@article {pmid30775415, year = {2018}, author = {Photos-Jones, E and Knapp, CW and Venieri, D and Christidis, GE and Elgy, C and Valsami-Jones, E and Gounaki, I and Andriopoulou, NC}, title = {Greco-Roman mineral (litho)therapeutics and their relationship to their microbiome: The case of the red pigment miltos.}, journal = {Journal of archaeological science, reports}, volume = {22}, number = {}, pages = {179-192}, doi = {10.1016/j.jasrep.2018.07.017}, pmid = {30775415}, issn = {2352-409X}, abstract = {This paper introduces a holistic approach to the study of Greco-Roman (G-R) lithotherapeutics. These are the minerals or mineral combinations that appear in the medical and scientific literature of the G-R world. It argues that they can best be described not simply in terms of their bulk chemistry/mineralogy but also their ecological microbiology and nanofraction component. It suggests that each individual attribute may have underpinned the bioactivity of the lithotherapeutic as an antibacterial, antifungal or other. We focus on miltos, the highly prized, naturally fine, red iron oxide-based mineral used as a pigment, in boat maintenance, agriculture and medicine. Five samples (four geological (from Kea, N. Cyclades) and one archaeological (from Lemnos, NE Aegean)) of miltos were analyzed with physical and biological science techniques. We show that: a. Kean miltos and Lemnian earth/miltos must have been chemically and mineralogically different; b. Lemnian miltos must have been more effective as an antibacterial against specific pathogens (Gram + and Gram - bacteria) than its Kean counterpart; c. two samples of Kean miltos, although similar, chemically, mineralogically and eco-microbiologically (phylum/class level), nevertheless, displayed different antibacterial action. We suggest that this may constitute proof of microbial ecology playing an important role in effecting bioactivity and, interestingly, at the more specific genus/species level. From the perspective of the historian of G-R science, we suggest that it may have been on account of its bioactivity, rather than simply its 'red-staining' effect, that miltos gained prominent entry into the scientific and medical literature of the G-R world.}, }
@article {pmid30772540, year = {2019}, author = {Reid, T and Droppo, IG and Chaganti, SR and Weisener, CG}, title = {Microbial metabolic strategies for overcoming low-oxygen in naturalized freshwater reservoirs surrounding the Athabasca Oil Sands: A proxy for End-Pit Lakes?.}, journal = {The Science of the total environment}, volume = {665}, number = {}, pages = {113-124}, doi = {10.1016/j.scitotenv.2019.02.032}, pmid = {30772540}, issn = {1879-1026}, abstract = {The success and sustainability of aquatic ecosystems are driven by the complex, cooperative metabolism of microbes. Ecological engineering strategies often strive to harness this syntrophic synergy of microbial metabolism for the reclamation of contaminated environments worldwide. Currently, there is a significant knowledge gap in our understanding of how the natural microbial ecology overcomes thermodynamic limitations in recovering contaminated environments. Here, we used in-situ metatranscriptomics and associated metataxonomic analyses on sediments collected from naturalized freshwater man-made reservoirs within the Athabasca Oil Sands region of Alberta, Canada. These reservoirs are unique since they are untouched by industrial mining processes and serve as representative endpoints for model landscape reconstruction. Results indicate that a microbial syntrophic cooperation has been established represented by the oxygenic and anoxygenic phototrophs, sustained through the efficient use of novel cellular mechanistic adaptations tailored to these unique thermodynamic conditions. Specifically, chemotaxis transcripts (cheY & MCPs-methyl-accepting chemotaxis proteins) were highly expressed, suggesting a highly active microbial response to gradients in environmental stimuli, resulting indirectly from hydrocarbon compound alteration. A high expression of photosynthetic activity, likely sustaining nutrient delivery to the similarly highly expressed methanogenic community acting in syntrophy during the breakdown of organics. Overall the more diversified functionality within sub-oxic sample locations indicates an ability to maintain efficient metabolism under thermodynamic constraints. This is the first study to holistically identify and characterize these types of in-situ, metabolic processes and address their thermodynamic feasibility within a global context for large landscape reconstruction. These characterizations of regional, natural landscapes surrounding the oil sands mining operation are severely lacking, but truly provide invaluable insight into end-point goals and targets for reclamation procedures.}, }
@article {pmid30771735, year = {2019}, author = {Petersen, C and Wankhade, UD and Bharat, D and Wong, K and Mueller, JE and Chintapalli, SV and Piccolo, BD and Jalili, T and Jia, Z and Symons, JD and Shankar, K and Anandh Babu, PV}, title = {Dietary supplementation with strawberry induces marked changes in the composition and functional potential of the gut microbiome in diabetic mice.}, journal = {The Journal of nutritional biochemistry}, volume = {66}, number = {}, pages = {63-69}, doi = {10.1016/j.jnutbio.2019.01.004}, pmid = {30771735}, issn = {1873-4847}, abstract = {Gut microbiota contributes to the biological activities of berry anthocyanins by transforming them into bioactive metabolites, and anthocyanins support the growth of specific bacteria, indicating a two-way relationship between anthocyanins and microbiota. In the present study, we tested the hypothesis that strawberry supplementation alters gut microbial ecology in diabetic db/db mice. Control (db/+) and diabetic (db/db) mice (7 weeks old) consumed standard diet or diet supplemented with 2.35% freeze-dried strawberry (db/db+SB) for 10 weeks. Colon contents were used to isolate bacterial DNA. V4 variable region of 16S rRNA gene was amplified. Data analyses were performed using standardized pipelines (QIIME 1.9 and R packages). Differences in predictive metagenomics function were identified by PICRUSt. Principal coordinate analyses confirmed that the microbial composition was significantly influenced by both host genotype and strawberry consumption. Further, α-diversity indices and β-diversity were different at the phylum and genus levels, and genus and operational taxonomical units levels, respectively (P<.05). At the phylum level, strawberry supplementation decreased the abundance of Verrucomicrobia in db/db+SB vs. db/db mice (P<.05). At the genus level, db/db mice exhibited a decrease in the abundance of Bifidobacterium, and strawberry supplementation increased Bifidobacterium in db/db+SB vs. db/db mice (P<.05). PICRUSt revealed significant differences in 45 predicted metabolic functions among the 3 groups. Our study provides evidence for marked changes in the composition and functional potential of the gut microbiome with strawberry supplementation in diabetic mice. Importantly, strawberry supplementation increased the abundance of beneficial bacteria Bifidobacterium which play a pivotal role in the metabolism of anthocyanins.}, }
@article {pmid30770943, year = {2019}, author = {Lewis, RW and Islam, A and Opdahl, L and Davenport, JR and Sullivan, TS}, title = {Comparative Genomics, Siderophore Production, and Iron Scavenging Potential of Root Zone Soil Bacteria Isolated from 'Concord' Grape Vineyards.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01324-8}, pmid = {30770943}, issn = {1432-184X}, support = {3319-3259//Washington State Concord Grape Research Council/ ; 3019-8894/3387//Washington State University Center for Sustaining Agriculture and Natural Resources/ ; }, abstract = {Iron (Fe) deficiency in crop production is a worldwide problem which often results in chlorosis in grapevines, particularly in calcareous soils. Siderophores secreted by microorganisms and Strategy II plants can chelate Fe and other metals in soil solution, and siderophore-Fe complexes can then be utilized by plants and microbes. Plants may also shift rhizosphere conditions to favor siderophore-producing microbes, which can increase plant available Fe. Between-row cover crops (barley, rye, wheat, wheat/vetch) were planted as living mulch to address grapevine chlorosis by enhancing soil health in two vineyards in central Washington. The objectives of the current study were to (1) enrich for siderophore-producing organisms from within the indigenous rooting zone community of 'Concord' grapevines, and (2) perform comparative genomics on putative siderophore producing organisms to assess potentially important Fe acquisition-related functional domains and protein families. A high-throughput, chrome azurol S (CAS)-based enrichment assay was used to select siderophore-producing microbes from 'Concord' grapevine root zone soil. Next-generation whole genome sequencing allowed the assembly and annotation of ten full genomes. Phylogenetic analysis revealed two distinct clades among the genomes using the 40 nearest neighbors available in the public database, all of which were of the Pseudomonas genus. Significant differences in functional domain abundances were observed between the clades including iron acquisition and metabolism of amino acids, carbon, nitrogen, phosphate, and sulfur. Diverse mechanisms of Fe uptake and siderophore production/uptake were identified in the protein families of the genomes. The sequenced organisms are likely pseudomonads which are well-suited for iron scavenging, suggesting a potential role in Fe turnover in vineyard systems.}, }
@article {pmid30769104, year = {2019}, author = {Conrads, G and Abdelbary, MMH}, title = {Challenges of Next-Generation Sequencing targeting Anaerobes.}, journal = {Anaerobe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.anaerobe.2019.02.006}, pmid = {30769104}, issn = {1095-8274}, abstract = {Next-generation sequencing allows for investigating the composition of microbiomes that are associated with infection (clinical microbiology) or dysbiosis (microbial ecology). The most commonly applied short-read sequencing technologies are Illumina MiSeq/HiSeq and Ion Torrent PGM, however, other platforms that generate long-reads are under way and optimized. A pre-condition for representative results is an appropriate method for contamination-free collection, homogenization, storage of specimens and a subsequent efficient DNA extraction protocol. As some of the anaerobes such as Clostridia or anaerobe Archaea are robust while others of the same environment, such as spirochetes, possess a very thin cell wall, a chemico-mechanical lysing strategy is recommended but with some precautions to avoid DNA-sheering and overheating. For amplicon sequencing, the Silva-TestPrime online tool helps to find the optimal 16S directed primers for individual studies. For metagenome profiling, the classifier tool has to be selected with helpful decision trees available but a combination based on different strategies seems to be indispensable. Further development of both hard- and software is needed before microbiome results become free of a substantial technology-dependent bias.}, }
@article {pmid30768364, year = {2019}, author = {Kain, V and Van Der Pol, W and Mariappan, N and Ahmad, A and Eipers, P and Gibson, DL and Gladine, C and Vigor, C and Durand, T and Morrow, C and Halade, GV}, title = {Obesogenic diet in aging mice disrupts gut microbe composition and alters neutrophil:lymphocyte ratio, leading to inflamed milieu in acute heart failure.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {}, number = {}, pages = {fj201802477R}, doi = {10.1096/fj.201802477R}, pmid = {30768364}, issn = {1530-6860}, abstract = {Calorie-dense obesogenic diet (OBD) is a prime risk factor for cardiovascular disease in aging. However, increasing age coupled with changes in the diet can affect the interaction of intestinal microbiota influencing the immune system, which can lead to chronic inflammation. How age and calorie-enriched OBD interact with microbial flora and impact leukocyte profiling is currently under investigated. Here, we tested the interorgan hypothesis to determine whether OBD in young and aging mice alters the gut microbe composition and the splenic leukocyte profile in acute heart failure (HF). Young (2-mo-old) and aging (18-mo-old) mice were supplemented with standard diet (STD, ∼4% safflower oil diet) and OBD (10% safflower oil) for 2 mo and then subjected to coronary artery ligation to induce myocardial infarction. Fecal samples were collected pre- and post-diet intervention, and the microbial flora were analyzed using 16S variable region 4 rRNA gene DNA sequencing and Quantitative Insights Into Microbial Ecology informatics. The STD and OBD in aging mice resulted in an expansion of the genus Allobaculum in the fecal microbiota. However, we found a pathologic change in the neutrophil:lymphocyte ratio in aging mice in comparison with their young counterparts. Thus, calorie-enriched OBD dysregulated splenic leukocytes by decreasing immune-responsive F4/80+ and CD169+ macrophages in aging mice. OBD programmed neutrophil swarming with an increase in isoprostanoid levels, with dysregulation of lipoxygenases, cytokines, and metabolite-sensing receptor expression. In summary, calorie-dense OBD in aging mice disrupted the composition of the gut microbiome, which correlates with the development of integrative and system-wide nonresolving inflammation in acute HF.-Kain, V., Van Der Pol, W., Mariappan, N., Ahmad, A., Eipers, P., Gibson, D. L., Gladine, C., Vigor, C., Durand, T., Morrow, C., Halade, G. V. Obesogenic diet in aging mice disrupts gut microbe composition and alters neutrophil:lymphocyte ratio, leading to inflamed milieu in acute heart failure.}, }
@article {pmid30767956, year = {2019}, author = {Bai, J and Jhaney, I and Daniel, G and Watkins Bruner, D}, title = {Pilot Study of Vaginal Microbiome Using QIIME 2™ in Women With Gynecologic Cancer Before and After Radiation Therapy.}, journal = {Oncology nursing forum}, volume = {46}, number = {2}, pages = {E48-E59}, doi = {10.1188/19.ONF.E48-E59}, pmid = {30767956}, issn = {1538-0688}, abstract = {OBJECTIVES: To characterize the vaginal microbiome using QIIME 2™ (Quantitative Insights Into Microbial Ecology 2) in women with gynecologic cancer.<br><br>SAMPLE &amp;AMP; SETTING: 19 women with gynecologic cancer before and after radiation therapy at a comprehensive cancer center in Atlanta, Georgia.<br><br>METHODS &amp;AMP; VARIABLES: This pilot study analyzed vaginal microbiome communities using a microbiome analysis pipeline, beginning with 16S rRNA gene sequencing and processing through use of a bioinformatics pipeline to downstream microbial statistical analysis.<br><br>RESULTS: The findings showed the methods to be robust, and most women with gynecologic cancer showed depletion of Lactobacillus. Compared to those pre-radiation therapy, women post-radiation therapy showed higher abundances of Mobiluncus, Atopobium, and Prevotella but lower abundances of Lactobacillus, Gardnerella, and Peptostreptococcus, which are associated with bacterial vaginosis.<br><br>IMPLICATIONS FOR NURSING: This study presents the fundamentals of human microbiome data collection and analysis methods to inform nursing science. Assessing the vaginal microbiome provides a potential pathway to develop interventions to ameliorate dysbiosis of the vaginal microbiome.}, }
@article {pmid30762095, year = {2019}, author = {Martínez-Rodríguez, P and Rolán-Alvarez, E and Del Mar Pérez-Ruiz, M and Arroyo-Yebras, F and Carpena-Catoira, C and Carvajal-Rodríguez, A and Bella, JL}, title = {Geographic and Temporal Variation of Distinct Intracellular Endosymbiont Strains of Wolbachia sp. in the Grasshopper Chorthippus parallelus: a Frequency-Dependent Mechanism?.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01338-2}, pmid = {30762095}, issn = {1432-184X}, support = {CGL2016-75482-P//Ministerio de Ciencia y Tecnolog?a/ ; BFU2013-44635//Ministerio de Econom?a, Industria y Competitividad, Gobierno de Espa?a/ ; }, abstract = {Wolbachia is an intracellular endosymbiont that can produce a range of effects on host fitness, but the temporal dynamics of Wolbachia strains have rarely been experimentally evaluated. We compare interannual strain frequencies along a geographical region for understanding the forces that shape Wolbachia strain frequency in natural populations of its host, Chorthippus parallelus (Orthoptera, Acrididae). General linear models show that strain frequency changes significantly across geographical and temporal scales. Computer simulation allows to reject the compatibility of the observed patterns with either genetic drift or sampling errors. We use consecutive years to estimate total Wolbachia strain fitness. Our estimation of Wolbachia fitness is significant in most cases, within locality and between consecutive years, following a negatively frequency-dependent trend. Wolbachia spp. B and F strains show a temporal pattern of variation that is compatible with a negative frequency-dependent natural selection mechanism. Our results suggest that such a mechanism should be at least considered in future experimental and theoretical research strategies that attempt to understand Wolbachia biodiversity.}, }
@article {pmid30761424, year = {2019}, author = {Parera-Valadez, Y and Yam-Puc, A and López-Aguiar, LK and Borges-Argáez, R and Figueroa-Saldivar, MA and Cáceres-Farfán, M and Márquez-Velázquez, NA and Prieto-Davó, A}, title = {Ecological Strategies Behind the Selection of Cultivable Actinomycete Strains from the Yucatan Peninsula for the Discovery of Secondary Metabolites with Antibiotic Activity.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01329-3}, pmid = {30761424}, issn = {1432-184X}, support = {CVU223481//Consejo Nacional de Ciencia y Tecnolog?a/ ; PNC//Consejo Nacional de Ciencia y Tecnolog?a/ ; TA200212, TA200415//Direcci?n General de Asuntos del Personal Acad?mico, Universidad Nacional Aut?noma de M?xico/ ; }, abstract = {The quest for novel natural products has recently focused on the marine environment as a source for novel microorganisms. Although isolation of marine-derived actinomycete strains is now common, understanding their distribution in the oceans and their adaptation to this environment can be helpful in the selection of isolates for further novel secondary metabolite discovery. This study explores the taxonomic diversity of marine-derived actinomycetes from distinct environments in the coastal areas of the Yucatan Peninsula and their adaptation to the marine environment as a first step towards novel natural product discovery. The use of simple ecological principles, for example, phylogenetic relatedness to previously characterized actinomycetes or seawater requirements for growth, to recognize isolates with adaptations to the ocean in an effort to select for marine-derived actinomycete to be used for further chemical studies. Marine microbial environments are an important source of novel bioactive natural products and, together with methods such as genome mining for detection of strains with biotechnological potential, ecological strategies can bring useful insights in the selection and identification of marine-derived actinomycetes for novel natural product discovery.}, }
@article {pmid30761423, year = {2019}, author = {Purahong, W and Kahl, T and Krüger, D and Buscot, F and Hoppe, B}, title = {Home-Field Advantage in Wood Decomposition Is Mainly Mediated by Fungal Community Shifts at &quot;Home&quot; Versus &quot;Away&quot;.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01334-6}, pmid = {30761423}, issn = {1432-184X}, support = {KR 3587/1-1, KR 3587/3-2//Deutsche Forschungsgemeinschaft/ ; BU 941/17-1//Deutsche Forschungsgemeinschaft/ ; }, abstract = {The home-field advantage (HFA) hypothesis has been used intensively to study leaf litter decomposition in various ecosystems. However, the HFA in woody substrates is still unexplored. Here, we reanalyzed and integrated existing datasets on various groups of microorganisms collected from natural deadwood of two temperate trees, Fagus sylvatica and Picea abies, from forests in which one or other of these species dominates but where both are present. Our aims were (i) to test the HFA hypothesis on wood decomposition rates of these two temperate tree species, and (ii) to investigate if HFA hypothesis can be explained by diversity and community composition of bacteria and in detail N-fixing bacteria (as determined by molecular 16S rRNA and nifH gene amplification) and fungi (as determined by molecular ITS rRNA amplification and sporocarp surveys). Our results showed that wood decomposition rates were accelerated at &quot;home&quot; versus &quot;away&quot; by 38.19% ± 20.04% (mean ± SE). We detected strong changes in fungal richness (increase 36-50%) and community composition (RANOSIM = 0.52-0.60, P < 0.05) according to HFA hypothesis. The changes of fungi were much stronger than for total bacteria and nitrogen fixing for both at richness and community composition levels. In conclusion, our results support the HFA hypothesis in deadwood: decomposition rate is accelerated at home due to specialization of fungal communities produced by the plant community above them. Furthermore, the higher richness of fungal sporocarps and nitrogen-fixing bacteria (nifH) may stimulate or at least stabilize wood decomposition rates at &quot;home&quot; versus &quot;away.&quot;}, }
@article {pmid30759613, year = {2019}, author = {Wang, X and Li, X and Yu, L and Huang, L and Xiu, J and Lin, W and Zhang, Y}, title = {Characterizing the microbiome in petroleum reservoir flooded by different water sources.}, journal = {The Science of the total environment}, volume = {653}, number = {}, pages = {872-885}, doi = {10.1016/j.scitotenv.2018.10.410}, pmid = {30759613}, issn = {1879-1026}, abstract = {Petroleum reservoir is an unusual subsurface biosphere, where indigenous microbes lived and evolved for million years. However, continual water injection changed the situation by introduction of new electron acceptors, donors and exogenous microbes. In this study, 16S-rRNA gene sequencing, comparative metagenomics and genomic bins reconstruction were employed to investigate the microbial community and metabolic potential in three typical water-flooded blocks of the Shen84 oil reservoir in Liaohe oil field, China. The results showed significant difference of microbial community compositions and metabolic characteristics existed between the injected water and the produced water/oil mixtures; however, there was considerable uniformity between the produced samples in different blocks. Microbial communities in the produced fluids were dominated by exogenous facultative microbes such as Pseudomonas and Thauera members from Proteobacteria phylum. Metabolic potentials for O2-dependent hydrocarbon degradation, dissimilarly nitrate reduction, and thiosulfate‑sulfur oxidation were much more abundant, whereas genes involved in dissimilatory sulfate reduction, anaerobic hydrocarbon degradation and methanogenesis were less abundant in the oil reservoir. Statistical analysis indicated the water composition had an obvious influence on microbial community composition and metabolic potential. The water-flooding process accompanied with introduction of nitrate or nitrite, and dissolved oxygen promoted the alteration of microbiome in oil reservoir from slow-growing anaerobic indigenous microbes (such as Thermotoga, Clostridia, and Syntrophobacter) to fast-growing opportunists as Beta- and Gama- Proteobacteria. The findings of this study shed light on the microbial ecology change in water flooded petroleum reservoir.}, }
@article {pmid30759269, year = {2019}, author = {Semenec, L and Vergara, IA and Laloo, AE and Mathews, ER and Bond, PL and Franks, AE}, title = {Enhanced Growth of Pilin-Deficient Geobacter sulfurreducens Mutants in Carbon Poor and Electron Donor Limiting Conditions.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01316-8}, pmid = {30759269}, issn = {1432-184X}, support = {N626909-13-1-N259//Office of Naval Research Global/ ; FA2386-14-1-4032//Asian Office of Aerospace Research and Development/ ; LP140100459//Australian Research Council/ ; }, abstract = {Geobacter sulfurreducens pili enable extracellular electron transfer and play a role in secretion of c-type cytochromes such as OmcZ. PilA-deficient mutants of G. sulfurreducens have previously been shown to accumulate cytochromes within their membranes. This cytochrome retaining phenotype allowed for enhanced growth of PilA-deficient mutants in electron donor and carbon-limited conditions where formate and fumarate are provided as the sole electron donor and acceptor with no supplementary carbon source. Conversely, wild-type G. sulfurreducens, which has normal secretion of cytochromes, has comparative limited growth in these conditions. This growth is further impeded for OmcZ-deficient and OmcS-deficient mutants. A PilB-deficient mutant which prevents pilin production but allows for secretion of OmcZ had moderate growth in these conditions, indicating a role for cytochrome localization to enabling survival in the electron donor and carbon-limited conditions. To determine which pathways enhanced growth using formate, Sequential Window Acquisition of all Theoretical Mass Spectra mass spectrometry (SWATH-MS) proteomics of formate adapted PilA-deficient mutants and acetate grown wild type was performed. PilA-deficient mutants had an overall decrease in tricarboxylic acid (TCA) cycle enzymes and significant upregulation of electron transport chain associated proteins including many c-type cytochromes and [NiFe]-hydrogenases. Whole genome sequencing of the mutants shows strong convergent evolution and emergence of genetic subpopulations during adaptation to growth on formate. The results described here suggest a role for membrane constrained c-type cytochromes to the enhancement of survival and growth in electron donor and carbon-limited conditions.}, }
@article {pmid30759084, year = {2019}, author = {Hawinkel, S and Kerckhof, FM and Bijnens, L and Thas, O}, title = {A unified framework for unconstrained and constrained ordination of microbiome read count data.}, journal = {PloS one}, volume = {14}, number = {2}, pages = {e0205474}, doi = {10.1371/journal.pone.0205474}, pmid = {30759084}, issn = {1932-6203}, abstract = {Explorative visualization techniques provide a first summary of microbiome read count datasets through dimension reduction. A plethora of dimension reduction methods exists, but many of them focus primarily on sample ordination, failing to elucidate the role of the bacterial species. Moreover, implicit but often unrealistic assumptions underlying these methods fail to account for overdispersion and differences in sequencing depth, which are two typical characteristics of sequencing data. We combine log-linear models with a dispersion estimation algorithm and flexible response function modelling into a framework for unconstrained and constrained ordination. The method is able to cope with differences in dispersion between taxa and varying sequencing depths, to yield meaningful biological patterns. Moreover, it can correct for observed technical confounders, whereas other methods are adversely affected by these artefacts. Unlike distance-based ordination methods, the assumptions underlying our method are stated explicitly and can be verified using simple diagnostics. The combination of unconstrained and constrained ordination in the same framework is unique in the field and facilitates microbiome data exploration. We illustrate the advantages of our method on simulated and real datasets, while pointing out flaws in existing methods. The algorithms for fitting and plotting are available in the R-package RCM.}, }
@article {pmid30758801, year = {2019}, author = {Kiewra, D and Czułowska, A and Dyczko, D and Zieliński, R and Plewa-Tutaj, K}, title = {First record of Haemaphysalis concinna (Acari: Ixodidae) in Lower Silesia, SW Poland.}, journal = {Experimental &amp; applied acarology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s10493-019-00344-w}, pmid = {30758801}, issn = {1572-9702}, abstract = {Haemaphysalis concinna Koch is one of 19 species of the genus Haemaphysalis which has been reported in the Palearctic region. In Europe, the presence of H. concinna ticks has been reported in numerous countries. In Poland, to date, the precise occurrence of H. concinna was known only from one site in the north-western region. This paper shows that H. concinna ticks can be considered a typical example of the tick fauna occurring in Lower Silesia, SW Poland. Tick monitoring was conducted using a standard flagging method in 24 sites in the various forest types of Lower Silesia. Among 1622 host-seeking ticks collected, H. concinna accounted for 2.7%. From the collected H. concinna there were: 25 (58.1%) larvae, 15 (34.9%) nymphs, 1 (2.3%) female, and 2 (4.7%) males. The presence of H. concinna was confirmed in 6 out of 24 tested sites in fresh mixed broadleaf forests, fresh mixed coniferous forests and in pastures.}, }
@article {pmid30756135, year = {2019}, author = {Singer, D and Metz, S and Unrein, F and Shimano, S and Mazei, Y and Mitchell, EAD and Lara, E}, title = {Contrasted Micro-Eukaryotic Diversity Associated with Sphagnum Mosses in Tropical, Subtropical and Temperate Climatic Zones.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01325-7}, pmid = {30756135}, issn = {1432-184X}, support = {310003A//Schweizerischer Nationalfonds zur F?rderung der Wissenschaftlichen Forschung/ ; 143960//Schweizerischer Nationalfonds zur F?rderung der Wissenschaftlichen Forschung/ ; ASTF 520 - 2015//European Molecular Biology Organization/ ; FONCyT PICT-2014-1290//Consejo Nacional de Investigaciones Cient?ficas y T?cnicas/ ; }, abstract = {Sphagnum-dominated ecosystem plays major roles as carbon sinks at the global level. Associated microbial communities, in particular, eukaryotes, play significant roles in nutrient fixation and turnover. In order to understand better the ecological processes driven by these organisms, the first step is to characterise these associated organisms. We characterised the taxonomic diversity, and from this, inferred the functional diversity of microeukaryotes in Sphagnum mosses in tropical, subtropical and temperate climatic zones through an environmental DNA diversity metabarcoding survey of the V9 region of the gene coding for the RNA of the small subunit of the ribosomes (SSU rRNA). As microbial processes are strongly driven by temperatures, we hypothesised that saprotrophy would be highest in warm regions, whereas mixotrophy, an optimal strategy in oligotrophic environments, would peak under colder climates. Phylotype richness was higher in tropical and subtropical climatic zones than in the temperate region, mostly due to a higher diversity of animal parasites (i.e. Apicomplexa). Decomposers, and especially opportunistic yeasts and moulds, were more abundant under warmer climates, while mixotrophic organisms were more abundant under temperate climates. The dominance of decomposers, suggesting a higher heterotrophic activity under warmer climates, is coherent with the generally observed faster nutrient cycling at lower latitudes; this phenomenon is likely enhanced by higher inputs of nutrients most probably brought in the system by Metazoa, such as arthropods.}, }
@article {pmid30755506, year = {2019}, author = {Hausmann, B and Pelikan, C and Rattei, T and Loy, A and Pester, M}, title = {Long-Term Transcriptional Activity at Zero Growth of a Cosmopolitan Rare Biosphere Member.}, journal = {mBio}, volume = {10}, number = {1}, pages = {}, doi = {10.1128/mBio.02189-18}, pmid = {30755506}, issn = {2150-7511}, abstract = {Microbial diversity in the environment is mainly concealed within the rare biosphere (all species with <0.1% relative abundance). While dormancy explains a low-abundance state very well, the mechanisms leading to rare but active microorganisms remain elusive. We used environmental systems biology to genomically and transcriptionally characterize &quot;Candidatus Desulfosporosinus infrequens,&quot; a low-abundance sulfate-reducing microorganism cosmopolitan to freshwater wetlands, where it contributes to cryptic sulfur cycling. We obtained its near-complete genome by metagenomics of acidic peat soil. In addition, we analyzed anoxic peat soil incubated under in situ-like conditions for 50 days by Desulfosporosinus-targeted qPCR and metatranscriptomics. The Desulfosporosinus population stayed at a constant low abundance under all incubation conditions, averaging 1.2 × 106 16S rRNA gene copies per cm³ soil. In contrast, transcriptional activity of &quot;Ca. Desulfosporosinus infrequens&quot; increased at day 36 by 56- to 188-fold when minor amendments of acetate, propionate, lactate, or butyrate were provided with sulfate, compared to the no-substrate-control. Overall transcriptional activity was driven by expression of genes encoding ribosomal proteins, energy metabolism, and stress response but not by expression of genes encoding cell growth-associated processes. Since our results did not support growth of these highly active microorganisms in terms of biomass increase or cell division, they had to invest their sole energy for maintenance, most likely counterbalancing acidic pH conditions. This finding explains how a rare biosphere member can contribute to a biogeochemically relevant process while remaining in a zero-growth state over a period of 50 days.IMPORTANCE The microbial rare biosphere represents the largest pool of biodiversity on Earth and constitutes, in sum of all its members, a considerable part of a habitat's biomass. Dormancy or starvation is typically used to explain the persistence of low-abundance microorganisms in the environment. We show that a low-abundance microorganism can be highly transcriptionally active while remaining in a zero-growth state for at least 7 weeks. Our results provide evidence that this zero growth at a high cellular activity state is driven by maintenance requirements. We show that this is true for a microbial keystone species, in particular a cosmopolitan but permanently low-abundance sulfate-reducing microorganism in wetlands that is involved in counterbalancing greenhouse gas emissions. In summary, our results provide an important step forward in understanding time-resolved activities of rare biosphere members relevant for ecosystem functions.}, }
@article {pmid30747342, year = {2019}, author = {Faulkner, M and Zhao, LS and Barrett, S and Liu, LN}, title = {Self-Assembly Stability and Variability of Bacterial Microcompartment Shell Proteins in Response to the Environmental Change.}, journal = {Nanoscale research letters}, volume = {14}, number = {1}, pages = {54}, doi = {10.1186/s11671-019-2884-3}, pmid = {30747342}, issn = {1931-7573}, support = {UF120411//Royal Society/ ; RG130442//Royal Society/ ; URF\R\180030//Royal Society/ ; RGF\EA\180233//Royal Society/ ; BB/M024202/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R003890/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {Bacterial microcompartments (BMCs) are proteinaceous self-assembling organelles that are widespread among the prokaryotic kingdom. By segmenting key metabolic enzymes and pathways using a polyhedral shell, BMCs play essential roles in carbon assimilation, pathogenesis, and microbial ecology. The BMC shell is composed of multiple protein homologs that self-assemble to form the defined architecture. There is tremendous interest in engineering BMCs to develop new nanobioreactors and molecular scaffolds. Here, we report the quantitative characterization of the formation and self-assembly dynamics of BMC shell proteins under varying pH and salt conditions using high-speed atomic force microscopy (HS-AFM). We show that 400-mM salt concentration is prone to result in larger single-layered shell patches formed by shell hexamers, and a higher dynamic rate of hexamer self-assembly was observed at neutral pH. We also visualize the variability of shell proteins from hexameric assemblies to fiber-like arrays. This study advances our knowledge about the stability and variability of BMC protein self-assemblies in response to microenvironmental changes, which will inform rational design and construction of synthetic BMC structures with the capacity of remodeling their self-assembly and structural robustness. It also offers a powerful toolbox for quantitatively assessing the self-assembly and formation of BMC-based nanostructures in biotechnology applications.}, }
