on workflow, NGS platforms, and knowledge bioinformatics devoted to fermented milk products. The knowledge that has been gained is vital in improving the monitoring, manipulation, and safety of these traditional fermented foods.}, }
@article {pmid33205286, year = {2021}, author = {Fernandez-Gonzalez, N and Braz, GHR and Regueiro, L and Lema, JM and Carballa, M}, title = {Microbial invasions in sludge anaerobic digesters.}, journal = {Applied microbiology and biotechnology}, volume = {105}, number = {1}, pages = {21-33}, pmid = {33205286}, issn = {1432-0614}, support = {2014-CE224//Centre for Industrial Technological Development/ ; ED431C 2017/29//Secretaria Xeral de Investigación e Desenvolvemento, Xunta de Galicia/ ; AGRUP2017/01//Secretaria Xeral de Investigación e Desenvolvemento, Xunta de Galicia/ ; BEX-2160/2015-03//Ministério da Educação/ ; }, abstract = {Among processes that control microbial community assembly, microbial invasion has received little attention until recently, especially in the field of anaerobic digestion. However, knowledge of the principles regulating the taxonomic and functional stability of microbial communities is key to truly develop better predictive models and effective management strategies for the anaerobic digestion process. To date, available studies focus on microbial invasions in digesters feed with activated sludge from municipal wastewater treatment plants. Herein, this review summarizes the importance of invasions for anaerobic digestion management, the ecological theories about microbial invasions, the traits of activated sludge microorganisms entering the digesters, and the resident communities of anaerobic reactors that are relevant for invasions and the current knowledge about the success and impacts of invasions, and discusses the research needs on this topic. The initial data indicate that the impact of invasions is low and only a small percentage of the mostly aerobic microorganisms present in the activated sludge feed are able to become stablished in the anaerobic digesters. However, there are still numerous unknowns about microbial invasions in anaerobic digestion including the influence of anaerobic feedstocks or process perturbances that new approaches on microbial ecology could unveil. KEY POINTS: • Microbial invasions are key processes to develop better strategies for digesters management. • Knowledge on pathogen invasions can improve anaerobic digestion microbial safety. • To date, the number of successful invasions on anaerobic digesters from activated sludge organisms is low. • Feed organisms detected in digesters are mostly inactive residual populations. • Need to expand the range of invaders and operational scenarios studied.}, }
@article {pmid33204208, year = {2020}, author = {Naseer, A and Garrido-Benavent, I and Khan, J and Ballarà, J and Mahiques, R and Khalid, AN and Sher, H}, title = {Cortinarius pakistanicus and C. pseudotorvus: two new species in oak forests in the Pakistan Himalayas.}, journal = {MycoKeys}, volume = {74}, number = {}, pages = {91-108}, pmid = {33204208}, issn = {1314-4049}, abstract = {The genus of basidiomycetous fungi Cortinarius occurs worldwide, from subtropical to boreal latitudes. Although molecular systematics has triggered the study of these fungi in the Americas and Europe in the last two decades, there is still limited research on its diversity in large portions of the planet, such as the high mountain ranges of Asia. Several collections of Cortinarius were made during mycological field trips conducted between 2014 and 2018 in pure oak forests in the Pakistan Himalayas. An integrative framework combining morphological and phylogenetic data was employed for their study. As a result, the two species C. pakistanicus and C. pseudotorvus are here described as new to science. Detailed macro- and micro-morphological descriptions, including SEM images of spores, and a molecular phylogenetic reconstruction based on nrITS sequence data are provided and used to discriminate the new species from morphologically and phylogenetically close taxa. Whereas our phylogenetic tree inference gave unequivocal support for the inclusion of C. pseudotorvus within C. sect. Telamonia, the assignment of C. pakistanicus to any known sections remained elusive. These species likely establish ectomycorrhizal associations with trees in the genus Quercus, making this type of forest in the Pakistan Himalayas a promising focus for future research on the diversity of Cortinarius.}, }
@article {pmid33203691, year = {2020}, author = {Jordaan, K and Lappan, R and Dong, X and Aitkenhead, IJ and Bay, SK and Chiri, E and Wieler, N and Meredith, LK and Cowan, DA and Chown, SL and Greening, C}, title = {Hydrogen-Oxidizing Bacteria Are Abundant in Desert Soils and Strongly Stimulated by Hydration.}, journal = {mSystems}, volume = {5}, number = {6}, pages = {}, pmid = {33203691}, issn = {2379-5077}, abstract = {How the diverse bacterial communities inhabiting desert soils maintain energy and carbon needs is much debated. Traditionally, most bacteria are thought to persist by using organic carbon synthesized by photoautotrophs following transient hydration events. Recent studies focused on Antarctic desert soils have revealed, however, that some bacteria use atmospheric trace gases, such as hydrogen (H2), to conserve energy and fix carbon independently of photosynthesis. In this study, we investigated whether atmospheric H2 oxidation occurs in four nonpolar desert soils and compared this process to photosynthesis. To do so, we first profiled the distribution, expression, and activities of hydrogenases and photosystems in surface soils collected from the South Australian desert over a simulated hydration-desiccation cycle. Hydrogenase-encoding sequences were abundant in the metagenomes and metatranscriptomes and were detected in actinobacterial, acidobacterial, and cyanobacterial metagenome-assembled genomes. Native dry soil samples mediated H2 oxidation, but rates increased 950-fold following wetting. Oxygenic and anoxygenic phototrophs were also detected in the community but at lower abundances. Hydration significantly stimulated rates of photosynthetic carbon fixation and, to a lesser extent, dark carbon assimilation. Hydrogenase genes were also widespread in samples from three other climatically distinct deserts, the Namib, Gobi, and Mojave, and atmospheric H2 oxidation was also greatly stimulated by hydration at these sites. Together, these findings highlight that H2 is an important, hitherto-overlooked energy source supporting bacterial communities in desert soils. Contrary to our previous hypotheses, however, H2 oxidation occurs simultaneously rather than alternately with photosynthesis in such ecosystems and may even be mediated by some photoautotrophs.IMPORTANCE Desert ecosystems, spanning a third of the earth's surface, harbor remarkably diverse microbial life despite having a low potential for photosynthesis. In this work, we reveal that atmospheric hydrogen serves as a major previously overlooked energy source for a large proportion of desert bacteria. We show that both chemoheterotrophic and photoautotrophic bacteria have the potential to oxidize hydrogen across deserts sampled across four continents. Whereas hydrogen oxidation was slow in native dry deserts, it increased by three orders of magnitude together with photosynthesis following hydration. This study revealed that continual harvesting of atmospheric energy sources may be a major way that desert communities adapt to long periods of water and energy deprivation, with significant ecological and biogeochemical ramifications.}, }
@article {pmid33200135, year = {2020}, author = {Shaffer, JP and Marotz, C and Belda-Ferre, P and Martino, C and Wandro, S and Estaki, M and Salido, RA and Carpenter, CS and Zaramela, LS and Minich, JJ and Bryant, MB and Sanders, K and Fraraccio, S and Ackermann, G and Humphrey, G and Swafford, AD and Miller-Montgomery, S and Knight, R}, title = {A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {33200135}, abstract = {One goal among microbial ecology researchers is to capture the maximum amount of information from all organisms in a sample. The recent COVID-19 pandemic, caused by the RNA virus SARS-CoV-2, has highlighted a gap in traditional DNA-based protocols, including the high-throughput methods we previously established as field standards. To enable simultaneous SARS-CoV-2 and microbial community profiling, we compare the relative performance of two total nucleic acid extraction protocols and our previously benchmarked protocol. We included a diverse panel of environmental and host-associated sample types, including body sites commonly swabbed for COVID-19 testing. Here we present results comparing the cost, processing time, DNA and RNA yield, microbial community composition, limit of detection, and well-to-well contamination, between these protocols.}, }
@article {pmid33199799, year = {2020}, author = {Perona-Vico, E and Feliu-Paradeda, L and Puig, S and Bañeras, L}, title = {Bacteria coated cathodes as an in-situ hydrogen evolving platform for microbial electrosynthesis.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {19852}, pmid = {33199799}, issn = {2045-2322}, abstract = {Hydrogen is a key intermediate element in microbial electrosynthesis as a mediator of the reduction of carbon dioxide (CO2) into added value compounds. In the present work we aimed at studying the biological production of hydrogen in biocathodes operated at - 1.0 V vs. Ag/AgCl, using a highly comparable technology and CO2 as carbon feedstock. Ten bacterial strains were chosen from genera Rhodobacter, Rhodopseudomonas, Rhodocyclus, Desulfovibrio and Sporomusa, all described as hydrogen producing candidates. Monospecific biofilms were formed on carbon cloth cathodes and hydrogen evolution was constantly monitored using a microsensor. Eight over ten bacteria strains showed electroactivity and H2 production rates increased significantly (two to eightfold) compared to abiotic conditions for two of them (Desulfovibrio paquesii and Desulfovibrio desulfuricans). D. paquesii DSM 16681 exhibited the highest production rate (45.6 ± 18.8 µM min-1) compared to abiotic conditions (5.5 ± 0.6 µM min-1), although specific production rates (per 16S rRNA copy) were similar to those obtained for other strains. This study demonstrated that many microorganisms are suspected to participate in net hydrogen production but inherent differences among strains do occur, which are relevant for future developments of resilient biofilm coated cathodes as a stable hydrogen production platform in microbial electrosynthesis.}, }
@article {pmid33196853, year = {2020}, author = {Sánchez-Soto, MF and Cerqueda-García, D and Alcántara-Hernández, RJ and Falcón, LI and Pech, D and Árcega-Cabrera, F and Aguirre-Macedo, ML and García-Maldonado, JQ}, title = {Assessing the Diversity of Benthic Sulfate-Reducing Microorganisms in Northwestern Gulf of Mexico by Illumina Sequencing of dsrB Gene.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01631-5}, pmid = {33196853}, issn = {1432-184X}, support = {201441//Mexican National Council for Science and Technology - Mexican Ministry of Energy Hydrocarbon Fund/ ; 251622 - 2015//Consejo Nacional de Ciencia y Tecnología/ ; }, abstract = {This study investigates the community composition, structure, and abundance of sulfate-reducing microorganisms (SRM) in surficial sediments of the Northwestern Gulf of Mexico (NWGoM) along a bathymetric gradient. For these purposes, Illumina sequencing and quantitative PCR (qPCR) of the dissimilatory sulfite reductase gene beta subunit (dsrB gene) were performed. Bioinformatic analyses indicated that SRM community was predominantly composed by members of Proteobacteria and Firmicutes across all the samples. However, Actinobacteria, Thermodesulfobacteria, and Chlorobi were also detected. Phylogenetic analysis indicated that unassigned dsrB sequences were related to Deltaproteobacteria and Nitrospirota superclusters, Euryarchaeota, and to environmental clusters. PCoA ordination revealed that samples clustered in three different groups. PERMANOVA indicated that water depth, temperature, redox, and nickel and cadmium content were the main environmental drivers for the SRM communities in the studied sites. Alpha diversity and abundance of SRM were lower for deeper sites, suggesting decreasing sulfate reduction activity with respect to water depth. This study contributes with the understanding of distribution and composition of dsrAB-containing microorganisms involved in sulfur transformations that may contribute to the resilience and stability of the benthic microbial communities facing metal and hydrocarbon pollution in the NWGoM, a region of recent development for oil and gas drilling.}, }
@article {pmid33194800, year = {2020}, author = {Jaiswal, S and Kumar, M and Mandeep,  and Sunita,  and Singh, Y and Shukla, P}, title = {Systems Biology Approaches for Therapeutics Development Against COVID-19.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {560240}, pmid = {33194800}, issn = {2235-2988}, mesh = {Animals ; Antiviral Agents/pharmacology ; COVID-19/*drug therapy/immunology/virology ; COVID-19 Vaccines/administration &amp; dosage/genetics/immunology ; Humans ; SARS-CoV-2/drug effects/genetics/immunology/*physiology ; Systems Biology ; }, abstract = {Understanding the systems biology approaches for promoting the development of new therapeutic drugs is attaining importance nowadays. The threat of COVID-19 outbreak needs to be vanished for global welfare, and every section of research is focusing on it. There is an opportunity for finding new, quick, and accurate tools for developing treatment options, including the vaccine against COVID-19. The review at this moment covers various aspects of pathogenesis and host factors for exploring the virus target and developing suitable therapeutic solutions through systems biology tools. Furthermore, this review also covers the extensive details of multiomics tools i.e., transcriptomics, proteomics, genomics, lipidomics, immunomics, and in silico computational modeling aiming towards the study of host-virus interactions in search of therapeutic targets against the COVID-19.}, }
@article {pmid33193238, year = {2020}, author = {Abdelhamid, MK and Quijada, NM and Dzieciol, M and Hatfaludi, T and Bilic, I and Selberherr, E and Liebhart, D and Hess, C and Hess, M and Paudel, S}, title = {Co-infection of Chicken Layers With Histomonas meleagridis and Avian Pathogenic Escherichia coli Is Associated With Dysbiosis, Cecal Colonization and Translocation of the Bacteria From the Gut Lumen.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {586437}, pmid = {33193238}, issn = {1664-302X}, abstract = {Histomonosis in chickens often appears together with colibacillosis in the field. Thus, we have experimentally investigated consequences of the co-infection of birds with Histomonas meleagridis and avian pathogenic Escherichia coli (APEC) on the pathology, host microbiota and bacterial translocation from the gut. Commercial chicken layers were infected via oral and cloacal routes with lux-tagged APEC with or without H. meleagridis whereas negative controls were left uninfected. Except one bird, which died due to colibacillosis, no clinical signs were recorded in birds infected with bioluminescence lux gene tagged E. coli. In co-infected birds, depression and ruffled feathers were observed in 4 birds and average body weight gain significantly decreased. Typhlitis caused by H. meleagridis was present only in co-infected birds, which also had pronounced microscopic lesions in systemic organs such as liver, heart and spleen. The 16S rRNA gene amplicon sequencing showed that in co-infected birds, corresponding to the severity of cecal lesions, microbial species richness and diversity in caeca greatly decreased and the abundance of the Escherichia group, Helicobacter and Bacteroides was relatively higher with a reduction of commensals. Most of the shared Amplicon Sequencing Variants between cecum and blood in co-infected birds belonged to Pseudomonas, Staphylococcus, and members of Enterobacteriaceae while those assigned as Lactobacillus and members of Ruminococcaceae and Lachnospiraceae were found mainly in negative controls. In infected birds, E. coli in the cecal lumen penetrated into deeper layers, a phenomenon noticed with higher incidence in the dead and co-infected birds. Furthermore, numbers of lux-tagged E. coli in caeca were significantly higher at every sampling date in co-infected birds. Altogether, infection of layers with H. meleagridis and E. coli resulted in more severe pathological changes, dramatic shift in the cecal mucosa-associated microbiota, higher tissue colonization of pathogenic bacteria such as avian pathogenic E. coli in the gut and increased penetration of E. coli from the cecal lumen toward peritoneum. This study provides novel insights into the parasite-bacteria interaction in vivo highlighting the role of H. meleagridis to support E. coli in the pathogenesis of colibacillosis in chickens.}, }
@article {pmid33193131, year = {2020}, author = {Straub, D and Blackwell, N and Langarica-Fuentes, A and Peltzer, A and Nahnsen, S and Kleindienst, S}, title = {Interpretations of Environmental Microbial Community Studies Are Biased by the Selected 16S rRNA (Gene) Amplicon Sequencing Pipeline.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {550420}, pmid = {33193131}, issn = {1664-302X}, abstract = {One of the major methods to identify microbial community composition, to unravel microbial population dynamics, and to explore microbial diversity in environmental samples is high-throughput DNA- or RNA-based 16S rRNA (gene) amplicon sequencing in combination with bioinformatics analyses. However, focusing on environmental samples from contrasting habitats, it was not systematically evaluated (i) which analysis methods provide results that reflect reality most accurately, (ii) how the interpretations of microbial community studies are biased by different analysis methods and (iii) if the most optimal analysis workflow can be implemented in an easy-to-use pipeline. Here, we compared the performance of 16S rRNA (gene) amplicon sequencing analysis tools (i.e., Mothur, QIIME1, QIIME2, and MEGAN) using three mock datasets with known microbial community composition that differed in sequencing quality, species number and abundance distribution (i.e., even or uneven), and phylogenetic diversity (i.e., closely related or well-separated amplicon sequences). Our results showed that QIIME2 outcompeted all other investigated tools in sequence recovery (>10 times fewer false positives), taxonomic assignments (>22% better F-score) and diversity estimates (>5% better assessment), suggesting that this approach is able to reflect the in situ microbial community most accurately. Further analysis of 24 environmental datasets obtained from four contrasting terrestrial and freshwater sites revealed dramatic differences in the resulting microbial community composition for all pipelines at genus level. For instance, at the investigated river water sites Sphaerotilus was only reported when using QIIME1 (8% abundance) and Agitococcus with QIIME1 or QIIME2 (2 or 3% abundance, respectively), but both genera remained undetected when analyzed with Mothur or MEGAN. Since these abundant taxa probably have implications for important biogeochemical cycles (e.g., nitrate and sulfate reduction) at these sites, their detection and semi-quantitative enumeration is crucial for valid interpretations. A high-performance computing conformant workflow was constructed to allow FAIR (Findable, Accessible, Interoperable, and Re-usable) 16S rRNA (gene) amplicon sequence analysis starting from raw sequence files, using the most optimal methods identified in our study. Our presented workflow should be considered for future studies, thereby facilitating the analysis of high-throughput 16S rRNA (gene) sequencing data substantially, while maximizing reliability and confidence in microbial community data analysis.}, }
@article {pmid33193120, year = {2020}, author = {Rosen, GL and Hammrich, P}, title = {Teaching Microbiome Analysis: From Design to Computation Through Inquiry.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {528051}, pmid = {33193120}, issn = {1664-302X}, abstract = {In this article, we present our three-class course sequence to educate students about microbiome analysis and metagenomics through experiential learning by taking them from inquiry to analysis of the microbiome: Molecular Ecology Lab, Bioinformatics, and Computational Microbiome Analysis. Students developed hypotheses, designed lab experiments, sequenced the DNA from microbiomes, learned basic python/R scripting, became proficient in at least one microbiome analysis software, and were able to analyze data generated from the microbiome experiments. While over 150 students (graduate and undergraduate) were impacted by the development of the series of courses, our assessment was only on undergraduate learning, where 45 students enrolled in at least one of the three courses and 4 students took all three. Students gained skills in bioinformatics through the courses, and several positive comments were received through surveys and private correspondence. Through a summative assessment, general trends show that students became more proficient in comparative genomic techniques and had positive attitudes toward their abilities to bridge biology and bioinformatics. While most students took individual or 2 of the courses, we show that pre- and post-surveys of these individual classes still showed progress toward learning objectives. It is expected that students trained will enter the workforce with skills needed to innovate in the biotechnology, health, and environmental industries. Students are trained to maximize impact and tackle real world problems in biology and medicine with their learned knowledge of data science and machine learning. The course materials for the new microbiome analysis course are available on Github: https://github.com/EESI/Comp_Metagenomics_resources.}, }
@article {pmid33190166, year = {2020}, author = {Yi, X and Guo, J and Wang, M and Xue, C and Ju, M}, title = {Inter-trophic Interaction of Gut Microbiota in a Tripartite System.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01640-4}, pmid = {33190166}, issn = {1432-184X}, support = {3207047 and 31760156//National Natural Science Foundation of China/ ; }, abstract = {Gut microbiota can be transmitted either environmentally or socially and vertically at intraspecific level; however, whether gut microbiota interact along trophic levels has been largely overlooked. Here, we characterized the gut bacterial communities of weevil larvae of Curculio arakawai that infest acorns of Mongolian oak (Quercus mongolica) as well as acorn-eating mammals, Siberian chipmunk (Tamias sibiricus), to test whether consumption of seed-borne larvae remodels the gut bacterial communities of T. sibiricus. Ingestion of weevil larvae of C. arakawai significantly altered the gut bacterial communities of T. sibiricus. Consequently, T. sibiricus fed larvae of C. arakawai showed higher capability to counter the negative effects of tannins, in terms of body weight maintenance, acorn consumption, N content in feces, urine pH, and blood ALT activity. Our results may first show that seed-borne insects as hidden players have a potential to alter the gut microbiota of seed predators in the tripartite system.}, }
@article {pmid33189472, year = {2020}, author = {Miao, Y and Heintz, MB and Bell, CH and Johnson, NW and Polasko, AL and Favero, D and Mahendra, S}, title = {Profiling microbial community structures and functions in bioremediation strategies for treating 1,4-dioxane-contaminated groundwater.}, journal = {Journal of hazardous materials}, volume = {}, number = {}, pages = {124457}, doi = {10.1016/j.jhazmat.2020.124457}, pmid = {33189472}, issn = {1873-3336}, abstract = {Microbial community compositions and functional profiles were analyzed in microcosms established using aquifer materials from a former automobile factory site, where 1,4-dioxane was identified as the primary contaminant of concern. Propane or oxygen biostimulation resulted in limited 1,4-dioxane degradation, which was markedly enhanced with the addition of nutrients, resulting in abundant Mycobacterium and Methyloversatilis taxa and high expressions of propane monooxygenase gene, prmA. In bioaugmented treatments, Pseudonocardia dioxanivorans CB1190 or Rhodococcus ruber ENV425 strains dominated immediately after augmentation and degraded 1,4-dioxane rapidly which was consistent with increased representation of xenobiotic and lipid metabolism-related functions. Although the bioaugmented microbes decreased due to insufficient growth substrates and microbial competition, they did continue to degrade 1,4-dioxane, presumably by indigenous propanotrophic and heterotrophic bacteria, inducing similar community structures across bioaugmentation conditions. In various treatments, functional redundancy acted as buffer capacity to ensure a stable microbiome, drove the restoration of the structure and microbial functions to original levels, and induced the decoupling between basic metabolic functions and taxonomy. The results of this study provided valuable information for design and decision-making for ex-situ bioreactors and in-situ bioremediation applications. A metagenomics-based understanding of the treatment process will enable efficient and accurate adjustments when encountering unexpected issues in bioremediation.}, }
@article {pmid33188444, year = {2020}, author = {Xu, Z and Wu, C and Lv, Y and Meng, F and Ban, Y}, title = {Effects of Aeration on the Formation of Arbuscular Mycorrhiza under a Flooded State and Copper Oxide Nanoparticle Removal in Vertical Flow Constructed Wetlands.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01637-z}, pmid = {33188444}, issn = {1432-184X}, abstract = {In this study, six vertical flow constructed wetlands (VFCWs) planted with Phragmites australis were operated at different aeration times (4 h day-1 and 8 h day-1), aeration modes (continuous and intermittent), and arbuscular mycorrhizal fungi (AMF) inoculation treatments (inoculation with Rhizophagus intraradices and no inoculation) to explore the effects of different aeration strategies on the formation of arbuscular mycorrhiza under a flooded state in VFCWs. In addition, these VFCWs were further used to treat copper oxide nanoparticle (CuO-NP) wastewater to evaluate the correlations among aeration, colonization, growth, and CuO-NP removal. The highest AMF 28S copy number (1.99×105) and colonization in reed roots, with values of 67%, 21%, and 1% for frequency (F%), intensity (M%), and arbuscule abundance (A%), were observed in the treatment with intermittent aeration for 4 h day-1. Aeration significantly increased the dissolved oxygen (DO) concentration and AMF colonization in VFCWs, thereby promoting plant growth and the purification of the CuO-NPs. However, excessive and continuous aeration had little positive effect on AMF colonization. This study provides a theoretical basis for the application of AMF for improving pollutant removal performance in constructed wetlands.}, }
@article {pmid33188298, year = {2020}, author = {Sakoula, D and Koch, H and Frank, J and Jetten, MSM and van Kessel, MAHJ and Lücker, S}, title = {Enrichment and physiological characterization of a novel comammox Nitrospira indicates ammonium inhibition of complete nitrification.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-020-00827-4}, pmid = {33188298}, issn = {1751-7370}, support = {339880//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Excellent Science (H2020 Priority Excellent Science)/ ; VI.Veni.192.086//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; 024.002.002//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; }, abstract = {The recent discovery of bacteria within the genus Nitrospira capable of complete ammonia oxidation (comammox) demonstrated that the sequential oxidation of ammonia to nitrate via nitrite can also be performed within a single bacterial cell. Although comammox Nitrospira exhibit a wide distribution in natural and engineered ecosystems, information on their physiological properties is scarce due to the limited number of cultured representatives. Additionally, most available genomic information is derived from metagenomic sequencing and high-quality genomes of Nitrospira in general are limited. In this study, we obtained a high (90%) enrichment of a novel comammox species, tentatively named &quot;Candidatus Nitrospira kreftii&quot;, and performed a detailed genomic and physiological characterization. The complete genome of &quot;Ca. N. kreftii&quot; allowed reconstruction of its basic metabolic traits. Similar to Nitrospira inopinata, the enrichment culture exhibited a very high ammonia affinity (Km(app)_NH3 ≈ 0.040 ± 0.01 µM), but a higher nitrite affinity (Km(app)_NO2- = 12.5 ± 4.0 µM), indicating an adaptation to highly oligotrophic environments. Furthermore, we observed partial inhibition of ammonia oxidation at ammonium concentrations as low as 25 µM. This inhibition of &quot;Ca. N. kreftii&quot; indicates that differences in ammonium tolerance rather than affinity could potentially be a niche determining factor for different comammox Nitrospira.}, }
@article {pmid33187698, year = {2020}, author = {Zheng, Z and Li, L and Makhalanyane, TP and Xu, C and Li, K and Xue, K and Xu, C and Qian, R and Zhang, B and Du, J and Yu, H and Cui, X and Wang, Y and Hao, Y}, title = {The composition of antibiotic resistance genes is not affected by grazing but is determined by microorganisms in grassland soils.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {143205}, doi = {10.1016/j.scitotenv.2020.143205}, pmid = {33187698}, issn = {1879-1026}, abstract = {Grazing is expected to exert a substantial influence on antibiotic resistance genes (ARGs) in grassland ecosystems. However, the precise effects of grazing on the composition of ARGs in grassland soils remain unclear. This is especially the case for grassland soils subject to long-term grazing. Here, we investigated ARGs and bacterial community composition in soils subject to long-term historic grazing (13-39 years) and corresponding ungrazed samples. Using a combination of shotgun metagenomics, amplicon analyses and associated soil physicochemical data, we provide novel insights regarding the structure of ARGs in grassland soils. Interestingly, our analysis revealed that long-term historic grazing had no impacts on the composition of ARGs in grassland soils. An average of 378 ARGs, conferring resistance to 14 major categories of antibiotics (80%), were identified in both grazing and ungrazed sites. Actinobacteria, Proteobacteria and Acidobacteria were the most prevalent predicted hosts in these soils and were also shown to harbour genetic capacity for multiple-resistant ARGs. Our results suggested that positive effects of bacterial community composition on ARGs could potentially be controlled by affecting MGEs. Soil properties had direct effects on the composition of ARGs through affecting the frequency of horizontal gene transfer among bacteria. Twelve novel ARGs were found in S. grandis steppe grasslands, indicating that different vegetation types might induce shifts in soil ARGs. Collectively, these findings suggest that soil properties, plants and microorganisms play critical roles in shaping ARG patterns in grasslands. Together, these data establish a solid baseline for understanding environmental antibiotic resistance in grasslands.}, }
@article {pmid33184503, year = {2021}, author = {Murray, AE and Freudenstein, J and Gribaldo, S and Hatzenpichler, R and Hugenholtz, P and Kämpfer, P and Konstantinidis, KT and Lane, CE and Papke, RT and Parks, DH and Rossello-Mora, R and Stott, MB and Sutcliffe, IC and Thrash, JC and Venter, SN and Whitman, WB and Acinas, SG and Amann, RI and Anantharaman, K and Armengaud, J and Baker, BJ and Barco, RA and Bode, HB and Boyd, ES and Brady, CL and Carini, P and Chain, PSG and Colman, DR and DeAngelis, KM and de Los Rios, MA and Estrada-de Los Santos, P and Dunlap, CA and Eisen, JA and Emerson, D and Ettema, TJG and Eveillard, D and Girguis, PR and Hentschel, U and Hollibaugh, JT and Hug, LA and Inskeep, WP and Ivanova, EP and Klenk, HP and Li, WJ and Lloyd, KG and Löffler, FE and Makhalanyane, TP and Moser, DP and Nunoura, T and Palmer, M and Parro, V and Pedrós-Alió, C and Probst, AJ and Smits, THM and Steen, AD and Steenkamp, ET and Spang, A and Stewart, FJ and Tiedje, JM and Vandamme, P and Wagner, M and Wang, FP and Yarza, P and Hedlund, BP and Reysenbach, AL}, title = {Author Correction: Roadmap for naming uncultivated Archaea and Bacteria.}, journal = {Nature microbiology}, volume = {6}, number = {1}, pages = {136}, doi = {10.1038/s41564-020-00827-2}, pmid = {33184503}, issn = {2058-5276}, support = {DEB-1841658//National Science Foundation (NSF)/ ; }, }
@article {pmid33184155, year = {2020}, author = {Yadav, B and Johri, AK and Dua, M}, title = {Metagenomic Analysis of the Microbial Diversity in Solid Waste from Okhla Landfill, New Delhi, India.}, journal = {Microbiology resource announcements}, volume = {9}, number = {46}, pages = {}, pmid = {33184155}, issn = {2576-098X}, abstract = {The Okhla landfill site is consistently in the news for having pollution levels higher than the city average. Here, we report the taxonomic characterization of the microbial diversity of Okhla landfill solid waste. The metagenome analyses revealed the microbial and metabolic diversity of the site.}, }
@article {pmid33183698, year = {2021}, author = {Chow, LKM and Ghaly, TM and Gillings, MR}, title = {A survey of sub-inhibitory concentrations of antibiotics in the environment.}, journal = {Journal of environmental sciences (China)}, volume = {99}, number = {}, pages = {21-27}, doi = {10.1016/j.jes.2020.05.030}, pmid = {33183698}, issn = {1001-0742}, mesh = {*Anti-Bacterial Agents ; Bacteria ; *Environmental Pollutants ; Humans ; Surveys and Questionnaires ; }, abstract = {Antibiotics are poorly metabolized, and can enter the environment via human waste streams, agricultural run-off and pharmaceutical effluent. We consequently expect to see a concentration gradient of antibiotic compounds radiating from areas of human population. Such antibiotics should be thought of as pollutants, as they can accumulate, and have biological effects. These antibiotic pollutants can increase rates of mutation and lateral transfer events, and continue to exert selection pressure even at sub-inhibitory concentrations. Here, we conducted a literature survey on environmental concentrations of antibiotics. We collated 887 data points from 40 peer-reviewed papers. We then determined whether these concentrations were biologically relevant by comparing them to their minimum selective concentrations, usually defined as between 1/4 and 1/230 of the minimum inhibitory concentration. Environmental concentrations of antibiotics surveyed often fall into this range. In general, the antibiotic concentrations recorded in aquatic and sediment samples were similar. These findings indicate that environmental concentrations of antibiotics are likely to be influencing microbial ecology, and to be driving the selection of antibiotic resistant bacteria.}, }
@article {pmid33182220, year = {2021}, author = {Li, M and Mi, T and He, H and Chen, Y and Zhen, Y and Yu, Z}, title = {Active bacterial and archaeal communities in coastal sediments: Biogeography pattern, assembly process and co-occurrence relationship.}, journal = {The Science of the total environment}, volume = {750}, number = {}, pages = {142252}, doi = {10.1016/j.scitotenv.2020.142252}, pmid = {33182220}, issn = {1879-1026}, mesh = {*Archaea/genetics ; *Bacteria/genetics ; China ; Geologic Sediments ; Oceans and Seas ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The biogeography of active microbial communities and the underlying mechanisms in marine sediments are important in microbial ecology but remain unclear. Here, using qPCR and high-throughput sequencing, we investigated bacterial and archaeal community abundances and activities by quantifying the abundance and expression of the 16S rRNA gene respectively, RNA-derived bacterial and archaeal community biogeography, assembly mechanisms and co-occurrence relationships in surface sediment samples from the Bohai Sea (BS), South Yellow Sea (SYS) and the north East China Sea (NECS) of the eastern Chinese marginal seas. The results revealed a higher heterogeneity of bacterial and archaeal community activities than of abundances and heterogeneous ecological functions among areas reflected by community compositions. Furthermore, clear geographic groups (i.e., the BS, SYS and NECS groups) were observed for all, abundant and rare active bacterial and archaeal communities, accompanied by significant distance-decay patterns. However, the abundant and rare taxa showed inconsistent geographic patterns. More importantly, deterministic processes played a greater role than stochastic processes in active bacterial and archaeal community assembly. The rare taxa had weaker abilities to disperse and/or adapt and more complex ecological processes than the abundant taxa. In addition, this study also showed that intertaxa competition was the dominant interaction between active bacterial and archaeal members, which could greatly contribute to dispersal limitation. Moreover, active bacterial and archaeal co-occurrence patterns showed significant distance-decay patterns, which were consistent with the community compositions.}, }
@article {pmid33178725, year = {2020}, author = {Vadopalas, L and Ruzauskas, M and Lele, V and Starkute, V and Zavistanaviciute, P and Zokaityte, E and Bartkevics, V and Pugajeva, I and Reinolds, I and Badaras, S and Klupsaite, D and Mozuriene, E and Dauksiene, A and Gruzauskas, R and Bartkiene, E}, title = {Combination of Antimicrobial Starters for Feed Fermentation: Influence on Piglet Feces Microbiota and Health and Growth Performance, Including Mycotoxin Biotransformation in vivo.}, journal = {Frontiers in veterinary science}, volume = {7}, number = {}, pages = {528990}, pmid = {33178725}, issn = {2297-1769}, abstract = {The aim of this study was to apply a combination of the microbial starters Lactobacillus uvarum LUHS245, Lactobacillus casei LUHS210, Pediococcus acidilactici LUHS29, and Pediococcus pentosaceus LUHS183 for feed fermentation and to evaluate the influence of fermentation on feed acidity and microbiological characteristics, as well as on the piglet feces microbiota, health, and growth performance. Additionally, mycotoxin biotransformation was analyzed, including masked mycotoxins, in feed and piglet feces samples. The 36-day experiment was conducted using 25-day-old Large White/Norwegian Landrace (LW/NL) piglets with an initial body weight of 6.9-7.0 kg, which were randomly distributed into two groups (in each 100 piglets): control group, fed with basal diet (based on barley, wheat, potato protein, soybean protein concentrate, and whey powder), and treated group, fed with fermented feed at 500 g kg-1 of total feed. Compared to a commercially available lactic acid bacteria (LAB) combination, the novel LAB mixture effectively reduced feed pH (on average pH 3.65), produced a 2-fold higher content of L(+) lactic acid, increased viable LAB count [on average 8.8 log10 colony-forming units (CFU) g-1], and led to stable feed fermentation during the entire test period (36 days). Fecal microbiota analysis showed an increased number of probiotic bacteria in the treated group, particularly Lactobacillus, when compared with the control group at the end of experiment. This finding indicates that fermented feed can modify microbial profile change in the gut of pigs. In treated piglets' blood (at day 61), the serum high-density lipoprotein (HDL) cholesterol and triglycerides (TG) were significantly higher, but the levels of T4, glucose, K, alkaline phosphatase (AP), and urea were significantly decreased (p ≤ 0.05) compared with the control group. Mycotoxin analysis showed that alternariol monomethyl ether (AME) and altenuene were found in 61-day-old control piglets' feces and in fermented feed samples. However, AME was not found in treated piglets' feces. Feed fermentation with the novel LAB combination is a promising means to modulate piglets' microbiota, which is essential to improve nutrient absorption, growth performance, and health parameters. The new LAB composition suggests a novel dietary strategy to positively manipulate fermented feed chemicals and bio-safety and the piglet gut microbial ecology to reduce antimicrobials use in pig production and increase local feed stock uses and economical effectiveness of the process.}, }
@article {pmid33175111, year = {2020}, author = {Pascoal, F and Costa, R and Magalhães, C}, title = {The microbial rare biosphere: current concepts, methods and ecological principles.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaa227}, pmid = {33175111}, issn = {1574-6941}, abstract = {Our ability to describe the highly diverse pool of low abundance populations present in natural microbial communities is increasing at an unprecedented pace. Yet we currently lack an integrative view of the key taxa, functions, and metabolic activity which make-up this communal pool, usually referred to as the 'rare biosphere', across the domains of life. In this context, this review examines the microbial rare biosphere in its broader sense, providing an historical perspective on representative studies which enabled to bridge the concept from macroecology to microbial ecology. It then addresses our current knowledge of the prokaryotic rare biosphere, and covers emerging insights into the ecology, taxonomy, and evolution of low abundance microeukaryotic, viral and host-associated communities. We also review recent methodological advances and provide a synthetic overview on how the rare biosphere fits into different conceptual models used to explain microbial community assembly mechanisms, composition, and function.}, }
@article {pmid33173062, year = {2020}, author = {Zakem, EJ and Polz, MF and Follows, MJ}, title = {Redox-informed models of global biogeochemical cycles.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {5680}, pmid = {33173062}, issn = {2041-1723}, mesh = {Bacteria/metabolism ; *Computer Simulation ; Ecology ; Ecosystem ; *Global Warming ; *Greenhouse Effect ; Greenhouse Gases/metabolism ; Methane/metabolism ; Models, Theoretical ; Nitrous Oxide/metabolism ; *Oxidation-Reduction ; }, abstract = {Microbial activity mediates the fluxes of greenhouse gases. However, in the global models of the marine and terrestrial biospheres used for climate change projections, typically only photosynthetic microbial activity is resolved mechanistically. To move forward, we argue that global biogeochemical models need a theoretically grounded framework with which to constrain parameterizations of diverse microbial metabolisms. Here, we explain how the key redox chemistry underlying metabolisms provides a path towards this goal. Using this first-principles approach, the presence or absence of metabolic functional types emerges dynamically from ecological interactions, expanding model applicability to unobserved environments.&quot;Nothing is less real than realism. It is only by selection, by elimination, by emphasis, that we get at the real meaning of things.&quot; -Georgia O'Keefe.}, }
@article {pmid33171770, year = {2020}, author = {Rico-Reséndiz, F and Cervantes-Pérez, SA and Espinal-Centeno, A and Dipp-Álvarez, M and Oropeza-Aburto, A and Hurtado-Bautista, E and Cruz-Hernández, A and Bowman, JL and Ishizaki, K and Arteaga-Vázquez, MA and Herrera-Estrella, L and Cruz-Ramírez, A}, title = {Transcriptional and Morpho-Physiological Responses of Marchantia polymorpha upon Phosphate Starvation.}, journal = {International journal of molecular sciences}, volume = {21}, number = {21}, pages = {}, pmid = {33171770}, issn = {1422-0067}, support = {PhD scholarships (No. 629985), (No. 420770), (No. 487660).//CONACYT/ ; (19H03247)//JSPS KAKENHI grant/ ; 19941-44//UCMEXUS/ ; 158550 &amp; A1-S-38383//CONACYT Ciencia Básica/ ; NA150181//Royal Society Newton Advanced Fellowship/ ; }, abstract = {Phosphate (Pi) is a pivotal nutrient that constraints plant development and productivity in natural ecosystems. Land colonization by plants, more than 470 million years ago, evolved adaptive mechanisms to conquer Pi-scarce environments. However, little is known about the molecular basis underlying such adaptations at early branches of plant phylogeny. To shed light on how early divergent plants respond to Pi limitation, we analyzed the morpho-physiological and transcriptional dynamics of Marchantia polymorpha upon Pi starvation. Our phylogenomic analysis highlights some gene networks present since the Chlorophytes and others established in the Streptophytes (e.g., PHR1-SPX1 and STOP1-ALMT1, respectively). At the morpho-physiological level, the response is characterized by the induction of phosphatase activity, media acidification, accumulation of auronidins, reduction of internal Pi concentration, and developmental modifications of rhizoids. The transcriptional response involves the induction of MpPHR1, Pi transporters, lipid turnover enzymes, and MpMYB14, which is an essential transcription factor for auronidins biosynthesis. MpSTOP2 up-regulation correlates with expression changes in genes related to organic acid biosynthesis and transport, suggesting a preference for citrate exudation. An analysis of MpPHR1 binding sequences (P1BS) shows an enrichment of this cis regulatory element in differentially expressed genes. Our study unravels the strategies, at diverse levels of organization, exerted by M. polymorpha to cope with low Pi availability.}, }
@article {pmid33170351, year = {2020}, author = {Rose, A and Padovan, A and Christian, K and van de Kamp, J and Kaestli, M and Tsoukalis, S and Bodrossy, L and Gibb, K}, title = {The Diversity of Nitrogen-Cycling Microbial Genes in a Waste Stabilization Pond Reveals Changes over Space and Time that Is Uncoupled to Changing Nitrogen Chemistry.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01639-x}, pmid = {33170351}, issn = {1432-184X}, support = {Australian Postgraduate Awards Scheme (APA)//Australian Government/ ; D2012/55671//PowerWater Corporation/ ; R-04202//OCE Science Leader Fellowship/ ; Environmental Genomics grant (R-02412)//CSIRO Oceans and Atmosphere/ ; }, abstract = {Nitrogen removal is an important process for wastewater ponds prior to effluent release. Bacteria and archaea can drive nitrogen removal if they possess the genes required to metabolize nitrogen. In the tropical savanna of northern Australia, we identified the previously unresolved microbial communities responsible for nitrogen cycling in a multi-pond wastewater stabilization system by measuring genomic DNA and cDNA for the following: nifH (nitrogen fixation); nosZ (denitrification); hzsA (anammox); archaeal AamoA and bacterial BamoA (ammonia oxidation); nxrB (nitrite oxidation); and nrfA (dissimilatory NO3 reduction to NH3). By collecting 160 DNA and 40 cDNA wastewater samples and measuring nitrogen (N)-cycling genes using a functional gene array, we found that genes from all steps of the N cycle were present and, except for nxrB, were also expressed. As expected, N-cycling communities showed daily, seasonal, and yearly shifts. However, contrary to our prediction, probes from most functional groups, excluding nosZ and AamoA, were different between ponds. Further, different genes that perform the same N-cycling role sometimes had different trends over space and time, resulting in only weak correlations between the different functional communities. Although N-cycling communities were correlated with wastewater nitrogen levels and physico-chemistry, the relationship was not strong enough to reliably predict the presence or diversity of N-cycling microbes. The complex and dynamic response of these genes to other functional groups and the changing physico-chemical environment provides insight into why altering wastewater pond conditions can result an abundance of some gene variants while others are lost.}, }
@article {pmid33169932, year = {2020}, author = {Heyse, J and Props, R and Kongnuan, P and De Schryver, P and Rombaut, G and Defoirdt, T and Boon, N}, title = {Rearing water microbiomes in white leg shrimp (Litopenaeus vannamei) larviculture assemble stochastically and are influenced by the microbiomes of live feed products.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.15310}, pmid = {33169932}, issn = {1462-2920}, support = {20180033//European Asian aquaculture Technology and innovation Platform (EURASTiP)/ ; 20180045//European Asian aquaculture Technology and innovation Platform (EURASTiP)/ ; 1S80618N//Flemish Fund for Scientific research (FWO-Vlaanderen)/ ; }, abstract = {The development of effective management strategies to reduce the occurrence of diseases in aquaculture is hampered by the limited knowledge on the microbial ecology of these systems. In this study, the dynamics and dominant community assembly processes in the rearing water of Litopenaeus vannamei larviculture tanks were determined. Additionally, the contribution of peripheral microbiomes, such as those of live and dry feeds, to the rearing water microbiome were quantified. The community assembly in the hatchery rearing water over time was dominated by stochasticity, which explains the observed heterogeneity between replicate cultivations. The community undergoes two shifts that match with the dynamics of the algal abundances in the rearing water. Source tracking analysis revealed that 37% of all bacteria in the hatchery rearing water were introduced either by the live or dry feeds, or during water exchanges. The contribution of the microbiome from the algae was the largest, followed by that of the Artemia, the exchange water and the dry feeds. Our findings provide fundamental knowledge on the assembly processes and dynamics of rearing water microbiomes and illustrate the crucial role of these peripheral microbiomes in maintaining health-promoting rearing water microbiomes.}, }
@article {pmid33169034, year = {2020}, author = {Aksenov, AA and Laponogov, I and Zhang, Z and Doran, SLF and Belluomo, I and Veselkov, D and Bittremieux, W and Nothias, LF and Nothias-Esposito, M and Maloney, KN and Misra, BB and Melnik, AV and Smirnov, A and Du, X and Jones, KL and Dorrestein, K and Panitchpakdi, M and Ernst, M and van der Hooft, JJJ and Gonzalez, M and Carazzone, C and Amézquita, A and Callewaert, C and Morton, JT and Quinn, RA and Bouslimani, A and Orio, AA and Petras, D and Smania, AM and Couvillion, SP and Burnet, MC and Nicora, CD and Zink, E and Metz, TO and Artaev, V and Humston-Fulmer, E and Gregor, R and Meijler, MM and Mizrahi, I and Eyal, S and Anderson, B and Dutton, R and Lugan, R and Boulch, PL and Guitton, Y and Prevost, S and Poirier, A and Dervilly, G and Le Bizec, B and Fait, A and Persi, NS and Song, C and Gashu, K and Coras, R and Guma, M and Manasson, J and Scher, JU and Barupal, DK and Alseekh, S and Fernie, AR and Mirnezami, R and Vasiliou, V and Schmid, R and Borisov, RS and Kulikova, LN and Knight, R and Wang, M and Hanna, GB and Dorrestein, PC and Veselkov, K}, title = {Auto-deconvolution and molecular networking of gas chromatography-mass spectrometry data.}, journal = {Nature biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41587-020-0700-3}, pmid = {33169034}, issn = {1546-1696}, abstract = {We engineered a machine learning approach, MSHub, to enable auto-deconvolution of gas chromatography-mass spectrometry (GC-MS) data. We then designed workflows to enable the community to store, process, share, annotate, compare and perform molecular networking of GC-MS data within the Global Natural Product Social (GNPS) Molecular Networking analysis platform. MSHub/GNPS performs auto-deconvolution of compound fragmentation patterns via unsupervised non-negative matrix factorization and quantifies the reproducibility of fragmentation patterns across samples.}, }
@article {pmid33167488, year = {2020}, author = {Oba, PM and Holscher, HD and Mathai, RA and Kim, J and Swanson, KS}, title = {Diet Influences the Oral Microbiota of Infants during the First Six Months of Life.}, journal = {Nutrients}, volume = {12}, number = {11}, pages = {}, pmid = {33167488}, issn = {2072-6643}, support = {USDA Hatch #ILLU 538-937//U.S. Department of Agriculture/ ; }, abstract = {Background: Oral microorganisms contribute to oral health and disease, but few have studied how infant feeding methods affect their establishment. Methods: Infant (n = 12) feeding records and tongue and cheek swabs were collected within 48 h of birth, and after 2, 4, and 6 mo. DNA was extracted from samples, bacterial and fungal amplicons were generated and sequenced using Illumina MiSeq, and sequences were analyzed using Quantitative Insights Into Microbial Ecology (QIIME) and Statistical Analysis System (SAS) to evaluate differences over time and among breast-fed, formula-fed, mixed-fed, and solid food-fed infants. Results: Considering all time points, breast milk- and mixed-fed infants had lower oral species richness than solid food-fed infants (p = 0.006). Regardless of feeding mode, species richness was lower at birth than at other time points (p = 0.006). Principal coordinates analysis (PCoA) of unique fraction metric (UniFrac) distances indicated that bacterial communities were impacted by feeding method (p < 0.005). Considering all time points, breast-fed infants had higher Streptococcus, while formula-fed infants had higher Actinomyces and Prevotella. Regardless of feeding mode, Propionibacterium, Porphyromonas, Prevotella, Gemella, Granulicatella, Veillonella, Fusobacterium, Leptotrichia, Neisseria, and Haemophilus increased with age, while Cloacibacterium and Dechloromonas decreased with age. Oral fungi were detected in infants but were not impacted by diet. Conclusions: These findings demonstrate that the establishment of oral bacteria depends on dietary composition and age. More research is necessary to determine whether this affects risk of oral caries and other health outcomes later in life.}, }
@article {pmid33166536, year = {2020}, author = {Goraj, W and Pytlak, A and Kowalska, B and Kowalski, D and Grządziel, J and Szafranek-Nakonieczna, A and Gałązka, A and Stępniewska, Z and Stępniewski, W}, title = {Influence of pipe material on biofilm microbial communities found in drinking water supply system.}, journal = {Environmental research}, volume = {}, number = {}, pages = {110433}, doi = {10.1016/j.envres.2020.110433}, pmid = {33166536}, issn = {1096-0953}, abstract = {The biofilms and water samples from a model installation built of PVC-U, PE-HD and cast iron pipes were investigated using standard heterotrophic plate count and 16S rRNA Next Generation Sequencing. The results of the high throughput identification imply that the construction material strongly influences the microbiome composition. PVC-U and PE-HD pipes were dominated with Proteobacteria (54-60%) while the cast pipe was overgrown by Nitrospirae (64%). It was deduced that the plastic pipes create a more convenient environment for the potentially pathogenic taxa than the cast iron. The 7-year old biofilms were described as complex habitats with sharp oxidation-reduction gradients, where co-existence of methanogenic and methanotrophic microbiota takes place. Furthermore, it was found that the drinking water distribution systems (DWDS) are a useful tool for studying the ecology of rare bacterial phyla. New ecophysiological aspects were described for Aquihabitans, Thermogutta and Vampirovibrio. The discrepancy between identity of HPC-derived bacteria and NGS-revealed composition of biofilm and water microbiomes point to the need of introducing new diagnostical protocols to enable proper assessment of the drinking water safety, especially in DWDSs operating without disinfection.}, }
@article {pmid33166079, year = {2020}, author = {Nie, Y and Wu, XL}, title = {Getting back to the nature of the microbial world: from the description and inductive reasoning to deductive study after 'meta-omics'.}, journal = {Microbial biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1751-7915.13681}, pmid = {33166079}, issn = {1751-7915}, support = {2018YFA0902100//National Key R&amp;D Program of China/ ; 2018YFA0902103//National Key R&amp;D Program of China/ ; 31761133006//National Natural Science Foundation of China/ ; 31770120//National Natural Science Foundation of China/ ; 31770118//National Natural Science Foundation of China/ ; }, abstract = {'Omics' studies have by now deposited massive amounts of data into the databases, and it is now time to return to the question as to what can we actually learn from them. Increased application of the deductive approach in synthetic microbial ecology and synthetic microbiome research will undoubtedly provide exciting new opportunities for advancing our understanding of microbial ecology.}, }
@article {pmid33164669, year = {2020}, author = {Zhu, M and Ji, J and Duan, X and Shi, W and Li, Y}, title = {First Report of Powdery Mildew Caused by Blumeria graminis f. sp. bromi on Bromus catharticus in China.}, journal = {Plant disease}, volume = {}, number = {}, pages = {}, doi = {10.1094/PDIS-09-20-1983-PDN}, pmid = {33164669}, issn = {0191-2917}, abstract = {Bromus catharticus, rescuegrass, is a brome grass that has been cultivated for herbage production, and been widely naturalized in many provinces of China, including Henan province. During April and May 2020, powdery mildew was found on leaves of Br. catharticus on the campus of Henan Normal University, Xinxiang city (35.3°N; 113.9°E), Henan Province, China. Abundant white or grayish irregular or coalesced circular powdery colonies were scattered on the adaxial surface of leaves and 70% of the leaf areas were affected. Some of the infected leaves either were chlorotic or senescent. About 60% of the observed plants showed powdery mildew symptoms. Conidiophores (n = 25) were 32 to 45 μm × 7 to 15 μm and composed of foot cells and conidia (mostly 6 conidia) in chains. Conidia (n = 50) were 25 to 35 μm × 10 to 15 μm, on average 30 × 13 μm, with a length/width ratio of 2.3. Chasmothecia were not found. Based on these morphologic characteristics, the pathogen was initially identified as Blumeria graminis f. sp. bromi (Braun and Cook 2012; Troch et al. 2014). B. graminis mycelia and conidia were collected, and total genomic DNA was extracted (Zhu et al. 2019). The rDNA internal transcribed spacer (ITS) region was amplified with primer pairs ITS1/ITS4. The amplicon was cloned and sequenced. The sequence (574 bp) was deposited into GenBank under Accession No. MT892940. BLASTn analysis revealed that MT892940 was 100% identical to B. graminis f. sp. bromi on Br. catharticus (AB000935, 550 of 550 nucleotides) (Takamatsu et al. 1998). Phylogenetic analysis of MT892940 and ITS of other B. graminis ff. spp. clearly indicated least two phylogenetically distinct clades of B. graminis f. sp. bromi and that MT892940 clustered with the Takamatsu vouchers. Leaf surfaces of five healthy plants were fixed at the base of a settling tower and then inoculated by blowing conidia from diseased leaves using pressurized air. Five non-inoculated plants served as controls. The inoculated and non-inoculated plants were maintained separately in two growth chambers (humidity, 60%; light/dark, 16 h/8 h; temperature, 18℃). Thirteen- to fifteen-days after inoculation, B. graminis signs and symptoms were visible on inoculated leaves, whereas control plants remained asymptomatic. The pathogenicity assays were repeated twice with the same results. The observed signs and symptoms were morphologically identical to those of the originally infected leaves. Accordingly, the causal organism of the powdery mildew was confirmed as B. graminis f. sp. bromi by morphological characteristics and ITS sequence data. B. graminis has been reported on Br. catharticus in the United States (Klingeman et al. 2018), Japan (Inuma et al. 2007) and Argentina (Delhey et al. 2003). To our best knowledge, this is the first report of B. graminis on Br. catharticus in China. Since hybridization of B. graminis ff. spp. is a mechanism of adaptation to new hosts, Br. catharticus may serve as a primary inoculum reservoir of B. graminis to infect other species (Menardo et al. 2016). This report provides fundamental information for the powdery mildew that can be used to develop control management of the disease in Br. catharticus herbage production.}, }
@article {pmid33162209, year = {2021}, author = {Hou, D and Hong, M and Wang, K and Yan, H and Wang, Y and Dong, P and Li, D and Liu, K and Zhou, Z and Zhang, D}, title = {Prokaryotic community succession and assembly on different types of microplastics in a mariculture cage.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {268}, number = {Pt A}, pages = {115756}, doi = {10.1016/j.envpol.2020.115756}, pmid = {33162209}, issn = {1873-6424}, mesh = {China ; Microplastics ; *Plastics ; RNA, Ribosomal, 16S ; *Water Pollutants, Chemical/analysis ; }, abstract = {Microplastics have emerged as a new anthropogenic substrate that can readily be colonized by microorganisms. Nevertheless, microbial community succession and assembly among different microplastics in nearshore mariculture cages remains poorly understood. Using an in situ incubation experiment, 16S rRNA gene amplicon sequencing, and the neutral model, we investigated the prokaryotic communities attached to polyethylene terephthalate (PET), polyethylene (PE), and polypropylene (PP) in a mariculture cage in Xiangshan Harbor, China. The α-diversities and compositions of microplastic-attached prokaryotic communities were significantly distinct from free-living and small particle-attached communities in the surrounding water but relatively similar to the large particle-attached communities. Although a distinct prokaryotic community was developed on each type of microplastic, the communities on PE and PP more closely resembled each other. Furthermore, the prokaryotic community dissimilarity among all media (microplastics and water fractions) tended to decrease over time. Hydrocarbon-degrading bacteria Alcanivorax preferentially colonized PE, and the genus Vibrio with opportunistically pathogenic members has the potential to colonize PET. Additionally, neutral processes dominated the prokaryotic community assembly on PE and PP, while selection was more responsible for the prokaryotic assembly on PET. The assembly of Planctomycetaceae and Thaumarchaeota Marine Group I taxa on three microplastics were mainly governed by selection and neutral processes, respectively. Our study provides further understanding of microplastic-associated microbial ecology in mariculture environments.}, }
@article {pmid33161552, year = {2021}, author = {Navarrete, AA and de Cássia Bonassi, R and Américo-Pinheiro, JHP and Vazquez, GH and Mendes, LW and de Souza Loureiro, E and Kuramae, EE and Tsai, SM}, title = {Methods to Identify Soil Microbial Bioindicators of Sustainable Management of Bioenergy Crops.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2232}, number = {}, pages = {251-263}, doi = {10.1007/978-1-0716-1040-4_19}, pmid = {33161552}, issn = {1940-6029}, abstract = {Here we describe a suite of methods to identify potential taxonomic and functional soil microbial indicators of soil quality and plant health in biofuel crops in various areas and land types. This approach draws on tools to assess microbial diversity, greenhouse gas fluxes, and soil physicochemical properties in bioenergy cropping systems. Integrative statistical models are then used to identify potential microbial indicators for sustainable management of bioenergy crops.}, }
@article {pmid33161546, year = {2021}, author = {Yeoh, YK}, title = {Removing Host-derived DNA Sequences from Microbial Metagenomes via Mapping to Reference Genomes.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2232}, number = {}, pages = {147-153}, doi = {10.1007/978-1-0716-1040-4_13}, pmid = {33161546}, issn = {1940-6029}, abstract = {DNA sequencing has become a common tool in environmental microbial ecology, facilitating characterization of microbial populations as well as complex microbial communities by circumventing culture bottlenecks. However, certain samples especially from host-associated environments (rhizosphere, human tissue) or complex communities (soils) can contain a high degree of DNA sequences derived from hosts (plants, human) or other organisms of non-interest (arthropods, unicellular eukaryotes). This chapter presents a simple in silico method to remove contaminating sequences in metagenomes based on aligning sequences to reference genomes of the target organism.}, }
@article {pmid33161522, year = {2020}, author = {Rosa, LH and Pinto, OHB and Convey, P and Carvalho-Silva, M and Rosa, CA and Câmara, PEAS}, title = {DNA Metabarcoding to Assess the Diversity of Airborne Fungi Present over Keller Peninsula, King George Island, Antarctica.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01627-1}, pmid = {33161522}, issn = {1432-184X}, abstract = {We assessed fungal diversity present in air samples obtained from King George Island, Antarctica, using DNA metabarcoding through high-throughput sequencing. We detected 186 fungal amplicon sequence variants (ASVs) dominated by the phyla Ascomycota, Basidiomycota, Mortierellomycota, Mucoromycota, and Chytridiomycota. Fungi sp. 1, Agaricomycetes sp. 1, Mortierella parvispora, Mortierella sp. 2, Penicillium sp., Pseudogymnoascus roseus, Microdochium lycopodinum, Mortierella gamsii, Arrhenia sp., Cladosporium sp., Mortierella fimbricystis, Moniliella pollinis, Omphalina sp., Mortierella antarctica, and Pseudogymnoascus appendiculatus were the most dominant ASVs. In addition, several ASVs could only be identified at higher taxonomic levels and may represent previously unknown fungi and/or new records for Antarctica. The fungi detected in the air displayed high indices of diversity, richness, and dominance. The airborne fungal diversity included saprophytic, mutualistic, and plant and animal opportunistic pathogenic taxa. The diversity of taxa detected reinforces the hypothesis that the Antarctic airspora includes fungal propagules of both intra- and inter-continental origin. If regional Antarctic environmental conditions ameliorate further in concert with climate warming, these fungi might be able to reactivate and colonize different Antarctic ecosystems, with as yet unknown consequences for ecosystem function in Antarctica. Further aeromycological studies are necessary to understand how and from where these fungi arrive and move within Antarctica and if environmental changes will encourage the development of non-native fungal species in Antarctica.}, }
@article {pmid33161521, year = {2020}, author = {Tanuwidjaja, I and Vogel, C and Pronk, GJ and Schöler, A and Kublik, S and Vestergaard, G and Kögel-Knabner, I and Mrkonjic Fuka, M and Schloter, M and Schulz, S}, title = {Microbial Key Players Involved in P Turnover Differ in Artificial Soil Mixtures Depending on Clay Mineral Composition.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01635-1}, pmid = {33161521}, issn = {1432-184X}, support = {SCHL 446/4-2//Deutsche Forschungsgemeinschaft (DE)/ ; KO 1035/33-1//Deutsche Forschungsgemeinschaft/ ; KO 1035/33-2//Deutsche Forschungsgemeinschaft/ ; 031B0509 B//Bundesministerium für Bildung und Forschung/ ; }, abstract = {Nutrient turnover in soils is strongly driven by soil properties, including clay mineral composition. One main nutrient is phosphorus (P), which is known to be easily immobilized in soil. Therefore, the specific surface characteristics of clay minerals might substantially influence P availability in soil and thus the microbial strategies for accessing P pools. We used a metagenomic approach to analyze the microbial potential to access P after 842 days of incubation in artificial soils with a clay mineral composition of either non-expandable illite (IL) or expandable montmorillonite (MT), which differ in their surface characteristics like soil surface area and surface charge. Our data indicate that microorganisms of the two soils developed different strategies to overcome P depletion, resulting in similar total P concentrations. Genes predicted to encode inorganic pyrophosphatase (ppa), exopolyphosphatase (ppx), and the pstSCAB transport system were higher in MT, suggesting effective P uptake and the use of internal poly-P stores. Genes predicted to encode enzymes involved in organic P turnover like alkaline phosphatases (phoA, phoD) and glycerophosphoryl diester phosphodiesterase were detected in both soils in comparable numbers. In addition, Po concentrations did not differ significantly. Most identified genes were assigned to microbial lineages generally abundant in agricultural fields, but some were assigned to lineages known to include oligotrophic specialists, such as Bacillaceae and Microchaetaceae.}, }
@article {pmid33160238, year = {2021}, author = {Gao, Y and Zhang, W and Li, Y and Wu, H and Yang, N and Hui, C}, title = {Dams shift microbial community assembly and imprint nitrogen transformation along the Yangtze River.}, journal = {Water research}, volume = {189}, number = {}, pages = {116579}, doi = {10.1016/j.watres.2020.116579}, pmid = {33160238}, issn = {1879-2448}, abstract = {Dams are important for flood control, water storage, irrigation, electric generation, navigation, and have been regarded as the largest anthropogenic disturbance in aquatic ecosystems. However, how dams impact nitrogen transformation on a large watershed scale remained less studied. To explicitly address the impact of dams on nitrogen transformation, we used 16S rRNA gene sequencing to investigate the microbial dynamics and ecological processes under different dam conditions along the Yangtze River, as microbial communities are playing a key role in aquatic nitrogen transformation. Compared with landforms, dams exerted a more significant impact on the distribution patterns of microbial communities along the Yangtze River. The results showed that, by controlling suspended sand concentration, dams filtered keystone species, reshaped distribution of metacommunities, and mediated ecological assembly processes of microbial communities. Moreover, direct causal relationships between dams and nitrogen transformation were chained via microbial communities. To summarize, by combining knowledge in hydrology, microbial ecology, and biogeochemistry, this research exhibited the impact of different dams on the nitrogen transformation along a large river, and the key roles of suspended sand and microbial communities were emphasized. We anticipate a more precise modelling and prediction of nitrogen transformation in large watersheds, which may provide new perspectives for controlling the nitrogen in aquatic environments.}, }
@article {pmid33158898, year = {2020}, author = {Jiang, Y and Brandt, BW and Buijs, MJ and Cheng, L and Exterkate, RAM and Crielaard, W and Deng, DM}, title = {Manipulation of saliva-derived microcosm biofilms to resemble dysbiotic subgingival microbiota.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.02371-20}, pmid = {33158898}, issn = {1098-5336}, abstract = {Periodontitis is a highly prevalent oral inflammatory disease triggered by dysbiotic subgingival microbiota. For the development of microbiome modulators that can reverse the dysbiotic state and re-establish a health-related microbiota, a high-throughput in vitro multi-species biofilm model is needed. Our aim is to establish a model that resembles a dysbiotic subgingival microbial biofilm by incorporating the major periodontal pathogen Porphyromonas gingivalis into microcosm biofilms cultured from pooled saliva of healthy volunteers. The biofilms were grown for 3, 7, and 10 days and analyzed for their microbial composition by 16S rDNA amplicon sequencing as well as dipeptidyl peptidase IV (DPP4) activity and butyric acid production. The addition of P. gingivalis increased its abundance in saliva-derived microcosm biofilms from 2.7% on day 3 to >50% on day 10, which significantly reduced the Shannon diversity, but did not affect the total number of operational taxonomic units (OTUs). The P. gingivalis-enriched biofilms displayed altered microbial composition as revealed by principle component analysis and reduced interactions among microbial species. Moreover, these biofilms exhibited enhanced DPP4 activity and butyric acid production. In conclusion, by adding P. gingivalis into saliva-derived microcosm biofilms, we established an in vitro pathogen-enriched dysbiotic microbiota, which resembles periodontitis-associated subgingival microbiota in terms of increased P. gingivalis abundance and higher DPP4 activity and butyric acid production. This model may allow for investigating factors that accelerate or hinder microbial shift from symbiosis to dysbiosis and for developing microbiome modulation strategies.IMPORTANCE In line with the new paradigm of the etiology of periodontitis, an inflammatory disorder initiated by dysbiotic subgingival microbiota, novel therapeutic strategies have been proposed, targeting reversing dysbiosis and restoring host-compatible microbiota, rather than eliminating the biofilms unselectively. Thus, appropriate laboratory models are required to evaluate the efficacy of potential microbiome modulators. In the present study, we used the easily obtainable saliva as an inoculum, spiked the microcosm biofilms with the periodontal pathogen Porphyromonas gingivalis, and obtained a P. gingivalis-enriched microbiota, which resembles the in vivo pathogen-enriched subgingival microbiota in severe periodontitis. This biofilm model circumvents the difficulties encountered when using subgingival plaque as the inoculum and achieves microbiota in dysbiotic state in a controlled and reproducible manner, which is required for high-throughput and large scale evaluation of strategies that can potentially modulate microbial ecology.}, }
@article {pmid33158547, year = {2020}, author = {Rahman, MS and Sikder, MNA and Xu, H}, title = {Insights into β-diversity of periphytic protozoan fauna along the water column of marine ecosystems.}, journal = {Marine pollution bulletin}, volume = {}, number = {}, pages = {111801}, doi = {10.1016/j.marpolbul.2020.111801}, pmid = {33158547}, issn = {1879-3363}, abstract = {It has been increasingly recognized that there is high relevance in determining the β-diversity of communities along an environmental gradient for bioassessment of environmental quality status. To evaluate the vertical variations in β-diversity of periphytic protozoan fauna, in response to environmental heterogeneity in marine ecosystems, a baseline survey was conducted at the four water depths in the coastal waters of the Yellow Sea, northern China. Results demonstrated that (1) the species distribution presented different patterns at four water depths; (2) both compositional and community structure showed a significant vertical variation in multivariate dispersions from surface layer to the deeper layers; and (3) β-diversity measures generally increased from depths of 1 m to 5 m. These findings suggest that the homogeneity in the periphytic communities are of a high variability along the water column of marine ecosystems.}, }
@article {pmid33158546, year = {2020}, author = {Gui, Y and Uroosa,  and Bai, X and Wang, Z and Xu, G and Xu, H}, title = {An approach to assessing ecological quality status due to microalgae bloom using biofilm-dwelling protozoa based on biological trait analysis.}, journal = {Marine pollution bulletin}, volume = {161}, number = {Pt A}, pages = {111795}, doi = {10.1016/j.marpolbul.2020.111795}, pmid = {33158546}, issn = {1879-3363}, mesh = {Biofilms ; *Biological Products ; Environmental Monitoring ; *Microalgae ; Water Quality ; }, abstract = {Functional diversity/distinctness measure based trait has been proved to be a robust indicator to summarize the description of community structures and to assess water quality in different types of aquatic environment. In this study, for identifying the shielding effect of microalgae against protozoan grazing, a nine-day survey was conducted by exposing protozoan communities to a series of concentration gradients (100 (control), 104, 105, 106 and 107 cells ml-1) of two microalgae, respectively. Our results showed clear resistance of two test microalgae against protozoan grazing in five treatments. The functional distinctness measures commonly represented a decreasing trend along the gradient of concentrations of both microalgae. Ellipse tests based on the paired functional distinctness indices revealed that community functioning represented an uptrend departure from the expected pattern with the concentrations of both microalgae increase. Therefore, we suggest that the functional distinctness measures might be a reliable approach to detect the ecological effect of microalgae against protozoan grazing.}, }