@article {pmid30746494, year = {2019}, author = {Tecon, R and Mitri, S and Ciccarese, D and Or, D and van der Meer, JR and Johnson, DR}, title = {Bridging the Holistic-Reductionist Divide in Microbial Ecology.}, journal = {mSystems}, volume = {4}, number = {1}, pages = {}, doi = {10.1128/mSystems.00265-18}, pmid = {30746494}, issn = {2379-5077}, abstract = {Microbial communities are inherently complex systems. To address this complexity, microbial ecologists are developing new, more elaborate laboratory models at an ever-increasing pace. These model microbial communities and habitats have opened up the exploration of new territories that lie between the simplicity and controllability of &quot;synthetic&quot; systems and the convolution and complexity of natural environments. Here, we discuss this classic methodological divide, we propose a conceptual perspective that integrates new research developments, and we sketch a 3-point possible roadmap to cross the divide between controllability and complexity in microbial ecology.}, }
@article {pmid30745899, year = {2018}, author = {Eveillard, D and Bouskill, NJ and Vintache, D and Gras, J and Ward, BB and Bourdon, J}, title = {Probabilistic Modeling of Microbial Metabolic Networks for Integrating Partial Quantitative Knowledge Within the Nitrogen Cycle.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3298}, doi = {10.3389/fmicb.2018.03298}, pmid = {30745899}, issn = {1664-302X}, abstract = {Understanding the interactions between microbial communities and their environment sufficiently to predict diversity on the basis of physicochemical parameters is a fundamental pursuit of microbial ecology that still eludes us. However, modeling microbial communities is problematic, because (i) communities are complex, (ii) most descriptions are qualitative, and (iii) quantitative understanding of the way communities interact with their surroundings remains incomplete. One approach to overcoming such complications is the integration of partial qualitative and quantitative descriptions into more complex networks. Here we outline the development of a probabilistic framework, based on Event Transition Graph (ETG) theory, to predict microbial community structure across observed chemical data. Using reverse engineering, we derive probabilities from the ETG that accurately represent observations from experiments and predict putative constraints on communities within dynamic environments. These predictions can feedback into the future development of field experiments by emphasizing the most important functional reactions, and associated microbial strains, required to characterize microbial ecosystems.}, }
@article {pmid30743865, year = {2018}, author = {Pikaar, I and de Vrieze, J and Rabaey, K and Herrero, M and Smith, P and Verstraete, W}, title = {Carbon emission avoidance and capture by producing in-reactor microbial biomass based food, feed and slow release fertilizer: Potentials and limitations.}, journal = {The Science of the total environment}, volume = {644}, number = {}, pages = {1525-1530}, doi = {10.1016/j.scitotenv.2018.07.089}, pmid = {30743865}, issn = {1879-1026}, abstract = {To adhere to the Paris Agreement of 2015, we need to store several Gigatonnes (Gt) of carbon annually. In the last years, a variety of technologies for carbon capture and storage (CCS) and carbon capture and usage (CCU) have been demonstrated. While conventional CCS and CCU are techno-economically feasible, their climate change mitigation potentials are limited, due to limited amount of CO2 that can be captured. Hence, there is an urgent need to explore other CCS and CCU routes. Here we discuss an interesting alternative route for capture of carbon dioxide from industrial point sources, using CO2-binding, so-called autotrophic aerobic bacteria to produce microbial biomass as a C-storage product. The produced microbial biomass is often referred to as microbial protein (MP) because it has a crude protein content of ~70-75%. Depending on the industrial production process and final quality of the produced MP, it can be used for human consumption as meat replacement, protein supplement in animal diets, or slow-release organic fertilizer thus providing both organic nitrogen and carbon to agricultural soils. Here, we discuss the potentials and limitations of this so far unexplored CCU approach. A preliminary assessment of the economic feasibility of the different routes for CO2 carbon avoidance, capture and utilization indicates that the value chain to food is becoming attractive and that the other end-points warrant close monitoring over the coming years.}, }
@article {pmid30742313, year = {2019}, author = {Noor, NM and Defoirdt, T and Alipiah, N and Karim, M and Daud, H and Natrah, I}, title = {Quorum sensing is required for full virulence of Vibrio campbellii towards tiger grouper (Epinephelus fuscoguttatus) larvae.}, journal = {Journal of fish diseases}, volume = {}, number = {}, pages = {}, doi = {10.1111/jfd.12946}, pmid = {30742313}, issn = {1365-2761}, support = {BOF-UGent//Universiteit Gent/ ; GP-HIP/2018/9598400//Universiti Putra Malaysia/ ; //Malaysian Ministry of Education/ ; }, abstract = {The link between quorum sensing in Vibrio campbellii and its virulence towards tiger grouper (Epinephelus fuscoguttatus) was investigated using V. campbellii wild type and quorum-sensing mutants with inactive quorum sensing or constitutively maximal quorum-sensing activity, and signal molecule synthase mutants. The results showed that wild-type V. campbellii is pathogenic to grouper larvae, causing more than 50% mortality after 4 days of challenge. Furthermore, the mortality of larvae challenged with the mutant with maximally active quorum sensing was significantly higher than that of larvae challenged with the wild type, whereas a higher survival was observed in the larvae challenged to the mutant with a completely inactive quorum-sensing system. Grouper larvae challenged with either the signal molecule synthase triple mutant, the harveyi autoinducer-1 (HAI-1) synthase mutant and the autoinducer-2 (AI-2) synthase mutant showed higher survival than larvae challenged with the wild type. In contrast, larvae challenged with the cholerae autoinducer-1 (CAI-1) synthase mutant showed high mortality. This indicates that HAI-1 and AI-2, but not CAI-1, are required for full virulence of V. campbellii towards grouper larvae. Our data suggest that quorum-sensing inhibition could be an effective strategy to control V. campbellii infections in tiger grouper.}, }
@article {pmid30740279, year = {2019}, author = {Lee, KM and Adams, M and Klassen, JL}, title = {Evaluation of DESS as a storage medium for microbial community analysis.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e6414}, doi = {10.7717/peerj.6414}, pmid = {30740279}, issn = {2167-8359}, abstract = {Microbial ecology research requires sampling strategies that accurately represent the microbial community under study. These communities must typically be transported from the collection location to the laboratory and then stored until they can be processed. However, there is a lack of consensus on how best to preserve microbial communities during transport and storage. Here, we evaluated dimethyl sulfoxide, ethylenediamine tetraacetic acid, saturated salt (DESS) solution as a broadly applicable preservative for microbial ecology experiments. We stored fungus gardens grown by the ant Trachymyrmex septentrionalis in DESS, 15% glycerol, and phosphate buffered saline (PBS) to test their impact on the fungus garden microbial community. Variation in microbial community structure due to differences in preservative type was minimal when compared to variation between ant colonies. Additionally, DESS preserved the structure of a defined mock community more faithfully than either 15% glycerol or PBS. DESS is inexpensive, easy to transport, and effective in preserving microbial community structure. We therefore conclude that DESS is a valuable preservative for use in microbial ecology research.}, }
@article {pmid30739147, year = {2019}, author = {Pastor, A and Freixa, A and Skovsholt, LJ and Wu, N and Romaní, AM and Riis, T}, title = {Microbial Organic Matter Utilization in High-Arctic Streams: Key Enzymatic Controls.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01330-w}, pmid = {30739147}, issn = {1432-184X}, support = {CF16-0325//Carlsbergfondet/ ; Postgraduate studies program//Fundaci?n Ram?n Areces/ ; }, abstract = {In the Arctic, climate changes contribute to enhanced mobilization of organic matter in streams. Microbial extracellular enzymes are important mediators of stream organic matter processing, but limited information is available on enzyme processes in this remote area. Here, we studied the variability of microbial extracellular enzyme activity in high-Arctic fluvial biofilms. We evaluated 12 stream reaches in Northeast Greenland draining areas exhibiting different geomorphological features with contrasting contents of soil organic matter to cover a wide range of environmental conditions. We determined stream nitrogen, phosphorus, and dissolved organic carbon concentrations, quantified algal biomass and bacterial density, and characterized the extracellular enzyme activities involved in catalyzing the cleavage of a range of organic matter compounds (e.g., β-glucosidase, phosphatase, β-xylosidase, cellobiohydrolase, and phenol oxidase). We found significant differences in microbial organic matter utilization among the study streams draining contrasting geomorphological features, indicating a strong coupling between terrestrial and stream ecosystems. Phosphatase and phenol oxidase activities were higher in solifluction areas than in alluvial areas. Besides dissolved organic carbon, nitrogen availability was the main driver controlling enzyme activities in the high-Arctic, which suggests enhanced organic matter mineralization at increased nutrient availability. Overall, our study provides novel information on the controls of organic matter usage by high-Arctic stream biofilms, which is of high relevance due to the predicted increase of nutrient availability in high-Arctic streams in global climate change scenarios.}, }
@article {pmid30739041, year = {2019}, author = {Camacho-Montealegre, CM and Rodrigues, EM and Tótola, MR}, title = {Microbial diversity and bioremediation of rhizospheric soils from Trindade Island - Brazil.}, journal = {Journal of environmental management}, volume = {236}, number = {}, pages = {358-364}, doi = {10.1016/j.jenvman.2019.02.013}, pmid = {30739041}, issn = {1095-8630}, abstract = {Pristine environments may harbor complex microbial communities with metabolic potential for use in bioremediation of organic pollutants. This study aimed to evaluate crude oil biodegradation by microbial communities present in rhizospheric soils of Bulbostylis nesiotis and Cyperus atlanticus on Trindade Island and the compositional structure of these communities. After 60 days under aerobic conditions, Total Petroleum Hydrocarbon biodegradation ranged from 66 to 75%, depending on the plant species and the origin of the soil samples. There was no response of petroleum biodegradation to fertilization with N:P:K (80:160:80 mg dm-3). Soil contamination with crude oil did not necessarily reduce microbial diversity. The richness and diversity increased in contaminated soils in some specific situations. We conclude that microbial communities from pristine soils have the ability to remove hydrocarbons through biodegradation and that Bulbostylis nesiotis and Cyperus atlanticus inhabiting Trindade Island harbor rhizospheric microbial communities with potential for application in rhizoremediation.}, }
@article {pmid30738110, year = {2019}, author = {Mateus-Barros, E and Meneghine, AK and Bagatini, IL and Fernandes, CC and Kishi, LT and Vieira, AAH and Sarmento, H}, title = {Comparison of two DNA extraction methods widely used in aquatic microbial ecology.}, journal = {Journal of microbiological methods}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.mimet.2019.02.005}, pmid = {30738110}, issn = {1872-8359}, abstract = {In recent years, the rapid advances of culture-independent methods and new molecular tools have revolutionized our understanding of microbial biodiversity and ecological functions. DNA extraction from microbial communities is a critical step in this process and several methods have been proposed and used, but the influence of the extraction method on the outcome and ultimately on ecological inferences from the results is not yet precisely determined. Here, we compared two of the most commonly used extraction methods in aquatic microbial ecology, and investigated whether the two methods yielded comparable results for community ecology analyses. We extracted DNA from 15 different shallow lakes with phenol:chloroform, a classical and widely used extraction method, and with the PowerSoil DNA isolation Kit, often suggested as the standard DNA extraction method, with some adaptations for aquatic environments. We found that although only 5% of all OTUs showed significant differences in pairwise comparisons (using the 15 lakes as replicates), these OTUs accounted for >35% (on average) of the relative abundance. Diversity and richness did not differ significantly between the two extraction methods, but the beta-dispersion of the communities indicated that the organic extraction yielded more homogeneous communities, while the kit extraction generated variability. Consequently, we conclude that despite the small number of OTUs with significant differences, their impact on the community composition obtained was not negligible, and therefore the results from these two extraction methods were not comparable.}, }
@article {pmid30735594, year = {2019}, author = {Ferguson, RMW and Garcia-Alcega, S and Coulon, F and Dumbrell, AJ and Whitby, C and Colbeck, I}, title = {Bioaerosol Biomonitoring: Sampling Optimisation for Molecular Microbial Ecology.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {}, doi = {10.1111/1755-0998.13002}, pmid = {30735594}, issn = {1755-0998}, abstract = {Bioaerosols (or biogenic aerosols) have largely been overlooked by molecular ecologists. However, this is rapidly changing as bioaerosols play key roles in public health, environmental chemistry, and the dispersal ecology of microbes. Due to the low environmental concentrations of bioaerosols, collecting sufficient biomass for molecular methods is challenging. Currently, no standardised methods for bioaerosol collection for molecular ecology research exist. Each study requires a process of optimisation, which greatly slows the advance of bioaerosol science. Here, we evaluated air filtration and liquid impingement for bioaerosol sampling across a range of environmental conditions. We also investigated the effect of sampling matrices, sample concentration strategies, and sampling duration on DNA yield. Air filtration using polycarbonate filters gave the highest recovery, but due to the faster sampling rates possible with impingement, we recommend this method for fine scale temporal/spatial ecological studies. We found that in order to prevent bias for the recovery of Gram-positive bacteria, the matrix for impingement should be phosphate buffered saline. The optimal method for bioaerosol concentration from the liquid matrix was centrifugation. However, we also present a method using syringe filters for rapid in-field recovery of bioaerosols from impingement samples, without compromising microbial diversity for High Throughput Sequencing approaches. Finally, we provide a resource that enables molecular ecologists to select the most appropriate sampling strategy for their specific research question. This article is protected by copyright. All rights reserved.}, }
@article {pmid30735001, year = {2019}, author = {Cassman, NA and Soares, JR and Pijl, A and Lourenço, KS and van Veen, JA and Cantarella, H and Kuramae, EE}, title = {Nitrification inhibitors effectively target N2 O-producing Nitrosospira spp. in tropical soil.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14557}, pmid = {30735001}, issn = {1462-2920}, abstract = {The nitrification inhibitors (NIs) 3,4-dimethylpyrazole (DMPP) and dicyandiamide (DCD) can effectively reduce N2 O emissions; however, which species are targeted and the effect of these NIs on the microbial nitrifier community is still unclear. Here we identified the ammonia oxidizing bacteria (AOB) species linked to N2 O emissions and evaluated the effects of urea and urea with DCD and DMPP on the nitrifying community in a 258-day field experiment under sugarcane. Using an amoA AOB amplicon sequencing approach and mining a previous dataset of 16S rRNA sequences, we characterized the most likely N2 O-producing AOB as a Nitrosospira spp. and identified Nitrosospira (AOB), Nitrososphaera (archaeal ammonia oxidizer) and Nitrospira (nitrite-oxidizer) as the most abundant, present nitrifiers. The fertilizer treatments had no effect on the alpha and beta diversities of the AOB communities. Interestingly, we found three clusters of co-varying variables with nitrifier operational taxonomic units (OTUs): the N2 O-producing AOB Nitrosospira with N2 O, NO3- , NH4+ , water-filled pore space (WFPS) and pH; AOA Nitrososphaera with NO3- , NH4+ and pH; and AOA Nitrososphaera and NOB Nitrospira with NH4+ , which suggests different drivers. These results support the co-occurrence of non-N2 O-producing Nitrososphaera and Nitrospira in the unfertilized soils and the promotion of N2 O-producing Nitrosospira under urea fertilization. Further, we suggest that DMPP is a more effective NI than DCD in tropical soil under sugarcane. This article is protected by copyright. All rights reserved.}, }
@article {pmid30727523, year = {2012}, author = {Rosenzweig, N and Tiedje, JM and Quensen, JF and Meng, Q and Hao, JJ}, title = {Microbial Communities Associated with Potato Common Scab-Suppressive Soil Determined by Pyrosequencing Analyses.}, journal = {Plant disease}, volume = {96}, number = {5}, pages = {718-725}, doi = {10.1094/PDIS-07-11-0571}, pmid = {30727523}, issn = {0191-2917}, abstract = {Potato common scab, caused by Streptomyces spp., is an annual production problem for potato growers, and not effectively controlled by current methods. A field with naturally occurring common scab suppression has been identified in Michigan, and confirmed to have a biological basis for this disease suppression. This field and an adjacent scab nursery conducive to disease were studied using pyrosequencing to compare the two microbial communities. Total DNA was extracted from both the disease-conducive and -suppressive soils. A phylogenetically taxon-informative region of the 16S rRNA gene was used to establish operational taxonomic units (OTUs) to characterize bacterial community richness and diversity. In total, 1,124 OTUs were detected and 565 OTUs (10% dissimilarity) were identified in disease-conducive soil and 859 in disease-suppressive soil, including 300 shared both between sites. Common phyla based on relative sequence abundance were Acidobacteria, Proteobacteria, and Firmicutes. Sequences of Lysobacter were found in significantly higher numbers in the disease-suppressive soil, as were sequences of group 4 and group 6 Acidobacteria. The relative abundance of sequences identified as the genus Bacillus was significantly higher by an order of magnitude in the disease-conducive soil.}, }
@article {pmid30729265, year = {2019}, author = {Bernard, C and Escalas, A and Villeriot, N and Agogué, H and Hugoni, M and Duval, C and Carré, C and Got, P and Sarazin, G and Jézéquel, D and Leboulanger, C and Grossi, V and Ader, M and Troussellier, M}, title = {Very Low Phytoplankton Diversity in a Tropical Saline-Alkaline Lake, with Co-dominance of Arthrospira fusiformis (Cyanobacteria) and Picocystis salinarum (Chlorophyta).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01332-8}, pmid = {30729265}, issn = {1432-184X}, support = {ANR-13-BS06-0001//Agence Nationale de la Recherche/ ; }, abstract = {Lake Dziani Dzaha (Mayotte Island, Indian Ocean) is a tropical thalassohaline lake which geochemical and biological conditions make it a unique aquatic ecosystem considered as a modern analogue of Precambrian environments. In the present study, we focused on the diversity of phytoplanktonic communities, which produce very high and stable biomass (mean2014-2015 = 652 ± 179 μg chlorophyll a L-1). As predicted by classical community ecology paradigms, and as observed in similar environments, a single species is expected to dominate the phytoplanktonic communities. To test this hypothesis, we sampled water column in the deepest part of the lake (18 m) during rainy and dry seasons for two consecutive years. Phytoplanktonic communities were characterized using a combination of metagenomic, microscopy-based and flow cytometry approaches, and we used statistical modeling to identify the environmental factors determining the abundance of dominant organisms. As hypothesized, the overall diversity of the phytoplanktonic communities was very low (15 OTUs), but we observed a co-dominance of two, and not only one, OTUs, viz., Arthrospira fusiformis (Cyanobacteria) and Picocystis salinarum (Chlorophyta). We observed a decrease in the abundance of these co-dominant taxa along the depth profile and identified the adverse environmental factors driving this decline. The functional traits measured on isolated strains of these two taxa (i.e., size, pigment composition, and concentration) are then compared and discussed to explain their capacity to cope with the extreme environmental conditions encountered in the aphotic, anoxic, and sulfidic layers of the water column of Lake Dziani Dzaha.}, }
@article {pmid30728279, year = {2019}, author = {Props, R and Monsieurs, P and Vandamme, P and Leys, N and Denef, VJ and Boon, N}, title = {Gene Expansion and Positive Selection as Bacterial Adaptations to Oligotrophic Conditions.}, journal = {mSphere}, volume = {4}, number = {1}, pages = {}, doi = {10.1128/mSphereDirect.00011-19}, pmid = {30728279}, issn = {2379-5042}, abstract = {We examined the genomic adaptations of prevalent bacterial taxa in a highly nutrient- and ion-depleted freshwater environment located in the secondary cooling water system of a nuclear research reactor. Using genome-centric metagenomics, we found that none of the prevalent bacterial taxa were related to typical freshwater bacterial lineages. We also did not identify strong signatures of genome streamlining, which has been shown to be one of the ecoevolutionary forces shaping the genome characteristics of bacterial taxa in nutrient-depleted environments. Instead, focusing on the dominant taxon, a novel Ramlibacter sp. which we propose to name Ramlibacter aquaticus, we detected extensive positive selection on genes involved in phosphorus and carbon scavenging pathways. These genes were involved in the high-affinity phosphate uptake and storage into polyphosphate granules, metabolism of nitrogen-rich organic matter, and carbon/energy storage into polyhydroxyalkanoate. In parallel, comparative genomics revealed a high number of paralogs and an accessory genome significantly enriched in environmental sensing pathways (i.e., chemotaxis and motility), suggesting extensive gene expansions in R. aquaticus The type strain of R. aquaticus (LMG 30558T) displayed optimal growth kinetics and productivity at low nutrient concentrations, as well as substantial cell size plasticity. Our findings with R. aquaticus LMG 30558T demonstrate that positive selection and gene expansions may represent successful adaptive strategies to oligotrophic environments that preserve high growth rates and cellular productivity.IMPORTANCE By combining a genome-centric metagenomic approach with a culture-based approach, we investigated the genomic adaptations of prevalent populations in an engineered oligotrophic freshwater system. We found evidence for widespread positive selection on genes involved in phosphorus and carbon scavenging pathways and for gene expansions in motility and environmental sensing to be important genomic adaptations of the abundant taxon in this system. In addition, microscopic and flow cytometric analysis of the first freshwater representative of this population (Ramlibacter aquaticus LMG 30558T) demonstrated phenotypic plasticity, possibly due to the metabolic versatility granted by its larger genome, to be a strategy to cope with nutrient limitation. Our study clearly demonstrates the need for the use of a broad set of genomic tools combined with culture-based physiological characterization assays to investigate and validate genomic adaptations.}, }
@article {pmid30687262, year = {2018}, author = {Zhou, C and Ontiveros-Valencia, A and Nerenberg, R and Tang, Y and Friese, D and Krajmalnik-Brown, R and Rittmann, BE}, title = {Hydrogenotrophic Microbial Reduction of Oxyanions With the Membrane Biofilm Reactor.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3268}, doi = {10.3389/fmicb.2018.03268}, pmid = {30687262}, issn = {1664-302X}, abstract = {Oxyanions, such as nitrate, perchlorate, selenate, and chromate are commonly occurring contaminants in groundwater, as well as municipal, industrial, and mining wastewaters. Microorganism-mediated reduction is an effective means to remove oxyanions from water by transforming oxyanions into harmless and/or immobilized forms. To carry out microbial reduction, bacteria require a source of electrons, called the electron-donor substrate. Compared to organic electron donors, H2 is not toxic, generates minimal secondary contamination, and can be readily obtained in a variety of ways at reasonable cost. However, the application of H2 through conventional delivery methods, such as bubbling, is untenable due to H2's low water solubility and combustibility. In this review, we describe the membrane biofilm reactor (MBfR), which is a technological breakthrough that makes H2 delivery to microorganisms efficient, reliable, and safe. The MBfR features non-porous gas-transfer membranes through which bubbleless H2 is delivered on-demand to a microbial biofilm that develops naturally on the outer surface of the membranes. The membranes serve as an active substratum for a microbial biofilm able to biologically reduce oxyanions in the water. We review the development of the MBfR technology from bench, to pilot, and to commercial scales, and we elucidate the mechanisms that control MBfR performance, particularly including methods for managing the biofilm's structure and function. We also give examples of MBfR performance for cases of treating single and co-occurring oxyanions in different types of contaminated water. In summary, the MBfR is an effective and reliable technology for removing oxyanion contaminants by accurately providing a biofilm with bubbleless H2 on demand. Controlling the H2 supply in accordance to oxyanion surface loading and managing the accumulation and activity of biofilm are the keys for process success.}, }
@article {pmid30530706, year = {2019}, author = {Holman, DB and Bearson, BL and Allen, HK and Shippy, DC and Loving, CL and Kerr, BJ and Bearson, SMD and Brunelle, BW}, title = {Chlortetracycline Enhances Tonsil Colonization and Fecal Shedding of Multidrug-Resistant Salmonella enterica Serovar Typhimurium DT104 without Major Alterations to the Porcine Tonsillar and Intestinal Microbiota.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {4}, pages = {}, doi = {10.1128/AEM.02354-18}, pmid = {30530706}, issn = {1098-5336}, abstract = {Salmonella spp. are estimated to cause 1.2 million cases of human foodborne illness each year in the United States, and pigs can often be asymptomatically colonized with Salmonella spp. (>50% of farms). Recent reports state that 18.3% of Salmonella enterica serovar Typhimurium isolates are resistant to ≥3 antimicrobial classes, and multidrug-resistant (MDR) strains are associated with an increased hospitalization rate and other complications. Chlortetracycline is commonly used in swine production to prevent/treat various diseases; therefore, chlortetracycline treatment of pigs unknowingly colonized with MDR Salmonella may have collateral effects on Salmonella spp. (and other gut bacteria). In this study, we determined the effect of in-feed chlortetracycline (400 g/ton) on shedding and colonization of pigs challenged with the MDR S Typhimurium strain DT104 (n = 11/group). We also assessed the impact on the fecal microbiota over the 12-day experimental period and on the ileum, cecum, and tonsil microbiota at 7 days postinoculation (dpi). In MDR S Typhimurium-inoculated pigs, chlortetracycline administration significantly increased fecal shedding at 2 dpi (+1.4 log10 CFU/g; P < 0.001) and enhanced tonsil colonization (+3.1 log10 CFU/g; P < 0.001). There were few major alterations detected in the gut or tonsillar microbiota of pigs treated with MDR S Typhimurium and/or chlortetracycline. The tonsillar transcriptome was largely unaffected despite increased colonization by MDR S Typhimurium following inoculation of the chlortetracycline-treated pigs. These results highlight the idea that chlortetracycline administration can enhance shedding and colonization of MDR S Typhimurium in pigs, which could increase the risk of environmental dissemination of MDR Salmonella strains.IMPORTANCESalmonella spp. are an important cause of foodborne illness in North America, and pork products are associated with sporadic cases and outbreaks of human salmonellosis. Isolates of Salmonella may be resistant to multiple antibiotics, and infections with multidrug-resistant (MDR) Salmonella spp. are more difficult to treat, leading to increased hospitalization rates. Swine operations commonly use antimicrobials, such as chlortetracycline, to prevent/treat infections, which may have collateral effects on pig microbial populations. Recently, we demonstrated that chlortetracycline induces the expression of genes associated with pathogenesis and invasion in MDR Salmonella enterica serovar Typhimurium in vitro In our current study, we show increased tonsillar colonization and fecal shedding of the MDR S Typhimurium strain DT104 from pigs administered chlortetracycline. Therefore, pigs unknowingly colonized with multidrug-resistant Salmonella spp. and receiving chlortetracycline for an unrelated infection may be at a greater risk for disseminating MDR Salmonella spp. to other pigs and to humans through environmental or pork product contamination.}, }
@article {pmid30726948, year = {2019}, author = {Wafa, A and Abrouk, D and Guyonnet, J and Barakat, M and Ortet, P and Simon, L and Lerondelle, C and Heulin, T and Haichar, FEZ}, title = {Plant hosts control microbial denitrification activity.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiz021}, pmid = {30726948}, issn = {1574-6941}, abstract = {In the rhizosphere, complex and dynamic interactions occur between plants and microbial networks that are primarily mediated by root exudation. Plants exude various metabolites that may influence the rhizosphere microbiota. However, few studies have sought to understand the role of root exudation in shaping the functional capacities of the microbiota. In this study, we aim to determine the impact of plants on the diversity of active microbiota and their ability to denitrify via root exudates. For that purpose, we grew four plant species, Triticum aestivum, Brassica napus, Medicago truncatula and Arabidopsis thaliana, separately in the same soil. We extracted RNA from the root-adhering soil and the root tissues, and we analysed the bacterial diversity by using 16S rRNA metabarcoding. We measured denitrification activity and denitrification gene expression (nirK and nirS) from each root-adhering soil sample and the root tissues using gas chromatography and quantitative PCR, respectively. We demonstrated that plant species shape denitrification activity and modulate the diversity of the active microbiota through root exudation. We observed a positive effect of T. aestivum and A. thaliana on denitrification activity and nirK gene expression on the root systems. Together, our results underscore the potential power of host plants in controlling microbial activities.}, }
@article {pmid30726571, year = {2019}, author = {Laforest-Lapointe, I and Whitaker, BK}, title = {Decrypting the phyllosphere microbiota: progress and challenges.}, journal = {American journal of botany}, volume = {}, number = {}, pages = {}, doi = {10.1002/ajb2.1229}, pmid = {30726571}, issn = {1537-2197}, }
@article {pmid30725170, year = {2019}, author = {Sun, X and Li, B and Han, F and Xiao, E and Xiao, T and Sun, W}, title = {Impacts of Arsenic and Antimony Co-Contamination on Sedimentary Microbial Communities in Rivers with Different Pollution Gradients.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01327-5}, pmid = {30725170}, issn = {1432-184X}, support = {41771301//National Natural Science Foundation of China/ ; 41420104007//National Natural Science Foundation of China/ ; }, abstract = {Arsenic (As) and antimony (Sb) are both toxic metalloids that are of primary concern for human health. Mining activity has introduced elevated levels of arsenic and antimony into the rivers and has increased the risks of drinking water contamination in China. Due to their mobility, the majority of the metalloids originating from mining activities are deposited in the river sediments. Thus, depending on various geochemical conditions, sediment could either be a sink or source for As and Sb in the water column. Microbes are key mediators for biogeochemical transformation and can both mobilize or precipitate As and Sb. To further understand the microbial community responses to As and Sb contamination, sediment samples with different contamination levels were collected from three rivers. The result of the study suggested that the major portions of As and Sb were in strong association with the sediment matrix and considered nonbioavailable. These fractions, however, were also suggested to have profound influences on the microbial community composition. As and Sb contamination caused strong reductions in microbial diversity in the heavily contaminated river sediments. Microorganisms were more sensitive to As comparing to Sb, as revealed by the co-occurrence network and random forest predictions. Operational taxonomic units (OTUs) that were potentially involved in As and Sb metabolism, such as Anaerolinea, Sphingomonas, and Opitutus, were enriched in the heavily contaminated samples. In contrast, many keystone taxa, including members of the Hyphomicrobiaceae and Bradyrhizobiaceae families, were inhibited by metalloid contamination, which could further impair crucial environmental services provided by these members.}, }
@article {pmid30724437, year = {2019}, author = {Ma, Y and Zilles, JL and Kent, AD}, title = {An evaluation of primers for detecting denitrifiers via their functional genes.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14555}, pmid = {30724437}, issn = {1462-2920}, abstract = {Microbial populations provide nitrogen cycling ecosystem services at the nexus of agriculture, environmental quality, and climate change. Denitrification, in particular, impacts socio-environmental systems in both positive and negative ways, through reduction of aquatic and atmospheric nitrogen pollution, but also reduction of soil fertility and production of greenhouse gases. However, denitrification rates are quite variable in time and space, and therefore difficult to model. Microbial ecology is working to improve the predictive ecology of denitrifiers by quantifying and describing the diversity of microbial functional groups. However, metagenomic sequencing has revealed previously undescribed diversity within these functional groups, and highlighted a need to reevaluate coverage of existing DNA primers for denitrification functional genes. We provide here a comprehensive in silico evaluation of primer sets that target diagnostic genes in the denitrification pathway. This analysis makes use of current DNA sequence data available for each functional gene. It contributes a comparative analysis of the strengths and limitations of each primer set for describing denitrifier functional groups. This analysis identifies genes for which development of new tools is needed, and aids in interpretation of existing datasets, both of which will facilitate application of molecular methods to further develop the predictive ecology of denitrifiers. This article is protected by copyright. All rights reserved.}, }
@article {pmid30721227, year = {2019}, author = {Marsland, R and Cui, W and Goldford, J and Sanchez, A and Korolev, K and Mehta, P}, title = {Available energy fluxes drive a transition in the diversity, stability, and functional structure of microbial communities.}, journal = {PLoS computational biology}, volume = {15}, number = {2}, pages = {e1006793}, doi = {10.1371/journal.pcbi.1006793}, pmid = {30721227}, issn = {1553-7358}, abstract = {A fundamental goal of microbial ecology is to understand what determines the diversity, stability, and structure of microbial ecosystems. The microbial context poses special conceptual challenges because of the strong mutual influences between the microbes and their chemical environment through the consumption and production of metabolites. By analyzing a generalized consumer resource model that explicitly includes cross-feeding, stochastic colonization, and thermodynamics, we show that complex microbial communities generically exhibit a transition as a function of available energy fluxes from a &quot;resource-limited&quot; regime where community structure and stability is shaped by energetic and metabolic considerations to a diverse regime where the dominant force shaping microbial communities is the overlap between species' consumption preferences. These two regimes have distinct species abundance patterns, different functional profiles, and respond differently to environmental perturbations. Our model reproduces large-scale ecological patterns observed across multiple experimental settings such as nestedness and differential beta diversity patterns along energy gradients. We discuss the experimental implications of our results and possible connections with disorder-induced phase transitions in statistical physics.}, }
@article {pmid30719551, year = {2019}, author = {Margesin, R and Collins, T}, title = {Microbial ecology of the cryosphere (glacial and permafrost habitats): current knowledge.}, journal = {Applied microbiology and biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00253-019-09631-3}, pmid = {30719551}, issn = {1432-0614}, support = {IF/01635/2014//Investigador FCT Programme/ ; }, abstract = {Microorganisms in cold ecosystems play a key ecological role in their natural habitats. Since these ecosystems are especially sensitive to climate changes, as indicated by the worldwide retreat of glaciers and ice sheets as well as permafrost thawing, an understanding of the role and potential of microbial life in these habitats has become crucial. Emerging technologies have added significantly to our knowledge of abundance, functional activity, and lifestyles of microbial communities in cold environments. The current knowledge of microbial ecology in glacial habitats and permafrost, the most studied habitats of the cryosphere, is reported in this review.}, }
@article {pmid30715579, year = {2019}, author = {Kivlin, SN and Kazenel, MR and Lynn, JS and Lee Taylor, D and Rudgers, JA}, title = {Plant Identity Influences Foliar Fungal Symbionts More Than Elevation in the Colorado Rocky Mountains.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01336-4}, pmid = {30715579}, issn = {1432-184X}, support = {DEB1354972//Directorate for Biological Sciences/ ; }, abstract = {Despite colonizing nearly every plant on Earth, foliar fungal symbionts have received little attention in studies on the biogeography of host-associated microbes. Evidence from regional scale studies suggests that foliar fungal symbiont distributions are influenced both by plant hosts and environmental variation in climate and soil resources. However, previous surveys have focused on either one plant host across an environmental gradient or one gradient and multiple plant hosts, making it difficult to disentangle the influence of host identity from the influence of the environment on foliar endophyte communities. We used a culture-based approach to survey fungal symbiont composition in the leaves of nine C3 grass species along replicated elevation gradients in grasslands of the Colorado Rocky Mountains. In these ecosystems, the taxonomic richness and composition of foliar fungal symbionts were mostly structured by the taxonomic identity of the plant host rather than by variation in climate. Plant traits related to size (height and leaf length) were the best predictors of foliar fungal symbiont composition and diversity, and composition did not vary predictably with plant evolutionary history. The largest plants had the most diverse and distinctive fungal communities. These results suggest that across the ~ 300 m elevation range that we sampled, foliar fungal symbionts may indirectly experience climate change by tracking the shifting distributions of plant hosts rather than tracking climate directly.}, }
@article {pmid30712793, year = {2019}, author = {Raabis, S and Li, W and Cersosimo, L}, title = {Effects and immune responses of probiotic treatment in ruminants.}, journal = {Veterinary immunology and immunopathology}, volume = {208}, number = {}, pages = {58-66}, doi = {10.1016/j.vetimm.2018.12.006}, pmid = {30712793}, issn = {1873-2534}, abstract = {Gut microbial colonization and establishment are vital to ruminant health and production. This review article focuses on current knowledge and methods used to understand and manipulate the gut microbial community in ruminant animals, with a special focus on probiotics treatment. This review highlights the most promising of studies in this area, including gut microbial colonization and establishment, effect of gastrointestinal tract microbial community on host mucosal innate immune function, impact of feeding strategies on gut microbial community, current probiotic treatments in ruminants, methods to manipulate the gut microbiota and associated antimicrobial compounds, and models and cell lines used in understanding the host immune response to probiotic treatments. As a lot of work in this area was done in humans and mice, this review article also includes up-to-date knowledge from relevant studies in human and mouse models. This review is a useful resource for scientists working in the areas of ruminant nutrition and health, and to researchers investigating the microbial ecology and its relation to animal health.}, }
@article {pmid30703910, year = {2014}, author = {Zablocki, ODJ and Rybicki, EP and Cowan, DA}, title = {First Report of a Potyvirus Infecting Albuca rautanenii in the Namib Desert.}, journal = {Plant disease}, volume = {98}, number = {12}, pages = {1749}, doi = {10.1094/PDIS-07-14-0737-PDN}, pmid = {30703910}, issn = {0191-2917}, abstract = {Chlorotic, streak-like symptoms were observed in April 2013 on a single specimen of Albuca rautanenii (Schinz) J.C.Manning &amp; Goldblatt (Family: Hyacinthaceae) found among other plants near Homeb in the Namib Desert, Namibia. No potential insect vectors (e.g., aphids) were observed on or around the infected plant. An extract from symptomatic leaves was assessed by transmission electron microscopy (leaf dip method) to ascertain if the symptoms were viral in origin. Long, flexuous threadlike particles 687 to 825 nm in length and 12.5 nm in diameter were observed. The morphology and size of the particles were indicative of a putative member of the taxonomic family Potyviridae. To confirm this, RT-PCR using universal potyvirus primers which amplify part of the nuclear inclusion b gene (NIb) was conducted (1) on total RNA extracted from leaf tissue (Qiagen RNeasy Plant Mini Kit). The triplicated reaction yielded amplicons of the expected size (~350 bp), which were cloned into the pJET 1.2 vector (Thermo Scientific, Waltham, MA) according to manufacturer's instructions. The sequences of 10 clones were trimmed to remove vector and primer ends and were deposited in the EBI database under the accession numbers LK995422 to LK995431. Curated sequences were used to search the GenBank database using BLASTn and tBLASTx, as well as for phylogenetic analysis. Intra-clonal nucleotide sequence similarity ranged from 97.99 to 99.72%. BLASTn searches showed all clones were 72% identical to Papaya ringspot virus isolate 1 accession JQ314105.1 (87% coverage), followed by Bean yellow mosaic virus clone Brn167 accession JF707769.1 (72% identity with 86% sequence coverage). The translated peptide fragment was most similar to Sugarcane mosaic virus isolate Beijing (AY042184.1), with a query cover of 98% and a similarity of 81%. Phylogenetic analysis was performed with a set of 57 reference potyvirus genomes, with their NIb regions aligned with the cloned nucleotide sequences according to the parameters used previously (1). The clones formed a distinct cluster, at a node with Cocksfoot streak virus (CSV) (NC_003742.1). An identity matrix of the aligned NIb clones and CSV showed a nucleotide identity range of 68.79 to 70.23%. These results suggest that the virus isolate belongs to the family Potyviridae, genus Potyvirus, supported by the characteristic morphological features of the virion and its relatedness to CSV. Moreover, the clustering of all sequences at a single node suggests a homogeneous viral population, without significant strain variation. Genetic distance inferred by phylogenetic analysis further suggests that the isolate is a novel species within the genus, which we tentatively name Albuca mosaic virus, AlbMV. To our knowledge, this is the first report of any plant virus infection in the native Namib Desert ecosystem. This is particularly relevant due to the scarcity and uniqueness of plant life in this hyperarid desert environment, and additional monitoring of this virus infection and other desert plant species is encouraged. Reference: (1) L. Zheng et al. Plant Pathol. 59:211, 2010.}, }
@article {pmid30706113, year = {2019}, author = {Ávila, MP and Oliveira-Junior, ES and Reis, MP and Hester, ER and Diamantino, C and Veraart, AJ and Lamers, LPM and Kosten, S and Nascimento, AMA}, title = {The Water Hyacinth Microbiome: Link Between Carbon Turnover and Nutrient Cycling.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01331-9}, pmid = {30706113}, issn = {1432-184X}, support = {APQ 01673/16//Funda??o de Amparo ? Pesquisa do Estado de Minas Gerais/ ; 306774/2016-0//Conselho Nacional de Desenvolvimento Cient?fico e Tecnol?gico (BR)/ ; BEX 13607/13-8//Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior/ ; 8631(2012)//Boeing/ ; 2017//Erasmus plus program/ ; }, abstract = {Water hyacinth (WH), a large floating plant, plays an important role in the biogeochemistry and ecology of many freshwaters globally. Its biogeochemical impact on wetland functioning is strongly mediated by the microbiome associated with its roots. However, little is known about the structure and function of this WH rhizobiome and its relation to wetland ecosystem functioning. Here, we unveil the core and transient rhizobiomes of WH and their key biogeochemical functions in two of the world's largest wetlands: the Amazon and the Pantanal. WH hosts a highly diverse microbial community shaped by spatiotemporal changes. Proteobacteria lineages were most common, followed by Actinobacteria and Planctomycetes. Deltaproteobacteria and Sphingobacteriia predominated in the core microbiome, potentially associated with polysaccharide degradation and fermentation of plant-derived carbon. Conversely, a plethora of lineages were transient, including highly abundant Acinetobacter, Acidobacteria subgroup 6, and methanotrophs, thus assuring diverse taxonomic signatures in the two different wetlands. Our findings point out that methanogenesis is a key driver of, and proxy for, community structure, especially during seasonal plant decline. We provide ecologically relevant insights into the WH microbiome, which is a key element linking plant-associated carbon turnover with other biogeochemical fluxes in tropical wetlands.}, }
@article {pmid30706112, year = {2019}, author = {Song, Y and Mao, G and Gao, G and Bartlam, M and Wang, Y}, title = {Structural and Functional Changes of Groundwater Bacterial Community During Temperature and pH Disturbances.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01333-7}, pmid = {30706112}, issn = {1432-184X}, support = {No.31670498 and 31322012//National Natural Science Foundation of China/ ; }, abstract = {In this study, we report the characteristics of a microbial community in sampled groundwater and elucidate the effects of temperature and pH disturbances on bacterial structure and nitrogen-cycling functions. The predominant phyla of candidate OD1, candidate OP3, and Proteobacteria represented more than half of the total bacteria, which clearly manifested as a &quot;low nucleic acid content (LNA) bacteria majority&quot; type via flow cytometric fingerprint. The results showed that LNA bacteria were more tolerant to rapid changes in temperature and pH, compared to high nucleic acid content (HNA) bacteria. A continuous temperature increase test demonstrated that the LNA bacterial group was less competitive than the HNA bacterial group in terms of maintaining their cell intactness and growth potential. In contrast, the percentage of intact LNA bacteria was maintained at nearly 70% with pH decrease, despite a 50% decrease in total intact cells. Next-generation sequencing results revealed strong resistance and growth potential of phylum Proteobacteria when the temperature increased or the pH decreased in groundwater, especially for subclasses α-, β-, and γ-Proteobacteria. In addition, relative abundance of nitrogen-related functional genes by qPCR showed no difference in nitrifiers or denitrifiers within 0.45 μm-captured and 0.45 μm-filterable bacteria due to phylogenetic diversity. One exception was the monophyletic anammox bacteria that belong to the phylum Planctomycetes, which were mostly captured on a 0.45-μm filter. Furthermore, we showed that both temperature increase and pH decrease could enhance the denitrification potential, whereas the nitrification and anammox potentials were weakened.}, }
@article {pmid30704595, year = {2019}, author = {Kamimura, BA and De Filippis, F and Sant'Ana, AS and Ercolini, D}, title = {Large-scale mapping of microbial diversity in artisanal Brazilian cheeses.}, journal = {Food microbiology}, volume = {80}, number = {}, pages = {40-49}, doi = {10.1016/j.fm.2018.12.014}, pmid = {30704595}, issn = {1095-9998}, abstract = {Brazilian artisanal cheeses are characterized by the use of raw milk and in some cases, natural starter cultures, known as &quot;pingo&quot;, as well as following simple and traditional manufacturing technology. In this study, a large-scale screening of the microbial ecology of 11 different types of artisanal cheeses produced in five geographical areas of Brazil was performed. Besides, the specific origin-related microbial signatures were identified. Clear geography- and technology-based differences in the microbiota were observed. Lactic acid bacteria dominated in all cheeses although Enterobacteriaceae and Staphylococcus also occurred in North, Northeast and Central cheeses. Differences in the lactic acid bacteria patterns were also highlighted: Streptococcus, Leuconostoc, Lactococcus and Lactobacillus were differently combined in terms of relative abundance according to product type and region of production. This study provides a comprehensive, unprecedented microbiological mapping of Brazilian cheeses, highlighting the impact of geographical origin and mode of production on microbial diversity. The results obtained will help to plan an evaluation of microbial contamination sources that will need to be studied for the improvement of cheese quality and safety.}, }
@article {pmid30701285, year = {2019}, author = {Ely, CS and Smets, BF}, title = {Guild Composition of Root-Associated Bacteria Changes with Increased Soil Contamination.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01326-6}, pmid = {30701285}, issn = {1432-184X}, support = {R829405//U.S. Environmental Protection Agency/ ; }, abstract = {The interaction of plants and root-associated bacteria encourage the removal of soil contaminants. Engineers and scientists have looked at this phenomenon as a possible means of soil treatment (rhizodegradation). In this study, root-associated bacteria were isolated and selected for growth on a model soil contaminant: polycyclic aromatic hydrocarbons. Isolates were compared genetically to see how plant-bacteria interactions change with soil contamination levels. Characterization of root-associated bacteria was performed using REP-PCR genetic fingerprinting and 16s rRNA gene alignments for identification. Genomic fingerprinting indicated that the composition of PAH-metabolizing bacteria (&quot;guild&quot;) was similar among plant species at each treatment level. However, guild composition changed with contamination level and differed from that of bulk soils, suggesting a common rhizosphere effect among plant species related to PAH contamination. PAH-metabolizing bacteria were identified through 16s rRNA gene alignment as members of the α-, β-, and γ-proteobacteria, Actinobacteria, and Bacilli classes. Burkholderia and Pseudomonas spp. were the only genera of bacteria isolated from all plant types in uncontaminated controls. Bacterial species found at the highest treatment included Achromobacter xylosoxidans, Rhodococcus spp., members of the Microbacteriae, Stenotrophomonas rhizophilia, as well as other members of the alpha-proteobacteria. Given their ability to grow on PAHs and inhabit highly contaminated rhizospheres, these bacteria appear good candidates for the promotion of rhizodegradation.}, }
@article {pmid30701133, year = {2019}, author = {De Paepe, K and Verspreet, J and Rezaei, MN and Hidalgo Martinez, S and Meysman, F and Van de Walle, D and Dewettinck, K and Raes, J and Courtin, C and Van de Wiele, T}, title = {Isolation of wheat bran-colonizing and metabolizing species from the human fecal microbiota.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e6293}, doi = {10.7717/peerj.6293}, pmid = {30701133}, issn = {2167-8359}, abstract = {Undigestible, insoluble food particles, such as wheat bran, are important dietary constituents that serve as a fermentation substrate for the human gut microbiota. The first step in wheat bran fermentation involves the poorly studied solubilization of fibers from the complex insoluble wheat bran structure. Attachment of bacteria has been suggested to promote the efficient hydrolysis of insoluble substrates, but the mechanisms and drivers of this microbial attachment and colonization, as well as subsequent fermentation remain to be elucidated. We have previously shown that an individually dependent subset of gut bacteria is able to colonize the wheat bran residue. Here, we isolated these bran-attached microorganisms, which can then be used to gain mechanistic insights in future pure culture experiments. Four healthy fecal donors were screened to account for inter-individual differences in gut microbiota composition. A combination of a direct plating and enrichment method resulted in the isolation of a phylogenetically diverse set of species, belonging to the Bacteroidetes, Firmicutes, Proteobacteria and Actinobacteria phyla. A comparison with 16S rRNA gene sequences that were found enriched on wheat bran particles in previous studies, however, showed that the isolates do not yet cover the entire diversity of wheat-bran colonizing species, comprising among others a broad range of Prevotella, Bacteroides and Clostridium cluster XIVa species. We, therefore, suggest several modifications to the experiment set-up to further expand the array of isolated species.}, }
@article {pmid30698709, year = {2019}, author = {Janssens, TKS and Tyc, O and Besselink, H and de Boer, W and Garbeva, P}, title = {Biological activities associated with the volatile compound 2,5-bis(1-methylethyl)-pyrazine.}, journal = {FEMS microbiology letters}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsle/fnz023}, pmid = {30698709}, issn = {1574-6968}, abstract = {Pyrazines are 1,4- diazabenzene based volatile organic compounds and known for their broad-spectrum antimicrobial activity. In the present study we assessed the antimicrobial activity of 2,5-bis(1-methylethyl)-pyrazine, produced by Paenibacillus sp. AD87 during co-culture with Burkholderia sp. AD24. In addition, we were using transcriptional reporter assays in E. coli and mammalian cells to decipher the possible mode of action. Bacterial and mammalian luciferase reporter strains were deployed to elucidate antimicrobial and toxicological effects of 2,5-bis(1-methylethyl)-pyrazine. At high levels of exposure, 2,5-bis(1-methylethyl)-pyrazine exerted strong DNA damage response. At lower concentrations, cell-wall damage response was observed. The activity was corroborated by a general toxicity reporter assay in E. coli ΔampD, defective in peptidoglycan turnover. The maximum E. coli cell-wall stress activity was measured at a concentration close to the onset of the mammalian cytotoxicity, while other adverse outcome pathways, such as the activation of aryl hydrocarbon and estrogenic receptor, the p53 tumor suppressor, and the oxidative stress related Nrf2 transcription factor, were induced at elevated concentrations compared to the response of mammalian cells. Because of its broad-spectrum antimicrobial activity at lower concentrations and the relatively low mammalian toxicity, 2,5-bis(1-methylethyl)-pyrazine is a potential bio-based fumigant with possible applications in food industry, agriculture or logistics.}, }
@article {pmid30697889, year = {2019}, author = {Eckert, EM and Quero, GM and Di Cesare, A and Manfredini, G and Mapelli, F and Borin, S and Fontaneto, D and Luna, GM and Corno, G}, title = {Antibiotic disturbance affects aquatic microbial community composition and foodweb interactions but not community resilience.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.15033}, pmid = {30697889}, issn = {1365-294X}, abstract = {Notwithstanding the fundamental role that environmental microbes play for ecosystem functioning, data on how microbes react to disturbances are still scarce, and most factors that confer stability to microbial communities are unknown. In this context, antibiotic discharge into the environment is considered a worldwide threat for ecosystems with potential risks to human health. We therefore tested resilience of microbial communities challenged by the presence of an antibiotic. In a continuous culture experiment we compared the abundance, composition and diversity of microbial communities undisturbed or disturbed by the constant addiction of tetracycline in low (10 μg L-1) or intermediate (100 μg L-1) concentration (press disturbance). Further, the bacterial communities in the three treatments had to face the sudden pulse disturbance of adding an allochthonous bacterium (Escherichia coli). Tetracycline, even at low concentrations, affected microbial communities by changing their phylogenetic composition and causing cell-aggregation. This, however, did not coincide with a reduced microbial diversity, but was mainly caused by a shift in dominance of specific bacterial families. Moreover, the less disturbed community (10 μg L-1 tetracycline) was sometimes more similar to the control and sometimes more similar to heavily disturbed community (100 μg L-1 tetracycline). All in all, we could not see a pattern where the communities disturbed with antibiotics were less resilient to a disturbance introducing E. coli, but they seemed to be able to buffer the input of the allochthonous strain in a similar manner as the control. This article is protected by copyright. All rights reserved.}, }
@article {pmid30694508, year = {2019}, author = {Pérez-Cobas, AE and Buchrieser, C}, title = {Analysis of the Pulmonary Microbiome Composition of Legionella pneumophila-Infected Patients.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1921}, number = {}, pages = {429-443}, doi = {10.1007/978-1-4939-9048-1_27}, pmid = {30694508}, issn = {1940-6029}, abstract = {The analysis of the lung microbiome composition is a field of research that recently emerged. It gained great interest in pulmonary diseases such as pneumonia since the microbiome seems to be involved in host immune responses, inflammation, and protection against pathogens. Thus, it is possible that the microbial communities living in the lungs play a role in the outcome and severity of lung infections such as Legionella-caused pneumonia and in the response to antibiotic therapy. In this chapter, all steps necessary for the characterization of the bacterial and fungal fraction of the lung microbiome using high-throughput sequencing approaches are explained, starting from the selection of clinical samples to the analysis of the taxonomic composition, diversity, and ecology of the microbiome.}, }
@article {pmid30694341, year = {2019}, author = {Ruiz-Ripa, L and Gómez, P and Alonso, CA and Camacho, MC and de la Puente, J and Fernández-Fernández, R and Ramiro, Y and Quevedo, MA and Blanco, JM and Zarazaga, M and Höfle, U and Torres, C}, title = {Detection of MRSA of Lineages CC130-mecC and CC398-mecA and Staphylococcus delphini-lnu(A) in Magpies and Cinereous Vultures in Spain.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01328-4}, pmid = {30694341}, issn = {1432-184X}, support = {SAF2016-76571-R//Ministerio de Econom?a, Industria y Competitividad, Gobierno de Espa?a/ ; }, abstract = {The aim of this study was to determine the carriage rate of coagulase-positive staphylococci (CoPS) in wild birds and to characterize recovered isolates. Tracheal samples from 324 wild birds, obtained in different Spanish regions during 2015-2016, were screened for CoPS carriage. The antimicrobial resistance profile and the virulence gene content were investigated. Molecular typing was performed by spa, agr, MLST, SCCmec, and S. delphini group classification. CoPS were recovered from 26 samples of wild birds (8.3%), and 27 isolates were further characterized. Two CoPS species were detected: S. aureus (n = 15; eight cinereous vultures and seven magpies) and S. delphini (n = 12; 11 cinereous vultures and one red kite). Thirteen S. aureus were methicillin-resistant (MRSA) and the remaining two strains were methicillin-susceptible (MSSA). Twelve MRSA were mecC-positive, typed as t843-ST1583/ST1945/ST1581/ST1571 (n = 11) and t1535-ST1945 (n = 1) (all of clonal-complex CC130); they were susceptible to the non-β-lactams tested. The remaining MRSA strain carried the mecA gene, was typed as t011-ST398-CC398-agrI-SCCmec-V, and showed a multiresistance phenotype. MSSA isolates were ascribed to lineages ST97-CC97 and ST425-CC425. All S. aureus lacked the studied virulence genes (lukS/F-PV, tst, eta, etb, and etd), and the IEC type E (with scn and sak genes) was detected in four mecC-positive and one MSSA isolates. S. delphini strains were methicillin-susceptible but showed resistance to at least one of the antimicrobials tested, with high penicillin (75%, with blaZ gene) and tetracycline [58%, with tet(K)± tet(L)] resistance rates. All S. delphini isolates presented the virulence genes lukS-I, siet, and se-int, and four carried the clindamycin-resistance lnu(A) gene.}, }
@article {pmid30689848, year = {2019}, author = {Xu, CQ and Liu, H and Zhou, SS and Zhang, DX and Zhao, W and Wang, S and Chen, F and Sun, YQ and Nie, S and Jia, KH and Jiao, SQ and Zhang, RG and Yun, QZ and Guan, W and Wang, X and Gao, Q and Bennetzen, JL and Maghuly, F and Porth, I and de Peer, YV and Wang, XR and Ma, Y and Mao, JF}, title = {Genome sequence of Malania oleifera, a tree with great value for nervonic acid production.}, journal = {GigaScience}, volume = {}, number = {}, pages = {}, doi = {10.1093/gigascience/giy164}, pmid = {30689848}, issn = {2047-217X}, abstract = {Background: Malania oleifera, a member of the Olacaceae family, is an IUCN Red Listed tree, endemic and restricted to the Karst region of South West China. This tree's seed is valued for its high content of precious fatty acids (especially nervonic acid). However, studies on its genetic make-up, and fatty acid biogenesis are severely hampered by a lack of molecular and genetic tools.<br><br>Findings: We generated 51 Gigabases (Gb) and 135 Gb of raw DNA sequences, using PacBio Single-Molecule Real-Time (SMRT) and 10x Genomics sequencing, respectively. A final genome assembly, with a scaffold N50 size of 4.65 Megabases (Mb) and a total length of 1.51 Gb, was obtained by primary assembly based on PacBio long reads plus scaffolding with 10x Genomics reads. Identified repeats constituted ∼82% of the genome, and 24,064 protein-coding genes were predicted with high support. The genome has low heterozygosity and shows no evidence for recent whole genome duplication. Metabolic pathway genes relating to the accumulation of long chain fatty acid were identified and studied in detail.<br><br>Conclusions: Here, we provide the first genome assembly and gene annotation for M. oleifera. The availability of these resources will be of great importance for conservation biology, and for the functional genomics of nervonic acid biosynthesis.}, }
@article {pmid30689307, year = {2019}, author = {Wackett, LP}, title = {Evolutionary microbial ecology: An annotated selection of World Wide Web sites relevant to the topics in environmental microbiology.}, journal = {Environmental microbiology reports}, volume = {11}, number = {1}, pages = {48-49}, doi = {10.1111/1758-2229.12734}, pmid = {30689307}, issn = {1758-2229}, }
@article {pmid30689286, year = {2019}, author = {Berg, JS and Pjevac, P and Sommer, T and Buckner, CRT and Philippi, M and Hach, PF and Liebeke, M and Holtappels, M and Danza, F and Tonolla, M and Sengupta, A and Schubert, CJ and Milucka, J and Kuypers, MMM}, title = {Dark aerobic sulfide oxidation by anoxygenic phototrophs in anoxic waters.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14543}, pmid = {30689286}, issn = {1462-2920}, abstract = {Anoxygenic phototrophic sulfide oxidation by green and purple sulfur bacteria (PSB) plays a key role in sulfide removal from anoxic shallow sediments and stratified waters. Although some PSB can also oxidize sulfide with nitrate and oxygen, little is known about the prevalence of this chemolithotrophic lifestyle in the environment. In this study, we investigated the role of these phototrophs in light-independent sulfide removal in the chemocline of Lake Cadagno. Our temporally resolved, high-resolution chemical profiles indicated that dark sulfide oxidation was coupled to high oxygen consumption rates of ~9 μM O2 ·h-1 . Single-cell analyses of lake water incubated with 13 CO2 in the dark revealed that Chromatium okenii was to a large extent responsible for aerobic sulfide oxidation and it accounted for up to 40 % of total dark carbon fixation. The genome of Chr. okenii reconstructed from the Lake Cadagno metagenome confirms its capacity for microaerophilic growth and provides further insights into its metabolic capabilities. Moreover, our genomic and single-cell data indicated that other PSB grow microaerobically in these apparently anoxic waters. Altogether, our observations suggest that aerobic respiration may not only play an underappreciated role in anoxic environments, but also that organisms typically considered strict anaerobes may be involved. This article is protected by copyright. All rights reserved.}, }
@article {pmid30687882, year = {2019}, author = {Liu, J and Tu, T and Gao, G and Bartlam, M and Wang, Y}, title = {Biogeography and Diversity of Freshwater Bacteria on a River Catchment Scale.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01323-9}, pmid = {30687882}, issn = {1432-184X}, support = {2015CB459000//Ministry of Science and Technology of the People's Republic of China/ ; 31670498//National Natural Science Foundation of China/ ; 31322012//National Natural Science Foundation of China/ ; }, abstract = {To illustrate how freshwater bacterial community changes with geographic gradient, we investigated the spatial changes of bacterial abundance and community structures from over 200 samples on a catchment scale in the Songhua River using heterotrophic plate counts, flow cytometry, denaturing gradient gel electrophoresis, and pyrosequencing analysis. The results showed that the mainstream had higher cultivable bacteria and total bacterial concentration than tributaries in the Songhua River catchment. Response model analysis demonstrated that the bacterial community exhibits a biogeographical signature even in an interconnected river network system, and the total bacterial concentration and biodiversity were significantly correlated to latitude (p < 0.001) and longitude (p < 0.001). Multivariate redundancy analysis indicated that temperature was the most important factor driving bacterial community structure in the Songhua River, which accounts for 35.30% variance of communities, then dissolved oxygen (17.60%), latitude (17.60%), longitude (11.80%), and pH (5.88%). High-throughput pyrosequencing revealed that at the phylum level, Proteobacteria was numerically dominant (89.6%) in river catchment, followed by Bacteroidetes (8.1%) and Cyanobacteria (1.2%). The overall results revealed that the bacterial community was driven by geographical distance regardless of the continuum of the river on a catchment scale.}, }
@article {pmid30687755, year = {2018}, author = {Kuang, X and Chen, V and Xu, X}, title = {Novel Approaches to the Control of Oral Microbial Biofilms.}, journal = {BioMed research international}, volume = {2018}, number = {}, pages = {6498932}, doi = {10.1155/2018/6498932}, pmid = {30687755}, issn = {2314-6141}, abstract = {Effective management of biofilm-related oral infectious diseases is a global challenge. Oral biofilm presents increased resistance to antimicrobial agents and elevated virulence compared with planktonic bacteria. Antimicrobial agents, such as chlorhexidine, have proven effective in the disruption/inhibition of oral biofilm. However, the challenge of precisely and continuously eliminating the specific pathogens without disturbing the microbial ecology still exists, which is a major factor in determining the virulence of a multispecies microbial consortium and the consequent development of oral infectious diseases. Therefore, several novel approaches are being developed to inhibit biofilm virulence without necessarily inducing microbial dysbiosis of the oral cavity. Nanoparticles, such as pH-responsive enzyme-mimic nanoparticles, have been developed to specifically target the acidic niches within the oral biofilm where tooth demineralization readily occurs, in effect controlling dental caries. Quaternary ammonium salts (QAS) such as dimethylaminododecyl methacrylate (DMADDM), when incorporated into dental adhesives or resin composite, have also shown excellent and durable antimicrobial activity and thus could effectively inhibit the occurrence of secondary caries. In addition, custom-designed small molecules, natural products and their derivatives, as well as basic amino acids such as arginine, have demonstrated ecological effects by modulating the virulence of the oral biofilm without universally killing the commensal bacteria, indicating a promising approach to the management of oral infectious diseases such as dental caries and periodontal diseases. This article aims to introduce these novel approaches that have shown potential in the control of oral biofilm. These methods may be utilized in the near future to effectively promote the clinical management of oral infectious diseases and thus benefit oral health.}, }
@article {pmid30685711, year = {2019}, author = {Vick, SHW and Greenfield, P and Pinetown, KL and Sherwood, N and Gong, S and Tetu, SG and Midgley, DJ and Paulsen, IT}, title = {Succession Patterns and Physical Niche Partitioning in Microbial Communities from Subsurface Coal Seams.}, journal = {iScience}, volume = {12}, number = {}, pages = {152-167}, doi = {10.1016/j.isci.2019.01.011}, pmid = {30685711}, issn = {2589-0042}, abstract = {The subsurface represents a largely unexplored frontier in microbiology. Here, coal seams present something of an oasis for microbial life, providing moisture, warmth, and abundant fossilized organic material. Microbes in coal seams are thought to syntrophically mobilize fossilized carbon from the geosphere to the biosphere. Despite the environmental and economic importance of this process, little is known about the microbial ecology of coal seams. In the current study, ecological succession and spatial niche partitioning are explored in three coal seam microbial communities. Scanning electron microscopic visualization and 16S rRNA sequencing track changes in microbial communities over time, revealing distinct attached and planktonic communities displaying patterns of ecological succession. Attachment to the coal surface is biofilm mediated on Surat coal, whereas microbes on Sydney and Gunnedah coal show different attachment processes. This study demonstrates that coal seam microbial communities undergo spatial niche partitioning during periods of succession as microbes colonize coal environments.}, }