@article {pmid33158141, year = {2020}, author = {Syrokou, MK and Themeli, C and Paramithiotis, S and Mataragas, M and Bosnea, L and Argyri, AA and Chorianopoulos, NG and Skandamis, PN and Drosinos, EH}, title = {Microbial Ecology of Greek Wheat Sourdoughs, Identified by a Culture-Dependent and a Culture-Independent Approach.}, journal = {Foods (Basel, Switzerland)}, volume = {9}, number = {11}, pages = {}, pmid = {33158141}, issn = {2304-8158}, support = {T1EDK-05339//European Union and Greek national funds/ ; }, abstract = {The aim of the present study was to assess the microecosystem of 13 homemade spontaneously fermented wheat sourdoughs from different regions of Greece, through the combined use of culture-dependent (classical approach; clustering by Random Amplified Polymorphic DNA-Polymerase Chain Reaction (RAPD-PCR) and identification by PCR species-specific for Lactiplantibacillus plantarum, and sequencing of the 16S-rRNA and 26S-rRNA gene, for Lactic Acid Bacteria (LAB) and yeasts, respectively) and independent approaches [DNA- and RNA-based PCR-Denaturing Gradient Gel Electrophoresis (DGGE)]. The pH and Total Titratable Acidity (TTA) values ranged from 3.64-5.05 and from 0.50-1.59% lactic acid, respectively. Yeast and lactic acid bacteria populations ranged within 4.60-6.32 and 6.28-9.20 log CFU/g, respectively. The yeast: LAB ratio varied from 1:23-1:10,000. A total of 207 bacterial and 195 yeast isolates were obtained and a culture-dependent assessment of their taxonomic affiliation revealed dominance of Lb. plantarum in three sourdoughs, Levilactobacillus brevis in four sourdoughs and co-dominance of these species in two sourdoughs. In addition, Companilactobacillusparalimentarius dominated in two sourdoughs and Fructilactobacillussanfranciscensis and Latilactobacillus sakei in one sourdough each. Lactococcus lactis, Lb. curvatus, Leuconostoc citreum, Ln. mesenteroides and Lb. zymae were also recovered from some samples. Regarding the yeast microbiota, it was dominated by Saccharomyces cerevisiae in 11 sourdoughs and Pichia membranifaciens and P. fermentans in one sourdough each. Wickerhamomyces anomalus and Kazachstania humilis were also recovered from one sample. RNA-based PCR-DGGE provided with nearly identical results with DNA-based one; in only one sample the latter provided an additional band. In general, the limitations of this approach, namely co-migration of amplicons from different species to the same electrophoretic position and multiband profile of specific isolates, greatly reduced resolution capacity, which resulted in only partial verification of the microbial ecology detected by culture-dependent approach in the majority of sourdough samples. Our knowledge regarding the microecosystem of spontaneously fermented Greek wheat-based sourdoughs was expanded, through the study of sourdoughs originating from regions of Greece that were not previously assessed.}, }
@article {pmid33157349, year = {2021}, author = {Kiewra, D and Szymanowski, M and Czułowska, A and Kolanek, A}, title = {The local-scale expansion of Dermacentor reticulatus ticks in Lower Silesia, SW Poland.}, journal = {Ticks and tick-borne diseases}, volume = {12}, number = {1}, pages = {101599}, doi = {10.1016/j.ttbdis.2020.101599}, pmid = {33157349}, issn = {1877-9603}, abstract = {The range of D. reticulatus is discontinuous in Europe, with a gap between the Western and Eastern European populations. Recent studies have shown, however, a decrease in the gap as a consequence of D. reticulatus spreading to new areas. This study aims to analyze the dynamic of local-scale changes in the D. reticulatus range in Lower Silesia, SW Poland. All sites of D. reticulatus presence recognized in our research were located in the north-western part of the study area (Wroclaw and its surroundings), whereas the south-eastern part was found to be free of these ticks. However, a five-year observation period (2014-2019) indicates the expansion of D. reticulatus on a local scale, with a general tendency to expand to the east, with northerly or southerly deviations from year to year. The settled sites differed in distance to the nearest built-up area, the density of resident population, as well as land development intensity in the immediate vicinity. The 100% probability isolines of D. reticulatus presence in Wroclaw and its surroundings allowed the determination of the rate of range change, which turned out to be uneven in terms of direction and speed. The average rate of change in the range of tick occurrence was estimated at 7 km in 3 years. A more accurate analysis of the estimated range changes-made using modeling and verification of predicted changes in the field-showed that the likely rate of range change can be estimated at around 0.6-2.3 km/year.}, }
@article {pmid33157023, year = {2020}, author = {Köstlbacher, S and Collingro, A and Halter, T and Domman, D and Horn, M}, title = {Coevolving Plasmids Drive Gene Flow and Genome Plasticity in Host-Associated Intracellular Bacteria.}, journal = {Current biology : CB}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cub.2020.10.030}, pmid = {33157023}, issn = {1879-0445}, abstract = {Plasmids are important in microbial evolution and adaptation to new environments. Yet, carrying a plasmid can be costly, and long-term association of plasmids with their hosts is poorly understood. Here, we provide evidence that the Chlamydiae, a phylum of strictly host-associated intracellular bacteria, have coevolved with their plasmids since their last common ancestor. Current chlamydial plasmids are amalgamations of at least one ancestral plasmid and a bacteriophage. We show that the majority of plasmid genes are also found on chromosomes of extant chlamydiae. The most conserved plasmid gene families are predominantly vertically inherited, while accessory plasmid gene families show significantly increased mobility. We reconstructed the evolutionary history of plasmid gene content of an entire bacterial phylum over a period of around one billion years. Frequent horizontal gene transfer and chromosomal integration events illustrate the pronounced impact of coevolution with these extrachromosomal elements on bacterial genome dynamics in host-dependent microbes.}, }
@article {pmid33156501, year = {2020}, author = {Trabelsi, ABH and Zaafouri, K and Friaa, A and Abidi, S and Naoui, S and Jamaaoui, F}, title = {Municipal sewage sludge energetic conversion as a tool for environmental sustainability: production of innovative biofuels and biochar.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, doi = {10.1007/s11356-020-11400-z}, pmid = {33156501}, issn = {1614-7499}, support = {Project : &quot;Thermo-chemical conversion of solid wastes into renewable biofuels and bio-products&quot;//Ministry of Higher Education and Scientific Research (MESRST) in Tunisia/ ; }, abstract = {In this study, municipal sewage sludge (MSS) is converted simultaneously into renewable biofuels (bio-oil, syngas) and high value-added products (biochar) using a fixed bed pyrolyzer. This work examines the combined effect of two factors: final pyrolysis temperature (°C) and MSS moisture content (%) on pyrogenic product yields and characteristics. A centered composite experimental design (CCD) is established for pyrolysis process optimization by adopting the response surface methodology (RSM). The statistical results indicate that the optimal conditions considering all studied factors and responses are 550 °C as final pyrolysis temperature and 15% as MSS moisture content. In these optimal conditions, biofuels yield is around 48 wt%, whereas biochar yield is about 52 wt%. The pyrolysis products characterizations reveal that (i) pyrolytic oil has a complex molecular composition rich with n-alkanes, n-alkenes, carboxylic acids, and aromatic compounds; (ii) bio-oil presents a high-energy content (high heating value HHV around 30.6 MJ/kg); (iii) syngas mixture has a good calorific value (HHV up to 8 MJ/kg), which could be used as renewable energy vector or for pyrolysis reactor heating; and (iv) biochar residue has good aliphatic and oxygenated group contents favoring its application as biofertilizer. These findings suggest that MSS conversion into biofuels and biochar is an appropriate approach for MSS treatment. MSS-to-energy could be proposed as an element for circular economy concept due to its effectiveness in producing high value-added and sustainable products and reducing environmental problems linked to MSS disposal.}, }
@article {pmid33156395, year = {2020}, author = {Addesso, R and Gonzalez-Pimentel, JL and D'Angeli, IM and De Waele, J and Saiz-Jimenez, C and Jurado, V and Miller, AZ and Cubero, B and Vigliotta, G and Baldantoni, D}, title = {Microbial Community Characterizing Vermiculations from Karst Caves and Its Role in Their Formation.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01623-5}, pmid = {33156395}, issn = {1432-184X}, support = {MINECO [CGL2016-75590-P]//European Regional Development Fund/ ; }, abstract = {The microbiota associated with vermiculations from karst caves is largely unknown. Vermiculations are enigmatic deposits forming worm-like patterns on cave walls all over the world. They represent a precious focus for geomicrobiological studies aimed at exploring both the microbial life of these ecosystems and the vermiculation genesis. This study comprises the first approach on the microbial communities thriving in Pertosa-Auletta Cave (southern Italy) vermiculations by next-generation sequencing. The most abundant phylum in vermiculations was Proteobacteria, followed by Acidobacteria > Actinobacteria > Nitrospirae > Firmicutes > Planctomycetes > Chloroflexi > Gemmatimonadetes > Bacteroidetes > Latescibacteria. Numerous less-represented taxonomic groups (< 1%), as well as unclassified ones, were also detected. From an ecological point of view, all the groups co-participate in the biogeochemical cycles in these underground environments, mediating oxidation-reduction reactions, promoting host rock dissolution and secondary mineral precipitation, and enriching the matrix in organic matter. Confocal laser scanning microscopy and field emission scanning electron microscopy brought evidence of a strong interaction between the biotic community and the abiotic matrix, supporting the role of microbial communities in the formation process of vermiculations.}, }
@article {pmid33155101, year = {2020}, author = {Torralba, MG and Aleti, G and Li, W and Moncera, KJ and Lin, YH and Yu, Y and Masternak, MM and Golusinski, W and Golusinski, P and Lamperska, K and Edlund, A and Freire, M and Nelson, KE}, title = {Oral Microbial Species and Virulence Factors Associated with Oral Squamous Cell Carcinoma.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01596-5}, pmid = {33155101}, issn = {1432-184X}, support = {R00 DE023584/DE/NIDCR NIH HHS/United States ; }, abstract = {The human microbiome has been the focus of numerous research efforts to elucidate the pathogenesis of human diseases including cancer. Oral cancer mortality is high when compared with other cancers, as diagnosis often occurs during late stages. Its prevalence has increased in the USA over the past decade and accounts for over 40,000 new cancer patients each year. Additionally, oral cancer pathogenesis is not fully understood and is likely multifactorial. To unravel the relationships that are associated with the oral microbiome and their virulence factors, we used 16S rDNA and metagenomic sequencing to characterize the microbial composition and functional content in oral squamous cell carcinoma (OSCC) tumor tissue, non-tumor tissue, and saliva from 18 OSCC patients. Results indicate a higher number of bacteria belonging to the Fusobacteria, Bacteroidetes, and Firmicutes phyla associated with tumor tissue when compared with all other sample types. Additionally, saliva metaproteomics revealed a significant increase of Prevotella in five OSCC subjects, while Corynebacterium was mostly associated with ten healthy subjects. Lastly, we determined that there are adhesion and virulence factors associated with Streptococcus gordonii as well as from known oral pathogens belonging to the Fusobacterium genera found mostly in OSCC tissues. From these results, we propose that not only will the methods utilized in this study drastically improve OSCC diagnostics, but the organisms and specific virulence factors from the phyla detected in tumor tissue may be excellent biomarkers for characterizing disease progression.}, }
@article {pmid33153747, year = {2020}, author = {Gu, Z and Liu, K and Pedersen, MW and Wang, F and Chen, Y and Zeng, C and Liu, Y}, title = {Community assembly processes underlying the temporal dynamics of glacial stream and lake bacterial communities.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {143178}, doi = {10.1016/j.scitotenv.2020.143178}, pmid = {33153747}, issn = {1879-1026}, abstract = {Community assembly processes are important in structuring aquatic microbial communities; however, the influence of these processes on the dynamics of bacterial communities in glacial streams and lakes remains largely unstudied. To investigate the assembly processes underlying the temporal variation of the bacterial community, we collected 50 water samples over five months in an ephemeral glacial stream and its downstream lake at the terminus of the Qiangyong glacier on the Tibetan Plateau. Using the V4 hypervariable region of the bacterial 16S rRNA gene combined with environmental measurements, such as water temperature, pH, total nitrogen (TN), dissolved organic carbon (DOC) and water conductivity, we found that temporal variation in the environmental factors promoted the shift in the proglacial stream and the lake bacterial communities. The quantification of ecological processes showed that the stream microbial communities were influenced by the ecological drift (40%) in June, then changed to homogeneous selection (40%) in July and variable selection (60%) in September, while the dynamic pattern of proglacial lake bacterioplankton was governed by homogeneous selection (≥ 50%) over the time. Overall, the dynamic of bacterial community in the proglacial stream and lake water is influenced by environmental factors, and the community composition assembly of the Qiangyong glacial stream and lake could be dynamic and primarily governed by deterministic processes.}, }
@article {pmid33151560, year = {2020}, author = {Yang, Q and Fu, S and Zou, P and Hao, J and Wei, D and Xie, G and Huang, J}, title = {Coordination of primary metabolism and virulence factors expression mediates the virulence of Vibrio parahaemolyticus towards cultured shrimp (Penaeus vannamei).}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jam.14922}, pmid = {33151560}, issn = {1365-2672}, support = {31702385//National Natural Science Foundation of China/ ; 81903372//National Natural Science Foundation of China/ ; QL202005//Youth Program of Education Department of Liaoning Province/ ; QNLM201706//Pilot National Laboratory for Marine Science and Technology (Qingdao)/ ; }, abstract = {AIMS: Acute hepatopancreatic necrosis disease (AHPND) caused by Vibrio parahaemolyticus has emerged as a severe bacterial disease of cultured shrimp. To identify the key virulence factors, two AHPND-causing V. parahaemolyticus (VpAHPND) strains (123 and 137) and two non-VpAHPND strains (HZ56 and ATCC 17082) were selected.<br><br>METHODS AND RESULTS: Challenge tests showed that the four strains exhibited different virulence towards shrimp with cumulative mortalities at 48 h postinfection (hpi) ranging from 10 to 92%. The expression of pirABVP in strain 123 and 137 was not significantly different. Genomic analysis revealed that the two VpAHPND strains contain a plasmid with the PirABVP toxins (pirABVP) flanked by the insertion sequence (ISVal1) that has been identified in various locations of chromosomes in VpAHPND strains. The two VpAHPND strains possessed almost identical virulence factors, while ISVal1 disrupted three genes related to flagellar motility in strain 137. Phenotype assay showed that strain 123 possessed the highest growth rate and swimming motility, followed by strain 137, suggesting that the disruption of essential genes mediated by ISVal1 significantly affected the virulence level. Transcriptome analysis of two VpAHPND strains (123 and 137) further suggested that virulence genes related to the capsule, flagella and primary metabolism were highly expressed in strain 123.<br><br>CONCLUSIONS: Here for the first time, it is demonstrated that the virulence of VpAHPND is not only determined by the expression of pirABVP , but also is mediated by ISVal1 which affects the genes involved in flagellar motility and primary metabolism.<br><br>The genomic and transcriptomic analysis of VpAHPND strains provides valuable information on the virulence factors affecting the pathogenicity of VpAHPND.}, }
@article {pmid33151140, year = {2020}, author = {Waite, DW and Chuvochina, M and Pelikan, C and Parks, DH and Yilmaz, P and Wagner, M and Loy, A and Naganuma, T and Nakai, R and Whitman, WB and Hahn, MW and Kuever, J and Hugenholtz, P}, title = {Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major functional capabilities.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {70}, number = {11}, pages = {5972-6016}, doi = {10.1099/ijsem.0.004213}, pmid = {33151140}, issn = {1466-5034}, abstract = {The class Deltaproteobacteria comprises an ecologically and metabolically diverse group of bacteria best known for dissimilatory sulphate reduction and predatory behaviour. Although this lineage is the fourth described class of the phylum Proteobacteria, it rarely affiliates with other proteobacterial classes and is frequently not recovered as a monophyletic unit in phylogenetic analyses. Indeed, one branch of the class Deltaproteobacteria encompassing Bdellovibrio-like predators was recently reclassified into a separate proteobacterial class, the Oligoflexia. Here we systematically explore the phylogeny of taxa currently assigned to these classes using 120 conserved single-copy marker genes as well as rRNA genes. The overwhelming majority of markers reject the inclusion of the classes Deltaproteobacteria and Oligoflexia in the phylum Proteobacteria. Instead, the great majority of currently recognized members of the class Deltaproteobacteria are better classified into four novel phylum-level lineages. We propose the names Desulfobacterota phyl. nov. and Myxococcota phyl. nov. for two of these phyla, based on the oldest validly published names in each lineage, and retain the placeholder name SAR324 for the third phylum pending formal description of type material. Members of the class Oligoflexia represent a separate phylum for which we propose the name Bdellovibrionota phyl. nov. based on priority in the literature and general recognition of the genus Bdellovibrio. Desulfobacterota phyl. nov. includes the taxa previously classified in the phylum Thermodesulfobacteria, and these reclassifications imply that the ability of sulphate reduction was vertically inherited in the Thermodesulfobacteria rather than laterally acquired as previously inferred. Our analysis also indicates the independent acquisition of predatory behaviour in the phyla Myxococcota and Bdellovibrionota, which is consistent with their distinct modes of action. This work represents a stable reclassification of one of the most taxonomically challenging areas of the bacterial tree and provides a robust framework for future ecological and systematic studies.}, }
@article {pmid33150937, year = {2020}, author = {Hopkins, JR and Semenova-Nelsen, T and Sikes, BA}, title = {Fungal community structure and seasonal trajectories respond similarly to fire across pyrophilic ecosystems.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {1}, pages = {}, doi = {10.1093/femsec/fiaa219}, pmid = {33150937}, issn = {1574-6941}, abstract = {Fire alters microbial community composition, and is expected to increase in frequency due to climate change. Testing whether microbes in different ecosystems will respond similarly to increased fire disturbance is difficult though, because fires are often unpredictable and hard to manage. Fire recurrent or pyrophilic ecosystems, however, may be useful models for testing the effects of frequent disturbance on microbes. We hypothesized that across pyrophilic ecosystems, fire would drive similar alterations to fungal communities, including altering seasonal community dynamics. We tested fire's effects on fungal communities in two pyrophilic ecosystems, a longleaf pine savanna and tallgrass prairie. Fire caused similar fungal community shifts, including (i) driving immediate changes that favored taxa able to survive fire and take advantage of post-fire environments and (ii) altering seasonal trajectories due to fire-associated changes to soil nutrient availability. This suggests that fire has predictable effects on fungal community structure and intra-annual community dynamics in pyrophilic ecosystems, and that these changes could significantly alter fungal function. Parallel fire responses in these key microbes may also suggest that recurrent fires drive convergent changes across ecosystems, including less fire-frequented systems that may start burning more often due to climate change.}, }
@article {pmid33150935, year = {2020}, author = {Landazuri, CFG and Gomez, JS and Raaijmakers, JM and Oyserman, BO}, title = {Restoring degraded microbiome function with self-assembled communities.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {12}, pages = {}, doi = {10.1093/femsec/fiaa225}, pmid = {33150935}, issn = {1574-6941}, abstract = {The natural microbial functions of many soils are severely degraded. Current state-of-the-art technology to restore these functions is through the isolation, screening, formulation and application of microbial inoculants and synthetic consortia. These approaches have inconsistent success, in part due to the incompatibility between the biofertilizer, crop, climate, existing soil microbiome and physicochemical characteristics of the soils. Here, we review the current state of the art in biofertilization and identify two key deficiencies in current strategies: the difficulty in designing complex multispecies biofertilizers and the bottleneck in scaling the production of complex multispecies biofertilizers. To address the challenge of producing scalable, multispecies biofertilizers, we propose to merge ecological theory with bioprocess engineering to produce 'self-assembled communities' enriched for particular functional guilds and adapted to a target soil and host plant. Using the nitrogen problem as an anchor, we review relevant ecology (microbial, plant and environmental), as well as reactor design strategies and operational parameters for the production of functionally enriched self-assembled communities. The use of self-assembled communities for biofertilization addresses two major hurdles in microbiome engineering: the importance of enriching microbes indigenous to (and targeted for) a specific environment and the recognized potential benefits of microbial consortia over isolates (e.g. functional redundancy). The proposed community enrichment model could also be instrumental for other microbial functions such as phosphorus solubilization, plant growth promotion or disease suppression.}, }
@article {pmid33150499, year = {2020}, author = {Rasmussen, AN and Damashek, J and Eloe-Fadrosh, EA and Francis, CA}, title = {In-depth Spatiotemporal Characterization of Planktonic Archaeal and Bacterial Communities in North and South San Francisco Bay.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01621-7}, pmid = {33150499}, issn = {1432-184X}, support = {OCE-0847266//Division of Ocean Sciences/ ; }, abstract = {Despite being the largest estuary on the west coast of North America, no in-depth survey of microbial communities in San Francisco Bay (SFB) waters currently exists. In this study, we analyze bacterioplankton and archaeoplankton communities at several taxonomic levels and spatial extents (i.e., North versus South Bay) to reveal patterns in alpha and beta diversity. We assess communities using high-throughput sequencing of the 16S rRNA gene in 177 water column samples collected along a 150-km transect over a 2-year monthly time-series. In North Bay, the microbial community is strongly structured by spatial salinity changes while in South Bay seasonal variations dominate community dynamics. Along the steep salinity gradient in North Bay, we find that operational taxonomic units (OTUs; 97% identity) have higher site specificity than at coarser taxonomic levels and turnover (&quot;species&quot; replacement) is high, revealing a distinct brackish community (in oligo-, meso-, and polyhaline samples) from fresh and marine end-members. At coarser taxonomic levels (e.g., phylum, class), taxa are broadly distributed across salinity zones (i.e., present/abundant in a large number of samples) and brackish communities appear to be a mix of fresh and marine communities. We also observe variations in brackish communities between samples with similar salinities, likely related to differences in water residence times between North and South Bay. Throughout SFB, suspended particulate matter is positively correlated with richness and influences changes in beta diversity. Within several abundant groups, including the SAR11 clade (comprising up to 30% of reads in a sample), OTUs appear to be specialized to a specific salinity range. Some other organisms also showed pronounced seasonal abundance, including Synechococcus, Ca. Actinomarina, and Nitrosopumilus-like OTUs. Overall, this study represents the first in-depth spatiotemporal survey of SFB microbial communities and provides insight into how planktonic microorganisms have specialized to different niches along the salinity gradient.}, }
@article {pmid33150498, year = {2020}, author = {Pino-Bodas, R and Stenroos, S}, title = {Global Biodiversity Patterns of the Photobionts Associated with the Genus Cladonia (Lecanorales, Ascomycota).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01633-3}, pmid = {33150498}, issn = {1432-184X}, support = {FLF program//Royal Botanical Gardens, Kew/ ; Juan de la Cierva-Incorporación 2015-23526//Ministerio de Ciencia, Innovación y Universidades/ ; }, abstract = {The diversity of lichen photobionts is not fully known. We studied here the diversity of the photobionts associated with Cladonia, a sub-cosmopolitan genus ecologically important, whose photobionts belong to the green algae genus Asterochloris. The genetic diversity of Asterochloris was screened by using the ITS rDNA and actin type I regions in 223 specimens and 135 species of Cladonia collected all over the world. These data, added to those available in GenBank, were compiled in a dataset of altogether 545 Asterochloris sequences occurring in 172 species of Cladonia. A high diversity of Asterochloris associated with Cladonia was found. The commonest photobiont lineages associated with this genus are A. glomerata, A. italiana, and A. mediterranea. Analyses of partitioned variation were carried out in order to elucidate the relative influence on the photobiont genetic variation of the following factors: mycobiont identity, geographic distribution, climate, and mycobiont phylogeny. The mycobiont identity and climate were found to be the main drivers for the genetic variation of Asterochloris. The geographical distribution of the different Asterochloris lineages was described. Some lineages showed a clear dominance in one or several climatic regions. In addition, the specificity and the selectivity were studied for 18 species of Cladonia. Potentially specialist and generalist species of Cladonia were identified. A correlation was found between the sexual reproduction frequency of the host and the frequency of certain Asterochloris OTUs. Some Asterochloris lineages co-occur with higher frequency than randomly expected in the Cladonia species.}, }
@article {pmid33149844, year = {2020}, author = {Skelly, E and Johnson, NW and Kapellas, K and Kroon, J and Lalloo, R and Weyrich, L}, title = {Response of Salivary Microbiota to Caries Preventive Treatment in Aboriginal and Torres Strait Islander Children.}, journal = {Journal of oral microbiology}, volume = {12}, number = {1}, pages = {1830623}, pmid = {33149844}, issn = {2000-2297}, abstract = {A once-annual caries preventive (Intervention) treatment was offered to Aboriginal and Torres Strait Islander schoolchildren-a population with disproportionately poorer oral health than non-Indigenous Australian children-in the Northern Peninsula Area (NPA) of Far North Queensland (FNQ), which significantly improved their oral health. Here, we examine the salivary microbiota of these children (mean age = 10 ± 2.96 years; n = 103), reconstructing the bacterial community composition with high-throughput sequencing of the V4 region of bacterial 16S rRNA gene. Microbial communities of children who received the Intervention had lower taxonomic diversity than those who did not receive treatment (Shannon, p < 0.05). Moreover, the Intervention resulted in further decreased microbial diversity in children with active carious lesions existing at the time of saliva collection. Microbial species associated with caries were detected; Lactobacillus salivarius, Lactobacillus reuteri, Lactobacillus gasseri, Prevotella multisaccharivorax, Parascardovia denticolens, and Mitsuokella HMT 131 were significantly increased (p < 0.05) in children with severe caries, especially in children who did not receive the Intervention. These insights into microbial associations and community differences prompt future considerations to the mechanisms behind caries-preventive therapy induced change; important for understanding the long-term implications of like treatment to improve oral health disparities within Australia. Trial registration: ANZCTR, ACTRN12615000693527. Registered 3 July 2015, https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=368750&amp;isReview=true.}, }
@article {pmid33149734, year = {2020}, author = {Pereira, LM and Messias, EA and Sorroche, BP and Oliveira, ADN and Arantes, LMRB and de Carvalho, AC and Tanaka-Azevedo, AM and Grego, KF and Carvalho, AL and Melendez, ME}, title = {In-depth transcriptome reveals the potential biotechnological application of Bothrops jararaca venom gland.}, journal = {The journal of venomous animals and toxins including tropical diseases}, volume = {26}, number = {}, pages = {e20190058}, pmid = {33149734}, issn = {1678-9199}, abstract = {Background: Lack of complete genomic data of Bothrops jararaca impedes molecular biology research focusing on biotechnological applications of venom gland components. Identification of full-length coding regions of genes is crucial for the correct molecular cloning design.<br><br>Methods: RNA was extracted from the venom gland of one adult female specimen of Bothrops jararaca. Deep sequencing of the mRNA library was performed using Illumina NextSeq 500 platform. De novo assembly of B. jararaca transcriptome was done using Trinity. Annotation was performed using Blast2GO. All predicted proteins after clustering step were blasted against non-redundant protein database of NCBI using BLASTP. Metabolic pathways present in the transcriptome were annotated using the KAAS-KEGG Automatic Annotation Server. Toxins were identified in the B. jararaca predicted proteome using BLASTP against all protein sequences obtained from Animal Toxin Annotation Project from Uniprot KB/Swiss-Pro database. Figures and data visualization were performed using ggplot2 package in R language environment.<br><br>Results: We described the in-depth transcriptome analysis of B. jararaca venom gland, in which 76,765 de novo assembled isoforms, 96,044 transcribed genes and 41,196 unique proteins were identified. The most abundant transcript was the zinc metalloproteinase-disintegrin-like jararhagin. Moreover, we identified 78 distinct functional classes of proteins, including toxins, inhibitors and tumor suppressors. Other venom proteins identified were the hemolytic lethal factors stonustoxin and verrucotoxin.<br><br>Conclusion: It is believed that the application of deep sequencing to the analysis of snake venom transcriptomes may represent invaluable insight on their biotechnological potential focusing on candidate molecules.}, }
@article {pmid33149208, year = {2020}, author = {Du, Q and Ren, B and He, J and Peng, X and Guo, Q and Zheng, L and Li, J and Dai, H and Chen, V and Zhang, L and Zhou, X and Xu, X}, title = {Candida albicans promotes tooth decay by inducing oral microbial dysbiosis.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-020-00823-8}, pmid = {33149208}, issn = {1751-7370}, support = {81771099//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81600858//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81870754//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Candida albicans has been detected in root carious lesions. The current study aimed to explore the action of this fungal species on the microbial ecology and the pathogenesis of root caries. Here, by analyzing C. albicans in supragingival dental plaque collected from root carious lesions and sound root surfaces of root-caries subjects as well as caries-free individuals, we observed significantly increased colonization of C. albicans in root carious lesions. Further in vitro and animal studies showed that C. albicans colonization increased the cariogenicity of oral biofilm by altering its microbial ecology, leading to a polymicrobial biofilm with enhanced acidogenicity, and consequently exacerbated tooth demineralization and carious lesion severity. More importantly, we demonstrated that the cariogenicity-promoting activity of C. albicans was dependent on PHR2. Deletion of PHR2 restored microbial equilibrium and led to a less cariogenic biofilm as demonstrated by in vitro artificial caries model or in vivo root-caries rat model. Our data indicate the critical role of C. albicans infection in the occurrence of root caries. PHR2 is the major factor that determines the ecological impact and caries-promoting activity of C. albicans in a mixed microbial consortium.}, }
@article {pmid33145650, year = {2020}, author = {Albornoz, FE and Orchard, S and Standish, RJ and Dickie, IA and Bending, GD and Hilton, S and Lardner, T and Foster, KJ and Gleeson, DB and Bougoure, J and Barbetti, MJ and You, MP and Ryan, MH}, title = {Evidence for Niche Differentiation in the Environmental Responses of Co-occurring Mucoromycotinian Fine Root Endophytes and Glomeromycotinian Arbuscular Mycorrhizal Fungi.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01628-0}, pmid = {33145650}, issn = {1432-184X}, support = {DP180103157//Australian Research Council (ARC) Discovery/ ; NE/S010270/1//Natural Environment Research Council/ ; FT140100103//ARC Future Fellowship/ ; ON-279//Australian Wool Innovation Ltd/ ; }, abstract = {Fine root endophytes (FRE) were traditionally considered a morphotype of arbuscular mycorrhizal fungi (AMF), but recent genetic studies demonstrate that FRE belong within the subphylum Mucoromycotina, rather than in the subphylum Glomeromycotina with the AMF. These findings prompt enquiry into the fundamental ecology of FRE and AMF. We sampled FRE and AMF in roots of Trifolium subterraneum from 58 sites across temperate southern Australia. We investigated the environmental drivers of composition, richness, and root colonization of FRE and AMF by using structural equation modelling and canonical correspondence analyses. Root colonization by FRE increased with increasing temperature and rainfall but decreased with increasing phosphorus (P). Root colonization by AMF increased with increasing soil organic carbon but decreased with increasing P. Richness of FRE decreased with increasing temperature and soil pH. Richness of AMF increased with increasing temperature and rainfall but decreased with increasing soil aluminium (Al) and pH. Aluminium, soil pH, and rainfall were, in decreasing order, the strongest drivers of community composition of FRE; they were also important drivers of community composition of AMF, along with temperature, in decreasing order: rainfall, Al, temperature, and soil pH. Thus, FRE and AMF showed the same responses to some (e.g. soil P, soil pH) and different responses to other (e.g. temperature) key environmental factors. Overall, our data are evidence for niche differentiation among these co-occurring mycorrhizal associates.}, }
@article {pmid33144313, year = {2020}, author = {Manus, MB and Kuthyar, S and Perroni-Marañón, AG and Núñez-de la Mora, A and Amato, KR}, title = {Infant Skin Bacterial Communities Vary by Skin Site and Infant Age across Populations in Mexico and the United States.}, journal = {mSystems}, volume = {5}, number = {6}, pages = {}, pmid = {33144313}, issn = {2379-5077}, abstract = {Daily practices put humans in close contact with the surrounding environment, and differences in these practices have an impact on human physiology, development, and health. There is mounting evidence that the microbiome represents an interface that mediates interactions between the human body and the environment. In particular, the skin microbiome serves as the primary interface with the external environment and aids in host immune function by contributing as the first line of defense against pathogens. Despite these important connections, we have only a basic understanding of how the skin microbiome is first established, or which environmental factors contribute to its development. To this end, this study compared the skin bacterial communities of infants (n = 47) living in four populations in Mexico and the United States that span the socioeconomic gradient, where we predicted that variation in physical and social environments would shape the infant skin microbiome. Results of 16S rRNA bacterial gene sequencing on 119 samples (armpit, hand, and forehead) showed that infant skin bacterial diversity and composition are shaped by population-level factors, including those related to socioeconomic status and household composition, and vary by skin site and infant age. Differences in infant-environment interactions, including with other people, appear to vary across the populations, likely influencing infant microbial exposures and, in turn, the composition of infant skin bacterial communities. These findings suggest that variation in microbial exposures stemming from the local environment in infancy can impact the establishment of the skin microbiome across body sites, with implications for developmental and health outcomes.IMPORTANCE This study contributes to the sparse literature on the infant skin microbiome in general, and the virtually nonexistent literature on the infant skin microbiome in a field setting. While microbiome research often addresses patterns at a national scale, this study addresses the influence of population-level factors, such as maternal socioeconomic status and contact with caregivers, on infant skin bacterial communities. This approach strengthens our understanding of how local variables influence the infant skin microbiome, and paves the way for additional studies to combine biological sample collection with questionnaires to adequately capture how specific behaviors dictate infant microbial exposures. Work in this realm has implications for infant care and health, as well as for investigating how the microbial communities of different body sites develop over time, with applications to specific health outcomes associated with the skin microbiome (e.g., immune system development or atopic dermatitis).}, }
@article {pmid33142974, year = {2020}, author = {Sánchez-Clemente, R and Guijo, MI and Nogales, J and Blasco, R}, title = {Carbon Source Influence on Extracellular pH Changes along Bacterial Cell-Growth.}, journal = {Genes}, volume = {11}, number = {11}, pages = {}, pmid = {33142974}, issn = {2073-4425}, support = {IB16062//Consejería de Educación y Empleo, Junta de Extremadura/ ; GR18031//European Regional Development Fund/ ; PID2019-108458RB-I00//European Commission/ ; }, abstract = {The effect of initial pH on bacterial cell-growth and its change over time was studied under aerobic heterotrophic conditions by using three bacterial strains: Escherichia coli ATCC 25922, Pseudomonas putida KT2440, and Pseudomonas pseudoalcaligenes CECT 5344. In Luria-Bertani (LB) media, pH evolved by converging to a certain value that is specific for each bacterium. By contrast, in the buffered Minimal Medium (MM), pH was generally more stable along the growth curve. In MM with glucose as carbon source, a slight acidification of the medium was observed for all strains. In the case of E. coli, a sudden drop in pH was observed during exponential cell growth that was later recovered at initial pH 7 or 8, but was irreversible below pH 6, thus arresting further cell-growth. When using other carbon sources in MM at a fixed initial pH, pH changes depended mainly on the carbon source itself. While glucose, glycerol, or octanoate slightly decreased extracellular pH, more oxidized carbon sources, such as citrate, 2-furoate, 2-oxoglutarate, and fumarate, ended up with the alkalinization of the medium. These observations are in accordance with pH change predictions using genome-scale metabolic models for the three strains, thus revealing the metabolic reasons behind pH change. Therefore, we conclude that the composition of the medium, specifically the carbon source, determines pH change during bacterial growth to a great extent and unravel the main molecular mechanism behind this phenotype. These findings pave the way for predicting pH changes in a given bacterial culture and may anticipate the interspecies interactions and fitness of bacteria in their environment.}, }
@article {pmid33142874, year = {2020}, author = {Van Herreweghen, F and Amberg, C and Marques, R and Callewaert, C}, title = {Biological and Chemical Processes that Lead to Textile Malodour Development.}, journal = {Microorganisms}, volume = {8}, number = {11}, pages = {}, pmid = {33142874}, issn = {2076-2607}, abstract = {The development of malodour on clothing is a well-known problem with social, economic and ecological consequences. Many people still think malodour is the result of a lack of hygiene, which causes social stigma and embarrassment. Clothing is washed more frequently due to odour formation or even discarded when permastink develops. The malodour formation process is impacted by many variables and processes throughout the textile lifecycle. The contact with the skin with consequent transfer of microorganisms, volatiles and odour precursors leads to the formation of a distinctive textile microbiome and volatilome. The washing and drying processes further shape the textile microbiome and impact malodour formation. These processes are impacted by interindividual differences and fabric type as well. This review describes the current knowledge on the volatilome and microbiome of the skin, textile and washing machine, the multiple factors that determine malodour formation on textiles and points out what information is still missing.}, }
@article {pmid33141643, year = {2020}, author = {Zhu, M and Ji, J and Shi, W and Li, Y}, title = {Occurrence of Powdery Mildew Caused by Blumeria graminis f. sp. poae on Poa pratensis in China.}, journal = {Plant disease}, volume = {}, number = {}, pages = {}, doi = {10.1094/PDIS-09-20-2051-PDN}, pmid = {33141643}, issn = {0191-2917}, abstract = {Poa pratensis, known as bluegrass, is a perennial grass and one of the best varieties with highly valued pasture and turf grass uses. It is widely grown on golf courses and used for lawns in squares and parks (Luo et al. 2020). During April and May 2020, powdery mildew-like signs and symptoms were observed on leaves of P. pratensis in Muye Park, Xinxiang city (35.3°N; 113.9°E), Henan Province, China. White or grayish powdery masses in spots- or coalesced lesions were abundant on the adaxial surfaces of leaves and covered up to 90 % of the leaf area. Some of the mildew-infested leaves appeared chlorotic or began senescence. Mildew-infested leaves were collected to microscopically observe the morphological characteristics of this pathogen. Conidiophores were composed of foot cells, followed by one or two cells, and conidia. The ellipsoid- shaped conidia (n = 50) were 25 - 36 × 10 - 15 μm (length × width), on average 30 × 13 μm, with a length/width ratio of 2.3. Foot-cells (n = 15) were 30 - 44 μm long and 7 - 15 μm wide. On leaf surfaces, germinated conidia produced a short primary germ tube and then a long secondary germ tube that finally differentiated into a hooked appressorium. Chasmothecia were not found. Based on these morphological characteristics, the pathogen was initially identified as B. graminis f. sp. poae, the known forma specialis (f. sp.) of B. graminis on P. pratensis (Braun and Cook 2012; Troch et al. 2014). Mycelia of the pathogen were scraped from infected leaves and total genomic DNA was isolated using the method described previously (Zhu et al. 2019). The rDNA internal transcribed spacer (ITS) region was amplified applying primer pairs ITS1/ITS4 (White et al. 1990). The amplicon was cloned and sequenced by Invitrogen (Shanghai, China). The obtained sequence for the pathogen was deposited into GenBank under Accession No. MT892956 and was 100 % identical (549/549 bp) to B. graminis on P. pratensis (AB273530) (Inuma et al. 2007). In addition, the phylogenetic analysis clearly showed that the identified fungus and B. graminis f. sp. poae were clustered in the same branch. To perform pathogenicity analysis, leaf surfaces of eight healthy plants were inoculated by dusting fungal conidia from diseased leaves. Eight non-inoculated plants served as a control. The non-inoculated and inoculated plants were separately maintained in two growth chambers (humidity, 60 %; light/dark, 16 h/8 h; temperature, 18 ℃). Twelve to fourteen days after inoculation, B. graminis signs were visible on inoculated leaves, while control plants remained healthy. The pathogenicity assays were repeated twice and showed same results. Therefore, based on the morphological characteristics and molecular analysis, the pathogen was identified and confirmed as B. graminis f. sp. poae. This pathogen has been reported on P. pratensis in Switzerland and Japan (Inuma et al. 2007). This is, to our best knowledge, the first disease note reporting B. graminis on P. pratensis in China. Because the hybridization of B. graminis formae speciales (ff. spp.). allow the pathogens to adapt to new hosts, P. pratensis may serve as a primary inoculum reservoir of B. graminis to threaten other species, including cereal crops (Klingeman et al. 2018; Menardo et al. 2016). In addition, powdery mildew may negatively affect the yield and quality of grasses. Our report expands the knowledge of B. graminis f. sp. poae and provides the fundamental information for future powdery mildew control.}, }
@article {pmid33140722, year = {2020}, author = {Sharma, K and Palatinszky, M and Nikolov, G and Berry, D and Shank, EA}, title = {Transparent soil microcosms for live-cell imaging and non-destructive stable isotope probing of soil microorganisms.}, journal = {eLife}, volume = {9}, number = {}, pages = {}, pmid = {33140722}, issn = {2050-084X}, support = {DE-SC0013887//Biological and Environmental Research/International ; DE-SC0019012//Biological and Environmental Research/International ; FunKeyGut 741623/ERC_/European Research Council/International ; }, abstract = {Microscale processes are critically important to soil ecology and biogeochemistry yet are difficult to study due to soil's opacity and complexity. To advance the study of soil processes, we constructed transparent soil microcosms that enable the visualization of microbes via fluorescence microscopy and the non-destructive measurement of microbial activity and carbon uptake in situ via Raman microspectroscopy. We assessed the polymer Nafion and the crystal cryolite as optically transparent soil substrates. We demonstrated that both substrates enable the growth, maintenance, and visualization of microbial cells in three dimensions over time, and are compatible with stable isotope probing using Raman. We applied this system to ascertain that after a dry-down/rewetting cycle, bacteria on and near dead fungal hyphae were more metabolically active than those far from hyphae. These data underscore the impact fungi have facilitating bacterial survival in fluctuating conditions and how these microcosms can yield insights into microscale microbial activities.}, }
@article {pmid33140283, year = {2020}, author = {Zhao, Y and Chen, J and Bai, B and Wang, Y and Zheng, J and Yu, Z and Deng, Q and Li, P}, title = {Pathogen determination from clinical abscess fluids using metagenomic next-generation sequencing.}, journal = {Folia microbiologica}, volume = {}, number = {}, pages = {}, doi = {10.1007/s12223-020-00829-x}, pmid = {33140283}, issn = {1874-9356}, support = {2020A1515010979//Natural Science Foundation of Guangdong Province/ ; JCYJ20170412143551332//Science, Technology and Innovation Commission of Shenzhen Municipality of key funds/ ; JCYJ20180302144721183//Science, Technology and Innovation Commission of Shenzhen Municipality of basic research funds/ ; JCYJ20180302144340004//Science, Technology and Innovation Commission of Shenzhen Municipality of basic research funds/ ; JCYJ20180302144345028//Science, Technology and Innovation Commission of Shenzhen Municipality of basic research funds/ ; JCYJ20180302144431923//Science, Technology and Innovation Commission of Shenzhen Municipality of basic research funds/ ; 2019001//Shenzhen Nanshan District Scientific Research Program of the People's Republic of China/ ; 2019004//Shenzhen Nanshan District Scientific Research Program of the People's Republic of China/ ; 2019005//Shenzhen Nanshan District Scientific Research Program of the People's Republic of China/ ; 2019027//Shenzhen Nanshan District Scientific Research Program of the People's Republic of China/ ; A2018163//provincial medical funds of Guangdong/ ; SZXK06162//Shenzhen Key Medical Discipline Construction Fund/ ; }, abstract = {Abscesses are often clinically manifested as local necrotic tissues in various organs or systems of the human body, which is commonly caused by microbial infection. Rapid and accurate identification of pathogens from clinical abscetic samples would greatly guide a clinician to make the precise choices of the antimicrobial treatment. Here, this study aimed to investigate the application of metagenomic next-generation sequencing (mNGS) in the microbial detection of clinical samples of abscess fluids from various organs or systems. Nine patients with abscess from various organs or systems were enrolled in this study. The pathogenic bacteria in abscess fluid were detected and compared by the conventional bacterial culture and mNGS respectively. The dominant pathogens of abscess fluids in 8 cases can be found directly from mNGS, dominating over 80% of the total reads abundance of the microbiome. Although the pathogens from 6 cases detected by mNGS were consistent with that from the conventional bacteria culture method, the fastidious obligate anaerobic bacteria in 2 cases additionally detected by mNGS were not found by the conventional culture method. Moreover, complex polymicrobial infection containing Parvimonas micra in one case negatively with conventional bacterial culture were demonstrated by the mNGS method. And the mNGS method can directly reflect the diversity of microbial ecology in the abscess fluids from the different parts of the human body. Conclusively, mNGS can be used as a supplemental method for the pathogen detection of clinically abscess fluids.}, }
@article {pmid33139872, year = {2020}, author = {Lecoeuvre, A and Ménez, B and Cannat, M and Chavagnac, V and Gérard, E}, title = {Microbial ecology of the newly discovered serpentinite-hosted Old City hydrothermal field (southwest Indian ridge).}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-020-00816-7}, pmid = {33139872}, issn = {1751-7370}, support = {ANR-14-CE01-0008-01//Agence Nationale de la Recherche (French National Research Agency)/ ; }, abstract = {Lost City (mid-Atlantic ridge) is a unique oceanic hydrothermal field where carbonate-brucite chimneys are colonized by a single phylotype of archaeal Methanosarcinales, as well as sulfur- and methane-metabolizing bacteria. So far, only one submarine analog of Lost City has been characterized, the Prony Bay hydrothermal field (New Caledonia), which nonetheless shows more microbiological similarities with ecosystems associated with continental ophiolites. This study presents the microbial ecology of the 'Lost City'-type Old City hydrothermal field, recently discovered along the southwest Indian ridge. Five carbonate-brucite chimneys were sampled and subjected to mineralogical and geochemical analyses, microimaging, as well as 16S rRNA-encoding gene and metagenomic sequencing. Dominant taxa and metabolisms vary between chimneys, in conjunction with the predicted redox state, while potential formate- and CO-metabolizing microorganisms as well as sulfur-metabolizing bacteria are always abundant. We hypothesize that the variable environmental conditions resulting from the slow and diffuse hydrothermal fluid discharge that currently characterizes Old City could lead to different microbial populations between chimneys that utilize CO and formate differently as carbon or electron sources. Old City discovery and this first description of its microbial ecology opens up attractive perspectives for understanding environmental factors shaping communities and metabolisms in oceanic serpentinite-hosted ecosystems.}, }
@article {pmid33138291, year = {2020}, author = {Lyu, Y and Debevere, S and Bourgeois, H and Ran, M and Broeckx, BJG and Vanhaecke, L and Wiele, TV and Hesta, M}, title = {Dose-Dependent Effects of Dietary Xylooligosaccharides Supplementation on Microbiota, Fermentation and Metabolism in Healthy Adult Cats.}, journal = {Molecules (Basel, Switzerland)}, volume = {25}, number = {21}, pages = {}, pmid = {33138291}, issn = {1420-3049}, abstract = {In order to investigate the effect and appropriate dose of prebiotics, this study evaluated the effect of two levels of xylooligosaccharides (XOS) in cats. Twenty-four healthy adult cats were divided into three groups: no-XOS control diet with 1% cellulose; low XOS supplementation (LXOS) with 0.04% XOS and 0.96% cellulose; and high XOS supplementation (HXOS) with 0.40% XOS and 0.60% cellulose. Both XOS groups increased blood 3-hydroxybutyryl carnitine levels and decreased hexadecanedioyl carnitine levels. Both XOS treatments displayed an increased bacterial abundance of Blautia, Clostridium XI, and Collinsella and a decreased abundance of Megasphaera and Bifidobacterium. LXOS groups increased fecal pH and bacterial abundance of Streptococcus and Lactobacillus, decreased blood glutaryl carnitine concentration, and Catenibacterium abundance. HXOS group showed a more distinct microbiome profile and higher species richness, and an increased bacterial abundance of Subdoligranulum, Ruminococcaceae genus (unassigned genus), Erysipelotrichaceae genus, and Lachnospiraceae. Correlations between bacterial abundances and blood and fecal parameters were also observed. In conclusion, XOS could benefit feline gut health by altering microbiota; its effects dependant on the dose. The higher-dose XOS increased bacterial populations that possibly promoted intestinal fermentation, while the lower dose altered populations of carbohydrate-metabolic microbiota and possibly modulated host metabolism. Low-dose prebiotics may become a trend in future studies.}, }
@article {pmid33134552, year = {2020}, author = {Latorre-Pérez, A and Pascual, J and Porcar, M and Vilanova, C}, title = {A lab in the field: applications of real-time, in situ metagenomic sequencing.}, journal = {Biology methods &amp; protocols}, volume = {5}, number = {1}, pages = {bpaa016}, pmid = {33134552}, issn = {2396-8923}, abstract = {High-throughput metagenomic sequencing is considered one of the main technologies fostering the development of microbial ecology. Widely used second-generation sequencers have enabled the analysis of extremely diverse microbial communities, the discovery of novel gene functions, and the comprehension of the metabolic interconnections established among microbial consortia. However, the high cost of the sequencers and the complexity of library preparation and sequencing protocols still hamper the application of metagenomic sequencing in a vast range of real-life applications. In this context, the emergence of portable, third-generation sequencers is becoming a popular alternative for the rapid analysis of microbial communities in particular scenarios, due to their low cost, simplicity of operation, and rapid yield of results. This review discusses the main applications of real-time, in situ metagenomic sequencing developed to date, highlighting the relevance of this technology in current challenges (such as the management of global pathogen outbreaks) and in the next future of industry and clinical diagnosis.}, }
@article {pmid33133427, year = {2020}, author = {Harvey, HJ and Wildman, RD and Mooney, SJ and Avery, SV}, title = {Challenges and approaches in assessing the interplay between microorganisms and their physical micro-environments.}, journal = {Computational and structural biotechnology journal}, volume = {18}, number = {}, pages = {2860-2866}, pmid = {33133427}, issn = {2001-0370}, abstract = {Spatial structure over scales ranging from nanometres to centimetres (and beyond) varies markedly in diverse habitats and the industry-relevant settings that support microbial activity. Developing an understanding of the interplay between a structured environment and the associated microbial processes and ecology is fundamental, but challenging. Several novel approaches have recently been developed and implemented to help address key questions for the field: from the use of imaging tools such as X-ray Computed Tomography to explore microbial growth in soils, to the fabrication of scratched materials to examine microbial-surface interactions, to the design of microfluidic devices to track microbial biofilm formation and the metabolic processes therein. This review discusses new approaches and challenges for incorporating structured elements into the study of microbial processes across different scales. We highlight how such methods can be pivotal for furthering our understanding of microbial interactions with their environments.}, }
@article {pmid33133035, year = {2020}, author = {Colby, GA and Ruuskanen, MO and St Pierre, KA and St Louis, VL and Poulain, AJ and Aris-Brosou, S}, title = {Warming Climate Is Reducing the Diversity of Dominant Microbes in the Largest High Arctic Lake.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {561194}, pmid = {33133035}, issn = {1664-302X}, abstract = {Temperatures in the Arctic are expected to increase dramatically over the next century, and transform high latitude watersheds. However, little is known about how microbial communities and their underlying metabolic processes will be affected by these environmental changes in freshwater sedimentary systems. To address this knowledge gap, we analyzed sediments from Lake Hazen, NU Canada. Here, we exploit the spatial heterogeneity created by varying runoff regimes across the watershed of this uniquely large high-latitude lake to test how a transition from low to high runoff, used as one proxy for climate change, affects the community structure and functional potential of dominant microbes. Based on metagenomic analyses of lake sediments along these spatial gradients, we show that increasing runoff leads to a decrease in taxonomic and functional diversity of sediment microbes. Our findings are likely to apply to other, smaller, glacierized watersheds typical of polar or high latitude ecosystems; we can predict that such changes will have far reaching consequences on these ecosystems by affecting nutrient biogeochemical cycling, the direction and magnitude of which are yet to be determined.}, }
@article {pmid33131854, year = {2020}, author = {Durán, J and Rodríguez, A and Heiðmarsson, S and Lehmann, JRK and Del Moral, Á and Garrido-Benavent, I and De Los Ríos, A}, title = {Cryptogamic cover determines soil attributes and functioning in polar terrestrial ecosystems.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {143169}, doi = {10.1016/j.scitotenv.2020.143169}, pmid = {33131854}, issn = {1879-1026}, abstract = {We still lack studies that provide evidence for direct links between the development of soil surface cryptogamic communities and soil attributes and functioning. This is particularly true in areas free of potentially confounding factors such as different soil types, land uses, or anthropogenic disturbances. Despite the ecological importance of polar ecosystems and their sensitivity to climate change, we are far from understanding how their soils function and will respond to climate change-driven alterations in above- and belowground features. We used two complementary approaches (i.e. cover gradients in the forefront of retreating glaciers as well as long-time deglaciated areas with well-developed cryptogamic cover types) to evaluate the role of cryptogams driving multiple soil biotic and abiotic attributes and functioning rates in polar terrestrial ecosystems. Increases in cryptogamic cover were consistently related to increases in organic matter accumulation, soil fertility, and bacterial diversity, but also in enhanced soil functioning rates in both sampling areas. However, we also show that the ability to influence soil attributes varies among different polar cryptogamic covers, indicating that their differential ability to thrive under climate-change scenarios will largely determine the fate of polar soils in coming decades.}, }
@article {pmid33130421, year = {2020}, author = {Boulard, L and Parrhysius, P and Jacobs, B and Dierkes, G and Wick, A and Buchmeier, G and Koschorreck, J and Ternes, TA}, title = {Development of an analytical method to quantify pharmaceuticals in fish tissues by liquid chromatography-tandem mass spectrometry detection and application to environmental samples.}, journal = {Journal of chromatography. A}, volume = {1633}, number = {}, pages = {461612}, doi = {10.1016/j.chroma.2020.461612}, pmid = {33130421}, issn = {1873-3778}, mesh = {Animals ; *Chromatography, Liquid ; Drug Residues/*analysis ; Environmental Monitoring/*methods ; *Fishes/metabolism ; Food Analysis/*methods ; Limit of Detection ; Rivers/*chemistry ; Solid Phase Extraction ; *Tandem Mass Spectrometry ; Waste Water/analysis ; Water Pollutants, Chemical/analysis ; }, abstract = {A sensitive multiresidue method was developed to quantify 35 pharmaceuticals and 28 metabolites/transformation products (TPs) in fish liver, fish fillet and fish plasma via LC-MS/MS. The method was designed to cover a broad range of substance polarities. This objective was realized by using non-discriminating sample clean-ups including separation technique based on size exclusion, namely restricted access media (RAM) chromatography. This universal clean-up allows for an easy integration of further organic micropollutants into the analytical method. Limits of quantification (LOQ) ranged from 0.05 to 5.5 ng/mL in fish plasma, from 0.1 to 19 ng/g d.w. (dry weight) in fish fillet and from 0.46 to 48 ng/g d.w. in fish liver. The method was applied for the analysis of fillets and livers of breams from the rivers Rhine and Saar, the Teltow Canal as well as carps kept in fish monitoring ponds fed by effluent from municipal wastewater treatment plants. This allowed for the first detection of 17 analytes including 10 metabolites/TPs such as gabapentin lactam and norlidocaine in fish tissues. These results highlight the importance of including metabolites and transformation products of pharmaceuticals in fish monitoring campaigns and further investigating their potential effects.}, }
@article {pmid33129268, year = {2020}, author = {Djemiel, C and Dequiedt, S and Karimi, B and Cottin, A and Girier, T and El Djoudi, Y and Wincker, P and Lelièvre, M and Mondy, S and Chemidlin Prévost-Bouré, N and Maron, PA and Ranjard, L and Terrat, S}, title = {BIOCOM-PIPE: a new user-friendly metabarcoding pipeline for the characterization of microbial diversity from 16S, 18S and 23S rRNA gene amplicons.}, journal = {BMC bioinformatics}, volume = {21}, number = {1}, pages = {492}, pmid = {33129268}, issn = {1471-2105}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; *Biodiversity ; Cluster Analysis ; Computational Biology/*methods ; Computer Simulation ; *DNA Barcoding, Taxonomic ; Databases, Genetic ; Fungi/*genetics ; *Genes, rRNA ; Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; *Software ; Soil Microbiology ; }, abstract = {BACKGROUND: The ability to compare samples or studies easily using metabarcoding so as to better interpret microbial ecology results is an upcoming challenge. A growing number of metabarcoding pipelines are available, each with its own benefits and limitations. However, very few have been developed to offer the opportunity to characterize various microbial communities (e.g., archaea, bacteria, fungi, photosynthetic microeukaryotes) with the same tool.<br><br>RESULTS: BIOCOM-PIPE is a flexible and independent suite of tools for processing data from high-throughput sequencing technologies, Roche 454 and Illumina platforms, and focused on the diversity of archaeal, bacterial, fungal, and photosynthetic microeukaryote amplicons. Various original methods were implemented in BIOCOM-PIPE to (1) remove chimeras based on read abundance, (2) align sequences with structure-based alignments of RNA homologs using covariance models, and (3) a post-clustering tool (ReClustOR) to improve OTUs consistency based on a reference OTU database. The comparison with two other pipelines (FROGS and mothur) and Amplicon Sequence Variant definition highlighted that BIOCOM-PIPE was better at discriminating land use groups.<br><br>CONCLUSIONS: The BIOCOM-PIPE pipeline makes it possible to analyze 16S, 18S and 23S rRNA genes in the same packaged tool. The new post-clustering approach defines a biological database from previously analyzed samples and performs post-clustering of reads with this reference database by using open-reference clustering. This makes it easier to compare projects from various sequencing runs, and increased the congruence among results. For all users, the pipeline was developed to allow for adding or modifying the components, the databases and the bioinformatics tools easily, giving high modularity for each analysis.}, }
@article {pmid33125668, year = {2020}, author = {Kim, S and Park, MS and Song, J and Kang, I and Cho, JC}, title = {High-throughput cultivation based on dilution-to-extinction with catalase supplementation and a case study of cultivating acI bacteria from Lake Soyang.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {58}, number = {11}, pages = {893-905}, doi = {10.1007/s12275-020-0452-2}, pmid = {33125668}, issn = {1976-3794}, abstract = {Multi-omics approaches, including metagenomics and single-cell amplified genomics, have revolutionized our understanding of the hidden diversity and function of microbes in nature. Even in the omics age, cultivation is an essential discipline in microbial ecology since microbial cultures are necessary to assess the validity of an in silico prediction about the microbial metabolism and to isolate viruses infecting bacteria and archaea. However, the ecophysiological characteristics of predominant freshwater bacterial lineages remain largely unknown due to the scarcity of cultured representatives. In an ongoing effort to cultivate the uncultured majority of freshwater bacteria, the most abundant freshwater Actinobacteria acI clade has recently been cultivated from Lake Soyang through catalase-supplemented high-throughput cultivation based on dilution-to-extinction. This method involves physical isolation of target microbes from mixed populations, culture media simulating natural habitats, and removal of toxic compounds. In this protocol, we describe detailed procedures for isolating freshwater oligotrophic microbes, as well as the essence of the dilution-to-extinction culturing. As a case study employing the catalase-supplemented dilution-to-extinction protocol, we also report a cultivation trial using a water sample collected from Lake Soyang. Of the 480 cultivation wells inoculated with a single lake-water sample, 75 new acI strains belonging to 8 acI tribes (acI-A1, A2, A4, A5, A6, A7, B1, B4, C1, and C2) were cultivated, and each representative strain per subclade could be revived from glycerol stocks. These cultivation results demonstrate that the protocol described in this study is efficient in isolating freshwater bacterioplankton harboring streamlined genomes.}, }
@article {pmid33123759, year = {2020}, author = {Janiszewska, M and Sobkowiak, S and Stefańczyk, E and Śliwka, J}, title = {Population Structure of Phytophthora infestans from a Single Location in Poland Over a Long Period of Time in Context of Weather Conditions.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01630-6}, pmid = {33123759}, issn = {1432-184X}, support = {PW Task 3.1//Polish Ministry of Agriculture and Rural Development/ ; 1-3-00-1-02//Polish Ministry of Science and Higher Education/ ; MN 1-3-00-3-01//Polish Ministry of Science and Higher Education/ ; }, abstract = {Phytophthora infestans (Mont.) de Bary is a destructive potato pathogen. Changing weather conditions are among the factors that influence the pathogen population structure. In this study, 237 P. infestans isolates were collected from a single unprotected experimental field in an area with high late-blight pressure located in Boguchwała in the southeastern part of Poland during 15 growing seasons (2000-2014). The isolates were assessed for mating type, mitochondrial haplotype, resistance to metalaxyl, virulence, and polymorphism of 14 single-sequence repeat markers (SSRs). The results revealed 89 unique genotypes among the 237 P. infestans isolates. Eighty-seven isolates belonged to genotype 34_A1, which was detected in all the years of research except 2012. Isolates of P. infestans from individual years were very similar to each other, as shown by Nei's genetic identity based on 14 SSR markers. The obtained results on isolate characteristics were analyzed in terms of meteorological data (air temperature and precipitation) and indicated that frost, long winters, and hot, dry summers did not directly affect the P. infestans population structure. We described the variability in metalaxyl resistance and virulence among isolates of the P. infestans genotype 34_A1.}, }
@article {pmid33123758, year = {2020}, author = {Tzuri, N and Caspi-Fluger, A and Betelman, K and Rohkin Shalom, S and Chiel, E}, title = {Horizontal Transmission of Microbial Symbionts Within a Guild of Fly Parasitoids.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01618-2}, pmid = {33123758}, issn = {1432-184X}, support = {435/2018//Israel science Foundation/ ; }, abstract = {Many insects harbor facultative microbial symbionts which affect the ecology of their hosts in diverse ways. Most symbionts are transmitted vertically with high fidelity, whereas horizontal transmission occurs rarely. Parasitoid larvae feed on a single host and are in close physical contact with it, providing an ecological opportunity for symbionts' horizontal transmission, but there is little empirical evidence documenting this. Here we studied horizontal transmission of three bacterial symbionts-Rickettsia, Sodalis, and Wolbachia-between three fly pupal ectoparasitoid species: Spalangia cameroni, S. endius, and Muscidifurax raptor. Muscidifurax raptor readily parasitized and successfully developed on the Spalangia spp., while the inverse did not happen. The two Spalangia spp. attacked each other and conspecifics in very low rates. Symbiont horizontal transmissions followed by stable vertical transmission in the recipient species were achieved, in low percentages, only between conspecifics: Wolbachia from infected to uninfected M. raptor, Rickettsia in S. endius, and Sodalis in S. cameroni. Low frequency of horizontal transmissions occurred in the interspecific combinations, but none of them persisted in the recipient species beyond F4, at most. Our study is one of few to demonstrate symbionts' horizontal transmission between hosts within the same trophic level and guild and highlights the rarity of such events.}, }
@article {pmid33123113, year = {2020}, author = {Mitchell, K and Ronas, J and Dao, C and Freise, AC and Mangul, S and Shapiro, C and Moberg Parker, J}, title = {PUMAA: A Platform for Accessible Microbiome Analysis in the Undergraduate Classroom.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {584699}, pmid = {33123113}, issn = {1664-302X}, abstract = {Improvements in high-throughput sequencing makes targeted amplicon analysis an ideal method for the study of human and environmental microbiomes by undergraduates. Multiple bioinformatics programs are available to process and interpret raw microbial diversity datasets, and the choice of programs to use in curricula is largely determined by student learning goals. Many of the most commonly used microbiome bioinformatics platforms offer end-to-end data processing and data analysis using a command line interface (CLI), but the downside for novice microbiome researchers is the steep learning curve often required. Alternatively, some sequencing providers include processing of raw data and taxonomy assignments as part of their pipelines. This, when coupled with available web-based or graphical user interface (GUI) analysis and visualization tools, eliminates the need for students or instructors to have extensive CLI experience. However, lack of universal data formats can make integration of these tools challenging. For example, tools for upstream and downstream analyses frequently use multiple different data formats which then require writing custom scripts or hours of manual work to make the files compatible. Here, we describe a microbial ecology bioinformatics curriculum that focuses on data analysis, visualization, and statistical reasoning by taking advantage of existing web-based and GUI tools. We created the Program for Unifying Microbiome Analysis Applications (PUMAA), which solves the problem of inconsistent files by formatting the output files from several raw data processing programs to seamlessly transition to a suite of GUI programs for analysis and visualization of microbiome taxonomic and inferred functional profiles. Additionally, we created a series of tutorials to accompany each of the microbiome analysis curricular modules. From pre- and post-course surveys, students in this curriculum self-reported conceptual and confidence gains in bioinformatics and data analysis skills. Students also demonstrated gains in biologically relevant statistical reasoning based on rubric-guided evaluations of open-ended survey questions and the Statistical Reasoning in Biology Concept Inventory. The PUMAA program and associated analysis tutorials enable students and researchers with no computational experience to effectively analyze real microbiome datasets to investigate real-world research questions.}, }
@article {pmid33123105, year = {2020}, author = {Navarro, MOP and Dilarri, G and Simionato, AS and Grzegorczyk, K and Dealis, ML and Cano, BG and Barazetti, AR and Afonso, L and Chryssafidis, AL and Ferreira, H and Andrade, G}, title = {Corrigendum: Determining the Targets of Fluopsin C Action on Gram-Negative and Gram-Positive Bacteria.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {574002}, doi = {10.3389/fmicb.2020.574002}, pmid = {33123105}, issn = {1664-302X}, abstract = {[This corrects the article DOI: 10.3389/fmicb.2020.01076.].}, }
@article {pmid33117398, year = {2020}, author = {Pirr, S and Viemann, D}, title = {Host Factors of Favorable Intestinal Microbial Colonization.}, journal = {Frontiers in immunology}, volume = {11}, number = {}, pages = {584288}, pmid = {33117398}, issn = {1664-3224}, abstract = {Gut microbial colonization starts with birth and initiates a complex process between the host and the microbiota. Successful co-development of both establishes a symbiotic mutual relationship and functional homeostasis, while alterations thereof predispose the individual life-long to inflammatory and metabolic diseases. Multiple data have been provided how colonizing microbes induce a reprogramming and maturation of immunity by providing crucial instructing information to the newborn immune system. Less is known about what host factors have influence on the interplay between intestinal immunity and the composition of the gut microbial ecology. Here we review existing evidence regarding host factors that contribute to a favorable development of the gut microbiome and thereby successful maturation of gut mucosal immunity.}, }