@article {pmid30684803, year = {2019}, author = {Kumar, M and Jaiswal, S and Sodhi, KK and Shree, P and Singh, DK and Agrawal, PK and Shukla, P}, title = {Antibiotics bioremediation: Perspectives on its ecotoxicity and resistance.}, journal = {Environment international}, volume = {124}, number = {}, pages = {448-461}, doi = {10.1016/j.envint.2018.12.065}, pmid = {30684803}, issn = {1873-6750}, abstract = {Antibiotic is one of the most significant discoveries and have brought a revolution in the field of medicine for human therapy. In addition to the medical uses, antibiotics have broad applications in agriculture and animal husbandry. In developing nations, antibiotics use have helped to increase the life expectancy by lowering the deaths due to bacterial infections, but the risks associated with antibiotics pollution is largely affecting people. Since antibiotics are released partially degraded and undegraded into environment creating antibiotic pollution, and its bioremediation is a challenging task. In the present review, we have discussed the primary antibiotic sources like hospitals, dairy, and agriculture causing antibiotic pollution and their innovative detection methods. The strong commitment towards the resistance prevention and participation, nations through strict policies and their implementations now come to fight against the antibiotic resistance under WHO. The review also deciphers the bacterial evolution based strategies to overcome the effects of antibiotics, so the antibiotic degradation and elimination from the environment and its health benefits. The present review focuses on the environmental sources of antibiotics, it's possible degradation mechanisms, health effects, and bacterial antibiotics resistance mechanisms.}, }
@article {pmid30680433, year = {2019}, author = {Goetghebuer, L and Bonal, M and Faust, K and Servais, P and George, IF}, title = {The Dynamic of a River Model Bacterial Community in Two Different Media Reveals a Divergent Succession and an Enhanced Growth of Most Strains Compared to Monocultures.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01322-w}, pmid = {30680433}, issn = {1432-184X}, support = {T.1037.14//Fonds De La Recherche Scientifique - FRS-FNRS (BE)/ ; }, abstract = {The dynamic of a community of 20 bacterial strains isolated from river water was followed in R2 broth and in autoclaved river water medium for 27 days in batch experiments. At an early stage of incubation, a fast-growing specialist strain, Acinetobater sp., dominated the community in both media. Later on, the community composition in both media diverged but was highly reproducible across replicates. In R2, several strains previously reported to degrade multiple simple carbon sources prevailed. In autoclaved river water, the community was more even and became dominated by several strains growing faster or exclusively in that medium. Those strains have been reported in the literature to degrade complex compounds. Their growth rate in the community was 1.5- to 7-fold greater than that observed in monoculture. Furthermore, those strains developed simultaneously in the community. Together, our results suggest the existence of cooperative interactions within the community incubated in autoclaved river water.}, }
@article {pmid30678814, year = {2019}, author = {Lavefve, L and Marasini, D and Carbonero, F}, title = {Microbial Ecology of Fermented Vegetables and Non-Alcoholic Drinks and Current Knowledge on Their Impact on Human Health.}, journal = {Advances in food and nutrition research}, volume = {87}, number = {}, pages = {147-185}, doi = {10.1016/bs.afnr.2018.09.001}, pmid = {30678814}, issn = {1043-4526}, abstract = {Fermented foods are currently experiencing a re-discovery, largely driven by numerous health benefits claims. While fermented dairy, beer, and wine (and other alcoholic fermented beverages) have been the subject of intensive research, other plant-based fermented foods that are in some case widely consumed (kimchi/sauerkraut, pickles, kombucha) have received less scientific attention. In this chapter, the current knowledge on the microbiology and potential health benefits of such plant-based fermented foods are presented. Kimchi is the most studied, characterized by primarily acidic fermentation by lactic acid bacteria. Anti-obesity and anti-hypertension properties have been reported for kimchi and other pickled vegetables. Kombucha is the most popular non-alcoholic fermented drink. Kombucha's microbiology is remarkable as it involves all fermenters described in known fermented foods: lactic acid bacteria, acetic acid bacteria, fungi, and yeasts. While kombucha is often hyped as a &quot;super-food,&quot; only antioxidant and antimicrobial properties toward foodborne pathogens are well established; and it is unknown if these properties incur beneficial impact, even in vitro or in animal models. The mode of action that has been studied and demonstrated the most is the probiotic one. However, it can be expected that fermentation metabolites may be prebiotic, or influence host health directly. To conclude, plant-based fermented foods and drinks are usually safe products; few negative reports can be found, but more research, especially human dietary intervention studies, are warranted to substantiate any health claim.}, }
@article {pmid30678161, year = {2019}, author = {Snelson, M and Coughlan, MT}, title = {Dietary Advanced Glycation End Products: Digestion, Metabolism and Modulation of Gut Microbial Ecology.}, journal = {Nutrients}, volume = {11}, number = {2}, pages = {}, doi = {10.3390/nu11020215}, pmid = {30678161}, issn = {2072-6643}, abstract = {The formation of advanced glycation end products (AGEs) in foods is accelerated with heat treatment, particularly within foods that are cooked at high temperatures for long periods of time using dry heat. The modern processed diet is replete with AGEs, and excessive AGE consumption is thought to be associated with a number of negative health effects. Many dietary AGEs have high molecular weight and are not absorbed in the intestine, and instead pass through to the colon, where they are available for metabolism by the colonic bacteria. Recent studies have been conducted to explore the effects of AGEs on the composition of the gut microbiota as well as the production of beneficial microbial metabolites, in particular, short-chain fatty acids. However, there is conflicting evidence regarding the impact of dietary AGEs on gut microbiota reshaping, which may be due, in part, to the formation of alternate compounds during the thermal treatment of foods. This review summarises the current evidence regarding dietary sources of AGEs, their gastrointestinal absorption and role in gut microbiota reshaping, provides a brief overview of the health implications of dietary AGEs and highlights knowledge gaps and avenues for future study.}, }
@article {pmid30677885, year = {2019}, author = {Young, JM and Skvortsov, T and Kelleher, BP and Mahaney, WC and Somelar, P and Allen, CCR}, title = {Effect of soil horizon stratigraphy on the microbial ecology of alpine paleosols.}, journal = {The Science of the total environment}, volume = {657}, number = {}, pages = {1183-1193}, doi = {10.1016/j.scitotenv.2018.11.442}, pmid = {30677885}, issn = {1879-1026}, abstract = {There is remarkable potential for research at the interface between the earth sciences and environmental microbiology that may lead to advances in our understanding of the role of bacterial communities in the surface or subsurface environment of our planet. One mainstay of sedimentary classification is the concept of differential soil and/or paleosol horizons being the result of primarily physical and chemical weathering, with relatively little understanding of how microbial communities between these stratified horizons differ, if at all. In this study we evaluate the differences in microbial community taxonomy and biogeochemical functional potential between stratified soil horizons in an alpine paleosol environment using next-generation sequencing (NGS) shotgun sequencing. Paleosols represent a unique environment to study the effect of differences soil horizon environments on the microbial community due to their relative isolation, and the fact that three distinct stratified soil horizons can be identified within the top 30 cm of the soil. This enables us to assess variation in microbial community composition that will be relatively distinct from variation due to distance alone. We test the hypothesis that variation in soil community composition is linked to variation in the physical and chemical parameters that define stratigraphy. Multivariate statistical analysis of sequencing reads from soil horizons across five sampling sites revealed that 1223 microbial genera vary significantly and consistently in abundance across stratified soil horizons at class level. Specifically Ktedonobacter, Bacilli and Betaproteobacteria responded most strongly to soil depth. Alpha diversity showed a positive correlation with soil depth. Beta diversity, however, did not differ significantly between horizons. Genes involved in carbohydrate and nitrogen metabolism were found to be more abundant in Ah horizon samples. Closer inspection of carbohydrate metabolism genes revealed that genes involved in CO2 fixation, fermentation and saccharide metabolism decreased in abundance with depth while one‑carbon metabolism increased down profile.}, }
@article {pmid30674322, year = {2019}, author = {Adela, R and Reddy, PNC and Ghosh, TS and Aggarwal, S and Yadav, AK and Das, B and Banerjee, SK}, title = {Serum protein signature of coronary artery disease in type 2 diabetes mellitus.}, journal = {Journal of translational medicine}, volume = {17}, number = {1}, pages = {17}, doi = {10.1186/s12967-018-1755-5}, pmid = {30674322}, issn = {1479-5876}, abstract = {BACKGROUND: Coronary artery disease (CAD) is the leading cause of morbidity and mortality in patients with type 2 diabetes mellitus (T2DM). The purpose of the present study was to discriminate the Indian CAD patients with or without T2DM by using multiple pathophysiological biomarkers.<br><br>METHODS: Using sensitive multiplex protein assays, we assessed 46 protein markers including cytokines/chemokines, metabolic hormones, adipokines and apolipoproteins for evaluating different pathophysiological conditions of control, T2DM, CAD and T2DM with CAD patients (T2DM_CAD). Network analysis was performed to create protein-protein interaction networks by using significantly (p < 0.05) altered protein markers in each disease using STRING 10.5 database. We used two supervised analysis methods i.e., between class analysis (BCA) and principal component analysis (PCA) to reveals distinct biomarkers profiles. Further, random forest classification (RF) was used to classify the diseases by the panel of markers.<br><br>RESULTS: Our two supervised analysis methods BCA and PCA revealed a distinct biomarker profiles and high degree of variability in the marker profiles for T2DM_CAD and CAD. Thereafter, the present study identified multiple potential biomarkers to differentiate T2DM, CAD, and T2DM_CAD patients based on their relative abundance in serum. RF classified T2DM based on the abundance patterns of nine markers i.e., IL-1β, GM-CSF, glucagon, PAI-I, rantes, IP-10, resistin, GIP and Apo-B; CAD by 14 markers i.e., resistin, PDGF-BB, PAI-1, lipocalin-2, leptin, IL-13, eotaxin, GM-CSF, Apo-E, ghrelin, adipsin, GIP, Apo-CII and IP-10; and T2DM _CAD by 12 markers i.e., insulin, resistin, PAI-1, adiponectin, lipocalin-2, GM-CSF, adipsin, leptin, Apo-AII, rantes, IL-6 and ghrelin with respect to the control subjects. Using network analysis, we have identified several cellular network proteins like PTPN1, AKT1, INSR, LEPR, IRS1, IRS2, IL1R2, IL6R, PCSK9 and MYD88, which are responsible for regulating inflammation, insulin resistance, and atherosclerosis.<br><br>CONCLUSION: We have identified three distinct sets of serum markers for diabetes, CAD and diabetes associated with CAD in Indian patients using nonparametric-based machine learning approach. These multiple marker classifiers may be useful for monitoring progression from a healthy person to T2DM and T2DM to T2DM_CAD. However, these findings need to be further confirmed in the future studies with large number of samples.}, }
@article {pmid30668615, year = {2019}, author = {Snelson, M and Kellow, NJ and Coughlan, MT}, title = {Modulation of the Gut Microbiota by Resistant Starch as a Treatment of Chronic Kidney Diseases: Evidence of Efficacy and Mechanistic Insights.}, journal = {Advances in nutrition (Bethesda, Md.)}, volume = {}, number = {}, pages = {}, doi = {10.1093/advances/nmy068}, pmid = {30668615}, issn = {2156-5376}, abstract = {Chronic kidney disease (CKD) has been associated with changes in gut microbial ecology, or &quot;dysbiosis,&quot; which may contribute to disease progression. Recent studies have focused on dietary approaches to favorably alter the composition of the gut microbial communities as a treatment method in CKD. Resistant starch (RS), a prebiotic that promotes proliferation of gut bacteria such as Bifidobacteria and Lactobacilli, increases the production of metabolites including short-chain fatty acids, which confer a number of health-promoting benefits. However, there is a lack of mechanistic insight into how these metabolites can positively influence renal health. Emerging evidence shows that microbiota-derived metabolites can regulate the incretin axis and mitigate inflammation via expansion of regulatory T cells. Studies from animal models and patients with CKD show that RS supplementation attenuates the concentrations of uremic retention solutes, including indoxyl sulfate and p-cresyl sulfate. Here, we present the current state of knowledge linking the microbiome to CKD, we explore the efficacy of RS in animal models of CKD and in humans with the condition, and we discuss how RS supplementation could be a promising dietary approach for slowing CKD progression.}, }
@article {pmid30666369, year = {2019}, author = {Zhou, D and Feng, H and Schuelke, T and De Santiago, A and Zhang, Q and Zhang, J and Luo, C and Wei, L}, title = {Rhizosphere Microbiomes from Root Knot Nematode Non-infested Plants Suppress Nematode Infection.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01319-5}, pmid = {30666369}, issn = {1432-184X}, support = {31601685//National Natural Science Foundation of China/ ; CARS-24-C-01//Agriculture Research System of China/ ; 201403032//Special Fund for Agro-scientific Research in the Public Interest/ ; 4921701//Key Research and Development Program of Jiangsu Province/ ; }, abstract = {Root knot nematodes (RKN, Meloidogyne spp.) are serious pathogens of numerous crops worldwide. Understanding the roles plant rhizosphere soil microbiome play during RKN infection is very important. The current study aims at investigating the impacts of soil microbiome on the activity of RKN. In this study, the 16S rRNA genes of the bacterial communities from nematode-infested and non-infested rhizosphere soils from four different plants were sequenced on the Illumina Hi-Seq platform. The soil microbiome effects on RKN infection were tested in a greenhouse assay. The non-infested soils had more microbial diversity than the infested soils from all plant rhizospheres, and both soil types had exclusive microbial communities. The inoculation of the microbiomes from eggplant and cucumber non-infested soils to tomato plants significantly alleviated the RKN infection, while the microbiome from infested soil showed increased the RKN infection. Furthermore, bacteria Pseudomonas sp. and Bacillus sp. were screened out from non-infested eggplant soil and exhibited biocontrol activity to RKN on tomato. Our findings suggest that microbes may regulate RKN infection in plants and are involved in biocontrol of RKN.}, }
@article {pmid30666368, year = {2019}, author = {Clifford, EL and Varela, MM and De Corte, D and Bode, A and Ortiz, V and Herndl, GJ and Sintes, E}, title = {Taurine Is a Major Carbon and Energy Source for Marine Prokaryotes in the North Atlantic Ocean off the Iberian Peninsula.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01320-y}, pmid = {30666368}, issn = {1432-184X}, support = {P27696-B22//Austrian Science Fund/ ; I486-B09//Austrian Science Fund/ ; Z194-B17//Austrian Science Fund/ ; 268595//FP7 Ideas: European Research Council (FP7/2007-2013)/ ; 10MMA604024PR, 2010-2012//Xunta de Galicia/ ; CTM2011-24008//Ministerio de Econom?a y Competitividad/ ; }, abstract = {Taurine, an amino acid-like compound, acts as an osmostress protectant in many marine metazoans and algae and is released via various processes into the oceanic dissolved organic matter pool. Taurine transporters are widespread among members of the marine prokaryotic community, tentatively indicating that taurine might be an important substrate for prokaryotes in the ocean. In this study, we determined prokaryotic taurine assimilation and respiration throughout the water column along two transects in the North Atlantic off the Iberian Peninsula. Taurine assimilation efficiency decreased from the epipelagic waters from 55 ± 14% to 27 ± 20% in the bathypelagic layers (means of both transects). Members of the ubiquitous alphaproteobacterial SAR11 clade accounted for a large fraction of cells taking up taurine, especially in surface waters. Archaea (Thaumarchaeota + Euryarchaeota) were also able to take up taurine in the upper water column, but to a lower extent than Bacteria. The contribution of taurine assimilation to the heterotrophic prokaryotic carbon biomass production ranged from 21% in the epipelagic layer to 16% in the bathypelagic layer. Hence, we conclude that dissolved free taurine is a significant carbon and energy source for prokaryotes throughout the oceanic water column being utilized with similar efficiencies as dissolved free amino acids.}, }
@article {pmid30666243, year = {2018}, author = {Zhang, F and Xu, X and Huo, Y and Xiao, Y}, title = {Trichoderma-Inoculation and Mowing Synergistically Altered Soil Available Nutrients, Rhizosphere Chemical Compounds and Soil Microbial Community, Potentially Driving Alfalfa Growth.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3241}, doi = {10.3389/fmicb.2018.03241}, pmid = {30666243}, issn = {1664-302X}, abstract = {Trichoderma spp. are proposed as major plant growth-promoting fungi (PGPF) to increase plants growth and productivity. Mowing can stimulate aboveground regrowth to improve plant biomass and nutritional quality. However, the synergistic effects of Trichoderma and mowing on plants growth, particularly the underlying microbial mechanisms mediated by rhizosphere soil chemical compounds, have rarely been reported. In the present study, we employed Trichoderma harzianum T-63 and conducted a pot experiment to investigate the synergistic effect of Trichoderma-inoculation and mowing on alfalfa growth, and the potential soil microbial ecological mechanisms were also explored. Alfalfa treated with Trichoderma-inoculation and/or mowing (T, M, and TM) had significant (P < 0.05) increases in plant shoot and root dry weights and soil available nutrients (N, P, and K), compared with those of the control (CK). Non-metric multidimensional scaling (NMDS) demonstrated that the rhizosphere chemical compounds and soil bacterial and fungal communities were, respectively, separated according to different treatments. There was a clear significant (P < 0.05) positive correlation between alfalfa biomass and the relative abundance of Trichoderma (R2 = 0.3451, P = 0.045). However, Pseudomonas, Flavobacterium, Arthrobacter, Bacillus, Agrobacterium, and Actinoplanes were not significantly correlated with alfalfa biomass. According to structure equation modeling (SEM), Trichoderma abundance and available P served as primary contributors to alfalfa growth promotion. Additionally, Trichoderma-inoculation and mowing altered rhizosphere soil chemical compounds to drive the soil microbial community, indirectly influencing alfalfa growth. Our research provides a basis for promoting alfalfa growth from a soil microbial ecology perspective and may provide a scientific foundation for guiding the farming of alfalfa.}, }
@article {pmid30666239, year = {2018}, author = {Dinakaran, V and Mandape, SN and Shuba, K and Pratap, S and Sakhare, SS and Tabatabai, MA and Smoot, DT and Farmer-Dixon, CM and Kesavalu, LN and Adunyah, SE and Southerland, JH and Gangula, PR}, title = {Identification of Specific Oral and Gut Pathogens in Full Thickness Colon of Colitis Patients: Implications for Colon Motility.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3220}, doi = {10.3389/fmicb.2018.03220}, pmid = {30666239}, issn = {1664-302X}, abstract = {Impaired colon motility is one of the leading problems associated with inflammatory bowel disease (IBD). An expanding body of evidence supports the role of microbiome in normal gut function and in progression of IBD. The objective of this work is to determine whether diseased full thickness colon specimens, including the neuromuscular region (critical for colon motility function), contain specific oral and gut pathogens. In addition, we compared the differences in colon microbiome between Caucasians (CA) and African Americans (AA). Thirty-nine human full thickness colon (diseased colon and adjacent healthy colon) specimens were collected from Crohn's Colitis (CC) or Ulcerative Colitis (UC) patients while they underwent elective colon surgeries. We isolated and analyzed bacterial ribosomal RNA (rRNA) from colon specimens by amplicon sequencing of the 16S rRNA gene region. The microbiome proportions were quantified into Operational Taxonomic Units (OTUs) by analysis with Quantitative Insights Into Microbial ecology (QIIME) platform. Two hundred twenty-eight different bacterial species were identified by QIIME analysis. However, we could only decipher the species name of fifty-three bacteria. Our results show that proportion of non-detrimental bacteria in CC or UC colon samples were altered compared to adjacent healthy colon specimens. We further show, for the first time in full thickness colon specimens, that microbiome of CC and UC diseased specimens is dominated by putative oral pathogens belonging to the Phyla Firmicutes (Streptococcus, Staphylococcus, Peptostreptococcus), and Fusobacteria (Fusobacterium). In addition, we have identified patterns of differences in microbiome levels between CA and AA specimens with potential implications for health disparities research. Overall, our results suggest a significant association between oral and gut microbes in the modulation of colon motility in colitis patients.}, }
@article {pmid30661111, year = {2019}, author = {Plotnikov, AO and Balkin, AS and Gogoleva, NE and Lanzoni, O and Khlopko, YA and Cherkasov, SV and Potekhin, AA}, title = {High-Throughput Sequencing of the 16S rRNA Gene as a Survey to Analyze the Microbiomes of Free-Living Ciliates Paramecium.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01321-x}, pmid = {30661111}, issn = {1432-184X}, support = {16-14-10157//Russian Science Foundation/ ; 14-04-01796//Russian Foundation for Basic Research/ ; }, abstract = {Ciliates are the largest group of ubiquitous aquatic bacterivorous protists, and many species are easily cultivated. However, only few studies reported prokaryotic communities naturally associated with ciliate cells. Herein, we analyzed the microbiome composition of several strains of Paramecium (Ciliophora) originating from different locations and belonging to two morpho-species by high-throughput sequencing (HTS) of the 16S rRNA gene. Possible reasons of HTS results bias were addressed comparing DNA libraries obtained using different primers and different number of ciliate cells. Microbiomes associated with ciliates and their environments were always significantly different by prokaryotic taxonomic composition and bacterial richness. There were also pronounced differences between Paramecium strains. Interestingly, potentially pathogenic bacteria were revealed in Paramecium microbiomes.}, }
@article {pmid30658982, year = {2019}, author = {Jiao, S and Chen, W and Wei, G}, title = {Resilience and Assemblage of Soil Microbiome in Response to Chemical Contamination Combined with Plant Growth.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.02523-18}, pmid = {30658982}, issn = {1098-5336}, abstract = {Lacking knowledge of the microbial responses to environmental change at the species and functional levels hinders our ability to understand the intrinsic mechanisms underlying the maintenance of microbial ecosystems. Here, we present results from temporal microcosms that introduced inorganic and organic contaminants into agro-soils for 90 days, with three common legume plants. Temporal dynamics and assemblage of soil microbial communities and functions in response to contamination under the influence of different plant growth were explored via sequencing of the 16S rRNA amplicon and shotgun metagenomics. Soil microbial alpha-diversity and structure at the taxonomic and functional levels exhibited resilience patterns. Functional profiles showed greater resilience than taxonomic ones. Different legume plants imposed stronger selection on taxonomic profiles compared with functional ones. Network and random forest analyses revealed that the functional potential of soil microbial communities was fostered by various taxonomic groups. Betaproteobacteria were important predictors of key functional traits such as amino acid metabolism, nucleic acid metabolism, and hydrocarbon degradation. Our study reveals strong resilience of soil microbiome to chemical contamination and sensitive responses of taxonomic rather than functional profiles to selection processes induced by different legume plants. This is pivotal to develop approaches and policies for the protection of soil microbial diversity and functions in agro-ecosystems with different response strategies from global environmental drivers, such as soil contamination and plant invasion.Importance Exploring the microbial responses to environmental disturbances is a central issue in microbial ecology. Understanding the dynamic responses of soil microbial communities to chemical contamination and the microbe-soil-plant interactions is essential for forecasting the long-term changes in soil ecosystems. Nevertheless, few studies have applied multi-omics approaches to assess the microbial responses to soil contamination and the microbe-soil-plant interactions at the taxonomic and functional levels simultaneously. Our study reveals clear succession and resilience patterns of soil microbial diversity and structure in response to chemical contamination. Different legume plants exerted stronger selection processes on taxonomic than functional profiles in contaminated soils, which could benefit plant growth and fitness as well as foster the potential abilities of hydrocarbon-degradation and metal-tolerance. These results provide new insight into the resilience and assemblage of soil microbiome in response to environmental disturbances in agro-ecosystems at the species and functional levels.}, }
@article {pmid30655101, year = {2018}, author = {Wolters, M and Ahrens, J and Romaní-Pérez, M and Watkins, C and Sanz, Y and Benítez-Páez, A and Stanton, C and Günther, K}, title = {Dietary fat, the gut microbiota, and metabolic health - A systematic review conducted within the MyNewGut project.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.clnu.2018.12.024}, pmid = {30655101}, issn = {1532-1983}, abstract = {BACKGROUND AND AIMS: Studies indicate that dietary fat quantity and quality influence the gut microbiota composition which may as a consequence impact metabolic health. This systematic review aims to summarize the results of available studies in humans on dietary fat intake (quantity and quality), the intestinal microbiota composition and related cardiometabolic health outcomes.<br><br>METHODS: We performed a systematic review (CRD42018088685) following PRISMA guidelines and searched for literature in Medline, EMBASE, and Cochrane databases.<br><br>RESULTS: From 796 records, 765 records were excluded based on title or abstract. After screening of 31 full-text articles six randomized controlled trials (RCT) and nine cross-sectional observational studies were included. Our results of interventional trials do not suggest strong effects of different amounts and types of dietary fat on the intestinal microbiota composition or on metabolic health outcomes while observational studies indicate associations with the microbiota and health outcomes. High intake of fat and saturated fatty acids (SFA) may negatively affect microbiota richness and diversity and diets high in monounsaturated fatty acids (MUFA) may decrease total bacterial numbers whereas dietary polyunsaturated fatty acids (PUFA) had no effect on richness and diversity.<br><br>CONCLUSIONS: High fat and high SFA diets can exert unfavorable effects on the gut microbiota and are associated with an unhealthy metabolic state. Also high MUFA diets may negatively affect gut microbiota whereas PUFA do not seem to negatively affect the gut microbiota or metabolic health outcomes. However, data are not consistent and most RCT and observational studies showed risks of bias.}, }
@article {pmid30654982, year = {2019}, author = {Mandalakis, M and Gavriilidou, A and Polymenakou, PN and Christakis, CA and Nomikou, P and Medvecký, M and Kilias, SP and Kentouri, M and Kotoulas, G and Magoulas, A}, title = {Microbial strains isolated from CO2-venting Kolumbo submarine volcano show enhanced co-tolerance to acidity and antibiotics.}, journal = {Marine environmental research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.marenvres.2019.01.002}, pmid = {30654982}, issn = {1879-0291}, abstract = {As ocean acidification intensifies, there is growing global concern about the impacts that future pH levels are likely to have on marine life and ecosystems. By analogy, a steep decrease of seawater pH with depth is encountered inside the Kolumbo submarine volcano (northeast Santorini) as a result of natural CO2 venting, making this system ideal for ocean acidification research. Here, we investigated whether the increase of acidity towards deeper layers of Kolumbo crater had any effect on relevant phenotypic traits of bacterial isolates. A total of 31 Pseudomonas strains were isolated from both surface- (SSL) and deep-seawater layers (DSL), with the latter presenting a significantly higher acid tolerance. In particular, the DSL strains were able to cope with H+ levels that were 18 times higher. Similarly, the DSL isolates exhibited a significantly higher tolerance than SSL strains against six commonly used antibiotics and As(III). More importantly, a significant positive correlation was revealed between antibiotics and acid tolerance across the entire set of SSL and DSL isolates. Our findings imply that Pseudomonas species with higher resilience to antibiotics could be favored by the prospect of acidifying oceans. Further studies are required to determine if this feature is universal across marine bacteria and to assess potential ecological impacts.}, }
@article {pmid30647456, year = {2019}, author = {Junghare, M and Spiteller, D and Schink, B}, title = {Anaerobic degradation of xenobiotic isophthalate by the fermenting bacterium Syntrophorhabdus aromaticivorans.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-019-0348-5}, pmid = {30647456}, issn = {1751-7370}, abstract = {Syntrophorhabdus aromaticivorans is a syntrophically fermenting bacterium that can degrade isophthalate (3-carboxybenzoate). It is a xenobiotic compound which has accumulated in the environment for more than 50 years due to its global industrial usage and can cause negative effects on the environment. Isophthalate degradation by the strictly anaerobic S. aromaticivorans was investigated to advance our understanding of the degradation of xenobiotics introduced into nature, and to identify enzymes that might have ecological significance for bioremediation. Differential proteome analysis of isophthalate- vs benzoate-grown cells revealed over 400 differentially expressed proteins of which only four were unique to isophthalate-grown cells. The isophthalate-induced proteins include a phenylacetate:CoA ligase, a UbiD-like decarboxylase, a UbiX-like flavin prenyltransferase, and a hypothetical protein. These proteins are encoded by genes forming a single gene cluster that putatively codes for anaerobic conversion of isophthalate to benzoyl-CoA. Subsequently, benzoyl-CoA is metabolized by the enzymes of the anaerobic benzoate degradation pathway that were identified in the proteomic analysis. In vitro enzyme assays with cell-free extracts of isophthalate-grown cells indicated that isophthalate is activated to isophthalyl-CoA by an ATP-dependent isophthalate:CoA ligase (IPCL), and subsequently decarboxylated to benzoyl-CoA by a UbiD family isophthalyl-CoA decarboxylase (IPCD) that requires a prenylated flavin mononucleotide (prFMN) cofactor supplied by UbiX to effect decarboxylation. Phylogenetic analysis revealed that IPCD is a novel member of the functionally diverse UbiD family (de)carboxylases. Homologs of the IPCD encoding genes are found in several other bacteria, such as aromatic compound-degrading denitrifiers, marine sulfate-reducers, and methanogenic communities in a terephthalate-degrading reactor. These results suggest that metabolic strategies adapted for degradation of isophthalate and other phthalate are conserved between microorganisms that are involved in the anaerobic degradation of environmentally relevant aromatic compounds.}, }
@article {pmid30640580, year = {2019}, author = {Cornut, J and De Respinis, S and Tonolla, M and Petrini, O and Bärlocher, F and Chauvet, E and Bruder, A}, title = {Rapid characterization of aquatic hyphomycetes by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.}, journal = {Mycologia}, volume = {}, number = {}, pages = {1-13}, doi = {10.1080/00275514.2018.1528129}, pmid = {30640580}, issn = {1557-2536}, abstract = {Protein fingerprinting using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI--TOF MS) is a rapid, reliable, and economical method to characterize isolates of terrestrial fungi and other microorganisms. The objective of our study was to evaluate the suitability of MALDI-TOF MS for the identification of aquatic hyphomycetes, a polyphyletic group of fungi that play crucial roles in stream ecosystems. To this end, we used 34 isolates of 21 aquatic hyphomycete species whose identity was confirmed by spore morphology and internal transcribed spacer (ITS1-5.8S-ITS2 = ITS) nuc rDNA sequencing. We tested the efficiency of three protein extraction methods, including chemical and mechanical treatments using 13 different protocols, with the objective of producing high-quality MALDI-TOF mass spectra. In addition to extraction protocols, mycelium age was identified as a key parameter affecting protein extraction efficiency. The dendrogram based on mass-spectrum similarity indicated good and relevant taxonomic discrimination; the tree structure was comparable to that of the phylogram based on ITS sequences. Consequently, MALDI-TOF MS could reliably identify the isolates studied and provided greater taxonomic accuracy than classical morphological methods. MALDI-TOF MS seems suited for rapid characterization and identification of aquatic hyphomycete species.}, }
@article {pmid30636276, year = {2019}, author = {Zak, DR and Pellitier, PT and Argiroff, WA and Castillo, B and James, TY and Nave, LE and Averill, C and Beidler, K and Bhatnagar, J and Blesh, J and Classen, AT and Craig, M and Fernandez, CW and Gundersen, P and Johansen, R and Koide, RT and Lilleskov, EA and Lindahl, BD and Nadelhoffer, KJ and Phillips, RP and Tunlid, A}, title = {Exploring the role of ectomycorrhizal fungi in soil carbon dynamics.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.15679}, pmid = {30636276}, issn = {1469-8137}, abstract = {The extent to which ectomycorrhizal fungi (ECM) enable plants to access organic nitrogen (N) bound in soil organic matter (SOM) and transfer this growth-limiting nutrient to their plant host, has important implications for our understanding of plant-fungal interactions and the cycling and storage of carbon (C) and N in terrestrial ecosystems. Empirical evidence currently supports a range of perspectives, suggesting that ECM vary in their ability to provide their host with N bound in SOM, and that this capacity can both positively and negatively influence soil C storage. To help resolve the multiplicity of observations, we gathered a group of researchers to explore the role of ECM fungi in soil C dynamics, and propose new directions that hold promise to resolve competing hypotheses and contrasting observations. In this Viewpoint, we summarize these deliberations and identify areas of inquiry that hold promise for increasing our understanding of these fundamental and widespread plant symbionts and their role in ecosystem level biogeochemistry. This article is protected by copyright. All rights reserved.}, }
@article {pmid30635381, year = {2019}, author = {Yao, Z and Du, S and Liang, C and Zhao, Y and Dini-Andreote, F and Wang, K and Zhang, D}, title = {Bacterial community assembly in a typical estuarine marsh with multiple environmental gradients.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.02602-18}, pmid = {30635381}, issn = {1098-5336}, abstract = {Bacterial communities play essential roles in estuarine marsh ecosystems, but the interplay of ecological processes underlying their community assembly are poorly understood. Here, we studied the sediment bacterial communities along a linear gradient extending from the water-land junction toward a high-marsh, using the 16S rRNA gene amplicon sequencing. Bacterial community composition differed significantly between sediment transects. Physico-chemical properties, particularly sediment nutrient levels [i.e., total nitrogen (TN) and available phosphorus (AP)], as well as sediment physical structure and pH (P < 0.05) were strongly associated with the overall community variations. In addition, the topological properties of bacterial co-occurrence networks varied with the distance to the water-land junction. Both node- and network-level topological features revealed the bacterial network of sediments farthest from the junction to be less intense in complexity and interactions compared with other sediments. Phylogenetic null modelling analysis showed a progressive transition from stochastic to deterministic community assembly for the water-land junction sites toward the emerging terrestrial system. Taken together, this study provides a detailed outline of the distribution pattern of sediment bacterial community across the estuarine marsh and inform on the mechanisms and processes mediating bacterial community assembly in marsh soils.IMPORTANCESalt marshes represent highly dynamic ecosystems where the atmosphere, continents and the ocean interact. The bacterial distribution in this ecosystem is of great ecological concern, as it provides essential functions acting on ecosystem services. However, ecological processes mediating the bacterial assembly are poorly understood in salt marshes, especially the ones located in estuaries. In this study, the distribution and assembly of bacterial communities in an estuarine marsh located in south Hangzhou Bay were investigated. The results revealed an intricate interplay between stochastic and deterministic processes mediating the assembly of bacterial communities in the studied gradient system. Collectively, our findings illustrate the main drivers of community assembly taking into consideration changes in sediment abiotic variables and potential biotic interactions. Thus, we offer new insights into estuarine bacterial communities and illustrate the interplay of ecological processes shaping the assembly of bacterial communities in estuarine marsh ecosystems.}, }
@article {pmid30633563, year = {2019}, author = {Tomás-Barberán, FA and Espín, JC}, title = {Effect of Food Structure and Processing on (Poly)phenol-Gut Microbiota Interactions and the Effects on Human Health.}, journal = {Annual review of food science and technology}, volume = {}, number = {}, pages = {}, doi = {10.1146/annurev-food-032818-121615}, pmid = {30633563}, issn = {1941-1413}, abstract = {The two-way interaction of food (poly)phenols with the human gut microbiota has been studied throughout the past ten years. Research has shown that this interaction can be relevant to explain the health effects of these phytochemicals. The effect of the food matrix and food processing on this interaction has only been partially studied. In this article, the studies within this field have been critically reviewed, with a special focus on the following groups of phenolic metabolites: citrus flavanones, pomegranate ellagitannins, and cocoa proanthocyanidins. The available research shows that both the food matrix and food processing can be relevant factors for gut microbiota reshaping to reach a healthier microbial ecology and for the conversion of polyphenols to bioactive and bioavailable metabolites. There are, however, some research gaps that indicate a more comprehensive research approach is needed to reach valid conclusions regarding the gut microbiota-mediated effects of polyphenols on human health.}, }
@article {pmid30629579, year = {2019}, author = {Miranda-CasoLuengo, R and Lu, J and Williams, EJ and Miranda-CasoLuengo, AA and Carrington, SD and Evans, ACO and Meijer, WG}, title = {Delayed differentiation of vaginal and uterine microbiomes in dairy cows developing postpartum endometritis.}, journal = {PloS one}, volume = {14}, number = {1}, pages = {e0200974}, doi = {10.1371/journal.pone.0200974}, pmid = {30629579}, issn = {1932-6203}, abstract = {Bacterial overgrowth in the uterus is a normal event after parturition. In contrast to the healthy cow, animals unable to control the infection within 21 days after calving develop postpartum endometritis. Studies on the Microbial Ecology of the bovine reproductive tract have focused on either vaginal or uterine microbiomes. This is the first study that compares both microbiomes in the same animals. Terminal Restriction Fragment Length Polymorphism of the 16S rRNA gene showed that despite large differences associated to individuals, a shared community exist in vagina and uterus during the postpartum period. The largest changes associated with development of endometritis were observed at 7 days postpartum, a time when vaginal and uterine microbiomes were most similar. 16S rRNA pyrosequencing of the vaginal microbiome at 7 days postpartum showed at least three different microbiome types that were associated with later development of postpartum endometritis. All three microbiome types featured reduced bacterial diversity. Taken together, the above findings support a scenario where disruption of the compartmentalization of the reproductive tract during parturition results in the dispersal and mixing of the vaginal and uterine microbiomes, which subsequently are subject to differentiation. This differentiation was observed early postpartum in the healthy cow. In contrast, loss of bacterial diversity and dominance of the microbiome by few bacterial taxa were related to a delayed succession at 7DPP in cows that at 21 DPP or later were diagnosed with endometritis.}, }
@article {pmid30627762, year = {2019}, author = {Treichel, NS and Prevoršek, Z and Mrak, V and Kostrić, M and Vestergaard, G and Foesel, B and Pfeiffer, S and Stres, B and Schöler, A and Schloter, M}, title = {Effect of the Nursing Mother on the Gut Microbiome of the Offspring During Early Mouse Development.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01317-7}, pmid = {30627762}, issn = {1432-184X}, abstract = {The development of the gut microbiome is influenced by several factors. It is acquired during and after birth and involves both maternal and environmental factors as well as the genetic disposition of the offspring. However, it is unclear if the microbiome development is directly triggered by the mode of delivery and very early contact with the mother or mostly at later stages of initial development mainly by breast milk provided by the mother. To investigate to what extent the gut microbiome composition of the offspring is determined by the nursing mother, providing breast milk, compared to the birth mother during early development, a cross-fostering experiment involving two genetically different mouse lines was developed, being prone to be obese or lean, respectively. The microbiome of the colon was analyzed by high-throughput 16S rRNA gene sequencing, when the mice were 3 weeks old. The nursing mother affected both α- and β-diversity of the offspring's gut microbiome and shaped its composition. Especially bacterial families directly transferred by breast milk, like Streptococcaceae, or families which are strongly influenced by the quality of the breast milk like Rikenellaceae, showed a strong response. The core microbiome transferred from the obese nursing mother showed a higher robustness in comparison to the microbiome transferred from the lean nursing mother. Overall, the nursing mother impacts the gut microbial composition of the offspring during early development and might play an important role for health and disease of the animals at later stages of life.}, }
@article {pmid30627761, year = {2019}, author = {Fokin, SI and Serra, V and Ferrantini, F and Modeo, L and Petroni, G}, title = {&quot;Candidatus Hafkinia simulans&quot; gen. nov., sp. nov., a Novel Holospora-Like Bacterium from the Macronucleus of the Rare Brackish Water Ciliate Frontonia salmastra (Oligohymenophorea, Ciliophora): Multidisciplinary Characterization of the New Endosymbiont and Its Host.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1311-0}, pmid = {30627761}, issn = {1432-184X}, support = {PRA_2018_63//Università di Pisa/ ; }, abstract = {We characterized a novel Holospora-like bacterium (HLB) (Alphaproteobacteria, Holosporales) living in the macronucleus of the brackish water ciliate Frontonia salmastra. This bacterium was morphologically and ultrastructurally investigated, and its life cycle and infection capabilities were described. We also obtained its 16S rRNA gene sequence and performed in situ hybridization experiments with a specifically-designed probe. A new taxon, &quot;Candidatus Hafkinia simulans&quot;, was established for this HLB. The phylogeny of the family Holosporaceae based on 16S rRNA gene sequences was inferred, adding to the already available data both the sequence of the novel bacterium and those of other Holospora and HLB species recently characterized. Our phylogenetic analysis provided molecular support for the monophyly of HLBs and placed the new endosymbiont as the sister genus of Holospora. Additionally, the host ciliate F. salmastra, recorded in Europe for the first time, was concurrently described through a multidisciplinary study. Frontonia salmastra's phylogenetic position in the subclass Peniculia and the genus Frontonia was assessed according to 18S rRNA gene sequencing. Comments on the biodiversity of this genus were added according to past and recent literature.}, }
@article {pmid30413475, year = {2019}, author = {Zerfaß, C and Christie-Oleza, JA and Soyer, OS}, title = {Manganese Oxide Biomineralization Provides Protection against Nitrite Toxicity in a Cell-Density-Dependent Manner.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {2}, pages = {}, doi = {10.1128/AEM.02129-18}, pmid = {30413475}, issn = {1098-5336}, abstract = {Manganese biomineralization is a widespread process among bacteria and fungi. To date, there is no conclusive experimental evidence for how and if this process impacts microbial fitness in the environment. Here, we show how a model organism for manganese oxidation is growth inhibited by nitrite, and that this inhibition is mitigated in the presence of manganese. We show that such manganese-mediated mitigation of nitrite inhibition is dependent on the culture inoculum size, and that manganese oxide (MnOX) forms granular precipitates in the culture, rather than sheaths around individual cells. We provide evidence that MnOX protection involves both its ability to catalyze nitrite oxidation into (nontoxic) nitrate under physiological conditions and its potential role in influencing processes involving reactive oxygen species (ROS). Taken together, these results demonstrate improved microbial fitness through MnOX deposition in an ecological setting, i.e., mitigation of nitrite toxicity, and point to a key role of MnOX in handling stresses arising from ROS.IMPORTANCE We present here a direct fitness benefit (i.e., growth advantage) for manganese oxide biomineralization activity in Roseobacter sp. strain AzwK-3b, a model organism used to study this process. We find that strain AzwK-3b in a laboratory culture experiment is growth inhibited by nitrite in manganese-free cultures, while the inhibition is considerably relieved by manganese supplementation and manganese oxide (MnOX) formation. We show that biogenic MnOX interacts directly with nitrite and possibly with reactive oxygen species and find that its beneficial effects are established through formation of dispersed MnOX granules in a manner dependent on the population size. These experiments raise the possibility that manganese biomineralization could confer protection against nitrite toxicity to a population of cells. They open up new avenues of interrogating this process in other species and provide possible routes to their biotechnological applications, including in metal recovery, biomaterials production, and synthetic community engineering.}, }
@article {pmid30625192, year = {2019}, author = {Ramírez-Fernández, L and Trefault, N and Carú, M and Orlando, J}, title = {Seabird and pinniped shape soil bacterial communities of their settlements in Cape Shirreff, Antarctica.}, journal = {PloS one}, volume = {14}, number = {1}, pages = {e0209887}, doi = {10.1371/journal.pone.0209887}, pmid = {30625192}, issn = {1932-6203}, abstract = {Seabirds and pinnipeds play an important role in biogeochemical cycling by transferring nutrients from aquatic to terrestrial environments. Indeed, soils rich in animal depositions have generally high organic carbon, nitrogen and phosphorus contents. Several studies have assessed bacterial diversity in Antarctic soils influenced by marine animals; however most have been conducted in areas with significant human impact. Thus, we chose Cape Shirreff, Livingston Island, an Antarctic Specially Protected Area designated mainly to protect the diversity of marine vertebrate fauna, and selected sampling sites with different types of animals coexisting in a relatively small space, and where human presence and impact are negligible. Using 16S rRNA gene analyses through massive sequencing, we assessed the influence of animal concentrations, via their modification of edaphic characteristics, on soil bacterial diversity and composition. The nutrient composition of soils impacted by Antarctic fur seals and kelp gulls was more similar to that of control soils (i.e. soils without visible presence of plants or animals), which may be due to the more active behaviour of these marine animals compared to other species. Conversely, the soils from concentrations of southern elephant seals and penguins showed greater differences in soil nutrients compared to the control. In agreement with this, the bacterial communities of the soils associated with these animals were most different from those of the control soils, with the soils of penguin colonies also possessing the lowest bacterial diversity. However, all the soils influenced by the presence of marine animals were dominated by bacteria belonging to Gammaproteobacteria, particularly those of the genus Rhodanobacter. Therefore, we conclude that the modification of soil nutrient composition by marine vertebrates promotes specific groups of bacteria, which could play an important role in the recycling of nutrients in terrestrial Antarctic ecosystems.}, }
@article {pmid30625112, year = {2019}, author = {Brooks, LE and Kaze, M and Sistrom, M}, title = {Where the plasmids roam: large-scale sequence analysis reveals plasmids with large host ranges.}, journal = {Microbial genomics}, volume = {}, number = {}, pages = {}, doi = {10.1099/mgen.0.000244}, pmid = {30625112}, issn = {2057-5858}, abstract = {Describing the role of plasmids and their contribution to the exchange of genetic material among bacteria is essential for understanding the fields of plasmid epidemiology, microbial ecology, and commercial and synthetic microbiology. Broad-host-range (BHR) plasmids are those that are found not only in a single bacterial species, but in members of different taxonomic groups and are of significant interest to researchers in many fields. We applied a novel approach to computationally identify new BHR plasmids, in which we searched for highly similar cognate plasmids within a comprehensive plasmid database. After identifying 125 plasmid groups with highly similar cognates found in multiple taxa, we closely examined BHR plasmids found in multiple families. The majority of our identified BHR plasmids are found in members of the Enterobacteriaceae and closely related taxa, while three BHR plasmids of potential commercial significance were found in two species of Cyanobacteria. One plasmid with an exceptionally broad host range was found in both Gram-positive and Gram-negative bacterial species. This analysis demonstrates the utility of this method in identifying new BHR plasmids while highlighting unknown ranges of previously documented plasmids.}, }
@article {pmid30625109, year = {2019}, author = {van der Aart, LT and Nouioui, I and Kloosterman, A and Ingual, JM and Willemse, J and Goodfellow, M and van Wezel, GP}, title = {Polyphasic classification of the gifted natural product producer Streptomyces roseifaciens sp. nov.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1099/ijsem.0.003215}, pmid = {30625109}, issn = {1466-5034}, abstract = {A polyphasic study was designed to establish the taxonomic status of a Streptomyces strain isolated from soil from the QinLing Mountains, Shaanxi Province, China, and found to be the source of known and new specialized metabolites. Strain MBT76T was found to have chemotaxonomic, cultural and morphological properties consistent with its classification in the genus Streptomyces. The strain formed a distinct branch in the Streptomyces16S rRNA gene tree and was closely related to the type strains of Streptomyces hiroshimensis and Streptomycesmobaraerensis. Multi-locus sequence analyses based on five conserved house-keeping gene alleles showed that strain MBT76T is closely related to the type strain of S. hiroshimensis, as was the case in analysis of a family of conserved proteins. The organism was also distinguished from S. hiroshimensis using cultural and phenotypic features. Average nucleotide identity and digital DNA-DNA hybridization values between the genomes of strain MBT76T and S. hiroshimensis DSM 40037T were 88.96 and 28.4±2.3%, respectively, which is in line with their assignment to different species. On the basis of this wealth of data it is proposed that strain MBT76T (=DSM 106196T=NCCB 100637T), be classified as a new species, Streptomycesroseifaciens sp. nov.}, }
@article {pmid30624643, year = {2019}, author = {Baldrian, P}, title = {The known and the unknown in soil microbial ecology.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiz005}, pmid = {30624643}, issn = {1574-6941}, abstract = {The methodical developments in the fields of molecular biology and analytical chemistry significantly increased the level of detail that we achieve when exploring soils and their microbial inhabitants. High-resolution description of microbial communities, detection of taxa with minor abundances, screening of gene expression or the detailed characterization of metabolomes are nowadays technically feasible. Despite all of this, our understanding of soil is limited in many ways. The imperfect tools to describe microbial communities and limited possibilities to assign traits to community members make it difficult to link microbes to functions. Also the analysis of processes exemplified by enzyme activity measurements is still imperfect. In the future, it is important to look at soil at a finer detail to obtain a better picture on the properties of individual microbes, their in situ interactions, metabolic rates and activity at a scale relevant to individual microbes. Scaling up is needed as well to get answers at ecosystem or biome levels and to enable global modelling. The recent development of novel tools including metabolomics, identification of genomes in metagenomics sequencing datasets or collection of trait data have the potential to bring soil ecology further. It will, however, always remain a highly demanding scientific discipline.}, }
@article {pmid30623212, year = {2019}, author = {de Sousa, AGG and Tomasino, MP and Duarte, P and Fernández-Méndez, M and Assmy, P and Ribeiro, H and Surkont, J and Leite, RB and Pereira-Leal, JB and Torgo, L and Magalhães, C}, title = {Diversity and Composition of Pelagic Prokaryotic and Protist Communities in a Thin Arctic Sea-Ice Regime.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-01314-2}, pmid = {30623212}, issn = {1432-184X}, support = {244646//Research Council of Norway/ ; NORTE-01-0145-FEDER-000031//Structured Program of R&amp;D&amp;I MarInfo/ ; Arktis 2030//Norwegian Ministries of Foreign Affairs and Climate and Environment/ ; NITROLIMIT - PTDC 2017 - PTDC/CTA-AMB/30997/2017//Funda??o para a Ci?ncia e a Tecnologia/ ; }, abstract = {One of the most prominent manifestations of climate change is the changing Arctic sea-ice regime with a reduction in the summer sea-ice extent and a shift from thicker, perennial multiyear ice towards thinner, first-year ice. These changes in the physical environment are likely to impact microbial communities, a key component of Arctic marine food webs and biogeochemical cycles. During the Norwegian young sea ICE expedition (N-ICE2015) north of Svalbard, seawater samples were collected at the surface (5 m), subsurface (20 or 50 m), and mesopelagic (250 m) depths on 9 March, 27 April, and 16 June 2015. In addition, several physical and biogeochemical data were recorded to contextualize the collected microbial communities. Through the massively parallel sequencing of the small subunit ribosomal RNA amplicon and metagenomic data, this work allows studying the Arctic's microbial community structure during the late winter to early summer transition. Results showed that, at compositional level, Alpha- (30.7%) and Gammaproteobacteria (28.6%) are the most frequent taxa across the prokaryotic N-ICE2015 collection, and also the most phylogenetically diverse. Winter to early summer trends were quite evident since there was a high relative abundance of thaumarchaeotes in the under-ice water column in late winter while this group was nearly absent during early summer. Moreover, the emergence of Flavobacteria and the SAR92 clade in early summer might be associated with the degradation of a spring bloom of Phaeocystis. High relative abundance of hydrocarbonoclastic bacteria, particularly Alcanivorax (54.3%) and Marinobacter (6.3%), was also found. Richness showed different patterns along the depth gradient for prokaryotic (highest at mesopelagic depth) and protistan communities (higher at subsurface depths). The microbial N-ICE2015 collection analyzed in the present study provides comprehensive new knowledge about the pelagic microbiota below drifting Arctic sea-ice. The higher microbial diversity found in late winter/early spring communities reinforces the need to continue with further studies to properly characterize the winter microbial communities under the pack-ice.}, }
@article {pmid30620427, year = {2019}, author = {Pasulka, A and Hu, SK and Countway, PD and Coyne, KJ and Cary, SC and Heidelberg, KB and Caron, DA}, title = {SSU-rRNA Gene Sequencing Survey of Benthic Microbial Eukaryotes from Guaymas Basin Hydrothermal Vent.}, journal = {The Journal of eukaryotic microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jeu.12711}, pmid = {30620427}, issn = {1550-7408}, abstract = {Microbial eukaryotes have important roles in marine food webs, but their diversity and activities in hydrothermal vent ecosystems are poorly characterized. In this study, we analyzed microbial eukaryotic communities associated with bacterial (Beggiatoa) mats in the 2,000 m deep-sea Guaymas Basin hydrothermal vent system using 18S rRNA gene high-throughput sequencing of the V4 region. We detected 6,954 distinct Operational Taxonomic Units (OTUs) across various mat systems. Of the sequences that aligned with known protistan phylotypes, most were affiliated with alveolates, especially dinoflagellates and ciliates, and cercozoans. OTU richness and community structure differed among sediment habitats (e.g., different mat types and cold sediments away from mats). Additionally, full-length 18S rRNA genes amplified and cloned from single-cells revealed the identities of some of the most commonly encountered, active ciliates in this hydrothermal vent ecosystem. Observations and experiments were also conducted to demonstrate that ciliates were trophically active and ingesting fluorescent bacteria or Beggiatoa trichomes. Our work suggests that the active and diverse protistan community at the Guaymas Basin hydrothermal vent ecosystem likely consumes substantial amounts of bacterial biomass, and that the different habitats, often defined by distances of just a few 10s of cm, select for particular assemblages and levels of diversity. This article is protected by copyright. All rights reserved.}, }
@article {pmid30619557, year = {2018}, author = {Duplouy, A and Minard, G and Lähteenaro, M and Rytteri, S and Saastamoinen, M}, title = {Silk properties and overwinter survival in gregarious butterfly larvae.}, journal = {Ecology and evolution}, volume = {8}, number = {24}, pages = {12443-12455}, doi = {10.1002/ece3.4595}, pmid = {30619557}, issn = {2045-7758}, abstract = {All organisms are challenged by encounters with parasites, which strongly select for efficient escape strategies in the host. The threat is especially high for gregarious species entering immobile periods, such as diapause. Larvae of the Glanville fritillary butterfly, Melitaea cinxia, spend the winter in diapause in groups of conspecifics each sheltered in a silk nest. Despite intensive monitoring of the population, we have little understanding of the ecological factors influencing larval survival over the winter in the field. We tested whether qualitative and quantitative properties of the silk nest contribute to larval survival over diapause. We used comparative proteomics, metabarcoding analyses, microscopic imaging, and in vitro experiments to compare protein composition of the silk, community composition of the silk-associated microbiota, and silk density from both wild-collected and laboratory-reared families, which survived or died in the field. Although most traits assessed varied across families, only silk density was correlated with overwinter survival in the field. The silk nest spun by gregarious larvae before the winter acts as an efficient breathable physical shield that positively affects larval survival during diapause. Such benefit may explain how this costly trait is conserved across populations of this butterfly species and potentially across other silk-spinning insect species.}, }
@article {pmid30619545, year = {2018}, author = {Alessi, AM and Redeker, KR and Chong, JPJ}, title = {A practical introduction to microbial molecular ecology through the use of isolation chips.}, journal = {Ecology and evolution}, volume = {8}, number = {24}, pages = {12286-12298}, doi = {10.1002/ece3.4748}, pmid = {30619545}, issn = {2045-7758}, abstract = {In the context of antimicrobial resistance as one of the most serious issues faced globally by health providers, we explored a practical introduction to molecular microbial ecology. We designed field work and practical experiments for third year members of a 4 year undergraduate Masters Program, in which the students employed traditional and novel isolation techniques to identify antimicrobial activities from soil dwelling microorganisms. Students gained experience in isolating DNA from complex microbial communities, amplifying 16S rRNA genes and applied richness/diversity indices as well as principal coordinate analyses to the interpretation of the data they obtained from high throughput sequencing. Our results confirmed that isolation chips facilitate the growth of a greater diversity and different species subset from the complex soil microorganism community than traditional plate spreading techniques. However, rarefaction of 16S rRNA amplicon sequencing data showed that the majority of observed species in soil remain unculturable by current methods. Based on the written reports produced by the students carrying out the work, we concluded that the described protocols are robust and informative, that these activities provide a good practical introduction to the theories and practice of molecular ecology and can be easily deployed to groups of six or more students in a cost-effective manner.}, }
@article {pmid30619197, year = {2018}, author = {Dyksma, S and Lenk, S and Sawicka, JE and Mußmann, M}, title = {Uncultured Gammaproteobacteria and Desulfobacteraceae Account for Major Acetate Assimilation in a Coastal Marine Sediment.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3124}, doi = {10.3389/fmicb.2018.03124}, pmid = {30619197}, issn = {1664-302X}, abstract = {Acetate is a key intermediate in anaerobic mineralization of organic matter in marine sediments. Its turnover is central to carbon cycling, however, the relative contribution of different microbial populations to acetate assimilation in marine sediments is unknown. To quantify acetate assimilation by in situ abundant bacterial populations, we incubated coastal marine sediments with 14C-labeled acetate and flow-sorted cells that had been labeled and identified by fluorescence in situ hybridization. Subsequently, scintillography determined the amount of 14C-acetate assimilated by distinct populations. This approach fostered a high-throughput quantification of acetate assimilation by phylogenetically identified populations. Acetate uptake was highest in the oxic-suboxic surface layer for all sorted bacterial populations, including deltaproteobacterial sulfate-reducing bacteria (SRB), which accounted for up to 32% of total bacterial acetate assimilation. We show that the family Desulfobulbaceae also assimilates acetate in marine sediments, while the more abundant Desulfobacteraceae dominated acetate assimilation despite lower uptake rates. Unexpectedly, members of Gammaproteobacteria accounted for the highest relative acetate assimilation in all sediment layers with up to 31-62% of total bacterial acetate uptake. We also show that acetate is used to build up storage compounds such as polyalkanoates. Together, our findings demonstrate that not only the usual suspects SRB but a diverse bacterial community may substantially contribute to acetate assimilation in marine sediments. This study highlights the importance of quantitative approaches to reveal the roles of distinct microbial populations in acetate turnover.}, }
@article {pmid30619181, year = {2018}, author = {Simonin, M and Cantarel, AAM and Crouzet, A and Gervaix, J and Martins, JMF and Richaume, A}, title = {Negative Effects of Copper Oxide Nanoparticles on Carbon and Nitrogen Cycle Microbial Activities in Contrasting Agricultural Soils and in Presence of Plants.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3102}, doi = {10.3389/fmicb.2018.03102}, pmid = {30619181}, issn = {1664-302X}, abstract = {Metal-oxide nanoparticles (NPs) such as copper oxide (CuO) NPs offer promising perspectives for the development of novel agro-chemical formulations of pesticides and fertilizers. However, their potential impact on agro-ecosystem functioning still remains to be investigated. Here, we assessed the impact of CuO-NPs (0.1, 1, and 100 mg/kg dry soil) on soil microbial activities involved in the carbon and nitrogen cycles in five contrasting agricultural soils in a microcosm experiment over 90 days. Additionally, in a pot experiment, we evaluated the influence of plant presence on the toxicity of CuO-NPs on soil microbial activities. CuO-NPs caused significant reductions of the three microbial activities measured (denitrification, nitrification, and soil respiration) at 100 mg/kg dry soil, but the low concentrations (0.1 and 1 mg/kg) had limited effects. We observed that denitrification was the most sensitive microbial activity to CuO-NPs in most soil types, while soil respiration and nitrification were mainly impacted in coarse soils with low organic matter content. Additionally, large decreases in heterotrophic microbial activities were observed in soils planted with wheat, even at 1 mg/kg for soil substrate-induced respiration, indicating that plant presence did not mitigate or compensate CuO-NP toxicity for microorganisms. These two experiments show that CuO-NPs can have detrimental effects on microbial activities in soils with contrasting physicochemical properties and previously exposed to various agricultural practices. Moreover, we observed that the negative effects of CuO-NPs increased over time, indicating that short-term studies (hours, days) may underestimate the risks posed by these contaminants in soils.}, }
@article {pmid30619134, year = {2018}, author = {Porcar, M and Louie, KB and Kosina, SM and Van Goethem, MW and Bowen, BP and Tanner, K and Northen, TR}, title = {Microbial Ecology on Solar Panels in Berkeley, CA, United States.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3043}, doi = {10.3389/fmicb.2018.03043}, pmid = {30619134}, issn = {1664-302X}, abstract = {Solar panels can be found practically all over the world and represent a standard surface that can be colonized by microbial communities that are resistant to harsh environmental conditions, including high irradiation, temperature fluctuations and desiccation. These properties make them not only ideal sources of stress-resistant bacteria, but also standard devices to study the microbial communities and their colonization process from different areas of Earth. We report here a comprehensive description of the microbial communities associated with solar panels in Berkeley, CA, United States. Cultivable bacteria were isolated to characterize their adhesive capabilities, and UV- and desiccation-resistance properties. Furthermore, a parallel culture-independent metagenomic and metabolomic approach has allowed us to gain insight on the taxonomic and functional nature of these communities. Metagenomic analysis was performed using the Illumina HiSeq2500 sequencing platform, revealing that the bacterial population of the Berkeley solar panels is composed mainly of Actinobacteria, Bacteroidetes and Proteobacteria, as well as lower amounts of Deinococcus-Thermus and Firmicutes. Furthermore, a clear predominance of Hymenobacter sp. was also observed. A functional analysis revealed that pathways involved in the persistence of microbes on solar panels (i.e., stress response, capsule development, and metabolite repair) and genes assigned to carotenoid biosynthesis were common to all metagenomes. On the other hand, genes involved in photosynthetic pathways and general autotrophic subsystems were rare, suggesting that these pathways are not critical for persistence on solar panels. Metabolomics was performed using a liquid chromatography tandem mass spectrometry (LC-MS/MS) approach. When comparing the metabolome of the solar panels from Berkeley and from Valencia (Spain), a very similar composition in polar metabolites could be observed, although some metabolites appeared to be differentially represented (for example, trigonelline, pantolactone and 5-valerolactone were more abundant in the samples from Valencia than in the ones from Berkeley). Furthermore, triglyceride metabolites were highly abundant in all the solar panel samples, and both locations displayed similar profiles. The comparison of the taxonomic profile of the Californian solar panels with those previously described in Spain revealed striking similarities, highlighting the central role of both selective pressures and the ubiquity of microbial populations in the colonization and establishment of microbial communities.}, }
@article {pmid30619117, year = {2018}, author = {López-García, A and Pineda-Quiroga, C and Atxaerandio, R and Pérez, A and Hernández, I and García-Rodríguez, A and González-Recio, O}, title = {Comparison of Mothur and QIIME for the Analysis of Rumen Microbiota Composition Based on 16S rRNA Amplicon Sequences.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3010}, doi = {10.3389/fmicb.2018.03010}, pmid = {30619117}, issn = {1664-302X}, abstract = {Background: Microbiome studies need to analyze massive sequencing data, which requires the use of sophisticated bioinformatics pipelines. Up to date, several tools are available, although the literature is scarce on studies that compare the performance of different bioinformatics pipelines on rumen microbiota when 16S rRNA amplicons are analyzed. The impact of the pipeline on the outcome of the results is also unknown, mainly in terms of the output from studies using these tools as an intermediate phenotype (pseudophenotypes). This study compares two commonly used software (Quantitative Insights Into Microbial Ecology) (QIIME) and mothur, and two microbial gene data bases (GreenGenes and SILVA) for 16S rRNA gene analysis, using metagenome read data collected from rumen content of a cohort of dairy cows. Results: We compared the relative abundance (RA) of the identified OTUs at the genus level. Both tools presented a high degree of agreement at identifying the most abundant genera: Bifidobacterium, Butyrivibrio, Methanobrevibacter, Prevotella, and Succiniclasticum (RA > 1%), regardless the database. There were no statistical differences between mothur and QIIME (P > 0.05) at estimating the overall RA of the most abundant (RA > 10%) genera, either using SILVA or GreenGenes. However, differences were found at RA < 10% (P < 0.05) when using GreenGenes as database, with mothur assigning OTUs to a larger number of genera and in larger RA for these less frequent microorganisms. With this database mothur resulted in larger richness (P < 0.05), more favorable rarefaction curves and a larger analytic sensitivity. These differences caused significant and relevant differences between tools at identifying the dissimilarity of microbiotas between pairs of animals. However, these differences were attenuated, but not erased, when SILVA was used as the reference database. Conclusion: The findings showed that the SILVA database seemed a preferred reference dataset for classifying OTUs from rumen microbiota. If this database was used, both QIIME and mothur produced comparable richness and diversity, and also in the RA of most common rumen microbes. However, important differences were found for less common microorganisms which impacted on the beta diversity calculated between pipelines. This may have relevant implications at studying global rumen microbiota.}, }