@article {pmid33116344, year = {2020}, author = {Crous, PW and Wingfield, MJ and Chooi, YH and Gilchrist, CLM and Lacey, E and Pitt, JI and Roets, F and Swart, WJ and Cano-Lira, JF and Valenzuela-Lopez, N and Hubka, V and Shivas, RG and Stchigel, AM and Holdom, DG and Jurjević, Ž and Kachalkin, AV and Lebel, T and Lock, C and Martín, MP and Tan, YP and Tomashevskaya, MA and Vitelli, JS and Baseia, IG and Bhatt, VK and Brandrud, TE and De Souza, JT and Dima, B and Lacey, HJ and Lombard, L and Johnston, PR and Morte, A and Papp, V and Rodríguez, A and Rodríguez-Andrade, E and Semwal, KC and Tegart, L and Abad, ZG and Akulov, A and Alvarado, P and Alves, A and Andrade, JP and Arenas, F and Asenjo, C and Ballarà, J and Barrett, MD and Berná, LM and Berraf-Tebbal, A and Bianchinotti, MV and Bransgrove, K and Burgess, TI and Carmo, FS and Chávez, R and Čmoková, A and Dearnaley, JDW and de A Santiago, ALCM and Freitas-Neto, JF and Denman, S and Douglas, B and Dovana, F and Eichmeier, A and Esteve-Raventós, F and Farid, A and Fedosova, AG and Ferisin, G and Ferreira, RJ and Ferrer, A and Figueiredo, CN and Figueiredo, YF and Reinoso-Fuentealba, CG and Garrido-Benavent, I and Cañete-Gibas, CF and Gil-Durán, C and Glushakova, AM and Gonçalves, MFM and González, M and Gorczak, M and Gorton, C and Guard, FE and Guarnizo, AL and Guarro, J and Gutiérrez, M and Hamal, P and Hien, LT and Hocking, AD and Houbraken, J and Hunter, GC and Inácio, CA and Jourdan, M and Kapitonov, VI and Kelly, L and Khanh, TN and Kisło, K and Kiss, L and Kiyashko, A and Kolařík, M and Kruse, J and Kubátová, A and Kučera, V and Kučerová, I and Kušan, I and Lee, HB and Levicán, G and Lewis, A and Liem, NV and Liimatainen, K and Lim, HJ and Lyons, MN and Maciá-Vicente, JG and Magaña-Dueñas, V and Mahiques, R and Malysheva, EF and Marbach, PAS and Marinho, P and Matočec, N and McTaggart, AR and Mešić, A and Morin, L and Muñoz-Mohedano, JM and Navarro-Ródenas, A and Nicolli, CP and Oliveira, RL and Otsing, E and Ovrebo, CL and Pankratov, TA and Paños, A and Paz-Conde, A and Pérez-Sierra, A and Phosri, C and Pintos, Á and Pošta, A and Prencipe, S and Rubio, E and Saitta, A and Sales, LS and Sanhueza, L and Shuttleworth, LA and Smith, J and Smith, ME and Spadaro, D and Spetik, M and Sochor, M and Sochorová, Z and Sousa, JO and Suwannasai, N and Tedersoo, L and Thanh, HM and Thao, LD and Tkalčec, Z and Vaghefi, N and Venzhik, AS and Verbeken, A and Vizzini, A and Voyron, S and Wainhouse, M and Whalley, AJS and Wrzosek, M and Zapata, M and Zeil-Rolfe, I and Groenewald, JZ}, title = {Fungal Planet description sheets: 1042-1111.}, journal = {Persoonia}, volume = {44}, number = {}, pages = {301-459}, pmid = {33116344}, issn = {0031-5850}, abstract = {Novel species of fungi described in this study include those from various countries as follows: Antarctica, Cladosporium arenosum from marine sediment sand. Argentina, Kosmimatamyces alatophylus (incl. Kosmimatamyces gen. nov.) from soil. Australia, Aspergillus banksianus, Aspergillus kumbius, Aspergillus luteorubrus, Aspergillus malvicolor and Aspergillus nanangensis from soil, Erysiphe medicaginis from leaves of Medicago polymorpha, Hymenotorrendiella communis on leaf litter of Eucalyptus bicostata, Lactifluus albopicri and Lactifluus austropiperatus on soil, Macalpinomyces collinsiae on Eriachne benthamii, Marasmius vagus on soil, Microdochium dawsoniorum from leaves of Sporobolus natalensis, Neopestalotiopsis nebuloides from leaves of Sporobolus elongatus, Pestalotiopsis etonensis from leaves of Sporobolus jacquemontii, Phytophthora personensis from soil associated with dying Grevillea mccutcheonii.Brazil, Aspergillus oxumiae from soil, Calvatia baixaverdensis on soil, Geastrum calycicoriaceum on leaf litter, Greeneria kielmeyerae on leaf spots of Kielmeyera coriacea. Chile, Phytophthora aysenensis on collar rot and stem of Aristotelia chilensis.Croatia, Mollisia gibbospora on fallen branch of Fagus sylvatica.Czech Republic, Neosetophoma hnaniceana from Buxus sempervirens.Ecuador, Exophiala frigidotolerans from soil. Estonia, Elaphomyces bucholtzii in soil. France, Venturia paralias from leaves of Euphorbia paralias.India, Cortinarius balteatoindicus and Cortinarius ulkhagarhiensis on leaf litter. Indonesia, Hymenotorrendiella indonesiana on Eucalyptus urophylla leaf litter. Italy, Penicillium taurinense from indoor chestnut mill. Malaysia, Hemileucoglossum kelabitense on soil, Satchmopsis pini on dead needles of Pinus tecunumanii.Poland, Lecanicillium praecognitum on insects' frass. Portugal, Neodevriesia aestuarina from saline water. Republic of Korea, Gongronella namwonensis from freshwater. Russia, Candida pellucida from Exomias pellucidus, Heterocephalacria septentrionalis as endophyte from Cladonia rangiferina, Vishniacozyma phoenicis from dates fruit, Volvariella paludosa from swamp. Slovenia, Mallocybe crassivelata on soil. South Africa, Beltraniella podocarpi, Hamatocanthoscypha podocarpi, Coleophoma podocarpi and Nothoseiridium podocarpi (incl. Nothoseiridium gen. nov.) from leaves of Podocarpus latifolius, Gyrothrix encephalarti from leaves of Encephalartos sp., Paraphyton cutaneum from skin of human patient, Phacidiella alsophilae from leaves of Alsophila capensis, and Satchmopsis metrosideri on leaf litter of Metrosideros excelsa.Spain, Cladophialophora cabanerensis from soil, Cortinarius paezii on soil, Cylindrium magnoliae from leaves of Magnolia grandiflora, Trichophoma cylindrospora (incl. Trichophoma gen. nov.) from plant debris, Tuber alcaracense in calcareus soil, Tuber buendiae in calcareus soil. Thailand, Annulohypoxylon spougei on corticated wood, Poaceascoma filiforme from leaves of unknown Poaceae.UK, Dendrostoma luteum on branch lesions of Castanea sativa, Ypsilina buttingtonensis from heartwood of Quercus sp. Ukraine, Myrmecridium phragmiticola from leaves of Phragmites australis.USA, Absidia pararepens from air, Juncomyces californiensis (incl. Juncomyces gen. nov.) from leaves of Juncus effusus, Montagnula cylindrospora from a human skin sample, Muriphila oklahomaensis (incl. Muriphila gen. nov.) on outside wall of alcohol distillery, Neofabraea eucalyptorum from leaves of Eucalyptus macrandra, Diabolocovidia claustri (incl. Diabolocovidia gen. nov.) from leaves of Serenoa repens, Paecilomyces penicilliformis from air, Pseudopezicula betulae from leaves of leaf spots of Populus tremuloides. Vietnam, Diaporthe durionigena on branches of Durio zibethinus and Roridomyces pseudoirritans on rotten wood. Morphological and culture characteristics are supported by DNA barcodes.}, }
@article {pmid33115951, year = {2020}, author = {Khan, S and Waliullah, S and Godfrey, V and Khan, MAW and Ramachandran, RA and Cantarel, BL and Behrendt, C and Peng, L and Hooper, LV and Zaki, H}, title = {Dietary simple sugars alter microbial ecology in the gut and promote colitis in mice.}, journal = {Science translational medicine}, volume = {12}, number = {567}, pages = {}, doi = {10.1126/scitranslmed.aay6218}, pmid = {33115951}, issn = {1946-6242}, abstract = {The higher prevalence of inflammatory bowel disease (IBD) in Western countries points to Western diet as a possible IBD risk factor. High sugar, which is linked to many noncommunicable diseases, is a hallmark of the Western diet, but its role in IBD remains unknown. Here, we studied the effects of simple sugars such as glucose and fructose on colitis pathogenesis in wild-type and Il10-/- mice. Wild-type mice fed 10% glucose in drinking water or high-glucose diet developed severe colitis induced by dextran sulfate sodium. High-glucose-fed Il10-/- mice also developed a worsened colitis compared to glucose-untreated Il10-/- mice. Short-term intake of high glucose or fructose did not trigger inflammatory responses in healthy gut but markedly altered gut microbiota composition. In particular, the abundance of the mucus-degrading bacteria Akkermansia muciniphila and Bacteroides fragilis was increased. Consistently, bacteria-derived mucolytic enzymes were enriched leading to erosion of the colonic mucus layer of sugar-fed wild-type and Il10-/- mice. Sugar-induced exacerbation of colitis was not observed when mice were treated with antibiotics or maintained in a germ-free environment, suggesting that altered microbiota played a critical role in sugar-induced colitis pathogenesis. Furthermore, germ-free mice colonized with microbiota from sugar-treated mice showed increased colitis susceptibility. Together, these data suggest that intake of simple sugars predisposes to colitis and enhances its pathogenesis via modulation of gut microbiota in mice.}, }
@article {pmid33115836, year = {2020}, author = {García-Timermans, C and Props, R and Zacchetti, B and Sakarika, M and Delvigne, F and Boon, N}, title = {Raman Spectroscopy-Based Measurements of Single-Cell Phenotypic Diversity in Microbial Populations.}, journal = {mSphere}, volume = {5}, number = {5}, pages = {}, pmid = {33115836}, issn = {2379-5042}, abstract = {Microbial cells experience physiological changes due to environmental change, such as pH and temperature, the release of bactericidal agents, or nutrient limitation. This has been shown to affect community assembly and physiological processes (e.g., stress tolerance, virulence, or cellular metabolic activity). Metabolic stress is typically quantified by measuring community phenotypic properties such as biomass growth, reactive oxygen species, or cell permeability. However, bulk community measurements do not take into account single-cell phenotypic diversity, which is important for a better understanding and the subsequent management of microbial populations. Raman spectroscopy is a nondestructive alternative that provides detailed information on the biochemical makeup of each individual cell. Here, we introduce a method for describing single-cell phenotypic diversity using the Hill diversity framework of Raman spectra. Using the biomolecular profile of individual cells, we obtained a metric to compare cellular states and used it to study stress-induced changes. First, in two Escherichia coli populations either treated with ethanol or nontreated and then in two Saccharomyces cerevisiae subpopulations with either high or low expression of a stress reporter. In both cases, we were able to quantify single-cell phenotypic diversity and to discriminate metabolically stressed cells using a clustering algorithm. We also described how the lipid, protein, and nucleic acid compositions changed after the exposure to the stressor using information from the Raman spectra. Our results show that Raman spectroscopy delivers the necessary resolution to quantify phenotypic diversity within individual cells and that this information can be used to study stress-driven metabolic diversity in microbial populations.IMPORTANCE Microbial cells that live in the same community can exist in different physiological and morphological states that change as a function of spatiotemporal variations in environmental conditions. This phenomenon is commonly known as phenotypic heterogeneity and/or diversity. Measuring this plethora of cellular expressions is needed to better understand and manage microbial processes. However, most tools to study phenotypic diversity only average the behavior of the sampled community. In this work, we present a way to quantify the phenotypic diversity of microbial samples by inferring the (bio)molecular profile of its constituent cells using Raman spectroscopy. We demonstrate how this tool can be used to quantify the phenotypic diversity that arises after the exposure of microbes to stress. Raman spectroscopy holds potential for the detection of stressed cells in bioproduction.}, }
@article {pmid33114469, year = {2020}, author = {Cornejo-Pareja, I and Ruiz-Limón, P and Gómez-Pérez, AM and Molina-Vega, M and Moreno-Indias, I and Tinahones, FJ}, title = {Differential Microbial Pattern Description in Subjects with Autoimmune-Based Thyroid Diseases: A Pilot Study.}, journal = {Journal of personalized medicine}, volume = {10}, number = {4}, pages = {}, pmid = {33114469}, issn = {2075-4426}, support = {CP16/00163, PI18/01160//Carlos III Health Institute-co-founded by Fondo Europeo de Desarrollo Regional - FEDER/ ; }, abstract = {The interaction between genetic susceptibility, epigenetic, endogenous, and environmental factors play a key role in the initiation and progression of autoimmune thyroid diseases (AITDs). Studies have shown that gut microbiota alterations take part in the development of autoimmune diseases. We have investigated the possible relationship between gut microbiota composition and the most frequent AITDs. A total of nine Hashimoto's thyroiditis (HT), nine Graves-Basedow's disease (GD), and 11 otherwise healthy donors (HDs) were evaluated. 16S rRNA pyrosequencing and bioinformatics analysis by Quantitative Insights into Microbial Ecology and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) were used to analyze the gut microbiota. Beta diversity analysis showed that gut microbiota from our groups was different. We observed an increase in bacterial richness in HT and a lower evenness in GD in comparison to the HDs. GD showed a significant increase of Fusobacteriaceae, Fusobacterium and Sutterella compared to HDs and the core microbiome features showed that Prevotellaceae and Prevotella characterized this group. Victivallaceae was increased in HT and was part of their core microbiome. Streptococcaceae, Streptococcus and Rikenellaceae were greater in HT compared to GD. Core microbiome features of HT were represented by Streptococcus, Alistipes, Anaerostipes, Dorea and Haemophilus. Faecalibacterium decreased in both AITDs compared to HDs. PICRUSt analysis demonstrated enrichment in the xenobiotics degradation, metabolism, and the metabolism of cofactors and vitamins in GD patients compared to HDs. Moreover, correlation studies showed that some bacteria were widely correlated with autoimmunity parameters. A prediction model evaluated a possible relationship between predominant concrete bacteria such as an unclassified genus of Ruminococcaceae, Sutterella and Faecalibacterium in AITDs. AITD patients present altered gut microbiota compared to HDs. These alterations could be related to the immune system development in AITD patients and the loss of tolerance to self-antigens.}, }
@article {pmid33111499, year = {2020}, author = {Zrimec, J}, title = {Multiple plasmid origin-of-transfer regions might aid the spread of antimicrobial resistance to human pathogens.}, journal = {MicrobiologyOpen}, volume = {9}, number = {12}, pages = {e1129}, pmid = {33111499}, issn = {2045-8827}, support = {Z2-7257//Javna Agencija za Raziskovalno Dejavnost RS/ ; }, abstract = {Antimicrobial resistance poses a great danger to humanity, in part due to the widespread horizontal gene transfer of plasmids via conjugation. Modeling of plasmid transfer is essential to uncovering the fundamentals of resistance transfer and for the development of predictive measures to limit the spread of resistance. However, a major limitation in the current understanding of plasmids is the incomplete characterization of the conjugative DNA transfer mechanisms, which conceals the actual potential for plasmid transfer in nature. Here, we consider that the plasmid-borne origin-of-transfer substrates encode specific DNA structural properties that can facilitate finding these regions in large datasets and develop a DNA structure-based alignment procedure for typing the transfer substrates that outperforms sequence-based approaches. Thousands of putative DNA transfer substrates are identified, showing that plasmid mobility can be twofold higher and span almost twofold more host species than is currently known. Over half of all putative mobile plasmids contain the means for mobilization by conjugation systems belonging to different mobility groups, which can hypothetically link previously confined host ranges across ecological habitats into a robust plasmid transfer network. This hypothetical network is found to facilitate the transfer of antimicrobial resistance from environmental genetic reservoirs to human pathogens, which might be an important driver of the observed rapid resistance development in humans and thus an important point of focus for future prevention measures.}, }
@article {pmid33110109, year = {2020}, author = {Bellone, R and Lequime, S and Jupille, H and Göertz, GP and Aubry, F and Mousson, L and Piorkowski, G and Yen, PS and Gabiane, G and Vazeille, M and Sakuntabhai, A and Pijlman, GP and de Lamballerie, X and Lambrechts, L and Failloux, AB}, title = {Experimental adaptation of dengue virus 1 to Aedes albopictus mosquitoes by in vivo selection.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {18404}, pmid = {33110109}, issn = {2045-2322}, abstract = {In most of the world, Dengue virus (DENV) is mainly transmitted by the mosquito Aedes aegypti while in Europe, Aedes albopictus is responsible for human DENV cases since 2010. Identifying mutations that make DENV more competent for transmission by Ae. albopictus will help to predict emergence of epidemic strains. Ten serial passages in vivo in Ae. albopictus led to select DENV-1 strains with greater infectivity for this vector in vivo and in cultured mosquito cells. These changes were mediated by multiple adaptive mutations in the virus genome, including a mutation at position 10,418 in the DENV 3'UTR within an RNA stem-loop structure involved in subgenomic flavivirus RNA production. Using reverse genetics, we showed that the 10,418 mutation alone does not confer a detectable increase in transmission efficiency in vivo. These results reveal the complex adaptive landscape of DENV transmission by mosquitoes and emphasize the role of epistasis in shaping evolutionary trajectories of DENV variants.}, }
@article {pmid33108474, year = {2020}, author = {Sahu, KP and Kumar, A and Patel, A and Kumar, M and Gopalakrishnan, S and Prakash, G and Rathour, R and Gogoi, R}, title = {Rice Blast Lesions: an Unexplored Phyllosphere Microhabitat for Novel Antagonistic Bacterial Species Against Magnaporthe oryzae.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01617-3}, pmid = {33108474}, issn = {1432-184X}, support = {09/083(0367)/2016-EMR-I//Council of Scientific and Industrial Research, India/ ; }, abstract = {Dark brown necrotic lesions caused by Magnaporthe oryzae on rice foliage is a contrasting microhabitat for leaf-colonizing microbiome as compared with the surrounding healthy chlorophyll-rich tissues. We explored culturable bacterial communities of blast lesions by adopting microbiological tools for isolating effective biocontrol bacterial strains against M. oryzae. 16S rRNA gene sequencing-based molecular identification revealed a total of 17 bacterial species belonging to Achromobacter (2), Comamonas (1), Curtobacterium (1), Enterobacter (1), Leclercia (2), Microbacterium (1), Pantoea (3), Sphingobacterium (1), and Stenotrophomonas (5) found colonizing the lesion. Over 50% of the bacterial isolates were able to suppress the mycelial growth of M. oryzae either by secretory or volatile metabolites. Volatiles released by Achromobacter sp., Curtobacterium luteum, Microbacterium oleivorans, Pantoea ananatis, Stenotrophomonas maltophilia, and Stenotrophomonas sp., and were found to be fungicidal while others showed fungistatic action. In planta pathogen challenged evaluation trial revealed the biocontrol potential of Stenotrophomonas sp. and Microbacterium oleivorans that showed over 60% blast severity suppression on the rice leaf. The lesion-associated bacterial isolates were found to trigger expression of defense genes such as OsCEBiP, OsCERK1, OsEDS1, and OsPAD4 indicating their capability to elicit innate defense in rice against blast disease. The investigation culminated in the identification of potential biocontrol agents for the management of rice blast disease.}, }
@article {pmid33105583, year = {2020}, author = {Rabieh, S and Bayaraa, O and Romeo, E and Amosa, P and Calnek, K and Idaghdour, Y and Ochsenkühn, MA and Amin, SA and Goldstein, G and Bromage, TG}, title = {MH-ICP-MS Analysis of the Freshwater and Saltwater Environmental Resources of Upolu Island, Samoa.}, journal = {Molecules (Basel, Switzerland)}, volume = {25}, number = {21}, pages = {}, pmid = {33105583}, issn = {1420-3049}, support = {UN-India Development Partnership Fund//United Nations Development Programme, United Nations United Nations Educational, Scientific and Cultural Organisation/ ; }, abstract = {The elemental composition of freshwater and saltwater samples around the South Pacific island of Upolu, Samoa has been investigated together with other indicators of water quality. Up to 69 elements from Li (3) to U (92) are measured in each sample, analyzed by Mattauch-Herzog-inductively coupled plasma-mass spectrometry (MH-ICP-MS). One hundred and seventy-six samples were collected from surface freshwater sources (24 rivers, two volcanic lakes, one dam) and from seawater sources from the surface to 30 m depth (45 inner reef, reef, and outer reef locations) around Upolu Island, including river mouths and estuaries. Principal component and hierarchical clustering correlation analyses were performed on quantile normalized log transformed elemental composition data to identify groups of samples with similar characteristics and to improve the visualization of the full spectrum of elements. Human activities, such as the use of herbicides and pesticides, may relate to observed elevated concentrations of some elements contained in chemicals known to have deleterious obesogenic effects on humans that may also cause coral reef decline. Furthermore, the salinity of some saltwater samples tested were very high, possibly due to climate variability, which may additionally harm the health and biodiversity of coral reefs.}, }
@article {pmid33099662, year = {2020}, author = {Sepehri, M and Khatabi, B}, title = {Combination of Siderophore-Producing Bacteria and Piriformospora indica Provides an Efficient Approach to Improve Cadmium Tolerance in Alfalfa.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01629-z}, pmid = {33099662}, issn = {1432-184X}, abstract = {Application of siderophore-producing microorganisms (SPMs), as an environmentally friendly approach, facilitates plant growth and survival under heavy metals toxicity. This study evaluated the effectiveness of SPMs, belonging to the bacterial genera Rhizobium and Pseudomonas and a root endophytic fungus (Piriformospora indica) to improve the fitness of alfalfa under cadmium (Cd) stress. A greenhouse experiment was performed as a randomized design with factorial arrangement of treatments. Treatments included microbial inoculations (Sinorhizobium meliloti, Pseudomonas fluorescence, and P. indica) and different Cd concentrations (0, 2, 5, 10 mg/kg) with three replications in potting media containing sand and sterile perlite (v/v, 2:1). The effect of Cd on plant growth and development, antioxidant enzymes activities, and accumulation of Cd and nutrients in alfalfa plant was investigated. Alfalfa inoculated with SPMs showed significantly higher biomass and nutrients uptake under both normal and Cd stress conditions than the controls. Under the highest Cd concentration (10 mg/kg), alfalfa plants inoculated with P. fluorescens and P. indica, either alone or in combination, showed the highest shoot dry weights. Cd-induced oxidative stress was mitigated by SPMs through enhanced antioxidant enzyme activities of catalase, ascorbate peroxidase, and guaiacol peroxidase. We showed that P. indica either alone or in combination with the siderophore producing bacteria (SPB) minimized the toxicity of Cd by enhanced growth rate and the lower Cd concentration in the shoots. In conclusion, metal-resistant SPMs could assist alfalfa to survive in Cd-contaminated soil by enhancing plant growth and development. Application of plant-associated microbes is an efficient, environmentally friendly approach to surmount the adverse effects of heavy metals toxicity on plants, animals, and humans. Graphical abstract.}, }
@article {pmid33099661, year = {2020}, author = {Kubera, Ł}, title = {Spread Patterns of Antibiotic Resistance in Faecal Indicator Bacteria Contaminating an Urbanized Section of the Brda River.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01624-4}, pmid = {33099661}, issn = {1432-184X}, support = {Grant No. 008/RID/2018/19//Ministerstwo Nauki i Szkolnictwa Wyższego/ ; }, abstract = {This paper presents the spatio-temporal distribution of faecal indicator bacteria (FIB) in the river section subject to anthropogenic stress and describes spread patterns of antibiotic resistance in the studied bacterial groups. The analysis involved 58 strains of Escherichia coli and 61 strains of enterococci. Antibiotic resistance profiles were prepared in accordance with the recommendations of the European Committee on Antimicrobial Susceptibility Testing (EUCAST). The results indicated a correlation between the location of a sampling site and the concentration of faecal bacteria. The highest average concentrations were recorded at the site located in the city centre, where the river is used mainly for recreation. Antibiotic resistance profiles showed that Escherichia coli had 100% sensitivity to tigecycline, levofloxacin and imipenem. The highest percentaage of strains (17%) were resistant to piperacillin. Enterococci were 100% sensitive to levofloxacin. No strains were vancomycin-resistant (VRE). The highest percentage of strains was resistant to imipenem (23%), and the lowest, to ampicillin (2%). The spatio-temporal distribution of antibiotic-resistant strains (ARS) indicated a high concentration of drug-resistant Escherichia coli (47%) in the summer season at the sampling site located in the last part of the river. At the same time, drug resistance in enterococci increased along the river course and was considerably higher in spring. There were no significant relationships between physico-chemical parameters of water and the levels of faecal bacteria. On the other hand, strong relationships were observed between the percentage of strains showing resistance to the applied antibiotics and physico-chemical and biological parameters of water. The percentage of antibiotic resistant strains of Escherichia coli was negatively correlated with dissolved oxygen concentration (r = - 0.9; p < 0.001) and BOD5 (r = - 0.85; p < 0.05). The percentage of antibiotic resistant strains of enterococci was most strongly correlated with water pH (r = - 0.92; p < 0.001).}, }
@article {pmid33099264, year = {2021}, author = {Gao, R and Bonin, L and Arroyo, JMC and Logan, BE and Rabaey, K}, title = {Separation and recovery of ammonium from industrial wastewater containing methanol using copper hexacyanoferrate (CuHCF) electrodes.}, journal = {Water research}, volume = {188}, number = {}, pages = {116532}, doi = {10.1016/j.watres.2020.116532}, pmid = {33099264}, issn = {1879-2448}, mesh = {*Ammonium Compounds ; Copper ; Electrodes ; Ferrocyanides ; Methanol ; *Waste Water ; }, abstract = {Ammonium is typically removed from wastewater by converting it to nitrogen gas using microorganisms, precluding its recovery. Copper hexacyanoferrate (CuHCF) is known to reversibly intercalate alkali cations in aqueous electrolytes due to the Prussian Blue crystal structure. We used this property to create a carbon-based intercalation electrode within an electrochemical cell. Depending on the electrode potential, it can recover NH4+ from wastewater via insertion/regeneration while leaving organics. In the first phase, different binders were evaluated towards creating a stable electrode matrix, with sodium carboxymethyl cellulose giving the best performance. Subsequently, based on voltammetry, we determined an intercalation potential for NH4+ removal of + 0.3 V vs. Ag/AgCl, while the regeneration potential of the electrode was + 1.1 V (vs. Ag/AgCl). Using the CuHCF electrodes 95% of the NH4+ in a synthetic wastewater containing 56 mM NH4+ and 68 mM methanol was removed with an energy input of 0.34 ± 0.01 Wh g-1 NH4+. A similar removal of 93% was obtained using an actual industrial wastewater (56 mM NH4+, 68 mM methanol, 0.02 mM NO2-, 0.05 mM NO3-, 0.04 mM SO42- and 0.34 mM ethanol), with an energy input of 0.40 ± 0.01 Wh g-1 NH4+. In both cases, there was negligible removal of organics. The stability of CuHCF electrodes was evaluated either by open circuit potential monitoring (61 h) or by cyclic voltammetry (50 h, 116 cycles). The stability during cycling of the electrode was determined in both synthetic and real streams for 25 h (125 cycles). The charge density (C cm-1) of the CuHCF electrodes declined by 17 % and 19% after 125 cycles in the synthetic stream and the actual wastewater, respectively. This study highlights the possibility of low-cost CuHCF coated electrodes for achieving separation of NH4+ from streams containing methanol. The stability of electrodes has been improved but needs to be further enhanced for large-scale applications and long-term operation.}, }
@article {pmid33098438, year = {2020}, author = {Gunnabo, AH and van Heerwaarden, J and Geurts, R and Wolde-Meskel, E and Degefu, T and Giller, KE}, title = {Phylogeography and Symbiotic Effectiveness of Rhizobia Nodulating Chickpea (Cicer arietinum L.) in Ethiopia.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01620-8}, pmid = {33098438}, issn = {1432-184X}, abstract = {Chickpea (Cicer arietinum L.) used to be considered a restrictive host that nodulated and fixed nitrogen only with Mesorhizobium ciceri and M. mediterraneum. Recent analysis revealed that chickpea can also establish effective symbioses with strains of several other Mesorhizobium species such as M. loti, M. haukuii, M. amorphae, M. muleiense, etc. These strains vary in their nitrogen fixation potential inviting further exploration. We characterized newly collected mesorhizobial strains isolated from various locations in Ethiopia to evaluate genetic diversity, biogeographic structure and symbiotic effectiveness. Symbiotic effectiveness was evaluated in Leonard Jars using a locally released chickpea cultivar &quot;Nattoli&quot;. Most of the new isolates belonged to a clade related to M. plurifarium, with very few sequence differences, while the total collection of strains contained three additional mesorhizobial genospecies associated with M. ciceri, M. abyssinicae and an unidentified Mesorhizobium species isolated from a wild host in Eritrea. The four genospecies identified represented a subset of the eight major Mesorhizobium clades recently reported for Ethiopia based on metagenomic data. All Ethiopian strains had nearly identical symbiotic genes that grouped them in a single cluster with M. ciceri, M. mediterraneum and M. muleiense, but not with M. plurifarium. Some phylogeographic structure was observed, with elevation and geography explaining some of the genetic differences among strains, but the relation between genetic identity and symbiotic effectiveness was observed to be weak.}, }
@article {pmid33096434, year = {2021}, author = {Prévoteau, A and Kerckhof, FM and Clauwaert, P and Rabaey, K}, title = {Electrochemical and phylogenetic comparisons of oxygen-reducing electroautotrophic communities.}, journal = {Biosensors &amp; bioelectronics}, volume = {171}, number = {}, pages = {112700}, doi = {10.1016/j.bios.2020.112700}, pmid = {33096434}, issn = {1873-4235}, abstract = {The mechanisms of extracellular electron transfer and the microbial taxa associated with the observed electroactivity are fundamental to oxygen-reducing microbial cathodes. Here we confirmed the apparent 'electroautotrophic' behavior of electroactive biofilms (EABs) grown on carbon electrodes at + 0.20V vs. Ag/AgCl under air. The EABs catalyzed O2 electroreduction into water ─ as demonstrated by a rotating ring disc experiment ─ and performed quasi-reversible heterogeneous electron transfer (HET). By using electrodes of low surface capacitance, we report for the first time nonturnover redox peaks that are very likely intrinsic to the redox protein(s) performing the HET. Because the formal potential of redox proteins is pH-dependent, we investigated the evolution of characteristic potentials of the EABs with the solution pH: (i) open circuit potential, (ii) half-wave potential, and (iii) averaged peak potential of nonturnover cyclic voltammograms, which is presumably the formal potential of the primary electron acceptor(s) for the community. In addition to describing the redox thermodynamics behind HET, we suggest that the corresponding data provides an electrochemical fingerprint that could help in comparing the electroactivity of diverse microbial communities. The taxon with the highest relative abundance in our EABs was an unclassified member of the Gammaproteobacteria that was phylogenetically closely related to most other abundant unclassified Gammaproteobacteria commonly reported in EABs reducing O2 at high potentials, further suggesting that those taxa are responsible for the bioelectroactivity. Phylogenetic and electrochemical similarities between reported EABs jointly support the hypothesis that similar biomolecular mechanisms may be responsible for this highly probable electroautotrophic metabolism.}, }
@article {pmid33096247, year = {2020}, author = {Pelusio, NF and Rossi, B and Parma, L and Volpe, E and Ciulli, S and Piva, A and D'Amico, F and Scicchitano, D and Candela, M and Gatta, PP and Bonaldo, A and Grilli, E}, title = {Effects of increasing dietary level of organic acids and nature-identical compounds on growth, intestinal cytokine gene expression and gut microbiota of rainbow trout (Oncorhynchus mykiss) reared at normal and high temperature.}, journal = {Fish &amp; shellfish immunology}, volume = {107}, number = {Pt A}, pages = {324-335}, doi = {10.1016/j.fsi.2020.10.021}, pmid = {33096247}, issn = {1095-9947}, abstract = {Organic acids (OA) and nature-identical compounds (NIC) such as monoterpenes and aldehydes are well-known growth and health promoters in terrestrial livestock while their application for fish production is recent and their mechanisms of action require further study. Hence, this study tested the increasing dietary level (D0, D250, D500, D1000; 0, 250, 500 and 1000 mg kg feed-1 respectively) of a microencapsulated blend containing citric and sorbic acid, thymol and vanillin over 82 days on rainbow trout to assess the effects on growth, feed utilization, intestine cytokine gene expression and gut microbiota (GM). Furthermore, the effects on intestinal cytokine gene expression and GM were also explored after one week at high water temperature (23 °C). OA and NIC improved specific growth rate (SGR) and feed conversion rate (FCR) during the second half (day 40-82) of the feeding trial, while at the end of the trial protein (PER) and lipid efficiency (LER) increased with increasing dietary level. GM diversity and composition and cytokine gene expression analysis showed no significant differences in fish fed with increasing doses of OA and NIC (82 days) demonstrating the absence of inflammatory activity in the intestinal mucosa. Although there were no statistical differences, GM structure showed a tendency in clustering D0 group separately from the other dietary groups and a trend towards reduction of Streptococcus spp. was observed in the D250 and D1000 groups. After exposure to high water temperature, lower GM diversity and increased gene expression of inflammatory intestinal cytokines were observed for both inclusions (D0 vs. D1000) compared to groups in standard condition. However, the gene up-regulation involved a limited number of cytokines showing the absence of a substantial inflammation process able to compromise the functional activity of the intestine. Despite further study should be conducted to fully clarify this mechanism, cytokines up-regulation seems to be concomitant to the reduction of the GM diversity and, particularly, to the reduction of specific lactic acid bacteria such as Leuconostoc. The application of the microencapsulate blend tested can be a useful strategy to improve growth and feed utilization in rainbow trout under normal temperature conditions. According to the results organic acids and nature-identical compounds did not revert the effects triggered by the increased temperature of water.}, }
@article {pmid33095158, year = {2020}, author = {Greenhalgh, R and Dermauw, W and Glas, JJ and Rombauts, S and Wybouw, N and Thomas, J and Alba, JM and Pritham, EJ and Legarrea, S and Feyereisen, R and Van de Peer, Y and Van Leeuwen, T and Clark, RM and Kant, MR}, title = {Genome streamlining in a minute herbivore that manipulates its host plant.}, journal = {eLife}, volume = {9}, number = {}, pages = {}, pmid = {33095158}, issn = {2050-084X}, support = {773902-SuperPests//Horizon 2020 - Research and Innovation Framework Programme/International ; STW-GAP/13550//Netherlands Organisation for Scientific Research/International ; 12T9818N//Research Foundation Flanders/International ; 772026-POLYADAPT//European Union Horizon 2020 research and innovation program/International ; 1457346//USA National Science Foundation/International ; 1274917N//Research Foundation Flanders/International ; 1457346//National Science Foundation/International ; STW-VIDI/13492//Netherlands Organisation for Scientific Research/International ; 773902-SuperPests//European Union Horizon 2020 research and innovation program/International ; }, abstract = {The tomato russet mite, Aculops lycopersici, is among the smallest animals on earth. It is a worldwide pest on tomato and can potently suppress the host's natural resistance. We sequenced its genome, the first of an eriophyoid, and explored whether there are genomic features associated with the mite's minute size and lifestyle. At only 32.5 Mb, the genome is the smallest yet reported for any arthropod and, reminiscent of microbial eukaryotes, exceptionally streamlined. It has few transposable elements, tiny intergenic regions, and is remarkably intron-poor, as more than 80% of coding genes are intronless. Furthermore, in accordance with ecological specialization theory, this defense-suppressing herbivore has extremely reduced environmental response gene families such as those involved in chemoreception and detoxification. Other losses associate with this species' highly derived body plan. Our findings accelerate the understanding of evolutionary forces underpinning metazoan life at the limits of small physical and genome size.}, }
@article {pmid33094372, year = {2020}, author = {Jeong, SY and Kim, TG}, title = {Effects of Plants on Metacommunities and Correlation Networks of Soil Microbial Groups in an Ecologically Restored Wetland.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01625-3}, pmid = {33094372}, issn = {1432-184X}, support = {2018R1D1A1B07048872//Ministry of Education/ ; }, abstract = {Plants may influence different aspects of the belowground microorganisms, including abundance, distribution, and interaction, in wetlands. Microbial communities were scrutinized in a 4-year-old restored wetland ecosystem with 5 distinct sites: a bare-soil site (10 local patches) and sites dominated by Miscanthus, Phragmites, Typha, and Zizania (20 patches per site). Ordination analysis revealed that plant-induced attributes (e.g., organic matter and total carbon and nitrogen) could explain the total environmental variance. Community comparisons showed that all groups (Bacteria, Fungi, Protista, and Metazoa) differed in community structure among the 5 sites (P < 0.05). Comparisons between the community and environmental ordination plots revealed that community structural variation among the sites correlated with the environmental change across all groups (R2 ≥ 0.61). This indicates that all groups were primarily influenced by plant detritus. In addition, correlation networks markedly varied in topology and composition among the sites across all groups. There was a strong coupling between the metacommunity and correlation network for both Bacteria and Fungi (R2 ≥ 0.58), indicating that the plants determined the spatial covariation patterns of microbial populations. Multi-group networks and group synchrony results revealed that Bacteria, Fungi, and Protista were synchronized with each other (R2 ≥ 0.52) as the key founders of the microbial systems, while Metazoa participated in the system only under Miscanthus. Our findings concluded that the plants shaped the communities by controlling the abundance and interaction of their populations.}, }
@article {pmid33087520, year = {2020}, author = {Tomkovich, S and Stough, JMA and Bishop, L and Schloss, PD}, title = {The Initial Gut Microbiota and Response to Antibiotic Perturbation Influence Clostridioides difficile Clearance in Mice.}, journal = {mSphere}, volume = {5}, number = {5}, pages = {}, pmid = {33087520}, issn = {2379-5042}, support = {U01 AI124255/AI/NIAID NIH HHS/United States ; UL1 TR002240/TR/NCATS NIH HHS/United States ; }, abstract = {The gut microbiota has a key role in determining susceptibility to Clostridioides difficile infections (CDIs). However, much of the mechanistic work examining CDIs in mouse models uses animals obtained from a single source. We treated mice from 6 sources (2 University of Michigan colonies and 4 commercial vendors) with clindamycin, followed by a C. difficile challenge, and then measured C. difficile colonization levels throughout the infection. The microbiota were profiled via 16S rRNA gene sequencing to examine the variation across sources and alterations due to clindamycin treatment and C. difficile challenge. While all mice were colonized 1 day postinfection, variation emerged from days 3 to 7 postinfection with animals from some sources colonized with C. difficile for longer and at higher levels. We identified bacteria that varied in relative abundance across sources and throughout the experiment. Some bacteria were consistently impacted by clindamycin treatment in all sources of mice, including Lachnospiraceae, Ruminococcaceae, and Enterobacteriaceae To identify bacteria that were most important to colonization regardless of the source, we created logistic regression models that successfully classified mice based on whether they cleared C. difficile by 7 days postinfection using community composition data at baseline, post-clindamycin treatment, and 1 day postinfection. With these models, we identified 4 bacterial taxa that were predictive of whether C. difficile cleared. They varied across sources (Bacteroides) or were altered by clindamycin (Porphyromonadaceae) or both (Enterobacteriaceae and Enterococcus). Allowing for microbiota variation across sources better emulates human interindividual variation and can help identify bacterial drivers of phenotypic variation in the context of CDIs.IMPORTANCEClostridioides difficile is a leading nosocomial infection. Although perturbation to the gut microbiota is an established risk, there is variation in who becomes asymptomatically colonized, develops an infection, or has adverse infection outcomes. Mouse models of C. difficile infection (CDI) are widely used to answer a variety of C. difficile pathogenesis questions. However, the interindividual variation between mice from the same breeding facility is less than what is observed in humans. Therefore, we challenged mice from 6 different breeding colonies with C. difficile We found that the starting microbial community structures and C. difficile persistence varied by the source of mice. Interestingly, a subset of the bacteria that varied across sources were associated with how long C. difficile was able to colonize. By increasing the interindividual diversity of the starting communities, we were able to better model human diversity. This provided a more nuanced perspective of C. difficile pathogenesis.}, }
@article {pmid33083833, year = {2021}, author = {Arca-Suárez, J and Lasarte-Monterrubio, C and Rodiño-Janeiro, BK and Cabot, G and Vázquez-Ucha, JC and Rodríguez-Iglesias, M and Galán-Sánchez, F and Beceiro, A and González-Bello, C and Oliver, A and Bou, G}, title = {Molecular mechanisms driving the in vivo development of OXA-10-mediated resistance to ceftolozane/tazobactam and ceftazidime/avibactam during treatment of XDR Pseudomonas aeruginosa infections.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {76}, number = {1}, pages = {91-100}, doi = {10.1093/jac/dkaa396}, pmid = {33083833}, issn = {1460-2091}, abstract = {BACKGROUND: The development of resistance to ceftolozane/tazobactam and ceftazidime/avibactam during treatment of Pseudomonas aeruginosa infections is concerning.<br><br>OBJECTIVES: Characterization of the mechanisms leading to the development of OXA-10-mediated resistance to ceftolozane/tazobactam and ceftazidime/avibactam during treatment of XDR P. aeruginosa infections.<br><br>METHODS: Four paired ceftolozane/tazobactam- and ceftazidime/avibactam-susceptible/resistant isolates were evaluated. MICs were determined by broth microdilution. STs, resistance mechanisms and genetic context of β-lactamases were determined by genotypic methods, including WGS. The OXA-10 variants were cloned in PAO1 to assess their impact on resistance. Models for the OXA-10 derivatives were constructed to evaluate the structural impact of the amino acid changes.<br><br>RESULTS: The same XDR ST253 P. aeruginosa clone was detected in all four cases evaluated. All initial isolates showed OprD deficiency, produced an OXA-10 enzyme and were susceptible to ceftazidime, ceftolozane/tazobactam, ceftazidime/avibactam and colistin. During treatment, the isolates developed resistance to all cephalosporins. Comparative genomic analysis revealed that the evolved resistant isolates had acquired mutations in the OXA-10 enzyme: OXA-14 (Gly157Asp), OXA-794 (Trp154Cys), OXA-795 (ΔPhe153-Trp154) and OXA-824 (Asn143Lys). PAO1 transformants producing the evolved OXA-10 derivatives showed enhanced ceftolozane/tazobactam and ceftazidime/avibactam resistance but decreased meropenem MICs in a PAO1 background. Imipenem/relebactam retained activity against all strains. Homology models revealed important changes in regions adjacent to the active site of the OXA-10 enzyme. The blaOXA-10 gene was plasmid borne and acquired due to transposition of Tn6746 in the pHUPM plasmid scaffold.<br><br>CONCLUSIONS: Modification of OXA-10 is a mechanism involved in the in vivo acquisition of resistance to cephalosporin/β-lactamase inhibitor combinations in P. aeruginosa.}, }
@article {pmid33082281, year = {2020}, author = {Allard, SM and Costa, MT and Bulseco, AN and Helfer, V and Wilkins, LGE and Hassenrück, C and Zengler, K and Zimmer, M and Erazo, N and Mazza Rodrigues, JL and Duke, N and Melo, VMM and Vanwonterghem, I and Junca, H and Makonde, HM and Jiménez, DJ and Tavares, TCL and Fusi, M and Daffonchio, D and Duarte, CM and Peixoto, RS and Rosado, AS and Gilbert, JA and Bowman, J}, title = {Introducing the Mangrove Microbiome Initiative: Identifying Microbial Research Priorities and Approaches To Better Understand, Protect, and Rehabilitate Mangrove Ecosystems.}, journal = {mSystems}, volume = {5}, number = {5}, pages = {}, pmid = {33082281}, issn = {2379-5077}, abstract = {Mangrove ecosystems provide important ecological benefits and ecosystem services, including carbon storage and coastline stabilization, but they also suffer great anthropogenic pressures. Microorganisms associated with mangrove sediments and the rhizosphere play key roles in this ecosystem and make essential contributions to its productivity and carbon budget. Understanding this nexus and moving from descriptive studies of microbial taxonomy to hypothesis-driven field and lab studies will facilitate a mechanistic understanding of mangrove ecosystem interaction webs and open opportunities for microorganism-mediated approaches to mangrove protection and rehabilitation. Such an effort calls for a multidisciplinary and collaborative approach, involving chemists, ecologists, evolutionary biologists, microbiologists, oceanographers, plant scientists, conservation biologists, and stakeholders, and it requires standardized methods to support reproducible experiments. Here, we outline the Mangrove Microbiome Initiative, which is focused around three urgent priorities and three approaches for advancing mangrove microbiome research.}, }
@article {pmid33078238, year = {2020}, author = {Jayakumar, A and Nair, IC and Radhakrishnan, EK}, title = {Environmental Adaptations of an Extremely Plant Beneficial Bacillus subtilis Dcl1 Identified Through the Genomic and Metabolomic Analysis.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01605-7}, pmid = {33078238}, issn = {1432-184X}, abstract = {Bacterial endophytes ubiquitously colonize the internal tissues of plants and promote the plant growth through diverse mechanisms. The current study describes the mechanistic basis of plant-specific adaptations present in an extremely beneficial endophytic bacterium. Here, the endophytic Bacillus subtilis Dcl1 isolated from the dried rhizome of Curcuma longa was found to have the drought tolerance, IAA and ACC deaminase production and phosphate solubilization properties. The whole genome sequencing and annotation further showed the genome of B. subtilis Dcl1 to have the size of 4,321,654 bp. This also showed the presence of genes for IAA, H2S, acetoin, butanediol, flagella and siderophore production along with phosphate solubilization and biofilm formation for the B. subtilis Dcl1. In addition, the genes responsible for the synthesis of surfactin, iturin, fengycin, bacillibactin, bacillaene, bacilysin, chitinase, chitosanase, protease and glycoside hydrolase could also be annotated from the genome of B. subtilis Dcl1. Identification of genes for the glycine betaine, glutamate and trehalose further indicated the drought stress tolerance features of B. subtilis Dcl1. The presence of the genetic basis to produce the catalase, superoxide dismutase, peroxidases, gamma-glutamyltranspeptidase, glutathione and glycolate oxidase also indicated the plant oxidative stress protective effect of B. subtilis Dcl1. Identification of these properties and the demonstration of its plant probiotic effect in Vigna unguiculata confirmed the applicability of B. subtilis Dcl1 as a biofertilizer, biocontrol and bioremediator agent to enhance the agricultural productivity.}, }
@article {pmid33077749, year = {2020}, author = {Yang, FS and Nie, S and Liu, H and Shi, TL and Tian, XC and Zhou, SS and Bao, YT and Jia, KH and Guo, JF and Zhao, W and An, N and Zhang, RG and Yun, QZ and Wang, XZ and Mannapperuma, C and Porth, I and El-Kassaby, YA and Street, NR and Wang, XR and Van de Peer, Y and Mao, JF}, title = {Chromosome-level genome assembly of a parent species of widely cultivated azaleas.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {5269}, pmid = {33077749}, issn = {2041-1723}, mesh = {Anthocyanins/biosynthesis ; Biosynthetic Pathways ; Carotenoids/metabolism ; Chromosomes, Plant/*genetics/metabolism ; Flowers/genetics/growth &amp; development/metabolism ; Gene Expression Regulation, Plant ; *Genome, Plant ; Multigene Family ; Plant Proteins/*genetics/metabolism ; Rhododendron/*genetics/growth &amp; development/metabolism ; Transcription Factors/genetics/metabolism ; }, abstract = {Azaleas (Ericaceae) comprise one of the most diverse ornamental plants, renowned for their cultural and economic importance. We present a chromosome-scale genome assembly for Rhododendron simsii, the primary ancestor of azalea cultivars. Genome analyses unveil the remnants of an ancient whole-genome duplication preceding the radiation of most Ericaceae, likely contributing to the genomic architecture of flowering time. Small-scale gene duplications contribute to the expansion of gene families involved in azalea pigment biosynthesis. We reconstruct entire metabolic pathways for anthocyanins and carotenoids and their potential regulatory networks by detailed analysis of time-ordered gene co-expression networks. MYB, bHLH, and WD40 transcription factors may collectively regulate anthocyanin accumulation in R. simsii, particularly at the initial stages of flower coloration, and with WRKY transcription factors controlling progressive flower coloring at later stages. This work provides a cornerstone for understanding the underlying genetics governing flower timing and coloration and could accelerate selective breeding in azalea.}, }
@article {pmid33075580, year = {2020}, author = {Francis, JS and Tatarko, AR and Richman, SK and Vaudo, AD and Leonard, AS}, title = {Microbes and pollinator behavior in the floral marketplace.}, journal = {Current opinion in insect science}, volume = {44}, number = {}, pages = {16-22}, doi = {10.1016/j.cois.2020.10.003}, pmid = {33075580}, issn = {2214-5753}, abstract = {Pollinator foraging decisions shape microbial dispersal, and microbes change floral phenotypes in ways perceivable by pollinators. Yet, the role microbes play in the cognitive ecology of pollination is relatively unexplored. Reviewing recent literature on floral microbial ecology and pollinator behavior, we advocate for further integration between these two fields. Insights into pollinator learning, memory, and decision-making can help explain their responses to microbially-altered floral phenotypes. Specifically, considering how pollinators forage for multiple nutrients, cope with uncertainty, structure foraging bouts, and move through their environment could inform predictions about microbial dispersal within plant communities. We highlight how behavior connects microbial changes in floral phenotype to downstream effects on both microbial dispersal and plant fitness.}, }
@article {pmid33072042, year = {2020}, author = {Sabino, YNV and de Araújo, KC and de Assis, FGDV and Moreira, SM and Lopes, TDS and Mendes, TAO and Huws, SA and Mantovani, HC}, title = {In silico Screening Unveil the Great Potential of Ruminal Bacteria Synthesizing Lasso Peptides.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {576738}, pmid = {33072042}, issn = {1664-302X}, abstract = {Studies of rumen microbial ecology suggest that the capacity to produce antimicrobial peptides could be a useful trait in species competing for ecological niches in the ruminal ecosystem. However, little is known about the synthesis of lasso peptides by ruminal microorganisms. Here we analyzed the distribution and diversity of lasso peptide gene clusters in 425 bacterial genomes from the rumen ecosystem. Genome mining was performed using antiSMASH 5, BAGEL4, and a database of well-known precursor sequences. The genomic context of the biosynthetic clusters was investigated to identify putative lasA genes and protein sequences from enzymes of the biosynthetic machinery were evaluated to identify conserved motifs. Metatranscriptome analysis evaluated the expression of the biosynthetic genes in the rumen microbiome. Several incomplete (n = 23) and complete (n = 11) putative lasso peptide clusters were detected in the genomes of ruminal bacteria. The complete gene clusters were exclusively found within the phylum Firmicutes, mainly (48%) in strains of the genus Butyrivibrio. The analysis of the genetic organization of complete putative lasso peptide clusters revealed the presence of co-occurring genes, including kinases (85%), transcriptional regulators (49%), and glycosyltransferases (36%). Moreover, a conserved pattern of cluster organization was detected between strains of the same genus/species. The maturation enzymes LasB, LasC, and LasD showed regions highly conserved, including the presence of a transglutaminase core in LasB, an asparagine synthetase domain in LasC, and an ABC-type transporter system in LasD. Phylogenetic trees of the essential biosynthetic proteins revealed that sequences split into monophyletic groups according to their shared single common ancestor. Metatranscriptome analyses indicated the expression of the lasso peptides biosynthetic genes within the active rumen microbiota. Overall, our in silico screening allowed the discovery of novel biosynthetic gene clusters in the genomes of ruminal bacteria and revealed several strains with the genetic potential to synthesize lasso peptides, suggesting that the ruminal microbiota represents a potential source of these promising peptides.}, }
@article {pmid33072023, year = {2020}, author = {Dias, T and Pimentel, V and Cogo, AJD and Costa, R and Bertolazi, AA and Miranda, C and de Souza, SB and Melo, J and Carolino, M and Varma, A and Eutrópio, F and Olivares, FL and Ramos, AC and Cruz, C}, title = {The Free-Living Stage Growth Conditions of the Endophytic Fungus Serendipita indica May Regulate Its Potential as Plant Growth Promoting Microbe.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {562238}, pmid = {33072023}, issn = {1664-302X}, abstract = {Serendipita indica (former Piriformospora indica) is a non-obligate endophytic fungus and generally a plant growth and defence promoter with high potential to be used in agriculture. However, S. indica may switch from biotrophy to saprotrophy losing its plant growth promoting traits. Our aim was to understand if the free-living stage growth conditions (namely C availability) regulate S. indica's phenotype, and its potential as plant-growth-promoting-microbe (PGPM). We grew S. indica in its free-living stage under increasing C availabilities (2-20 g L-1 of glucose or sucrose). We first characterised the effect of C availability during free-living stage growth on fungal phenotype: colonies growth and physiology (plasma membrane proton pumps, stable isotopic signatures, and potential extracellular decomposing enzymes). The effect of the C availability during the free-living stage of the PGPM was evaluated on wheat. We observed that C availability during the free-living stage regulated S. indica's growth, ultrastructure and physiology, resulting in two distinct colony phenotypes: compact and explorer. The compact phenotype developed at low C, used peptone as the major C and N source, and displayed higher decomposing potential for C providing substrates; while the explorer phenotype developed at high C, used glucose and sucrose as major C sources and casein and yeast extract as major N sources, and displayed higher decomposing potential for N and P providing substrates. The C availability, or the C/N ratio, during the free-living stage left a legacy to the symbiosis stage, regulating S. indica's potential to promote plant growth: wheat growth promotion by the explorer phenotype was ± 40% higher than that by the compact phenotype. Our study highlights the importance of considering microbial ecology in designing PGPM/biofertilizers. Further studies are needed to test the phenotypes under more extreme conditions, and to understand if the in vitro acquired characteristics persist under field conditions.}, }
@article {pmid33072015, year = {2020}, author = {Zhu, C and Bass, D and Wang, Y and Shen, Z and Song, W and Yi, Z}, title = {Environmental Parameters and Substrate Type Drive Microeukaryotic Community Structure During Short-Term Experimental Colonization in Subtropical Eutrophic Freshwaters.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {555795}, pmid = {33072015}, issn = {1664-302X}, abstract = {Microeukaryotes are key components of aquatic ecosystems and play crucial roles in aquatic food webs. However, influencing factors and potential assembly mechanisms for microeukaryotic community on biofilms are rarely studied. Here, those of microeukaryotic biofilms in subtropical eutrophic freshwaters were investigated for the first time based on 2,585 operational taxonomic units (OTUs) from 41 samples, across different environmental conditions and substrate types. Following conclusions were drawn: (1) Environmental parameters were more important than substrate types in structuring microeukaryotic community of biofilms in subtropical eutrophic freshwaters. (2) In the fluctuating river, there was a higher diversity of OTUs and less predictability of community composition than in the stable lake. Sessile species were more likely to be enriched on smooth surfaces of glass slides, while both free-swimming and attached organisms occurred within holes inside PFUs (polyurethane foam units). (3) Both species sorting and neutral process were mechanisms for assembly of microeukaryotic biofilms, but their importance varied depending on different habitats and substrates. (4) The effect of species sorting was slightly higher than the neutral process in river biofilms due to stronger environmental filtering. Species sorting was a stronger force structuring communities on glass slides than PFUs with more niche availability. Our study sheds light on assembly mechanisms for microeukaryotic community on different habitat and substrate types, showing that the resulting communities are determined by both sets of variables, in this case primarily habitat type. The balance of neutral process and species sorting differed between habitats, but the high alpha diversity of microeukaryotes in both led to similar sets of lifecycle traits being selected for in each case.}, }
@article {pmid33072010, year = {2020}, author = {Shang, Y and Wu, X and Wei, Q and Dou, H and Wang, X and Chen, J and Zhang, H and Ma, S and Zhang, H}, title = {Total Arsenic, pH, and Sulfate Are the Main Environmental Factors Affecting the Microbial Ecology of the Water and Sediments in Hulun Lake, China.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {548607}, pmid = {33072010}, issn = {1664-302X}, abstract = {Bacteria have the metabolic potential to produce a diverse array of secondary metabolites, which have important roles in biogeochemical cycling processes. However, for Hulun Lake and the rivers that enter into it, the bacterial community structures and their effects have not previously been widely studied, limiting our ecological understanding of this habitat. To address this, we have analyzed the bacterial communities in the water ecosystem of the Hulun Lake Basin. 16S rRNA high-throughput sequencing identified 64 phyla, 165 classes, 218 orders, 386 families, and 740 genera of bacteria across all samples. The dominant phyla in the central area of the lake were Proteobacteria, Actinobacteria, Firmicutes, and Cyanobacteria, while in all other areas, Proteobacteria, Actinobacteria, and Bacteroidetes were dominant. The microbial community structures were significantly affected by environmental factors [arsenic (As), pH, and sulfate (SO42-)] and their location in the lake. The species richness in the sediments of Hulun Lake was higher than in the water, and this ecosystem harbored the highest proportion of unclassified sequences, representing unclassified bacteria. This study provides basic data for future investigations into the Hulun lake ecosystem and for water microbial monitoring and protection measures.}, }
@article {pmid33072003, year = {2020}, author = {Brown, JM and Labonté, JM and Brown, J and Record, NR and Poulton, NJ and Sieracki, ME and Logares, R and Stepanauskas, R}, title = {Single Cell Genomics Reveals Viruses Consumed by Marine Protists.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {524828}, pmid = {33072003}, issn = {1664-302X}, abstract = {The predominant model of the role of viruses in the marine trophic web is that of the &quot;viral shunt,&quot; where viral infection funnels a substantial fraction of the microbial primary and secondary production back to the pool of dissolved organic matter. Here, we analyzed the composition of non-eukaryotic DNA associated with individual cells of small, planktonic protists in the Gulf of Maine (GoM) and the Mediterranean Sea. We found viral DNA associated with a substantial fraction cells from the GoM (51%) and the Mediterranean Sea (35%). While Mediterranean SAGs contained a larger proportion of cells containing bacterial sequences (49%), a smaller fraction of cells contained bacterial sequences in the GoM (19%). In GoM cells, nearly identical bacteriophage and ssDNA virus sequences where found across diverse lineages of protists, suggesting many of these viruses are non-infective. The fraction of cells containing viral DNA varied among protistan lineages and reached 100% in Picozoa and Choanozoa. These two groups also contained significantly higher numbers of viral sequences than other identified taxa. We consider mechanisms that may explain the presence of viral DNA in protistan cells and conclude that protistan predation on free viral particles contributed to the observed patterns. These findings confirm prior experiments with protistan isolates and indicate that the viral shunt is complemented by a viral link in the marine microbial food web. This link may constitute a sink of viral particles in the ocean and has implications for the flow of carbon through the microbial food web.}, }
@article {pmid33070212, year = {2020}, author = {Xu, S and Jiang, L and Qiao, G and Chen, J}, title = {Diversity of bacterial symbionts associated with Myzus persicae (Sulzer) (Hemiptera: Aphididae: Aphidinae) revealed by 16S rRNA Illumina sequencing.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01622-6}, pmid = {33070212}, issn = {1432-184X}, support = {2016YFE0203100//National Key R &amp; D Program of China/ ; 31620103916//National Natural Science Foundation of China (CN)/ ; 31772492//National Natural Science Foundation of China/ ; XDA19050303//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 2020087//Youth Innovation Promotion Association of Chinese Academy of Sciences/ ; }, abstract = {Aphids are known to be associated with a variety of symbiotic bacteria. To improve our knowledge of the bacterial diversity of polyphagous aphids, in the present study, we investigated the microbiota of the cosmopolitan agricultural pest Myzus persicae (Sulzer). Ninety-two aphid samples collected from different host plants in various regions of China were examined using high-throughput amplicon sequencing. We comprehensively characterized the symbiont diversity of M. persicae and assessed the variations in aphid-associated symbiont communities. We detected a higher diversity of symbionts than has been previously observed. M. persicae hosted the primary endosymbiont Buchnera aphidicola and seven secondary symbionts, among which Wolbachia was the most prevalent and Rickettsia, Arsenophonus, and Spiroplasma were reported for the first time. Ordination analyses and statistical tests revealed that the symbiont flora associated with M. persicae did not change with respect to host plant or geography, which may be due to frequent migrations between different aphid populations. These findings will advance our knowledge of the microbiota of polyphagous insects and will enrich our understanding of assembly of host-microbiome systems.}, }
@article {pmid33069997, year = {2021}, author = {Dai, H and Gao, J and Li, D and Wang, Z and Duan, W}, title = {Metagenomics combined with DNA-based stable isotope probing provide comprehensive insights of active triclosan-degrading bacteria in wastewater treatment.}, journal = {Journal of hazardous materials}, volume = {404}, number = {Pt B}, pages = {124192}, doi = {10.1016/j.jhazmat.2020.124192}, pmid = {33069997}, issn = {1873-3336}, abstract = {The biotransformation of triclosan (TCS) during wastewater treatment occurred frequently, while little researches are known the identity of microorganisms involved in the biodegradation process. In this work, DNA-based stable isotope probing (DNA-SIP) was occupied to investigate the TCS assimilation microbes originated from a full-scale cyclic activated sludge system in Beijing. Results of TCS removal pathway showed that the TCS removal in nitrification process was mainly contributed by the metabolism of heterotrophic bacteria, accounting for about 18.54%. DNA-SIP assay indicated that Sphingobium dominated the degradation of TCS. Oligotyping analysis further indicated that oligotype GCTAAT and ATGTTA of Sphingobium played important roles in degrading TCS. Furthermore, the Kyoto Encyclopedia of Genes and Genomes functional abundance statistics based on PICRUSt2 showed that glutathione transferase was the most prevalent enzyme involved in TCS metabolism, and TCS might be removed through microbial carbon metabolism. Metagenomics made clear that Sphingobium might play irrelevant role on the propagation of antibiotics resistance genes (ARGs), even though, it could degrade TCS. Thauera and Dechloromonas were identified as the key hosts of most ARGs. This study revealed the potential metabolic pathway and microbial ecology of TCS biodegradation in nitrification process of wastewater treatment system.}, }
@article {pmid33068395, year = {2020}, author = {Lebre, PH and Bottos, E and Makhalanyane, TP and Hogg, I and Cowan, DA}, title = {Islands in the sand: are all hypolithic microbial communities the same?.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {1}, pages = {}, doi = {10.1093/femsec/fiaa216}, pmid = {33068395}, issn = {1574-6941}, abstract = {Hypolithic microbial communities (hypolithons) are complex assemblages of phototrophic and heterotrophic organisms associated with the ventral surfaces of translucent minerals embedded in soil surfaces. Past studies on the assembly, structure and function of hypolithic communities have tended to use composite samples (i.e. bulked hypolithic biomass) with the underlying assumption that samples collected from within a 'homogeneous' locality are phylogenetically homogeneous. In this study, we question this assumption by analysing the prokaryote phylogenetic diversity of multiple individual hypolithons: i.e. asking the seemingly simple question of 'Are all hypolithons the same'? Using 16S rRNA gene-based phylogenetic analysis of hypolithons recovered for a localized moraine region in the Taylor Valley, McMurdo Dry Valleys, Antarctica, we demonstrate that these communities are heterogeneous at very small spatial scales (<5 m). Using null models of phylogenetic turnover, we showed that this heterogeneity between hypolithons is probably due to stochastic effects such as dispersal limitations, which is entirely consistent with the physically isolated nature of the hypolithic communities ('islands in the sand') and the almost complete absence of a liquid continuum as a mode of microbial transport between communities.}, }
@article {pmid33067657, year = {2020}, author = {Han, D and Richter-Heitmann, T and Kim, IN and Choy, E and Park, KT and Unno, T and Kim, J and Nam, SI}, title = {Survey of Bacterial Phylogenetic Diversity During the Glacier Melting Season in an Arctic Fjord.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01616-4}, pmid = {33067657}, issn = {1432-184X}, support = {NRF-2015M1A5A1037243//National Research Foundation of Korea/ ; NRF-2018R1D1A3B07041743//National Research Foundation of Korea/ ; NRF-2019R1I1A1A01058140//National Research Foundation of Korea/ ; }, abstract = {To understand bacterial biogeography in response to the hydrographic impact of climate change derived from the Arctic glacier melting, we surveyed bacterial diversity and community composition using bacterial 16S rRNA gene metabarcoding in the seawaters of Kongsfjorden, Svalbard, during summer 2016. In the present study, bacterial biogeography in the Kongsfjorden seawaters showed distinct habitat patterns according to water mass classification and habitat transition between Atlantic and fjord surface waters. Moreover, we estimated phylogenetic diversity of bacterial communities using the net relatedness, nearest taxon, and beta nearest taxon indices. We found the influence of freshwater input from glacier melting in shaping bacterial assemblage composition through the stochastic model. We further evaluated bacterial contributions to phytoplankton-derived dimethylsulfoniopropionate (DMSP) using a quantitative PCR (qPCR) measurement with demethylation (dmdA) and cleavage (dddP) genes of two fundamentally different processes. Our qPCR results imply that bacterial DMSP degradation follows the Atlantic inflow during summer in Kongsfjorden. These findings suggest that the Atlantic inflow and glacial melting influence bacterial community composition and assembly processes and thus affect the degradation of phytoplankton-derived organic matter in an Arctic fjord.}, }
@article {pmid33067588, year = {2020}, author = {Mueller, AJ and Jung, MY and Strachan, CR and Herbold, CW and Kirkegaard, RH and Wagner, M and Daims, H}, title = {Genomic and kinetic analysis of novel Nitrospinae enriched by cell sorting.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-020-00809-6}, pmid = {33067588}, issn = {1751-7370}, support = {W1257//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; W1257//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; 294343//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; }, abstract = {Chemolithoautotrophic nitrite-oxidizing bacteria (NOB) are key players in global nitrogen and carbon cycling. Members of the phylum Nitrospinae are the most abundant, known NOB in the oceans. To date, only two closely affiliated Nitrospinae species have been isolated, which are only distantly related to the environmentally abundant uncultured Nitrospinae clades. Here, we applied live cell sorting, activity screening, and subcultivation on marine nitrite-oxidizing enrichments to obtain novel marine Nitrospinae. Two binary cultures were obtained, each containing one Nitrospinae strain and one alphaproteobacterial heterotroph. The Nitrospinae strains represent two new genera, and one strain is more closely related to environmentally abundant Nitrospinae than previously cultured NOB. With an apparent half-saturation constant of 8.7 ± 2.5 µM, this strain has the highest affinity for nitrite among characterized marine NOB, while the other strain (16.2 ± 1.6 µM) and Nitrospina gracilis (20.1 ± 2.1 µM) displayed slightly lower nitrite affinities. The new strains and N. gracilis share core metabolic pathways for nitrite oxidation and CO2 fixation but differ remarkably in their genomic repertoires of terminal oxidases, use of organic N sources, alternative energy metabolisms, osmotic stress and phage defense. The new strains, tentatively named &quot;Candidatus Nitrohelix vancouverensis&quot; and &quot;Candidatus Nitronauta litoralis&quot;, shed light on the niche differentiation and potential ecological roles of Nitrospinae.}, }
@article {pmid33067398, year = {2020}, author = {Shibl, AA and Isaac, A and Ochsenkühn, MA and Cárdenas, A and Fei, C and Behringer, G and Arnoux, M and Drou, N and Santos, MP and Gunsalus, KC and Voolstra, CR and Amin, SA}, title = {Diatom modulation of select bacteria through use of two unique secondary metabolites.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {44}, pages = {27445-27455}, pmid = {33067398}, issn = {1091-6490}, abstract = {Unicellular eukaryotic phytoplankton, such as diatoms, rely on microbial communities for survival despite lacking specialized compartments to house microbiomes (e.g., animal gut). Microbial communities have been widely shown to benefit from diatom excretions that accumulate within the microenvironment surrounding phytoplankton cells, known as the phycosphere. However, mechanisms that enable diatoms and other unicellular eukaryotes to nurture specific microbiomes by fostering beneficial bacteria and repelling harmful ones are mostly unknown. We hypothesized that diatom exudates may tune microbial communities and employed an integrated multiomics approach using the ubiquitous diatom Asterionellopsis glacialis to reveal how it modulates its naturally associated bacteria. We show that A. glacialis reprograms its transcriptional and metabolic profiles in response to bacteria to secrete a suite of central metabolites and two unusual secondary metabolites, rosmarinic acid and azelaic acid. While central metabolites are utilized by potential bacterial symbionts and opportunists alike, rosmarinic acid promotes attachment of beneficial bacteria to the diatom and simultaneously suppresses the attachment of opportunists. Similarly, azelaic acid enhances growth of beneficial bacteria while simultaneously inhibiting growth of opportunistic ones. We further show that the bacterial response to azelaic acid is numerically rare but globally distributed in the world's oceans and taxonomically restricted to a handful of bacterial genera. Our results demonstrate the innate ability of an important unicellular eukaryotic group to modulate select bacteria in their microbial consortia, similar to higher eukaryotes, using unique secondary metabolites that regulate bacterial growth and behavior inversely across different bacterial populations.}, }
@article {pmid33067195, year = {2020}, author = {Co, R and Hug, LA}, title = {A Need for Improved Cellulase Identification from Metagenomic Sequence Data.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {1}, pages = {}, pmid = {33067195}, issn = {1098-5336}, abstract = {Improved sequencing technologies and the maturation of metagenomic approaches allow the identification of gene variants with potential industrial applications, including cellulases. Cellulase identification from metagenomic environmental surveys is complicated by inconsistent nomenclature and multiple categorization systems. Here, we summarize the current classification and nomenclature systems, with recommendations for improvements to these systems. Addressing the issues described will strengthen the annotation of cellulose-active enzymes from environmental sequence data sets-a rapidly growing resource in environmental and applied microbiology.}, }
@article {pmid33066774, year = {2020}, author = {Yan, H and Yu, B and Degroote, J and Spranghers, T and Van Noten, N and Majdeddin, M and Van Poucke, M and Peelman, L and De Vrieze, J and Boon, N and Gielen, I and Smet, S and Chen, D and Michiels, J}, title = {Antibiotic affects the gut microbiota composition and expression of genes related to lipid metabolism and myofiber types in skeletal muscle of piglets.}, journal = {BMC veterinary research}, volume = {16}, number = {1}, pages = {392}, pmid = {33066774}, issn = {1746-6148}, support = {CARS-36//earmarked fund for the China Agriculture Research System/ ; 31672436//National Natural Science Foundation of China/ ; 31730091//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Early-life antibiotic administration is known to affect gut microbiota and host adiposity, but the effects of antibiotic exposure on skeletal muscle properties remain unknown. The present study evaluated the changes in skeletal muscle properties including myofiber characteristics and composition, as well as intramuscular fat (IMF) content in skeletal muscle of piglets when exposed to a tylosin-containing diet.<br><br>RESULTS: A total of 18 piglets (28 days of age) were randomly allocated into two groups: control basal diet (Control) and Control + 100 mg tylosin phosphate/kg of feed (Antibiotic). The trial lasted for 39 days. High-throughput amplicon sequencing revealed that no significant difference in initial gut microbiota composition was existed between Control and Antibiotic groups. Antibiotic administration increased body weight and growth rate and decreased feed to gain ratio of pigs (P < 0.05). The carcass lean and fat volumes of pigs were increased by the tylosin administration (P < 0.05). Antibiotic treatment increased myofiber density and the expression of genes related to type I and type IIb myofibers in longissimus muscle (P < 0.05). The IMF content in longissimus muscle was increased by antibiotic exposure (P < 0.05). Antibiotic administration increased expression of genes related to fatty acid uptake and de novo synthesis, and decreased expression of genes related to triglyceride hydrolysis (P < 0.05). Tylosin administration affected taxonomic distribution and beta diversity of the caecal and colonic microbiota of piglets.<br><br>CONCLUSION: These results confirm that the growth performance, myofiber composition and muscle lipid metabolism are affected by antibiotic administration, which may be associated with an altered gut microbiota, suggesting that the gut microbiota could be served as a potential target for modulating skeletal muscle properties of host.}, }
@article {pmid33066697, year = {2020}, author = {Amat, S and Lantz, H and Munyaka, PM and Willing, BP}, title = {Prevotella in Pigs: The Positive and Negative Associations with Production and Health.}, journal = {Microorganisms}, volume = {8}, number = {10}, pages = {}, pmid = {33066697}, issn = {2076-2607}, abstract = {A diverse and dynamic microbial community (known as microbiota) resides within the pig gastrointestinal tract (GIT). The microbiota contributes to host health and performance by mediating nutrient metabolism, stimulating the immune system, and providing colonization resistance against pathogens. Manipulation of gut microbiota to enhance growth performance and disease resilience in pigs has recently become an active area of research in an era defined by increasing scrutiny of antimicrobial use in swine production. In order to develop microbiota-targeted strategies, or to identify potential next-generation probiotic strains originating from the endogenous members of GIT microbiota in pigs, it is necessary to understand the role of key commensal members in host health. Many, though not all, correlative studies have associated members of the genus Prevotella with positive outcomes in pig production, including growth performance and immune response; therefore, a comprehensive review of the genus in the context of pig production is needed. In the present review, we summarize the current state of knowledge about the genus Prevotella in the intestinal microbial community of pigs, including relevant information from other animal species that provide mechanistic insights, and identify gaps in knowledge that must be addressed before development of Prevotella species as next-generation probiotics can be supported.}, }