@article {pmid30618066, year = {2019}, author = {Flores-Uribe, J and Hevroni, G and Ghai, R and Pushkarev, A and Inoue, K and Kandori, H and Béjà, O}, title = {Heliorhodopsins are absent in diderm (Gram-negative) bacteria: Some thoughts and possible implications for activity.}, journal = {Environmental microbiology reports}, volume = {}, number = {}, pages = {}, doi = {10.1111/1758-2229.12730}, pmid = {30618066}, issn = {1758-2229}, abstract = {Microbial heliorhodopsins are a new type of rhodopsins, currently believed to engage in light sensing, with an opposite membrane topology compared to type-1 and type-2 rhodopsins. We determined heliorhodopsins presence/absence is monoderms and diderms representatives from the Tara Oceans and freshwater metagenomes as well as metagenome assembled genome collections. Heliorhodopsins are absent in diderms, confirming our previous observations in cultured Proteobacteria. We do not rule out the possibility that heliorhodopsins serve as light sensors. However, this does not easily explain their absence from diderms. Based on these observations, we speculate on the putative role of heliorhodopsins in light-driven transport of amphiphilic molecules. This article is protected by copyright. All rights reserved.}, }
@article {pmid30613848, year = {2019}, author = {Ye, S and Bhattacharjee, M and Siemann, E}, title = {Thermal Tolerance in Green Hydra: Identifying the Roles of Algal Endosymbionts and Hosts in a Freshwater Holobiont Under Stress.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-01315-1}, pmid = {30613848}, issn = {1432-184X}, abstract = {It has been proposed that holobionts (host-symbiont units) could swap endosymbionts, rapidly alter the hologenome (host plus symbiont genome), and increase their stress tolerance. However, experimental tests of individual and combined contributions of hosts and endosymbionts to holobiont stress tolerance are needed to test this hypothesis. Here, we used six green hydra (Hydra viridissima) strains to tease apart host (hydra) and symbiont (algae) contributions to thermal tolerance. Heat shock experiments with (1) hydra with their original symbionts, (2) aposymbiotic hydra (algae removed), (3) novel associations (a single hydra strain hosting different algae individually), and (4) control hydra (aposymbiotic hydra re-associated with their original algae) showed high variation in thermal tolerance in each group. Relative tolerances of strains were the same within original, aposymbiotic, and control treatments, but reversed in the novel associations group. Aposymbiotic hydra had similar or higher thermal tolerance than hydra with algal symbionts. Selection on the holobiont appears to be stronger than on either partner alone, suggesting endosymbiosis could become an evolutionary trap under climate change. Our results suggest that green hydra thermal tolerance is strongly determined by the host, with a smaller, non-positive role for the algal symbiont. Once temperatures exceed host tolerance limits, swapping symbionts is unlikely to allow these holobionts to persist. Rather, increases in host tolerance through in situ adaptation or migration of pre-adapted host strains appear more likely to increase local thermal tolerance. Overall, our results indicate green hydra is a valuable system for studying aquatic endosymbiosis under changing environmental conditions, and demonstrate how the host and the endosymbiont contribute to holobiont stress tolerance.}, }
@article {pmid30612185, year = {2019}, author = {Murphy, AE and Kolkmeyer, R and Song, B and Anderson, IC and Bowen, J}, title = {Bioreactivity and Microbiome of Biodeposits from Filter-Feeding Bivalves.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-01312-4}, pmid = {30612185}, issn = {1432-184X}, support = {OCE 1062882//National Science Foundation/ ; OCE 1233801//National Science Foundation/ ; LTER 0080381//National Science Foundation/ ; NA10OAR4170085//Virginia Sea Grant, Virginia Institute of Marine Science/ ; }, abstract = {Bivalves serve an important ecosystem function in delivering organic matter from pelagic to benthic zones and are important in mediating eutrophication. However, the fate of this organic matter (i.e., biodeposits) is an important consideration when assessing the ecological roles of these organisms in coastal ecosystems. In addition to environmental conditions, the processing of biodeposits is dependent on its composition and the metabolic capacity of the associated microbial community. The objectives of this study were to compare the biological reactivity, potential denitrification rates, and microbial communities of biodeposits sourced from different bivalve species: hard clam (Mercenaria mercenaria), eastern oyster (Crassostrea virginica), and ribbed mussel (Geukensia demissa). To our knowledge, this is the first study to investigate and compare the microbiome of bivalve biodeposits using high-throughput sequencing and provide important insight into the mechanisms by which bivalves may alter sediment microbial communities and benthic biogeochemical cycles. We show that clam biodeposits had significantly higher bioreactivity compared to mussel and oyster biodeposits, as reflected in higher dissolved inorganic carbon and ammonium production rates in controlled incubations. Potential denitrification rates were also significantly higher for clam biodeposits compared to oyster and mussel biodeposits. The microbial communities associated with the biodeposits were significantly different across bivalve species, with significantly greater abundances of Alteromonadales, Chitinophagales, Rhodobacterales, and Thiotrichales associated with the clam biodeposits. These bioreactivity and microbial differences across bivalve species are likely due to differences in bivalve physiology and feeding behavior and should be considered when evaluating the effects of bivalves on water quality and ecosystem function.}, }
@article {pmid30612184, year = {2019}, author = {Pan, J and Chen, Y and Wang, Y and Zhou, Z and Li, M}, title = {Vertical Distribution of Bathyarchaeotal Communities in Mangrove Wetlands Suggests Distinct Niche Preference of Bathyarchaeota Subgroup 6.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1309-7}, pmid = {30612184}, issn = {1432-184X}, support = {41506163,31622002,91851105//National Natural Science Foundation of China/ ; 31600093//National Natural Science Foundation of China/ ; }, abstract = {Bathyarchaeota is a diverse, abundant, and widespread archaeal phylum that may play an important role in global carbon cycling. The vertical distribution of Bathyarchaeota and environmental impact on bathyarchaeotal community in deep-sea and lake sediments are known; however, little information is available on Bathyarchaeota in eutrophic and brackish environments, such as mangrove wetlands. In the current study, we investigated the bathyarchaeotal community in the mangrove ecosystem of Futian Nature Reserve, Shenzhen. By slicing the profile into 2-cm layers from the surface to bottom, 110 sediment samples were obtained from three mangrove and three mud flat profiles. High-throughput sequencing of archaeal 16S rRNA genes, quantification of bathyarchaeotal 16S rRNA genes with optimized quantitative primers, and the ensuing statistical analyses revealed the vertical distribution of Bathyarchaeota in the mangrove ecosystem, indicating that Bathyarchaeota was the dominant archaeal phylum therein, with Bathyarchaeota subgroups 6, 8, 15, and 17 as the most abundant subgroups. The abundance of Bathyarchaeota was higher in the mangrove than in the mud flat and other oligotrophic or freshwater habitats. Total organic carbon (TOC) and nitric oxide were significantly correlated with the abundance of Bathyarchaeota, and pH was the major factor shaping the community composition. Further, the data suggested that Bathyarchaeota subgroup 6 preferentially dwelled in slightly acidic, high TOC, and subsurface environments, indicating a potentially distinct role in the global geochemical cycle. These findings expand the knowledge of the distribution and niche preference of Bathyarchaeota, emphasizing the need for continuous characterization of bathyarchaeotal subgroups.}, }
@article {pmid30612183, year = {2019}, author = {Ding, W and Zhang, W and Alikunhi, NM and Batang, Z and Pei, B and Wang, R and Chen, L and Al-Suwailem, A and Qian, PY}, title = {Metagenomic Analysis of Zinc Surface-Associated Marine Biofilms.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-01313-3}, pmid = {30612183}, issn = {1432-184X}, abstract = {Biofilms are a significant source of marine biofouling. Marine biofilm communities are established when microorganisms adhere to immersed surfaces. Despite the microbe-inhibiting effect of zinc surfaces, microbes can still attach to the surface and form biofilms. However, the diversity of biofilm-forming microbes that can attach to zinc surfaces and their common functional features remain elusive. Here, by analyzing 9,000,000 16S rRNA gene amplicon sequences and 270 Gb of metagenomic data, we comprehensively explored the taxa and functions related to biofilm formation in subtidal zones of the Red Sea. A clear difference was observed between the biofilm and adjacent seawater microbial communities in terms of the taxonomic structure at phylum and genus levels, and a huge number of genera were only present in the biofilms. Saturated alpha-diversity curves suggested the existence of more than 14,000 operational taxonomic units in one biofilm sample, which is much higher than previous estimates. Remarkably, the biofilms contained abundant and diverse transposase genes, which were localized along microbial chromosomal segments and co-existed with genes related to metal ion transport and resistance. Genomic analyses of two cyanobacterial strains that were abundant in the biofilms revealed a variety of metal ion transporters and transposases. Our analyses revealed the high diversity of biofilm-forming microbes that can attach to zinc surfaces and the ubiquitous role of transposase genes in microbial adaptation to toxic metal surfaces.}, }
@article {pmid30612083, year = {2018}, author = {Zhu, X and Campanaro, S and Treu, L and Kougias, PG and Angelidaki, I}, title = {Novel ecological insights and functional roles during anaerobic digestion of saccharides unveiled by genome-centric metagenomics.}, journal = {Water research}, volume = {151}, number = {}, pages = {271-279}, doi = {10.1016/j.watres.2018.12.041}, pmid = {30612083}, issn = {1879-2448}, abstract = {In typical anaerobic digestion (AD) systems, the microbial functional assertion is hampered by synchronised versatile metabolism required for heterogeneous substrates degradation. Thus, the intricate methanogenic process from organic compounds remains an enigma after decades of empirical operation. In this study, simplified AD microbial communities were obtained with substrate specifications and continuous reactor operation. Genome-centric metagenomic approach was followed to holistically investigate the metabolic pathways of the AD and the microbial synergistic networks. In total, 63 metagenome assembled genomes (MAGs) were assembled from 8 metagenomes acquired in specific methanogenic niches. The metabolic pathways were reconstructed from the annotated genes and their dynamicity under experimental conditions. The results show that the methanogenic niches nourish unique metabolism beyond current knowledge acquired from cultivation-based methods. A novel glucose mineralization model without acetate formation was proposed and asserted in a pair of syntrophs: Clostridiaceae sp. and Methanoculleus thermophilus. Moreover, the catabolic pathway was elucidated in uncharacterized syntrophic acetate oxidizers, Synergistaceae spp. A remarkable evolutionary insight is the discovery that electron transport and energy conservation mechanisms impose selective pressure on syntrophic partners. Overall, the functional roles of the individual microbes tightly rely on the catabolic pathways and cannot always be physiologically defined in accordance with conventional four-step AD concept. The substrate-specific systems provided a traceable microbial community to dissecting the AD process. The genome-centric metagenomics successfully constructed genomes of microbes that have not been previously isolated and illustrated metabolic pathways that beyond the current knowledge of AD process. This study provides new perspectives to unravel the AD microbial ecology and suggests more attention should be paid on uncharacterized metabolism specifically harboured by AD microbial communities.}, }
@article {pmid30610256, year = {2019}, author = {Mikhailov, IS and Zakharova, YR and Bukin, YS and Galachyants, YP and Petrova, DP and Sakirko, MV and Likhoshway, YV}, title = {Correction to: Co-occurrence Networks Among Bacteria and Microbial Eukaryotes of Lake Baikal During a Spring Phytoplankton Bloom.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1307-9}, pmid = {30610256}, issn = {1432-184X}, abstract = {The original version of this article unfortunately contained mistakes in the legends of figures.}, }
@article {pmid30610255, year = {2019}, author = {Xia, X and Cheung, S and Endo, H and Suzuki, K and Liu, H}, title = {Latitudinal and Vertical Variation of Synechococcus Assemblage Composition Along 170° W Transect From the South Pacific to the Arctic Ocean.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1308-8}, pmid = {30610255}, issn = {1432-184X}, support = {JPMJCR11A5//JST CREST program/ ; 24121004//JSPS Grant-in-Aid for Scientific Research on Innovative Areas/ ; 16128416 and 16101917//Research Grant Council of Hong Kong/ ; }, abstract = {Synechococcus is one of the most widely distributed and abundant picocyanobacteria in the global oceans. Although latitudinal variation of Synechococcus assemblage in marine surface waters has been observed, few studies compared Synechococcus assemblage composition in surface and subsurface waters at the basin scale. Here, we report marine Synechococcus diversity in the surface and deep chlorophyll maximum (DCM) layers along 170° W from the South Pacific to the Arctic Ocean in summer. Along the transect, spatial niche partitioning of Synechococcus lineages in the surface waters was clearly observed. Species richness of surface Synechococcus assemblage was positively correlated with water temperature. Clade CRD1 was dominant in the areas (15° S-10° N and 35-40° N) associated with upwelling, and there were 3 different subclades with distinct distribution. CRD1-A was restricted in the North Equatorial Current (5-10° N), CRD1-B dominated in the equatorial upwelling region (15° S-0.17° N), and CRD1-C was only distributed in the North Pacific Current (35-40° N). Similarities between the Synechococcus assemblages in the surface and DCM layers were high at the upwelling regions and areas where the mixed layer was deep, while low in the Subtropical Gyres with strong stratification. Clade I, CRD1-B, and CRD1-C were major Synechococcus lineages in the DCM layer. In particular, clade I, which is composed of 7 subclades with distinct thermal niches, was widely distributed in the DCM layer. Overall, our results provide new insights into not only the latitudinal distribution of Synechococcus assemblages, but also their vertical variation in the central Pacific.}, }
@article {pmid30610231, year = {2019}, author = {Andrei, AŞ and Salcher, MM and Mehrshad, M and Rychtecký, P and Znachor, P and Ghai, R}, title = {Niche-directed evolution modulates genome architecture in freshwater Planctomycetes.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-018-0332-5}, pmid = {30610231}, issn = {1751-7370}, support = {MSM200961801//Akademie Věd České Republiky (Academy of Sciences of the Czech Republic)/ ; PPPLZ: L200961651//Akademie Věd České Republiky (Academy of Sciences of the Czech Republic)/ ; 17-04828S//Grantová Agentura České Republiky (Grant Agency of the Czech Republic)/ ; 17-04828S//Grantová Agentura České Republiky (Grant Agency of the Czech Republic)/ ; }, abstract = {Freshwater environments teem with microbes that do not have counterparts in culture collections or genetic data available in genomic repositories. Currently, our apprehension of evolutionary ecology of freshwater bacteria is hampered by the difficulty to establish organism models for the most representative clades. To circumvent the bottlenecks inherent to the cultivation-based techniques, we applied ecogenomics approaches in order to unravel the evolutionary history and the processes that drive genome architecture in hallmark freshwater lineages from the phylum Planctomycetes. The evolutionary history inferences showed that sediment/soil Planctomycetes transitioned to aquatic environments, where they gave rise to new freshwater-specific clades. The most abundant lineage was found to have the most specialised lifestyle (increased regulatory genetic circuits, metabolism tuned for mineralization of proteinaceous sinking aggregates, psychrotrophic behaviour) within the analysed clades and to harbour the smallest freshwater Planctomycetes genomes, highlighting a genomic architecture shaped by niche-directed evolution (through loss of functions and pathways not needed in the newly acquired freshwater niche).}, }
@article {pmid30607437, year = {2019}, author = {Lupatini, M and Suleiman, AKA and Jacques, RJS and Lemos, LN and Pylro, VS and Van Veen, JA and Kuramae, EE and Roesch, LFW}, title = {Moisture Is More Important than Temperature for Assembly of Both Potentially Active and Whole Prokaryotic Communities in Subtropical Grassland.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1310-1}, pmid = {30607437}, issn = {1432-184X}, abstract = {Moisture and temperature play important roles in the assembly and functioning of prokaryotic communities in soil. However, how moisture and temperature regulate the function of niche- versus neutral-based processes during the assembly of these communities has not been examined considering both the total microbial community and the sole active portion with potential for growth in native subtropical grassland. We set up a well-controlled microcosm-based experiment to investigate the individual and combined effects of moisture and temperature on soil prokaryotic communities by simulating subtropical seasons in grassland. The prokaryotic populations with potential for growth and the total prokaryotic community were assessed by 16S rRNA transcript and 16S rRNA gene analyses, respectively. Moisture was the major factor influencing community diversity and structure, with a considerable effect of this factor on the total community. The prokaryotic populations with potential for growth and the total communities were influenced by the same assembly rules, with the niche-based mechanism being more influential in communities under dry condition. Our results provide new information regarding moisture and temperature in microbial communities of soil and elucidate how coexisting prokaryotic populations, under different physiological statuses, are shaped in native subtropical grassland soil.}, }
@article {pmid30604790, year = {2019}, author = {De Paepe, K and Verspreet, J and Rezaei, MN and Martinez, SH and Meysman, F and Van de Walle, D and Dewettinck, K and Courtin, CM and Van de Wiele, T}, title = {Modification of wheat bran particle size and tissue composition affects colonisation and metabolism by human faecal microbiota.}, journal = {Food &amp; function}, volume = {}, number = {}, pages = {}, doi = {10.1039/c8fo01272e}, pmid = {30604790}, issn = {2042-650X}, abstract = {Dietary modulation can alter the gut microbiota composition and activity, in turn affecting health. Particularly, dietary fibre rich foods, such as wheat bran, are an important nutrient source for the gut microbiota. Several processing methods have been developed to modify the functional, textural and breadmaking properties of wheat bran, which can affect the gut microbiota. We therefore studied the effect of enzyme treatment, particle size reduction and wheat kernel pearling on the faecal microbiota of ten healthy individuals. The most commonly studied health marker, associated to the gut microbiota activity is Short Chain Fatty Acid (SCFA) production. This study shows that modifying wheat bran physicochemical properties allows control over the extent and the rate of SCFA production by the faecal microbiota. Wheat bran pericarp fractions, depleted in starch and enriched in cellulose and highly branched arabinoxylans, were poorly fermentable compared to unmodified wheat bran, thus resulting in a reduced SCFA production with up to 20 mM. The nature of the SCFA, however, largely depends on the donor and can be linked to the individual's gut microbiota composition. The latter changed in an individually dependent manner in response to wheat bran modification. Some product dependent significant differences could still be identified across the ten donors. This product effect is more pronounced in the microbial community attached to the wheat bran residue as compared to the luminal microbial community. Generally, we find lower levels of Firmicutes, Bacteroidetes and Bifidobacterium and a higher abundance of Proteobacteria in the pericarp enriched wheat bran fractions, compared to unmodified wheat bran.}, }
@article {pmid30603770, year = {2019}, author = {Ishizawa, H and Kuroda, M and Inoue, K and Inoue, D and Morikawa, M and Ike, M}, title = {Colonization and Competition Dynamics of Plant Growth-Promoting/Inhibiting Bacteria in the Phytosphere of the Duckweed Lemna minor.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1306-x}, pmid = {30603770}, issn = {1432-184X}, support = {JPJMAL1108//Advanced Low Carbon Technology Research and Development Program/ ; JP18J10181//Japan Society for the Promotion of Science/ ; }, abstract = {Despite the considerable role of aquatic plant-associated bacteria in host plant growth and nutrient cycling in aquatic environments, the mode of their plant colonization has hardly been understood. This study examined the colonization and competition dynamics of a plant growth-promoting bacterium (PGPB) and two plant growth-inhibiting bacteria (PGIB) in the aquatic plant Lemna minor (common duckweed). When inoculated separately to L. minor, each bacterial strain quickly colonized at approximately 106 cells per milligram (plant fresh weight) and kept similar populations throughout the 7-day cultivation time. The results of two-membered co-inoculation assays revealed that the PGPB strain Aquitalea magnusonii H3 consistently competitively excluded the PGIB strain Acinetobacter ursingii M3, and strain H3 co-existed at almost 1:1 proportion with another PGIB strain, Asticcacaulis excentricus M6, regardless of the inoculation ratios (99:1-1:99) and inoculation order. We also found that A. magnusonii H3 exerted its growth-promoting effect over the negative effects of the two PGIB strains even when only a small amount was inoculated, probably due to its excellent competitive colonization ability. These experimental results demonstrate that there is a constant ecological equilibrium state involved in the bacterial colonization of aquatic plants.}, }
@article {pmid30603713, year = {2018}, author = {Nakato, GV and Wicker, E and Coutinho, TA and Mahuku, G and Studholme, DJ}, title = {A highly specific tool for identification of Xanthomonas vasicola pv. musacearum based on five Xvm-specific coding sequences.}, journal = {Heliyon}, volume = {4}, number = {12}, pages = {e01080}, doi = {10.1016/j.heliyon.2018.e01080}, pmid = {30603713}, issn = {2405-8440}, abstract = {Xanthomonas vasicola pv. musacearum (Xvm) is a bacterial pathogen responsible for the economically important Xanthomonas wilt disease on banana and enset crops in Sub-Saharan Africa. Given that the symptoms are similar to those of other diseases, molecular diagnosis is essential to unambiguously identify this pathogen and distinguish it from closely related strains not pathogenic on these hosts. Currently, Xvm identification is based on polymerase chain reaction (PCR) with GspDm primers, targeting the gene encoding general secretory protein D. Experimental results and examination of genomic sequences revealed poor specificity of the GspDm PCR. Here, we present and validate five new Xvm-specific primers amplifying only Xvm strains.}, }
@article {pmid30602074, year = {2016}, author = {Nemchenko, UM and Rakova, EB and Savelkaieva, MV and Serdiuk, LV and Ivanova, EI and Shabanova, NM and Bukharova, EV}, title = {[The complex evaluation of condition of intestinal and nasopharyngeal microbiocenosis in alumni of children's home].}, journal = {Klinicheskaia laboratornaia diagnostika}, volume = {61}, number = {8}, pages = {508-512}, pmid = {30602074}, issn = {0869-2084}, abstract = {The examination of nasopharyngeal and intestinal microbiocenoses was implemented in orphan children aged 1-3 years residing in children;s home of Cheremkhovo of the Irkutskaia oblast. All children had compromised anamnesis: prematurity, hypotrophy, chicken pox, frequent acute respiratory viral infections, intestinal infections, atopic dermatitis. The study was carried out to comprehensively evaluate conditions of intestinal and nasopharyngeal biotops in children residing in closed children’s institution - children’s home. The microbiological analysis of qualitative and quantitative composition of content of intestine and nasopharynx was implemented according standard techniques. The analysis established in 81.2±6.90% of examined children deficiency of Bifidobacterium flora, decreasing of level of population density of bifidobacteria up to 6.9±1.53% lg KOE/g, in 31.2±8.1% - deficiency of normal colibacillus, in 78.1±7.3% - increased level of opportunistic flora. The analysis also established high rate of isolation of Escherichia coli with decreased enzyme activity and in 28.1±7.9% - Escherichia coli with hemolytic activity. The enterococci were permanent participants of nasopharyngeal and intestinal biotop (58.6±8.7%). From opportunistic flora, in nasopharynx were registered pathogenic streptococci - S.pyogenes, S.pneumonia and also pathogenic fungi Candida andpoly-resistant strains S. aureus. The study results demonstrated characteristics of microbial ecology of intestinal and nasopharyngeal biotops of orphan children in conditions of children institution of closed type where the circulation of pathogenic and opportunistic microorganisms occurs intensively, including strains with high medicinal resistance. All this determines necessity to attribute alumni of children’s homes to risk group of infectious pathology and requires constant micro-ecological monitoring for timely correction of microbiocenoses.}, }
@article {pmid30602082, year = {2018}, author = {Jeon, SJ and Galvão, KN}, title = {An Advanced Understanding of Uterine Microbial Ecology Associated with Metritis in Dairy Cows.}, journal = {Genomics &amp; informatics}, volume = {16}, number = {4}, pages = {e21}, doi = {10.5808/GI.2018.16.4.e21}, pmid = {30602082}, issn = {1598-866X}, abstract = {Metritis, the inflammation of the uterus caused by polymicrobial infections, is a prevalent and costly disease to the dairy industry as it decreases milk yield, survival, and the welfare of dairy cows. Although the antibiotic ceftiofur is widely used for the treatment of metritis, endometrium and ovary function is compromised, resulting in subfertility and infertility. According to culture-dependent studies, uterine pathogens include Escherichia coli, Trueperella pyogenes, Fusobacterium necrophorum, and Prevotella melaninogenica. Recent studies using high-throughput sequencing claimed that metritis is a microbiota-associated disease. Herein, we propose that metritis is associated with uterine microbiota with high abundance of Bacteroides, Porphyromonas, and Fusobacterium, but rare bacteria such as Escherichia coli and Helcococcus ovis cannot be ignored.}, }
@article {pmid30599206, year = {2018}, author = {Zwaenepoel, A and Li, Z and Lohaus, R and Van de Peer, Y}, title = {Finding evidence for whole genome duplications: a reappraisal.}, journal = {Molecular plant}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.molp.2018.12.019}, pmid = {30599206}, issn = {1752-9867}, }
@article {pmid30598728, year = {2019}, author = {Rafeek, R and Carrington, CVF and Gomez, A and Harkins, D and Torralba, M and Kuelbs, C and Addae, J and Moustafa, A and Nelson, KE}, title = {Xylitol and sorbitol effects on the microbiome of saliva and plaque.}, journal = {Journal of oral microbiology}, volume = {11}, number = {1}, pages = {1536181}, doi = {10.1080/20002297.2018.1536181}, pmid = {30598728}, issn = {2000-2297}, abstract = {Chewing gum containing xylitol may help prevent caries by reducing levels of mutans streptococci (MS) and lactobacilli in saliva and plaque. Very little is known about other species which are possibly beneficial to oral health. In this study, we employed high-throughput sequencing of the 16S rRNA gene to profile microbial communities of saliva and plaque following short-term consumption of xylitol and sorbitol containing chewing gum. Participants (n = 30) underwent a washout period and were randomly assigned to one of two groups. Each group chewed either xylitol or sorbitol gum for three weeks, before undergoing a second four-week washout period after which they switched to the alternate gum for three weeks. Analysis of samples collected before and after each intervention identified distinct plaque and saliva microbial communities that altered dependent on the order in which gum treatments were given. Neither the xylitol nor sorbitol treatments significantly affected the bacterial composition of plaque. Lactobacilli were undetected and the number of Streptococcus mutans sequence reads was very low and unaffected by either xylitol or sorbitol. However, sorbitol affected several other streptococcal species in saliva including increasing the abundance of S. cristatus, an oral commensal shown to inhibit bacteria associated with chronic periodontitis.}, }
@article {pmid30595029, year = {2018}, author = {Tian, L and Tan, Y and Chen, G and Wang, G and Sun, J and Ou, S and Chen, W and Bai, W}, title = {Metabolism of anthocyanins and consequent effects on the gut microbiota.}, journal = {Critical reviews in food science and nutrition}, volume = {}, number = {}, pages = {1-10}, doi = {10.1080/10408398.2018.1533517}, pmid = {30595029}, issn = {1549-7852}, abstract = {Anthocyanins are natural water-soluble polyphenols present in fruits and vegetables. Health-promoting effects attributed to anthocyanins are mainly associated with oxidative stress inhibition and gut microbiota modulation. Dietary anthocyanins undergo a complex metabolism after ingestion and interact with endogenous and microbial enzymes, leading to the production of a large number of circulating and excreted anthocyanin metabolites and catabolic products. To date, the bioavailability and health benefits of anthocyanins have been widely documented. Although there are several papers that illustrated the metabolism of anthocyanins, the effects of dietary anthocyanins on the modulation of the gut microbial ecology and on the growth of certain microbial species are still poorly understood. The present paper summarizes the recent data on the absorption of anthocyanins in the upper gastrointestine and the metabolism of anthocyanins by gut microbiota. The modulatory effects of anthocyanins from different sources on gut microbiota are also discussed.}, }
@article {pmid30594092, year = {2018}, author = {Garner, E and Inyang, M and Garvey, E and Parks, J and Glover, C and Grimaldi, A and Dickenson, E and Sutherland, J and Salveson, A and Edwards, MA and Pruden, A}, title = {Impact of blending for direct potable reuse on premise plumbing microbial ecology and regrowth of opportunistic pathogens and antibiotic resistant bacteria.}, journal = {Water research}, volume = {151}, number = {}, pages = {75-86}, doi = {10.1016/j.watres.2018.12.003}, pmid = {30594092}, issn = {1879-2448}, abstract = {Little is known about how introducing recycled water intended for direct potable reuse (DPR) into distribution systems and premise plumbing will affect water quality at the point of use, particularly with respect to effects on microbial communities and regrowth. The examination of potential growth of opportunistic pathogens (OPs) and spread of antibiotic resistance genes (ARGs), each representing serious and growing public health concerns, by introducing DPR water has not previously been evaluated. In this study, the impact of blending purified DPR water with traditional drinking water sources was investigated with respect to treatment techniques, blending location, and blending ratio. Water from four U.S. utility partners was treated in bench- and pilot-scale treatment trains to simulate DPR with blending. Water was incubated in simulated premise plumbing rigs made of PVC pipe containing brass coupons to measure regrowth of total bacteria (16S rRNA genes, heterotrophic plate count), OPs (Legionella spp., Mycobacterium spp., Pseudomonas aeruginosa), ARGs (qnrA, vanA), and an indicator of horizontal gene transfer and multi-drug resistance (intI1). The microbial community composition was profiled and the resistome (i.e., all ARGs present) was characterized in select samples using next generation sequencing. While regrowth of total bacteria (16S rRNA genes) from the start of the incubation through week eight consistently occurred across tested scenarios (Wilcoxon, p ≤ 0.0001), total bacteria were not more abundant in the water or biofilm of any DPR scenario than in the corresponding conventional potable condition (p ≥ 0.0748). Regrowth of OP marker genes, qnrA, vanA, and intI1 were not significantly greater in water or biofilm for any DPR blends treated with advanced oxidation compared to corresponding potable water (p ≥ 0.1047). This study of initial bacteria colonizing pipes after introduction of blended DPR water revealed little evidence (i.e., one target in one water type) of exacerbated regrowth of total bacteria, OPs, or ARGs in premise plumbing.}, }
@article {pmid30593603, year = {2018}, author = {Bachran, M and Kluge, S and Lopez-Fernandez, M and Cherkouk, A}, title = {Microbial Diversity in an Arid, Naturally Saline Environment.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1301-2}, pmid = {30593603}, issn = {1432-184X}, abstract = {The Arava Valley in is a rock desert within the Great African Rift valley. Soil from this area is covered with a salt crust. Here, we report microbial diversity from arid, naturally saline samples collected near Ein Yahav from the Arava Valley by culture-independent as well as culture-dependent analysis. High-throughput sequencing of the hypervariable region V4 of the 16S rRNA gene revealed that the microbial community consists of halophiles from the domain Bacteria as well as Archaea. Bacterial diversity was mainly represented by the genus Salinimicrobium of the order Flavobacteriales within the phylum Bacteroidetes, from the gammaproteobacterial orders Alteromonadales and Oceanospirillales as well as representatives from the order Bacillales of the phylum Firmicutes. Archaeal diversity was dominated by euryarchaeal Halobacteria from the orders Halobacteriales, Haloferacales, and Natrialbales. But more than 40% of the sequences affiliated with Archaea were assigned to unknown or unclassified archaea. Even if taxonomic resolution of the 16S rRNA gene V4 region for Archaea is limited, this study indicates the need of further and more detailed studies of Archaea. By using culture-dependent analysis, bacteria of the order Bacillales as well as archaea from all three halobacterial orders Halobacteriales, Haloferacales, and Natrialbales including potentially novel species from the genera Halorubrum and Haloparvum were isolated.}, }