@article {pmid33065340, year = {2020}, author = {Jacquemyn, H and Pozo, MI and Álvarez-Pérez, S and Lievens, B and Fukami, T}, title = {Yeast-nectar interactions: metacommunities and effects on pollinators.}, journal = {Current opinion in insect science}, volume = {44}, number = {}, pages = {35-40}, doi = {10.1016/j.cois.2020.09.014}, pmid = {33065340}, issn = {2214-5753}, abstract = {About 90% of all flowering plant species are pollinated by animals. Animals are attracted to flowers because they often provide food in the form of nectar and pollen. While floral nectar is assumed to be initially sterile, it commonly becomes colonized by yeasts after animals have visited the flowers. Although yeast communities in floral nectar appear simple, community assembly depends on a complex interaction between multiple factors. Yeast colonization has a significant effect on the scent of floral nectar, foraging behavior of insects and nectar consumption. Consumption of nectar colonized by yeasts has been shown to improve bee fitness, but effects largely depended on yeast species. Altogether, these results indicate that dispersal, colonization history and nectar chemistry strongly interact and have pronounced effects on yeast metacommunities and, as a result, on bee foraging behavior and fitness. Future research directions to better understand the dynamics of plant-microbe-pollinator interactions are discussed.}, }
@article {pmid33062716, year = {2020}, author = {Almugadam, BS and Liu, Y and Chen, SM and Wang, CH and Shao, CY and Ren, BW and Tang, L}, title = {Alterations of Gut Microbiota in Type 2 Diabetes Individuals and the Confounding Effect of Antidiabetic Agents.}, journal = {Journal of diabetes research}, volume = {2020}, number = {}, pages = {7253978}, pmid = {33062716}, issn = {2314-6753}, abstract = {Type 2 diabetes is a leading cause of morbidity and a common risk of several disorders. Identifying the microbial ecology changes is essential for disease prediction, therapy, and prevention. Thus, our study is aimed at investigating the intestinal microbiota among healthy and type 2 diabetes individuals and exploring the effect of antidiabetic agents on gut bacterial flora. 24 type 2 diabetes (metformin, glimepiride, and nontherapeutic subgroups; N = 8) and 24 healthy control subjects were enrolled in this study, and intestinal bacterial microbiota was investigated by analyzing V3-V4 regions of 16S rRNA gene sequence. Numerous alterations were observed in the gut microbial community of diabetic individuals. These changes were characterized by a significant lowered abundance of Faecalibacterium, Fusobacterium, Dialister, and Elusimicrobium in the nontherapeutic subgroup compared to the healthy control group. Likewise, correlation analysis showed a substantial decline in gut microbiota richness and diversity with the duration of illness. Furthermore, antidiabetic agents restored to some extent the richness and diversity of gut microbiota and improved the abundance of many beneficial bacteria with a significant increase of Methanobrevibacter in the metformin subcategory compared to the nontherapeutic subgroup. In return, they decreased the abundance of some opportunistic pathogens. The findings of this study have added a novel understanding about the pathogenesis of the disease and the mechanisms underlying antidiabetic therapy, which are of potential interest for therapeutic lines and further studies.}, }
@article {pmid33059158, year = {2021}, author = {Chique, C and Hynds, P and Burke, LP and Morris, D and Ryan, MP and O'Dwyer, J}, title = {Contamination of domestic groundwater systems by verotoxigenic escherichia coli (VTEC), 2003-2019: A global scoping review.}, journal = {Water research}, volume = {188}, number = {}, pages = {116496}, doi = {10.1016/j.watres.2020.116496}, pmid = {33059158}, issn = {1879-2448}, mesh = {*Groundwater ; Humans ; Prospective Studies ; *Shiga-Toxigenic Escherichia coli ; Water Supply ; *Waterborne Diseases ; }, abstract = {Verocytotoxin-producing E. coli (VTEC) are important agents of diarrhoeal disease in humans globally. As a noted waterborne disease, emphasis has been given to the study VTEC in surface waters, readily susceptible to microbial contamination. Conversely, the status of VTEC in potable groundwater sources, generally regarded as a &quot;safe&quot; drinking-water supply remains largely understudied. As such, this investigation presents the first scoping review seeking to determine the global prevalence of VTEC in groundwater supply sources intended for human consumption. Twenty-three peer-reviewed studies were identified and included for data extraction. Groundwater sample and supply detection rates (estimated 0.6 and 1.3%, respectively) indicate VTEC is infrequently present in domestic groundwater sources. However, where generic (fecal indicator) E. coli are present, the VTEC to E. coli ratio was found to be 9.9%, representing a latent health concern for groundwater consumers. Geographically, extracted data indicates higher VTEC detection rates in urban (5.4%) and peri‑urban (4.9%) environments than in rural areas (0.9%); however, this finding is confounded by the predominance of research studies in lower income regions. Climate trends indicate local environments classified as 'temperate' (14/554; 2.5%) and 'cold' (8/392; 2%) accounted for a majority of supply sources with VTEC present, with similar detection rates encountered among supplies sampled during periods typically characterized by 'high' precipitation (15/649; 2.3%). Proposed prevalence figures may find application in preventive risk-based catchment and groundwater quality management including development of Quantitative Microbial Risk Assessments (QMRA). Notwithstanding, to an extent, a large geographical disparity in available investigations, lack of standardized reporting, and bias in source selection, restrict the transferability of research findings. Overall, the mechanisms responsible for VTEC transport and ingress into groundwater supplies remain ambiguous, representing a critical knowledge gap, and denoting a distinctive lack of integration between hydrogeological and public health research. Key recommendations and guidelines are provided for prospective studies directed at increasingly integrative and multi-disciplinary research.}, }
@article {pmid33059136, year = {2021}, author = {Ávila, C and García-Galán, MJ and Borrego, CM and Rodríguez-Mozaz, S and García, J and Barceló, D}, title = {New insights on the combined removal of antibiotics and ARGs in urban wastewater through the use of two configurations of vertical subsurface flow constructed wetlands.}, journal = {The Science of the total environment}, volume = {755}, number = {Pt 2}, pages = {142554}, doi = {10.1016/j.scitotenv.2020.142554}, pmid = {33059136}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents ; Drug Resistance, Microbial ; Genes, Bacterial ; Waste Disposal, Fluid ; *Waste Water/analysis ; *Wetlands ; }, abstract = {The occurrence and removal of 49 antibiotics and 11 selected antibiotic resistance genes (ARGs) were investigated in 2 vertical subsurface flow (VF) constructed wetlands (1.5 m2 each): an unsaturated (UVF) unit and a partially saturated (SVF) unit (0.35 m saturated out of 0.8 m) operating in parallel and treating urban wastewater. Thirteen antibiotics were detected in influent wastewater, 6 of which were present in all samples. The SVF showed statistical significance on the removal of 4 compounds (namely ciprofloxacin, ofloxacin, pipemidic acid and azithromycin), suggesting that the wider range of pH and/or redox conditions of this configuration might promote the microbial degradation of some antibiotics. In contrast, the concentration of the latter (except pipemidic acid) and also clindamycin was higher in the effluent than in the influent of the UVF. Five ARGs were detected in influent wastewater, sul1 and sul2, blaTEM, ermB and qnrS. All of them were detected also in the biofilm of both wetlands, except qnrS. Average removal rates of ARGs showed no statistical differences between both wetland units, and ranged between 46 and 97% for sul1, 33 and 97% for sul2, 9 and 99% for ermB, 18 and 97% for qnrS and 11 and 98% for blaTEM.}, }
@article {pmid33054775, year = {2020}, author = {Roussel, C and De Paepe, K and Galia, W and De Bodt, J and Chalancon, S and Leriche, F and Ballet, N and Denis, S and Alric, M and Van de Wiele, T and Blanquet-Diot, S}, title = {Spatial and temporal modulation of enterotoxigenic E. coli H10407 pathogenesis and interplay with microbiota in human gut models.}, journal = {BMC biology}, volume = {18}, number = {1}, pages = {141}, pmid = {33054775}, issn = {1741-7007}, abstract = {BACKGROUND: Enterotoxigenic Escherichia coli (ETEC) substantially contributes to the burden of diarrheal illnesses in developing countries. With the use of complementary in vitro models of the human digestive environment, TNO gastrointestinal model (TIM-1), and Mucosal Simulator of the Human Intestinal Microbial Ecosystem (M-SHIME), we provided the first detailed report on the spatial-temporal modulation of ETEC H10407 survival, virulence, and its interplay with gut microbiota. These systems integrate the main physicochemical parameters of the human upper digestion (TIM-1) and simulate the ileum vs ascending colon microbial communities and luminal vs mucosal microenvironments, captured from six fecal donors (M-SHIME).<br><br>RESULTS: A loss of ETEC viability was noticed upon gastric digestion, while a growth renewal was found at the end of jejunal and ileal digestion. The remarkable ETEC mucosal attachment helped to maintain luminal concentrations above 6 log10 mL-1 in the ileum and ascending colon up to 5 days post-infection. Seven ETEC virulence genes were monitored. Most of them were switched on in the stomach and switched off in the TIM-1 ileal effluents and in a late post-infectious stage in the M-SHIME ascending colon. No heat-labile enterotoxin production was measured in the stomach in contrast to the ileum and ascending colon. Using 16S rRNA gene-based amplicon sequencing, ETEC infection modulated the microbial community structure of the ileum mucus and ascending colon lumen.<br><br>CONCLUSIONS: This study provides a better understanding of the interplay between ETEC and gastrointestinal cues and may serve to complete knowledge on ETEC pathogenesis and inspire novel prophylactic strategies for diarrheal diseases.}, }
@article {pmid33054212, year = {2020}, author = {Li, Y and Wang, T and Camps-Arbestain, M and Suárez-Abelenda, M and Whitby, CP}, title = {Lime and/or Phosphate Application Affects the Stability of Soil Organic Carbon: Evidence from Changes in Quantity and Chemistry of the Soil Water-Extractable Organic Matter.}, journal = {Environmental science &amp; technology}, volume = {54}, number = {21}, pages = {13908-13916}, doi = {10.1021/acs.est.0c01341}, pmid = {33054212}, issn = {1520-5851}, abstract = {The mechanisms by which lime and/or phosphate addition impacts the preservation of soil organic matter (OM) are poorly understood. We explored the changes in quantity and chemistry of water-extractable organic matter (WEOM) in the bulk soil and its heavy density fraction (>1.6 g/cm3) of an unmanaged C-rich volcanic soil caused by lime and/or phosphate application. The addition of lime or phosphate caused (i) a significant increase in the WEOM, along with a decrease in its C/N ratio and an increase in its aromaticity, and (ii) changes in the WEOM chemical composition, measured with pyrolysis-gas chromatography/mass spectrometry, this being most impacted by lime application. The combined effect of lime and phosphate addition on the quantity and chemistry of WEOM was larger than the effects of separate lime and phosphate additions. By comparing the response of the bulk soil and the heavy fraction, we infer that phosphate has a greater contribution to the destabilization of vulnerable particulate OM, while lime causes a comparable disruption in the particulate OM and that in the heavy fraction. These findings provide a mechanistic insight into the decreased OM stability after liming and/or P fertilizing Andosols. They have implications for designing climate-smart management practices for these soils.}, }
@article {pmid33051738, year = {2020}, author = {Zhang, W and Wang, X and Li, Y and Liu, Z and Li, D and Wen, X and Feng, Y and Zhang, X}, title = {Pinewood Nematode Alters the Endophytic and Rhizospheric Microbial Communities of Pinus massoniana.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01619-1}, pmid = {33051738}, issn = {1432-184X}, support = {2018YFC1200400//National Key R &amp; D Program of China/ ; 31901315//Young Scientists Fund/ ; }, abstract = {Pinewood nematode, Bursaphelenchus xylophilus, is one of the greatest threats to pine trees and is spreading all over the world. During the nematode's pathogenesis, plant microorganisms play important roles. However, many microbial communities, such as that in Pinus massoniana, a major host of B. xylophilus that is widely distributed in China, are not well studied, especially the fungal communities. Here, the endophytic and rhizospheric bacterial and fungal communities associated with healthy and B. xylophilus-infected P. massoniana were analyzed. The results showed that 7639 bacterial and 3108 fungal OTUs were annotated from samples of P. massoniana, the rhizosphere, and B. xylophilus. There were significant diversity differences of endophytic microbes between healthy and infected P. massoniana. The abundances of endophytic bacteria Paenibacillus, unidentified_Burkholderiaceae, Serratia, Erwinia, and Pseudoxanthomonas and fungi Penicillifer, Zygoascus, Kirschsteiniothelia, Cyberlindnera, and Sporothrix in infected pines were greater than those in healthy pines, suggesting an association of particular microbial abundances with the pathogenesis of B. xylophilus in pines. Meanwhile, the abundances of microbes of unidentified_Burkholderiaceae, Saitozyma, and Pestalotiopsis were greater and Acidothermus and Trichoderma were lower in the rhizosphere under infected pines than those under healthy pines and the differences might be caused by B. xylophilus-induced weakening of the health of pines. Our study explored the endophytic and rhizospheric microbial community changes potentially caused by B. xylophilus infection of pines.}, }
@article {pmid33049639, year = {2021}, author = {Ni, N and Li, X and Yao, S and Shi, R and Kong, D and Bian, Y and Jiang, X and Song, Y}, title = {Biochar applications combined with paddy-upland rotation cropping systems benefit the safe use of PAH-contaminated soils: From risk assessment to microbial ecology.}, journal = {Journal of hazardous materials}, volume = {404}, number = {Pt A}, pages = {124123}, doi = {10.1016/j.jhazmat.2020.124123}, pmid = {33049639}, issn = {1873-3336}, abstract = {This study aimed to establish a method allowing the safe use of polycyclic aromatic hydrocarbon (PAH)-contaminated soils through the combination of biochar applications and different cropping systems. The impact of biochar applications under different cropping systems on the human health risks of PAHs and soil microbiology was elucidated. The residual PAHs were the lowest in rhizosphere soils amended with 2% corn straw-derived biochar pyrolyzed at 300 °C (CB300) under the paddy-upland rotation cropping (PURC) system. Human health risks resulting from the ingestion of PAH-contaminated carrot roots / rice grains under the PURC system were significantly lower than those under continuous upland cropping systems. The greatest diversity, richness and network complexity of soil microbial communities occurred under the PURC system combined with the 2% CB300 treatment. Soil microbial functions associated with soil health and PAH biodegradation were enhanced under this strategy, while the pathogen group was inhibited. Primarily owing to its high sorption capacity, bamboo-derived biochar pyrolyzed at 700 °C realized in the reduction of PAHs, but weakly influenced shifts in soil microbial communities. Overall, the combination of PURC systems and low-temperature-pyrolyzed nutrient-rich biochar could efficiently reduce the human health risks of PAHs and improve soil microbial ecology in agricultural fields.}, }
@article {pmid33047413, year = {2020}, author = {Dini-Andreote, F and Kowalchuk, GA and Prosser, JI and Raaijmakers, JM}, title = {Towards meaningful scales in ecosystem microbiome research.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.15276}, pmid = {33047413}, issn = {1462-2920}, }
@article {pmid33043868, year = {2020}, author = {Seto, M and Iwasa, Y}, title = {Microbial material cycling, energetic constraints and ecosystem expansion in subsurface ecosystems.}, journal = {Proceedings. Biological sciences}, volume = {287}, number = {1931}, pages = {20200610}, pmid = {33043868}, issn = {1471-2954}, mesh = {*Ecological and Environmental Phenomena ; *Ecosystem ; *Environmental Microbiology ; }, abstract = {To harvest energy from chemical reactions, microbes engage in diverse catabolic interactions that drive material cycles in the environment. Here, we consider a simple mathematical model for cycling reactions between alternative forms of an element (A and Ae), where reaction 1 converts A to Ae and reaction 2 converts Ae to A. There are two types of microbes: type 1 microbes harness reaction 1, and type 2 microbes harness reaction 2. Each type receives its own catabolic resources from the other type and provides the other type with the by-products as the catabolic resources. Analyses of the model show that each type increases its steady-state abundance in the presence of the other type. The flux of material flow becomes faster in the presence of microbes. By coupling two catabolic reactions, types 1 and 2 can also expand their realized niches through the abundant resource premium, the effect of relative quantities of products and reactants on the available chemical energy, which is especially important for microbes under strong energetic limitations. The plausibility of mutually beneficial interactions is controlled by the available chemical energy (Gibbs energy) of the system. We conclude that mutualistic catabolic interactions can be an important factor that enables microbes in subsurface ecosystems to increase ecosystem productivity and expand the ecosystem.}, }
@article {pmid33042180, year = {2020}, author = {Otlewska, A and Migliore, M and Dybka-Stępień, K and Manfredini, A and Struszczyk-Świta, K and Napoli, R and Białkowska, A and Canfora, L and Pinzari, F}, title = {When Salt Meddles Between Plant, Soil, and Microorganisms.}, journal = {Frontiers in plant science}, volume = {11}, number = {}, pages = {553087}, pmid = {33042180}, issn = {1664-462X}, abstract = {In extreme environments, the relationships between species are often exclusive and based on complex mechanisms. This review aims to give an overview of the microbial ecology of saline soils, but in particular of what is known about the interaction between plants and their soil microbiome, and the mechanisms linked to higher resistance of some plants to harsh saline soil conditions. Agricultural soils affected by salinity is a matter of concern in many countries. Soil salinization is caused by readily soluble salts containing anions like chloride, sulphate and nitrate, as well as sodium and potassium cations. Salinity harms plants because it affects their photosynthesis, respiration, distribution of assimilates and causes wilting, drying, and death of entire organs. Despite these life-unfavorable conditions, saline soils are unique ecological niches inhabited by extremophilic microorganisms that have specific adaptation strategies. Important traits related to the resistance to salinity are also associated with the rhizosphere-microbiota and the endophytic compartments of plants. For some years now, there have been studies dedicated to the isolation and characterization of species of plants' endophytes living in extreme environments. The metabolic and biotechnological potential of some of these microorganisms is promising. However, the selection of microorganisms capable of living in association with host plants and promoting their survival under stressful conditions is only just beginning. Understanding the mechanisms of these processes and the specificity of such interactions will allow us to focus our efforts on species that can potentially be used as beneficial bioinoculants for crops.}, }
@article {pmid33040164, year = {2020}, author = {Wisnoski, NI and Lennon, JT}, title = {Microbial community assembly in a multi-layer dendritic metacommunity.}, journal = {Oecologia}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00442-020-04767-w}, pmid = {33040164}, issn = {1432-1939}, support = {DEB-1442246//National Science Foundation (US)/ ; W911NF-14-1-0411//Army Research Office/ ; }, abstract = {A major goal of metacommunity ecology is to infer the local- and regional-scale processes that underlie community assembly. In dendritic ecological networks, branching patterns and directional flow can alter the balance between local and regional factors during assembly. Vertical habitat structure may further affect community assembly in dendritic metacommunities. In this study, we analyzed the bacterial metacommunity of a fifth-order mountain stream network to assess differences in community assembly (1) between planktonic and benthic habitats, (2) across spatial scales, and (3) between headwater and downstream regions of the network. Using taxonomic and phylogenetic null modeling, we found habitat-specific spatial patterns of community assembly across the dendritic network. Compositional differences between planktonic and benthic communities were maintained by variable selection, but we also found evidence of local dispersal limitation between the two habitats. Planktonic community assembly was scale dependent, transitioning from homogeneous selection at local scales to variable selection at regional scales, while benthic community assembly was less scale dependent. Variable selection structured headwaters in both habitat types, but downstream communities were primarily structured by homogeneous selection, especially in sediments. Taken together, our results show that vertical habitat structure contributes to the scale-dependent processes of community assembly across the dendritic metacommunity.}, }
@article {pmid33039899, year = {2020}, author = {Douterelo, I and Dutilh, BE and Calero, C and Rosales, E and Martin, K and Husband, S}, title = {Impact of phosphate dosing on the microbial ecology of drinking water distribution systems: Fieldwork studies in chlorinated networks.}, journal = {Water research}, volume = {187}, number = {}, pages = {116416}, doi = {10.1016/j.watres.2020.116416}, pmid = {33039899}, issn = {1879-2448}, abstract = {Phosphate is routinely dosed to ensure regulatory compliance for lead in drinking water distribution systems. Little is known about the impact of the phosphate dose on the microbial ecology in these systems and in particular the endemic biofilms. Disturbance of the biofilms and embedded material in distribution can cause regulatory failures for turbidity and metals. To investigate the impact of phosphate on developing biofilms, pipe wall material from four independent pipe sections was mobilised and collected using two twin-flushing operations a year apart in a chlorinated UK network pre- and post-phosphate dosing. Intensive monitoring was undertaken, including turbidity and water physico-chemistry, traditional microbial culture-based indicators, and microbial community structure via sequencing the 16S rRNA gene for bacteria and the ITS2 gene for fungi. Whole metagenome sequencing was used to study shifts in functional characteristics following the addition of phosphate. As an operational consequence, turbidity responses from the phosphate-enriched water were increased, particularly from cast iron pipes. Differences in the taxonomic composition of both bacteria and fungi were also observed, emphasising a community shift towards microorganisms able to use or metabolise phosphate. Phosphate increased the relative abundance of bacteria such as Pseudomonas, Paenibacillus, Massilia, Acinetobacter and the fungi Cadophora, Rhizophagus and Eupenicillium. Whole metagenome sequencing showed with phosphate a favouring of sequences related to Gram-negative bacterium type cell wall function, virions and thylakoids, but a reduction in the number of sequences associated to vitamin binding, methanogenesis and toxin biosynthesis. With current faecal indicator tests only providing risk detection in bulk water samples, this work improves understanding of how network changes effect microbial ecology and highlights the potential for new approaches to inform future monitoring or control strategies to protect drinking water quality.}, }
@article {pmid33039841, year = {2021}, author = {Alloul, A and Muys, M and Hertoghs, N and Kerckhof, FM and Vlaeminck, SE}, title = {Cocultivating aerobic heterotrophs and purple bacteria for microbial protein in sequential photo- and chemotrophic reactors.}, journal = {Bioresource technology}, volume = {319}, number = {}, pages = {124192}, doi = {10.1016/j.biortech.2020.124192}, pmid = {33039841}, issn = {1873-2976}, mesh = {Kinetics ; *Proteobacteria ; Rhodobacter ; *Rhodopseudomonas ; Waste Water ; }, abstract = {Aerobic heterotrophic bacteria (AHB) and purple non-sulfur bacteria (PNSB) are typically explored as two separate types of microbial protein, yet their properties as respectively a bulk and added-value feed ingredient make them appealing for combined use. The feasibility of cocultivation in a sequential photo- and chemotrophic approach was investigated. First, mapping the chemotrophic growth kinetics for four Rhodobacter, Rhodopseudomonas and Rhodospirillum species on different carbon sources showed a preference for fructose (µmax 2.4-3.9 d-1 28 °C; protein 36-59%DW). Secondly, a continuous photobioreactor inoculated with Rhodobacter capsulatus (VFA as C-source) delivered the starter culture for an aerobic batch reactor (fructose as C-source). This two-stage system showed an improved nutritional quality compared to AHB production: higher protein content (45-71%DW), more attractive amino/fatty acid profile and contained up to 10% PNSB. The findings strengthen protein production with cocultures and might enable the implementation of the technology for resource recovery on streams such as wastewater.}, }
@article {pmid33037304, year = {2020}, author = {De Rudder, C and Garcia-Tímermans, C and De Boeck, I and Lebeer, S and Van de Wiele, T and Calatayud Arroyo, M}, title = {Lacticaseibacillus casei AMBR2 modulates the epithelial barrier function and immune response in a donor-derived nasal microbiota manner.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {16939}, pmid = {33037304}, issn = {2045-2322}, abstract = {Live biotherapeutic products (LBP) are emerging as alternative treatment strategies for chronic rhinosinusitis. The selection of interesting candidate LBPs often involves model systems that do not include the polymicrobial background (i.e. the host microbiota) in which they will be introduced. Here, we performed a screening in a simplified model system of upper respiratory epithelium to assess the effect of nasal microbiota composition on the ability to attach and grow of a potential LBP, Lacticaseibacillus casei AMBR2, in this polymicrobial background. After selecting the most permissive and least permissive donor, L. casei AMBR2 colonisation in their respective polymicrobial backgrounds was assessed in more physiologically relevant model systems. We examined cytotoxicity, epithelial barrier function, and cytokine secretion, as well as bacterial cell density and phenotypic diversity in differentiated airway epithelium based models, with or without macrophage-like cells. L. casei AMBR2 could colonize in the presence of both selected donor microbiota and increased epithelial barrier resistance in presence of donor-derived nasal bacteria, as well as anti-inflammatory cytokine secretion in the presence of macrophage-like cells. This study highlights the potential of L. casei AMBR2 as LBP and the necessity to employ physiologically relevant model systems to investigate host-microbe interaction in LBP research.}, }
@article {pmid33033618, year = {2020}, author = {Medina, WRM and Eramo, A and Tu, M and Fahrenfeld, NL}, title = {Sewer biofilm microbiome and antibiotic resistance genes as function of pipe material, source of microbes, and disinfection: field and laboratory studies.}, journal = {Environmental science : water research &amp; technology}, volume = {6}, number = {8}, pages = {2122-2137}, pmid = {33033618}, issn = {2053-1400}, support = {R25 GM058389/GM/NIGMS NIH HHS/United States ; }, abstract = {Wastewater systems are recognized pathways for the spread of antibiotic resistant bacteria, but relatively little is known about the microbial ecology of the sewer environment. Sewer biofilm colonization by antibiotic resistance gene (ARG) carrying bacteria may impact interpretations of sewage epidemiology data, water quality during sewer overflows, and hazard to utility workers. The objectives of this research were to evaluate the (1) microbiome of real and simulated sewer biofilms and their potential to accumulate ARGs and (2) susceptibility of simulated sewer biofilms to bleach disinfection. First, biofilm samples were collected from sewer municipal systems. Next, an annular biofilm reactor was used to simulate the sewer environment while controlling the pipe material (concrete vs. PVC). The reactor was operated either as fed semi-batch with sewer sediment and synthetic wastewater (Sed-SB) or fed with a continuous flow of raw sewage (WW-CF). The abundance of ARGs, human fecal marker HF183, and 16S rRNA gene copies in these biofilm samples was measured with qPCR. Amplicon sequencing was performed to compare the prokaryotic diversity between samples. Finally, the susceptibility of reactor biofilm to a 4.6% bleach disnfection protocol was evaluated using viability qPCR and amplicon sequencing. Field and WW-CF biofilms contained the most ARG copies and the microbial community compositions varied between the different biofilm samples (field, Sed-SB, and WW-CF). Pipe material did not affect the abundance of ARGs in the reactor samples. However, log removal following bleach treatment suggested that the biofilm grown on PVC surface was primarily dislodged from the surface by the bleach treatment whereas more bacteria were lysed within the biofilm that remained on the concrete surface. Viable bacteria carrying ARGs were observed following 10 minutes of treatment. This study showed that sewer biofilms can accumulate bacteria carrying ARGs and that while bleach can reduce sewer biofilm density, the protocol tested here will not completely remove the biofilms.}, }
@article {pmid33033140, year = {2020}, author = {Peruzzo, A and Salerno, B and Tiengo, A and Petrin, S and Barco, L and Losasso, C and Orsini, M}, title = {Genome Sequence of a Persistent Campylobacter jejuni Strain, 2016-IZSVE-19-111250.}, journal = {Microbiology resource announcements}, volume = {9}, number = {41}, pages = {}, pmid = {33033140}, issn = {2576-098X}, abstract = {In this report, we present the whole-genome sequence of a Campylobacter jejuni strain isolated recursively for the last 3 years from an Italian poultry farm.}, }
@article {pmid33032584, year = {2020}, author = {Zhu, L and Xu, F and Wan, W and Yu, B and Tang, L and Yang, Y and Du, Y and Chen, Z and Xu, H}, title = {Correction to: Gut microbial characteristics of adult patients with allergy rhinitis.}, journal = {Microbial cell factories}, volume = {19}, number = {1}, pages = {192}, doi = {10.1186/s12934-020-01441-x}, pmid = {33032584}, issn = {1475-2859}, abstract = {An amendment to this paper has been published and can be accessed via the original article.}, }
@article {pmid33032128, year = {2021}, author = {Zhang, S and Xia, X and Ke, Y and Song, S and Shen, Z and Cheung, S and Liu, H}, title = {Population dynamics and interactions of Noctiluca scintillans and Mesodinium rubrum during their successive blooms in a subtropical coastal water.}, journal = {The Science of the total environment}, volume = {755}, number = {Pt 1}, pages = {142349}, doi = {10.1016/j.scitotenv.2020.142349}, pmid = {33032128}, issn = {1879-1026}, mesh = {*Dinoflagellida ; Environmental Monitoring ; *Phytoplankton ; Population Dynamics ; Water ; }, abstract = {A time series field survey were conducted in Port Shelter, a subtropical coastal water in NW Pacific, beginning before the onset of a chain of Noctiluca scintillans and/or Mesodinium rubrum blooms, and ending after the blooms had declined. At the first mixed bloom stage, seed of N. scintillans and the consequent outbreak of both N. scintillans and M. rubrum were largely due to the physical forcing. Plenty food supply and their different feeding habits supported N. scintillans and M. rubrum to bloom massively and concomitantly. Following that, there was a small N. scintillans bloom followed by a small crest of M. rubrum. Their initiation and scale were mainly affected by limited food supply and/or the inferior food source. Sudden change of wind from mild northeast wind to strong southeast wind might contribute to the termination of N. scintillans bloom. Finally, physical accumulation was the most important driving factors of the formation and dispersal of the third and largest bloom of N. scintillans. Formation of these bloom events may involve vertical migration and/or the concentrating mechanism of M. rubrum and N. scintillans. Meanwhile, biotic interactions such as mutual supportive relationship between N. scintillans and M. rubrum, and O. hongkongense fed on the progametes of N. scintillans, as well as other abiotic factors like seawater temperature and rainfall, also play important roles in this series of bloom events. Our findings have important implications for coastal zones worldwide, which are affected recurrently by these two ubiquitous red tide-forming species.}, }
@article {pmid33031481, year = {2020}, author = {Klaps, J and de Vega, C and Herrera, CM and Junker, RR and Lievens, B and Álvarez-Pérez, S}, title = {Candida metrosideri pro tempore sp. nov. and Candida ohialehuae pro tempore sp. nov., two antifungal-resistant yeasts associated with Metrosideros polymorpha flowers in Hawaii.}, journal = {PloS one}, volume = {15}, number = {10}, pages = {e0240093}, pmid = {33031481}, issn = {1932-6203}, mesh = {Amphotericin B/pharmacology ; Antifungal Agents/pharmacology ; Candida/*classification/drug effects/genetics/isolation &amp; purification ; Drug Resistance, Fungal ; Flowers/microbiology ; Hawaii ; Microbial Sensitivity Tests ; Myrtaceae/*microbiology ; Phenotype ; Phylogeny ; RNA, Ribosomal/classification/genetics/metabolism ; }, abstract = {Flowers produce an array of nutrient-rich exudates in which microbes can thrive, making them hotspots for microbial abundance and diversity. During a diversity study of yeasts inhabiting the flowers of Metrosideros polymorpha (Myrtaceae) in the Hawai'i Volcanoes National Park (HI, USA), five isolates were found to represent two novel species. Morphological and physiological characterization, and sequence analysis of the small subunit ribosomal RNA (rRNA) genes, the D1/D2 domains of the large subunit rRNA genes, the internal transcribed spacer (ITS) regions, and the genes encoding the largest and second largest subunits of the RNA polymerase II (RPB1 and RPB2, respectively), classified both species in the family Metschnikowiaceae, and we propose the names Candida metrosideri pro tempore sp. nov. (JK22T = CBS 16091 = MUCL 57821) and Candida ohialehuae pro tempore sp. nov. (JK58.2T = CBS 16092 = MUCL 57822) for such new taxa. Both novel Candida species form a well-supported subclade in the Metschnikowiaceae containing species associated with insects, flowers, and a few species of clinical importance. The ascosporic state of the novel species was not observed. The two novel yeast species showed elevated minimum inhibitory concentrations to the antifungal drug amphotericin B (>4 μg/mL). The ecology and phylogenetic relationships of C. metrosideri and C. ohialehuae are also discussed.}, }
@article {pmid33027736, year = {2020}, author = {Dettling, A and Wedel, C and Huptas, C and Hinrichs, J and Scherer, S and Wenning, M}, title = {High counts of thermophilic spore formers in dairy powders originate from persisting strains in processing lines.}, journal = {International journal of food microbiology}, volume = {335}, number = {}, pages = {108888}, doi = {10.1016/j.ijfoodmicro.2020.108888}, pmid = {33027736}, issn = {1879-3460}, mesh = {Animals ; Colony Count, Microbial ; Dairy Products/*microbiology ; Endospore-Forming Bacteria/classification/genetics/*isolation &amp; purification ; *Food Handling ; Food Microbiology ; Genome, Bacterial/genetics ; Germany ; Milk/microbiology ; Spores, Bacterial/classification/genetics/*isolation &amp; purification ; }, abstract = {During the last decades, thermophilic spore counts became a very important quality parameter for manufacturers with regard to powdered dairy products. Low-spore count powders are highly demanded but challenging to produce when high production volume and long process times are intended. In this study a detailed monitoring of microbial levels in three skim milk powder plants was conducted. Anoxybacillus flavithermus was found to be primarily responsible for increased spore levels with increasing spore numbers being detected after 6-8 h already during initial processing steps. Simultaneously, the species composition shifted from a diverse bulk tank milk microbiota where different Bacillus species represented around 90% of the thermophilic bacteria to a dominance of A. flavithermus in the end product. The analysis of A. flavithermus isolates from different powder batches with RAPD PCR revealed recurring patterns in each of the eight German manufacturers sampled over several months. The high relatedness of isolates exhibiting identical RAPD patterns was exemplified by cgMLST based on whole genome sequences. We assume that A. flavithermus strains persisted in production plants and were not eliminated by cleaning. It is concluded that such persisting strains recurrently recontaminated subsequent powder productions. The data highlight that a targeted optimization of cleaning and disinfection procedures is the most promising measure to effectively reduce thermophilic spore counts in German dairy powders.}, }
@article {pmid33026073, year = {2020}, author = {Thomas, S and Lucie, EM and Adeline, S and Pascale, M and Christophe, C and Tom, VW and Stéphanie, BD}, title = {Tripartite relationship between gut microbiota, intestinal mucus and dietary fibers: towards preventive strategies against enteric infections.}, journal = {FEMS microbiology reviews}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsre/fuaa052}, pmid = {33026073}, issn = {1574-6976}, abstract = {The human gut is inhabited by a large variety of microorganims involved in many physiological processes and collectively refered as to gut microbiota. Disrupted microbiome has been associated with negative health outcomes and especially could promote the onset of enteric infections. To sustain their growth and persistence within the human digestive tract, gut microbes and enteric pathogens rely on two main polysaccharide compartments, namely dietary fibers and mucus carbohydrates. Several evidences suggest that the three-way relationship between gut microbiota, dietary fibers and mucus layer could unravel the capacity of enteric pathogens to colonize the human digestive tract and ultimately lead to infection. The review starts by shedding light on similarities and differences between dietary fibers and mucus carbohydrates structures and functions. Next, we provide an overview of the interactions of these two components with the third partner, namely the gut microbiota, under health and diseased situations. The review will then provide insights into the relevance of using dietary fibers interventions to prevent enteric infections with a focus on gut microbial imbalance and impaired-mucus integrity. Facing the numerous challenges in studying microbiota-pathogen-dietary fiber-mucus interactions, we lastly describe the characteristics and potentialities of currently available in vitro models of the human gut.}, }
@article {pmid33025063, year = {2020}, author = {Gomard, Y and Flores, O and Vittecoq, M and Blanchon, T and Toty, C and Duron, O and Mavingui, P and Tortosa, P and McCoy, KD}, title = {Changes in Bacterial Diversity, Composition and Interactions During the Development of the Seabird Tick Ornithodoros maritimus (Argasidae).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01611-9}, pmid = {33025063}, issn = {1432-184X}, support = {ESPEVEC (ANR blanc ANR-13-BSV7-0018-01)//Agence Nationale de la Recherche/ ; DISTIC//Labex CeMEB (Centre Méditerranéen de l'Environnement et de la Biodiversité)/ ; }, abstract = {Characterising within-host microbial interactions is essential to understand the drivers that shape these interactions and their consequences for host ecology and evolution. Here, we examined the bacterial microbiota hosted by the seabird soft tick Ornithodoros maritimus (Argasidae) in order to uncover bacterial interactions within ticks and how these interactions change over tick development. Bacterial communities were characterised through next-generation sequencing of the V3-V4 hypervariable region of the bacterial 16S ribosomal RNA gene. Bacterial co-occurrence and co-exclusion were determined by analysing networks generated from the metagenomic data obtained at each life stage. Overall, the microbiota of O. maritimus was dominated by four bacterial genera, namely Coxiella, Rickettsia, Brevibacterium and Arsenophonus, representing almost 60% of the reads. Bacterial diversity increased over tick development, and adult male ticks showed higher diversity than did adult female ticks. Bacterial networks showed that co-occurrence was more frequent than co-exclusion and highlighted substantial shifts across tick life stages; interaction networks changed from one stage to the next with a steady increase in the number of interactions through development. Although many bacterial interactions appeared unstable across life stages, some were maintained throughout development and were found in both sexes, such as Coxiella and Arsenophonus. Our data support the existence of a few stable interactions in O. maritimus ticks, on top of which bacterial taxa accumulate from hosts and/or the environment during development. We propose that stable associations delineate core microbial interactions, which are likely to be responsible for key biological functions.}, }
@article {pmid33025062, year = {2020}, author = {Baeza, N and Mercade, E}, title = {Relationship Between Membrane Vesicles, Extracellular ATP and Biofilm Formation in Antarctic Gram-Negative Bacteria.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01614-6}, pmid = {33025062}, issn = {1432-184X}, support = {CTQ2014-59632-R//Ministerio de Ciencia, Innovación y Universidades/ ; BES-2015-074582//Ministerio de Ciencia, Innovación y Universidades/ ; 2014SGR1017//Departament d'Innovació, Universitats i Empresa, Generalitat de Catalunya/ ; }, abstract = {Biofilms offer a safe environment that favors bacterial survival; for this reason, most pathogenic and environmental bacteria live integrated in biofilm communities. The development of biofilms is complex and involves many factors, which need to be studied in order to understand bacterial behavior and control biofilm formation when necessary. We used a collection of cold-adapted Antarctic Gram-negative bacteria to study whether their ability to form biofilms is associated with a capacity to produce membrane vesicles and secrete extracellular ATP. In most of the studied strains, no correlation was found between biofilm formation and these two factors. Only Shewanella vesiculosa M7T secreted high levels of extracellular ATP, and its membrane vesicles caused a significant increase in the speed and amount of biofilm formation. In this strain, an important portion of the exogenous ATP was contained in membrane vesicles, where it was protected from apyrase treatment. These results confirm that ATP influences biofilm formation. Although the role of extracellular ATP in prokaryotes is still not well understood, the metabolic cost of its production suggests it has an important function, such as a role in biofilm formation. Thus, the liberation of extracellular ATP through membrane vesicles and its function deserve further study.}, }
@article {pmid33025061, year = {2020}, author = {Boraks, A and Plunkett, GM and Doro, TM and Alo, F and Sam, C and Tuiwawa, M and Ticktin, T and Amend, AS}, title = {Scale-Dependent Influences of Distance and Vegetation on the Composition of Aboveground and Belowground Tropical Fungal Communities.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01608-4}, pmid = {33025061}, issn = {1432-184X}, support = {1555793//National Science Foundation (US)/ ; 1555657//National Science Foundation/ ; }, abstract = {Fungi provide essential ecosystem services and engage in a variety of symbiotic relationships with trees. In this study, we investigate the spatial relationship of trees and fungi at a community level. We characterized the spatial dynamics for above- and belowground fungi using a series of forest monitoring plots, at nested spatial scales, located in the tropical South Pacific, in Vanuatu. Fungal communities from different habitats were sampled using metagenomic analysis of the nuclear ribosomal ITS1 region. Fungal communities exhibited strong distance-decay of similarity across our entire sampling range (3-110,000 m) and also at small spatial scales (< 50 m). Unexpectedly, this pattern was inverted at an intermediate scale (3.7-26 km). At large scales (80-110 km), belowground and aboveground fungal communities responded inversely to increasing geographic distance. Aboveground fungal community turnover (beta diversity) was best explained, at all scales, by geographic distance. In contrast, belowground fungal community turnover was best explained by geographic distance at small scales and tree community composition at large scales. Fungal communities from various habitats respond differently to the influences of habitat and geographic distance. At large geographic distances (80-110 km), community turnover for aboveground fungi is better explained by spatial distance, whereas community turnover for belowground fungi is better explained by plant community turnover. Future syntheses of spatial dynamics among fungal communities must explicitly consider geographic scale to appropriately contextualize community turnover.}, }
@article {pmid33025060, year = {2020}, author = {Fernandes, NM and Campello-Nunes, PH and Paiva, TS and Soraes, CAG and Silva-Neto, ID}, title = {Ciliate Diversity From Aquatic Environments in the Brazilian Atlantic Forest as Revealed by High-Throughput DNA Sequencing.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01612-8}, pmid = {33025060}, issn = {1432-184X}, support = {E-26/202.325/2018//Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ)/ ; E-26/202.326/2018//Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ)/ ; 426648/2016-1//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, abstract = {Rainforest aquatic ecosystems include complex habitats with scarce information on their unicellular eukaryote diversity and community structure. We have investigated the diversity of ciliates in freshwater and brackish environments along the Brazilian Atlantic Forest, based on the hypervariable V4 region of the 18S-rDNA obtained by high-throughput DNA sequencing. Our analyses detected 409 ciliate taxonomic units (OTUs), mostly attributed to the classes Oligohymenophorea and Spirotrichea. A total of 11 classes, 12 subclasses, 112 genera, and 144 species were reported. We found the following: (a) the ciliate communities are more diverse in freshwater- than in Atlantic Forest-associated brackish environments; (b) the ciliate communities are composed by a small amount of highly abundant OTUs, but a high number of low-abundant or rare OTUs; (c) nearly one-third of the ciliate OTUs share less than 97% sequence identity to reference sequences and (d) phylogenetic inference supports the hypothesis that the V4 region of the Ciliophora 18S-rDNA is a suitable marker for accurate evolutionary inferences at class level. Our results showed that a considerable fraction of the HTS-detected diversity of ciliates from Brazilian Atlantic Forest is not represented in the currently available molecular databases.}, }
@article {pmid33024291, year = {2020}, author = {Giguere, AT and Eichorst, SA and Meier, DV and Herbold, CW and Richter, A and Greening, C and Woebken, D}, title = {Acidobacteria are active and abundant members of diverse atmospheric H2-oxidizing communities detected in temperate soils.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-020-00750-8}, pmid = {33024291}, issn = {1751-7370}, support = {P 26392/FWF_/Austrian Science Fund FWF/Austria ; 636928//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; P26392-B20//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; }, abstract = {Significant rates of atmospheric dihydrogen (H2) consumption have been observed in temperate soils due to the activity of high-affinity enzymes, such as the group 1h [NiFe]-hydrogenase. We designed broadly inclusive primers targeting the large subunit gene (hhyL) of group 1h [NiFe]-hydrogenases for long-read sequencing to explore its taxonomic distribution across soils. This approach revealed a diverse collection of microorganisms harboring hhyL, including previously unknown groups and taxonomically not assignable sequences. Acidobacterial group 1h [NiFe]-hydrogenase genes were abundant and expressed in temperate soils. To support the participation of acidobacteria in H2 consumption, we studied two representative mesophilic soil acidobacteria, which expressed group 1h [NiFe]-hydrogenases and consumed atmospheric H2 during carbon starvation. This is the first time mesophilic acidobacteria, which are abundant in ubiquitous temperate soils, have been shown to oxidize H2 down to below atmospheric concentrations. As this physiology allows bacteria to survive periods of carbon starvation, it could explain the success of soil acidobacteria. With our long-read sequencing approach of group 1h [NiFe]-hydrogenase genes, we show that the ability to oxidize atmospheric levels of H2 is more widely distributed among soil bacteria than previously recognized and could represent a common mechanism enabling bacteria to persist during periods of carbon deprivation.}, }
@article {pmid33022257, year = {2020}, author = {Koskella, B}, title = {The phyllosphere.}, journal = {Current biology : CB}, volume = {30}, number = {19}, pages = {R1143-R1146}, doi = {10.1016/j.cub.2020.07.037}, pmid = {33022257}, issn = {1879-0445}, abstract = {There is longstanding interest in studying microbial communities below ground, while little attention has historically been paid to the above ground portions of plants (the phyllosphere). The phyllosphere has been estimated to make up around 60% of the biomass across all taxa on Earth, making it a key habitat for microbial organisms. The more we study these complex and dynamic communities, the more we come to realize their importance to the health of plant hosts. Overall, the phyllosphere is proving to be both an important microbial habitat and a tractable model system for asking questions in microbial ecology and evolution.}, }
@article {pmid33021904, year = {2020}, author = {Taparia, T and Hendrix, E and Hendriks, M and Krijger, M and de Boer, W and Van der Wolf, J}, title = {Comparative studies on the disease prevalence and population dynamics of ginger blotch and brown blotch pathogens of button mushrooms.}, journal = {Plant disease}, volume = {}, number = {}, pages = {}, doi = {10.1094/PDIS-06-20-1260-RE}, pmid = {33021904}, issn = {0191-2917}, abstract = {INTRODUCTION: Bacterial blotch is one of the most economically important diseases of button mushrooms. Knowledge on mechanisms of disease expression, inoculum thresholds and disease management is limited to the most-well known pathogen, Pseudomonas tolaasii. Recent outbreaks in Western Europe have been attributed to 'P. gingeri' and P. salomonii for ginger and brown blotch, respectively, although information on their identity, infection dynamics and pathogenicity is largely lacking.<br><br>METHODS: The disease pressure in an experimental mushroom cultivation facility was evaluated for 'P. gingeri' and P. salomonii over varying inoculation densities, casing soil types, environmental humidity and cultivation cycles. The pathogen population structures in the casing soils were simultaneously tracked across the cropping cycle using highly specific and sensitive TaqmanTM-qPCR assays.<br><br>RESULTS: 'P. gingeri' caused disease outbreaks at lower inoculum thresholds (104 cfu/g) in the soil than P. salomonii (105 cfu/g). Ginger blotch generically declined in later harvest cycles, although brown blotch did not. Casing soils were differentially suppressive to blotch diseases, based on their composition and supplementation. Endemic pathogen populations increased across the cultivation cycle although the inoculated pathogen populations were consistent between the 1st and 2nd flush.<br><br>CONCLUSION: 'P. gingeri' and P. salomonii have unique infection and population dynamics, that vary over soil types. Their endemic populations are also differently abundant in peat-based casing soils. This knowledge is essential to interpret diagnostic results from screening mushroom farms and design localized disease control strategies.}, }
@article {pmid33021677, year = {2020}, author = {Kolátková, V and Čepička, I and Hoffman, R and Vohník, M}, title = {Marinomyxa Gen. Nov. Accommodates Gall-Forming Parasites of the Tropical to Subtropical Seagrass Genus Halophila and Constitutes a Novel Deep-Branching Lineage Within Phytomyxea (Rhizaria: Endomyxa).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01615-5}, pmid = {33021677}, issn = {1432-184X}, support = {1308218//Grantová Agentura, Univerzita Karlova/ ; }, abstract = {Marine representatives of Phytomyxea (SAR: Rhizaria: Endomyxa), a peculiar class of obligate endobiotic parasites, are a greatly understudied ecological group of protists infecting many algal, diatom, and seagrass species. Very little is known about the actual diversity, ecology, and pathogenic potential of these organisms and their taxonomic treatment in many cases follows outdated morphotaxonomic concepts. Here we focused on resolving the phylogenetic relations of the phytomyxean parasites of the widespread seagrass genus Halophila. We report the first finding of Plasmodiophora halophilae, the parasite of ovate-leaf Halophila species, after more than 100 years since its original description in 1913. We provide additional information on its anatomy, morphology, distribution, and host range, together with a phylogenetic evidence that it is congeneric with the recently rediscovered species infecting the invasive seagrass Halophila stipulacea in the Mediterranean Sea. Despite the previously hypothesized affiliation of the latter to Tetramyxa, our phylogenetic analyses of the 18S rRNA gene place Tetramyxa parasitica (a parasite of brackish water phanerogams and the type species of the genus) in the freshwater/terrestrial phytomyxean order Plasmodiophorida and reveal that phytomyxids associated with Halophila spp. form a separate deep-branching clade within the class proposed here as Marinomyxa gen. nov. We further argue that M. marina infecting H. stipulacea is most likely a species-specific parasite and implies their comigration through the Suez Canal.}, }
@article {pmid33013993, year = {2020}, author = {Jueterbock, A and Boström, C and Coyer, JA and Olsen, JL and Kopp, M and Dhanasiri, AKS and Smolina, I and Arnaud-Haond, S and Van de Peer, Y and Hoarau, G}, title = {The Seagrass Methylome Is Associated With Variation in Photosynthetic Performance Among Clonal Shoots.}, journal = {Frontiers in plant science}, volume = {11}, number = {}, pages = {571646}, pmid = {33013993}, issn = {1664-462X}, abstract = {Evolutionary theory predicts that clonal organisms are more susceptible to extinction than sexually reproducing organisms, due to low genetic variation and slow rates of evolution. In agreement, conservation management considers genetic variation as the ultimate measure of a population's ability to survive over time. However, clonal plants are among the oldest living organisms on our planet. Here, we test the hypothesis that clonal seagrass meadows display epigenetic variation that complements genetic variation as a source of phenotypic variation. In a clonal meadow of the seagrass Zostera marina, we characterized DNA methylation among 42 shoots. We also sequenced the whole genome of 10 shoots to correlate methylation patterns with photosynthetic performance under exposure to and recovery from 27°C, while controlling for somatic mutations. Here, we show for the first time that clonal seagrass shoots display DNA methylation variation that is independent from underlying genetic variation, and associated with variation in photosynthetic performance under experimental conditions. It remains unknown to what degree this association could be influenced by epigenetic responses to transplantation-related stress, given that the methylomes showed a strong shift under acclimation to laboratory conditions. The lack of untreated control samples in the heat stress experiment did not allow us to distinguish methylome shifts induced by acclimation from such induced by heat stress. Notwithstanding, the co-variation in DNA methylation and photosynthetic performance may be linked via gene expression because methylation patterns varied in functionally relevant genes involved in photosynthesis, and in the repair and prevention of heat-induced protein damage. While genotypic diversity has been shown to enhance stress resilience in seagrass meadows, we suggest that epigenetic variation plays a similar role in meadows dominated by a single genotype. Consequently, conservation management of clonal plants should consider epigenetic variation as indicator of resilience and stability.}, }
@article {pmid33013873, year = {2020}, author = {Ou, J and Liang, S and Guo, XK and Hu, X}, title = {α-Defensins Promote Bacteroides Colonization on Mucosal Reservoir to Prevent Antibiotic-Induced Dysbiosis.}, journal = {Frontiers in immunology}, volume = {11}, number = {}, pages = {2065}, pmid = {33013873}, issn = {1664-3224}, abstract = {In addition to their established functions in host defense, accumulating evidence has suggested an emerging role for antimicrobial proteins (AMPs) in shaping commensal microbiota. However, the role of α-defensins, the most abundant AMPs of intestine, in regulating microbial ecology remains inconclusive. Here, we report that α-defensins promote commensal Bacteroides colonization by enhancing bacterial adhesion to the mucosal reservoir. Experiments utilizing mice deficient in matrix metalloproteinase 7 (MMP7), the α-defensin-activating enzyme, with rigorous littermate controls showed that α-defensin deficiency did not significantly influence steady-state intestinal microbiota. In contrast, α-defensins are essential for replenishment of commensal Bacteroides from the mucosal reservoir following antibiotics-induced dysbiosis, shown by markedly compromised recovery of Bacteroides in Mmp7-/- animals. Mechanistically, α-defensins promote Bacteroides colonization on epithelial surfaces in vivo and adhesion to epithelial cells in vitro. Moreover, α-defensins unexpectedly does not show any microbicidal activities against Bacteroides. Together, we propose that α-defensins promote commensal bacterial colonization and recovery to maintain microbial diversity upon environmental challenges.}, }
@article {pmid33013780, year = {2020}, author = {Yang, Y and Zhang, Y and Cápiro, NL and Yan, J}, title = {Genomic Characteristics Distinguish Geographically Distributed Dehalococcoidia.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {546063}, pmid = {33013780}, issn = {1664-302X}, abstract = {Dehalococcoidia (Dia) class microorganisms are frequently found in various pristine and contaminated environments. Metagenome-assembled genomes (MAGs) and single-cell amplified genomes (SAGs) studies have substantially improved the understanding of Dia microbial ecology and evolution; however, an updated thorough investigation on the genomic and evolutionary characteristics of Dia microorganisms distributed in geographically distinct environments has not been implemented. In this study, we analyzed available genomic data to unravel Dia evolutionary and metabolic traits. Based on the phylogeny of 16S rRNA genes retrieved from sixty-seven genomes, Dia microorganisms can be categorized into three groups, the terrestrial cluster that contains all Dehalococcoides and Dehalogenimonas strains, the marine cluster I, and the marine cluster II. These results reveal that a higher ratio of horizontally transferred genetic materials was found in the Dia marine clusters compared to that of the Dia terrestrial cluster. Pangenome analysis further suggests that Dia microorganisms have evolved cluster-specific enzymes (e.g., dehalogenase in terrestrial Dia, sulfite reductase in marine Dia) and biosynthesis capabilities (e.g., siroheme biosynthesis in marine Dia). Marine Dia microorganisms are likely adapted to versatile metabolisms for energy conservation besides organohalide respiration. The genomic differences between marine and terrestrial Dia may suggest distinct functions and roles in element cycling (e.g., carbon, sulfur, chlorine), which require interdisciplinary approaches to unravel the physiology and evolution of Dia in various environments.}, }
@article {pmid33013755, year = {2020}, author = {Whitworth, DE and Jurkevitch, E and Pérez, J and Fuhrmann, G and Koval, SF}, title = {Editorial: Mechanisms of Prokaryotic Predation.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {2071}, doi = {10.3389/fmicb.2020.02071}, pmid = {33013755}, issn = {1664-302X}, }
@article {pmid33013480, year = {2020}, author = {Turroni, S and Magnani, M and Kc, P and Lesnik, P and Vidal, H and Heer, M}, title = {Gut Microbiome and Space Travelers' Health: State of the Art and Possible Pro/Prebiotic Strategies for Long-Term Space Missions.}, journal = {Frontiers in physiology}, volume = {11}, number = {}, pages = {553929}, pmid = {33013480}, issn = {1664-042X}, abstract = {The upcoming exploration missions will imply a much longer duration than any of the missions flown so far. In these missions, physiological adaptation to the new environment leads to changes in different body systems, such as the cardiovascular and musculoskeletal systems, metabolic and neurobehavioral health and immune function. To keep space travelers healthy on their trip to Moon, Mars and beyond and their return to Earth, a variety of countermeasures need to be provided to maintain body functionality. From research on the International Space Station (ISS) we know today, that for instance prescribing an adequate training regime for each individual with the devices available in the respective spacecraft is still a challenge. Nutrient supply is not yet optimal and must be optimized in exploration missions. Food intake is intrinsically linked to changes in the gut microbiome composition. Most of the microbes that inhabit our body supply ecosystem benefit to the host-microbe system, including production of important resources, bioconversion of nutrients, and protection against pathogenic microbes. The gut microbiome has also the ability to signal the host, regulating the processes of energy storage and appetite perception, and influencing immune and neurobehavioral function. The composition and functionality of the microbiome most likely changes during spaceflight. Supporting a healthy microbiome by respective measures in space travelers might maintain their health during the mission but also support rehabilitation when being back on Earth. In this review we are summarizing the changes in the gut microbiome observed in spaceflight and analog models, focusing particularly on the effects on metabolism, the musculoskeletal and immune systems and neurobehavioral disorders. Since space travelers are healthy volunteers, we focus on the potential of countermeasures based on pre- and probiotics supplements.}, }
@article {pmid33008820, year = {2020}, author = {Stracke, C and Meyer, BH and Hagemann, A and Jo, E and Lee, A and Albers, SV and Cha, J and Bräsen, C and Siebers, B}, title = {Salt Stress Response of Sulfolobus acidocaldarius Involves Complex Trehalose Metabolism Utilizing a Novel Trehalose-6-Phosphate Synthase (TPS)/Trehalose-6-Phosphate Phosphatase (TPP) Pathway.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {24}, pages = {}, pmid = {33008820}, issn = {1098-5336}, mesh = {Archaeal Proteins/*genetics/metabolism ; Glucosyltransferases/genetics/metabolism ; Metabolic Networks and Pathways ; Phosphoric Monoester Hydrolases/genetics/metabolism ; Salt Stress/*genetics ; Sulfolobus acidocaldarius/*enzymology ; Trehalose/*metabolism ; }, abstract = {The crenarchaeon Sulfolobus acidocaldarius has been described to synthesize trehalose via the maltooligosyltrehalose synthase (TreY) and maltooligosyltrehalose trehalohydrolase (TreZ) pathway, and the trehalose glycosyltransferring synthase (TreT) pathway has been predicted. Deletion mutant analysis of strains with single and double deletions of ΔtreY and ΔtreT in S. acidocaldarius revealed that in addition to these two pathways, a third, novel trehalose biosynthesis pathway is operative in vivo: the trehalose-6-phosphate (T6P) synthase/T6P phosphatase (TPS/TPP) pathway. In contrast to known TPS proteins, which belong to the GT20 family, the S. acidocaldarius TPS belongs to the GT4 family, establishing a new function within this group of enzymes. This novel GT4-like TPS was found to be present mainly in the Sulfolobales The ΔtreY ΔtreT Δtps triple mutant of S. acidocaldarius, which lacks the ability to synthesize trehalose, showed no altered phenotype under standard conditions or heat stress but was unable to grow under salt stress. Accordingly, in the wild-type strain, a significant increase of intracellular trehalose formation was observed under salt stress. Quantitative real-time PCR showed a salt stress-mediated induction of all three trehalose-synthesizing pathways. This demonstrates that in Archaea, trehalose plays an essential role for growth under high-salt conditions.IMPORTANCE The metabolism and function of trehalose as a compatible solute in Archaea was not well understood. This combined genetic and enzymatic approach at the interface of microbiology, physiology, and microbial ecology gives important insights into survival under stress, adaptation to extreme environments, and the role of compatible solutes in Archaea Here, we unraveled the complexity of trehalose metabolism, and we present a comprehensive study on trehalose function in stress response in S. acidocaldarius This sheds light on the general microbiology and the fascinating metabolic repertoire of Archaea, involving many novel biocatalysts, such as glycosyltransferases, with great potential in biotechnology.}, }
@article {pmid33007535, year = {2021}, author = {Wang, H and Chen, J and Ren, P and Zhang, Y and Omondi Onyango, S}, title = {Ultrasound irradiation alters the spatial structure and improves the antioxidant activity of the yellow tea polysaccharide.}, journal = {Ultrasonics sonochemistry}, volume = {70}, number = {}, pages = {105355}, doi = {10.1016/j.ultsonch.2020.105355}, pmid = {33007535}, issn = {1873-2828}, abstract = {In this study, the impact of ultrasound irradiation on the structural characteristics and antioxidant properties of yellow tea polysaccharides with different molecular weights (Mw) were investigated. Native yellow tea polysaccharide containing YTPS-3N, YTPS-5N and YTPS-7N were prepared through precipitation with ethanol at various concentrations of 30%, 50%, and 70%, respectively, and irradiated with high intensity ultrasound (20 kHz) for 55 min to yield yellow tea polysaccharide including YTPS-3U, YTPS-5U and YTPS-7U. The molecular weight (Mw) of YTPS-3N (from 37.7 to 15.1 kDa) and YTPS-5N (from 14.6 to 5.2 kDa) sharply decreased upon ultrasound irradiation, coincidentally particle size (Zavg) was also significantly reduced for YTPS-3N (40%), YTPS-5N (48%) and YTPS-7N (54%). The high-performance liquid chromatography and Fourier transform-infrared spectroscopy analysis revealed a partial degradation of native yellow tea polysaccharide treated with ultrasound, though the monosaccharide composition was not altered. Furthermore, changes in morphology and the breakdown of native yellow tea polysaccharide upon irradiation was confirmed with the circular dichroism spectrum, atomic force and scanning electron microscopy. As a consequence, irradiation of yellow tea polysaccharide increased free radical scavenging activity with YTPS-7U exhibiting the highest levels of 2, 2-diphenyl-1-picrylhydrazyl free radical, superoxide and hydroxyl radicals scavenging activity. These results suggest that the alteration of the spatial structure of yellow tea polysaccharide can enhance its antioxidant activity which is an important property for functional foods or medicines.}, }
@article {pmid33006023, year = {2020}, author = {Gao, X and Xu, H and Yuan, X}, title = {The Overlooked Genetic Diversity in the Dryland Soil Surface-Dwelling Cyanobacterium Nostoc flagelliforme as Revealed by the Marker Gene wspA.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01610-w}, pmid = {33006023}, issn = {1432-184X}, support = {31670104//the National Natural Science Foundation of China/ ; 2020JZ-51//Natural Science Foundation of Shaanxi Province (CN)/ ; }, abstract = {Biodiversity is recognized to be relatively low in the dryland ecosystem. However, we might overlook the accumulating genetic variation in those dryland micro-populations, which should eventually increase the dryland biodiversity. In the xeric steppes of western and northwestern China, there are two soil surface-dwelling and genetically close cyanobacterial species, Nostoc commune and Nostoc flagelliforme. They respectively exhibit lamellate and filamentous colony shapes. Their individual colony is consisted of hundreds of trichomes and the common exopolysaccharide matrix. N. flagelliforme is exclusively distributed in the dryland and supposed to be evolved from N. commune. We previously reported that the morphological diversity of N. flagelliforme colonies was very limited, being either cylindrical or strip-like. In this communication, we performed single-nucleotide polymorphism (SNP) analysis of the marker gene wspA as well as phylogenetic analysis of the WspA protein in N. flagelliforme colonies to gain insights into its genetic diversity. SNP analysis suggested that there existed plentiful nucleotide variations in the individual colonies and meanwhile these variations shared certain evolutionary regularity. Phylogenetic analysis of the deduced proteins from the cloned wspA sequences suggested that the relatively regular variations were possibly dispersed in the N. flagelliforme populations of different regions. Thus, these results presented a scenario of the underestimated genetic diversity hidden behind the limited morphotype of dryland cyanobacteria. Maybe, we can consider the individual cyanobacterial colony as a potential biodiversity pool in the drylands.}, }
@article {pmid33004967, year = {2020}, author = {Walker, SP and Barrett, M and Hogan, G and Flores Bueso, Y and Claesson, MJ and Tangney, M}, title = {Non-specific amplification of human DNA is a major challenge for 16S rRNA gene sequence analysis.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {16356}, pmid = {33004967}, issn = {2045-2322}, support = {12/RC/2273/SFI_/Science Foundation Ireland/Ireland ; 15/CDA/3630/SFI_/Science Foundation Ireland/Ireland ; MRCG2016-25/HRBI_/Health Research Board/Ireland ; }, mesh = {Bacteria/genetics ; Breast Neoplasms/genetics ; DNA, Bacterial/*genetics ; Female ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; RNA, Ribosomal, 16S/*analysis ; Sequence Analysis, DNA/*methods ; }, abstract = {The targeted sequencing of the 16S rRNA gene is one of the most frequently employed techniques in the field of microbial ecology, with the bacterial communities of a wide variety of niches in the human body have been characterised in this way. This is performed by targeting one or more hypervariable (V) regions within the 16S rRNA gene in order to produce an amplicon suitable in size for next generation sequencing. To date, all technical research has focused on the ability of different V regions to accurately resolve the composition of bacterial communities. We present here an underreported artefact associated with 16S rRNA gene sequencing, namely the off-target amplification of human DNA. By analysing 16S rRNA gene sequencing data from a selection of human sites we highlighted samples susceptible to this off-target amplification when using the popular primer pair targeting the V3-V4 region of the gene. The most severely affected sample type identified (breast tumour samples) were then re-analysed using the V1-V2 primer set, showing considerable reduction in off target amplification. Our data indicate that human biopsy samples should preferably be amplified using primers targeting the V1-V2 region. It is shown here that these primers result in on average 80% less human genome aligning reads, allowing for more statistically significant analysis of the bacterial communities residing in these samples.}, }
@article {pmid33002118, year = {2020}, author = {Song, J and Klümper, U and Riber, L and Dechesne, A and Smets, BF and Sørensen, SJ and Brandt, KK}, title = {A converging subset of soil bacterial taxa is permissive to the IncP-1 plasmid pKJK5 across a range of soil copper contamination.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {11}, pages = {}, doi = {10.1093/femsec/fiaa200}, pmid = {33002118}, issn = {1574-6941}, abstract = {Stressors like metals or antibiotics can affect bacterial community permissiveness for plasmid uptake, but there is little knowledge about long-term effects of such stressors on the evolution of community permissiveness. We assessed the effect of more than 90 years of soil Cu contamination on bacterial community permissiveness (i.e. uptake ability) toward a gfp-tagged IncP-1 plasmid (pKJK5) introduced via an Escherichia coli donor. Plasmid transfer events from the donor to the recipient soil bacterial community were quantified and transconjugants were subsequently isolated by fluorescence activated cell sorting and identified by 16S rRNA gene amplicon sequencing. Transfer frequency of plasmid pKJK5 was reduced in bacterial communities extracted from highly Cu contaminated (4526 mg kg-1) soil compared to corresponding communities extracted from moderately (458 mg kg-1) Cu contaminated soil and a low Cu reference soil (15 mg kg-1). The taxonomic composition of the transconjugal pools showed remarkable similarities irrespective of the degree of soil Cu contamination and despite contrasting compositions of the extracted recipient communities and the original soil communities. Permissiveness assessed at the level of individual operational taxonomic units (OTUs; 16S rRNA gene 97% sequence similarity threshold) was only slightly affected by soil Cu level and high replicate variability of OTU-level permissiveness indicated a role of stochastic events in IncP-1 plasmid transfer or strain-to-strain permissiveness variability.}, }
@article {pmid33001506, year = {2020}, author = {Beier, S and Andersson, AF and Galand, PE and Hochart, C and Logue, JB and McMahon, K and Bertilsson, S}, title = {The environment drives microbial trait variability in aquatic habitats.}, journal = {Molecular ecology}, volume = {29}, number = {23}, pages = {4605-4617}, doi = {10.1111/mec.15656}, pmid = {33001506}, issn = {1365-294X}, support = {BE5937/2-1//Deutsche Forschungsgemeinschaft/ ; MCB-0702395//United States National Science Foundation/ ; CSP1977//Joint Genome Institute/ ; ANR-14-CE02-0004-01//Agence Nationale de la Recherche/ ; NTL-LTER DEB-1440297//Long-Term Ecological Research Program/ ; DEB-1344254//INSPIRE Award/ ; //Swedish Research Council (VR)/ ; }, abstract = {A prerequisite to improve the predictability of microbial community dynamics is to understand the mechanisms of microbial assembly. To study factors that contribute to microbial community assembly, we examined the temporal dynamics of genes in five aquatic metagenome time-series, originating from marine offshore or coastal sites and one lake. With this trait-based approach we expected to find gene-specific patterns of temporal allele variability that depended on the seasonal metacommunity size of carrier-taxa and the variability of the milieu and the substrates to which the resulting proteins were exposed. In more detail, we hypothesized that a larger seasonal metacommunity size would result in increased temporal variability of functional units (i.e., gene alleles), as shown previously for taxonomic units. We further hypothesized that multicopy genes would feature higher temporal variability than single-copy genes, as gene multiplication can result from high variability in substrate quality and quantity. Finally, we hypothesized that direct exposure of proteins to the extracellular environment would result in increased temporal variability of the respective gene compared to intracellular proteins that are less exposed to environmental fluctuations. The first two hypotheses were confirmed in all data sets, while significant effects of the subcellular location of gene products was only seen in three of the five time-series. The gene with the highest allele variability throughout all data sets was an iron transporter, also representing a target for phage infection. Previous work has emphasized the role of phage-prokaryote interactions as a major driver of microbial diversity. Our finding therefore points to a potentially important role of iron transporter-mediated phage infections for the assembly and maintenance of diversity in aquatic prokaryotes.}, }