@article {pmid30593565, year = {2018}, author = {Vallespir Lowery, N and Ursell, T}, title = {Structured environments fundamentally alter dynamics and stability of ecological communities.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {}, number = {}, pages = {}, doi = {10.1073/pnas.1811887116}, pmid = {30593565}, issn = {1091-6490}, abstract = {The dynamics and stability of ecological communities are intimately linked with the specific interactions-like cooperation or predation-between constituent species. In microbial communities, like those found in soils or the mammalian gut, physical anisotropies produced by fluid flow and chemical gradients impact community structure and ecological dynamics, even in structurally isotropic environments. Although natural communities existing in physically unstructured environments are rare, the role of environmental structure in determining community dynamics and stability remains poorly studied. To address this gap, we used modified Lotka-Volterra simulations of competitive microbial communities to characterize the effects of surface structure on community dynamics. We find that environmental structure has profound effects on communities, in a manner dependent on the specific pattern of interactions between community members. For two mutually competing species, eventual extinction of one competitor is effectively guaranteed in isotropic environments. However, addition of environmental structure enables long-term coexistence of both species via local &quot;pinning&quot; of competition interfaces, even when one species has a significant competitive advantage. In contrast, while three species competing in an intransitive loop (as in a game of rock-paper-scissors) coexist stably in isotropic environments, structural anisotropy disrupts the spatial patterns on which coexistence depends, causing chaotic population fluctuations and subsequent extinction cascades. These results indicate that the stability of microbial communities strongly depends on the structural environment in which they reside. Therefore, a more complete ecological understanding, including effective manipulation and interventions in natural communities of interest, must account for the physical structure of the environment.}, }
@article {pmid30586832, year = {2019}, author = {Yang, S and Zheng, Q and Yuan, M and Shi, Z and Chiariello, NR and Docherty, KM and Dong, S and Field, CB and Gu, Y and Gutknecht, J and Hungate, BA and Le Roux, X and Ma, X and Niboyet, A and Yuan, T and Zhou, J and Yang, Y}, title = {Long-term elevated CO2 shifts composition of soil microbial communities in a Californian annual grassland, reducing growth and N utilization potentials.}, journal = {The Science of the total environment}, volume = {652}, number = {}, pages = {1474-1481}, doi = {10.1016/j.scitotenv.2018.10.353}, pmid = {30586832}, issn = {1879-1026}, abstract = {The continuously increasing concentration of atmospheric CO2 has considerably altered ecosystem functioning. However, few studies have examined the long-term (i.e. over a decade) effect of elevated CO2 on soil microbial communities. Using 16S rRNA gene amplicons and a GeoChip microarray, we investigated soil microbial communities from a Californian annual grassland after 14 years of experimentally elevated CO2 (275 ppm higher than ambient). Both taxonomic and functional gene compositions of the soil microbial community were modified by elevated CO2. There was decrease in relative abundance for taxa with higher ribosomal RNA operon (rrn) copy number under elevated CO2, which is a functional trait that responds positively to resource availability in culture. In contrast, taxa with lower rrn copy number were increased by elevated CO2. As a consequence, the abundance-weighted average rrn copy number of significantly changed OTUs declined from 2.27 at ambient CO2 to 2.01 at elevated CO2. The nitrogen (N) fixation gene nifH and the ammonium-oxidizing gene amoA significantly decreased under elevated CO2 by 12.6% and 6.1%, respectively. Concomitantly, nitrifying enzyme activity decreased by 48.3% under elevated CO2, albeit this change was not significant. There was also a substantial but insignificant decrease in available soil N, with both nitrate (NO3-) (-27.4%) and ammonium (NH4+) (-15.4%) declining. Further, a large number of microbial genes related to carbon (C) degradation were also affected by elevated CO2, whereas those related to C fixation remained largely unchanged. The overall changes in microbial communities and soil N pools induced by long-term elevated CO2 suggest constrained microbial N decomposition, thereby slowing the potential maximum growth rate of the microbial community.}, }
@article {pmid30585386, year = {2018}, author = {Cholet, F and Ijaz, UZ and Smith, CJ}, title = {Differential ratio amplicons (Ramp) for the evaluation of RNA integrity extracted from complex environmental samples.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14516}, pmid = {30585386}, issn = {1462-2920}, abstract = {Reliability and reproducibility of transcriptomics-based studies are dependent on RNA integrity. In microbial ecology, microfluidics-based techniques, such as the Ribosomal Integrity Number (RIN), targeting rRNA are currently the only approaches to evaluate RNA integrity. However, the relationship between rRNA and mRNA integrity is unknown. Here we present an integrity index, the Ratio Amplicon, Ramp , adapted from human clinical studies, to directly monitor mRNA integrity from complex environmental samples. We show, in a suite of experimental degradations of RNA extracted from sediment, that while the RIN generally reflected the degradation status of RNA the Ramp mapped mRNA degradation better. Furthermore, we examined the effect of degradation on transcript community structure by amplicon sequencing of 16S rRNA, amoA and glnA transcripts. We successfully sequenced transcripts for all three targets even from highly-degraded RNA samples. While RNA degradation changed the community structure of the mRNA profiles, no changes were observed for the 16S rRNA transcript profiles. Since both RT-Q-PCR and sequencing results were obtained, even from highly degraded samples, we strongly recommend evaluating RNA integrity prior to downstream processing to ensure meaningful results. For this both the RIN and Ramp are useful, with the Ramp better evaluating mRNA integrity in this study. This article is protected by copyright. All rights reserved.}, }
@article {pmid30581429, year = {2018}, author = {Brenzinger, K and Drost, SM and Korthals, G and Bodelier, PLE}, title = {Organic Residue Amendments to Modulate Greenhouse Gas Emissions From Agricultural Soils.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3035}, doi = {10.3389/fmicb.2018.03035}, pmid = {30581429}, issn = {1664-302X}, abstract = {Organic fertilizers have been shown to stimulate CH4 uptake from agricultural soils. Managing fertilizer application to maximize this effect and to minimize emission of other greenhouse gasses offers possibilities to increase sustainability of agriculture. To tackle this challenge, we incubated an agricultural soil with different organic amendments (compost, sewage sludge, digestate, cover crop residues mixture), either as single application or in a mixture and subjected it to different soil moisture concentrations using different amounts of organic amendments. GHG fluxes and in vitro CH4 oxidation rates were measured repeatedly, while changes in organic matter and abundance of GHG relevant microbial groups (nitrifiers, denitrifiers, methanotrophs, methanogens) were measured at the end of the incubation. Overall the dynamics of the analyzed GHGs differed significantly. While CO2 and N2O differed considerably between the treatments, CH4 fluxes remained stable. In contrast, in vitro CH4 oxidation showed a clear increase for all amendments over time. CO2 fluxes were mostly dependent on the amount of organic residue that was used, while N2O fluxes were affected more by soil moisture. Several combinations of amendments led to reductions of CO2, CH4, and/or N2O emissions compared to un-amended soil. Most optimal GHG balance was obtained by compost amendments, which resulted in a similar overall GHG balance as compared to the un-amended soil. However, compost is not very nutrient rich potentially leading to lower crop yield when applied as single fertilizer. Hence, the combination of compost with one of the more nutrient rich organic amendments (sewage sludge, digestate) provides a trade-off between maintaining crop yield and minimizing GHG emissions. Additionally, we could observe a strong increase in microbial communities involved in GHG consumption in all amendments, with the strongest increase associated with cover crop residue mixtures. Future research should focus on the interrelation of plants, soil, and microbes and their impact on the global warming potential in relation to applied organic amendments.}, }
@article {pmid30580396, year = {2019}, author = {Williams, MR and Hashsham, SA}, title = {Direct or DNA Extraction-Free Amplification and Quantification of Foodborne Pathogens.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1918}, number = {}, pages = {21-33}, doi = {10.1007/978-1-4939-9000-9_2}, pmid = {30580396}, issn = {1940-6029}, abstract = {The use of direct nucleic acid amplification of pathogens from food matrices has the potential to reduce time to results over DNA extraction-based approaches as well as traditional culture-based approaches. Here we describe protocols for assay design and experiments for direct amplification of foodborne pathogens in food sample matrices using loop-mediated isothermal amplification (LAMP) and polymerase chain reaction (PCR). The examples provided include the detection Escherichia coli in milk samples and Salmonella in pork meat samples. This protocol includes relevant reagents and methods including obtaining target sequences, assay design, sample processing, and amplification. These methods, though used for specific example matrices, could be applied to many other foodborne pathogens and sample types.}, }
@article {pmid30579209, year = {2018}, author = {Bains, W and Petkowski, JJ and Sousa-Silva, C and Seager, S}, title = {New environmental model for thermodynamic ecology of biological phosphine production.}, journal = {The Science of the total environment}, volume = {658}, number = {}, pages = {521-536}, doi = {10.1016/j.scitotenv.2018.12.086}, pmid = {30579209}, issn = {1879-1026}, abstract = {We present a new model for the biological production of phosphine (PH3). Phosphine is found globally, in trace amounts, in the Earth's atmosphere. It has been suggested as a key molecule in the phosphorus cycle, linking atmospheric, lithospheric and biological phosphorus chemistry. Phosphine's production is strongly associated with marshes, swamps and other sites of anaerobic biology. However the mechanism of phosphine's biological production has remained controversial, because it has been believed that reduction of phosphate to phosphine is endergonic. In this paper we show through thermodynamic calculations that, in specific environments, the combined action of phosphate reducing and phosphite disproportionating bacteria can produce phosphine. Phosphate-reducing bacteria can capture energy from the reduction of phosphate to phosphite through coupling phosphate reduction to NADH oxidation. Our hypothesis describes how the phosphate chemistry in an environmental niche is coupled to phosphite generation in ground water, which in turn is coupled to the phosphine production in water and atmosphere, driven by a specific microbial ecology. Our hypothesis provides clear predictions on specific complex environments where biological phosphine production could be widespread. We propose tests of our hypothesis in fieldwork.}, }
@article {pmid30577137, year = {2018}, author = {Abreu-Junior, CH and de Lima Brossi, MJ and Monteiro, RT and Cardoso, PHS and da Silva Mandu, T and Nogueira, TAR and Ganga, A and Filzmoser, P and de Oliveira, FC and Firme, LP and He, Z and Capra, GF}, title = {Effects of sewage sludge application on unfertile tropical soils evaluated by multiple approaches: A field experiment in a commercial Eucalyptus plantation.}, journal = {The Science of the total environment}, volume = {655}, number = {}, pages = {1457-1467}, doi = {10.1016/j.scitotenv.2018.11.334}, pmid = {30577137}, issn = {1879-1026}, abstract = {Sewage sludge (SS) reuse in forest plantation as soil fertilizer/amendment has tremendously increased in recent years. However, SS may have high concentrations of potentially toxic elements (PTE), representing a potential risk for soil and the whole ecosystem. This paper was aimed to assess the toxicity of PTE in unfertile tropical soils amended with SS in a commercial Eucalyptus plantation, with an integrated multiple approaches combining: i) the use of a battery of bioassays (Daphnia magna, Pseudokcrichirella subcapitata, Lactuca sativa, and Allium cepa); and ii) the evaluation of some PTE (Cd, Cr, Cu, Fe, Mn, Ni, Pb, and Zn) and their availability into the pedoenvironment. Differences in total and available PTE between SS doses and time of treatments were evaluated using ANOVA; correlations between PTE and bioassays by a sparse partial robust M-regression (SPRM), while multiple correlations among parameters were performed by principal factor analysis (PFA). Results show that PTE contents in soils tended to increase with SS application doses. However this cannot be assumed as a general rule since in all the investigated treatments the PTE concentrations were consistently below both soil natural background concentrations and quality reference values. Bioassays showed a generalized low eco- and genotoxicity of SS with an increase in toxicity at increasing SS doses but with a clear decreasing trend as time went by. A. cepa was the most sensitive bioassay followed by P. subcapitata > D. magna > L. sativa. Overall, the results indicate that in realistic open field conditions SS risk may be lower than expected due to dynamic decrease in PTE toxicity with time after application. This study has an important implication that open-field trials should be strongly encouraged for evaluating environmental risk of SS application in forestry.}, }
@article {pmid30577127, year = {2018}, author = {Wang, D and Li, T and Huang, K and He, X and Zhang, XX}, title = {Roles and correlations of functional bacteria and genes in the start-up of simultaneous anammox and denitrification system for enhanced nitrogen removal.}, journal = {The Science of the total environment}, volume = {655}, number = {}, pages = {1355-1363}, doi = {10.1016/j.scitotenv.2018.11.321}, pmid = {30577127}, issn = {1879-1026}, abstract = {Simultaneous anammox and denitrification (SAD) is a newly developed wastewater treatment process efficient in nitrogen removal, but its underlying microbiological mechanisms during start-up remains unknown. This study investigated the changing patterns of functional bacteria and genes, as well as their correlation during the start-up (260 d) of the SAD systems in two lab-scale up-flow anaerobic sludge blanket bioreactors separately inoculated with anaerobic granular sludge (R1) and aerobic floccular sludge (R2). Results showed that high total nitrogen removal was achieved in the SAD systems of both R1 (88.25%) and R2 (89.42%). High-throughput sequencing of 16S rRNA gene amplicons revealed that Armatimonadetes phylum had a high abundance (44.34%) in R2, while was not detectable in R1 during the anammox stage. However, the SAD bioreactors retained inherent microbial community and the inoculation with different sludge showed less notable effects on their microbial composition. In the SAD systems, Candidatus Brocadia had high abundance in R1 (2.93%) and R2 (4.64%) and played important role in anammox. Network analysis indicated that Denitratisoma and Dokdonella were positively correlated with nitrite reductase genes nirS and nirK (p < 0.05), while Thermomonas and Pseudomonas showing a positive correlation with nitrate reductase gene narG (p < 0.05) were mainly responsible for the nitrate reduction in the SAD systems. Moreover, the overwhelming dominance of narG v.s. napA revealed the crucial roles of respiratory nitrate reduction in the bioreactors. The results extend our knowledge regarding the microbial ecology of the SAD system, which might be practically helpful for application of the process in wastewater treatment.}, }
@article {pmid30574650, year = {2018}, author = {Weiss, R and Palatinszky, M and Wagner, M and Niessner, R and Elsner, M and Seidel, M and Ivleva, NP}, title = {Surface-enhanced Raman spectroscopy of microorganisms: limitations and applicability on the single-cell level.}, journal = {The Analyst}, volume = {}, number = {}, pages = {}, doi = {10.1039/c8an02177e}, pmid = {30574650}, issn = {1364-5528}, abstract = {Detection and characterization of microorganisms is essential for both clinical diagnostics and environmental studies. An emerging technique to analyse microbes at single-cell resolution is surface-enhanced Raman spectroscopy (surface-enhanced Raman scattering: SERS). Optimised SERS procedures enable fast analytical read-outs with specific molecular information, providing insight into the chemical composition of microbiological samples. Knowledge about the origin of microbial SERS signals and parameter(s) affecting their occurrence, intensity and/or reproducibility is crucial for reliable SERS-based analyses. In this work, we explore the feasibility and limitations of the SERS approach for characterizing microbial cells and investigate the applicability of SERS for single-cell sorting as well as for three-dimensional visualization of microbial communities. Analyses of six different microbial species (an archaeon, two Gram-positive bacteria, three Gram-negative bacteria) showed that for several of these organisms distinct features in their SERS spectra were lacking. As additional confounding factor, the physiological conditions of the cells (as influenced by e.g., storage conditions or deuterium-labelling) were systematically addressed, for which we conclude that the respective SERS signal at the single-cell level is strongly influenced by the metabolic activity of the analysed cells. While this finding complicates the interpretation of SERS data, it may on the other hand enable probing of the metabolic state of individual cells within microbial populations of interest.}, }
@article {pmid30574135, year = {2018}, author = {Vander Roost, J and Daae, FL and Steen, IH and Thorseth, IH and Dahle, H}, title = {Distribution Patterns of Iron-Oxidizing Zeta- and Beta-Proteobacteria From Different Environmental Settings at the Jan Mayen Vent Fields.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3008}, doi = {10.3389/fmicb.2018.03008}, pmid = {30574135}, issn = {1664-302X}, abstract = {Iron oxidizers are widespread in marine environments and play an important role in marine iron cycling. However, little is known about the overall distribution of iron oxidizers within hydrothermal systems, including settings with little hydrothermal activity. Moreover, the extent to which different phylogenetic groups of iron oxidizers exhibit niche specialization toward different environmental settings, remains largely unknown. Obtaining such knowledge is critical to unraveling the impact of the activity of iron oxidizers and how they are adapted. Here, we used 16S rRNA sequencing to characterize the distribution of iron oxidizers in different environmental settings within the Jan Mayen hydrothermal vent fields (JMVFs). Putative iron oxidizers affiliated to Zetaproteobacteria and Betaproteobacteria were detected within iron mounds, bottom seawater, basalt surfaces, and surface layers of sediments. The detected iron oxidizers were compared to sequence types previously observed in patchily distributed iron mats associated with diffuse venting at the JMVFs. Most OTUs of iron oxidizers reoccurred under different environmental settings, suggesting a limited degree of niche specialization. Consequently, most of the detected iron oxidizers seem to be generalists with a large habitat range. Our study highlights the importance of gathering information about the overall distribution of iron oxidizers in hydrothermal systems to fully understand the role of this metabolic group regarding cycling of iron. Furthermore, our results provide further evidence of the presence of iron-oxidizing members of Betaproteobacteria in marine environments.}, }
@article {pmid30572962, year = {2018}, author = {Du Preez, S and Corbitt, M and Cabanas, H and Eaton, N and Staines, D and Marshall-Gradisnik, S}, title = {A systematic review of enteric dysbiosis in chronic fatigue syndrome/myalgic encephalomyelitis.}, journal = {Systematic reviews}, volume = {7}, number = {1}, pages = {241}, doi = {10.1186/s13643-018-0909-0}, pmid = {30572962}, issn = {2046-4053}, abstract = {BACKGROUND: Chronic fatigue syndrome or myalgic encephalomyelitis (CFS/ME) is an illness characterised by profound and pervasive fatigue in addition to a heterogeneous constellation of symptoms. The aetiology of this condition remains unknown; however, it has been previously suggested that enteric dysbiosis is implicated in the pathogenesis of CFS/ME. This review examines the evidence currently available for the presence of abnormal microbial ecology in CFS/ME in comparison to healthy controls, with one exception being probiotic-supplemented CFS/ME patients, and whether the composition of the microbiome plays a role in symptom causation.<br><br>METHODS: EMBASE, Medline (via EBSCOhost), Pubmed and Scopus were systematically searched from 1994 to March 2018. All studies that investigated the gut microbiome composition of CFS/ME patients were initially included prior to the application of specific exclusion criteria. The association between these findings and patient-centred outcomes (fatigue, quality of life, gastrointestinal symptoms, psychological wellbeing) are also reported.<br><br>RESULTS: Seven studies that met the inclusion criteria were included in the review. The microbiome composition of CFS/ME patients was compared with healthy controls, with the exception of one study that compared to probiotic-supplemented CFS/ME patients. Differences were reported in each study; however, only three were considered statistically significant, and the findings across all studies were inconsistent. The quality of the studies included in this review scored between poor (< 54%), fair (54-72%) and good (94-100%) using the Downs and Black checklist.<br><br>CONCLUSIONS: There is currently insufficient evidence for enteric dysbiosis playing a significant role in the pathomechanism of CFS/ME. Recommendations for future research in this field include the use of consistent criteria for the diagnosis of CFS/ME, reduction of confounding variables by controlling factors that influence microbiome composition prior to sample collection and including more severe cases of CFS/ME.}, }
@article {pmid30568671, year = {2018}, author = {Bardin, M and Leyronas, C and Troulet, C and Morris, CE}, title = {Striking Similarities Between Botrytis cinerea From Non-agricultural and From Agricultural Habitats.}, journal = {Frontiers in plant science}, volume = {9}, number = {}, pages = {1820}, doi = {10.3389/fpls.2018.01820}, pmid = {30568671}, issn = {1664-462X}, abstract = {Investigations into life history of microorganisms that cause plant diseases have been limited mostly to contexts where they are in interaction with plants, and with cropped or otherwise managed vegetation. Therefore, knowledge about the diversity of plant pathogens, about potential reservoirs of inoculum and about the processes that contribute to their survival and adaptation is limited to these contexts. The agro-centric perspective of plant pathogen life histories is incoherent with respect to the capacity of many of them to persist as saprophytes on various substrates. In this context we have investigated the ubiquity of the broad host range necrotrophic fungus Botrytis cinerea, outside of agricultural settings and have determined if the populations in these natural habitats can be distinguished phenotypically and phylogenetically from populations isolated from diseased crops. Over a period of 5 years, we isolated B. cinerea from 235 samples of various substrates collected in France including rainfall, snowpack, river, and lake water, epilithic biofilms in mountain streams, leaf litter and plant debris, rock surfaces, bird feathers and healthy wild plants from outside of agricultural fields. All substrates except rock surfaces harbored B. cinerea leading us to establish a collection of purified strains that were compared to B. cinerea from diseased tomato, grapes and various other crops in France. Phylogenetic comparisons of 321 strains from crop plants and 100 strains from environmental substrates based on sequences of 9 microsatellite markers revealed that strains from crops and the environment could not be distinguished. Furthermore, the genetic diversity of strains outside of agriculture was just as broad as within agriculture. In tests to determine the aggressiveness of strains on tomato stems, the mean disease severity caused by strains from environmental substrates was statistically identical to the severity of disease caused by strains from tomato, but was significantly greater than the severity caused by strains from grape or other crops. Our results suggest that highly diverse populations of this plant pathogen persist outside of agriculture in association with substrates other than plants and that this part of their life history is compatible with its capacity to maintain its potential as plant pathogen.}, }
@article {pmid30565880, year = {2018}, author = {Thorn, CE and Bergesch, C and Joyce, A and Sambrano, G and McDonnell, K and Brennan, F and Heyer, R and Benndorf, D and Abram, F}, title = {A robust, cost-effective method for DNA, RNA and protein co-extraction from soil, other complex microbiomes, and pure cultures.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {}, doi = {10.1111/1755-0998.12979}, pmid = {30565880}, issn = {1755-0998}, abstract = {The soil microbiome is inherently complex with high biological diversity, and spatial heterogeneity typically occurring on the sub-millimetre scale. To study the microbial ecology of soils, and other microbiomes, biomolecules i.e. nucleic acids and proteins, must be efficiently and reliably co-recovered from the same biological samples. Commercial kits are currently available for the co-extraction of DNA, RNA and proteins but none has been developed for soil samples. We present a new protocol drawing on existing phenol-chloroform based methods for nucleic acids co-extraction but incorporating targeted precipitation of proteins from the phenol phase. The protocol is cost-effective and robust, and easily implemented using reagents commonly available in laboratories. The method is estimated to be eight times cheaper than using disparate commercial kits for the isolation of DNA and/or RNA, and proteins, from soil. The method is effective, providing good quality biomolecules from a diverse range of soil types, with clay contents varying from 9.5 to 35.1%, which we successfully used for downstream, high-throughput gene sequencing and metaproteomics. Additionally, we demonstrate that the protocol can also be easily implemented for biomolecule co-extraction from other complex microbiome samples, including cattle slurry and microbial communities recovered from anaerobic bioreactors, as well as from Gram-positive and Gram-negative pure cultures. This article is protected by copyright. All rights reserved.}, }
@article {pmid30565684, year = {2018}, author = {Wang, JC and Bergeron, M and Andersen, H and Tikhtman, R and Haslam, D and Hunter, T and Herr, AB and de Alarcon, A}, title = {Feasibility of shotgun metagenomics to assess microbial ecology of pediatric tracheostomy tubes.}, journal = {The Laryngoscope}, volume = {}, number = {}, pages = {}, doi = {10.1002/lary.27356}, pmid = {30565684}, issn = {1531-4995}, abstract = {OBJECTIVE: Biofilm formation on medical devices such as tracheostomy tubes (TTs) is a serious problem. The clinical impact of biofilms on the airway is still unclear. Biofilms may play a role in granulation tissue development, recurrent airway infections, and failure of laryngotracheal reconstructions. The microbial ecology on TTs has yet to be elucidated. The purpose of this study was to determine the feasibility of shotgun metagenomics to assess the biodistribution of microorganisms on TTs.<br><br>METHODS: Four TTs were collected from pediatric patients (1.4-10.2 years) with (n = 2) and without (n = 2) granulation tissue formation. Duration of TT placement prior to retrieval from patients ranged from 5 to 365 days. DNA extraction was performed using the MO BIO UltraClean Microbial Isolation (Mo Bio Laboratories, Carlsbad, CA). Library generation using Nextera XT adapters (Illumina Inc., San Diego, CA) and metagenomic shotgun sequencing was performed using the Illumina NextSeq500 (Illumina Inc, San Diego, CA). Salinibacter ruber, a species not found in mammalian microbiome communities, was used as a DNA standard and represented 0.7% to 5.7% of the microbiome, ensuring good quality and abundance of sample DNA.<br><br>RESULTS: Metagenomic shotgun sequencing was successful for all patients. In TTs associated with granuloma, Fusobacterium nucleatum, Haemophilus influenzae, Moraxella catarrhalis, and Streptococcus pneumoniae were predominant, most of which are considered pathogens. From TTs without granulomas, Neisseria mucosa, Neisseria sicca, Acinetobacter baumannii, and Haemophilus parainfluenzae were identified, primarily consistent with respiratory microbiome.<br><br>CONCLUSION: This study reveals that metagenomic shotgun sequencing of biofilms formed on pediatric TTs is feasible with an apparent difference in microbiome for patients with granulation tissue. Further studies are necessary to elucidate the pathogenesis of microbial ecology and its role in airway disease in patients with TTs.<br><br>LEVEL OF EVIDENCE: 2c. Laryngoscope, 2018.}, }
@article {pmid30565024, year = {2018}, author = {Lee, JC and Song, JS and Whang, KS}, title = {Sphingobium pinisoli sp. nov., isolated from the rhizosphere soil of a Korean native pine tree.}, journal = {Antonie van Leeuwenhoek}, volume = {}, number = {}, pages = {}, doi = {10.1007/s10482-018-01215-x}, pmid = {30565024}, issn = {1572-9699}, support = {PJ01287601//Department of Agriculture and Rural Development/ ; }, abstract = {A Gram-stain negative, aromatic compound degrading bacterium, designated strain ASA28T, was isolated from the rhizosphere soil of a pine tree at Anmyon island, Taean in Korea. Strain ASA28T was found to be strictly aerobic, non-motile, short rods which can grow at 15-28 °C (optimum, 25-28 °C), at pH 5.0-11.0 (optimum, pH 7.0) and at salinities of 0-1.0% (w/v) NaCl (optimum, 0% NaCl). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain ASA28T belongs to the genus Sphingobium, showing high sequence similarity to Sphingobium scionense WP01T (97.8%), Sphingobium vermicocomposti VC-230T (96.8%), Sphingobium yanoikuyae ATCC 51230T (96.5%) and Sphingobium herbicidovorans MHT (95.6%). The predominant ubiquinone and polyamine components were identified as Q-10 and spermidine, respectively. The major fatty acids were identified as C18:1ω7c, C16:0, C14:0 2-OH and C16:1ω7c and/or C15:0 iso 2-OH. The major polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylcholine, sphingoglycolipid, phosphoglycolipid, four unidentified aminophospholipids, an unidentified aminolipid, two unidentified phospholipids and six unidentified lipids. The DNA G+C content of this novel isolate was determined to be 63.0 mol%. DNA-DNA relatedness between strain ASA28T and S. herbicidovorans KCTC 2939T, S. vermicocomposti DSM 21299T and S. scionense DSM 19371T was determined to be 32 ± 5%, 30 ± 4% and 25 ± 5%, respectively. On the basis of the phylogenetic, phenotypic and chemotaxonomic analyses in this study, strain ASA28T is considered to represent a novel species of the genus Sphingobium, for which the name Sphingobium pinisoli sp. nov. is proposed. The type strain is ASA28T (= KACC 18700T = NBRC 112246T).}, }
@article {pmid30564217, year = {2018}, author = {Ramírez, GA and Jørgensen, SL and Zhao, R and D'Hondt, S}, title = {Minimal Influence of Extracellular DNA on Molecular Surveys of Marine Sedimentary Communities.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2969}, doi = {10.3389/fmicb.2018.02969}, pmid = {30564217}, issn = {1664-302X}, abstract = {Extracellular DNA has been reported to comprise a large fraction of total DNA in near-seafloor sediment. However, the potential effect of extracellular DNA, arising from dead or moribund cells, on sequencing surveys is a critical concern that has largely not been addressed for marine sedimentary habitats. To address this concern, we interrogated freshly collected Arctic and Pacific sediment for extracellular 16S rRNA genes using the photoactive DNA-binding dye Propidium Monoazide. Significant differences between relative abundances of total (intracellular + extracellular) Bacterial 16S rRNA genes and relative abundances of intracellular Bacterial 16S rRNA genes are only detected in three of twelve shallow [10 cm below seafloor (cmbsf)] samples. Relative abundances of total Bacterial 16S rRNA genes are statistically indistinguishable from relative abundances of intracellular Bacterial 16S rRNA genes in all interrogated samples from depths greater than 10 cmbsf. 16S rRNA gene sequencing shows that even where significantly higher abundances of extracellular genes are detected, they have little or no influence on prokaryote community composition. Taxon-level analyses suggest that extracellular DNA, arising from in situ death, may be sourced from different organisms in sediment of different ages. However, the overall effect of extracellular genes on sequencing surveys of marine sedimentary prokaryotes is minimal.}, }
@article {pmid30564202, year = {2018}, author = {Too, CC and Keller, A and Sickel, W and Lee, SM and Yule, CM}, title = {Microbial Community Structure in a Malaysian Tropical Peat Swamp Forest: The Influence of Tree Species and Depth.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2859}, doi = {10.3389/fmicb.2018.02859}, pmid = {30564202}, issn = {1664-302X}, abstract = {Tropical peat swamp forests sequester globally significant stores of carbon in deep layers of waterlogged, anoxic, acidic and nutrient-depleted peat. The roles of microbes in supporting these forests through the formation of peat, carbon sequestration and nutrient cycling are virtually unknown. This study investigated physicochemical peat properties and microbial diversity between three dominant tree species: Shorea uliginosa (Dipterocarpaceae), Koompassia malaccensis (legumes associated with nitrogen-fixing bacteria), Eleiodoxa conferta (palm) and depths (surface, 45 and 90 cm) using microbial 16S rRNA gene amplicon sequencing. Water pH, oxygen, nitrogen, phosphorus, total phenolic contents and C/N ratio differed significantly between depths, but not tree species. Depth also strongly influenced microbial diversity and composition, while both depth and tree species exhibited significant impact on the archaeal communities. Microbial diversity was highest at the surface, where fresh leaf litter accumulates, and nutrient supply is guaranteed. Nitrogen was the core parameter correlating to microbial communities, but the interactive effects from various environmental variables displayed significant correlation to relative abundance of major microbial groups. Proteobacteria was the dominant phylum and the most abundant genus, Rhodoplanes, might be involved in nitrogen fixation. The most abundant methanogens and methanotrophs affiliated, respectively, to families Methanomassiliicoccaceae and Methylocystaceae. Our results demonstrated diverse microbial communities and provide valuable insights on microbial ecology in these extreme ecosystems.}, }