@article {pmid33001224, year = {2020}, author = {Yavitt, JB and Roco, CA and Debenport, SJ and Barnett, SE and Shapleigh, JP}, title = {Community Organization and Metagenomics of Bacterial Assemblages Across Local Scale pH Gradients in Northern Forest Soils.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01613-7}, pmid = {33001224}, issn = {1432-184X}, support = {1007286//Agricultural Research Service/ ; }, abstract = {Soil pH has shown to predict bacterial diversity, but mechanisms are still poorly understood. To investigate how bacteria distribute themselves as a function of soil pH, we assessed community composition, diversity, assembly, and gene abundance across local (ca. 1 km) scale gradients in soil pH from ~ 3.8 to 6.5 created by differences in soil parent material in three northern forests. Plant species were the same on all sites, with no evidence of agriculture in the past. Concentrations of extractable calcium, iron, and phosphorus also varied significantly across the pH gradients. Among taxa, Alphaproteobacteria and Acidobacteria were more common in soils with acidic pH values. Overall richness and diversity of OTUs peaked at intermediate pH values. Variations in OTU richness and diversity also had a quadratic fit with concentrations of extractable calcium and phosphorus. Community assembly was via homogeneous deterministic processes in soils with acidic pH values, whereas stochastic processes dominated in soils with near-neutral pH values. Although we expected selection via genes for acid tolerance response in acidic soils, genes for genetic information processing were more selective. Taxa in higher pH soils had differential abundance of transporter genes, suggesting adaptation to acquire metabolic substrates from soils. Soil bacterial communities in northern forest soils are incredibly diverse, and we still have much to learn about how soil pH and co-varying soil parameters directly drive gene selection in this critical component of ecosystem structure.}, }
@article {pmid33001029, year = {2020}, author = {Nelson, CW and Ardern, Z and Goldberg, TL and Meng, C and Kuo, CH and Ludwig, C and Kolokotronis, SO and Wei, X}, title = {Dynamically evolving novel overlapping gene as a factor in the SARS-CoV-2 pandemic.}, journal = {eLife}, volume = {9}, number = {}, pages = {}, pmid = {33001029}, issn = {2050-084X}, support = {Postdoctoral Research Fellowship//Academia Sinica/International ; Grant//National Philanthropic Trust/International ; John D. MacArthur Professorship Chair//University of Wisconsin-Madison/International ; IOS grants #1755370 and #1758800//National Science Foundation/International ; John D MacArthur Professorship Chair//University of Wisconsin-Madison/International ; }, mesh = {Amino Acid Sequence ; Animals ; Antibodies, Viral/immunology ; Antibody Specificity ; Antigens, Viral/biosynthesis/genetics/immunology ; Betacoronavirus/*genetics/pathogenicity/physiology ; COVID-19 ; China/epidemiology ; Chiroptera/virology ; Coronavirus/genetics ; Coronavirus Infections/epidemiology/*virology ; Epitopes/genetics/immunology ; Europe/epidemiology ; Eutheria/virology ; *Evolution, Molecular ; Gene Expression Regulation, Viral ; *Genes, Overlapping ; *Genes, Viral ; Genetic Variation ; Haplotypes/genetics ; Host Specificity/*genetics ; Humans ; Models, Molecular ; Mutation ; Open Reading Frames/*genetics ; *Pandemics ; Phylogeny ; Pneumonia, Viral/epidemiology/*virology ; Protein Biosynthesis ; Protein Conformation ; RNA, Viral/genetics ; SARS-CoV-2 ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; Viral Proteins/biosynthesis/genetics/immunology ; }, abstract = {Understanding the emergence of novel viruses requires an accurate and comprehensive annotation of their genomes. Overlapping genes (OLGs) are common in viruses and have been associated with pandemics but are still widely overlooked. We identify and characterize ORF3d, a novel OLG in SARS-CoV-2 that is also present in Guangxi pangolin-CoVs but not other closely related pangolin-CoVs or bat-CoVs. We then document evidence of ORF3d translation, characterize its protein sequence, and conduct an evolutionary analysis at three levels: between taxa (21 members of Severe acute respiratory syndrome-related coronavirus), between human hosts (3978 SARS-CoV-2 consensus sequences), and within human hosts (401 deeply sequenced SARS-CoV-2 samples). ORF3d has been independently identified and shown to elicit a strong antibody response in COVID-19 patients. However, it has been misclassified as the unrelated gene ORF3b, leading to confusion. Our results liken ORF3d to other accessory genes in emerging viruses and highlight the importance of OLGs.}, }
@article {pmid33000311, year = {2020}, author = {Silva-Lima, AW and Froes, AM and Garcia, GD and Tonon, LAC and Swings, J and Cosenza, CAN and Medina, M and Penn, K and Thompson, JR and Thompson, CC and Thompson, FL}, title = {Mussismilia braziliensis White Plague Disease Is Characterized by an Affected Coral Immune System and Dysbiosis.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01588-5}, pmid = {33000311}, issn = {1432-184X}, support = {Biocomp, IODP//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; PQ//Conselho Nacional de Desenvolvimento Científico e Tecnológico (BR)/ ; CNE//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; }, abstract = {Infectious diseases are one of the major drivers of coral reef decline worldwide. White plague-like disease (WPL) is a widespread disease with a complex etiology that infects several coral species, including the Brazilian endemic species Mussismilia braziliensis. Gene expression profiles of healthy and WPL-affected M. braziliensis were analyzed in winter and summer seasons. The de novo assembly of the M. braziliensis transcriptome from healthy and white plague samples produced a reference transcriptome containing 119,088 transcripts. WPL-diseased samples were characterized by repression of immune system and cellular defense processes. Autophagy and cellular adhesion transcripts were also repressed in WPL samples, suggesting exhaustion of the coral host defenses. Seasonal variation leads to plasticity in transcription with upregulation of intracellular signal transduction, apoptosis regulation, and oocyte development in the summer. Analysis of the active bacterial rRNA indicated that Pantoea bacteria were more abundant in WPL corals, while Tistlia, Fulvivirga, and Gammaproteobacteria Ga0077536 were more abundant in healthy samples. Cyanobacteria proliferation was also observed in WPL, mostly in the winter. These results indicate a scenario of dysbiosis in WPL-affected M. braziliensis, with the loss of potentially symbiotic bacteria and proliferation of opportunistic microbes after the start of the infection process.}, }
@article {pmid32998695, year = {2020}, author = {Soverini, M and Rampelli, S and Turroni, S and Brigidi, P and Biagi, E and Candela, M}, title = {Do the human gut metagenomic species possess the minimal set of core functionalities necessary for life?.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {678}, pmid = {32998695}, issn = {1471-2164}, abstract = {BACKGROUND: Advances in bioinformatics recently allowed for the recovery of 'metagenomes assembled genomes' from human microbiome studies carried on with shotgun sequencing techniques. Such approach is used as a mean to discover new unclassified metagenomic species, putative biological entities having distinct metabolic traits.<br><br>RESULTS: In the present analysis we compare 400 genomes from isolates available on NCBI database and 10,000 human gut metagenomic species, screening all of them for the presence of a minimal set of core functionalities necessary, but not sufficient, for life. As a result, the metagenome-assembled genomes resulted systematically depleted in genes encoding for essential functions apparently needed to support autonomous bacterial life.<br><br>CONCLUSIONS: The relevant degree of lacking core functionalities that we observed in metagenome-assembled genomes raises some concerns about the effective completeness of metagenome-assembled genomes, suggesting caution in extrapolating biological information about their metabolic propensity and ecology in a complex environment like the human gastrointestinal tract.}, }
@article {pmid32996612, year = {2021}, author = {Moisan, K and Raaijmakers, JM and Dicke, M and Lucas-Barbosa, D and Cordovez, V}, title = {Volatiles from soil-borne fungi affect directional growth of roots.}, journal = {Plant, cell &amp; environment}, volume = {44}, number = {1}, pages = {339-345}, doi = {10.1111/pce.13890}, pmid = {32996612}, issn = {1365-3040}, abstract = {Volatiles play major roles in mediating ecological interactions between soil (micro)organisms and plants. It is well-established that microbial volatiles can increase root biomass and lateral root formation. To date, however, it is unknown whether microbial volatiles can affect directional root growth. Here, we present a novel method to study belowground volatile-mediated interactions. As proof-of-concept, we designed a root Y-tube olfactometer, and tested the effects of volatiles from four different soil-borne fungi on directional growth of Brassica rapa roots in soil. Subsequently, we compared the fungal volatile organic compounds (VOCs) previously profiled with Gas Chromatography-Mass Spectrometry (GC-MS). Using our newly designed setup, we show that directional root growth in soil is differentially affected by fungal volatiles. Roots grew more frequently toward volatiles from the root pathogen Rhizoctonia solani, whereas volatiles from the other three saprophytic fungi did not impact directional root growth. GC-MS profiling showed that six VOCs were exclusively emitted by R. solani. These findings verify that this novel method is suitable to unravel the intriguing chemical cross-talk between roots and soil-borne fungi and its impact on root growth.}, }
@article {pmid32996237, year = {2021}, author = {Barbera, P and Czech, L and Lutteropp, S and Stamatakis, A}, title = {SCRAPP: A tool to assess the diversity of microbial samples from phylogenetic placements.}, journal = {Molecular ecology resources}, volume = {21}, number = {1}, pages = {340-349}, pmid = {32996237}, issn = {1755-0998}, support = {//Klaus Tschira Stiftung/ ; }, abstract = {Microbial ecology research is currently driven by the continuously decreasing cost of DNA sequencing and the improving accuracy of data analysis methods. One such analysis method is phylogenetic placement, which establishes the phylogenetic identity of the anonymous environmental sequences in a sample by means of a given phylogenetic reference tree. However, assessing the diversity of a sample remains challenging, as traditional methods do not scale well with the increasing data volumes and/or do not leverage the phylogenetic placement information. Here, we present scrapp, a highly parallel and scalable tool that uses a molecular species delimitation algorithm to quantify the diversity distribution over the reference phylogeny for a given phylogenetic placement of the sample. scrapp employs a novel approach to cluster phylogenetic placements, called placement space clustering, to efficiently perform dimensionality reduction, so as to scale on large data volumes. Furthermore, it uses the phylogeny-aware molecular species delimitation method mPTP to quantify diversity. We evaluated scrapp using both, simulated and empirical data sets. We use simulated data to verify our approach. Tests on an empirical data set show that scrapp-derived metrics can classify samples by their diversity-correlated features equally well or better than existing, commonly used approaches. scrapp is available at https://github.com/pbdas/scrapp.}, }
@article {pmid32995929, year = {2020}, author = {Wang, H and Zhang, Y and Bartlett, DH and Xiao, X}, title = {Transcriptomic Analysis Reveals Common Adaptation Mechanisms Under Different Stresses for Moderately Piezophilic Bacteria.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01609-3}, pmid = {32995929}, issn = {1432-184X}, support = {2018YFC0309800//National Key Research and Development Program of China/ ; 41776173//National Natural Science Foundation of China/ ; 41530967//National Natural Science Foundation of China/ ; 91951117//National Natural Science Foundation of China/ ; 41921006//National Natural Science Foundation of China/ ; }, abstract = {Piezophiles, by the commonly accepted definition, grow faster under high hydrostatic pressure (HHP) than under ambient pressure and are believed to exist only in pressurized environments where life has adapted to HHP during evolution. However, recent findings suggest that piezophiles have developed a common adaptation strategy to cope with multiple types of stresses including HHP. These results raise a question on the ecological niches of piezophiles: are piezophiles restricted to habitats with HHP? In this study, we observed that the bacterial strains Sporosarcina psychrophila DSM 6497 and Lysinibacillus sphaericus LMG 22257, which were isolated from surface environments and then transferred under ambient pressure for half a century, possess moderately piezophilic characteristics with optimal growth pressures of 7 and 20 MPa, respectively. Their tolerance to HHP was further enhanced by MgCl2 supplementation under the highest tested pressure of 50 MPa. Transcriptomic analysis was performed to compare gene expression with and without MgCl2 supplementation under 50 MPa for S. psychrophila DSM 6497. Among 4390 genes or transcripts obtained, 915 differentially expressed genes (DEGs) were identified. These DEGs are primarily associated with the antioxidant defense system, intracellular compatible solute accumulation, and membrane lipid biosynthesis, which have been reported to be essential for cells to cope with HHP. These findings indicate no in situ pressure barrier for piezophile isolation, and cells may adopt a common adaptation strategy to cope with different stresses.}, }
@article {pmid32994415, year = {2020}, author = {Guo, X and Gao, Q and Yuan, M and Wang, G and Zhou, X and Feng, J and Shi, Z and Hale, L and Wu, L and Zhou, A and Tian, R and Liu, F and Wu, B and Chen, L and Jung, CG and Niu, S and Li, D and Xu, X and Jiang, L and Escalas, A and Wu, L and He, Z and Van Nostrand, JD and Ning, D and Liu, X and Yang, Y and Schuur, EAG and Konstantinidis, KT and Cole, JR and Penton, CR and Luo, Y and Tiedje, JM and Zhou, J}, title = {Gene-informed decomposition model predicts lower soil carbon loss due to persistent microbial adaptation to warming.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {4897}, pmid = {32994415}, issn = {2041-1723}, mesh = {Acclimatization/genetics ; Archaea/genetics/isolation &amp; purification/metabolism ; Bacteria/genetics/isolation &amp; purification/metabolism ; Carbon/*analysis/metabolism ; Carbon Cycle ; Cellulose/metabolism ; Environmental DNA/genetics/isolation &amp; purification ; Fungi/genetics/isolation &amp; purification/metabolism ; Global Warming ; Grassland ; Hot Temperature/adverse effects ; Metagenome/*genetics ; Metagenomics ; Microbiota/*physiology ; Models, Genetic ; Plant Roots/chemistry ; Poaceae/chemistry ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Soil microbial respiration is an important source of uncertainty in projecting future climate and carbon (C) cycle feedbacks. However, its feedbacks to climate warming and underlying microbial mechanisms are still poorly understood. Here we show that the temperature sensitivity of soil microbial respiration (Q10) in a temperate grassland ecosystem persistently decreases by 12.0 ± 3.7% across 7 years of warming. Also, the shifts of microbial communities play critical roles in regulating thermal adaptation of soil respiration. Incorporating microbial functional gene abundance data into a microbially-enabled ecosystem model significantly improves the modeling performance of soil microbial respiration by 5-19%, and reduces model parametric uncertainty by 55-71%. In addition, modeling analyses show that the microbial thermal adaptation can lead to considerably less heterotrophic respiration (11.6 ± 7.5%), and hence less soil C loss. If such microbially mediated dampening effects occur generally across different spatial and temporal scales, the potential positive feedback of soil microbial respiration in response to climate warming may be less than previously predicted.}, }
@article {pmid32994285, year = {2020}, author = {Trego, AC and O'Sullivan, S and Quince, C and Mills, S and Ijaz, UZ and Collins, G}, title = {Size Shapes the Active Microbiome of Methanogenic Granules, Corroborating a Biofilm Life Cycle.}, journal = {mSystems}, volume = {5}, number = {5}, pages = {}, pmid = {32994285}, issn = {2379-5077}, abstract = {Methanogenic archaea are key players in cycling organic matter in nature but also in engineered waste treatment systems, where they generate methane, which can be used as a renewable energy source. In such systems in the built environment, complex methanogenic consortia are known to aggregate into highly organized, spherical granular biofilms comprising the interdependent microbial trophic groups mediating the successive stages of the anaerobic digestion (AD) process. This study separated methanogenic granules into a range of discrete size fractions, hypothesizing different biofilm growth stages, and separately supplied each with specific substrates to stimulate the activity of key AD trophic groups, including syntrophic acid oxidizers and methanogens. Rates of specific methanogenic activity were measured, and amplicon sequencing of 16S rRNA gene transcripts was used to resolve phylotranscriptomes across the series of size fractions. Increased rates of methane production were observed in each of the size fractions when hydrogen was supplied as the substrate compared with those of volatile fatty acids (acetate, propionate, and butyrate). This was connected to a shift toward hydrogenotrophic methanogenesis dominated by Methanobacterium and Methanolinea Interestingly, the specific active microbiomes measured in this way indicated that size was significantly more important than substrate in driving the structure of the active community in granules. Multivariate integration studywise discriminant analysis identified 56 genera shaping changes in the active community across both substrate and size. Half of those were found to be upregulated in the medium-sized granules, which were also the most active and potentially of the most important size, or life stage, for precision management of AD systems.IMPORTANCE Biological wastewater conversion processes collectively constitute one of the single biggest worldwide applications of microbial communities. There is an obvious requirement, therefore, to study the microbial systems central to the success of such technologies. Methanogenic granules, in particular, are architecturally fascinating biofilms that facilitate highly organized cooperation within the metabolic network of the anaerobic digestion (AD) process and, thus, are especially intriguing model systems for microbial ecology. This study, in a way not previously reported, provoked syntrophic and methanogenic activity and the structure of the microbial community, using specific substrates targeting the key trophic groups in AD. Unexpectedly, granule size more strongly than substrate shaped the active portion of the microbial community. Importantly, the findings suggest the size, or age, of granules inherently shapes the active microbiome linked to a life cycle. This provides exciting insights into the function of, and the potential for additional modeling of biofilm development in, methanogenic granules.}, }
@article {pmid32993824, year = {2020}, author = {Hanley-Cook, GT and Argaw, AA and de Kok, BP and Vanslambrouck, KW and Toe, LC and Kolsteren, PW and Jones, AD and Lachat, CK}, title = {EAT-Lancet diet score requires minimum intake values to predict higher micronutrient adequacy of diets in rural women of reproductive age from five low- and middle-income countries.}, journal = {The British journal of nutrition}, volume = {}, number = {}, pages = {1-9}, doi = {10.1017/S0007114520003864}, pmid = {32993824}, issn = {1475-2662}, abstract = {The EAT-Lancet Commission promulgated a universal reference diet. Subsequently, researchers constructed an EAT-Lancet diet score (0-14 points), with minimum intake values for various dietary components set at 0 g/d, and reported inverse associations with risks of major health outcomes in a high-income population. We assessed associations between EAT-Lancet diet scores, without or with lower bound values, and the mean probability of micronutrient adequacy (MPA) among nutrition-insecure women of reproductive age (WRA) from low- and middle-income countries (LMIC). We analysed single 24-h diet recall data (n 1950) from studies in rural DRC, Ecuador, Kenya, Sri Lanka and Vietnam. Associations between EAT-Lancet diet scores and MPA were assessed by fitting linear mixed-effects models. Mean EAT-Lancet diet scores were 8·8 (SD 1·3) and 1·9 (SD 1·1) without or with minimum intake values, respectively. Pooled MPA was 0·58 (SD 0·22) and energy intake was 10·5 (SD 4·6) MJ/d. A one-point increase in the EAT-Lancet diet score, without minimum intake values, was associated with a 2·6 (SD 0·7) percentage points decrease in MPA (P < 0·001). In contrast, the EAT-Lancet diet score, with minimum intake values, was associated with a 2·4 (SD 1·3) percentage points increase in MPA (P = 0·07). Further analysis indicated positive associations between EAT-Lancet diet scores and MPA adjusted for energy intake (P < 0·05). Our findings indicate that the EAT-Lancet diet score requires minimum intake values for nutrient-dense dietary components to avoid positively scoring non-consumption of food groups and subsequently predicting lower MPA of diets, when applied to rural WRA in LMIC.}, }
@article {pmid32993503, year = {2020}, author = {De Maayer, P and Pillay, T and Coutinho, TA}, title = {Flagella by numbers: comparative genomic analysis of the supernumerary flagellar systems among the Enterobacterales.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {670}, pmid = {32993503}, issn = {1471-2164}, support = {SFH180109299856//National Research Foundation/ ; }, abstract = {BACKGROUND: Flagellar motility is an efficient means of movement that allows bacteria to successfully colonize and compete with other microorganisms within their respective environments. The production and functioning of flagella is highly energy intensive and therefore flagellar motility is a tightly regulated process. Despite this, some bacteria have been observed to possess multiple flagellar systems which allow distinct forms of motility.<br><br>RESULTS: Comparative genomic analyses showed that, in addition to the previously identified primary peritrichous (flag-1) and secondary, lateral (flag-2) flagellar loci, three novel types of flagellar loci, varying in both gene content and gene order, are encoded on the genomes of members of the order Enterobacterales. The flag-3 and flag-4 loci encode predicted peritrichous flagellar systems while the flag-5 locus encodes a polar flagellum. In total, 798/4028 (~ 20%) of the studied taxa incorporate dual flagellar systems, while nineteen taxa incorporate three distinct flagellar loci. Phylogenetic analyses indicate the complex evolutionary histories of the flagellar systems among the Enterobacterales.<br><br>CONCLUSIONS: Supernumerary flagellar loci are relatively common features across a broad taxonomic spectrum in the order Enterobacterales. Here, we report the occurrence of five (flag-1 to flag-5) flagellar loci on the genomes of enterobacterial taxa, as well as the occurrence of three flagellar systems in select members of the Enterobacterales. Considering the energetic burden of maintaining and operating multiple flagellar systems, they are likely to play a role in the ecological success of members of this family and we postulate on their potential biological functions.}, }
@article {pmid32992776, year = {2020}, author = {García-Vega, ÁS and Corrales-Agudelo, V and Reyes, A and Escobar, JS}, title = {Diet Quality, Food Groups and Nutrients Associated with the Gut Microbiota in a Nonwestern Population.}, journal = {Nutrients}, volume = {12}, number = {10}, pages = {}, pmid = {32992776}, issn = {2072-6643}, abstract = {Diet plays an important role in shaping gut microbiota. However, much remains to be learned regarding this association. We analyzed dietary intake and gut microbiota in a community-dwelling cohort of 441 Colombians. Diet quality, intake of food groups and nutrient consumption were paired with microbial diversity and composition using linear regressions, Procrustes analyses and a random-forest machine-learning algorithm. Analyses were adjusted for potential confounders, including the five cities from where the participants originated, sex (male, female), age group (18-40 and 41-62 years), BMI (lean, overweight, obese) and socioeconomic status. Microbial diversity was higher in individuals with increased intake of nutrients obtained from plant-food sources, whereas the intake of food groups and nutrients correlated with microbiota structure. Random-forest regressions identified microbial communities associated with different diet components. Two remarkable results confirmed previous expectations regarding the link between diet and microbiota: communities composed of short-chain fatty acid (SCFA) producers were more prevalent in the microbiota of individuals consuming diets rich in fiber and plant-food sources, such as fruits, vegetables and beans. In contrast, an inflammatory microbiota composed of bile-tolerant and putrefactive microorganisms along with opportunistic pathogens thrived in individuals consuming diets enriched in animal-food sources and of low quality, i.e., enriched in ultraprocessed foods and depleted in dietary fiber. This study expands our understanding of the relationship between dietary intake and gut microbiota. We provide evidence that diet is strongly associated with the gut microbial community and highlight generalizable connections between them.}, }
@article {pmid32990279, year = {2020}, author = {Zhu, Y and Xiong, Y and Gu, Y and Li, Q and Liu, Y}, title = {Chiropractic Therapy Modulated Gut Microbiota and Attenuated Allergic Airway Inflammation in an Immature Rat Model.}, journal = {Medical science monitor : international medical journal of experimental and clinical research}, volume = {26}, number = {}, pages = {e926039}, pmid = {32990279}, issn = {1643-3750}, abstract = {BACKGROUND As a type of traditional Chinese massage, chiropractic therapy is applied to prevent and treat children with asthma in China. However, its mechanism of action is unclear. Allergic airway inflammation plays a key role in the occurrence and development of asthma, in which changes in gut microbiota are involved. The present study investigated the influence of chiropractic therapy on allergic airway inflammation (AAI) and gut microbiota in an immature rat model. MATERIAL AND METHODS Three-week-old male Sprague-Dawley rats were divided randomly into control (CN), AAI, and chiropractic (CP) groups. AAI and CP groups were sensitized and challenged with ovalbumin (OVA) to induce AAI. The CP group received chiropractic therapy during AAI modelling. AAI was assessed by cell counts in bronchoalveolar lavage fluid and HE staining of lung tissues. Plasma OVA-sIgE, IFN-γ, IL-4, and IL-10 levels were detected by ELISA. DNA extraction from feces samples was used for 16S rRNA gene sequencing and analyzed for gut microbiota by Quantitative Insights Into Microbial Ecology (QIIME). RESULTS AAI group had significantly lower richness and diversity of gut microbiota along with Th2 response and allergic airway inflammation. Moreover, the AAI group had lower abundance of butyrate-producing bacterial taxa with more Lactobacillus. Chiropractic therapy significantly increased the richness and diversity of gut microbiota and increased butyrate-producing bacterial taxa and decreased Lactobacillus, along with attenuating Th2 response and allergic airway inflammation during AAI modelling. CONCLUSIONS Chiropractic therapy attenuated allergic airway inflammation and optimized gut microbiota in an immature rat model, which might promote the development of adult-like butyrogenic milieu, immunotolerance, and inflammation attenuation.}, }
@article {pmid32989484, year = {2020}, author = {González-Hourcade, M and Del Campo, EM and Casano, LM}, title = {The Under-explored Extracellular Proteome of Aero-Terrestrial Microalgae Provides Clues on Different Mechanisms of Desiccation Tolerance in Non-Model Organisms.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01604-8}, pmid = {32989484}, issn = {1432-184X}, support = {CGL2016-80259-P//Ministerio de Ciencia, Innovación y Universidades/ ; }, abstract = {Trebouxia sp. (TR9) and Coccomyxa simplex (Csol) are desiccation-tolerant lichen microalgae with different adaptive strategies in accordance with the prevailing conditions of their habitats. The remodelling of cell wall and extracellular polysaccharides depending on water availability are key elements in the tolerance to desiccation of both microalgae. Currently, there is no information about the extracellular proteins of these algae and other aero-terrestrial microalgae in response to limited water availability. To our knowledge, this is the first report on the proteins associated with the extracellular polymeric substances (EPS) of aero-terrestrial microalgae subjected to cyclic desiccation/rehydration. LC-MS/MS and bioinformatic analyses of the EPS-associated proteins in the two lichen microalgae submitted to four desiccation/rehydration cycles allowed the compilation of 111 and 121 identified proteins for TR9 and Csol, respectively. Both sets of EPS-associated proteins shared a variety of predicted biological functions but showed a constitutive expression in Csol and partially inducible in TR9. In both algae, the EPS-associated proteins included a number of proteins of unknown functions, some of which could be considered as small intrinsically disordered proteins related with desiccation-tolerant organisms. Differences in the composition and the expression pattern between the studied EPS-associated proteins would be oriented to preserve the biochemical and biophysical properties of the extracellular structures under the different conditions of water availability in which each alga thrives.}, }
@article {pmid32984478, year = {2020}, author = {Hassen, AI and Pierneef, R and Swanevelder, ZH and Bopape, FL}, title = {Microbial and functional diversity of Cyclopia intermedia rhizosphere microbiome revealed by analysis of shotgun metagenomics sequence data.}, journal = {Data in brief}, volume = {32}, number = {}, pages = {106288}, pmid = {32984478}, issn = {2352-3409}, abstract = {Cyclopia spp., commonly referred to as honeybush due to the honey scented flowers, are indigenous legumes mainly growing in the Cape Floristic Region of the Western Cape, South Africa. Dozens of species, including Cyclopia intermedia, C. subternata, C. plicata, C. genistoides are used to make the well-known, popular and widely enjoyed beverage called 'honeybush tea'. In the past, most rhizosphere microbial studies associated with Cyclopia spp. focused mainly on the taxonomy and diversity of the root nodule associated symbiotic nitrogen fixing rhizobia. The work presented here is the first report on the microbial and functional diversity of rhizosphere microbiome associated with Cyclopia intermedia. Metagenomic shotgun sequencing was performed on the rhizosphere soil sample collected from this Cyclopia sp. using illumina Hiseq 2500 platform which resulted in an α- diversity of 312 species. Analysis of the metagenome sequence using the Metagenomic analysis server (MG-RAST) indicated that bacteria constitute the dominant domain followed by Eukaryota, Archaea and other sequences derived from fungi and viruses. Functional diversity of the metagenome based on analysis using the Cluster Orthologous Group (COG) method showed metabolism as the most important function in the community. The raw sequence data is uploaded in FASTQ format on MG-RAST server with ID mgm4855911.3 which can be accessed at http://www.mg-rast.org/linkin.cgi?project=mgp90368. The data on the microbial and functional diversity of the rhizosphere community of Cyclopia intermedia generates a baseline information about the microbial ecology of this indigenous legume. The microbial profile data can also be used as indicators of soil health characteristic of the rhizosphere of this important legume.}, }
@article {pmid32983401, year = {2020}, author = {Lequime, S and Bastide, P and Dellicour, S and Lemey, P and Baele, G}, title = {nosoi: A stochastic agent-based transmission chain simulation framework in r.}, journal = {Methods in ecology and evolution}, volume = {11}, number = {8}, pages = {1002-1007}, pmid = {32983401}, issn = {2041-210X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {The transmission process of an infectious agent creates a connected chain of hosts linked by transmission events, known as a transmission chain. Reconstructing transmission chains remains a challenging endeavour, except in rare cases characterized by intense surveillance and epidemiological inquiry. Inference frameworks attempt to estimate or approximate these transmission chains but the accuracy and validity of such methods generally lack formal assessment on datasets for which the actual transmission chain was observed.We here introduce nosoi, an open-source r package that offers a complete, tunable and expandable agent-based framework to simulate transmission chains under a wide range of epidemiological scenarios for single-host and dual-host epidemics. nosoi is accessible through GitHub and CRAN, and is accompanied by extensive documentation, providing help and practical examples to assist users in setting up their own simulations.Once infected, each host or agent can undergo a series of events during each time step, such as moving (between locations) or transmitting the infection, all of these being driven by user-specified rules or data, such as travel patterns between locations. nosoi is able to generate a multitude of epidemic scenarios, that can-for example-be used to validate a wide range of reconstruction methods, including epidemic modelling and phylodynamic analyses. nosoi also offers a comprehensive framework to leverage empirically acquired data, allowing the user to explore how variations in parameters can affect epidemic potential. Aside from research questions, nosoi can provide lecturers with a complete teaching tool to offer students a hands-on exploration of the dynamics of epidemiological processes and the factors that impact it. Because the package does not rely on mathematical formalism but uses a more intuitive algorithmic approach, even extensive changes of the entire model can be easily and quickly implemented.}, }
@article {pmid32983187, year = {2020}, author = {de Souza, RSC and Armanhi, JSL and Arruda, P}, title = {From Microbiome to Traits: Designing Synthetic Microbial Communities for Improved Crop Resiliency.}, journal = {Frontiers in plant science}, volume = {11}, number = {}, pages = {1179}, pmid = {32983187}, issn = {1664-462X}, abstract = {Plants teem with microorganisms, whose tremendous diversity and role in plant-microbe interactions are being increasingly explored. Microbial communities create a functional bond with their hosts and express beneficial traits capable of enhancing plant performance. Therefore, a significant task of microbiome research has been identifying novel beneficial microbial traits that can contribute to crop productivity, particularly under adverse environmental conditions. However, although knowledge has exponentially accumulated in recent years, few novel methods regarding the process of designing inoculants for agriculture have been presented. A recently introduced approach is the use of synthetic microbial communities (SynComs), which involves applying concepts from both microbial ecology and genetics to design inoculants. Here, we discuss how to translate this rationale for delivering stable and effective inoculants for agriculture by tailoring SynComs with microorganisms possessing traits for robust colonization, prevalence throughout plant development and specific beneficial functions for plants. Computational methods, including machine learning and artificial intelligence, will leverage the approaches of screening and identifying beneficial microbes while improving the process of determining the best combination of microbes for a desired plant phenotype. We focus on recent advances that deepen our knowledge of plant-microbe interactions and critically discuss the prospect of using microbes to create SynComs capable of enhancing crop resiliency against stressful conditions.}, }
@article {pmid32983012, year = {2020}, author = {Hounmanou, YMG and Dalsgaard, A and Sopacua, TF and Uddin, GMN and Leekitcharoenphon, P and Hendriksen, RS and Olsen, JE and Larsen, MH}, title = {Molecular Characteristics and Zoonotic Potential of Salmonella Weltevreden From Cultured Shrimp and Tilapia in Vietnam and China.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1985}, pmid = {32983012}, issn = {1664-302X}, abstract = {Salmonella Weltevreden is increasingly reported from aquatic environments, seafood, and patients in several Southeast Asian countries. Using genome-wide analysis, we characterized S. Weltevreden isolated from cultured shrimp and tilapia from Vietnam and China to study their genetic characteristics and relatedness to clinical isolates of S. Weltevreden ST-365. The phylogenetic analysis revealed up to 312 single-nucleotide polymorphism (SNP) difference between tilapia isolates, whereas isolates from shrimp were genetically more closely related. Epidemiologically unrelated isolates from Vietnam were closely related to isolates from China, e.g., 20 SNPs differences between strains 28V and 75C. In comparison with strains from other parts of the world, our environmental isolates predominantly clustered within the continental South Asia lineage, constituted mostly of strains from human stool with as low as seven SNPs difference, e.g., 30V versus Cont_ERR495254. All sequenced isolates were MLST type ST-365 and contained the major virulence-related genes encoded by the Salmonella Pathogenicity Islands 1-5. Ten of the isolates harbored the IncFII(S) plasmid similar to the virulence genes-mediated plasmid pSPCV of S. Paratyphi C, and one isolate had the IncQ1 plasmid on the same contig with strA/B, sul2, and tetA resistance genes similar to the IncQ1 type, pNUC of S. Typhimurium. A pangenomic analysis yielded 7891 genes including a core genome of 4892 genes, with a closely related accessory genome content between clinical and environmental isolates (Benjamini p > 0.05). In a search for differences that could explain the higher prevalence of S. Weltevreden in aquatic samples, genomes were compared with those of other Salmonella enterica serovars. S. Weltevreden revealed specific regions harboring glpX (Fructose-1;6-bisphosphatase; class II), rfbC (dTDP-4-dehydrorhamnose 3;5-epimerase), and cmtB (PTS Mannitol-specific cryptic phosphotransferase enzyme IIA component) involved in carbohydrate biosynthesis pathways. Our study builds grounds for future experiments to determine genes or pathways that are essential when S. Weltevreden are in aquatic environments and microbial interactions providing survival advantages to S. Weltevreden in such environments.}, }
@article {pmid32982988, year = {2020}, author = {van der Goot, E and van Spronsen, FJ and Falcão Salles, J and van der Zee, EA}, title = {A Microbial Community Ecology Perspective on the Gut-Microbiome-Brain Axis.}, journal = {Frontiers in endocrinology}, volume = {11}, number = {}, pages = {611}, pmid = {32982988}, issn = {1664-2392}, }
@article {pmid32979812, year = {2020}, author = {Meyer, KM and Morris, AH and Webster, K and Klein, AM and Kroeger, ME and Meredith, LK and Brændholt, A and Nakamura, F and Venturini, A and Fonseca de Souza, L and Shek, KL and Danielson, R and van Haren, J and Barbosa de Camargo, P and Tsai, SM and Dini-Andreote, F and de Mauro, JMS and Barlow, J and Berenguer, E and Nüsslein, K and Saleska, S and Rodrigues, JLM and Bohannan, BJM}, title = {Belowground changes to community structure alter methane-cycling dynamics in Amazonia.}, journal = {Environment international}, volume = {145}, number = {}, pages = {106131}, doi = {10.1016/j.envint.2020.106131}, pmid = {32979812}, issn = {1873-6750}, abstract = {Amazonian rainforest is undergoing increasing rates of deforestation, driven primarily by cattle pasture expansion. Forest-to-pasture conversion has been associated with increases in soil methane (CH4) emission. To better understand the drivers of this change, we measured soil CH4 flux, environmental conditions, and belowground microbial community structure across primary forests, cattle pastures, and secondary forests in two Amazonian regions. We show that pasture soils emit high levels of CH4 (mean: 3454.6 ± 9482.3 μg CH4 m-2 d-1), consistent with previous reports, while forest soils on average emit CH4 at modest rates (mean: 9.8 ± 120.5 μg CH4 m-2 d-1), but often act as CH4 sinks. We report that secondary forest soils tend to consume CH4 (mean: -10.2 ± 35.7 μg CH4 m-2 d-1), demonstrating that pasture CH4 emissions can be reversed. We apply a novel computational approach to identify microbial community attributes associated with flux independent of soil chemistry. While this revealed taxa known to produce or consume CH4 directly (i.e. methanogens and methanotrophs, respectively), the vast majority of identified taxa are not known to cycle CH4. Each land use type had a unique subset of taxa associated with CH4 flux, suggesting that land use change alters CH4 cycling through shifts in microbial community composition. Taken together, we show that microbial composition is crucial for understanding the observed CH4 dynamics and that microorganisms provide explanatory power that cannot be captured by environmental variables.}, }
@article {pmid32978127, year = {2020}, author = {Xia, WW and Zhao, J and Zheng, Y and Zhang, HM and Zhang, JB and Chen, RR and Lin, XG and Jia, ZJ}, title = {Active Soil Nitrifying Communities Revealed by In Situ Transcriptomics and Microcosm-Based Stable-Isotope Probing.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {23}, pages = {}, pmid = {32978127}, issn = {1098-5336}, mesh = {Archaea/genetics/*isolation &amp; purification ; Bacteria/genetics/*isolation &amp; purification ; Fertilizers/analysis ; Gene Expression Profiling ; High-Throughput Nucleotide Sequencing ; Nitrogen/*metabolism ; RNA, Archaeal/analysis ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Real-Time Polymerase Chain Reaction ; *Soil Microbiology ; Transcription, Genetic ; }, abstract = {Long-term nitrogen field fertilization often results in significant changes in nitrifying communities that catalyze a key step in the global N cycle. However, whether microcosm studies are able to inform the dynamic changes in communities of ammonia-oxidizing bacteria (AOB) and archaea (AOA) under field conditions remains poorly understood. This study aimed to evaluate the transcriptional activities of nitrifying communities under in situ conditions, and we found that they were largely similar to those of 13C-labeled nitrifying communities in the urea-amended microcosms of soils that had received different N fertilization regimens for 22 years. High-throughput sequencing of 16S rRNA genes and transcripts suggested that Nitrosospira cluster 3-like AOB and Nitrososphaera viennensis-like AOA were significantly stimulated in N-fertilized fresh soils. Real-time quantitative PCR demonstrated that the significant increase of AOA and AOB in fresh soils upon nitrogen fertilization could be preserved in the air-dried soils. DNA-based stable-isotope probing (SIP) further revealed the greatest labeling of Nitrosospira cluster 3-like AOB and Nitrosospira viennensis-like AOA, despite the strong advantage of AOB over AOA in the N-fertilized soils. Nitrobacter-like nitrite-oxidizing bacteria (NOB) played more important roles than Nitrospira-like NOB in urea-amended SIP microcosms, while the situation was the opposite under field conditions. Our results suggest that long-term fertilization selected for physiologically versatile AOB and AOA that could have been adapted to a wide range of substrate ammonium concentrations. It also provides compelling evidence that the dominant communities of transcriptionally active nitrifiers under field conditions were largely similar to those revealed in 13C-labeled microcosms.IMPORTANCE The role of manipulated microcosms in microbial ecology has been much debated, because they cannot entirely represent the in situ situation. We collected soil samples from 20 field plots, including 5 different treatments with and without nitrogen fertilizers for 22 years, in order to assess active nitrifying communities by in situ transcriptomics and microcosm-based stable-isotope probing. The results showed that chronic N enrichment led to competitive advantages of Nitrosospira cluster 3-like AOB over N. viennensis-like AOA in soils under field conditions. Microcosm labeling revealed similar results for active AOA and AOB, although an apparent discrepancy was observed for nitrite-oxidizing bacteria. This study suggests that the soil microbiome represents a relatively stable community resulting from complex evolutionary processes over a large time scale, and microcosms can serve as powerful tools to test the theory of environmental filtering on the key functional microbial guilds.}, }
@article {pmid32975888, year = {2020}, author = {Goelen, T and Vuts, J and Sobhy, IS and Wäckers, F and Caulfield, JC and Birkett, MA and Rediers, H and Jacquemyn, H and Lievens, B}, title = {Identification and application of bacterial volatiles to attract a generalist aphid parasitoid: from laboratory to greenhouse assays.}, journal = {Pest management science}, volume = {}, number = {}, pages = {}, doi = {10.1002/ps.6102}, pmid = {32975888}, issn = {1526-4998}, support = {HBC.2018/2022//Agentschap Innoveren en Ondernemen/ ; 1S15116316N//Fonds Wetenschappelijk Onderzoek/ ; }, abstract = {BACKGROUND: Recent studies have shown that microorganisms emit volatile compounds that affect insect behaviour. However, it remains largely unclear whether microbes can be exploited as a source of attractants to improve biological control of insect pests. In this study, we used a combination of coupled gas chromatography-electroantennography (GC-EAG) and Y-tube olfactometer bioassays to identify attractive compounds in the volatile extracts of three bacterial strains that are associated with the habitat of the generalist aphid parasitoid Aphidius colemani, and to create mixtures of synthetic compounds to find attractive blends for A. colemani. Subsequently, the most attractive blend was evaluated in two-choice cage experiments under greenhouse conditions.<br><br>RESULTS: GC-EAG analysis revealed 20 compounds that were linked to behaviourally attractive bacterial strains. A mixture of two EAG-active compounds, styrene and benzaldehyde applied at a respective dose of 1 μg and 10 ng, was more attractive than the single compounds or the culture medium of the bacteria in Y-tube olfactometer bioassays. Application of this synthetic mixture under greenhouse conditions resulted in significant attraction of the parasitoids, and outperformed application of the bacterial culture medium.<br><br>CONCLUSION: Compounds isolated from bacterial blends were capable of attracting parasitoids both in laboratory and greenhouse assays, indicating that microbial cultures are an effective source of insect attractants. This opens new opportunities to attract and retain natural enemies of pest species and to enhance biological pest control.}, }
@article {pmid32975751, year = {2020}, author = {Garbisu, C and Alkorta, I and Kidd, P and Epelde, L and Mench, M}, title = {Keep and promote biodiversity at polluted sites under phytomanagement.}, journal = {Environmental science and pollution research international}, volume = {27}, number = {36}, pages = {44820-44834}, doi = {10.1007/s11356-020-10854-5}, pmid = {32975751}, issn = {1614-7499}, support = {SOE1/P5/E0189//Interreg/ ; }, mesh = {Biodegradation, Environmental ; Biodiversity ; Biomass ; Ecosystem ; Soil ; *Soil Pollutants/analysis ; }, abstract = {The phytomanagement concept combines a sustainable reduction of pollutant linkages at risk-assessed contaminated sites with the generation of both valuable biomass for the (bio)economy and ecosystem services. One of the potential benefits of phytomanagement is the possibility to increase biodiversity in polluted sites. However, the unique biodiversity present in some polluted sites can be severely impacted by the implementation of phytomanagement practices, even resulting in the local extinction of endemic ecotypes or species of great conservation value. Here, we highlight the importance of promoting measures to minimise the potential adverse impact of phytomanagement on biodiversity at polluted sites, as well as recommend practices to increase biodiversity at phytomanaged sites without compromising its effectiveness in terms of reduction of pollutant linkages and the generation of valuable biomass and ecosystem services.}, }
@article {pmid32975677, year = {2020}, author = {Ouarabi, L and Drider, D and Taminiau, B and Daube, G and Bendali, F and Lucau-Danila, A}, title = {Vaginal Microbiota: Age Dynamic and Ethnic Particularities of Algerian Women.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01606-6}, pmid = {32975677}, issn = {1432-184X}, abstract = {The composition of the vaginal microbiota is a key element for maintaining gynecological and reproductive health. With the aim of obtaining an accurate overview of the vaginal microbiota of Algerian women, in terms of their age and ethnic group, we conducted a 16S rRNA gene targeted metagenomic analysis of 100 vaginal samples taken from healthy childbearing and menopausal women. These data were used to establish the pattern of the vaginal microbiota during reproductive and postreproductive phases. Hormone levels were correlated to changes in microbial composition for menopausal women. The ethnic comparison revealed a particular microbiota profile for Algerian women, with a dominance of CST III and CST I. A rapid qPCR method developed by the authors was successfully used to identify the vaginal bacterial pattern for a customized gynecological management.}, }
@article {pmid32975666, year = {2020}, author = {Lee, CW and Lim, JH and Heng, PL and Marican, NF and Narayanan, K and Sim, EUH and Bong, CW}, title = {Influence of elevated river flow on hypoxia occurrence, nutrient concentration and microbial dynamics in a tropical estuary.}, journal = {Environmental monitoring and assessment}, volume = {192}, number = {10}, pages = {660}, doi = {10.1007/s10661-020-08625-3}, pmid = {32975666}, issn = {1573-2959}, support = {HiCOE (IOES-2014D)//Ministry of Higher Education/ ; FRGS (FP061-2018A)//Ministry of Higher Education/ ; }, mesh = {Chlorophyll A ; Environmental Monitoring ; *Estuaries ; Humans ; Hypoxia ; Nutrients ; *Rivers ; Seasons ; }, abstract = {We sampled the Klang estuary during the inter-monsoon and northeast monsoon period (July-Nov 2011, Oct-Nov 2012), which coincided with higher rainfall and elevated Klang River flow. The increased freshwater inflow into the estuary resulted in water column stratification that was observed during both sampling periods. Dissolved oxygen (DO) dropped below 63 μM, and hypoxia was observed. Elevated river flow also transported dissolved inorganic nutrients, chlorophyll a and bacteria to the estuary. However, bacterial production did not correlate with DO concentration in this study. As hypoxia was probably not due to in situ heterotrophic processes, deoxygenated waters were probably from upstream. We surmised this as DO correlated with salinity (R2 = 0.664, df = 86, p < 0.001). DO also decreased with increasing flushing time (R2 = 0.556, df = 11, p < 0.01), suggesting that when flushing time (> 6.7 h), hypoxia could occur at the Klang estuary. Here, we presented a model that related riverine flow rate to the post-heavy rainfall hypoxia that explicated the episodic hypoxia at Klang estuary. As Klang estuary supports aquaculture and cockle culture, our results could help protect the aquaculture and cockle culture industry here.}, }
@article {pmid32975419, year = {2021}, author = {Trueba-Santiso, A and Wasmund, K and Soder-Walz, JM and Marco-Urrea, E and Adrian, L}, title = {Genome Sequence, Proteome Profile, and Identification of a Multiprotein Reductive Dehalogenase Complex in Dehalogenimonas alkenigignens Strain BRE15M.}, journal = {Journal of proteome research}, volume = {20}, number = {1}, pages = {613-623}, doi = {10.1021/acs.jproteome.0c00569}, pmid = {32975419}, issn = {1535-3907}, abstract = {Bacteria of the genus Dehalogenimonas respire with vicinally halogenated alkanes via dihaloelimination. We aimed to describe involved proteins and their supermolecular organization. Metagenomic sequencing of a Dehalogenimonas-containing culture resulted in a 1.65 Mbp draft genome of Dehalogenimonas alkenigignens strain BRE15M. It contained 31 full-length reductive dehalogenase homologous genes (rdhA), but only eight had cognate rdhB gene coding for membrane-anchoring proteins. Shotgun proteomics of cells grown with 1,2-dichloropropane as an electron acceptor identified 1152 proteins representing more than 60% of the total proteome. Ten RdhA proteins were detected, including a DcpA ortholog, which was the strongest expressed RdhA. Blue native gel electrophoresis (BNE) demonstrating maximum activity was localized in a protein complex of 146-242 kDa. Protein mass spectrometry revealed the presence of DcpA, its membrane-anchoring protein DcpB, two hydrogen uptake hydrogenase subunits (HupL and HupS), an iron-sulfur protein (HupX), and subunits of a redox protein with a molybdopterin-binding motif (OmeA and OmeB) in the complex. BNE after protein solubilization with different detergent concentrations revealed no evidence for an interaction between the putative respiratory electron input module (HupLS) and the OmeA/OmeB/HupX module. All detected RdhAs comigrated with the organohalide respiration complex. Based on genomic and proteomic analysis, we propose quinone-independent respiration in Dehalogenimonas.}, }
@article {pmid32974747, year = {2020}, author = {Souza, UA and Webster, A and Dall'Agnol, B and Morel, AP and Peters, FB and Favarini, MO and Mazim, FD and Soares, JBG and Tirelli, FP and Tortato, MA and de Lemos, ERS and Trigo, TC and Soares, JF and Reck, J}, title = {Molecular and Serological Survey of the Cat-Scratch Disease Agent (Bartonella henselae) in Free-Ranging Leopardus geoffroyi and Leopardus wiedii (Carnivora: Felidae) From Pampa Biome, Brazil.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01601-x}, pmid = {32974747}, issn = {1432-184X}, abstract = {The genus Bartonella comprises emerging bacteria that affect humans and other mammals worldwide. Felids represent an important reservoir for several Bartonella species. Domestic cats are the main reservoir of Bartonella henselae, the agent of cat scratch disease (CSD). It can be transmitted directly by scratches and bites from infected cats and via cat fleas. This study aims to investigate the circulation of Bartonella spp. in free-ranging Neotropical wild felids from Southern Brazil using serological and molecular methods. In this study, 53 live-trapped free-ranging wild felids were sampled, 39 Leopardus geoffroyi and 14 Leopardus wiedii, from five municipalities in the Rio Grande, do Sul state, southern Brazil. All captured animals were clinically healthy. Two blood samples of L. geoffroyi were positive, by PCR, for the presence of B. henselae DNA. Conversely, none of L. wiedii blood samples were positive when tested using PCR. Indirect immunofluorescence assay (IFA) showed that 28% of serum samples of wild felids were reactive (seropositive) for B. henselae by immunofluorescence, with titers ranging from 64 to 256. The results presented here provide the first evidence of a Bartonella-enzootic cycle involving L. geoffroyi and L. wiedii, which may account for the spillover of the emerging zoonotic pathogen B. henselae for the indigenous fauna in Southern Brazil.}, }
@article {pmid32974213, year = {2020}, author = {de Souza-Basqueira, M and Ribeiro, RM and de Oliveira, LC and Moreira, CHV and Martins, RCR and Franco, DC and Amado, PPP and Mayer, MPA and Sabino, EC}, title = {Gut Dysbiosis in Chagas Disease. A Possible Link to the Pathogenesis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {402}, pmid = {32974213}, issn = {2235-2988}, support = {U19 AI098461/AI/NIAID NIH HHS/United States ; }, abstract = {Chagas disease is caused by the flagellate protozoan Trypanosoma cruzi. Cardiomyopathy and damage to gastrointestinal tissue are the main disease manifestations. There are data suggesting that the immune response to T. cruzi depends on the intestinal microbiota. We hypothesized that Chagas disease is associated with an altered gut microbiome and that these changes are related to the disease phenotype. The stool microbiome from 104 individuals, 73 with Chagas disease (30 with the cardiac, 11 with the digestive, and 32 with the indeterminate form), and 31 healthy controls was characterized using 16S rRNA amplification and sequencing. The QIIME (Quantitative Insights Into Microbial Ecology) platform was used to analyze the data. Alpha and beta diversity indexes did not indicate differences between the groups. However, the relative abundance of Verrucomicrobia, represented primarily by the genus Akkermansia, was significantly lower in the Chagas disease groups, especially the cardiac group, compared to the controls. Furthermore, differences in the relative abundances of Alistipes, Bilophila, and Dialister were observed between the groups. We conclude that T. cruzi infection results in changes in the gut microbiome that may play a role in the myocardial and intestinal inflammation seen in Chagas disease.}, }
@article {pmid32974121, year = {2020}, author = {Lee, NLY and Huang, D and Quek, ZBR and Lee, JN and Wainwright, BJ}, title = {Distinct fungal communities associated with different organs of the mangrove Sonneratia alba in the Malay Peninsula.}, journal = {IMA fungus}, volume = {11}, number = {}, pages = {17}, pmid = {32974121}, issn = {2210-6340}, abstract = {Mangrove forests are key tropical marine ecosystems that are rich in fungi, but our understanding of fungal communities associated with mangrove trees and their various organs remains limited because much of the diversity lies within the microbiome. In this study, we investigated the fungal communities associated with the mangrove tree Sonneratia alba throughout Peninsular Malaysia and Singapore. At each sampling location, we collected leaves, fruits, pneumatophores and sediment samples and performed amplicon sequencing of the ribosomal internal transcribed spacer 1 to characterise the associated communities. Results show distinct fungal communities at each sampled location with further differentiation according to the plant part. We find a significant distance decay of similarity, particularly for sediment samples due to the greater variability of sediment environments relative to the more stable fungal habitats provided by living plant organs. We are able to assign taxonomy to the majority of sequences from leaves and fruits, but a much larger portion of the sequences recovered from pneumatophores and sediment samples could not be identified. This pattern underscores the limited mycological research performed in marine environments and demonstrates the need for a concerted research effort on multiple species to fully characterise the coastal microbiome and its role in the functioning of marine ecosystems.}, }
@article {pmid32973727, year = {2020}, author = {Kuznecova, J and Šulčius, S and Vogts, A and Voss, M and Jürgens, K and Šimoliūnas, E}, title = {Nitrogen Flow in Diazotrophic Cyanobacterium Aphanizomenon flos-aquae Is Altered by Cyanophage Infection.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {2010}, pmid = {32973727}, issn = {1664-302X}, abstract = {Viruses can significantly influence cyanobacteria population dynamics and activity, and through this the biogeochemical cycling of major nutrients. However, surprisingly little attention has been given to understand how viral infections alter the ability of diazotrophic cyanobacteria for atmospheric nitrogen fixation and its release to the environment. This study addressed the importance of cyanophages for net 15N2 assimilation rate, expression of nitrogenase reductase gene (nifH) and changes in nitrogen enrichment (15N/14N) in the diazotrophic cyanobacterium Aphanizomenon flos-aquae during infection by the cyanophage vB_AphaS-CL131. We found that while the growth of A. flos-aquae was inhibited by cyanophage addition (decreased from 0.02 h-1 to 0.002 h-1), there were no significant differences in nitrogen fixation rates (control: 22.7 × 10-7 nmol N heterocyte-1; infected: 23.9 × 10-7 nmol N heterocyte-1) and nifH expression level (control: 0.6-1.6 transcripts heterocyte-1; infected: 0.7-1.1 transcripts heterocyte-1) between the infected and control A. flos-aquae cultures. This implies that cyanophage genome replication and progeny production within the vegetative cells does not interfere with the N2 fixation reactions in the heterocytes of these cyanobacteria. However, higher 15N enrichment at the poles of heterocytes of the infected A. flos-aquae, revealed by NanoSIMS analysis indicates the accumulation of fixed nitrogen in response to cyanophage addition. This suggests reduced nitrogen transport to vegetative cells and the alterations in the flow of fixed nitrogen within the filaments. In addition, we found that cyanophage lysis resulted in a substantial release of ammonium into culture medium. Cyanophage infection seems to substantially redirect N flow from cyanobacterial biomass to the production of N storage compounds and N release.}, }
@article {pmid32973299, year = {2020}, author = {Hernández-Del Amo, E and Dolinová, I and la Ramis-Jorba, G and Gich, F and Bañeras, L}, title = {Limited effect of radial oxygen loss on ammonia oxidizers in Typha angustifolia root hairs.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {15694}, pmid = {32973299}, issn = {2045-2322}, mesh = {Ammonia/*metabolism ; Microbiota ; Nitrification/*physiology ; Oxygen/metabolism ; Plant Roots/*metabolism ; RNA, Ribosomal, 16S/genetics ; Typhaceae/*metabolism ; }, abstract = {The benefits of plant-microbe interactions have been exploited extensively for nutrient removal. Radial oxygen loss in aquatic macrophytes potentially promotes nitrification and accelerates nitrogen removal through coupled nitrification-denitrification process. Nitrification is likely the limiting activity for an effective nitrogen removal in wetlands. In this work, we have quantified the effect of radial oxygen losses in Typha angustifolia plants in environments of contrasting salinities, including a temporary lagoon, a constructed wetland, and a river estuary. In all sites, radial oxygen diffusion occurred mainly at a narrow band, from 1 to 5 cm from the root tip, and were almost absent at the tip and basal sections of the root (> 5 cm). Root sections with active oxygen diffusion tended to show higher bacterial and archaeal densities in the rhizoplane according to 16S rRNA gene abundance data, except at higher salinities. Archaeal amoA /bacterial amoA gene ratios were highly variable among sites. Archaeal nitrifiers were only favoured over bacteria on the root surface of Typha collected from the constructed wetland. Collectively, radial oxygen loss had little effect on the nitrifying microbial community at the smaller scale (differences according to root-section), and observed differences were more likely related to prevailing physicochemical conditions of the studied environments or to long-term effects of the root microenvironment (root vs sediment comparisons).}, }
@article {pmid32970805, year = {2020}, author = {Sakarika, M and Sosa, DAT and Depoortere, M and Rottiers, H and Ganigué, R and Dewettinck, K and Rabaey, K}, title = {The type of microorganism and substrate determines the odor fingerprint of dried bacteria targeting microbial protein production.}, journal = {FEMS microbiology letters}, volume = {367}, number = {18}, pages = {}, doi = {10.1093/femsle/fnaa138}, pmid = {32970805}, issn = {1574-6968}, abstract = {The rapidly increasing demand for protein has led to the pursuit of new protein sources, among which microbial protein (MP) is one of the most promising. Although the nutritional properties of MP are important and often well-studied, the sensory properties of the microbial cells will in part determine the commercial success of the product and are much less investigated. Here we assessed the odor fingerprint of dried bacteria originating from pure cultures and enriched mixed microbial communities using an electronic nose (e-nose). The e-nose discriminated between the different MP sources, while the choice of culture and substrate substantially affected their volatile organic compound (VOC) profile. The most dominant odor descriptors (>20% of VOC peak area) were sweet, fruity and fishy, while the mixed cultures presented higher peak areas indicating potentially more intense aromas than the pure cultures. The e-nose can detect the suitability of new MP sources and determine their best end-use.}, }
@article {pmid32969526, year = {2020}, author = {Niemeier-Walsh, C and Ryan, PH and Meller, J and Ollberding, NJ and Adhikari, A and Indugula, R and Reponen, T}, title = {The mycobiomes and bacteriomes of sputum, saliva, and home dust.}, journal = {Indoor air}, volume = {}, number = {}, pages = {}, doi = {10.1111/ina.12750}, pmid = {32969526}, issn = {1600-0668}, support = {T42OH008432/OH/NIOSH CDC HHS/United States ; 5UL1TR001425-04/TR/NCATS NIH HHS/United States ; R21ES024807/ES/NIEHS NIH HHS/United States ; }, abstract = {Respiratory microbiome is an understudied area of research compared to other microbiomes of the human body. The respiratory tract is exposed to an array of environmental pollutants, including microbes. Yet, we know very little about the relationship between environmental and respiratory microbiome. The primary aim of our study was to compare the mycobiomes and bacteriomes between three sample types from the same participants, including home dust, saliva, and sputum. Samples were collected from 40 adolescents in a longitudinal cohort. We analyzed the samples using 16s bacterial rDNA and ITS fungal rDNA gene sequencing, as well as quantitative PCR with universal fungal and bacterial primers. Results showed that home dust had the greatest alpha diversity between the three sample types for both bacteria and fungi. Dust had the highest total fungal load and the lowest total bacterial load. Sputum had greater bacterial diversity than saliva, but saliva had greater fungal diversity than sputum. The distribution of major bacterial phyla differed between all sample types. However, the distribution of major fungal classes differed only between sputum and saliva. Future research should examine the biological significance of the taxa found in each sample type based on microbial ecology and associations with health effects.}, }
@article {pmid32968841, year = {2020}, author = {Zhao, D and Zhang, Z and Niu, H and Guo, H}, title = {Win by Quantity: a Striking Rickettsia-Bias Symbiont Community Revealed by Seasonal Tracking in the Whitefly Bemisia tabaci.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01607-5}, pmid = {32968841}, issn = {1432-184X}, support = {31701797//the National Natural Science Foundation of China/ ; BK20170598//the Natural Science Foundation of Jiangsu Province, China/ ; BE2010342//the Key Research and Development Program of Jiangsu Province, China/ ; }, abstract = {Maintaining an adaptive seasonality is a basic ecological requisite for cold-blooded organism insects which usually harbor various symbionts. However, how coexisting symbionts coordinate in insects during seasonal progress is still unknown. The whitefly Bemisia tabaci in China harbors the obligate symbiont Portiera that infects each individual, as well as various facultative symbionts. In this study, we investigated whitefly populations in cucumber and cotton fields from May to December 2019, aiming to reveal the fluctuations of symbiont infection frequencies, symbiont coordination in multiple infected individuals, and host plants effects on symbiont infections. The results indicated that the facultative symbionts Hamiltonella (H), Rickettsia (R), and Cardinium (C) exist in field whiteflies, with single (H) and double (HC and HR) infections occurring frequently. Infection frequencies of Hamiltonella (always 100%) and Cardinium (29.50-34.38%) remained steady during seasonal progression. Rickettsia infection frequency in the cucumber whitefly population decreased from 64.47% in summer to 35.29% in winter. Significantly lower Rickettsia infection frequency (15.55%) was identified in cotton whitefly populations and was not subject to seasonal fluctuation. Nevertheless, Rickettsia had a significantly quantitative advantage in the symbiont community of whitefly individuals and populations from both cucumber and cotton field all through the seasons. Moreover, higher Portiera and Hamiltonella densities were found in HC and HR whitefly than in H whitefly, suggesting these symbionts may contribute to producing nutrients for their symbiont partners. These results provide ample cues to further explore the interactions between coexisting symbionts, the coevolutionary relationship between symbionts and host symbiont-induced effects on host plant use.}, }
@article {pmid32967081, year = {2020}, author = {Ortiz, M and Bosch, J and Coclet, C and Johnson, J and Lebre, P and Salawu-Rotimi, A and Vikram, S and Makhalanyane, T and Cowan, D}, title = {Microbial Nitrogen Cycling in Antarctic Soils.}, journal = {Microorganisms}, volume = {8}, number = {9}, pages = {}, pmid = {32967081}, issn = {2076-2607}, abstract = {The Antarctic continent is widely considered to be one of the most hostile biological habitats on Earth. Despite extreme environmental conditions, the ice-free areas of the continent, which constitute some 0.44% of the total continental land area, harbour substantial and diverse communities of macro-organisms and especially microorganisms, particularly in the more &quot;hospitable&quot; maritime regions. In the more extreme non-maritime regions, exemplified by the McMurdo Dry Valleys of South Victoria Land, nutrient cycling and ecosystem servicing processes in soils are largely driven by microbial communities. Nitrogen turnover is a cornerstone of ecosystem servicing. In Antarctic continental soils, specifically those lacking macrophytes, cold-active free-living diazotrophic microorganisms, particularly Cyanobacteria, are keystone taxa. The diazotrophs are complemented by heterotrophic bacterial and archaeal taxa which show the genetic capacity to perform elements of the entire N cycle, including nitrification processes such as the anammox reaction. Here, we review the current literature on nitrogen cycling genes, taxa, processes and rates from studies of Antarctic soils. In particular, we highlight the current gaps in our knowledge of the scale and contribution of these processes in south polar soils as critical data to underpin viable predictions of how such processes may alter under the impacts of future climate change.}, }
@article {pmid32963580, year = {2020}, author = {Floková, K and Shimels, M and Andreo Jimenez, B and Bardaro, N and Strnad, M and Novák, O and Bouwmeester, HJ}, title = {An improved strategy to analyse strigolactones in complex sample matrices using UHPLC-MS/MS.}, journal = {Plant methods}, volume = {16}, number = {}, pages = {125}, pmid = {32963580}, issn = {1746-4811}, abstract = {Background: Strigolactones represent the most recently described group of plant hormones involved in many aspects of plant growth regulation. Simultaneously, root exuded strigolactones mediate rhizosphere signaling towards beneficial arbuscular mycorrhizal fungi, but also attract parasitic plants. The seed germination of parasitic plants induced by host strigolactones leads to serious agricultural problems worldwide. More insight in these signaling molecules is hampered by their extremely low concentrations in complex soil and plant tissue matrices, as well as their instability. So far, the combination of tailored isolation-that would replace current unspecific, time-consuming and labour-intensive processing of large samples-and a highly sensitive method for the simultaneous profiling of a broad spectrum of strigolactones has not been reported.<br><br>Results: Depending on the sample matrix, two different strategies for the rapid extraction of the seven structurally similar strigolactones and highly efficient single-step pre-concentration on polymeric RP SPE sorbent were developed and validated. Compared to conventional methods, controlled temperature during the extraction and the addition of an organic modifier (acetonitrile, acetone) to the extraction solvent helped to tailor strigolactone isolation from low initial amounts of root tissue (150 mg fresh weight, FW) and root exudate (20 ml), which improved both strigolactone stability and sample purity. We have designed an efficient UHPLC separation with sensitive MS/MS detection for simultaneous analysis of seven natural strigolactones including their biosynthetic precursors-carlactone and carlactonoic acid. In combination with the optimized UHPLC-MS/MS method, attomolar detection limits were achieved. The new method allowed successful profiling of seven strigolactones in small exudate and root tissue samples of four different agriculturally important plant species-sorghum, rice, pea and tomato.<br><br>Conclusion: The established method provides efficient strigolactone extraction with aqueous mixtures of less nucleophilic organic solvents from small root tissue and root exudate samples, in combination with rapid single-step pre-concentration. This method improves strigolactone stability and eliminates the co-extraction and signal of matrix-associated contaminants during the final UHPLC-MS/MS analysis with an electrospray interface, which dramatically increases the overall sensitivity of the analysis. We show that the method can be applied to a variety of plant species.}, }
@article {pmid32963001, year = {2020}, author = {Dueholm, MS and Andersen, KS and McIlroy, SJ and Kristensen, JM and Yashiro, E and Karst, SM and Albertsen, M and Nielsen, PH}, title = {Generation of Comprehensive Ecosystem-Specific Reference Databases with Species-Level Resolution by High-Throughput Full-Length 16S rRNA Gene Sequencing and Automated Taxonomy Assignment (AutoTax).}, journal = {mBio}, volume = {11}, number = {5}, pages = {}, pmid = {32963001}, issn = {2150-7511}, abstract = {High-throughput 16S rRNA gene amplicon sequencing is an essential method for studying the diversity and dynamics of microbial communities. However, this method is presently hampered by the lack of high-identity reference sequences for many environmental microbes in the public 16S rRNA gene reference databases and by the absence of a systematic and comprehensive taxonomy for the uncultured majority. Here, we demonstrate how high-throughput synthetic long-read sequencing can be applied to create ecosystem-specific full-length 16S rRNA gene amplicon sequence variant (FL-ASV) resolved reference databases that include high-identity references (>98.7% identity) for nearly all abundant bacteria (>0.01% relative abundance) using Danish wastewater treatment systems and anaerobic digesters as an example. In addition, we introduce a novel sequence identity-based approach for automated taxonomy assignment (AutoTax) that provides a complete seven-rank taxonomy for all reference sequences, using the SILVA taxonomy as a backbone, with stable placeholder names for unclassified taxa. The FL-ASVs are perfectly suited for the evaluation of taxonomic resolution and bias associated with primers commonly used for amplicon sequencing, allowing researchers to choose those that are ideal for their ecosystem. Reference databases processed with AutoTax greatly improves the classification of short-read 16S rRNA ASVs at the genus- and species-level, compared with the commonly used universal reference databases. Importantly, the placeholder names provide a way to explore the unclassified environmental taxa at different taxonomic ranks, which in combination with in situ analyses can be used to uncover their ecological roles.}, }
@article {pmid32962223, year = {2020}, author = {Rothman, JA and Cox-Foster, DL and Andrikopoulos, C and McFrederick, QS}, title = {Diet Breadth Affects Bacterial Identity but Not Diversity in the Pollen Provisions of Closely Related Polylectic and Oligolectic Bees.}, journal = {Insects}, volume = {11}, number = {9}, pages = {}, pmid = {32962223}, issn = {2075-4450}, support = {NNX15AP99A/NASA/NASA/United States ; 2018-67011- 28123//U.S. Department of Agriculture/ ; CA-R-ENT-5109-H//U.S. Department of Agriculture/ ; 1929572//National Science Foundation/ ; Pollinating Insect Research Unit Base Funds//U.S. Department of Agriculture/ ; }, abstract = {Mounting evidence suggests that microbes found in the pollen provisions of wild and solitary bees are important drivers of larval development. As these microbes are also known to be transmitted via the environment, most likely from flowers, the diet breadth of a bee may affect the diversity and identity of the microbes that occur in its pollen provisions. Here, we tested the hypothesis that, due to the importance of floral transmission of microbes, diet breadth affects pollen provision microbial community composition. We collected pollen provisions at four sites from the polylectic bee Osmia lignaria and the oligolectic bee Osmia ribifloris. We used high-throughput sequencing of the bacterial 16S rRNA gene to characterize the bacteria found in these provisions. We found minimal overlap in the specific bacterial variants in pollen provisions across the host species, even when the bees were constrained to foraging from the same flowers in cages at one site. Similarly, there was minimal overlap in the specific bacterial variants across sites, even within the same host species. Together, these findings highlight the importance of environmental transmission and host specific sorting influenced by diet breadth for microbes found in pollen provisions. Future studies addressing the functional consequences of this filtering, along with tests for differences between more species of oligoletic and polylectic bees will provide rich insights into the microbial ecology of solitary bees.}, }
@article {pmid32962069, year = {2020}, author = {Cold, F and Kousgaard, SJ and Halkjaer, SI and Petersen, AM and Nielsen, HL and Thorlacius-Ussing, O and Hansen, LH}, title = {Fecal Microbiota Transplantation in the Treatment of Chronic Pouchitis: A Systematic Review.}, journal = {Microorganisms}, volume = {8}, number = {9}, pages = {}, pmid = {32962069}, issn = {2076-2607}, support = {7076-00129B//Danish Innovation Fund/ ; }, abstract = {The objective was to evaluate available literature on treatment of chronic pouchitis with fecal microbiota transplantation (FMT) focusing on clinical outcomes, safety, and different approaches to FMT preparation and delivery. A systematic review of electronic databases was conducted using Medline, EMBASE, and the Cochrane Central Register of Controlled Trials Library from inception through April 2020. Human studies of all study types reporting results of FMT to treat chronic pouchitis were included. Nine studies, reporting FMT treatment of 69 patients with chronic pouchitis were found eligible for the review. Most studies were case series and cohort studies rated as having fair to poor quality due to high risk of bias and small sample size. Only one randomized controlled trial was included, finding no beneficial effect of FMT. In total clinical response after FMT was reported in 14 (31.8%) out of 44 evaluated patients at various timepoints after FMT, and clinical remission in ten (22.7%) patients. Only minor self-limiting adverse events were reported. FMT varied greatly regarding preparation, length of treatment, and route of delivery. The effects of FMT on symptoms of chronic pouchitis are not established, though some studies show promising results. Future controlled well-designed studies are warranted.}, }
@article {pmid32962009, year = {2020}, author = {Pantanella, F and Lekunberri, I and Gagliardi, A and Venuto, G and Sànchez-Melsió, A and Fabiani, M and Balcázar, JL and Schippa, S and De Giusti, M and Borrego, C and Solimini, A}, title = {Effect of Urban Wastewater Discharge on the Abundance of Antibiotic Resistance Genes and Antibiotic-Resistant Escherichia coli in Two Italian Rivers.}, journal = {International journal of environmental research and public health}, volume = {17}, number = {18}, pages = {}, pmid = {32962009}, issn = {1660-4601}, mesh = {Anti-Bacterial Agents ; *Drug Resistance, Microbial/genetics ; *Escherichia coli/drug effects/genetics ; *Genes, Bacterial ; Italy ; RNA, Ribosomal, 16S ; *Waste Water/analysis ; }, abstract = {BACKGROUND: Wastewater treatment plants (WWTPs) are microbial factories aimed to reduce the amount of nutrients and pathogenic microorganisms in the treated wastewater before its discharge into the environment. We studied the impact of urban WWTP effluents on the abundance of antibiotic resistance genes (ARGs) and antibiotic-resistant Escherichia coli (AR-E. coli) in the last stretch of two rivers (Arrone and Tiber) in Central Italy that differ in size and flow volume.<br><br>METHODS: Water samples were collected in three seasons upstream and downstream of the WWTP, at the WWTP outlet, and at sea sites near the river mouth, and analyzed for the abundance of ARGs by qPCR and AR-E. coli using cultivation followed by disk diffusion assays.<br><br>RESULTS: For all studied genes (16S rRNA, intI1, sul1, ermB, blaTEM, tetW and qnrS), absolute concentrations were significantly higher in the Tiber than in the Arrone at all sampling sites, despite their collection date, but the prevalence of target ARGs within bacterial communities in both rivers was similar. The absolute concentrations of most ARGs were also generally higher in the WWTP effluent with median levels between log 4 and log 6 copies per ml but did not show differences along the studied stretches of rivers. Statistically significant site effect was found for E. coli phenotypic resistance to tetracycline and ciprofloxacin in the Arrone but not in the Tiber.<br><br>CONCLUSIONS: In both rivers, diffuse or point pollution sources other than the studied WWTP effluents may account for the observed resistance pattern, although the Arrone appears as more sensitive to the wastewater impact considering its lower flow volume.}, }
@article {pmid32961710, year = {2020}, author = {Yacoub, A and Magnin, N and Gerbore, J and Haidar, R and Bruez, E and Compant, S and Guyoneaud, R and Rey, P}, title = {The Biocontrol Root-Oomycete, Pythium Oligandrum, Triggers Grapevine Resistance and Shifts in the Transcriptome of the Trunk Pathogenic Fungus, Phaeomoniella Chlamydospora.}, journal = {International journal of molecular sciences}, volume = {21}, number = {18}, pages = {}, pmid = {32961710}, issn = {1422-0067}, abstract = {The worldwide increase in grapevine trunk diseases, mainly esca, represents a major threat for vineyard sustainability. Biocontrol of a pioneer fungus of esca, Phaeomoniella chlamydospora, was investigated here by deciphering the tripartite interaction between this trunk-esca pathogen, grapevine and the biocontrol-oomycete, Pythium oligandrum. When P. oligandrum colonizes grapevine roots, it was observed that the wood necroses caused by P. chlamydospora were significantly reduced. Transcriptomic analyses of plant and fungus responses were performed to determine the molecular events occurring, with the aim to relate P.chlamydospora degradation of wood to gene expression modulation. Following P. oligandrum-root colonization, major transcriptomic changes occurred both, in the grapevine-defense system and in the P. chlamydospore-virulence factors. Grapevine-defense was enhanced in response to P. chlamydospora attacks, with P. oligandrum acting as a plant-systemic resistance inducer, promoting jasmonic/ethylene signaling pathways and grapevine priming. P. chlamydospora pathogenicity genes, such as those related to secondary metabolite biosynthesis, carbohydrate-active enzymes and transcription regulators, were also affected in their expression. Shifts in grapevine responses and key-fungal functions were associated with the reduction of P. chlamydospora wood necroses. This study provides evidence of wood fungal pathogen transcriptional changes induced by a root biocontrol agent, P. oligandrum, in which there is no contact between the two microorganisms.}, }
@article {pmid32961324, year = {2020}, author = {de Souza, CM and Garcia, MT and de Barros, PP and Pedroso, LLC and Ward, RADC and Strixino, JF and Melo, VMM and Junqueira, JC}, title = {Chitosan enhances the antimicrobial photodynamic inactivation mediated by Photoditazine® against Streptococcus mutans.}, journal = {Photodiagnosis and photodynamic therapy}, volume = {32}, number = {}, pages = {102001}, doi = {10.1016/j.pdpdt.2020.102001}, pmid = {32961324}, issn = {1873-1597}, abstract = {Chitosan (CS), a biopolymer with intrinsic antimicrobial activity, can increase antimicrobial photodynamic inactivation (aPDI). The aim of this study was to evaluate the capacity of CS to potentiate the efficacy of Photoditazine® (PDZ)-mediated aPDI of the cariogenic bacterium Streptococcus mutans. CS effectively augmented the effects of aPDI, with reductions of approximately 4.5 logs in both planktonic and biofilm states. The combined treatment was also capable of reducing the number of S. mutans cells and amount of extracellular matrix in biofilms formed on enamel surfaces, which were characterized using scanning electron microscopy analysis. Furthermore, CS increased the absorption of PDZ by S. mutans cells. The combination of CS with PDZ-mediated aPDI is hence a promising antimicrobial approach against S. mutans and may be useful to control dental caries.}, }
@article {pmid32960315, year = {2020}, author = {Sodhi, KK and Kumar, M and Singh, DK}, title = {Assessing the bacterial diversity and functional profiles of the River Yamuna using Illumina MiSeq sequencing.}, journal = {Archives of microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00203-020-02045-0}, pmid = {32960315}, issn = {1432-072X}, abstract = {A small percentage of the total freshwater on Earth is represented by river water. Microbes have an essential role to play in the biogeochemical cycles, mineralization of organic water, along with xenobiotics degradation. Microbial dynamics are susceptible to environmental stressors which includes pollutants such as antibiotics, metals, and other degradants. River Yamuna is polluted extensively by domestic and industrial wastes. Xenobiotics, when released into the environment, can lead to water pollution. The present study evaluates the microbial diversity in Yamuna River (28°40'5.53'' N, 77°15'0.35'' E) along with the prediction of the metagenome function. In this context, the metagenomic DNA was extracted and sequencing was done on Illumina@MiSeq platform. The total number of OTUs picked was 41,994, out of which 74% were classified within the kingdom Bacteria. 35% of the OTUs were assigned to phylum Proteobacteria, followed by Bacteriodetes (22%), whereas 26% of OTUs were unassigned. PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) was used to predict metagenomic functions using 16S rDNA as a marker. Metagenomic reads were assigned to the Kyoto Encyclopedia of Genes and Genomes (KEGG), Cluster of Orthologous (COG), and Gene Ontology (GO). Functional characterization reveals the presence of methyl-accepting chemotaxis protein which is an important adaptation for the microbes in the environment. The enzymes can be mapped for the bioremediation of xenobiotics. Information obtained from the amplicon sequencing of River Yamuna, collaborated with &quot;omic&quot; studies, may help in the design of bioremediation strategies and can be used for environmental clean-up of pollutants.}, }
@article {pmid32958725, year = {2020}, author = {Wünsch, D and Strijkstra, A and Wöhlbrand, L and Freese, HM and Scheve, S and Hinrichs, C and Trautwein, K and Maczka, M and Petersen, J and Schulz, S and Overmann, J and Rabus, R}, title = {Global Response of Phaeobacter inhibens DSM 17395 to Deletion of Its 262-kb Chromid Encoding Antibiotic Synthesis.}, journal = {Microbial physiology}, volume = {30}, number = {1-6}, pages = {9-24}, doi = {10.1159/000508591}, pmid = {32958725}, issn = {2673-1673}, abstract = {The marine alphaproteobacterium Phaeobacter inhibens DSM 17395, a member of the Roseobacter group, was recently shown to markedly enhance growth upon deletion of its 262-kb chromid encoding biosynthesis of tropodithietic acid (TDA). To scrutinize the metabolic/regulatory adaptations that underlie enhanced growth of the Δ262 mutant, its transcriptome and proteome compared to the wild type were investigated in process-controlled bioreactors with Casamino Acids as growth substrate. Genome resequencing revealed only few additional genetic changes (a heterogenic insertion, prophage activation, and several point mutations) between wild type and Δ262 mutant, albeit with no conceivable effect on the studied growth physiology. The abundances of the vast majority of transcripts and proteins involved in the catabolic network for complete substrate oxidation to CO2 were found to be unchanged, suggesting that the enhanced amino acid utilization of the Δ262 mutant did not require elevated synthesis of most enzymes of the catabolic network. Similarly, constituents of genetic information processing and cellular processes remained mostly unchanged. In contrast, 426 genes displayed differential expression, of which 410 were localized on the 3.2-Mb chromosome, 5 on the 65-kb chromid, and 11 on the 78-kb chromid. Notably, the branched-chain amino transferase IlvE acting on rapidly utilized Val, Ile, and Leu was upregulated. Moreover, the transportome was reconfigured, as evidenced from increased abundances of transcripts and proteins of several uptake systems for amino acids and inorganic nutrients (e.g., phosphate). Some components of the respiratory chain were also upregulated, which correlates with the higher respiration rates of the Δ262 mutant. Furthermore, chromosomally encoded transcripts and proteins that are peripherally related to TDA biosynthesis (e.g., the serine acyl transferase CysE) were strongly downregulated in the Δ262 mutant. Taken together, these observations reflect adaptations to enhanced growth as well as the functional interconnectivity of the replicons of P. inhibens DSM 17395.}, }
@article {pmid32957572, year = {2020}, author = {Wang, Q and Fu, S and Yang, Q and Hao, J and Zhou, C and Liu, Y}, title = {The Impact of Water Intrusion on Pathogenic Vibrio Species to Inland Brackish Waters of China.}, journal = {International journal of environmental research and public health}, volume = {17}, number = {18}, pages = {}, pmid = {32957572}, issn = {1660-4601}, mesh = {China ; Multilocus Sequence Typing ; *Seawater/virology ; *Vibrio cholerae ; *Vibrio parahaemolyticus/genetics ; Water ; Water Microbiology ; Water Movements ; }, abstract = {The estuary is the ecological niche of pathogenic Vibrio spp. as it provides abundant organic and inorganic nutrients from seawater and rivers. However, little is known about the ecology of these Vibrio species in the inland brackish water area. In this study, their co-occurrence and relationships to key environmental constraints (salinity and temperature) in the Hun-Tai River of China were examined using the most probable number polymerase chain reaction (MPN-PCR) approach. We hereby report 2-year continuous surveillance based on six water indices of the Hun-Tai River. The results showed that seawater intrusion maximally reached inland as far as 26.5 km for the Hun-Tai River. Pathogenic Vibrio spp. were detected in 21.9% of the water samples. In particular, V. cholerae, V. parahaemolyticus, and V. vulnificus were isolated in 10 (10.4%), 20 (20.8.5%), and 2 (2.08%) samples, respectively. All V. parahaemolyticus strains were tdh gene negative, 10% were positive for the trh gene. Multi-locus sequence typing (MLST) divided V. parahaemolyticus strains into 12 sequence types (STs) for the Hun-Tai River. Five STs were respectively present in various locations along the Hun-Tai River. The PCR assay for detecting six virulence genes and Vibrio seventh pandemic island I and II revealed three genotypes in 12 V. cholerae isolates. The results of our study showed that seawater intrusion and salinity have profound effects on the distribution of pathogenic Vibrio spp. in the inland river, suggesting a potential health risk associated with the waters of the Hun-Tai River used for irrigation and drinking.}, }
@article {pmid32950135, year = {2020}, author = {Peruzy, MF and Aponte, M and Proroga, YTR and Capuano, F and Cristiano, D and Delibato, E and Houf, K and Murru, N}, title = {Yersinia enterocolitica detection in pork products: Evaluation of isolation protocols.}, journal = {Food microbiology}, volume = {92}, number = {}, pages = {103593}, doi = {10.1016/j.fm.2020.103593}, pmid = {32950135}, issn = {1095-9998}, abstract = {Conventional methods for Yersinia enterocolitica detection in food samples are generally considered inadequate. Problems arise from the presence of the so-called &quot;background flora&quot;, coupled to the low contamination level of the pathogen. Since, data on the microbial ecology occurring in competitive microflora are still lacking, MALDI TOF MS was used for strains 'identification after enrichment in PSB or ITC broths, and after plating on selective CIN medium at different incubation times. SYBR Green Real time PCR was used for the Y. enterocolitica strains' detection (4/O:3, 1A/O:5) in experimentally contaminated foods, as well as in naturally contaminated samples. A higher number of different bacterial genera (10 on CIN and 18 on PCA) was recorded after enrichment in PSB, whilst enrichment in ITC led to recovery of 6 and 10 genera on CIN and PCA, respectively. Yersiniaceae was the dominant family on the first day of incubation, but on the second day the percentage of isolation considerably decreased. By testing experimentally contaminated samples, substantial difficulties were encountered. The biotype 1A was always detected, whereas strain 4/O:3 proved to be poorly competitive. Based on the data, the enrichment media PSB and ITC, currently proposed for Y. enterocolitica detection, need to be improved to promote a successful pathogen's recovery.}, }
@article {pmid32949457, year = {2020}, author = {Hermans, SM and Buckley, HL and Curran-Cournane, F and Taylor, M and Lear, G}, title = {Temporal variation in soil bacterial communities can be confounded with spatial variation.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {12}, pages = {}, doi = {10.1093/femsec/fiaa192}, pmid = {32949457}, issn = {1574-6941}, abstract = {Investigating temporal variation in soil bacterial communities advances our fundamental understanding of the causal processes driving biological variation, and how the composition of these important ecosystem members may change into the future. Despite this, temporal variation in soil bacteria remains understudied, and the effects of spatial heterogeneity in bacterial communities on the detection of temporal changes is largely unknown. Using 16S rRNA gene amplicon sequencing, we evaluated temporal patterns in soil bacterial communities from indigenous forest and human-impacted sites sampled repeatedly over a 5-year period. Temporal variation appeared to be greater when fewer spatial samples per site were analysed, as well as in human-impacted compared to indigenous sites (P < 0.01 for both). The biggest portion of variation in bacterial community richness and composition was explained by soil physicochemical variables (13-24%) rather than spatial distance or sampling time (<1%). These results highlight the importance of adequate spatiotemporal replication when sampling soil communities for environmental monitoring, and the importance of conducting temporal research across a wide variety of land uses. This will ensure we have a true understanding of how bacterial communities change over space and time; the work presented here provides important considerations for how such research should be designed.}, }
@article {pmid32948906, year = {2020}, author = {Jeong, SY and Kim, TG}, title = {Spatial Variance of Species Distribution Predicts the Interspecies Interactions within a Microbial Metacommunity.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01603-9}, pmid = {32948906}, issn = {1432-184X}, support = {2018R1D1A1B07048872//Ministry of Education/ ; }, abstract = {Interspecies interactions have a profound influence on spatial distribution of coexisting microbial species. We explored whether spatial variance of species distribution (SVSD) predicts the degree of interspecies interactions within a microbial metacommunity. Simulations were used to determine the relationships from random, lake, soil, and biofilm metacommunity datasets (1,000 times). All of the bacterial datasets showed a negative correlation between the habitat breadth (inverse to SVSD) and the numbers of total, positive, and negative interspecies interactions (P < 0.05); the only exception was the relationship between habitat breadth and negative interactions in the biofilm dataset. The random dataset had no significant relationships (P > 0.05). We repeated the simulations to determine the degree of correlation and reproducibility (100 times). Habitat breadth was negatively correlated with the total and positive interactions in all of the real datasets (P < 0.05), and the negative relationships persisted across repetitions. Despite variability in the slope of total interactions, the slope values of positive interactions were similar for the real datasets (- 19.9, - 19.2, and - 25.8 for lake, soil, and biofilm, respectively). In conclusion, our results demonstrate the patterns of species interaction-distribution and show that interspecies interactions are positively correlated with the SVSD.}, }
@article {pmid32948905, year = {2020}, author = {Mars Brisbin, M and Conover, AE and Mitarai, S}, title = {Influence of Regional Oceanography and Hydrothermal Activity on Protist Diversity and Community Structure in the Okinawa Trough.}, journal = {Microbial ecology}, volume = {80}, number = {4}, pages = {746-761}, doi = {10.1007/s00248-020-01583-w}, pmid = {32948905}, issn = {1432-184X}, abstract = {Microbial eukaryotes (protists) contribute substantially to ecological functioning in marine ecosystems, but the relative importance of factors shaping protist diversity, such as environmental selection and dispersal, remains difficult to parse. Water masses of a back-arc basin with hydrothermal activity provide a unique opportunity for studying the effects of dispersal and environmental selection on protist communities. In this study, we used metabarcoding to characterize protist communities in the Okinawa Trough, a back-arc spreading basin containing at least twenty-five active hydrothermal vent fields. Water was sampled from four depths at fourteen stations spanning the length of the Okinawa Trough, including three sites influenced by nearby hydrothermal vent sites. While significant differences in community structure reflecting water depth were present, protist communities were mostly homogeneous horizontally. Protist communities in the bottom waters affected by hydrothermal activity were significantly different from communities in other bottom waters, suggesting that environmental factors can be especially important in shaping community composition under specific conditions. Amplicon sequence variants that were enriched in hydrothermally influenced bottom waters largely derived from cosmopolitan protists that were present, but rare, in other near-bottom samples, thus highlighting the importance of the rare biosphere.}, }
@article {pmid32948266, year = {2020}, author = {Morimoto, D and Šulčius, S and Tominaga, K and Yoshida, T}, title = {Predetermined clockwork microbial worlds: Current understanding of aquatic microbial diel response from model systems to complex environments.}, journal = {Advances in applied microbiology}, volume = {113}, number = {}, pages = {163-191}, doi = {10.1016/bs.aambs.2020.06.001}, pmid = {32948266}, issn = {0065-2164}, abstract = {In the photic zone of aquatic ecosystems, microorganisms with different metabolisms and their viruses form complex interactions and food webs. Within these interactions, phototrophic microorganisms such as eukaryotic microalgae and cyanobacteria interact directly with sunlight, and thereby generate circadian rhythms. Diel cycling originally generated in microbial phototrophs is directly transmitted toward heterotrophic microorganisms utilizing the photosynthetic products as they are excreted or exuded. Such diel cycling seems to be indirectly propagated toward heterotrophs as a result of complex biotic interactions. For example, cell death of phototrophic microorganisms induced by viral lysis and protistan grazing provides additional resources of dissolved organic matter to the microbial community, and so generates diel cycling in other heterotrophs with different nutrient dependencies. Likewise, differences in the diel transmitting pathway via complex interactions among heterotrophs, and between heterotrophs and their viruses, may also generate higher variation and time lag diel rhythms in different heterotrophic taxa. Thus, sunlight and photosynthesis not only contribute energy and carbon supply, but also directly or indirectly control diel cycling of the microbial community through complex interactions in the photic zone of aquatic ecosystems.}, }
@article {pmid32945836, year = {2020}, author = {Pajdak-Stós, A and Fiałkowski, W and Fiałkowska, E}, title = {Rotifers weaken the efficiency of the cyanobacterium defence against ciliate grazers.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {11}, pages = {}, doi = {10.1093/femsec/fiaa189}, pmid = {32945836}, issn = {1574-6941}, abstract = {Cyanobacteria can protect themselves through limited dispersion and by increasing the compactness of the mucilage-covered cyanobacterial mat as well as by producing sheaths covering their trichomes. These features have been used in research to measure their degree of inducible defence. The influence of the presence of the rotifers Lecane inermis on the effectiveness of Phormidium sp. (Ph2) cyanobacterium defence was investigated. Experiments were conducted on the ciliates Pseudomicrothorax dubius and Furgasonia blochmanni, specialised in the ingestion of filamentous cyanobacteria. The most compact were cyanobacterial mats that were subjected exclusively to ciliates and the most dispersed were mats in the presence of rotifers alone. The presence of rotifers feeding on cyanobacterial mucilage led to the decreased effectiveness of the defence in two ways, by increasing the dispersion of cyanobacterial trichomes, thus loosening the cyanobacterial mat, and through the ingestion of the exopolysaccharide material covering the trichomes. As a result, in the presence of rotifers and the high density of ciliates, almost all the trichomes were removed. Moreover, in comparison with other treatments, a higher number of ciliates and rotifers remained active until the end of the experiments. This is the first report to show how rotifers can weaken the defence of cyanobacteria.}, }
@article {pmid32939928, year = {2020}, author = {Masetti, R and Zama, D and Leardini, D and Muratore, E and Turroni, S and Prete, A and Brigidi, P and Pession, A}, title = {The gut microbiome in pediatric patients undergoing allogeneic hematopoietic stem cell transplantation.}, journal = {Pediatric blood &amp; cancer}, volume = {67}, number = {12}, pages = {e28711}, doi = {10.1002/pbc.28711}, pmid = {32939928}, issn = {1545-5017}, abstract = {The gut microbiome (GM) has been associated with different clinical outcomes in the context of allogeneic hematopoietic stem cell transplantation (HSCT). Large multicenter cohort studies in adults have found significant correlations with overall survival, relapse, and incidence of complications. Moreover, GM is already a promising target for therapeutic interventions. However, few data are available in children, a population presenting unique features and challenges. During childhood, the GM evolves rapidly with large structural fluctuations, alongside with the maturation of the immune system. Furthermore, the HSCT procedure presents significant differences in children. These considerations underline the importance of a specific focus on the pediatric setting, and the role of GM and its age-dependent trajectory in influencing the immunity reconstitution and clinical outcomes. This review provides a comprehensive overview of the available evidence in the field of GM and pediatric HSCT, highlighting age-specific issues and discussing GM-based therapeutic approaches.}, }
@article {pmid32935184, year = {2020}, author = {He, Y and Zhou, Y and Weng, R and Wang, J and Chen, J and Huang, M}, title = {Responses of Ammonia-Oxidizing Archaea and Bacteria in Malodorous River Sediments to Different Remediation Techniques.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01597-4}, pmid = {32935184}, issn = {1432-184X}, support = {41877477//National Natural Science Foundation of China/ ; 18DZ1203806//Shanghai Science and Technology Development Funds/ ; 2017ZX07207001//National Science and Technology Major Project for Water Pollution Control and Treatment/ ; 2018ZX07208008//National Science and Technology Major Project for Water Pollution Control and Treatment/ ; }, abstract = {In this study, the joint use of high throughput sequencing, real-time quantitative PCR, and ammonia-oxidizing bacteria (AOB)-inhibiting allylthiourea was used to differentiate between the contributions of ammonia-oxidizing archaea (AOA) vs AOB to ammonia oxidation and ascertain how AOA and AOB responded to two widely used river remediation techniques (aeration and Ca(NO3)2 injection). Results showed that ammonia oxidation was largely attributed to ATU-sensitive AOB rather than AOA and Nitrosomonas was the predominant AOB-related genus (53.86%) in the malodorous river. The contribution of AOB to ammonia oxidation in the context of aeration and Ca(NO3)2 injection was 75.51 ± 2.77% and 60.19 ± 10.44%, respectively. The peak of AOB/AOA ratio and the marked increase of relative abundances of Nitrosomonas and Nitrosospira in aeration runs further demonstrated aeration favored the ammonia oxidation of AOB. Comparatively, Ca(NO3)2 injection could increase the ammonia oxidation contribution of AOA from 31.32 ± 6.06 to 39.81 ± 10.44% and was significantly correlated with Nitrosococcus of AOB (r = 0.796, p < 0.05), Candidatus_Nitrosopelagicus of AOA (r = 0.986, p < 0.01), and AOA Simpson diversity (r = - 0.791, p < 0.05). Moreover, Candidatus_Nitrosopelagicus was only present in Ca(NO3)2 runs. Taken together, Ca(NO3)2 was recognized as an important factor in mediating the growth and ecological niches of ammonia oxidizers.Graphical abstract.}, }
@article {pmid32935183, year = {2020}, author = {Phoma, BS and Makhalanyane, TP}, title = {Depth-Dependent Variables Shape Community Structure and Functionality in the Prince Edward Islands.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01589-4}, pmid = {32935183}, issn = {1432-184X}, abstract = {Physicochemical variables limit and control the distribution of microbial communities in all environments. In the oceans, this may significantly influence functional processes such the consumption of dissolved organic material and nutrient sequestration. Yet, the relative contributions of physical factors, such as water mass variability and depth, on functional processes are underexplored. We assessed microbial community structure and functionality in the Prince Edward Islands (PEIs) using 16S rRNA gene amplicon analysis and extracellular enzymatic activity assays, respectively. We found that depth and nutrients substantially drive the structural patterns of bacteria and archaea in this region. Shifts from epipelagic to bathypelagic zones were linked to decreases in the activities of several extracellular enzymes. These extracellular enzymatic activities were positively correlated with several phyla including several Alphaproteobacteria (including members of the SAR 11 clade and order Rhodospirillales) and Cyanobacteria. We show that depth-dependent variables may be essential drivers of community structure and functionality in the PEIs.}, }
@article {pmid32930890, year = {2020}, author = {Gupta, D and Guzman, MS and Bose, A}, title = {Extracellular electron uptake by autotrophic microbes: physiological, ecological, and evolutionary implications.}, journal = {Journal of industrial microbiology &amp; biotechnology}, volume = {47}, number = {9-10}, pages = {863-876}, pmid = {32930890}, issn = {1476-5535}, support = {MCB2021822//National Science Foundation/ ; 201563111//David and Lucile Packard Foundation/ ; DESC0014613//U.S. Department of Energy/ ; W911NF-18-1-0037//U.S. Department of Defense/ ; }, abstract = {Microbes exchange electrons with their extracellular environment via direct or indirect means. This exchange is bidirectional and supports essential microbial oxidation-reduction processes, such as respiration and photosynthesis. The microbial capacity to use electrons from insoluble electron donors, such as redox-active minerals, poised electrodes, or even other microbial cells is called extracellular electron uptake (EEU). Autotrophs with this capability can thrive in nutrient and soluble electron donor-deficient environments. As primary producers, autotrophic microbes capable of EEU greatly impact microbial ecology and play important roles in matter and energy flow in the biosphere. In this review, we discuss EEU-driven autotrophic metabolisms, their mechanism and physiology, and highlight their ecological, evolutionary, and biotechnological implications.}, }
@article {pmid32929739, year = {2020}, author = {Raymond, NS and Gómez-Muñoz, B and van der Bom, FJT and Nybroe, O and Jensen, LS and Müller-Stöver, DS and Oberson, A and Richardson, AE}, title = {Phosphate-solubilising microorganisms for improved crop productivity: a critical assessment.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.16924}, pmid = {32929739}, issn = {1469-8137}, abstract = {Phosphate-solubilising microorganisms (PSM) are often reported to have positive effects on crop productivity through enhanced phosphorus (P) nutrition. Our aim was to evaluate the validity of this concept. Most studies that report 'positive effects' of PSM on plant growth have been conducted under controlled conditions, whereas field experiments more frequently fail to demonstrate a positive response. Many studies have indicated that the mechanisms seen in vitro do not translate into improved crop P nutrition in complex soil-plant systems. Furthermore, associated mechanisms are often not rigorously assessed. We suggest that PSM do not mobilise sufficient P to change the crops' nutritional environment under field conditions. The current concept, in which PSM solubilise P 'for the plant' should thus be revised. Although PSM have the capacity to solubilise P to meet their own needs, it is the turnover of the microbial biomass that subsequently provides P to plants over a longer time. Therefore, the existing concept of PSM function is unlikely to deliver a reliable strategy for increasing crop P nutrition. A further mechanistic understanding is needed to determine how P mobilisation by PSM as a component of the whole soil community can be manipulated to become more effective for plant P nutrition.}, }
@article {pmid32925728, year = {2020}, author = {Berentsen, B and Nagaraja, BH and Teige, EP and Lied, GA and Lundervold, AJ and Lundervold, K and Steinsvik, EK and Hillestad, ER and Valeur, J and Brønstad, I and Gilja, OH and Osnes, B and Hatlebakk, JG and Haász, J and Labus, J and Gupta, A and Mayer, EA and Benitez-Páez, A and Sanz, Y and Lundervold, A and Hausken, T}, title = {Study protocol of the Bergen brain-gut-microbiota-axis study: A prospective case-report characterization and dietary intervention study to evaluate the effects of microbiota alterations on cognition and anatomical and functional brain connectivity in patients with irritable bowel syndrome.}, journal = {Medicine}, volume = {99}, number = {37}, pages = {e21950}, pmid = {32925728}, issn = {1536-5964}, mesh = {Adolescent ; Adult ; Aged ; Brain/microbiology/physiopathology ; Case-Control Studies ; Cognition/physiology ; Diet, Carbohydrate-Restricted/*methods ; Female ; Fermentation ; Gastrointestinal Microbiome/*physiology ; Humans ; Irritable Bowel Syndrome/*diet therapy/*microbiology/psychology ; Male ; Middle Aged ; Prospective Studies ; Young Adult ; }, abstract = {INTRODUCTION: Irritable bowel syndrome (IBS) is a common clinical label for medically unexplained gastrointestinal (GI) symptoms, recently described as a disturbance of the brain-gut-microbiota (BGM) axis. To gain a better understanding of the mechanisms underlying the poorly understood etiology of IBS, we have designed a multifaceted study that aim to stratify the complex interaction and dysfunction between the brain, the gut, and the microbiota in patients with IBS.<br><br>METHODS: Deep phenotyping data from patients with IBS (n = 100) and healthy age- (between 18 and 65) and gender-matched controls (n = 40) will be collected between May 2019 and December 2021. Psychometric tests, questionnaires, human biological tissue/samples (blood, faeces, saliva, and GI biopsies from antrum, duodenum, and sigmoid colon), assessment of gastric accommodation and emptying using transabdominal ultrasound, vagal activity, and functional and structural magnetic resonance imaging (MRI) of the brain, are included in the investigation of each participant. A subgroup of 60 patients with IBS-D will be further included in a 12-week low FODMAP dietary intervention-study to determine short and long-term effects of diet on GI symptoms, microbiota composition and functions, molecular GI signatures, cognitive, emotional and social functions, and structural and functional brain signatures. Deep machine learning, prediction tools, and big data analyses will be used for multivariate analyses allowing disease stratification and diagnostic biomarker detection.<br><br>DISCUSSION: To our knowledge, this is the first study to employ unsupervised machine learning techniques and incorporate systems-based interactions between the central and the peripheral components of the brain-gut-microbiota axis at the levels of the multiomics, microbiota profiles, and brain connectome of a cohort of 100 patients with IBS and matched controls; study long-term safety and efficacy of the low-FODMAP diet on changes in nutritional status, gut microbiota composition, and metabolites; and to investigate changes in the brain and gut connectome after 12 weeks strict low-FODMAP-diet in patients with IBS. However, there are also limitations to the study. As a restrictive diet, the low-FODMAP diet carries risks of nutritional inadequacy and may foster disordered eating patterns. Strict FODMAP restriction induces a potentially unfavourable gut microbiota, although the health effects are unknown.<br><br>TRIAL REGISTRATION NUMBER: NCT04296552 (ClinicalTrials.gov).}, }
@article {pmid32923720, year = {2020}, author = {Giongo, A and Dos Anjos Borges, LG and Marconatto, L and de Lara Palhano, P and Serbent, MP and Moreira-Silva, E and de Abreu Siqueira, T and Martinho, CT and Barili, R and Paz, LV and Moser, LI and De Marco Veríssimo, C and Ketzer, JMM and Medina-Silva, R}, title = {Adaption of microbial communities to the hostile environment in the Doce River after the collapse of two iron ore tailing dams.}, journal = {Heliyon}, volume = {6}, number = {8}, pages = {e04778}, pmid = {32923720}, issn = {2405-8440}, abstract = {In November 2015, two iron ore tailing dams collapsed in the city of Mariana, Brazil. The dams' collapse generated a wave of approximately 50 million m3 of a mixture of mining waste and water. It was a major environmental tragedy in Brazilian history, which damaged rivers, and cities 660 km away in the Doce River basin until it reached the ocean coast. Shortly after the incident, several reports informed that the concentration of metals in the water was above acceptable legal limits under Brazilian laws. Here the microbial communities in samples of water, mud, foam, and rhizosphere of Eichhornia from Doce River were analyzed for 16S and 18S rRNA-based amplicon sequencing, along with microbial isolation, chemical and mineralogical analyses. Samples were collected one month and thirteen months after the collapse. Prokaryotic communities from mud shifted drastically over time (33% Bray-Curtis similarity), while water samples were more similar (63% Bray-Curtis similarity) in the same period. After 12 months, mud samples remained with high levels of heavy metals and a reduction in the diversity of microeukaryotes was detected. Amoebozoans increased in mud samples, reaching 49% of microeukaryote abundance, with Discosea and Lobosa groups being the most abundant. The microbial communities' structure in mud samples changed adapting to the new environment condition. The characterization of microbial communities and metal-tolerant organisms from such impacted environments is essential for understanding the ecological consequences of massive anthropogenic impacts and strategies for the restoration of contaminated sites such as the Doce River.}, }
@article {pmid32923454, year = {2020}, author = {Ardern, Z and Neuhaus, K and Scherer, S}, title = {Are Antisense Proteins in Prokaryotes Functional?.}, journal = {Frontiers in molecular biosciences}, volume = {7}, number = {}, pages = {187}, pmid = {32923454}, issn = {2296-889X}, abstract = {Many prokaryotic RNAs are transcribed from loci outside of annotated protein coding genes. Across bacterial species hundreds of short open reading frames antisense to annotated genes show evidence of both transcription and translation, for instance in ribosome profiling data. Determining the functional fraction of these protein products awaits further research, including insights from studies of molecular interactions and detailed evolutionary analysis. There are multiple lines of evidence, however, that many of these newly discovered proteins are of use to the organism. Condition-specific phenotypes have been characterized for a few. These proteins should be added to genome annotations, and the methods for predicting them standardized. Evolutionary analysis of these typically young sequences also may provide important insights into gene evolution. This research should be prioritized for its exciting potential to uncover large numbers of novel proteins with extremely diverse potential practical uses, including applications in synthetic biology and responding to pathogens.}, }
@article {pmid32920672, year = {2020}, author = {Valverde, A and Cason, ED and Gómez-Arias, A and Bozkale, D and Govender, D and Riddell, E and Cowan, D}, title = {Pollution shapes the microbial communities in river water and sediments from the Olifants River catchment, South Africa.}, journal = {Archives of microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00203-020-02035-2}, pmid = {32920672}, issn = {1432-072X}, abstract = {Human activities such as agriculture and mining are leading causes of water pollution worldwide. Individual contaminants are known to negatively affect microbial communities. However, the effect of multifaceted pollution on these communities is less well understood. We investigated, using next-generation sequencing of the 16S rRNA genes, the effects of multisource (i.e., fertilizer industry and mining) chronic pollution on bacterial and archaeal communities in water and sediments from the Olifants River catchment, South Africa. Water samples showed less microbial species diversity than sediments and both habitats displayed different microbial communities. Within each of these habitats, pollution had no effect on alpha diversity but shaped the microbial composition and taxonomy-based predicted functions. Certain prokaryotic taxa and functional groups were indicative of different degrees of pollution. Heterotrophic taxa (e.g., Flavobacterium sp.) and sulphur-oxidizing bacteria (i.e., Thiobacillus sp.) were indicators of pollution in water and sediments, respectively. Ultimately, this information could be used to develop microbial indicators of water quality degradation.}, }
@article {pmid32920671, year = {2020}, author = {Lee, JC and Whang, KS}, title = {Lysobacter telluris sp. nov., isolated from Korean rhizosphere soil.}, journal = {Archives of microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00203-020-02032-5}, pmid = {32920671}, issn = {1432-072X}, abstract = {A Gram-stain-negative, aerobic, non-motile, non-spore-forming light-yellow-coloured rod-shaped bacterial strain, designated YJ15T, was isolated from soil at Bigeum island in Korea. Growth was observed at 10-37 °C (optimum, 28 °C), at pH 6.0-7.5 (optimum, pH 7.0) and in the absence of NaCl. Based on 16S rRNA gene sequence analysis, strain YJ15T was closely related to 'Lysobacter tongrenensis' YS037T (97.8%), Lysobacter pocheonensis Gsoil193T (96.5%) and Lysobacter daecheongensis Dae08T (95.8%) and phylogenetically grouped together with 'Lysobacter tongrenensis' YS037T, Lysobacter dokdonensis DS-58T and Lysobacter pocheonensis Gsoil 193T. The DNA-DNA relatedness between strain YJ15T and 'Lysobacter tongrenensis' KCTC 52206T was 12% and the phylogenomic analysis based on the whole genome sequence demonstrated that strain YJ20T formed a distinct phyletic line with Lysobacterlter dokdonensis DS-58T showing average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values of 76.3 and 21.3%, respectively. The predominant ubiquinone was identified as Q-8, and polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and two unidentified aminolipids. The major fatty acids were iso-C17:1 ω9c, iso-C15:0, iso-C16:0 and iso-C17:0. The genomic DNA G + C content was 68.2 mol %. On the basis of phenotypic, chemotaxonomic properties and phylogenetic analyses in this study, strain YJ15T is considered to represent a novel species of the genus Lysobacter, for which the name Lysobacter telluris sp. nov. is proposed. The type strain is YJ15T (= KACC 19552T = NBRC 113197T).}, }
@article {pmid32920663, year = {2020}, author = {Paz, C and Öpik, M and Bulascoschi, L and Bueno, CG and Galetti, M}, title = {Dispersal of Arbuscular Mycorrhizal Fungi: Evidence and Insights for Ecological Studies.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01582-x}, pmid = {32920663}, issn = {1432-184X}, support = {2018/16697-4//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2018/00212-1//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; }, abstract = {Dispersal is a critical ecological process that modulates gene flow and contributes to the maintenance of genetic and taxonomic diversity within ecosystems. Despite an increasing global understanding of the arbuscular mycorrhizal (AM) fungal diversity, distribution and prevalence in different biomes, we have largely ignored the main dispersal mechanisms of these organisms. To provide a geographical and scientific overview of the available data, we systematically searched for the direct evidence on the AM fungal dispersal agents (abiotic and biotic) and different propagule types (i.e. spores, extraradical hyphae or colonized root fragments). We show that the available data (37 articles) on AM fungal dispersal originates mostly from North America, from temperate ecosystems, from biotic dispersal agents (small mammals) and AM fungal spores as propagule type. Much lesser evidence exists from South American, Asian and African tropical systems and other dispersers such as large-bodied birds and mammals and non-spore propagule types. We did not find strong evidence that spore size varies across dispersal agents, but wind and large animals seem to be more efficient dispersers. However, the data is still too scarce to draw firm conclusions from this finding. We further discuss and propose critical research questions and potential approaches to advance the understanding of the ecology of AM fungi dispersal.}, }
@article {pmid32920539, year = {2020}, author = {Zhang, R and Weinbauer, MG and Peduzzi, P}, title = {Aquatic Viruses and Climate Change.}, journal = {Current issues in molecular biology}, volume = {41}, number = {}, pages = {357-380}, doi = {10.21775/cimb.041.357}, pmid = {32920539}, issn = {1467-3045}, abstract = {The viral component in aquatic systems clearly needs to be incorporated into future ocean and inland water climate models. Viruses have the potential to influence carbon and nutrient cycling in aquatic ecosystems significantly. Changing climate likely has both direct and indirect influence on virus-mediated processes, among them an impact on food webs, biogeochemical cycles and on the overall metabolic performance of whole ecosystems. Here we synthesise current knowledge on potential climate-related consequences for viral assemblages, virus-host interactions and virus functions, and in turn, viral processes contributing to climate change. There is a need to increase the accuracy of predictions of climate change impacts on virus- driven processes, particularly of those linked to biological production and biogeochemical cycles. Comprehension of the relationships between microbial/viral processes and global phenomena is essential to predict the influence on as well as the response of the biosphere to global change.}, }
@article {pmid32920408, year = {2021}, author = {Soh, YNA and Kunacheva, C and Menon, S and Webster, RD and Stuckey, DC}, title = {Comparison of soluble microbial product (SMP) production in full-scale anaerobic/aerobic industrial wastewater treatment and a laboratory based synthetic feed anaerobic membrane system.}, journal = {The Science of the total environment}, volume = {754}, number = {}, pages = {142173}, doi = {10.1016/j.scitotenv.2020.142173}, pmid = {32920408}, issn = {1879-1026}, mesh = {Anaerobiosis ; Bioreactors ; Sewage ; *Waste Disposal, Fluid ; *Waste Water ; }, abstract = {This study focused on the characterisation of soluble microbial products (SMPs) produced from a full-scale multi-stage (anaerobic/aerobic) industrial wastewater treatment plant, and contrasted them to the SMPs detected in the effluent of a lab-scale AnMBR treating synthetic wastewater to determine if there were any common solutes detected irrespective of the feed organics. Recently developed analytical methods using gas chromatography coupled mass spectrometry (GC-MS) and liquid chromatography coupled quadrupole-time-of-flight (LC-Q-ToF) for SMP characterisation in a wide molecular weight (MW) range of 30-2000 Da (Da) were applied. Samples collected from the Industrial Wastewater plant were the upflow anaerobic sludge blanket (UASB) influent and effluent, and aerobic membrane bioreactor (MBR) effluent before discharge. The GC-MS detected a spike in cyclooctasulphur in the UASB effluent, an indicator of shock-loading, which disappeared after the MBR process. Alkanes, acids and nitrogenous compounds were found to be the end-products from the GC-MS results, while LC-Q-ToF analysis revealed that eicosanoids, a group of cell-signalling molecules, were produced in the aerobic MBR, and made up 71% of its effluent. A comparison of the submerged anaerobic membrane bioreactor (SAMBR) and aerobic MBR effluents using GC-MS showed that there was only a small degree of similarity between the SMPs, comprising mainly long chain alkanes and phthalate. On the other hand, LC-Q-ToF showed a large contrast in compound composition, mostly having cell-signalling functions, which deepened our understanding of the different metabolic processes occurring in aerobic and anaerobic systems. These data could be useful for future work in various areas such as controlling quorum-sensing and biofilm formation, process optimisation and control, and microbial ecology.}, }
@article {pmid32920334, year = {2020}, author = {Candry, P and Radić, L and Favere, J and Carvajal-Arroyo, JM and Rabaey, K and Ganigué, R}, title = {Mildly acidic pH selects for chain elongation to caproic acid over alternative pathways during lactic acid fermentation.}, journal = {Water research}, volume = {186}, number = {}, pages = {116396}, doi = {10.1016/j.watres.2020.116396}, pmid = {32920334}, issn = {1879-2448}, mesh = {*Caproates ; Carbohydrates ; Fermentation ; Hydrogen-Ion Concentration ; *Lactic Acid ; }, abstract = {Carbohydrate-rich waste streams can be used for bioproduction of medium-chain carboxylic acids (MCCA) such as caproic acid. The carbohydrates in these streams can be converted to lactic acid as the initial fermentation product, which can then be fermented to MCCA by chain elongation. In this process, chain elongators compete for lactic acid with other bacterial groups that, for instance, ferment lactic acid to propionic and acetic acid. Understanding the drivers that control the competition between these two pathways is essential to maximizing MCCA production. This study aimed to investigate the competition between chain elongating and propionic acid producing organisms as a function of operational pH. Operation of long-term lactic acid fermenting reactors with varying pH values showed that pH values above 6 resulted in a propionic acid producing community dominated by Veillonella and Aminobacterium. At pH values below 6, the community moved towards chain elongation, with communities dominated by Caproiciproducens. Short-term incubations showed that rates of lactic acid consumption were strongly reduced at pH below 6 (7.7 ± 1.2 mM lactic acid·h-1 at pH 6.5; 0.74 ± 0.33 mM lactic acid·h-1 at pH 5.5). Similar to observations in long-term reactors, when a chain elongating community adapted to pH 5.5 was used for short-term incubations at pH 6.5, propionic acid was the dominant product. The results of this study show that pH below 6 stimulate lactic acid chain elongators through kinetic effects, and potentially improved energetics, providing a tool for microbial management of MCCA-producing systems.}, }
@article {pmid32919387, year = {2020}, author = {Casterline, BW and Paller, AS}, title = {Early development of the skin microbiome: therapeutic opportunities.}, journal = {Pediatric research}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41390-020-01146-2}, pmid = {32919387}, issn = {1530-0447}, abstract = {As human skin hosts a diverse microbiota in health and disease, there is an emerging consensus that dysregulated interactions between host and microbiome may contribute to chronic inflammatory disease of the skin. Neonatal skin is a unique habitat, structurally similar to the adult but with a different profile of metabolic substrates, environmental stressors, and immune activity. The surface is colonized within moments of birth with a bias toward maternal strains. Initial colonists are outcompeted as environmental exposures increase and host skin matures. Nonetheless, early life microbial acquisitions may have long-lasting effects on health through modulation of host immunity and competitive interactions between bacteria. Microbial ecology and its influence on health have been of interest to dermatologists for >50 years, and an explosion of recent interest in the microbiome has prompted ongoing investigations of several microbial therapeutics for dermatological disease. In this review, we consider how recent insight into the host and microbial factors driving development of the skin microbiome in early life offers new opportunities for therapeutic intervention. IMPACT: Advancement in understanding molecular mechanisms of bacterial competition opens new avenues of investigation into dermatological disease. Primary development of the skin microbiome is determined by immunological features of the cutaneous habitat. Understanding coordinated microbial and immunological development in the pediatric patient requires a multidisciplinary synthesis of primary literature.}, }
@article {pmid32919372, year = {2020}, author = {Frommeyer, B and Fiedler, AW and Oehler, SR and Hanson, BT and Loy, A and Franchini, P and Spiteller, D and Schleheck, D}, title = {Environmental and Intestinal Phylum Firmicutes Bacteria Metabolize the Plant Sugar Sulfoquinovose via a 6-Deoxy-6-sulfofructose Transaldolase Pathway.}, journal = {iScience}, volume = {23}, number = {9}, pages = {101510}, pmid = {32919372}, issn = {2589-0042}, abstract = {Bacterial degradation of the sugar sulfoquinovose (SQ, 6-deoxy-6-sulfoglucose) produced by plants, algae, and cyanobacteria, is an important component of the biogeochemical carbon and sulfur cycles. Here, we reveal a third biochemical pathway for primary SQ degradation in an aerobic Bacillus aryabhattai strain. An isomerase converts SQ to 6-deoxy-6-sulfofructose (SF). A novel transaldolase enzyme cleaves the SF to 3-sulfolactaldehyde (SLA), while the non-sulfonated C3-(glycerone)-moiety is transferred to an acceptor molecule, glyceraldehyde phosphate (GAP), yielding fructose-6-phosphate (F6P). Intestinal anaerobic bacteria such as Enterococcus gilvus, Clostridium symbiosum, and Eubacterium rectale strains also express transaldolase pathway gene clusters during fermentative growth with SQ. The now three known biochemical strategies for SQ catabolism reflect adaptations to the aerobic or anaerobic lifestyle of the different bacteria. The occurrence of these pathways in intestinal (family) Enterobacteriaceae and (phylum) Firmicutes strains further highlights a potential importance of metabolism of green-diet SQ by gut microbial communities to, ultimately, hydrogen sulfide.}, }
@article {pmid32918562, year = {2020}, author = {Ennis, NJ and Dharumaduri, D and Bryce, JG and Tisa, LS}, title = {Metagenome Across a Geochemical Gradient of Indian Stone Ruins Found at Historic Sites in Tamil Nadu, India.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01598-3}, pmid = {32918562}, issn = {1432-184X}, abstract = {Although stone surfaces seem unlikely to be habitable, they support microbial life. Life on these surfaces are subjected to many varying harsh conditions and require the inhabitants to exhibit resistance to environmental factors including UV irradiation, toxic metal exposure, and fluctuating temperatures and humidity. Here we report the effect of hosting stone geochemistry on the microbiome of stone ruins found in Tamil Nadu, India. The microbial communities found on the two lithologies, granite and granodiorite, hosted distinct populations of bacteria. Geochemical composition analysis of sampled stones revealed quartz mineral content as a major driver of microbial community structure, particularly promoting community richness and proportions of Cyanobacteria and Deinococcus-Thermus. Other geochemical parameters including ilmenite, albite, anorthite, and orthoclase components or elemental concentrations (Ti, Fe, Mn, Na, and K) also influenced community structure to a lesser degree than quartz. Core members of the stone microbiome community found on both lithologies were also identified and included Cyanobacteria (Chroococcidiopsaceae and Dapisostemonum CCIBt 3536), Rubrobacter, and Deinococcus. A cluster of taxa including Sphingomonas, Geodermatophilus, and Truepera were mostly found in the granodiorite samples. Community diversity correlated with quartz mineral content in these samples may indicate that the microbial communities that attach to quartz surfaces may be transient and regularly changing. This work has expanded our understanding of built-stone microbial community structure based on lithology and geochemistry.}, }
@article {pmid32918153, year = {2020}, author = {Sajjad, W and Ali, B and Bahadur, A and Ghimire, PS and Kang, S}, title = {Bacterial Diversity and Communities Structural Dynamics in Soil and Meltwater Runoff at the Frontier of Baishui Glacier No.1, China.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01600-y}, pmid = {32918153}, issn = {1432-184X}, abstract = {Comprehensive knowledge of bacterial ecology mainly in supraglacial habitats is pivotal particularly at the frontier of accelerated glacier retreat. In this study, bacterial diversity and community composition in glacial soil and meltwater runoff at the frontier of Baishui Glacier No.1 were evaluated using high throughput sequencing. Significant variations in the physiochemical parameters formed an ecological gradient between soil and meltwater runoff. Based on the richness and evenness indexes, the bacterial diversity was relatively higher in soil compared with meltwater runoff. Hierarchical clustering and bi-plot ordination revealed that the taxonomic composition of soil samples was highly similar and significantly influenced by the ecological parameters than the meltwater runoff. The overall relative abundance trend of bacterial phyla and genera were greatly varied in soil and water samples. The relative abundance of Proteobacteria was higher in water runoff samples (40.5-87%) compared with soil samples (32-52.7%). Proteobacteria, Firmicutes, and a little part of Cyanobacteria occupied a major portion of water runoff while the soil was dominated by Acidobacteria (6-16.2%), Actinobacteria (5-16%), Bacteroidetes (0.5-8.8%), and Cyanobacteria (0.1-8.3%) besides Proteobacteria and Firmicutes. Higher numbers of biomarkers were found in soil group compared with the water group. The study area is diverse in terms of richness, while community structures are not evenly distributed. This study provides a preliminary understanding of the bacterial diversity and shifts in community structure in soil and meltwater runoff at the frontier of the glacial. The findings revealed that the environmental factors are a significantly strong determinant of bacterial community structures in such a closely linked ecosystem.}, }
@article {pmid32917751, year = {2020}, author = {Park, SJ and Andrei, AŞ and Bulzu, PA and Kavagutti, VS and Ghai, R and Mosier, AC}, title = {Expanded Diversity and Metabolic Versatility of Marine Nitrite-Oxidizing Bacteria Revealed by Cultivation- and Genomics-Based Approaches.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {22}, pages = {}, pmid = {32917751}, issn = {1098-5336}, mesh = {Bacteria/*classification/isolation &amp; purification/*metabolism ; Geologic Sediments/microbiology ; Metabolic Networks and Pathways ; *Microbiota ; Nitrites/*metabolism ; Oxidation-Reduction ; Republic of Korea ; Seawater/microbiology ; }, abstract = {Nitrite-oxidizing bacteria (NOB) are ubiquitous and abundant microorganisms that play key roles in global nitrogen and carbon biogeochemical cycling. Despite recent advances in understanding NOB physiology and taxonomy, currently very few cultured NOB or representative NOB genome sequences from marine environments exist. In this study, we employed enrichment culturing and genomic approaches to shed light on the phylogeny and metabolic capacity of marine NOB. We successfully enriched two marine NOB (designated MSP and DJ) and obtained a high-quality metagenome-assembled genome (MAG) from each organism. The maximum nitrite oxidation rates of the MSP and DJ enrichment cultures were 13.8 and 30.0 μM nitrite per day, respectively, with these optimum rates occurring at 0.1 mM and 0.3 mM nitrite, respectively. Each enrichment culture exhibited a different tolerance to various nitrite and salt concentrations. Based on phylogenomic position and overall genome relatedness indices, both NOB MAGs were proposed as novel taxa within the Nitrospinota and Nitrospirota phyla. Functional predictions indicated that both NOB MAGs shared many highly conserved metabolic features with other NOB. Both NOB MAGs encoded proteins for hydrogen and organic compound metabolism and defense mechanisms for oxidative stress. Additionally, these organisms may have the genetic potential to produce cobalamin (an essential enzyme cofactor that is limiting in many environments) and, thus, may play an important role in recycling cobalamin in marine sediment. Overall, this study appreciably expands our understanding of the Nitrospinota and Nitrospirota phyla and suggests that these NOB play important biogeochemical roles in marine habitats.IMPORTANCE Nitrification is a key process in the biogeochemical and global nitrogen cycle. Nitrite-oxidizing bacteria (NOB) perform the second step of aerobic nitrification (converting nitrite to nitrate), which is critical for transferring nitrogen to other organisms for assimilation or energy. Despite their ecological importance, there are few cultured or genomic representatives from marine systems. Here, we obtained two NOB (designated MSP and DJ) enriched from marine sediments and estimated the physiological and genomic traits of these marine microbes. Both NOB enrichment cultures exhibit distinct responses to various nitrite and salt concentrations. Genomic analyses suggest that these NOB are metabolically flexible (similar to other previously described NOB) yet also have individual genomic differences that likely support distinct niche distribution. In conclusion, this study provides more insights into the ecological roles of NOB in marine environments.}, }
@article {pmid32917275, year = {2020}, author = {Modin, O and Liébana, R and Saheb-Alam, S and Wilén, BM and Suarez, C and Hermansson, M and Persson, F}, title = {Hill-based dissimilarity indices and null models for analysis of microbial community assembly.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {132}, doi = {10.1186/s40168-020-00909-7}, pmid = {32917275}, issn = {2049-2618}, abstract = {BACKGROUND: High-throughput amplicon sequencing of marker genes, such as the 16S rRNA gene in Bacteria and Archaea, provides a wealth of information about the composition of microbial communities. To quantify differences between samples and draw conclusions about factors affecting community assembly, dissimilarity indices are typically used. However, results are subject to several biases, and data interpretation can be challenging. The Jaccard and Bray-Curtis indices, which are often used to quantify taxonomic dissimilarity, are not necessarily the most logical choices. Instead, we argue that Hill-based indices, which make it possible to systematically investigate the impact of relative abundance on dissimilarity, should be used for robust analysis of data. In combination with a null model, mechanisms of microbial community assembly can be analyzed. Here, we also introduce a new software, qdiv, which enables rapid calculations of Hill-based dissimilarity indices in combination with null models.<br><br>RESULTS: Using amplicon sequencing data from two experimental systems, aerobic granular sludge (AGS) reactors and microbial fuel cells (MFC), we show that the choice of dissimilarity index can have considerable impact on results and conclusions. High dissimilarity between replicates because of random sampling effects make incidence-based indices less suited for identifying differences between groups of samples. Determining a consensus table based on count tables generated with different bioinformatic pipelines reduced the number of low-abundant, potentially spurious amplicon sequence variants (ASVs) in the data sets, which led to lower dissimilarity between replicates. Analysis with a combination of Hill-based indices and a null model allowed us to show that different ecological mechanisms acted on different fractions of the microbial communities in the experimental systems.<br><br>CONCLUSIONS: Hill-based indices provide a rational framework for analysis of dissimilarity between microbial community samples. In combination with a null model, the effects of deterministic and stochastic community assembly factors on taxa of different relative abundances can be systematically investigated. Calculations of Hill-based dissimilarity indices in combination with a null model can be done in qdiv, which is freely available as a Python package (https://github.com/omvatten/qdiv). In qdiv, a consensus table can also be determined from several count tables generated with different bioinformatic pipelines. Video Abstract.}, }
@article {pmid32916620, year = {2020}, author = {Lukumbuzya, M and Kristensen, JM and Kitzinger, K and Pommerening-Röser, A and Nielsen, PH and Wagner, M and Daims, H and Pjevac, P}, title = {A refined set of rRNA-targeted oligonucleotide probes for in situ detection and quantification of ammonia-oxidizing bacteria.}, journal = {Water research}, volume = {186}, number = {}, pages = {116372}, doi = {10.1016/j.watres.2020.116372}, pmid = {32916620}, issn = {1879-2448}, mesh = {*Ammonia ; *Ecosystem ; In Situ Hybridization, Fluorescence ; Oligonucleotide Probes/genetics ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Ammonia-oxidizing bacteria (AOB) of the betaproteobacterial genera Nitrosomonas and Nitrosospira are key nitrifying microorganisms in many natural and engineered ecosystems. Since many AOB remain uncultured, fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes has been one of the most widely used approaches to study the community composition, abundance, and other features of AOB directly in environmental samples. However, the established and widely used AOB-specific 16S rRNA-targeted FISH probes were designed up to two decades ago, based on much smaller rRNA gene sequence datasets than available today. Several of these probes cover their target AOB lineages incompletely and suffer from a weak target specificity, which causes cross-hybridization of probes that should detect different AOB lineages. Here, a set of new highly specific 16S rRNA-targeted oligonucleotide probes was developed and experimentally evaluated that complements the existing probes and enables the specific detection and differentiation of the known, major phylogenetic clusters of betaproteobacterial AOB. The new probes were successfully applied to visualize and quantify AOB in activated sludge and biofilm samples from seven pilot- and full-scale wastewater treatment systems. Based on its improved target group coverage and specificity, the refined probe set will facilitate future in situ analyses of AOB.}, }
@article {pmid32915303, year = {2020}, author = {Chan, YF and Chiang, PW and Tandon, K and Rogozin, D and Degermendzhi, A and Zykov, V and Tang, SL}, title = {Spatiotemporal Changes in the Bacterial Community of the Meromictic Lake Uchum, Siberia.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01592-9}, pmid = {32915303}, issn = {1432-184X}, support = {No. 19-05-00428//Российский Фонд Фундаментальных Исследований (РФФИ) (RU)/ ; No. 18-45-243002//Krasnoyarsk Regional Fund of Science/ ; 105-2923-B-001-001-MY3//Ministry of Science and Technology, Taiwan/ ; 108-2811-M-001-603//Ministry of Science and Technology, Taiwan/ ; }, abstract = {Lake Uchum is a newly defined meromictic lake in Siberia with clear seasonal changes in its mixolimnion. This study characterized the temporal dynamics and vertical profile of bacterial communities in oxic and anoxic zones of the lake across all four seasons: October (autumn), March (winter), May (spring), and August (summer). Bacterial richness and diversity in the anoxic zone varied widely between time points. Proteobacteria was the dominant bacterial phylum throughout the oxic and anoxic zones across all four seasons. Alphaproteobacteria (Loktanella) and Gammaproteobacteria (Aliidiomarina) exhibited the highest abundance in the oxic and anoxic zone, respectively. Furthermore, there was a successional shift in sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria in the anoxic zone across the seasons. The most dominant SRB, Desulfonatronovibrio sp., is likely one of the main producers of hydrogen sulfide (H2S) and typically accumulates the most H2S in winter. The representative anoxygenic phototrophic bacterial group in Lake Uchum was purple sulfur bacteria (PSB). PSB were dominant (60.76%) in summer, but only had 0.2-1.5% relative abundance from autumn to spring. Multivariate analysis revealed that the abundance of these SRB and PSB correlated to the concentration of H2S in Lake Uchum. Taken together, this study provides insights into the relationships between changes in bacterial community and environmental features in Lake Uchum.}, }
@article {pmid32914254, year = {2020}, author = {Chen, J and Xie, P and Yu, D and Xie, L and Zeng, C and Chen, J}, title = {Dynamic Change of Sedimental Microbial Community During Black Bloom-an In Situ Enclosure Simulation Study.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01561-2}, pmid = {32914254}, issn = {1432-184X}, support = {2012ZX07101-010//Major Science and Technology Program for Water Pollution Control and Treatment/ ; 2014FBZ02, 2014FB15//State Key Laboratory of Freshwater Ecology and Biotechnology/ ; 31901081//National Natural Science Foundation of China/ ; }, abstract = {Black bloom is a worldwide environmental problem. Sediment microbes play important roles in the process of black bloom. The dynamic change of sedimental microbial community and their potential link between taste and odor compounds during black bloom was investigated in an in situ black bloom enclosure simulation experiment. Through high-throughput sequencing and analysis, pronounced shifts of sedimental microbial community were observed on the 3rd and 7th day in the black bloom group. Microbes in Cyanobacteria, Verrucomicrobia, Planctomycetes, and Actinobacteria were obviously increased, while microbes from the phyla OP8, Chloroflexi, and Acidobacteria were decreased significantly. RDA analysis revealed that the concentrations of chlorophyll a (Chla), total phosphorus (TP), and turbidity (NTU) in the water and the TP, TN concentrations in the sediment were the main environmental factors that affect the microbial community in the sediment. Correlation analysis revealed that microbes Dechloromonas sp. (OTU003567 and OTU000093), Desulfococcus sp. (OTU000911), Chromatiaceae (OTU001222), and Methanosaeta sp. (OTU004809) were positively correlated with the taste and odor substances in the sediment, such as dimethyl sulfide (DMS), β-ionone, β-cyclocitral and geosmin. The sedimental microbial community gradually recovered in the late phase of black bloom, indicating the stability and self-recovery ability of the sedimental microbial community during black bloom. Noteworthily, we observed many possible pathogens increased significantly during the black bloom, which alerts us to keep away from contaminated sediment when black bloom occurred.}, }
@article {pmid32911871, year = {2020}, author = {Mbareche, H and Dumont-Leblond, N and Bilodeau, GJ and Duchaine, C}, title = {An Overview of Bioinformatics Tools for DNA Meta-Barcoding Analysis of Microbial Communities of Bioaerosols: Digest for Microbiologists.}, journal = {Life (Basel, Switzerland)}, volume = {10}, number = {9}, pages = {}, pmid = {32911871}, issn = {2075-1729}, abstract = {High-throughput DNA sequencing (HTS) has changed our understanding of the microbial composition present in a wide range of environments. Applying HTS methods to air samples from different environments allows the identification and quantification (relative abundance) of the microorganisms present and gives a better understanding of human exposure to indoor and outdoor bioaerosols. To make full use of the avalanche of information made available by these sequences, repeated measurements must be taken, community composition described, error estimates made, correlations of microbiota with covariates (variables) must be examined, and increasingly sophisticated statistical tests must be conducted, all by using bioinformatics tools. Knowing which analysis to conduct and which tools to apply remains confusing for bioaerosol scientists, as a litany of tools and data resources are now available for characterizing microbial communities. The goal of this review paper is to offer a guided tour through the bioinformatics tools that are useful in studying the microbial ecology of bioaerosols. This work explains microbial ecology features like alpha and beta diversity, multivariate analyses, differential abundances, taxonomic analyses, visualization tools and statistical tests using bioinformatics tools for bioaerosol scientists new to the field. It illustrates and promotes the use of selected bioinformatic tools in the study of bioaerosols and serves as a good source for learning the &quot;dos and don'ts&quot; involved in conducting a precise microbial ecology study.}, }
@article {pmid32910439, year = {2020}, author = {Callewaert, C and Ravard Helffer, K and Lebaron, P}, title = {Skin Microbiome and its Interplay with the Environment.}, journal = {American journal of clinical dermatology}, volume = {21}, number = {Suppl 1}, pages = {4-11}, pmid = {32910439}, issn = {1179-1888}, abstract = {Advances in sequencing, bioinformatics and analytics now allow the structure, function and interrelations of whole microbial communities to be studied in greater detail. Collaborative efforts and multidisciplinary studies, crossing the boundary between environmental and medical microbiology, have allowed specific environmental, animal and human microbiomes to be characterized. One of the main challenges for microbial ecology is to link the phylogenetic diversity of host-associated microbes to their functional roles within the community. Much remains to be learned on the way microbes colonize the skin of different living organisms and the way the skin microbiome reacts to the surrounding environment (air, water, etc.). In this review, we discuss examples of recent studies that have used modern technology to provide insights into microbial communities in water and on skin, such as those in natural resources (thermal spring water), large mammals (humpback whales) and humans (the skin microbiome). The results of these studies demonstrate how a greater understanding of the structure and functioning of microbiota, together with their interactions with the environment, may facilitate the discovery of new probiotics or postbiotics, provide indicators for the quality of the environment, and show how changes in lifestyle and living environment, such as urbanization, can impact on the skin microbiome and skin health and disease in humans.}, }
@article {pmid32909073, year = {2020}, author = {Mootapally, C and Mahajan, MS and Nathani, NM}, title = {Sediment Plasmidome of the Gulfs of Kathiawar Peninsula and Arabian Sea: Insights Gained from Metagenomics Data.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01587-6}, pmid = {32909073}, issn = {1432-184X}, support = {PDF/2016/001239//Science and Engineering Research Board/ ; PDF/2016/000190//Science and Engineering Research Board/ ; }, abstract = {Plasmidomes have become the research area of interest for ecologists exploring bacteria rich ecosystems. Marine environments are among such niche that host a huge number of microbes and have a complex environment which pose the need to study these bacterial indicators of horizontal gene transfer events for survival and stability. The plasmid content of the metagenomics data from 8 sediment samples of the Gulfs of Kathiawar and an open Arabian Sea sample was screened. The reads corresponding to hits against the plasmid database were assembled and studied for diversity using Kraken and functional content using MG-RAST. The sequences were also checked for resistome and virulence factors. The replicon hosts were overall dominated by Proteobacteria, Firmicutes, and Actinobacteria while red algae specific to the Kutch samples. The genes encoded were dominant in the flagella motility and type VI secretion systems. Overall, results from the study confirmed that the plasmids encoded traits for metal, antibiotic, and phage resistance along with virulence systems, and these would be conferring benefit to the hosts. The study throws insights into the environmental role of the plasmidome in adaptation of the microbes in the studied sites to the environmental stresses.}, }
@article {pmid32906802, year = {2020}, author = {Nakai, R and Naganuma, T and Tazato, N and Morohoshi, S and Koide, T}, title = {Cell Plasticity and Genomic Structure of a Novel Filterable Rhizobiales Bacterium that Belongs to a Widely Distributed Lineage.}, journal = {Microorganisms}, volume = {8}, number = {9}, pages = {}, pmid = {32906802}, issn = {2076-2607}, support = {KAKENHI Grant Number JP13J03441//Japan Society for the Promotion of Science/ ; KAKENHI Grant Number JP15H05620//Japan Society for the Promotion of Science/ ; KAKENHI Grant Number JP19H05683//Ministry of Education, Culture, Sports, Science and Technology/ ; KAKENHI Grant Number JP19H05679//Ministry of Education, Culture, Sports, Science and Technology/ ; KAKENHI Grant Number JP23570117//Japan Society for the Promotion of Science/ ; }, abstract = {Rhizobiales bacterium strain IZ6 is a novel filterable bacterium that was isolated from a suspension filtrate (<0.22 µm) of soil collected in Shimane Prefecture, western Japan. Additional closely related isolates were recovered from filterable fractions of terrestrial environmental samples collected from other places in Japan; the Gobi Desert, north-central China; and Svalbard, Arctic Norway. These findings indicate a wide distribution of this lineage. This study reports the cell variation and genomic structure of IZ6. When cultured at lower temperatures (4 °C and 15 °C), this strain contained ultra-small cells and cell-like particles in the filtrate. PacBio sequencing revealed that this chromosome (3,114,641 bp) contained 3150 protein-coding, 51 tRNA, and three rRNA genes. IZ6 showed low 16S rRNA gene sequence identity (<97%) and low average nucleotide identity (<76%) with its closest known relative, Flaviflagellibacter deserti. Unlike the methylotrophic bacteria and nitrogen-fixing bacteria in related genera, there were no genes that encoded enzymes for one-carbon-compound utilization and nitrogen fixation in the IZ6 genome; the genes related to nitrate and nitrite reductase are retained and those related to the cell membrane function tend to be slightly enriched in the genome. This genomic information helps elucidate the eco-physiological function of a phenotypically heterogeneous and diverse Rhizobiales group.}, }
@article {pmid32903459, year = {2020}, author = {Álvarez-Rodríguez, I and Arana, L and Ugarte-Uribe, B and Gómez-Rubio, E and Martín-Santamaría, S and Garbisu, C and Alkorta, I}, title = {Type IV Coupling Proteins as Potential Targets to Control the Dissemination of Antibiotic Resistance.}, journal = {Frontiers in molecular biosciences}, volume = {7}, number = {}, pages = {201}, pmid = {32903459}, issn = {2296-889X}, abstract = {The increase of infections caused by multidrug-resistant bacteria, together with the loss of effectiveness of currently available antibiotics, represents one of the most serious threats to public health worldwide. The loss of human lives and the economic costs associated to the problem of the dissemination of antibiotic resistance require immediate action. Bacteria, known by their great genetic plasticity, are capable not only of mutating their genes to adapt to disturbances and environmental changes but also of acquiring new genes that allow them to survive in hostile environments, such as in the presence of antibiotics. One of the major mechanisms responsible for the horizontal acquisition of new genes (e.g., antibiotic resistance genes) is bacterial conjugation, a process mediated by mobile genetic elements such as conjugative plasmids and integrative conjugative elements. Conjugative plasmids harboring antibiotic resistance genes can be transferred from a donor to a recipient bacterium in a process that requires physical contact. After conjugation, the recipient bacterium not only harbors the antibiotic resistance genes but it can also transfer the acquired plasmid to other bacteria, thus contributing to the spread of antibiotic resistance. Conjugative plasmids have genes that encode all the proteins necessary for the conjugation to take place, such as the type IV coupling proteins (T4CPs) present in all conjugative plasmids. Type VI coupling proteins constitute a heterogeneous family of hexameric ATPases that use energy from the ATP hydrolysis for plasmid transfer. Taking into account their essential role in bacterial conjugation, T4CPs are attractive targets for the inhibition of bacterial conjugation and, concomitantly, the limitation of antibiotic resistance dissemination. This review aims to compile present knowledge on T4CPs as a starting point for delving into their molecular structure and functioning in future studies. Likewise, the scientific literature on bacterial conjugation inhibitors has been reviewed here, in an attempt to elucidate the possibility of designing T4CP-inhibitors as a potential solution to the dissemination of multidrug-resistant bacteria.}, }
@article {pmid32903319, year = {2020}, author = {Møller, TE and van der Bilt, WGM and Roerdink, DL and Jørgensen, SL}, title = {Microbial Community Structure in Arctic Lake Sediments Reflect Variations in Holocene Climate Conditions.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1520}, pmid = {32903319}, issn = {1664-302X}, abstract = {The reconstruction of past climate variability using physical and geochemical parameters from lake sedimentary records is a well-established and widely used approach. These geological records are also known to contain large and active microbial communities, believed to be responsive to their surroundings at the time of deposition, and proceed to interact intimately with their physical and chemical environment for millennia after deposition. However, less is known about the potential legacy of past climate conditions on the contemporary microbial community structure. We analysed two Holocene-length (past 10 ka BP) sediment cores from the glacier-fed Ymer Lake, located in a highly climate-sensitive region on south-eastern Greenland. By combining physical proxies, solid as well as fluid geochemistry, and microbial population profiling in a comprehensive statistical framework, we show that the microbial community structure clusters according to established lithological units, and thus captures past environmental conditions and climatic transitions. Further, comparative analyses of the two sedimentary records indicates that the manifestation of regional climate depends on local settings such as water column depth, which ultimately constrains microbial variability in the deposited sediments. The strong coupling between physical and geochemical shifts in the lake and microbial variation highlights the potential of molecular microbiological data to strengthen and refine existing sedimentological classifications of past environmental conditions and transitions. Furthermore, this coupling implies that microbially controlled transformation and partitioning of geochemical species (e.g., manganese and sulphate) in Ymer lake today is still affected by climatic conditions that prevailed thousands of years back in time.}, }
@article {pmid32901388, year = {2020}, author = {González-Dominici, LI and Saati-Santamaría, Z and García-Fraile, P}, title = {Genome Analysis and Genomic Comparison of the Novel Species Arthrobacter ipsi Reveal Its Potential Protective Role in Its Bark Beetle Host.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01593-8}, pmid = {32901388}, issn = {1432-184X}, support = {19-09072S//Grantová Agentura České Republiky/ ; CLU-2018-04//Junta de Castilla y León (ES)/ ; }, abstract = {The pine engraver beetle, Ips acuminatus Gyll, is a bark beetle that causes important damages in Scots pine (Pinus sylvestris) forests and plantations. As almost all higher organisms, Ips acuminatus harbours a microbiome, although the role of most members of its microbiome is not well understood. As part of a work in which we analysed the bacterial diversity associated to Ips acuminatus, we isolated the strain Arthrobacter sp. IA7. In order to study its potential role within the bark beetle holobiont, we sequenced and explored its genome and performed a pan-genome analysis of the genus Arthrobacter, showing specific genes of strain IA7 that might be related with its particular role in its niche. Based on these investigations, we suggest several potential roles of the bacterium within the beetle. Analysis of genes related to secondary metabolism indicated potential antifungal capability, confirmed by the inhibition of several entomopathogenic fungal strains (Metarhizium anisopliae CCF0966, Lecanicillium muscarium CCF6041, L. muscarium CCF3297, Isaria fumosorosea CCF4401, I. farinosa CCF4808, Beauveria bassiana CCF4422 and B. brongniartii CCF1547). Phylogenetic analyses of the 16S rRNA gene, six concatenated housekeeping genes (tuf-secY-rpoB-recA-fusA-atpD) and genome sequences indicated that strain IA7 is closely related to A. globiformis NBRC 12137T but forms a new species within the genus Arthrobacter; this was confirmed by digital DNA-DNA hybridization (37.10%) and average nucleotide identity (ANIb) (88.9%). Based on phenotypic and genotypic features, we propose strain IA7T as the novel species Arthrobacter ipsi sp. nov. (type strain IA7T = CECT 30100T = LMG 31782T) and suggest its protective role for its host.}, }
@article {pmid32901387, year = {2020}, author = {Wu, C and Wei, X and Hu, Z and Liu, Y and Hu, Y and Qin, H and Chen, X and Wu, J and Ge, T and Zhran, M and Su, Y}, title = {Diazotrophic Community Variation Underlies Differences in Nitrogen Fixation Potential in Paddy Soils Across a Climatic Gradient in China.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01591-w}, pmid = {32901387}, issn = {1432-184X}, support = {2017YFD0800104//National Key Research and Development program/ ; 41977100//National Natural Science Foundation of China/ ; 41771300//National Natural Science Foundation of China/ ; 2018WK4012//Hunan Province Base for Scientific and Technological Innovation Cooperation/ ; 2017QNCXTD_GTD//Youth Innovation Team Project of Institute of Subtropical Agriculture, Chinese Academy of Sciences/ ; 2019JJ10003//Natural Science Foundation of Hunan Province/ ; }, abstract = {Biological nitrogen (N2) fixation as a source of new N input into the soil by free-living diazotrophs is important for achieving sustainable rice agriculture. However, the dominant environmental drivers or factors influencing N2 fixation and the functional significance of the diazotroph community structure in paddy soil across a climatic gradient are not yet well understood. Thus, we characterized the diazotroph community and identified the ecological predictors of N2 fixation potential in four different climate zones (mid-temperate, warm-temperate, subtropical, and tropical paddy soils) in eastern China. Comprehensive nifH gene sequencing, functional activity detection, and correlation analysis with environmental factors were estimated. The potential nitrogenase activity (PNA) was highest in warm-temperate regions, where it was 6.2-, 2.9-, and 2.2-fold greater than in the tropical, subtropical, and mid-temperate regions, respectively; nifH gene abundance was significantly higher in warm-temperate and subtropical zones than in the tropical or mid-temperate zones. Diazotroph diversity was significantly higher in the tropical climate zone and significantly lower in the mid-temperate zone. Non-metric multidimensional scaling and canonical correlation analysis indicated that paddy soil diazotroph populations differed significantly among the four climate zones, mainly owing to differences in climate and soil pH. Structural equation models and automatic linear models revealed that climate and nutrients indirectly affected PNA by affecting soil pH and diazotroph community, respectively, while diazotroph community, C/P, and nifH gene abundance directly affected PNA. And C/P ratio, pH, and the diazotroph community structure were the main predictors of PNA in paddy soils. Collectively, the differences in diazotroph community structure have ecological significance, with important implications for the prediction of soil N2-fixing functions under climate change scenarios.}, }
@article {pmid32901386, year = {2020}, author = {Petrzik, K and Lukavský, J and Koloniuk, I}, title = {Novel Virus on Filamentous Arthronema africanum Cyanobacterium.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01599-2}, pmid = {32901386}, issn = {1432-184X}, support = {RVO60077344//institutional support/ ; RVO67985939//institutional support/ ; Biocirtech T01000048//Technologická Agentura České Republiky/ ; }, abstract = {Widely distributed in water environments and in soil, cyanobacteria are hosts of lysogenic or lytic bacterioviruses. A novel, probably lysogenic virus (phage) for which the name Arthronema africanum virus TR020 (Aa-TR020) is proposed, has been isolated from filamentous freshwater cyanobacterium Arthronema africanum. The virus formed turbid plaques on plate culture of A. africanum strain 1980/01 but not on other Arthronema strain and other bacterial species. The genome of Aa-TR020 is linear molecule of dsDNA, 44,805 bp in length with 216 bp long terminal repeats and with G + C content of 46%. Fifty-five genes organized on plus and minus strands were predicted there. The genome size, gene arrangement, and selected protein sequences showed relatedness to Phormidium virus Pf-WMP3 and other viruses known to infect cyanobacteria and classified in the family Podoviridae.}, }
@article {pmid32897365, year = {2020}, author = {Rodrigues, GR and Pinto, OHB and Schroeder, LF and Fernandes, GDR and Costa, OYA and Quirino, BF and Kuramae, EE and Barreto, CC}, title = {Unraveling the xylanolytic potential of Acidobacteria bacterium AB60 from Cerrado soils.}, journal = {FEMS microbiology letters}, volume = {367}, number = {18}, pages = {}, doi = {10.1093/femsle/fnaa149}, pmid = {32897365}, issn = {1574-6968}, abstract = {The presence of genes for glycosyl hydrolases in many Acidobacteria genomes indicates an important role in the degradation of plant cell wall material. Acidobacteria bacterium AB60 was obtained from Cerrado oligotrophic soil in Brazil, where this phylum is abundant. The 16S rRNA gene analyses showed that AB60 was closely related to the genera Occallatibacter and Telmatobacter. However, AB60 grew on xylan as carbon source, which was not observed in Occallatibacter species; but growth was not detected on medium containing carboxymethyl cellulose, as observed in Telmatobacter. Nevertheless, the genome analysis of AB60 revealed genes for the enzymes involved in cellulose as well as xylan degradation. In addition to enzymes involved in xylan degradation, α-l-rhamnosidase was detected in the cultures of AB60. Functional screening of a small-insert genomic library did not identify any clones capable of carboxymethyl cellulose degradation, but open reading frames coding α-l-arabinofuranosidase and α-l-rhamnosidase were present in clones showing xylan degradation halos. Both enzymes act on the lateral chains of heteropolymers such as pectin and some hemicelluloses. These results indicate that the hydrolysis of α-linked sugars may offer a metabolic niche for slow-growing Acidobacteria, allowing them to co-exist with other plant-degrading microbes that hydrolyze β-linked sugars from cellulose or hemicellulose backbones.}, }
@article {pmid32897356, year = {2020}, author = {Bandini, F and Misci, C and Taskin, E and Cocconcelli, PS and Puglisi, E}, title = {Biopolymers modulate microbial communities in municipal organic waste digestion.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {10}, pages = {}, doi = {10.1093/femsec/fiaa183}, pmid = {32897356}, issn = {1574-6941}, abstract = {The development of biopolymers has raised issues about their recalcitrance in the environment. Their disposal is mainly carried out with the organic fraction of municipal solid waste (OFMSW) through thermophilic anaerobic digestion and aerobic composting, bioprocesses aimed at turning organic matter into biogas and compost. However, the effects of biopolymers on OFMSW treatment, on the final compost and on the microbial communities involved are partly unexplored. In this study, the OFMSW treatment was reproduced on a laboratory-scale respecting real plant conditions and testing the impacts of mixing polylactic acid (PLA) and starch-based bioplastic (SBB) separately. The dynamics of bacterial, archaeal and fungal communities during the process was screened by high-throughput sequencing (HTS) of phylogenetic amplicons. Starch-based bioplastic showed a minor and heterogeneous microbial diversity between the anaerobic and aerobic phases. Contrariwise, PLA treatment resulted in wider and more diverse bacterial and fungal communities for the compost and the aerobic biofilm. Since the biodiversity in compost may play a crucial role in its stability and safety, the modulation of environmental microbial communities induced by higher concentrations of PLA in OFMSW treatment can pose relevant issues.}, }
@article {pmid32896070, year = {2020}, author = {Fei, C and Ochsenkühn, MA and Shibl, AA and Isaac, A and Wang, C and Amin, SA}, title = {Quorum sensing regulates 'swim-or-stick' lifestyle in the phycosphere.}, journal = {Environmental microbiology}, volume = {22}, number = {11}, pages = {4761-4778}, pmid = {32896070}, issn = {1462-2920}, support = {AD179//New York University Abu Dhabi/ ; NA19NOS4780183//National Oceanic and Atmospheric Administration (NOAA)/ ; }, abstract = {Interactions between phytoplankton and bacteria play major roles in global biogeochemical cycles and oceanic nutrient fluxes. These interactions occur in the microenvironment surrounding phytoplankton cells, known as the phycosphere. Bacteria in the phycosphere use either chemotaxis or attachment to benefit from algal excretions. Both processes are regulated by quorum sensing (QS), a cell-cell signalling mechanism that uses small infochemicals to coordinate bacterial gene expression. However, the role of QS in regulating bacterial attachment in the phycosphere is not clear. Here, we isolated a Sulfitobacter pseudonitzschiae F5 and a Phaeobacter sp. F10 belonging to the marine Roseobacter group and an Alteromonas macleodii F12 belonging to Alteromonadaceae, from the microbial community of the ubiquitous diatom Asterionellopsis glacialis. We show that only the Roseobacter group isolates (diatom symbionts) can attach to diatom transparent exopolymeric particles. Despite all three bacteria possessing genes involved in motility, chemotaxis, and attachment, only S. pseudonitzschiae F5 and Phaeobacter sp. F10 possessed complete QS systems and could synthesize QS signals. Using UHPLC-MS/MS, we identified three QS molecules produced by both bacteria of which only 3-oxo-C16:1 -HSL strongly inhibited bacterial motility and stimulated attachment in the phycosphere. These findings suggest that QS signals enable colonization of the phycosphere by algal symbionts.}, }
@article {pmid32894355, year = {2020}, author = {He, W and Zhang, M and Jin, G and Sui, X and Zhang, T and Song, F}, title = {Effects of Nitrogen Deposition on Nitrogen-Mineralizing Enzyme Activity and Soil Microbial Community Structure in a Korean Pine Plantation.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01595-6}, pmid = {32894355}, issn = {1432-184X}, support = {31971527//National Natural Science Foundation of China/ ; TD2019C002//Natural Science Foudation of Heilongjiang Province/ ; }, abstract = {To predict the effects of nitrogen deposition on nitrogen-mineralizing enzyme activity and soil microbial community structure in artificial temperate forests in northern China, we studied the soil properties, nitrogen-mineralizing enzyme activity, and microbial community structure in the soil of a Korean pine plantation in which different concentrations (0, 20, 40, 80 kg N ha-1 year-1) of ammonium nitrate were applied for 5 consecutive years. The results showed that nitrogen addition at different concentrations did not significantly affect the soil pH. High nitrogen addition (80 kg N ha-1 year-1) significantly increased the soil organic matter, ammonium nitrogen, and nitrate nitrogen content in the Korean pine plantation, and ammonium nitrogen was the key factor that influenced the soil fungal community structure. The urease activity under the moderate nitrogen addition treatment (40 kg N ha-1 year-1) was significantly lower than that under the control (0 kg N ha-1 year-1), and the protease activity in the three treatments was also significantly lower than that in the control. There was no significant correlation between microbial community structure and the four mineralizing enzymes. After nitrogen addition at different concentrations, the Simpson and Shannon indexes of soil bacteria decreased significantly under low nitrogen addition (20 kg N ha-1 year-1), but the α-diversity index of soil fungi did not show significant differences under nitrogen addition. The microbial community composition was significantly changed by the different treatments. PLS-DA analysis showed that Tardiphaga was an important genus that made the greatest contribution to the differences in bacterial community composition among treatments, as was Taeniolella for fungal community composition. The low level of nitrogen addition inhibited nitrogen mineralization in the Korean pine plantation by reducing the relative abundances of Nitrosomonadaceae and Betaproteobacteriales and by reducing the abundances of symbiotrophic fungi. Berkelbacteria and Polyporales were bacteria and fungi, respectively, that changed significantly under the high nitrogen addition treatment (80 kg N ha-1 year-1). This study provides more data to support predictions of the changes in nitrogen-mineralizing enzyme activity and microbial community structure in artificial temperate forest soils in response to increased nitrogen deposition.}, }
@article {pmid32893477, year = {2020}, author = {Castledine, M and Padfield, D and Buckling, A}, title = {Experimental (co)evolution in a multi-species microbial community results in local maladaptation.}, journal = {Ecology letters}, volume = {23}, number = {11}, pages = {1673-1681}, doi = {10.1111/ele.13599}, pmid = {32893477}, issn = {1461-0248}, support = {BB/T002522/1//NERC National Environmental research council/ ; NE/S000771/1//NERC National Environmental research council/ ; NE/P001130/1//NERC National Environmental research council/ ; }, mesh = {Acclimatization ; Adaptation, Physiological ; Biological Evolution ; *Microbiota ; }, abstract = {Interspecific coevolutionary interactions can result in rapid biotic adaptation, but most studies have focused only on species pairs. Here, we (co)evolved five microbial species in replicate polycultures and monocultures and quantified local adaptation. Specifically, growth rate assays were used to determine adaptations of each species' populations to (1) the presence of the other four species in general and (2) sympatric vs. allopatric communities. We found that species did not show an increase in net biotic adaptation:ancestral, polyculture- and monoculture-evolved populations did not have significantly different growth rates within communities. However, 4/5 species' growth rates were significantly lower within the community they evolved in relative to an allopatric community. 'Local maladaptation' suggests that species evolved increased competitive interactions to sympatric species' populations. This increased competition did not affect community stability or productivity. Our results suggest that (co)evolution within communities can increase competitive interactions that are specific to (co)evolved community members.}, }
@article {pmid32892232, year = {2020}, author = {Dwidar, M and Jang, H and Sangwan, N and Mun, W and Im, H and Yoon, S and Choi, S and Nam, D and Mitchell, RJ}, title = {Diffusible Signaling Factor, a Quorum-Sensing Molecule, Interferes with and Is Toxic Towards Bdellovibrio bacteriovorus 109J.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01585-8}, pmid = {32892232}, issn = {1432-184X}, support = {2020R1A2C2012158//National Research Foundation of Korea/ ; 2017M1A3A3A02016642//National Research Foundation of Korea/ ; }, abstract = {Bdellovibrio bacteriovorus 109J is a predatory bacterium which lives by predating on other Gram-negative bacteria to obtain the nutrients it needs for replication and survival. Here, we evaluated the effects two classes of bacterial signaling molecules (acyl homoserine lactones (AHLs) and diffusible signaling factor (DSF)) have on B. bacteriovorus 109J behavior and viability. While AHLs had a non-significant impact on predation rates, DSF considerably delayed predation and bdelloplast lysis. Subsequent experiments showed that 50 μM DSF also reduced the motility of attack-phase B. bacteriovorus 109J cells by 50% (38.2 ± 14.9 vs. 17 ± 8.9 μm/s). Transcriptomic analyses found that DSF caused genome-wide changes in B. bacteriovorus 109J gene expression patterns during both the attack and intraperiplasmic phases, including the significant downregulation of the flagellum assembly genes and numerous serine protease genes. While the former accounts for the reduced speeds observed, the latter was confirmed experimentally with 50 μM DSF completely blocking protease secretion from attack-phase cells. Additional experiments found that 30% of the total cellular ATP was released into the supernatant when B. bacteriovorus 109J was exposed to 200 μM DSF, implying that this QS molecule negatively impacts membrane integrity.}, }
@article {pmid32889760, year = {2021}, author = {Harrison, JG and John Calder, W and Shuman, B and Alex Buerkle, C}, title = {The quest for absolute abundance: The use of internal standards for DNA-based community ecology.}, journal = {Molecular ecology resources}, volume = {21}, number = {1}, pages = {30-43}, doi = {10.1111/1755-0998.13247}, pmid = {32889760}, issn = {1755-0998}, support = {EPS-1655726//National Science Foundation/ ; }, abstract = {To characterize microbiomes and other ecological assemblages, ecologists routinely sequence and compare loci that differ among focal taxa. Counts of these sequences convey information regarding the occurrence and relative abundances of taxa, but provide no direct measure of their absolute abundances, due to the technical limitations of the sequencing process. The relative abundances in compositional data are inherently constrained and difficult to interpret. The incorporation of internal standards (ISDs; colloquially referred to as 'spike-ins') into DNA pools can ameliorate the problems posed by relative abundance data and allow absolute abundances to be approximated. Unfortunately, many laboratory and sampling biases cause ISDs to underperform or fail. Here, we discuss how careful deployment of ISDs can avoid these complications and be an integral component of well-designed studies seeking to characterize ecological assemblages via sequencing of DNA.}, }
@article {pmid32888042, year = {2020}, author = {Dickey, JR and Fordyce, JA and Lebeis, SL}, title = {Bacterial communities of the Salvia lyrata rhizosphere explained by spatial structure and sampling grain.}, journal = {Microbial ecology}, volume = {80}, number = {4}, pages = {846-858}, doi = {10.1007/s00248-020-01594-7}, pmid = {32888042}, issn = {1432-184X}, support = {DEB1638922//National Science Foundation (USA)/ ; }, abstract = {Advancements in molecular technology have reduced the constraints that the grain of observation, or the spatial resolution and volume of the sampling unit, has on the characterization of plant-associated microbiomes. With discrete ecological sampling and massive parallel sequencing, we can more precisely portray microbiome community assembly and microbial recruitment to host tissue over space and time. Here, we differentiate rarefied community richness and relative abundance in bacterial microbiomes of Salvia lyrata dependent on three spatial depths, which are discrete physical distances from the soil surface within the rhizosphere microhabitat as a proxy for the root system zones. To assess the impact of sampling grain on rarefied community richness and relative abundance, we evaluated the variation of these metrics between samples pooled prior to DNA extraction and samples pooled after sequencing. A distance-based redundancy analysis with the quantitative Jaccard distance revealed that rhizosphere microbiomes vary in richness between rhizosphere soil depths. At all orders of diversity, rarefied microbial richness was consistently lowest at the deepest samples taken (approximately 4 cm from soil surface) in comparison with other rhizosphere soil depths. We additionally show that finer grain sampling (i.e., three samples of equal volume pooled after sequencing) recovers greater microbial richness when using 16S rRNA gene sequencing to describe microbial communities found within the rhizosphere system. In summary, to further elucidate the extent host-specific microbiomes assemble within the rhizosphere, the grain at which bacterial communities are sampled should reflect and encompass fine-scale heterogeneity of the system.}, }
@article {pmid32887945, year = {2021}, author = {Gao, CH and Cao, H and Cai, P and Sørensen, SJ}, title = {The initial inoculation ratio regulates bacterial coculture interactions and metabolic capacity.}, journal = {The ISME journal}, volume = {15}, number = {1}, pages = {29-40}, pmid = {32887945}, issn = {1751-7370}, abstract = {Coculture is an important model system in microbial ecology studies. As a key experimental parameter, the initial inoculation ratio has a crucial impact on the results of the coculture system. However, such an effect has never been investigated under multiple niche conditions. In this study, we established a simple coculture system with two model bacteria in various carbon sources and investigated the influence of initial inoculum ratios of 1:1000 to 1000:1 on community structure, function, and bacterial interaction. We found that the final ratio of the cocultures with different initial inoculum ratios differed in approximately five-sixths of the carbon sources, suggesting that the final ratio is highly dependent on the initial inoculum ratio, while the carbon source preferences of bacteria could not predict the final ratio of cocultures. Furthermore, we found that the initial ratio could regulate the metabolic capacity of the coculture, as only cocultures with initial ratios of 1:1 and 1000:1 gained high capacity on 14 specific carbon sources. The underlying reason may be that the pattern of species interaction is changed by the initial ratio. In conclusion, we showed that the initial ratio can induce emergent properties in coculture. These findings suggest that the initial ratio not only impacts the reproducibility of coculture experiments but also can influence our understanding of generic microbial ecology.}, }
@article {pmid32887010, year = {2020}, author = {Oliveira, BB and Veigas, B and Carlos, FF and Sánchez-Melsió, A and Balcázar, JL and Borrego, CM and Baptista, PV}, title = {Water safety screening via multiplex LAMP-Au-nanoprobe integrated approach.}, journal = {The Science of the total environment}, volume = {741}, number = {}, pages = {140447}, doi = {10.1016/j.scitotenv.2020.140447}, pmid = {32887010}, issn = {1879-1026}, mesh = {*Escherichia coli ; Feces ; *Nucleic Acid Amplification Techniques ; Real-Time Polymerase Chain Reaction ; Sensitivity and Specificity ; }, abstract = {Contaminated water resources remain a major global concern regarding public health. The majority of water safety protocols include indicators of microbial contamination to evaluate the potential risk to public health and are key elements of quality guidelines. Among these, markers for total coliforms and fecal coliforms are strong indicators of co-contamination with other pathogens. Traditional methods, recurring to slow and cumbersome culture-based approaches, have been gradually replaced by molecular methods, capable of faster and more specific screening. These are usually PCR-based methods that may allow for multiple pathogen detection but require dedicated laboratory equipment, hindering the rapid on-site assessment. Here, we used a multiplex Loop-Mediated Isothermal Amplification (mLAMP) strategy for the amplification of two markers associated with the contamination by total and fecal coliforms (e.g. Escherichia coli) - lacZ and uidA genes, respectively - thus allowing for single tube multiplex detection. The mLAMP products were then subject to an Au-nanoprobe colorimetric detection assay for precise discrimination of targets. This approach was validated in 22 water samples that were also screened for the presence of lacZ and uidA using standard and quantitative PCR, with the capability for discriminating the contamination level, e.g. a semi-quantitative evaluation of water quality.}, }
@article {pmid32885507, year = {2020}, author = {Wall, CB and Egan, CP and Swift, SIO and Hynson, NA}, title = {Three decades post-reforestation has not led to the reassembly of arbuscular mycorrhizal fungal communities associated with remnant primary forests.}, journal = {Molecular ecology}, volume = {29}, number = {21}, pages = {4234-4247}, doi = {10.1111/mec.15624}, pmid = {32885507}, issn = {1365-294X}, abstract = {The negative effects of deforestation can potentially be ameliorated through ecological restoration. However, reforestation alone may not reassemble the same ecological communities or functions as primary forests. In part, this failure may be owed to forest ecosystems inherently involving complex interactions among guilds of organisms. Plants, which structure forest food webs, rely on intimate associations with symbiotic microbes such as root-inhabiting mycorrhizal fungi. Here, we leverage a large-scale reforestation project on Hawai'i Island underway for over three decades to assess whether arbuscular mycorrhizal (AM) fungal communities have concurrently been restored. The reference ecosystem for this restoration project is a remnant montane native Hawaiian forest that provides critical habitat for endangered birds. We sampled soils from 12 plots within remnant and restored forest patches and characterized AM fungal communities using high-throughput amplicon sequencing. While some AM fungal community metrics were comparable between remnant and restored forest (e.g. species richness), other key characteristics were not. Specifically, community membership and the identity of AM fungal keystone species differed between the two habitat types, as well as the primary environmental factors influencing community composition. Remnant forest AM fungal communities were strongly associated with soil chemical properties, especially pH, while restored forest communities were influenced by the spatial proximity to remnant forests. We posit that combined, these differences in soil AM fungal communities could be negatively affecting the recruitment of native plant hosts and that future restoration efforts should consider plant-microbe interactions as an important facet of forest health.}, }
@article {pmid32884655, year = {2020}, author = {Duplouy, A and Minard, G and Saastamoinen, M}, title = {The gut bacterial community affects immunity but not metabolism in a specialist herbivorous butterfly.}, journal = {Ecology and evolution}, volume = {10}, number = {16}, pages = {8755-8769}, pmid = {32884655}, issn = {2045-7758}, abstract = {Plant tissues often lack essential nutritive elements and may contain a range of secondary toxic compounds. As nutritional imbalance in food intake may affect the performances of herbivores, the latter have evolved a variety of physiological mechanisms to cope with the challenges of digesting their plant-based diet. Some of these strategies involve living in association with symbiotic microbes that promote the digestion and detoxification of plant compounds or supply their host with essential nutrients missing from the plant diet. In Lepidoptera, a growing body of evidence has, however, recently challenged the idea that herbivores are nutritionally dependent on their gut microbial community. It is suggested that many of the herbivorous Lepidopteran species may not host a resident microbial community, but rather a transient one, acquired from their environment and diet. Studies directly testing these hypotheses are however scarce and come from an even more limited number of species.By coupling comparative metabarcoding, immune gene expression, and metabolomics analyses with experimental manipulation of the gut microbial community of prediapause larvae of the Glanville fritillary butterfly (Melitaea cinxia, L.), we tested whether the gut microbial community supports early larval growth and survival, or modulates metabolism or immunity during early stages of development.We successfully altered this microbiota through antibiotic treatments and consecutively restored it through fecal transplants from conspecifics. Our study suggests that although the microbiota is involved in the up-regulation of an antimicrobial peptide, it did not affect the life history traits or the metabolism of early instars larvae.This study confirms the poor impact of the microbiota on diverse life history traits of yet another Lepidoptera species. However, it also suggests that potential eco-evolutionary host-symbiont strategies that take place in the gut of herbivorous butterfly hosts might have been disregarded, particularly how the microbiota may affect the host immune system homeostasis.}, }
@article {pmid32882545, year = {2021}, author = {Li, L and Ning, D and Jeon, Y and Ryu, H and Santo Domingo, JW and Kang, DW and Kadudula, A and Seo, Y}, title = {Ecological insights into assembly processes and network structures of bacterial biofilms in full-scale biologically active carbon filters under ozone implementation.}, journal = {The Science of the total environment}, volume = {751}, number = {}, pages = {141409}, doi = {10.1016/j.scitotenv.2020.141409}, pmid = {32882545}, issn = {1879-1026}, mesh = {Bacteria ; Biofilms ; Charcoal ; *Ozone ; *Water Purification ; }, abstract = {To address the adverse effects of harmful algal blooms, there are increased demands over the implementation of ozone coupled with biologically active carbon (BAC) filters in the drinking water treatment plants. Although the microbial biofilms are vital elements to support the proper performance of BAC filters, except for taxonomic affiliations, little is known about the assembly mechanisms of microbial communities in the full-scale BAC filters. This study aimed to examine how the assembly processes and their associated factors (e.g., influent characteristics, biological interactions) drive the temporal dynamics of bacterial communities in full-scale BAC filters, which underwent ozone implementation (five consecutive seasons from 2017 to 2018). The results revealed that along with the increase of bacterial taxonomic richness and evenness, stochastic processes became more crucial to determine the bacterial community assembly in the summer and autumn after ozone implementation (relative contribution: 61.23% and 83.75%, respectively). Moreover, their corresponding networks possessed simple network structures with lower modularity than other seasons, which implied lesser biological interactions among bacterial populations. The correlation between taxonomic and predicted functional diversities using functional redundancy index indicated that relatively high levels of bacterial functional redundancy (>0.83) were generally present in BAC filters. However, compared to other seasons, significantly higher degrees of functional redundancy existed in the summer and autumn after ozone implementation (0.85 ± 0.01 and 0.86 ± 0.01, respectively). Overall, this work improves our understanding of the microbial ecology of full-scale BAC filters by providing a conceptual framework that characterizes bacterial biofilm assembly processes relevant to performance optimization of full-scale BAC filters.}, }
@article {pmid32880700, year = {2020}, author = {Sabu, EA and Gonsalves, MJ and Sreepada, RA and Shivaramu, MS and Ramaiah, N}, title = {Evaluation of the Physiological Bacterial Groups in a Tropical Biosecured, Zero-Exchange System Growing Whiteleg Shrimp, Litopenaeus vannamei.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01575-w}, pmid = {32880700}, issn = {1432-184X}, support = {PSC 0206//Council of Scientific and Industrial Research, India/ ; }, abstract = {To elucidate the individual and multiple roles of physiological bacterial groups involved in biogeochemical cycles of carbon, nitrogen, phosphorus and sulfur, the changes in the abundance of aerobic bacteria (heterotrophs, methane oxidizers, ammonia oxidizers, sulfur oxidizers, phosphate solubilizers, phosphate accumulators) and anaerobic bacteria (total anaerobes, nitrate reducers, denitrifiers and sulfate reducers) were investigated in a biosecured, zero-exchange system stocked with whiteleg shrimp, Litopenaeus vannamei for one production cycle. Key water quality parameters during the 96-day production cycle fell within the normal range for L. vannamei culture. Results of Spearman's correlation matrix revealed that different sets of variables correlated at varying levels of significance of the interrelationships between bacterial abundances and water quality parameters. The three nitrogenous species (ammonia, nitrite and nitrate) strongly influenced the physiological bacterial groups' abundance. The strong relationship of bacterial groups with phytoplankton biomass and abundance clearly showed the trophic interconnections in nutrient exchange/recycling. Canonical correspondence analysis performed to assess the total variation revealed that the three dissolved nitrogen species followed by salinity, temperature, phytoplankton biomass and pH collectively accounted for as much as 82% of the total variation. In conclusion, the results of the study revealed that the major drivers that interweaved biogeochemical cycles are the three dissolved nitrogen species, which microbially mediated various aerobic-anaerobic assimilation/dissimilation processes in the pond ecosystem. Considering the pond microbial ecology becoming an important management tool where applied research could improve the economic and environmental sustainability of the aquaculture industry, the findings of the present study are practically relevant.}, }
@article {pmid32880699, year = {2020}, author = {Wei, J and Segraves, KA and Li, WZ and Yang, XK and Xue, HJ}, title = {Gut bacterial communities and their contribution to performance of specialist Altica flea beetles.}, journal = {Microbial ecology}, volume = {80}, number = {4}, pages = {946-959}, doi = {10.1007/s00248-020-01590-x}, pmid = {32880699}, issn = {1432-184X}, support = {31672334//National Natural Science Foundation of China/ ; }, abstract = {Host plant shifts are a common mode of speciation in herbivorous insects. Although insects can evolve adaptations to successfully incorporate a new host plant, it is becoming increasingly recognized that the gut bacterial community may play a significant role in allowing insects to detoxify novel plant chemical defenses. Here, we examined differences in gut bacterial communities between Altica flea beetle species that feed on phylogenetically unrelated host plants in sympatry. We surveyed the gut bacterial communities of three closely related flea beetles from multiple locations using 16S rRNA amplicon sequencing. The results showed that the beetle species shared a high proportion (80.7%) of operational taxonomic units. Alpha-diversity indicators suggested that gut bacterial diversity did not differ among host species, whereas geography had a significant effect on bacterial diversity. In contrast, analyses of beta-diversity showed significant differences in gut bacterial composition among beetle species when we used species composition and relative abundance metrics, but there was no difference in composition when species presence/absence and phylogenetic distance indices were used. Within host beetle species, gut bacterial composition varied significantly among sites. A metagenomic functionality analysis predicted that the gut microbes had functions involved in xenobiotic biodegradation and metabolism as well as metabolism of terpenoids and polyketides. These predictions, however, did not differ among beetle host species. Antibiotic curing experiments showed that development time was significantly prolonged, and there was a significant decline in body weight of newly emerged adults in beetles lacking gut bacteria, suggesting the beetles may receive a potential benefit from the gut microbe-insect interaction. On the whole, our results suggest that although the gut bacterial community did not show clear host-specific patterns among Altica species, spatiotemporal variability is an important determinant of gut bacterial communities. Furthermore, the similarity of communities among these beetle species suggests that microbial facilitation may not be a determinant of host plant shifts in Altica.}, }
@article {pmid32879989, year = {2020}, author = {Gonzalo, M and Deveau, A and Aigle, B}, title = {Inhibitions Dominate but Stimulations and Growth Rescues Are Not Rare Among Bacterial Isolates from Grains of Forest Soil.}, journal = {Microbial ecology}, volume = {80}, number = {4}, pages = {872-884}, doi = {10.1007/s00248-020-01579-6}, pmid = {32879989}, issn = {1432-184X}, support = {ANR-11-LABX 0002 01//ANR/ ; }, abstract = {Soil is a complex environment made of multiple microhabitats in which a wide variety of microorganisms co-exist and interact to form dynamic communities. While the abiotic factors that regulate the structure of these communities are now quite well documented, our knowledge of how bacteria interact with each other within these communities is still insufficient. Literature reveals so far contradictory results and is mainly focused on antagonistic interactions. To start filling this gap, we isolated 35 different bacterial isolates from grains of soil assuming that, at this scale, these bacteria would have been likely interacting in their natural habitat. We tested pairwise interactions between all isolates from each grain and scored positive and negative interactions. We compared the effects of simultaneous versus delayed co-inoculations, allowing or not to a strain to modify first its environment. One hundred fifty-seven interactions, either positive or negative, were recorded among the 525 possible one's. Members of the Bacillus subtilis, Pseudomonas and Streptomyces genera were responsible for most inhibitions, while positive interactions occurred between isolates of the Bacillales order and only in delayed inoculation conditions. Antagonist isolates had broad spectral abilities to acquire nutrients from organic and inorganic matter, while inhibited isolates tended to have little potentials. Despite an overall domination of antagonistic interactions (87%), a third of the isolates were able to stimulate or rescue the growth of other isolates, suggesting that cooperation between bacteria may be underestimated.}, }
@article {pmid32879459, year = {2021}, author = {Rubbens, P and Props, R and Kerckhof, FM and Boon, N and Waegeman, W}, title = {Cytometric fingerprints of gut microbiota predict Crohn's disease state.}, journal = {The ISME journal}, volume = {15}, number = {1}, pages = {354-358}, pmid = {32879459}, issn = {1751-7370}, support = {BOFSTA2015000501//Universiteit Gent (UGent)/ ; }, abstract = {Variations in the gut microbiome have been associated with changes in health state such as Crohn's disease (CD). Most surveys characterize the microbiome through analysis of the 16S rRNA gene. An alternative technology that can be used is flow cytometry. In this report, we reanalyzed a disease cohort that has been characterized by both technologies. Changes in microbial community structure are reflected in both types of data. We demonstrate that cytometric fingerprints can be used as a diagnostic tool in order to classify samples according to CD state. These results highlight the potential of flow cytometry to perform rapid diagnostics of microbiome-associated diseases.}, }
@article {pmid32879458, year = {2021}, author = {Mooshammer, M and Kitzinger, K and Schintlmeister, A and Ahmerkamp, S and Nielsen, JL and Nielsen, PH and Wagner, M}, title = {Flow-through stable isotope probing (Flow-SIP) minimizes cross-feeding in complex microbial communities.}, journal = {The ISME journal}, volume = {15}, number = {1}, pages = {348-353}, pmid = {32879458}, issn = {1751-7370}, support = {EXC 309//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 294343//EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: &quot;Ideas&quot; Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))/ ; W 1257//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; }, abstract = {Stable isotope probing (SIP) is a key tool for identifying the microorganisms catalyzing the turnover of specific substrates in the environment and to quantify their relative contributions to biogeochemical processes. However, SIP-based studies are subject to the uncertainties posed by cross-feeding, where microorganisms release isotopically labeled products, which are then used by other microorganisms, instead of incorporating the added tracer directly. Here, we introduce a SIP approach that has the potential to strongly reduce cross-feeding in complex microbial communities. In this approach, the microbial cells are exposed on a membrane filter to a continuous flow of medium containing isotopically labeled substrate. Thereby, metabolites and degradation products are constantly removed, preventing consumption of these secondary substrates. A nanoSIMS-based proof-of-concept experiment using nitrifiers in activated sludge and 13C-bicarbonate as an activity tracer showed that Flow-SIP significantly reduces cross-feeding and thus allows distinguishing primary consumers from other members of microbial food webs.}, }
@article {pmid32877326, year = {2020}, author = {Lee, HJ and Kim, SY and Whang, KS}, title = {Cellulomonas citrea sp. nov., isolated from paddy soil.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {70}, number = {10}, pages = {5304-5311}, doi = {10.1099/ijsem.0.004409}, pmid = {32877326}, issn = {1466-5034}, mesh = {Bacterial Typing Techniques ; Base Composition ; Cellulomonas/*classification/isolation &amp; purification ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Nucleic Acid Hybridization ; *Oryza ; *Phylogeny ; Pigmentation ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Sequence Analysis, DNA ; *Soil Microbiology ; Vitamin K 2/analogs &amp; derivatives/chemistry ; }, abstract = {Two Gram-stain-positive, facultatively anaerobic, motile, aerobic, rod-shaped and non-spore-forming actinobacteria, strains AO-9T and AO-18, were isolated from paddy soil collected from Daejeon, Republic of Korea. Colonies were smooth, lemon-yellow and circular and 0.5-0.8×2.0-2.4 µm in diameter after 3 days of incubation at 28 °C on tryptic soy agar. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strains AO-9T and AO-18 belonged to the genus Cellulomonas, showing the highest sequence similarities to Cellulomonas marina FXJ8.089T (96.6 %), Cellulomonas endophytica SYSUP0004T (96.5 %), Cellulomonas gelida DSM 20111T (96.2 %), Cellulomonas uda DSM 20107T (96.1 %), Cellulomonas rhizosphaerae NEAU-TCZ24T (96.1 %), Cellulomonas composti TR7-06T (96.0 %), Cellulomonas persica JCM 18111T (96.0 %) and less than 96 % to other closely related species. The DNA-DNA hybridization values between strains AO-9T and AO-18 were 87 %. The average nucleotide identity and digital DNA-DNA hybridization values between strain AO-9T and type strains of related species of the genus Cellulomonas were 84.0-85.8 % and 20.3-20.9 %, respectively. The major cellular fatty acids are anteiso-C15:0 (49.9 %), C14:0 (12.9 %) and iso-C14:0 (12.1 %). The predominant isoprenoid quinone was MK-9 (H4). The polar lipid profile consists of diphosphatidylglycerol, phosphatidylglycerol and one unidentified lipid. The DNA G+C content was 72.9 mol%. Based on its distinctive phenotypic, phylogenetic and chemotaxonomic characteristics, the two strains are considered to represent novel species of the genus Cellulomonas, for which the name Cellulomonas citrea sp. nov. is proposed. The type strain is AO-9T (=KACC 19069T=NBRC 112523T).}, }
@article {pmid32875141, year = {2020}, author = {Corbin, KD and Krajmalnik-Brown, R and Carnero, EA and Bock, C and Emerson, R and Rittmann, BE and Marcus, AK and Davis, T and Dirks, B and Ilhan, ZE and Champagne, C and Smith, SR}, title = {Integrative and quantitative bioenergetics: Design of a study to assess the impact of the gut microbiome on host energy balance.}, journal = {Contemporary clinical trials communications}, volume = {19}, number = {}, pages = {100646}, pmid = {32875141}, issn = {2451-8654}, abstract = {The literature is replete with clinical studies that characterize the structure, diversity, and function of the gut microbiome and correlate the results to different disease states, including obesity. Whether the microbiome has a direct impact on obesity has not been established. To address this gap, we asked whether the gut microbiome and its bioenergetics quantitatively change host energy balance. This paper describes the design of a randomized crossover clinical trial that combines outpatient feeding with precisely controlled metabolic phenotyping in an inpatient metabolic ward. The target population was healthy, weight-stable individuals, age 18-45 and with a body mass index ≤30 kg/m2. Our primary objective was to determine within-participant differences in energy balance after consuming a control Western Diet versus a Microbiome Enhancer Diet intervention specifically designed to optimize the gut microbiome for positive impacts on host energy balance. We assessed the complete energy-balance equation via whole-room calorimetry, quantified energy intake, fecal energy losses, and methane production. We implemented conditions of tight weight stability and balance between metabolizable energy intake and predicted energy expenditure. We explored key factors that modulate the balance between host and microbial nutrient accessibility by measuring enteroendocrine hormone profiles, appetite/satiety, gut transit and gastric emptying. By integrating these clinical measurements with future bioreactor experiments, gut microbial ecology analysis, and mathematical modeling, our goal is to describe initial cause-and-effect mechanisms of gut microbiome metabolism on host energy balance. Our innovative methods will enable subsequent studies on the interacting roles of diet, the gut microbiome, and human physiology.<br><br>Clinicaltrialsgov identifier: NCT02939703. The present study reference can be found here: https://clinicaltrials.gov/ct2/show/NCT02939703.}, }
@article {pmid32874778, year = {2020}, author = {Marchioro, GM and Glasl, B and Engelen, AH and Serrão, EA and Bourne, DG and Webster, NS and Frade, PR}, title = {Microbiome dynamics in the tissue and mucus of acroporid corals differ in relation to host and environmental parameters.}, journal = {PeerJ}, volume = {8}, number = {}, pages = {e9644}, pmid = {32874778}, issn = {2167-8359}, abstract = {Corals are associated with diverse microbial assemblages; however, the spatial-temporal dynamics of intra-species microbial interactions are poorly understood. The coral-associated microbial community varies substantially between tissue and mucus microhabitats; however, the factors controlling the occurrence, abundance, and distribution of microbial taxa over time have rarely been explored for different coral compartments simultaneously. Here, we test (1) differentiation in microbiome diversity and composition between coral compartments (surface mucus and tissue) of two Acropora hosts (A. tenuis and A. millepora) common along inshore reefs of the Great Barrier Reef, as well as (2) the potential linkage between shifts in individual coral microbiome families and underlying host and environmental parameters. Amplicon based 16S ribosomal RNA gene sequencing of 136 samples collected over 14 months, revealed significant differences in bacterial richness, diversity and community structure among mucus, tissue and the surrounding seawater. Seawater samples were dominated by members of the Synechococcaceae and Pelagibacteraceae bacterial families. The mucus microbiome of Acropora spp. was dominated by members of Flavobacteriaceae, Synechococcaceae and Rhodobacteraceae and the tissue was dominated by Endozoicimonaceae. Mucus microbiome in both Acropora species was primarily correlated with seawater parameters including levels of chlorophyll a, ammonium, particulate organic carbon and the sum of nitrate and nitrite. In contrast, the correlation of the tissue microbiome to the measured environmental (i.e., seawater parameters) and host health physiological factors differed between host species, suggesting host-specific modulation of the tissue-associated microbiome to intrinsic and extrinsic factors. Furthermore, the correlation between individual coral microbiome members and environmental factors provides novel insights into coral microbiome-by-environment dynamics and hence has potential implications for current reef restoration and management efforts (e.g. microbial monitoring and observatory programs).}, }
@article {pmid32873609, year = {2020}, author = {Kloosterman, AM and Shelton, KE and van Wezel, GP and Medema, MH and Mitchell, DA}, title = {RRE-Finder: a Genome-Mining Tool for Class-Independent RiPP Discovery.}, journal = {mSystems}, volume = {5}, number = {5}, pages = {}, pmid = {32873609}, issn = {2379-5077}, support = {R01 AI144967/AI/NIAID NIH HHS/United States ; T32 GM070421/GM/NIGMS NIH HHS/United States ; }, abstract = {Many ribosomally synthesized and posttranslationally modified peptide classes (RiPPs) are reliant on a domain called the RiPP recognition element (RRE). The RRE binds specifically to a precursor peptide and directs the posttranslational modification enzymes to their substrates. Given its prevalence across various types of RiPP biosynthetic gene clusters (BGCs), the RRE could theoretically be used as a bioinformatic handle to identify novel classes of RiPPs. In addition, due to the high affinity and specificity of most RRE-precursor peptide complexes, a thorough understanding of the RRE domain could be exploited for biotechnological applications. However, sequence divergence of RREs across RiPP classes has precluded automated identification based solely on sequence similarity. Here, we introduce RRE-Finder, a new tool for identifying RRE domains with high sensitivity. RRE-Finder can be used in precision mode to confidently identify RREs in a class-specific manner or in exploratory mode to assist in the discovery of novel RiPP classes. RRE-Finder operating in precision mode on the UniProtKB protein database retrieved ∼25,000 high-confidence RREs spanning all characterized RRE-dependent RiPP classes, as well as several yet-uncharacterized RiPP classes that require future experimental confirmation. Finally, RRE-Finder was used in precision mode to explore a possible evolutionary origin of the RRE domain. The results suggest RREs originated from a co-opted DNA-binding transcriptional regulator domain. Altogether, RRE-Finder provides a powerful new method to probe RiPP biosynthetic diversity and delivers a rich data set of RRE sequences that will provide a foundation for deeper biochemical studies into this intriguing and versatile protein domain.IMPORTANCE Bioinformatics-powered discovery of novel ribosomal natural products (RiPPs) has historically been hindered by the lack of a common genetic feature across RiPP classes. Herein, we introduce RRE-Finder, a method for identifying RRE domains, which are present in a majority of prokaryotic RiPP biosynthetic gene clusters (BGCs). RRE-Finder identifies RRE domains 3,000 times faster than current methods, which rely on time-consuming secondary structure prediction. Depending on user goals, RRE-Finder can operate in precision mode to accurately identify RREs present in known RiPP classes or in exploratory mode to assist with novel RiPP discovery. Employing RRE-Finder on the UniProtKB database revealed several high-confidence RREs in novel RiPP-like clusters, suggesting that many new RiPP classes remain to be discovered.}, }
@article {pmid32873292, year = {2020}, author = {Zhu, L and Xu, F and Wan, W and Yu, B and Tang, L and Yang, Y and Du, Y and Chen, Z and Xu, H}, title = {Gut microbial characteristics of adult patients with allergy rhinitis.}, journal = {Microbial cell factories}, volume = {19}, number = {1}, pages = {171}, doi = {10.1186/s12934-020-01430-0}, pmid = {32873292}, issn = {1475-2859}, support = {81900541//National Natural Science Foundation of China/ ; 2019J05005//Natural Science Foundation of Fujian Province/ ; }, abstract = {BACKGROUND: Although recent studies have indicated that intestinal microbiota dweller are involved in the pathogenesis of allergy rhinitis (AR), the influence of gut microbiota on AR adult has not been fully elucidated yet. Hence, we carried out this study to uncover the distinctive bacterial taxa that differentiate allergy rhinitis patients from healthy individuals. Feces samples from thirty three AR patients and thirty one healthy individuals were analyzed by 16S rRNA gene sequencing.<br><br>RESULTS: Results showed that the bacterial diversity in AR group was significantly higher than that of the non-AR group. Bacterial communities between AR and non-AR group were significantly differentiated as revealed by Principal coordinates analysis (PCoA) and the variation within non-AR were higher than that of the counterpart. Firmicutes, Fusobacteria, Actinobacteria, Cyanobacteria and Chloroflexi were the significantly differed phyla taxa and the top significantly distinguished bacterial genus included Prevotella_9, Phascolarctobacterium, Roseburia, Megamonas, Alistipes, Lachnoclostridium and Fusobacterium. The higher network complexity in AR group were dominated by taxa belonging to Firmicutes. The predicted function, alpha linolenic acid metabolism and bacterial invasion of epithelial cells pathway were higher in non-AR group while gonadotropin-releasing hormone (GnRH) signaling pathway, Fc γ-R mediated phagocytosis and endocytosis were higher in AR patients. Although the bacterial diversity between moderate and severe AR patients showed no significant difference, the significant correlation between featured genus and total nasal symptom score or rhinoconjunctivitis quality of life questionnaire, such as Butyricicoccus and Eisenbergiella, revealed the potential to intervene the AR status by means of gut microbiota.<br><br>CONCLUSIONS: In conclusion, patients with allergy rhinitis had distinguished gut microbiota characteritics in comparison with healthy controls. The results suggest that gut microbiota might play crucial roles in influencing the course and different symptoms of AR. Trial registration ChiCTR, ChiCTR1900028613. Registered 29 December 2019, https://www.chictr.org.cn/showproj.aspx?proj=47650 .}, }
@article {pmid32870508, year = {2020}, author = {Kedia, S and Ghosh, TS and Jain, S and Desigamani, A and Kumar, A and Gupta, V and Bopanna, S and Yadav, DP and Goyal, S and Makharia, G and Travis, SPL and Das, B and Ahuja, V}, title = {Gut microbiome diversity in acute severe colitis is distinct from mild to moderate ulcerative colitis.}, journal = {Journal of gastroenterology and hepatology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jgh.15232}, pmid = {32870508}, issn = {1440-1746}, support = {//Intramural THSTI research funds/ ; //Scheme for Promotion of Academic and Research Collaboration (SPARC)/ ; }, abstract = {BACKGROUND AND AIM: Although the gut microbiome of patients with ulcerative colitis (UC) has been characterized, no study has characterized the gut microbiome in acute severe colitis (ASC). We compared the gut microbiome of patients with UC, ASC, and healthy controls (HCs).<br><br>METHODS: Patients with mild to moderate UC (n = 24), ASC (n = 19 with 21 episodes) and HCs (n = 50) were recruited prospectively. A 16SrDNA amplicon approach was used to explore gut microbial diversity and taxonomic repertoires. UC was diagnosed using European Crohn's and Colitis Organization guidelines, and ASC was diagnosed using Truelove and Witts' criteria.<br><br>RESULTS: The normalized alpha diversity was significantly lower in ASC than mild-moderately active UC (P < 0.05) or HC (P < 0.001). The gut microbiome in ASC was highly unstable, as characterized by high intracohort variation (analyzed using J-divergence measure), which was significantly greater than in UC or HC. On principal coordinate analysis, the microbiome of HC and UC were similar, with the ASC cohort being distinct from both. Comparison of ranked abundances identified four distinct clusters of genera (G1, G2, G3, and G4), with specific trends in their abundance across three groups: G1/G2A clusters had the least, whereas G3 had the highest abundance in the ASC cohort.<br><br>CONCLUSIONS: Gut microbial diversity is lower in ASC than mild-moderate UC or HCs. Gut microbiome composition is increasingly unstable in ASC, with a distinct abundance of specific genera varying between HCs and ASC. Mild-moderate UC lies within the spectrum.}, }
@article {pmid32862246, year = {2020}, author = {Starke, R and Pylro, VS and Morais, DK}, title = {16S rRNA Gene Copy Number Normalization Does Not Provide More Reliable Conclusions in Metataxonomic Surveys.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01586-7}, pmid = {32862246}, issn = {1432-184X}, support = {18-25706S//Grantová Agentura České Republiky/ ; 20-02022Y//Grantová Agentura České Republiky/ ; }, abstract = {Sequencing 16S rRNA gene amplicons is the gold standard to uncover the composition of prokaryotic communities. The presence of multiple copies of this gene makes the community abundance data distorted and gene copy normalization (GCN) necessary for correction. Even though GCN of 16S data provided a picture closer to the metagenome before, it should also be compared with communities of known composition due to the fact that library preparation is prone to methodological biases. Here, we process 16S rRNA gene amplicon data from eleven simple mock communities with DADA2 and estimate the impact of GCN. In all cases, the mock community composition derived from the 16S sequencing differs from those expected, and GCN fails to improve the classification for most of the analysed communities. Our approach provides empirical evidence that GCN does not improve the 16S target sequencing analyses in real scenarios. We therefore question the use of GCN for metataxonomic surveys until a more comprehensive catalogue of copy numbers becomes available.}, }
@article {pmid32861933, year = {2020}, author = {Uroosa,  and Kazmi, SSUH and Xu, G and Xu, H}, title = {Insights into the effects of harmful algal bloom on ecological quality status using body-size spectrum of biofilm-dwelling ciliates in marine ecosystems.}, journal = {Marine pollution bulletin}, volume = {160}, number = {}, pages = {111596}, doi = {10.1016/j.marpolbul.2020.111596}, pmid = {32861933}, issn = {1879-3363}, mesh = {Biofilms ; *Ciliophora ; *Dinoflagellida ; Ecosystem ; Harmful Algal Bloom ; }, abstract = {The effects of two harmful algae Alexandrium tamarense and Gymnodinium catenatum on ecological quality status were identified using biofilm-dwelling ciliate assemblage as test organism communities. The body-size spectra of the test ciliates were observed at a gradient of cell concentrations of both algal species: 100 (control), followed by102, 103, 104 and 105 cells ml-1. The test ciliates showed clear variations in body-size spectra along the concentration gradients of both algal species. In terms of probability density, the ciliates generally peaked at low levels of algal concentrations (100-104 cells ml-1) in small size forms, followed by the forms with large sizes at the concentration of 105 cells ml-1 of both algal species. Bootstrapped-average analysis demonstrated a significant change in body-size spectrum when algal concentrations were higher than 104 cells ml-1. It is suggested that the body-size spectrum of the ciliates may be used to indicate the effects of harmful algal bloom.}, }
@article {pmid32860516, year = {2020}, author = {Virta, L and Soininen, J and Norkko, A}, title = {Biodiversity Loss Threatens the Current Functional Similarity of Beta Diversity in Benthic Diatom Communities.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01576-9}, pmid = {32860516}, issn = {1432-184X}, support = {294853//Academy of Finland/ ; }, abstract = {The global biodiversity loss has increased the need to understand the effects of decreasing diversity, but our knowledge on how species loss will affect the functioning of communities and ecosystems is still very limited. Here, the levels of taxonomic and functional beta diversity and the effect of species loss on functional beta diversity were investigated in an estuary that provides a naturally steep environmental gradient. The study was conducted using diatoms that are among the most important microorganisms in all aquatic ecosystems and globally account for 40% of marine primary production. Along the estuary, the taxonomic beta diversity of diatom communities was high (Bray-Curtis taxonomic similarity 0.044) and strongly controlled by the environment, particularly wind exposure, salinity, and temperature. In contrast, the functional beta diversity was low (Bray-Curtis functional similarity 0.658) and much less controlled by the environment. Thus, the diatom communities stayed functionally almost similar despite large changes in species composition and environment. This may indicate that, through high taxonomic diversity and redundancy in functions, microorganisms provide an insurance effect against environmental change. However, when studying the effect of decreasing species richness on functional similarity of communities, simulated species loss to 45% of the current species richness decreased functional similarity significantly. This suggests that decreasing species richness may increase variability and reduce the stability and resilience of communities. These results highlight the importance of high taxonomic biodiversity for the stable functioning of benthic communities.}, }
@article {pmid32860076, year = {2020}, author = {Câmara, PEAS and Carvalho-Silva, M and Pinto, OHB and Amorim, ET and Henriques, DK and da Silva, TH and Pellizzari, F and Convey, P and Rosa, LH}, title = {Diversity and Ecology of Chlorophyta (Viridiplantae) Assemblages in Protected and Non-protected Sites in Deception Island (Antarctica, South Shetland Islands) Assessed Using an NGS Approach.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01584-9}, pmid = {32860076}, issn = {1432-184X}, support = {23/2018//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, abstract = {Assessment of the diversity of algal assemblages in Antarctica has until now largely relied on traditional microbiological culture approaches. Here we used DNA metabarcoding through high-throughput sequencing (HTS) to assess the uncultured algal diversity at two sites on Deception Island, Antarctica. The first was a relatively undisturbed site within an Antarctic Specially Protected Area (ASPA 140), and the second was a site heavily impacted by human visitation, the Whalers Bay historic site. We detected 65 distinct algal taxa, 50 from within ASPA 140 and 61 from Whalers Bay. Of these taxa, 46 were common to both sites, and 19 only occurred at one site. Algal richness was about six times greater than reported in previous studies using culture methods. A high proportion of DNA reads obtained was assigned to the highly invasive species Caulerpa webbiana at Whalers Bay, and the potentially pathogenic genus Desmodesmus was found at both sites. Our data demonstrate that important differences exist between these two protected and human-impacted sites on Deception Island in terms of algal diversity, richness, and abundance. The South Shetland Islands have experienced considerable effects of climate change in recent decades, while warming through geothermal activity on Deception Island itself makes this island one of the most vulnerable to colonization by non-native species. The detection of DNA of non-native taxa highlights concerns about how human impacts, which take place primarily through tourism and national research operations, may influence future biological colonization processes in Antarctica.}, }
@article {pmid32859925, year = {2020}, author = {Jurburg, SD and Konzack, M and Eisenhauer, N and Heintz-Buschart, A}, title = {The archives are half-empty: an assessment of the availability of microbial community sequencing data.}, journal = {Communications biology}, volume = {3}, number = {1}, pages = {474}, pmid = {32859925}, issn = {2399-3642}, support = {FZT 118//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, abstract = {As DNA sequencing has become more popular, the public genetic repositories where sequences are archived have experienced explosive growth. These repositories now hold invaluable collections of sequences, e.g., for microbial ecology, but whether these data are reusable has not been evaluated. We assessed the availability and state of 16S rRNA gene amplicon sequences archived in public genetic repositories (SRA, EBI, and DDJ). We screened 26,927 publications in 17 microbiology journals, identifying 2015 16S rRNA gene sequencing studies. Of these, 7.2% had not made their data public at the time of analysis. Among a subset of 635 studies sequencing the same gene region, 40.3% contained data which was not available or not reusable, and an additional 25.5% contained faults in data formatting or data labeling, creating obstacles for data reuse. Our study reveals gaps in data availability, identifies major contributors to data loss, and offers suggestions for improving data archiving practices.}, }
@article {pmid32859275, year = {2020}, author = {Lu, J and Salzberg, SL}, title = {Ultrafast and accurate 16S rRNA microbial community analysis using Kraken 2.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {124}, pmid = {32859275}, issn = {2049-2618}, support = {R01 HG006677/HG/NHGRI NIH HHS/United States ; R35 GM130151/GM/NIGMS NIH HHS/United States ; }, abstract = {BACKGROUND: For decades, 16S ribosomal RNA sequencing has been the primary means for identifying the bacterial species present in a sample with unknown composition. One of the most widely used tools for this purpose today is the QIIME (Quantitative Insights Into Microbial Ecology) package. Recent results have shown that the newest release, QIIME 2, has higher accuracy than QIIME, MAPseq, and mothur when classifying bacterial genera from simulated human gut, ocean, and soil metagenomes, although QIIME 2 also proved to be the most computationally expensive. Kraken, first released in 2014, has been shown to provide exceptionally fast and accurate classification for shotgun metagenomics sequencing projects. Bracken, released in 2016, then provided users with the ability to accurately estimate species or genus relative abundances using Kraken classification results. Kraken 2, which matches the accuracy and speed of Kraken 1, now supports 16S rRNA databases, allowing for direct comparisons to QIIME and similar systems.<br><br>METHODS: For a comprehensive assessment of each tool, we compare the computational resources and speed of QIIME 2's q2-feature-classifier, Kraken 2, and Bracken in generating the three main 16S rRNA databases: Greengenes, SILVA, and RDP. For an evaluation of accuracy, we evaluated each tool using the same simulated 16S rRNA reads from human gut, ocean, and soil metagenomes that were previously used to compare QIIME, MAPseq, mothur, and QIIME 2. We evaluated accuracy based on the accuracy of the final genera read counts assigned by each tool. Finally, as Kraken 2 is the only tool providing per-read taxonomic assignments, we evaluate the sensitivity and precision of Kraken 2's per-read classifications.<br><br>RESULTS: For both the Greengenes and SILVA database, Kraken 2 and Bracken are up to 100 times faster at database generation. For classification, using the same data as previous studies, Kraken 2 and Bracken are up to 300 times faster, use 100x less RAM, and generate results that more accurate at 16S rRNA profiling than QIIME 2's q2-feature-classifier.<br><br>CONCLUSION: Kraken 2 and Bracken provide a very fast, efficient, and accurate solution for 16S rRNA metataxonomic data analysis. Video Abstract.}, }
@article {pmid32857837, year = {2020}, author = {Ho, A and Mendes, LW and Lee, HJ and Kaupper, T and Mo, Y and Poehlein, A and Bodelier, PLE and Jia, Z and Horn, MA}, title = {Response of a methane-driven interaction network to stressor intensification.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {10}, pages = {}, doi = {10.1093/femsec/fiaa180}, pmid = {32857837}, issn = {1574-6941}, abstract = {Microorganisms may reciprocally select for specific interacting partners, forming a network with interdependent relationships. The methanotrophic interaction network, comprising methanotrophs and non-methanotrophs, is thought to modulate methane oxidation and give rise to emergent properties beneficial for the methanotrophs. Therefore, microbial interaction may become relevant for community functioning under stress. However, empirical validation of the role and stressor-induced response of the interaction network remains scarce. Here, we determined the response of a complex methane-driven interaction network to a stepwise increase in NH4Cl-induced stress (0.5-4.75 g L-1, in 0.25-0.5 g L-1 increments) using enrichment of a naturally occurring complex community derived from a paddy soil in laboratory-scale incubations. Although ammonium and intermediates of ammonium oxidation are known to inhibit methane oxidation, methanotrophic activity was unexpectedly detected even in incubations with high ammonium levels, albeit rates were significantly reduced. Sequencing analysis of the 16S rRNA and pmoA genes consistently revealed divergent communities in the reference and stressed incubations. The 16S rRNA-based co-occurrence network analysis revealed that NH4Cl-induced stress intensification resulted in a less complex and modular network, likely driven by less stable interaction. Interestingly, the non-methanotrophs formed the key nodes, and appear to be relevant members of the community. Overall, stressor intensification unravels the interaction network, with adverse consequences for community functioning.}, }
@article {pmid32855435, year = {2021}, author = {Fodelianakis, S and Valenzuela-Cuevas, A and Barozzi, A and Daffonchio, D}, title = {Direct quantification of ecological drift at the population level in synthetic bacterial communities.}, journal = {The ISME journal}, volume = {15}, number = {1}, pages = {55-66}, pmid = {32855435}, issn = {1751-7370}, support = {Baseline fund to DD//King Abdullah University of Science and Technology (KAUST)/ ; OSR-2018-CARF-1973//King Abdullah University of Science and Technology (KAUST)/ ; }, abstract = {In community ecology, drift refers to random births and deaths in a population. In microbial ecology, drift is estimated indirectly via community snapshots but in this way, it is almost impossible to distinguish the effect of drift from the effect of other ecological processes. Controlled experiments where drift is quantified in isolation from other processes are still missing. Here we isolate and quantify drift in a series of controlled experiments on simplified and tractable bacterial communities. We detect drift arising randomly in the populations within the communities and resulting in a 1.4-2% increase in their growth rate variability on average. We further use our experimental findings to simulate complex microbial communities under various conditions of selection and dispersal. We find that the importance of drift increases under high selection and low dispersal, where it can lead to ~5% of species loss and to ~15% increase in β-diversity. The species extinct by drift are mainly rare, but they become increasingly less rare when selection increases, and dispersal decreases. Our results provide quantitative insights regarding the properties of drift in bacterial communities and suggest that it accounts for a consistent fraction of the observed stochasticity in natural surveys.}, }
@article {pmid32854141, year = {2020}, author = {Altinli, M and Lequime, S and Atyame, C and Justy, F and Weill, M and Sicard, M}, title = {Wolbachia modulates prevalence and viral load of Culex pipiens densoviruses in natural populations.}, journal = {Molecular ecology}, volume = {29}, number = {20}, pages = {4000-4013}, doi = {10.1111/mec.15609}, pmid = {32854141}, issn = {1365-294X}, abstract = {The inadequacy of standard mosquito control strategies calls for ecologically safe novel approaches, for example the use of biological agents such as the endosymbiotic α-proteobacteria Wolbachia or insect-specific viruses (ISVs). Understanding the ecological interactions between these &quot;biocontrol endosymbionts&quot; is thus a fundamental step. Wolbachia are transmitted vertically from mother to offspring and modify their hosts' phenotypes, including reproduction (e.g., cytoplasmic incompatibility) and survival (e.g., viral interference). In nature, Culex pipiens (sensu lato) mosquitoes are always found infected with genetically diverse Wolbachia called wPip that belong to five phylogenetic groups. In recent years, ISVs have also been discovered in these mosquito species, although their interactions with Wolbachia in nature are unknown. Here, we studied the interactions between a widely prevalent ISV, the Culex pipiens densovirus (CpDV, Densovirinae), and Wolbachia in northern Tunisian C. pipiens populations. We showed an influence of different Wolbachia groups on CpDV prevalence and a general positive correlation between Wolbachia and CpDV loads. By investigating the putative relationship between CpDV diversification and wPip groups in the different sites, we detected a signal linked to wPip groups in CpDV phylogeny in sites where all larvae were infected by the same wPip group. However, no such signal was detected where the wPip groups coexisted, suggesting CpDV horizontal transfer between hosts. Overall, our results provide good evidence for an ecological influence of Wolbachia on an ISV, CpDV, in natural populations and highlight the importance of integrating Wolbachia in our understanding of ISV ecology in nature.}, }
@article {pmid32853201, year = {2020}, author = {Buongiorno, J and Sipes, K and Wasmund, K and Loy, A and Lloyd, KG}, title = {Woeseiales transcriptional response to shallow burial in Arctic fjord surface sediment.}, journal = {PloS one}, volume = {15}, number = {8}, pages = {e0234839}, pmid = {32853201}, issn = {1932-6203}, mesh = {Arctic Regions ; Bacterial Proteins/genetics ; Estuaries ; Gammaproteobacteria/classification/*genetics/metabolism ; Genome, Bacterial ; Geologic Sediments/*microbiology ; Heat-Shock Proteins/genetics ; Metagenome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Svalbard ; Transcriptome ; }, abstract = {Distinct lineages of Gammaproteobacteria clade Woeseiales are globally distributed in marine sediments, based on metagenomic and 16S rRNA gene analysis. Yet little is known about why they are dominant or their ecological role in Arctic fjord sediments, where glacial retreat is rapidly imposing change. This study combined 16S rRNA gene analysis, metagenome-assembled genomes (MAGs), and genome-resolved metatranscriptomics uncovered the in situ abundance and transcriptional activity of Woeseiales with burial in four shallow sediment sites of Kongsfjorden and Van Keulenfjorden of Svalbard (79°N). We present five novel Woeseiales MAGs and show transcriptional evidence for metabolic plasticity during burial, including sulfur oxidation with reverse dissimilatory sulfite reductase (dsrAB) down to 4 cm depth and nitrite reduction down to 6 cm depth. A single stress protein, spore protein SP21 (hspA), had a tenfold higher mRNA abundance than any other transcript, and was a hundredfold higher on average than other transcripts. At three out of the four sites, SP21 transcript abundance increased with depth, while total mRNA abundance and richness decreased, indicating a shift in investment from metabolism and other cellular processes to build-up of spore protein SP21. The SP21 gene in MAGs was often flanked by genes involved in membrane-associated stress response. The ability of Woeseiales to shift from sulfur oxidation to nitrite reduction with burial into marine sediments with decreasing access to overlying oxic bottom waters, as well as enter into a dormant state dominated by SP21, may account for its ubiquity and high abundance in marine sediments worldwide, including those of the rapidly shifting Arctic.}, }
@article {pmid32852571, year = {2020}, author = {Hubert, J and Nesvorna, M and Green, SJ and Klimov, PB}, title = {Microbial Communities of Stored Product Mites: Variation by Species and Population.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01581-y}, pmid = {32852571}, issn = {1432-184X}, support = {GA19-09998S//Grantová Agentura České Republiky/ ; 19-14-00004//Russian Science Foundation/ ; }, abstract = {Arthropod-associated microorganisms are important because they affect host fitness, protect hosts from pathogens, and influence the host's ability to vector pathogens. Stored product mites (Astigmata) often establish large populations in various types of food items, damaging the food by direct feeding and introducing contaminants, including their own bodies, allergen-containing feces, and associated microorganisms. Here we access the microbial structure and abundance in rearing diets, eggs, feces fraction, and mite bodies of 16 mite populations belonging to three species (Carpoglyphus lactis, Acarus siro, and Tyrophagus putrescentiae) using quantitative PCR and 16S ribosomal RNA (rRNA) gene amplicon sequencing. The mite microbiomes had a complex structure dominated by the following bacterial taxa (OTUs): (a) intracellular symbionts of the genera Cardinium and Wolbachia in the mite bodies and eggs; (b) putative gut symbionts of the genera Solitalea, Bartonella, and Sodalis abundant in mite bodies and also present in mite feces; (c) feces-associated or environmental bacteria of the genera Bacillus, Staphylococcus, and Kocuria in the diet, mite bodies, and feces. Interestingly and counterintuitively, the differences between microbial communities in various conspecific mite populations were higher than those between different mite species. To explain some of these differences, we hypothesize that the intracellular bacterial symbionts can affect microbiome composition in mite bodies, causing differences between microbial profiles. Microbial profiles differed between various sample types, such as mite eggs, bodies, and the environment (spent growth medium-SPGM). Low bacterial abundances in eggs may result in stochastic effects in parent-offspring microbial transmission, except for the intracellular symbionts. Bacteria in the rearing diet had little effect on the microbial community structure in SPGM and mite bodies. Mite fitness was positively correlated with bacterial abundance in SPGM and negatively correlated with bacterial abundances in mite bodies. Our study demonstrates critical host-microbe interactions, affecting all stages of mite growth and leading to alteration of the environmental microbiome. Correlational evidence based on absolute quantitation of bacterial 16S rRNA gene copies suggests that mite-associated microorganisms are critical for modulating important pest properties of mites by altering population growth.}, }
@article {pmid32850972, year = {2020}, author = {Álvarez-Rodríguez, I and Ugarte-Uribe, B and de la Arada, I and Arrondo, JLR and Garbisu, C and Alkorta, I}, title = {Conjugative Coupling Proteins and the Role of Their Domains in Conjugation, Secondary Structure and in vivo Subcellular Location.}, journal = {Frontiers in molecular biosciences}, volume = {7}, number = {}, pages = {185}, pmid = {32850972}, issn = {2296-889X}, abstract = {Type IV Coupling Proteins (T4CPs) are essential elements in many type IV secretion systems (T4SSs). The members of this family display sequence, length, and domain architecture heterogeneity, being the conserved Nucleotide-Binding Domain the motif that defines them. In addition, most T4CPs contain a Transmembrane Domain (TMD) in the amino end and an All-Alpha Domain facing the cytoplasm. Additionally, a few T4CPs present a variable domain at the carboxyl end. The structural paradigm of this family is TrwBR388, the T4CP of conjugative plasmid R388. This protein has been widely studied, in particular the role of the TMD on the different characteristics of TrwBR388. To gain knowledge about T4CPs and their TMD, in this work a chimeric protein containing the TMD of TraJpKM101 and the cytosolic domain of TrwBR388 has been constructed. Additionally, one of the few T4CPs of mobilizable plasmids, MobBCloDF13 of mobilizable plasmid CloDF13, together with its TMD-less mutant MobBΔTMD have been studied. Mating studies showed that the chimeric protein is functional in vivo and that it exerted negative dominance against the native proteins TrwBR388 and TraJpKM101. Also, it was observed that the TMD of MobBCloDF13 is essential for the mobilization of CloDF13 plasmid. Analysis of the secondary structure components showed that the presence of a heterologous TMD alters the structure of the cytosolic domain in the chimeric protein. On the contrary, the absence of the TMD in MobBCloDF13 does not affect the secondary structure of its cytosolic domain. Subcellular localization studies showed that T4CPs have a unipolar or bipolar location, which is enhanced by the presence of the remaining proteins of the conjugative system. Unlike what has been described for TrwBR388, the TMD is not an essential element for the polar location of MobBCloDF13. The main conclusion is that the characteristics described for the paradigmatic TrwBR388 T4CP should not be ascribed to the whole T4CP family. Specifically, it has been proven that the mobilizable plasmid-related MobBCloDF13 presents different characteristics regarding the role of its TMD. This work will contribute to better understand the T4CP family, a key element in bacterial conjugation, the main mechanism responsible for antibiotic resistance spread.}, }
@article {pmid32850744, year = {2020}, author = {Song, C and Zhu, F and Carrión, VJ and Cordovez, V}, title = {Beyond Plant Microbiome Composition: Exploiting Microbial Functions and Plant Traits via Integrated Approaches.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {8}, number = {}, pages = {896}, pmid = {32850744}, issn = {2296-4185}, abstract = {Plants recruit specific microorganisms to live inside and outside their roots that provide essential functions for plant growth and health. The study of the microbial communities living in close association with plants helps in understanding the mechanisms involved in these beneficial interactions. Currently, most of the research in this field has been focusing on the description of the taxonomic composition of the microbiome. Therefore, a focus on the plant-associated microbiome functions is pivotal for the development of novel agricultural practices which, in turn, will increase plant fitness. Recent advances in microbiome research using model plant species started to shed light on the functions of specific microorganisms and the underlying mechanisms of plant-microbial interaction. Here, we review (1) microbiome-mediated functions associated with plant growth and protection, (2) insights from native and agricultural habitats that can be used to improve soil health and crop productivity, (3) current -omics and new approaches for studying the plant microbiome, and (4) challenges and future perspectives for exploiting the plant microbiome for beneficial outcomes. We posit that integrated approaches will help in translating fundamental knowledge into agricultural practices.}, }
@article {pmid32849473, year = {2020}, author = {Sedlacek, CJ}, title = {It Takes a Village: Discovering and Isolating the Nitrifiers.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1900}, pmid = {32849473}, issn = {1664-302X}, abstract = {It has been almost 150 years since Jean-Jacques Schloesing and Achille Müntz discovered that the process of nitrification, the oxidation of ammonium to nitrate, is a biological process carried out by microorganisms. In the following 15 years, numerous researchers independently contributed paradigm shifting discoveries that formed the foundation of nitrification and nitrification-related research. One of them was Sergei Winogradsky, whose major accomplishments include the discovery of both lithotrophy (in sulfur-oxidizing bacteria) and chemoautotrophy (in nitrifying bacteria). However, Winogradsky often receives most of the credit for many other foundational nitrification discoveries made by his contemporaries. This accumulation of credit over time is at least in part due to the increased attention, Winogradsky receives in the scientific literature and textbooks as a &quot;founder of microbiology&quot; and &quot;the founder of microbial ecology.&quot; Here, some light is shed on several other researchers who are often overlooked, but whose work was instrumental to the emerging field of nitrification and to the work of Winogradsky himself. Specifically, the discovery of the biological process of nitrification by Schloesing and Müntz, the isolation of the first nitrifier by Grace and Percy Frankland, and the observation that nitrification is carried out by two distinct groups of microorganisms by Robert Warington are highlighted. Finally, the more recent discoveries of the chemolithoautotrophic ammonia-oxidizing archaea and complete ammonia oxidizers are put into this historical context.}, }
@article {pmid32849470, year = {2020}, author = {Nagler, M and Podmirseg, SM and Mayr, M and Ascher-Jenull, J and Insam, H}, title = {Quantities of Intra- and Extracellular DNA Reveal Information About Activity and Physiological State of Methanogenic Archaea.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1894}, pmid = {32849470}, issn = {1664-302X}, abstract = {Although being a common aim of many microbial ecology studies, measuring individual physiological conditions of a microbial group or species within a complex consortium is still a challenge. Here, we propose a novel approach that is based on the quantification of sequentially extracted extracellular (exDNA) and intracellular DNA (iDNA) and reveals information about cell lysis and activity of methanogenic archaea within a biogas-producing microbial community. We monitored the methane production rates of differently treated batch anaerobic cultures and compared the concentrations of the alpha subunit of the methyl coenzyme M reductase gene of methanogenic archaea in extracellular and intracellular DNA fractions and in the classically extracted total DNA pool. Our results showed that this fine-tuned DNA approach coupled with the interpretation of the ratio between free exDNA and iDNA considerably improved microbial activity tracking compared to the classical extraction/quantification of total DNA. Additionally, it allowed to identify and quantify methanogenic populations that are inactive and those that are strongly influenced by cell lysis. We argue that despite the need of further studies, this method represents a novel approach to gain specific physiological information from a complex environmental sample and holds the potential to be applied to other microbes of interest.}, }
@article {pmid32849423, year = {2020}, author = {Moonga, HB and Schoustra, SE and van den Heuvel, J and Linnemann, AR and Samad, MS and Shindano, J and Smid, EJ}, title = {Composition and Diversity of Natural Bacterial Communities in Mabisi, a Traditionally Fermented Milk.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1816}, pmid = {32849423}, issn = {1664-302X}, abstract = {Many traditionally fermented milk products such as mabisi involve spontaneous fermentation, which can result in bacterial community composition variation due to selection pressure. The aim of this study was to determine the composition of bacterial communities in the different types of mabisi produced across Zambia and identify the factors that influence their composition. Samples of mabisi were collected across the country, and analyzed for pH and bacterial communities using 16S rRNA amplicon sequencing. We found that the bacterial community composition was dominated by members of two phyla, i.e., Firmicutes and Proteobacteria, from which the top 10 most abundant genera were Lactococcus, Lactobacillus, Streptococcus, Enterobacter, Citrobacter, Klebsiella, Kluyvera, Buttiauxella, Aeromonas, and Acinetobacter. The most dominant genus was Lactococcus, which was present in all types of mabisi produced from all regions. The mabisi products from traditional mabisi production regions (TMPRs) were dominated by lactic acid bacteria (LAB) whereas products from non-TMPRs were dominated by non-LAB species. Tonga mabisi, the most popular type of mabisi produced in non-TMPRs, had the most complex and diverse bacterial community composition compared to the other types, which included barotse, backslopping, creamy, and thick-tonga mabisi. Other factors that influenced bacterial community composition were geographical location, fermentation duration and pH while the type of fermentation container and producer did not. This study provides new insights that can be applied in starter culture development as well as microbial functionality studies.}, }
@article {pmid32849396, year = {2020}, author = {Huang, J and Yang, J and Jiang, H and Wu, G and Liu, W and Wang, B and Xiao, H and Han, J}, title = {Microbial Responses to Simulated Salinization and Desalinization in the Sediments of the Qinghai-Tibetan Lakes.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1772}, pmid = {32849396}, issn = {1664-302X}, abstract = {Uncovering microbial response to salinization or desalinization is of great importance to understanding of the influence of global climate change on lacustrine microbial ecology. In this study, to simulate salinization and desalinization, sediments from Erhai Lake (salinity 0.3-0.8 g/L) and Chaka Lake (salinity 299.3-350.7 g/L) on the Qinghai-Tibetan Plateau were transplanted into different lakes with a range of salinity of 0.3-299.3 g/L, followed by in situ incubation for 50 days and subsequent geochemical and microbial analyses. Desalinization was faster than salinization in the transplanted sediments. The salinity of the transplanted sediment increased and decreased in the salinization and desalinization simulation experiments, respectively. The TOC contents of the transplanted sediments were lower than that of their undisturbed counterparts in the salinization experiments, whereas they had a strong negative linear relationship with salinity in the desalinization experiments. Microbial diversity decreased in response to salinization and desalinization, and microbial community dissimilarity significantly (P < 0.01) increased with salinity differences between the transplanted sediments and their undisturbed counterparts. Microbial groups belonging to Gammaproteobacteria and Actinobacteria became abundant in salinization whereas Bacteroidetes and Chloroflexi became dominant in desalinization. Among the predicted microbial functions, hydrogenotrophic methanogenesis, methanogenesis through CO2 reduction with H2, nitrate/nitrogen respiration, and nitrification increased in salinization; in desalinization, enhancement was observed for respiration of sulfur compounds, sulfate respiration, sulfur respiration, thiosulfate respiration, hydrocarbon degradation, chemoheterotrophy, and fermentation, whereas depressing was found for aerobic ammonia oxidation, nitrate/nitrogen respiration, nitrification, nitrite respiration, manganese oxidation, aerobic chemoheterotrophy, and phototrophy. Such microbial variations could be explained by changes of transplantation, salinity, and covarying variables. In summary, salinization and desalinization had profound influence on the geochemistry, microbial community, and function in lakes.}, }
@article {pmid32849356, year = {2020}, author = {Arbour, TJ and Gilbert, B and Banfield, JF}, title = {Diverse Microorganisms in Sediment and Groundwater Are Implicated in Extracellular Redox Processes Based on Genomic Analysis of Bioanode Communities.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1694}, pmid = {32849356}, issn = {1664-302X}, abstract = {Extracellular electron transfer (EET) between microbes and iron minerals, and syntrophically between species, is a widespread process affecting biogeochemical cycles and microbial ecology. The distribution of this capacity among microbial taxa, and the thermodynamic controls on EET in complex microbial communities, are not fully known. Microbial electrochemical cells (MXCs), in which electrodes serve as the electron acceptor or donor, provide a powerful approach to enrich for organisms capable of EET and to study their metabolism. We used MXCs coupled with genome-resolved metagenomics to investigate the capacity for EET in microorganisms present in a well-studied aquifer near Rifle, CO. Electroactive biofilms were established and maintained for almost 4 years on anodes poised mostly at -0.2 to -0.25 V vs. SHE, a range that mimics the redox potential of iron-oxide minerals, using acetate as the sole carbon source. Here we report the metagenomic characterization of anode-biofilm and planktonic microbial communities from samples collected at timepoints across the study period. From two biofilm and 26 planktonic samples we reconstructed draft-quality and near-complete genomes for 84 bacteria and 2 archaea that represent the majority of organisms present. A novel Geobacter sp. with at least 72 putative multiheme c-type cytochromes (MHCs) was the dominant electrode-attached organism. However, a diverse range of other electrode-associated organisms also harbored putative MHCs with at least 10 heme-binding motifs, as well as porin-cytochrome complexes and e-pili, including Actinobacteria, Ignavibacteria, Chloroflexi, Acidobacteria, Firmicutes, Beta- and Gammaproteobacteria. Our results identify a small subset of the thousands of organisms previously detected in the Rifle aquifer that may have the potential to mediate mineral redox transformations.}, }
@article {pmid32849338, year = {2020}, author = {Presley, GN and Zhang, J and Purvine, SO and Schilling, JS}, title = {Functional Genomics, Transcriptomics, and Proteomics Reveal Distinct Combat Strategies Between Lineages of Wood-Degrading Fungi With Redundant Wood Decay Mechanisms.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1646}, pmid = {32849338}, issn = {1664-302X}, abstract = {Wood-degrading fungi vary in their strategies for deconstructing wood, and their competitive successes shape the rate and fate of carbon released from wood, Earth's largest pool of aboveground terrestrial carbon. In this study, one-on-one interspecific interactions between two model brown rot (carbohydrate-selective) fungi, Gloeophyllum trabeum and Rhodonia (Postia) placenta, were studied on wood wafers where a clearly resolved interaction zone (IZ) could be generated, reproducibly. Comparative RNAseq and proteomics between the IZ and non-interacting hyphae of each species identified combative strategies for each fungus. Glycoside hydrolases were a relatively smaller portion of the interaction secretome compared to non-interacting hyphae. The interaction zone showed higher pectinase specific activity than all other sampling locations, and higher laminarinase specific activity (branched β-glucan proxy) was seen in the IZ secretome relative to equivalent hyphae in single-species cultures. Our efforts also identified two distinct competitive strategies in these two fungi with a shared nutritional mode (brown rot) but polyphyletic ancestral lineages. Gloeophyllum trabeum (Gloeophyllum clade) upregulated more secondary metabolite (SM) synthesis genes in response to a competitor than did R. placenta. R. placenta (Antrodia clade) upregulated a larger variety of uncharacterized oxidoreductases in interacting hyphae, suggesting that these may play a role in mediating competitor response in this fungus. Both species produced several hypothetical proteins exclusively in the interaction zone, leaving questions as to the function of these proteins. This work supports the existence of multiple interaction strategies among brown rot fungi and highlights the functional diversity among wood decay fungi.}, }
@article {pmid32849330, year = {2020}, author = {Floc'h, JB and Hamel, C and Lupwayi, N and Harker, KN and Hijri, M and St-Arnaud, M}, title = {Bacterial Communities of the Canola Rhizosphere: Network Analysis Reveals a Core Bacterium Shaping Microbial Interactions.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1587}, pmid = {32849330}, issn = {1664-302X}, abstract = {The rhizosphere hosts a complex web of prokaryotes interacting with one another that may modulate crucial functions related to plant growth and health. Identifying the key factors structuring the prokaryotic community of the plant rhizosphere is a necessary step toward the enhancement of plant production and crop yield with beneficial associative microorganisms. We used a long-term field experiment conducted at three locations in the Canadian prairies to verify that: (1) the level of cropping system diversity influences the α- and β-diversity of the prokaryotic community of canola (Brassica napus) rhizosphere; (2) the canola rhizosphere community has a stable prokaryotic core; and (3) some highly connected taxa of this community fit the description of hub-taxa. We sampled the rhizosphere of canola grown in monoculture, in a 2-phase rotation (canola-wheat), in a 3-phase rotation (pea-barley-canola), and in a highly diversified 6-phase rotation, five and eight years after cropping system establishment. We detected only one core bacterial Amplicon Sequence Variant (ASV) in the prokaryotic component of the microbiota of canola rhizosphere, a hub taxon identified as cf. Pseudarthrobacter sp. This ASV was also the only hub taxon found in the networks of interactions present in both years and at all three sites. We highlight a cohort of bacteria and archaea that were always connected with the core taxon in the network analyses.}, }
@article {pmid32846525, year = {2020}, author = {Jilani, H and Cilla, A and Barberá, R and Hamdi, M}, title = {Antiproliferative activity of green, black tea and olive leaves polyphenols subjected to biosorption and in vitro gastrointestinal digestion in Caco-2 cells.}, journal = {Food research international (Ottawa, Ont.)}, volume = {136}, number = {}, pages = {109317}, doi = {10.1016/j.foodres.2020.109317}, pmid = {32846525}, issn = {1873-7145}, abstract = {Olive (Olea europaea L.) leaves and tea (Camellia sinensis) are rich sources of bioactive compounds, especially polyphenols. Our previous studies have evidenced the potential use of Saccharomyces cerevisiae as a natural delivery system for these antioxidants and a means to improve their bioaccessibility in the human gut. In the present work, the antiproliferative effect of green tea (GT), black tea (BT) and olive leaves (OL) infusions and suspensions of S. cerevisiae were evaluated, for the first time, in human colon cancer cells (Caco-2) after biosorption and in vitro gastrointestinal digestion. The bioaccessible fractions (BF) were not overtly cytotoxic, not affecting cell viability. ROS and mitochondrial membrane potential changes (Δψm) values were reduced compared with control cells. Moreover, all the BF after biosorption induced a significant (p < 0.05) increase in cell proportions in S-phase. The arrest of the cell cycle was reversible without induction of apoptosis, suggesting that the biosorbed phenolics in both infusions and suspensions act as cytostatic agents.}, }
@article {pmid32845305, year = {2020}, author = {Imchen, M and Kumavath, R}, title = {Shotgun metagenomics reveals a heterogeneous prokaryotic community and a wide array of antibiotic resistance genes in mangrove sediment.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {10}, pages = {}, doi = {10.1093/femsec/fiaa173}, pmid = {32845305}, issn = {1574-6941}, abstract = {Saline tolerant mangrove forests partake in vital biogeochemical cycles. However, they are endangered due to deforestation as a result of urbanization. In this study, we have carried out a metagenomic snapshot of the mangrove ecosystem from five countries to assess its taxonomic, functional and antibiotic resistome structure. Chao1 alpha diversity varied significantly (P < 0.001) between the countries (Brazil, Saudi Arabia, China, India and Malaysia). All datasets were composed of 33 phyla dominated by eight major phyla covering >90% relative abundance. Comparative analysis of mangrove with terrestrial and marine ecosystems revealed the strongest heterogeneity in the mangrove microbial community. We also observed that the mangrove community shared similarities to both the terrestrial and marine microbiome, forming a link between the two contrasting ecosystems. The antibiotic resistant genes (ARG) resistome was comprised of nineteen level 3 classifications dominated by multidrug resistance efflux pumps (46.7 ± 4.3%) and BlaR1 family regulatory sensor-transducer disambiguation (25.2 ± 4.8%). ARG relative abundance was significantly higher in Asian countries and in human intervention datasets at a global scale. Our study shows that the mangrove microbial community and its antibiotic resistance are affected by geography as well as human intervention and are unique to the mangrove ecosystem. Understanding changes in the mangrove microbiome and its ARG is significant for sustainable development and public health.}, }
@article {pmid32845128, year = {2020}, author = {Ceron-Chafla, P and Kleerebezem, R and Rabaey, K and van Lier, JB and Lindeboom, REF}, title = {Direct and Indirect Effects of Increased CO2 Partial Pressure on the Bioenergetics of Syntrophic Propionate and Butyrate Conversion.}, journal = {Environmental science &amp; technology}, volume = {54}, number = {19}, pages = {12583-12592}, pmid = {32845128}, issn = {1520-5851}, abstract = {Simultaneous digestion and in situ biogas upgrading in high-pressure bioreactors will result in elevated CO2 partial pressure (pCO2). With the concomitant increase in dissolved CO2, microbial conversion processes may be affected beyond the impact of increased acidity. Elevated pCO2 was reported to affect the kinetics and thermodynamics of biochemical conversions because CO2 is an intermediate and end-product of the digestion process and modifies the carbonate equilibrium. Our results showed that increasing pCO2 from 0.3 to 8 bar in lab-scale batch reactors decreased the maximum substrate utilization rate (rsmax) for both syntrophic propionate and butyrate oxidation. These kinetic limitations are linked to an increased overall Gibbs free energy change (ΔGOverall) and a potential biochemical energy redistribution among syntrophic partners, which showed interdependence with hydrogen partial pressure (pH2). The bioenergetics analysis identified a moderate, direct impact of elevated pCO2 on propionate oxidation and a pH-mediated effect on butyrate oxidation. These constraints, combined with physiological limitations on growth exerted by increased acidity and inhibition due to higher concentrations of undissociated volatile fatty acids, help to explain the observed phenomena. Overall, this investigation sheds light on the role of elevated pCO2 in delicate biochemical syntrophic conversions by connecting kinetic, bioenergetic, and physiological effects.}, }
@article {pmid32844509, year = {2020}, author = {Zhu, X and Jackson, RD and DeLucia, EH and Tiedje, JM and Liang, C}, title = {The soil microbial carbon pump: From conceptual insights to empirical assessments.}, journal = {Global change biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/gcb.15319}, pmid = {32844509}, issn = {1365-2486}, support = {31930070//National Natural Science Foundation of China/ ; 41977051//National Natural Science Foundation of China/ ; GJTD-2019-10//K.C. Wong Education Foundation/ ; }, abstract = {The global soil carbon (C) pool is massive, so relatively small changes in soil organic carbon (SOC) stocks can significantly alter atmospheric C and global climate. The recently proposed concept of the soil microbial carbon pump (MCP) emphasizes the active role of soil microbes in SOC storage by integrating the continual microbial transformation of organic C from labile to persistent anabolic forms. However, the concept has not been evaluated with data. Here, we combine datasets, including microbial necromass biomarker amino sugars and SOC, from two long-term agricultural field studies conducted by large United States bioenergy research programs. We interrogate the soil MCP concept by investigating the asynchronous responses of microbial necromass and SOC to land-use change. Microbial necromass appeared to preferentially accumulate in soil and be the dominant contributor to SOC accrual in diversified perennial bioenergy crops. Specifically, ~92% of the additional SOC enhanced by plant diversity was estimated to be microbial necromass C, and >76% of the additional SOC enhanced by land-use transition from annual to perennial crops was estimated to be microbial necromass. This suggests that the soil MCP was stimulated in diversified perennial agroecosystems. We further delineate and suggest two parameters-soil MCP capacity and efficacy-reflecting the conversion of plant C into microbial necromass and the contribution of microbial necromass to SOC, respectively, that should serve as valuable metrics for future studies evaluating SOC storage under alternative management in changing climates.}, }
@article {pmid32843743, year = {2021}, author = {Khoruts, A and Staley, C and Sadowsky, MJ}, title = {Faecal microbiota transplantation for Clostridioides difficile: mechanisms and pharmacology.}, journal = {Nature reviews. Gastroenterology &amp; hepatology}, volume = {18}, number = {1}, pages = {67-80}, pmid = {32843743}, issn = {1759-5053}, abstract = {Faecal microbiota transplantation (FMT) has emerged as a remarkably successful treatment for recurrent Clostridioides difficile infection that cannot be cured with antibiotics alone. Understanding the complex biology and pathogenesis of C. difficile infection, which we discuss in this Perspective, is essential for understanding the potential mechanisms by which FMT cures this disease. Although FMT has already entered clinical practice, different microbiota-based products are currently in clinical trials and are vying for regulatory approval. However, all these therapeutics belong to an entirely new class of agents that require the development of a new branch of pharmacology. Characterization of microbiota therapeutics uses novel and rapidly evolving technologies and requires incorporation of microbial ecology concepts. Here, we consider FMT within a pharmacological framework, including its essential elements: formulation, pharmacokinetics and pharmacodynamics. From this viewpoint, multiple gaps in knowledge become apparent, identifying areas that require systematic research. This knowledge is needed to help clinical providers use microbiota therapeutics appropriately and to facilitate development of next-generation microbiota products with improved safety and efficacy. The discussion here is limited to FMT as a representative of microbiota therapeutics and recurrent C. difficile as the indication; however, consideration of the intrinsic basic principles is relevant to this entire class of microbiota-based therapeutics.}, }
@article {pmid32843539, year = {2020}, author = {Santillan, E and Constancias, F and Wuertz, S}, title = {Press Disturbance Alters Community Structure and Assembly Mechanisms of Bacterial Taxa and Functional Genes in Mesocosm-Scale Bioreactors.}, journal = {mSystems}, volume = {5}, number = {4}, pages = {}, pmid = {32843539}, issn = {2379-5077}, abstract = {Press disturbances are of interest in microbial ecology, as they can drive microbial communities to alternative stable states. However, the effect of press disturbances in community assembly mechanisms, particularly with regard to taxa and functional genes at different levels of abundance (i.e., common and rare), remains largely unknown. Here, we tested the effect of a continuous alteration in substrate feeding scheme on the structure, function, and assembly of bacterial communities. Two sets of replicate 5-liter sequencing batch reactors were operated at two different organic carbon loads for a period of 74 days, following 53 days of acclimation after inoculation with sludge from a full-scale treatment plant. Temporal dynamics of community taxonomic and functional gene structure were derived from metagenomics and 16S rRNA gene metabarcoding data. Disturbed reactors exhibited different community function, structure, and assembly compared to undisturbed reactors. Bacterial taxa and functional genes showed dissimilar α-diversity and community assembly patterns. Deterministic assembly mechanisms were generally stronger in disturbed reactors and in common fractions compared to rare ones. Function quickly recovered after the disturbance was removed, but community structure did not. Our results highlight that functional gene data from metagenomics can indicate patterns of community assembly that differ from those obtained from taxon data. This study reveals how a joint evaluation of assembly mechanisms and community structure of bacterial taxa and functional genes as well as ecosystem function can unravel the response of complex microbial systems to a press disturbance.IMPORTANCE Ecosystem management must be viewed in the context of increasing frequencies and magnitudes of various disturbances that occur at different scales. This work provides a glimpse of the changes in assembly mechanisms found in microbial communities exposed to sustained changes in their environment. These mechanisms, deterministic or stochastic, can cause communities to reach a similar or variable composition and function. For a comprehensive view, we use a joint evaluation of temporal dynamics in assembly mechanisms and community structure for both bacterial taxa and their functional genes at different abundance levels, in both disturbed and undisturbed states. We further reverted the disturbance state to contrast recovery of function with community structure. Our findings are relevant, as very few studies have employed such an approach, while there is a need to assess the relative importance of assembly mechanisms for microbial communities across different spatial and temporal scales, environmental gradients, and types of disturbance.}, }
@article {pmid32842646, year = {2020}, author = {Finore, I and Vigneron, A and Vincent, WF and Leone, L and Di Donato, P and Schiano Moriello, A and Nicolaus, B and Poli, A}, title = {Novel Psychrophiles and Exopolymers from Permafrost Thaw Lake Sediments.}, journal = {Microorganisms}, volume = {8}, number = {9}, pages = {}, pmid = {32842646}, issn = {2076-2607}, support = {UMI-MicroMeNu//Program Sentinel North financed by the Canada First Research Excellence Fund (CFREF); the Natural Sciences and Engineering Research Council of Canada (NSERC); the CNR (Italy)-Université Laval UMI-MicroMeNu program; the Fonds de Recherche du Québec-Nature/ ; }, abstract = {Thermokarst lakes are one of the most abundant types of microbial ecosystems in the circumpolar North. These shallow basins are formed by the thawing and collapse of ice-rich permafrost, with subsequent filling by snow and ice melt. Until now, permafrost thaw lakes have received little attention for isolation of microorganisms by culture-based analysis. The discovery of novel psychrophiles and their biomolecules makes these extreme environments suitable sources for the isolation of new strains, including for potential biotechnological applications. In this study, samples of bottom sediments were collected from three permafrost thaw lakes in subarctic Québec, Canada. Their diverse microbial communities were characterized by 16S rRNA gene amplicon analysis, and subsamples were cultured for the isolation of bacterial strains. Phenotypic and genetic characterization of the isolates revealed affinities to the genera Pseudomonas, Paenibacillus, Acinetobacter,Staphylococcus and Sphingomonas. The isolates were then evaluated for their production of extracellular enzymes and exopolymers. Enzymes of potential biotechnological interest included α and β-glucosidase, α and β-maltosidase, β-xylosidase and cellobiohydrolase. One isolate, Pseudomonas extremaustralis strain 2ASCA, also showed the capability to produce, in the loosely bound cell fraction, a levan-type polysaccharide with a yield of 613 mg/L of culture, suggesting its suitability as a candidate for eco-sustainable alternatives to commercial polymers.}, }
@article {pmid32841483, year = {2020}, author = {Mammola, S and Amorim, IR and Bichuette, ME and Borges, PAV and Cheeptham, N and Cooper, SJB and Culver, DC and Deharveng, L and Eme, D and Ferreira, RL and Fišer, C and Fišer, Ž and Fong, DW and Griebler, C and Jeffery, WR and Jugovic, J and Kowalko, JE and Lilley, TM and Malard, F and Manenti, R and Martínez, A and Meierhofer, MB and Niemiller, ML and Northup, DE and Pellegrini, TG and Pipan, T and Protas, M and Reboleira, ASPS and Venarsky, MP and Wynne, JJ and Zagmajster, M and Cardoso, P}, title = {Fundamental research questions in subterranean biology.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {95}, number = {6}, pages = {1855-1872}, doi = {10.1111/brv.12642}, pmid = {32841483}, issn = {1469-185X}, support = {N1-0069//Javna Agencija za Raziskovalno Dejavnost RS/ ; 745530//H2020 Marie Skłodowska-Curie Actions/ ; eLTER//Horizon 2020 Framework Programme/ ; R01 EY024941/EY/NEI NIH HHS/United States ; 678193//Horizon 2020 Framework Programme/ ; CF19-0609//Carlsbergfondet/ ; 15471//Villum Fonden/ ; 882221//H2020 Marie Skłodowska-Curie Actions/ ; ANR-15-CE32-0005//Agence Nationale de la Recherche/ ; RDP 00092-18//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; }, abstract = {Five decades ago, a landmark paper in Science titled The Cave Environment heralded caves as ideal natural experimental laboratories in which to develop and address general questions in geology, ecology, biogeography, and evolutionary biology. Although the 'caves as laboratory' paradigm has since been advocated by subterranean biologists, there are few examples of studies that successfully translated their results into general principles. The contemporary era of big data, modelling tools, and revolutionary advances in genetics and (meta)genomics provides an opportunity to revisit unresolved questions and challenges, as well as examine promising new avenues of research in subterranean biology. Accordingly, we have developed a roadmap to guide future research endeavours in subterranean biology by adapting a well-established methodology of 'horizon scanning' to identify the highest priority research questions across six subject areas. Based on the expert opinion of 30 scientists from around the globe with complementary expertise and of different academic ages, we assembled an initial list of 258 fundamental questions concentrating on macroecology and microbial ecology, adaptation, evolution, and conservation. Subsequently, through online surveys, 130 subterranean biologists with various backgrounds assisted us in reducing our list to 50 top-priority questions. These research questions are broad in scope and ready to be addressed in the next decade. We believe this exercise will stimulate research towards a deeper understanding of subterranean biology and foster hypothesis-driven studies likely to resonate broadly from the traditional boundaries of this field.}, }
@article {pmid32840670, year = {2020}, author = {Nikouli, E and Meziti, A and Smeti, E and Antonopoulou, E and Mente, E and Kormas, KA}, title = {Gut Microbiota of Five Sympatrically Farmed Marine Fish Species in the Aegean Sea.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01580-z}, pmid = {32840670}, issn = {1432-184X}, abstract = {In this study, we hypothesized that sympatrically grown farmed fish, i.e. fish which experience similar environmental conditions and nutritionally similar diets, would have more convergent gut microbiota. Using a &quot;common garden&quot; approach, we identified the core microbiota and bacterial community structure differences between five fish species farmed in the same aquaculture site on the west coast of the Aegean Sea, Greece. The investigated individuals were at similar developmental stages and reared in adjacent (< 50 m) aquaculture cages; each cage had 15 kg fish m-3. The diets were nutritionally similar to support optimal growth for each fish species. DNA from the midgut of 3-6 individuals per fish species was extracted and sequenced for the V3-V4 region of the bacterial 16S rRNA. Only 3.9% of the total 181 operational taxonomic units (OTUs) were shared among all fish. Between 5 and 74 OTUs were unique to each fish species. Each of the investigated fish species had a distinct profile of dominant OTUs, i.e. cumulative relative abundance of ≥ 80%. Co-occurrence network analysis for each fish species showed that all networks were strongly dominated by positive correlations between the abundances of their OTUs. However, each fish species had different network characteristics suggesting the differential significance of the OTUs in each of the five fish species midgut. The results of the present study may provide evidence that adult fish farmed in the Mediterranean Sea have a rather divergent and species-specific gut microbiota profile, which are shaped independently of the similar environmental conditions under which they grow.}, }
@article {pmid32840024, year = {2020}, author = {Sizikov, S and Burgsdorf, I and Handley, KM and Lahyani, M and Haber, M and Steindler, L}, title = {Characterization of sponge-associated Verrucomicrobia: microcompartment-based sugar utilization and enhanced toxin-antitoxin modules as features of host-associated Opitutales.}, journal = {Environmental microbiology}, volume = {22}, number = {11}, pages = {4669-4688}, doi = {10.1111/1462-2920.15210}, pmid = {32840024}, issn = {1462-2920}, support = {1243/16//Israel Science Foundation/ ; }, abstract = {Bacteria of the phylum Verrucomicrobia are ubiquitous in marine environments and can be found as free-living organisms or as symbionts of eukaryotic hosts. Little is known about host-associated Verrucomicrobia in the marine environment. Here we reconstructed two genomes of symbiotic Verrucomicrobia from bacterial metagenomes derived from the Atlanto-Mediterranean sponge Petrosia ficiformis and three genomes from strains that we isolated from offshore seawater of the Eastern Mediterranean Sea. Phylogenomic analysis of these five strains indicated that they are all members of Verrucomicrobia subdivision 4, order Opitutales. We compared these novel sponge-associated and seawater-isolated genomes to closely related Verrucomicrobia. Genomic analysis revealed that Planctomycetes-Verrucomicrobia microcompartment gene clusters are enriched in the genomes of symbiotic Opitutales including sponge symbionts but not in free-living ones. We hypothesize that in sponge symbionts these microcompartments are used for degradation of l-fucose and l-rhamnose, which are components of algal and bacterial cell walls and therefore may be found at high concentrations in the sponge tissue. Furthermore, we observed an enrichment of toxin-antitoxin modules in symbiotic Opitutales. We suggest that, in sponges, verrucomicrobial symbionts utilize these modules as a defence mechanism against antimicrobial activity deriving from the abundant microbial community co-inhabiting the host.}, }
@article {pmid32839879, year = {2020}, author = {Noskov, YA and Kabilov, MR and Polenogova, OV and Yurchenko, YA and Belevich, OE and Yaroslavtseva, ON and Alikina, TY and Byvaltsev, AM and Rotskaya, UN and Morozova, VV and Glupov, VV and Kryukov, VY}, title = {A Neurotoxic Insecticide Promotes Fungal Infection in Aedes aegypti Larvae by Altering the Bacterial Community.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01567-w}, pmid = {32839879}, issn = {1432-184X}, support = {18-74-00090//Russian Science Foundation (RU)/ ; }, abstract = {Symbiotic bacteria have a significant impact on the formation of defensive mechanisms against fungal pathogens and insecticides. The microbiome of the mosquito Aedes aegypti has been well studied; however, there are no data on the influence of insecticides and pathogenic fungi on its structure. The fungus Metarhizium robertsii and a neurotoxic insecticide (avermectin complex) interact synergistically, and the colonization of larvae with hyphal bodies is observed after fungal and combined (conidia + avermectins) treatments. The changes in the bacterial communities (16S rRNA) of Ae. aegypti larvae under the influence of fungal infection, avermectin toxicosis, and their combination were studied. In addition, we studied the interactions between the fungus and the predominant cultivable bacteria in vitro and in vivo after the coinfection of the larvae. Avermectins increased the total bacterial load and diversity. The fungus decreased the diversity and insignificantly increased the bacterial load. Importantly, avermectins reduced the relative abundance of Microbacterium (Actinobacteria), which exhibited a strong antagonistic effect towards the fungus in in vitro and in vivo assays. The avermectin treatment led to an increased abundance of Chryseobacterium (Flavobacteria), which exerted a neutral effect on mycosis development. In addition, avermectin treatment led to an elevation of some subdominant bacteria (Pseudomonas) that interacted synergistically with the fungus. We suggest that avermectins change the bacterial community to favor the development of fungal infection.}, }
@article {pmid32836127, year = {2020}, author = {Li, X and Wang, T and Chang, SX and Jiang, X and Song, Y}, title = {Biochar increases soil microbial biomass but has variable effects on microbial diversity: A meta-analysis.}, journal = {The Science of the total environment}, volume = {749}, number = {}, pages = {141593}, doi = {10.1016/j.scitotenv.2020.141593}, pmid = {32836127}, issn = {1879-1026}, mesh = {Biomass ; *Carbon ; Charcoal ; *Soil ; Soil Microbiology ; }, abstract = {Biochar has been extensively studied as a soil amendment for carbon sequestration and for improving soil quality; however, a systematic understanding of the responses of soil microbial biomass and diversity to biochar addition is lacking. Here, a meta-analysis of 999 paired data points from 194 studies shows that biochar increases microbial biomass but has variable effects on microbial diversity. Generally, the effects of biochar on microbial biomass are dependent on biochar properties, while that on microbial diversity is dependent on soil properties. The application of biochar, particularly that produced under low temperature and from nutrient-rich feedstocks, could better increase soil microbial biomass (based on phospholipid fatty acid analysis (MBCPLFA)) and diversity. The increases of total microbial biomass with biochar addition are greater in the field than in laboratory studies, in sandy than in clay soils, and when measured by fumigation-extraction (MBCFE) than by MBCPLFA. The bacterial biomass only significantly increases in laboratory studies and fungal biomass only in soils with pH ≤ 7.5 and soil organic carbon ≤30 g kg-1. The increases in total microbial diversity with biochar addition were greater in acidic and sandy soils with low soil organic carbon content and in laboratory incubation studies. In addition, long-term and low-rate addition of biochar always increases microbial diversity. To better guide the use of biochar as a soil amendment, we suggest that establishing long-term and field studies, using a standard method for measuring microbial communities, on different soil types should be our emphasis in future research.}, }
@article {pmid32835181, year = {2020}, author = {Kirubakaran, R and ArulJothi, KN and Revathi, S and Shameem, N and Parray, JA}, title = {Emerging priorities for microbial metagenome research.}, journal = {Bioresource technology reports}, volume = {11}, number = {}, pages = {100485}, pmid = {32835181}, issn = {2589-014X}, abstract = {Overwhelming anthropogenic activities lead to deterioration of natural resources and the environment. The microorganisms are considered desirable, due to their suitability for easy genetic manipulation and handling. With the aid of modern biotechnological techniques, the culturable microorganisms have been widely exploited for the benefit of mankind. Metagenomics, a powerful tool to access the abundant biodiversity of the environmental samples including the unculturable microbes, to determine microbial diversity and population structure, their ecological roles and expose novel genes of interest. This review focuses on the microbial adaptations to the adverse environmental conditions, metagenomic techniques employed towards microbial biotechnology. Metagenomic approach helps to understand microbial ecology and to identify useful microbial derivatives like antibiotics, toxins, and enzymes with diverse and enhanced function. It also summarizes the application of metagenomics in clinical diagnosis, improving microbial ecology, therapeutics, xenobiotic degradation and impact on agricultural crops.}, }
@article {pmid32834061, year = {2020}, author = {D'Abramo, F and Neumeyer, S}, title = {A historical and political epistemology of microbes.}, journal = {Centaurus; international magazine of the history of science and medicine}, volume = {62}, number = {2}, pages = {321-330}, pmid = {32834061}, issn = {0008-8994}, abstract = {This article traces the historical co-evolution of microbiology, bacteriology, and virology, framed within industrial and agricultural contexts, as well as their role in colonial and national history between the end of the 19th century and the first decades of the 20th century. The epistemology of germ theory, coupled with the economic interests of European colonies, has shaped the understanding of human-microbial relationships in a reductionist way. We explore a brief history of the medical and biological sciences, focusing on microbes and the difficulty of implementing germ theory outside of biology laboratories. Furthermore, we highlight the work of Lynn Margulis, who conceptualized microbes within their ecological contexts. Such research shows the active role microbes play in handling life-sustaining biological and biochemical processes. We outline how the industrial and technological advancements of the last two centuries not only impacted almost all human societies, but also changed the world on microbial, biological, and geological levels. The narration of these histories is a complex task, and depends on how national, international, and intergovernmental institutions (such as the World Health Organization) conceive of the selective environmental pressures exerted by industry and biotechnological companies.}, }
@article {pmid32832265, year = {2020}, author = {Li, X and Li, Z and He, Y and Li, P and Zhou, H and Zeng, N}, title = {Regional distribution of Christensenellaceae and its associations with metabolic syndrome based on a population-level analysis.}, journal = {PeerJ}, volume = {8}, number = {}, pages = {e9591}, pmid = {32832265}, issn = {2167-8359}, abstract = {The link between the gut microbiota and metabolic syndrome (MetS) has attracted widespread attention. Christensenellaceae was recently described as an important player in human health, while its distribution and relationship with MetS in Chinese population is still unknown. This study sought to observe the association between Christensenellaceae and metabolic indexes in a large sample of residents in South China. A total of 4,781 people from the GGMP project were included, and the fecal microbiota composition of these individuals was characterized by 16S rRNA sequencing and analyzed the relation between Christensenellaceae and metabolism using QIIME (Quantitative Insight Into Microbial Ecology, Version 1.9.1). The results demonstrated that microbial richness and diversity were increased in the group with a high abundance of Christensenellaceae, who showed a greater complexity of the co-occurrence network with other bacteria than residents who lacked Christensenellaceae. The enriched bacterial taxa were predominantly represented by Oscillospira, Ruminococcaceae, RF39, Rikenellaceae and Akkermansia as the Christensenellaceae abundance increased, while the abundances of Veillonella, Fusobacterium and Klebsiella were significantly reduced. Furthermore, Christensenellaceae was negatively correlated with the pathological features of MetS, such as obesity, hypertriglyceridemia and body mass index (BMI). We found reduced levels of lipid biosynthesis and energy metabolism pathways in people with a high abundance of Christensenellaceae, which may explain the negative relationship between body weight and Christensenellaceae. In conclusion, we found a negative correlation between Christensenellaceae and MetS in a large Chinese population and reported the geographical distribution of Christensenellaceae in the GGMP study. The association data from this population-level research support the investigation of strains within Christensenellaceae as potentially beneficial gut microbes.}, }
@article {pmid32830554, year = {2020}, author = {Van Hul, M and Karnik, K and Canene-Adams, K and De Souza, M and Van den Abbeele, P and Marzorati, M and Delzenne, NM and Everard, A and Cani, PD}, title = {Comparison of the effects of soluble corn fiber and fructooligosaccharides on metabolism, inflammation, and gut microbiome of high-fat diet-fed mice.}, journal = {American journal of physiology. Endocrinology and metabolism}, volume = {319}, number = {4}, pages = {E779-E791}, doi = {10.1152/ajpendo.00108.2020}, pmid = {32830554}, issn = {1522-1555}, mesh = {Animals ; Body Composition ; Body Weight ; Diet, High-Fat/*adverse effects ; Dietary Fiber/*pharmacology ; Energy Metabolism/drug effects ; Gastrointestinal Microbiome/*drug effects ; *Inflammation ; Insulin Resistance ; Male ; Metabolism/*drug effects ; Mice ; Mice, Inbred C57BL ; Oligosaccharides/*pharmacology ; Probiotics ; *Zea mays ; }, abstract = {Dietary fibers are essential components of a balanced diet and have beneficial effects on metabolic functions. To gain insight into their impact on host physiology and gut microbiota, we performed a direct comparison of two specific prebiotic fibers in mice. During an 8-wk follow up, mice fed a high-fat diet (HFD) were compared with mice on a normal diet (basal condition, controls) and to mice fed the HFD but treated with one of the following prebiotics: fructooligosaccharides (FOS) or soluble corn fiber (SCF). Both prebiotic fibers led to a similar reduction of body weight and fat mass, lower inflammation and improved metabolic parameters. However, these health benefits were the result of different actions of the fibers, as SCF impacted energy excretion, whereas FOS did not. Interestingly, both fibers had very distinct gut microbial signatures with different short-chain fatty acid profiles, indicating that they do not favor the growth of the same bacterial communities. Although the prebiotic potential of different fibers may seem physiologically equivalent, our data show that the underlying mechanisms of action are different, and this by targeting different gut microbes. Altogether, our data provide evidence that beneficial health effects of specific dietary fibers must be documented to be considered a prebiotic and that studies devoted to understanding how structures relate to specific microbiota modulation and metabolic effects are warranted.}, }
@article {pmid32830371, year = {2020}, author = {Mukherjee, I and Salcher, MM and Andrei, AŞ and Kavagutti, VS and Shabarova, T and Grujčić, V and Haber, M and Layoun, P and Hodoki, Y and Nakano, SI and Šimek, K and Ghai, R}, title = {A freshwater radiation of diplonemids.}, journal = {Environmental microbiology}, volume = {22}, number = {11}, pages = {4658-4668}, doi = {10.1111/1462-2920.15209}, pmid = {32830371}, issn = {1462-2920}, support = {MSM200961801//Akademie Věd České Republiky/ ; 17-04828S//Grant Agency of the Czech Republic/ ; 19-23469S//Grant Agency of the Czech Republic/ ; 20-12496X//Grant Agency of the Czech Republic/ ; 022/2019/P//Grant Agency of the University of South Bohemia/ ; 116/2019/P//Grant Agency of the University of South Bohemia/ ; JSPS-17-17//JSPS Bilateral Japanese-Czech Joint Research Project/ ; 310030_185108/SNSF_/Swiss National Science Foundation/Switzerland ; }, abstract = {Diplonemids are considered marine protists and have been reported among the most abundant and diverse eukaryotes in the world oceans. Recently we detected the presence of freshwater diplonemids in Japanese deep freshwater lakes. However, their distribution and abundances in freshwater ecosystems remain unknown. We assessed abundance and diversity of diplonemids from several geographically distant deep freshwater lakes of the world by amplicon-sequencing, shotgun metagenomics and catalysed reporter deposition-fluorescent in situ hybridization (CARD-FISH). We found diplonemids in all the studied lakes, albeit with low abundances and diversity. We assembled long 18S rRNA sequences from freshwater diplonemids and showed that they form a new lineage distinct from the diverse marine clades. Freshwater diplonemids are a sister-group to a marine clade, which are mainly isolates from coastal and bay areas, suggesting a recent habitat transition from marine to freshwater habitats. Images of CARD-FISH targeted freshwater diplonemids suggest they feed on bacteria. Our analyses of 18S rRNA sequences retrieved from single-cell genomes of marine diplonemids show they encode multiple rRNA copies that may be very divergent from each other, suggesting that marine diplonemid abundance and diversity both have been overestimated. These results have wider implications on assessing eukaryotic abundances in natural habitats by using amplicon-sequencing alone.}, }
@article {pmid32829442, year = {2020}, author = {Cabrerizo, MJ and Marañón, E}, title = {Grazing Pressure Is Independent of Prey Size in a Generalist Herbivorous Protist: Insights from Experimental Temperature Gradients.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01578-7}, pmid = {32829442}, issn = {1432-184X}, support = {PGC2018-094553B-I00//Ministerio de Ciencia, Innovación y Universidades/ ; FJCI2017-32318//Ministerio de Ciencia, Innovación y Universidades/ ; }, abstract = {Grazing by herbivorous protists contributes to structuring plankton communities through its effect on the growth, biomass, and competitiveness of prey organisms and also impacts the transfer of primary production towards higher trophic levels. Previous evidence shows that heterotrophic processes (grazing rates, g) are more sensitive to temperature than autotrophic ones (phytoplankton growth rates, μ) and also that small cells tend to be more heavily predated than larger ones; however, it remains unresolved how the interplay between changes in temperature and cell size modulates grazing pressure (i.e., g:μ ratio). We addressed this problem by conducting an experiment with four phytoplankton populations, from pico- to microphytoplankton, over a 12 °C gradient and in the presence/absence of a generalist herbivorous protist, Oxyrrhis marina. We found that highest g rates coincided with highest μ rates, which corresponded to intermediate cell sizes. There were no significant differences in either μ or g between the smallest and largest cell sizes considered. The g:μ ratio was largely independent of cell size and C:N ratios, and its thermal dependence was low although species-specific differences were large. We suggest that the similar g:μ found could be the consequence that the energetic demand imposed by rising temperatures would be a more important issue than the mechanical constriction to ingestion derived from prey cell size. Despite the difficulty of quantifying μ and g in natural planktonic communities, we suggest that the g:μ ratio is a key response variable to evaluate thermal sensitivity of food webs because it gives a more integrative view of trophic functioning than both rates separately.}, }
@article {pmid32829441, year = {2020}, author = {Silveira, R and Silva, MRSS and de Roure Bandeira de Mello, T and Alvim, EACC and Marques, NCS and Kruger, RH and da Cunha Bustamante, MM}, title = {Bacteria and Archaea Communities in Cerrado Natural Pond Sediments.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01574-x}, pmid = {32829441}, issn = {1432-184X}, support = {process number 193.000.567/2009//Fundação de Apoio à Pesquisa do Distrito Federal/ ; }, abstract = {Natural ponds in the Brazilian Cerrado harbor high biodiversity but are still poorly studied, especially their microbial assemblage. The characterization of the microbial community in aquatic environments is fundamental for understanding its functioning, particularly under the increasing pressure posed by land conversion and climate change. Here, we aim to characterize the structure (abundance, richness, and diversity) and composition of the Bacteria and Archaea in the sediment of two natural ponds belonging to different basins that primarily differ in size and depth in the Cerrado. Sediment samples were collected in the dry and rainy seasons and the transition periods between both. The structure and composition of Bacteria and Archaea were assessed by 16S rRNA gene pyrosequencing. We identified 45 bacterial and four archaeal groups. Proteobacteria and Acidobacteria dominated the bacterial community, while Euryarchaeota and Thaumarchaeota dominated the archaeal community. Seasonal fluctuations in the relative abundance of microbial taxa were observed, but pond characteristics were more determinant to community composition differences. Microbial communities are highly diverse, and local variability could partially explain the microbial structure's main differences. Functional predictions based in 16S rRNA gene accessed with Tax4Fun indicated an enriched abundance of predicted methane metabolism in the deeper pond, where higher abundance of methanogenic archaea Methanocella, Methanosaeta, and Methanomicrobiaceae was detected. Our dataset encompasses the more comprehensive survey of prokaryotic microbes in Cerrado's aquatic environments. Here, we present basic and essential information about composition and diversity, for initial insights into the ecology of Bacteria and Archaea in these environments.}, }
@article {pmid32829154, year = {2021}, author = {Jamwal, R and Amit,  and Kumari, S and Balan, B and Kelly, S and Cannavan, A and Singh, DK}, title = {Rapid and non-destructive approach for the detection of fried mustard oil adulteration in pure mustard oil via ATR-FTIR spectroscopy-chemometrics.}, journal = {Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy}, volume = {244}, number = {}, pages = {118822}, doi = {10.1016/j.saa.2020.118822}, pmid = {32829154}, issn = {1873-3557}, abstract = {Attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy integrated with chemometrics was effectively applied for the rapid detection and accurate quantification of fried mustard oil (FMO) adulteration in pure mustard oil (PMO). PMO was adulterated with FMO in the range of 0.5-50% v/v. Principal component analysis (PCA) elucidated the studied adulteration using two components with an explained variance of 97%. The linear discriminant analysis (LDA) was adopted to classify the adulterated PMO samples with FMO. LDA model showed 100% accuracy initially, as well as when cross-validated. To enhance the overall quality of models, characteristic spectral regions were optimized, and principal component regression (PCR) and partial least square regression (PLS-R) models were constructed with high accuracy and precision. PLS-R model for the 2nd derivative of the optimized spectral region 1260-1080 cm-1 showed best results for prediction sample sets in terms of high R2 and residual predictive deviation (RPD) value of 0.999 and 31.91 with low root mean square error (RMSE) and relative prediction error (RE %) of 0.53% v/v and 3.37% respectively. Thus, the suggested method can detect up to 0.5% v/v of adulterated FMO in PMO in a short time interval.}, }
@article {pmid32829116, year = {2020}, author = {Sakarika, M and Candry, P and Depoortere, M and Ganigué, R and Rabaey, K}, title = {Impact of substrate and growth conditions on microbial protein production and composition.}, journal = {Bioresource technology}, volume = {317}, number = {}, pages = {124021}, doi = {10.1016/j.biortech.2020.124021}, pmid = {32829116}, issn = {1873-2976}, mesh = {Biomass ; *Carbon ; }, abstract = {Production of microbial protein (MP) from recovered resources - e.g. CO2-sourced formate and acetate - could provide protein while enabling CO2 capture. To assess the protein quality obtained from this process, pure cultures and enriched communities were selected and characterized kinetically, stoichiometrically and nutritionally. Growth on acetate resulted in up to 5.3 times higher maximum specific growth rate (μmax) than formate (i.e. 0.15-0.41 h-1 for acetate compared to 0.061-0.29 h-1 for formate at pH = 7). The protein content was a function of the growth phase, with the highest values during stationary phase, ranging between 18 and 82%CDW protein depending on the organism and substrate. The negative correlation between biomass productivity and protein content indicated a trade-off between production rate and product quality. The final product (i.e. dried MP) quality was in most cases superior to soybean and all cultures were rich in threonine, phenylalanine and tyrosine, regardless of the carbon source.}, }
@article {pmid32827977, year = {2020}, author = {Dai, H and Gao, J and Wang, S and Li, D and Wang, Z}, title = {The key active degrader, metabolic pathway and microbial ecology of triclosan biodegradation in an anoxic/oxic system.}, journal = {Bioresource technology}, volume = {317}, number = {}, pages = {124014}, doi = {10.1016/j.biortech.2020.124014}, pmid = {32827977}, issn = {1873-2976}, mesh = {Bacteria/genetics ; Biodegradation, Environmental ; Drug Resistance, Microbial ; Metabolic Networks and Pathways ; *Triclosan ; }, abstract = {A lab-scale anoxic/oxic (A/O) system was used to reveal the key active triclosan-degrading bacteria (TCS-DB) in this study. The results showed that TCS was mainly removed by metabolism of heterotrophic bacteria (accounting for about 62%), and the potential metabolic pathway was the break of ether bond in TCS formed 2,4-dichlorophenol, and further dechlorination formed phenol or other metabolic end products. DNA-based stable isotope probing (DNA-SIP) assay further revealed that Methylobacillus accounting for 20.75% in 13C sample was the key active TCS-DB. Furthermore, methylotrophy and methanol oxidation were found to be the potential metabolic routes of TCS degradation by functional annotation of prokaryotic taxa analysis. Interestingly, TCS accelerated the propagation of antibiotic resistance genes (fabI) and intI1 which positively correlated with several functional microorganisms (p < 0.05). This study contributes to comprehend the potential mechanism, metabolic pathway and microbial ecology of TCS biodegradation in A/O system.}, }
@article {pmid32827089, year = {2020}, author = {Maher, AMD and Asaiyah, M and Quinn, S and Burke, R and Wolff, H and Bode, HB and Griffin, CT}, title = {Competition and Co-existence of Two Photorhabdus Symbionts with a Nematode Host.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01573-y}, pmid = {32827089}, issn = {1432-184X}, support = {16/RI/3399/SFI_/Science Foundation Ireland/Ireland ; }, abstract = {Photorhabdus spp. (Enterobacteriales: Morganellaceae) occur exclusively as symbionts of Heterorhabditis nematodes for which they provide numerous services, including killing insects and providing nutrition and defence within the cadavers. Unusually, two species (Photorhabdus cinerea and Photorhabdus temperata) associate with a single population of Heterorhabditis downesi at a dune grassland site. Building on previous work, we investigated competition between these two Photorhabdus species both at the regional (between insects) and local (within insect) level by trait comparison and co-culture experiments. There was no difference between the species with respect to supporting nematode reproduction and protection of cadavers against invertebrate scavengers, but P. cinerea was superior to P. temperata in several traits: faster growth rate, greater antibacterial and antifungal activity and colonisation of a higher proportion of nematodes in co-culture. Moreover, where both bacterial symbionts colonised single nematode infective juveniles, P. cinerea tended to dominate in numbers. Differences between Photorhabdus species were detected in the suite of secondary metabolites produced: P. temperata produced several compounds not produced by P. cinerea including anthraquinone pigments. Bioluminescence emitted by P. temperata also tended to be brighter than that from P. cinerea. Bioluminescence and pigmentation may protect cadavers against scavengers that rely on sight. We conclude that while P. cinerea may show greater local level (within-cadaver) competitive success, co-existence of the two Photorhabdus species in the spatially heterogeneous environment of the dunes is favoured by differing specialisations in defence of the cadaver against differing locally important threats.}, }
@article {pmid32826215, year = {2020}, author = {Gofstein, TR and Perkins, M and Field, J and Leigh, MB}, title = {The Interactive Effects of Crude Oil and Corexit 9500 on Their Biodegradation in Arctic Seawater.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {21}, pages = {}, pmid = {32826215}, issn = {1098-5336}, support = {RL5 GM118990/GM/NIGMS NIH HHS/United States ; TL4 GM118992/GM/NIGMS NIH HHS/United States ; UL1 GM118991/GM/NIGMS NIH HHS/United States ; }, mesh = {Arctic Regions ; Bacteria/*metabolism ; Biodegradation, Environmental ; *Lipids ; *Microbiota ; Petroleum/*metabolism ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Seawater/microbiology ; }, abstract = {The risk of petroleum spills coupled with the potential application of chemical dispersants as a spill response strategy necessitates further understanding of the fate of oil and dispersants and their interactive effects during biodegradation. Using Arctic seawater mesocosms amended with either crude oil, Corexit 9500, or both together, we quantified the chemical losses of crude oil and Corexit 9500 and identified microbial taxa implicated in their biodegradation based on shifts in the microbial community structure over a 30-day time course. Chemical analyses included total petroleum hydrocarbons (TPH), n-alkanes, branched alkanes, and polycyclic aromatic hydrocarbons (PAHs) for oil loss and the surfactant components dioctyl sodium sulfosuccinate (DOSS), Span 80, Tween 80, Tween 85, and the DOSS metabolite ethylhexyl sulfosuccinate (EHSS) for Corexit loss. Changes to the microbial communities and identification of key taxa were determined by 16S rRNA gene amplicon sequencing. The nonionic surfactants of Corexit 9500 (Span 80 and Tweens 80 and 85) biodegraded rapidly, dropping to below the limits of detection within 5 days and prior to any detectable initiation of oil biodegradation. This resulted in no observable suppression of petroleum biodegradation in the presence of Corexit compared to that of oil alone. In contrast, biodegradation of DOSS was delayed in the presence of oil, based on the prolonged presence of DOSS and accumulation of the degradation intermediate EHSS that did not occur in the absence of oil. Microbial analyses revealed that oil and Corexit enriched different overall microbial communities, with the presence of both resulting in a community composition that shifted from one more similar to that of Corexit only to one reflecting the oil-only community over time, in parallel with the degradation of predominantly Corexit and then oil components. Some microbial taxa (Oleispira, Pseudofulvibacter, and Roseobacter) responded to either oil or Corexit, suggesting that some organisms may be capable of utilizing both substrates. Together, these findings reveal interactive effects of crude oil and Corexit 9500 on chemical losses and microbial communities as they biodegrade, providing further insight into their fate when copresent in the environment.IMPORTANCE Chemical dispersants such as Corexit 9500 are commonly used in oil spill response and are currently under consideration for use in the Arctic, where their fate and effects have not been well studied. This research was performed to determine the interactive effects of the copresence of crude oil and Corexit 9500 on the degradation of components from each mixture and the associated microbial community structure over time in Arctic seawater. These findings will help yield a better understanding of the biodegradability of dispersant components applied to an oi