@article {pmid30562060, year = {2018}, author = {Arora, T and Rudenko, O and Egerod, KL and Husted, AS and Kovatcheva-Datchary, P and Akrami, R and Kristensen, M and Schwartz, TW and Bäckhed, F}, title = {Microbial fermentation of flaxseed fibers modulates the transcriptome of GPR41-expressing enteroendocrine cells and protects mice against diet-induced obesity.}, journal = {American journal of physiology. Endocrinology and metabolism}, volume = {}, number = {}, pages = {}, doi = {10.1152/ajpendo.00391.2018}, pmid = {30562060}, issn = {1522-1555}, abstract = {Dietary fibers, an integral part of the human diet, require the enzymatic activity of the gut microbiota for complete metabolism into short chain fatty acids (SCFAs). SCFAs are important modulators of host metabolism and physiology and act in part as signaling molecules by activating G-protein coupled receptors (GPR) such as GPR41. Flaxseed fibers improve metabolism in rodents and mice, but their fermentation profiles, effects on enteroendocrine cells and associated metabolic benefits are unknown. We fed GPR41-RFP mice, an enteroendocrine reporter mouse strain, chow, high fat diet (HFD) or HFD supplemented either with 10% non-fermentable fiber cellulose or fermentable flaxseed fibers for 12 weeks to assess changes in cecal gut microbiota, enteroendocrine cell transcriptome in ileum and colon, and physiological parameters. We observed that flaxseed fibers restructured the gut microbiota and promoted proliferation of the genera Bifidobacterium and Akkermansia compared with HFD. The shifts in cecal bacterial composition restored levels of the SCFAs butyrate similar to the chow diet, resulting in colonic, but not ileal, enteroendocrine cell transcriptional changes in genes related to cell cycle, mRNA and protein transport compared with HFD. Consistent with effects on enteroendocrine functions, flaxseed fibers also protected mice from diet-induced obesity, potentially by preventing reduction in energy expenditure induced by HFD. Our study shows that flaxseed fibers alter cecal microbial ecology, are fermented to SCFAs in cecum, and modulate enteroendocrine cell transcriptome in colon, which may contribute to their metabolically favorable phenotype.}, }
@article {pmid30559748, year = {2018}, author = {Guyonnet, JP and Guillemet, M and Dubost, A and Simon, L and Ortet, P and Barakat, M and Heulin, T and Achouak, W and Haichar, FEZ}, title = {Plant Nutrient Resource Use Strategies Shape Active Rhizosphere Microbiota Through Root Exudation.}, journal = {Frontiers in plant science}, volume = {9}, number = {}, pages = {1662}, doi = {10.3389/fpls.2018.01662}, pmid = {30559748}, issn = {1664-462X}, abstract = {Plant strategies for soil nutrient uptake have the potential to strongly influence plant-microbiota interactions, due to the competition between plants and microorganisms for soil nutrient acquisition and/or conservation. In the present study, we investigate whether these plant strategies could influence rhizosphere microbial activities via root exudation, and contribute to the microbiota diversification of active bacterial communities colonizing the root-adhering soil (RAS) and inhabiting the root tissues. We applied a DNA-based stable isotope probing (DNA-SIP) approach to six grass species distributed along a gradient of plant nutrient resource strategies, from conservative species, characterized by low nitrogen (N) uptake, a long lifespans and low root exudation level, to exploitative species, characterized by high rates of photosynthesis, rapid rates of N uptake and high root exudation level. We analyzed their (i) associated microbiota composition involved in root exudate assimilation and soil organic matter (SOM) degradation by 16S-rRNA-based metabarcoding. (ii) We determine the impact of root exudation level on microbial activities (denitrification and respiration) by gas chromatography. Measurement of microbial activities revealed an increase in denitrification and respiration activities for microbial communities colonizing the RAS of exploitative species. This increase of microbial activities results probably from a higher exudation rate and more diverse metabolites by exploitative plant species. Furthermore, our results demonstrate that plant nutrient resource strategies have a role in shaping active microbiota. We present evidence demonstrating that plant nutrient use strategies shape active microbiota involved in root exudate assimilation and SOM degradation via root exudation.}, }
@article {pmid30403856, year = {2018}, author = {Calatayud, M and Xiong, C and Du Laing, G and Raber, G and Francesconi, K and van de Wiele, T}, title = {Salivary and Gut Microbiomes Play a Significant Role in in Vitro Oral Bioaccessibility, Biotransformation, and Intestinal Absorption of Arsenic from Food.}, journal = {Environmental science &amp; technology}, volume = {52}, number = {24}, pages = {14422-14435}, doi = {10.1021/acs.est.8b04457}, pmid = {30403856}, issn = {1520-5851}, abstract = {The release of a toxicant from a food matrix during the gastrointestinal digestion is a crucial determinant of the toxicant's oral bioavailability. We present a modified setup of the human simulator of the gut microbial ecosystem (SHIME), with four sequential gastrointestinal reactors (oral, stomach, small intestine, and colon), including the salivary and colonic microbiomes. Naturally arsenic-containing rice, mussels, and nori seaweed were digested in the presence of microorganisms and in vitro oral bioaccessibility, bioavailability, and metabolism of arsenic species were evaluated following analysis by using HPLC/mass spectrometry. When food matrices were digested with salivary bacteria, the soluble arsenic in the gastric digestion stage increased for mussel and nori samples, but no coincidence impact was found in the small intestinal and colonic digestion stages. However, the simulated small intestinal absorption of arsenic was increased in all food matrices (1.2-2.7 fold higher) following digestion with salivary microorganisms. No significant transformation of the arsenic species occurred except for the arsenosugars present in mussels and nori. In those samples, conversions between the oxo arsenosugars were observed in the small intestinal digestion stage whereupon the thioxo analogs became major metabolites. These results expand our knowledge on the likely metabolism and oral bioavailabiltiy of arsenic during human digestion, and provide valuable information for future risk assessments of dietary arsenic.}, }
@article {pmid30555445, year = {2018}, author = {Ilgrande, C and Leroy, B and Wattiez, R and Vlaeminck, SE and Boon, N and Clauwaert, P}, title = {Metabolic and Proteomic Responses to Salinity in Synthetic Nitrifying Communities of Nitrosomonas spp. and Nitrobacter spp.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2914}, doi = {10.3389/fmicb.2018.02914}, pmid = {30555445}, issn = {1664-302X}, abstract = {Typically, nitrification is a two-stage microbial process and is key in wastewater treatment and nutrient recovery from waste streams. Changes in salinity represent a major stress factor that can trigger response mechanisms, impacting the activity and the physiology of bacteria. Despite its pivotal biotechnological role, little information is available on the specific response of nitrifying bacteria to varying levels of salinity. In this study, synthetic communities of ammonia-oxidizing bacteria (AOB Nitrosomonas europaea and/or Nitrosomonas ureae) and nitrite-oxidizing bacteria (NOB Nitrobacter winogradskyi and/or Nitrobacter vulgaris) were tested at 5, 10, and 30 mS cm-1 by adding sodium chloride to the mineral medium (0, 40, and 200 mM NaCl, respectively). Ammonia oxidation activity was less affected by salinity than nitrite oxidation. AOB, on their own or in combination with NOB, showed no significant difference in the ammonia oxidation rate among the three conditions. However, N. winogradskyi improved the absolute ammonia oxidation rate of both N. europaea and N. ureae. N. winogradskyi's nitrite oxidation rate decreased to 42% residual activity upon exposure to 30 mS cm-1, also showing a similar behavior when tested with Nitrosomonas spp. The nitrite oxidation rate of N. vulgaris, as a single species, was not affected when adding sodium chloride up to 30 mS cm-1, however, its activity was completely inhibited when combined with Nitrosomonas spp. in the presence of ammonium/ammonia. The proteomic analysis of a co-culture of N. europaea and N. winogradskyi revealed the production of osmolytes, regulation of cell permeability and an oxidative stress response in N. europaea and an oxidative stress response in N. winogradskyi, as a result of increasing the salt concentration from 5 to 30 mS cm-1. A specific metabolic response observed in N. europaea suggests the role of carbon metabolism in the production of reducing power, possibly to meet the energy demands of the stress response mechanisms, induced by high salinity. For the first time, metabolic modifications and response mechanisms caused by the exposure to salinity were described, serving as a tool toward controllability and predictability of nitrifying systems exposed to salt fluctuations.}, }
@article {pmid30555443, year = {2018}, author = {Tanaka, K and Yokoe, S and Igarashi, K and Takashino, M and Ishikawa, M and Hori, K and Nakanishi, S and Kato, S}, title = {Extracellular Electron Transfer via Outer Membrane Cytochromes in a Methanotrophic Bacterium Methylococcus capsulatus (Bath).}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2905}, doi = {10.3389/fmicb.2018.02905}, pmid = {30555443}, issn = {1664-302X}, abstract = {Electron exchange reactions between microbial cells and solid materials, referred to as extracellular electron transfer (EET), have attracted attention in the fields of microbial physiology, microbial ecology, and biotechnology. Studies of model species of iron-reducing, or equivalently, current-generating bacteria such as Geobacter spp. and Shewanella spp. have revealed that redox-active proteins, especially outer membrane c-type cytochromes (OMCs), play a pivotal role in the EET process. Recent (meta)genomic analyses have revealed that diverse microorganisms that have not been demonstrated to have EET ability also harbor OMC-like proteins, indicating that EET via OMCs could be more widely preserved in microorganisms than originally thought. A methanotrophic bacterium Methylococcus capsulatus (Bath) was reported to harbor multiple OMC genes whose expression is elevated by Cu starvation. However, the physiological role of these genes is unknown. Therefore, in this study, we explored whether M. capsulatus (Bath) displays EET abilities via OMCs. In electrochemical analysis, M. capsulatus (Bath) generated anodic current only when electron donors such as formate were available, and could reduce insoluble iron oxides in the presence of electron donor compounds. Furthermore, the current-generating and iron-reducing activities of M. capsulatus (Bath) cells that were cultured in a Cu-deficient medium, which promotes high levels of OMC expression, were higher than those cultured in a Cu-supplemented medium. Anodic current production by the Cu-deficient cells was significantly suppressed by disruption of MCA0421, a highly expressed OMC gene, and by treatment with carbon monoxide (CO) gas (an inhibitor of c-type cytochromes). Our results provide evidence of EET in M. capsulatus (Bath) and demonstrate the pivotal role of OMCs in this process. This study raises the possibility that EET to solid compounds is a novel survival strategy of methanotrophic bacteria.}, }
@article {pmid30554808, year = {2018}, author = {Sutherland, WJ and Broad, S and Butchart, SHM and Clarke, SJ and Collins, AM and Dicks, LV and Doran, H and Esmail, N and Fleishman, E and Frost, N and Gaston, KJ and Gibbons, DW and Hughes, AC and Jiang, Z and Kelman, R and LeAnstey, B and le Roux, X and Lickorish, FA and Monk, KA and Mortimer, D and Pearce-Higgins, JW and Peck, LS and Pettorelli, N and Pretty, J and Seymour, CL and Spalding, MD and Wentworth, J and Ockendon, N}, title = {A Horizon Scan of Emerging Issues for Global Conservation in 2019.}, journal = {Trends in ecology &amp; evolution}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tree.2018.11.001}, pmid = {30554808}, issn = {1872-8383}, abstract = {We present the results of our tenth annual horizon scan. We identified 15 emerging priority topics that may have major positive or negative effects on the future conservation of global biodiversity, but currently have low awareness within the conservation community. We hope to increase research and policy attention on these areas, improving the capacity of the community to mitigate impacts of potentially negative issues, and maximise the benefits of issues that provide opportunities. Topics include advances in crop breeding, which may affect insects and land use; manipulations of natural water flows and weather systems on the Tibetan Plateau; release of carbon and mercury from melting polar ice and thawing permafrost; new funding schemes and regulations; and land-use changes across Indo-Malaysia.}, }
@article {pmid30554770, year = {2018}, author = {Cordier, T and Lanzén, A and Apothéloz-Perret-Gentil, L and Stoeck, T and Pawlowski, J}, title = {Embracing Environmental Genomics and Machine Learning for Routine Biomonitoring.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2018.10.012}, pmid = {30554770}, issn = {1878-4380}, abstract = {Genomics is fast becoming a routine tool in medical diagnostics and cutting-edge biotechnologies. Yet, its use for environmental biomonitoring is still considered a futuristic ideal. Until now, environmental genomics was mainly used as a replacement of the burdensome morphological identification, to screen known morphologically distinguishable bioindicator taxa. While prokaryotic and eukaryotic microbial diversity is of key importance in ecosystem functioning, its implementation in biomonitoring programs is still largely unappreciated, mainly because of difficulties in identifying microbes and limited knowledge of their ecological functions. Here, we argue that the combination of massive environmental genomics microbial data with machine learning algorithms can be extremely powerful for biomonitoring programs and pave the way to fill important gaps in our understanding of microbial ecology.}, }
@article {pmid30554323, year = {2018}, author = {Jiang, N and Liu, H and Wang, P and Huang, J and Han, H and Wang, Q}, title = {Illumina MiSeq Sequencing Investigation of Microbiota in Bronchoalveolar Lavage Fluid and Cecum of the Swine Infected with PRRSV.}, journal = {Current microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00284-018-1613-y}, pmid = {30554323}, issn = {1432-0991}, support = {No. 81172777//the National Natural Science Foundation of China under Grant/ ; No. 2014B11NC096//the Dalian Science and Technological Project under Grant/ ; }, abstract = {Porcine reproductive and respiratory syndrome virus (PRRSV) causes significant animal morbidity and mortality and economic losses worldwide. In this study, we analyzed the microbiota in bronchoalveolar lavage fluid (BAL), mucosa, and feces in cecum of the PRRSV-challenged pigs using the Illumina MiSeq sequencing platform, to investigate the role of microbiota in the pathogenesis and development of porcine reproductive and respiratory syndrome (PRRS). Quantitative insights into microbial ecology analyses indicated that the dominant bacterial groups in the lung from the PRRSV-challenged pigs were Haemophilus parasuis and Mycoplasma hyorhinis, with a relative abundance of 35-48% and 27-41%, respectively. Our results were consistent with the clinical observation that the PRRSV-infected pigs are always co-infected with other bacteria, such as Haemophilus and Mycoplasma. On the other hand, Campylobacter and Clostridium became the two most abundant bacteria in the mucosal and luminal microbiota of the cecum of the PRRSV-challenged pigs, and the relative abundance was four times higher than that in the healthy pigs. This suggested that Campylobacter and Clostridium might be associated with the pathogenesis of diarrhea in PRRS. Linear discriminant analysis effect size reveals significant microbial dysbiosis of BAL, mucosa, and feces in cecum of the PRRSV-challenged pigs. We have identified a structural imbalance of the microbiota, characterized by a reduced diversity of microbiota and abundance alterations of certain bacteria in the PRRSV-challenged pigs. The observed microbiota dysbiosis in this study provides insight into the roles of the microbiota in the complications of the PRRSV infection.}, }
@article {pmid30552443, year = {2018}, author = {Rothman, JA and Andrikopoulos, C and Cox-Foster, D and McFrederick, QS}, title = {Floral and Foliar Source Affect the Bee Nest Microbial Community.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1300-3}, pmid = {30552443}, issn = {1432-184X}, support = {NNX15AP99A//National Aeronautics and Space Administration/ ; 2018-67011-28123//National Institute of Food and Agriculture/ ; CA-R-ENT-5109-H//National Institute of Food and Agriculture/ ; }, abstract = {Managed pollinators such as the alfalfa leafcutting bee, Megachile rotundata, are essential to the production of a wide variety of agricultural crops. These pollinators encounter a diverse array of microbes when foraging for food and nest-building materials on various plants. To test the hypothesis that food and nest-building source affects the composition of the bee-nest microbiome, we exposed M. rotundata adults to treatments that varied both floral and foliar source in a 2 × 2 factorial design. We used 16S rRNA gene and internal transcribed spacer (ITS) sequencing to capture the bacterial and fungal diversity of the bee nests. We found that nest microbial communities were significantly different between treatments, indicating that bee nests become inoculated with environmentally derived microbes. We did not find evidence of interactions between the fungi and bacteria within our samples. Furthermore, both the bacterial and fungal communities were quite diverse and contained numerous exact sequence variants (ESVs) of known plant and bee pathogens that differed based on treatment. Our research indicates that bees deposit plant-associated microbes into their nests, including multiple plant pathogens such as smut fungi and bacteria that cause blight and wilt. The presence of plant pathogens in larval pollen provisions highlights the potential for bee nests to act as disease reservoirs across seasons. We therefore suggest that future research should investigate the ability of bees to transmit pathogens from nest to host plant.}, }
@article {pmid30547761, year = {2018}, author = {Morales-Cruz, A and Figueroa-Balderas, R and García, JF and Tran, E and Rolshausen, PE and Baumgartner, K and Cantu, D}, title = {Profiling grapevine trunk pathogens in planta: a case for community-targeted DNA metabarcoding.}, journal = {BMC microbiology}, volume = {18}, number = {1}, pages = {214}, doi = {10.1186/s12866-018-1343-0}, pmid = {30547761}, issn = {1471-2180}, support = {2016-1798//American Vineyard Foundation/ ; 2017-1798//American Vineyard Foundation/ ; 2018-1798//American Vineyard Foundation/ ; 2012-51181-19954//National Institute of Food and Agriculture/ ; }, abstract = {BACKGROUND: DNA metabarcoding, commonly used in exploratory microbial ecology studies, is a promising method for the simultaneous in planta-detection of multiple pathogens associated with disease complexes, such as the grapevine trunk diseases. Profiling of pathogen communities associated with grapevine trunk diseases is particularly challenging, due to the presence within an individual wood lesion of multiple co-infecting trunk pathogens and other wood-colonizing fungi, which span a broad range of taxa in the fungal kingdom. As such, we designed metabarcoding primers, using as template the ribosomal internal transcribed spacer of grapevine trunk-associated ascomycete fungi (GTAA) and compared them to two universal primer widely used in microbial ecology.<br><br>RESULTS: We first performed in silico simulations and then tested the primers by high-throughput amplicon sequencing of (i) multiple combinations of mock communities, (ii) time-course experiments with controlled inoculations, and (iii) diseased field samples from vineyards under natural levels of infection. All analyses showed that GTAA had greater affinity and sensitivity, compared to those of the universal primers. Importantly, with GTAA, profiling of mock communities and comparisons with shotgun-sequencing metagenomics of field samples gave an accurate representation of genera of important trunk pathogens, namely Phaeomoniella, Phaeoacremonium, and Eutypa, the abundances of which were over- or under-estimated with universal primers.<br><br>CONCLUSIONS: Overall, our findings not only demonstrate that DNA metabarcoding gives qualitatively and quantitatively accurate results when applied to grapevine trunk diseases, but also that primer customization and testing are crucial to ensure the validity of DNA metabarcoding results.}, }
@article {pmid30547194, year = {2018}, author = {Visvalingam, J and Zhang, P and Ells, TC and Yang, X}, title = {Dynamics of Biofilm Formation by Salmonella Typhimurium and Beef Processing Plant Bacteria in Mono- and Dual-Species Cultures.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1304-z}, pmid = {30547194}, issn = {1432-184X}, support = {A-1603 and A-1637//Agriculture and Agri-Food Canada/ ; }, abstract = {This study aimed to determine the impact of bacteria from a beef plant conveyor belt on the biofilm formation of Salmonella in dual-species cultures. Beef plant isolates (50) including 18 Gram-negative aerobes (GNA), 8 Gram-positive aerobes (GPA), 5 lactic acid bacteria (LAB), 9 Enterobacteriaceae (EB), and 10 generic Escherichia coli (GEC) were included for developing biofilms in mono- and co-culture with S. Typhimurium at 15 °C for 6 days. Five selected cultures in planktonic form and in biofilms were tested for susceptibility to two commonly used sanitizers (i.e. E-San and Perox-E Plus). In mono-cultures, ≥ 80, 67, 61, 20, and 13% of GEC, EB, GNA, LAB, and GPA, respectively, developed measurable biofilms after 2 days, while all co-culture pairings with S. Typhimurium achieved some level of biofilm production. The predominant effect of EB and only effect of GEC strains on the biofilm formation of S. Typhimurium was antagonistic, while that of Gram-positive bacteria was synergistic, with the effect being more prominent on day 6. The effect was highly variable for the GNA isolates. Six aerobic isolates that formed moderate/strong biofilms by day 2 greatly boosted the co-culture biofilm formation. Seven Gram-negative bacteria were antagonistic against the biofilm formation of the co-cultures. Both sanitizers completely inactivated the selected planktonic cultures, but were largely ineffective against biofilms. In conclusion, all beef plant isolates assessed formed biofilms when paired with S. Typhimurium. Aerobic biofilm formers may create a more favorable condition for Salmonella biofilm formation, while some beef plant isolates have potential as a biocontrol strategy for Salmonella biofilms.}, }
@article {pmid30545051, year = {2018}, author = {Haro, C and Villatoro, M and Vaquero, L and Pastor, J and Giménez, MJ and Ozuna, CV and Sánchez-León, S and García-Molina, MD and Segura, V and Comino, I and Sousa, C and Vivas, S and Landa, BB and Barro, F}, title = {The Dietary Intervention of Transgenic Low-Gliadin Wheat Bread in Patients with Non-Celiac Gluten Sensitivity (NCGS) Showed No Differences with Gluten Free Diet (GFD) but Provides Better Gut Microbiota Profile.}, journal = {Nutrients}, volume = {10}, number = {12}, pages = {}, doi = {10.3390/nu10121964}, pmid = {30545051}, issn = {2072-6643}, support = {Projects AGL2013-48946-C3-1-R, AGL2013-48946-C and AGL2016-80566-P//Ministerio de Economía, Industria y Competitividad, Gobierno de España/ ; }, abstract = {The study evaluated the symptoms, acceptance, and digestibility of bread made from transgenic low-gliadin wheat, in comparison with gluten free bread, in Non-coeliac gluten sensitivity (NCGS) patients, considering clinical/sensory parameters and gut microbiota composition. This study was performed in two phases of seven days each, comprising a basal phase with gluten free bread and an E82 phase with low-gliadin bread. Gastrointestinal clinical symptoms were evaluated using the Gastrointestinal Symptom Rating Scale (GSRS) questionnaire, and stool samples were collected for gluten immunogenic peptides (GIP) determination and the extraction of gut microbial DNA. For the basal and E82 phases, seven and five patients, respectively, showed undetectable GIPs content. The bacterial 16S rRNA gene V1-V2 hypervariable regions were sequenced using the Illumina MiSeq platform and downstream analysis was done using a Quantitative Insights into Microbial Ecology (QIIME) pipeline. No significant differences in the GSRS questionnaires were observed between the two phases. However, we observed a significantly lower abundance of some gut genera Oscillospira, Dorea, Blautia, Bacteroides, Coprococcus, and Collinsella, and a significantly higher abundance of Roseburia and Faecalibacterium genera during the E82 phase compared with the basal phase. The consumption of low-gliadin bread E82 by NCGS subjects induced potentially positive changes in the gut microbiota composition, increasing the butyrate-producing bacteria and favoring a microbial profile that is suggested to have a key role in the maintenance or improvement of gut permeability.}, }
@article {pmid30544668, year = {2018}, author = {Kaboré, WAD and Dembélé, R and Bagré, TS and Konaté, A and Boisramé, S and Chevalier, V and Konsem, T and Traoré, AS and Barro, N}, title = {Characterization and Antimicrobial Susceptibility of Lactococcus lactis Isolated from Endodontic Infections in Ouagadougou, Burkina Faso.}, journal = {Dentistry journal}, volume = {6}, number = {4}, pages = {}, doi = {10.3390/dj6040069}, pmid = {30544668}, issn = {2304-6767}, abstract = {BACKGROUND: This study aimed to characterize and test the antimicrobial susceptibility of Lactococcus lactis isolated in endodontic infections in Burkina Faso.<br><br>MATERIAL AND METHODS: This was a prospective study conducted at the Municipal Oral Health Center of Ouagadougou, Burkina Faso, from June to October 2014. Clinical data were collected using a questionnaire form. The method of streaking on selective medium was used to isolate bacteria. Identification was made using the API 20 Strep gallery. Antibiotic susceptibility was performed by the diffusion method on solid medium.<br><br>RESULTS: One hundred and twenty-five (125) patients were received with a significant proportion from the age group of 19 to 40 years (55.2%). Apical periodontitis accounted for 50.4% and cellulitis for 49.6% of cases. Lactococcus lactis ssp. lactis was identified in five exudate samples. Isolates were 100% resistant to cefixime and metronidazole, 80% to ceftriaxone, cefuroxime, cefotaxime, chloramphenicol and 60% to penicillin G, amoxicillin, amoxicillin clavulanic acid. A multidrug resistance of more than three families of antibiotics was noticed. No strains produced extended spectrum ß-lactamases.<br><br>CONCLUSION: Lactococcus lactis is part of endodontic biofilm. The reported strong antibiotic resistance involving endodontic therapy will focus on the effect of the disinfectant solution and the mechanical action of the canal instruments.}, }
@article {pmid30544592, year = {2018}, author = {Bosmans, L and Pozo, MI and Verreth, C and Crauwels, S and Wäckers, F and Jacquemyn, H and Lievens, B}, title = {Hibernation Leads to Altered Gut Communities in Bumblebee Queens (Bombus terrestris).}, journal = {Insects}, volume = {9}, number = {4}, pages = {}, doi = {10.3390/insects9040188}, pmid = {30544592}, issn = {2075-4450}, abstract = {Many reptiles, amphibians, mammals, and insects practice some form of hibernation during which their metabolic rate is drastically reduced. This allows them to conserve energy and survive the harsh winter conditions with little or no food. While it can be expected that a reduction in host metabolism has a substantial influence on the gut microbial community, little is known about the effects of hibernation on the composition of the microbial gut community, especially for insects. In this study, we assessed and compared the bacterial gut community composition within the midgut and ileum of indoor-reared queens of Bombus terrestris before and after an artificial hibernation period of 16 weeks. Deep sequencing of 16S ribosomal RNA gene amplicons and clustering of sequence reads into operational taxonomic units (OTUs) at a similarity threshold of 97% revealed several bacterial taxa that are known to be strongly associated with corbiculate bees. Bacterial community composition after hibernation compared to before hibernation was characterized by higher OTU richness and evenness, with decreased levels of the core bacteria Gilliamella (Proteobacteria, Orbaceae) and Snodgrassella (Proteobacteria, Neisseriaceae), and increased relative abundance of non-core bacteria, including several psychrophilic and psychrotrophic taxa.}, }
@article {pmid30542336, year = {2018}, author = {Okazaki, Y and Salcher, MM and Callieri, C and Nakano, SI}, title = {The Broad Habitat Spectrum of the CL500-11 Lineage (Phylum Chloroflexi), a Dominant Bacterioplankton in Oxygenated Hypolimnia of Deep Freshwater Lakes.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2891}, doi = {10.3389/fmicb.2018.02891}, pmid = {30542336}, issn = {1664-302X}, abstract = {CL500-11 (phylum Chloroflexi) is one of the most ubiquitous and abundant bacterioplankton lineages in deep freshwater lakes inhabiting the oxygenated hypolimnion. While metagenomics predicted possible eco-physiological characteristics of this uncultured lineage, no consensus on their ecology has so far been reached, partly because their niche is not clearly understood due to a limited number of quantitative field observations. This study investigated the abundance and distribution of CL500-11 in seven deep perialpine lakes using catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). Samples were taken vertically (5-12 depths in each lake) and temporally (in two lakes) at the deepest point of the lakes located in Switzerland, Italy, and Austria with varying depth, trophic state, mixing regime, and water retention time. The results showed a dominance of CL500-11 in all the lakes; their proportion to total prokaryotes ranged from 4.3% (Mondsee) to 24.3% (Lake Garda) and their abundance ranged from 0.65 × 105 (Mondsee) to 1.77 × 105 (Lake Garda) cells mL-1. By summarizing available information on CL500-11 occurrence to date, we demonstrated their broad habitat spectrum, ranging from ultra-oligotrophic to meso-eutrophic lakes, while low abundances or complete absence was observed in lakes with shallow depth, low pH, and/or short water retention time (<1 year). Together with available metagenomic and geochemical evidences from literatures, here we reviewed potential substrates supporting growth of CL500-11. Overall, the present study further endorsed ubiquity and quantitative significance of CL500-11 in deep freshwater systems and narrowed the focus on their physiological characteristics and ecological importance.}, }
@article {pmid30542078, year = {2018}, author = {Scoma, A and Heyer, R and Rifai, R and Dandyk, C and Marshall, I and Kerckhof, FM and Marietou, A and Boshker, HTS and Meysman, FJR and Malmos, KG and Vosegaard, T and Vermeir, P and Banat, IM and Benndorf, D and Boon, N}, title = {Reduced TCA cycle rates at high hydrostatic pressure hinder hydrocarbon degradation and obligate oil degraders in natural, deep-sea microbial communities.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-018-0324-5}, pmid = {30542078}, issn = {1751-7370}, abstract = {Petroleum hydrocarbons reach the deep-sea following natural and anthropogenic factors. The process by which they enter deep-sea microbial food webs and impact the biogeochemical cycling of carbon and other elements is unclear. Hydrostatic pressure (HP) is a distinctive parameter of the deep sea, although rarely investigated. Whether HP alone affects the assembly and activity of oil-degrading communities remains to be resolved. Here we have demonstrated that hydrocarbon degradation in deep-sea microbial communities is lower at native HP (10 MPa, about 1000 m below sea surface level) than at ambient pressure. In long-term enrichments, increased HP selectively inhibited obligate hydrocarbon-degraders and downregulated the expression of beta-oxidation-related proteins (i.e., the main hydrocarbon-degradation pathway) resulting in low cell growth and CO2 production. Short-term experiments with HP-adapted synthetic communities confirmed this data, revealing a HP-dependent accumulation of citrate and dihydroxyacetone. Citrate accumulation suggests rates of aerobic oxidation of fatty acids in the TCA cycle were reduced. Dihydroxyacetone is connected to citrate through glycerol metabolism and glycolysis, both upregulated with increased HP. High degradation rates by obligate hydrocarbon-degraders may thus be unfavourable at increased HP, explaining their selective suppression. Through lab-scale cultivation, the present study is the first to highlight a link between impaired cell metabolism and microbial community assembly in hydrocarbon degradation at high HP. Overall, this data indicate that hydrocarbons fate differs substantially in surface waters as compared to deep-sea environments, with in situ low temperature and limited nutrients availability expected to further prolong hydrocarbons persistence at deep sea.}, }
@article {pmid30524385, year = {2018}, author = {Rilling, JI and Acuña, JJ and Sadowsky, MJ and Jorquera, MA}, title = {Putative Nitrogen-Fixing Bacteria Associated With the Rhizosphere and Root Endosphere of Wheat Plants Grown in an Andisol From Southern Chile.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2710}, doi = {10.3389/fmicb.2018.02710}, pmid = {30524385}, issn = {1664-302X}, abstract = {Acidic ash derived volcanic soils (Andisols) support 50% of cereal production in Chile. Nitrogen (N) is essential for cereal crops and commonly added as urea with consequent environmental concerns due to leaching. Despite the relevance of N to plant growth, few studies have focused on understanding the application, management and ecological role of N2-fixing bacterial populations as tool for improve the N nutrition of cereal crops in Chile. It is known that N2-fixing bacteria commonly inhabits diverse plant compartments (e.g., rhizosphere and root endosphere) where they can supply N for plant growth. Here, we used culture-independent and dependent approaches to characterize and compare the putative N2-fixing bacteria associated with the rhizosphere and root endosphere of wheat plants grown in an Andisol from southern Chile. Our results showed significantly greater bacterial loads in the rhizosphere than the root endosphere. Quantitative PCR results indicated that the copy number of the 16S rRNA gene ranged from 1012~1013 and 107~108 g-1 sample in rhizosphere and root endosphere, respectively. The nifH gene copy number ranged from 105~106 and 105 g-1 sample in rhizosphere and root endosphere, respectively. The total culturable bacteria number ranged from 109~1010 and 107~108 CFU g-1 sample in rhizosphere and 104~105 and 104 CFU g-1 sample in root endosphere using LB and NM-1 media, respectively. Indirect counts of putative N2-fixing bacteria were 103 and 102~103 CFU g-1 sample in rhizosphere and root endosphere using NFb medium, respectively. Sequencing of 16S rRNA genes from randomly selected putative N2-fixing bacteria revealed the presence of members of Proteobacteria (Bosea and Roseomonas), Actinobacteria (Georgenia, Mycobacterium, Microbacterium, Leifsonia, and Arthrobacter), Bacteroidetes (Chitinophaga) and Firmicutes (Bacillus and Psychrobacillus) taxa. Differences in 16S rRNA and putative nifH-containing bacterial communities between rhizosphere and root endosphere were shown by denaturing gradient gel electrophoresis (DGGE). This study shows a compartmentalization between rhizosphere and root endosphere for both the abundance and diversity of total (16S rRNA) and putative N2-fixing bacterial communities on wheat plants grown in Chilean Andisols. This information can be relevant for the design and application of agronomic strategies to enhance sustainable N-utilization in cereal crops in Chile.}, }
@article {pmid30522433, year = {2018}, author = {Mohr, T and Aliyu, H and Küchlin, R and Zwick, M and Cowan, D and Neumann, A and de Maayer, P}, title = {Comparative genomic analysis of Parageobacillus thermoglucosidasius strains with distinct hydrogenogenic capacities.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {880}, doi = {10.1186/s12864-018-5302-9}, pmid = {30522433}, issn = {1471-2164}, support = {031B0180//Bundesministerium für Bildung und Forschung/ ; }, abstract = {BACKGROUND: The facultatively anaerobic thermophile Parageobacillus thermoglucosidasius produces hydrogen gas (H2) by coupling CO oxidation to proton reduction in the water-gas shift (WGS) reaction via a carbon monoxide dehydrogenase-hydrogenase enzyme complex. Although little is known about the hydrogenogenic capacities of different strains of this species, these organisms offer a potentially viable process for the synthesis of this alternative energy source.<br><br>RESULTS: The WGS-catalyzed H2 production capacities of four distinct P. thermoglucosidasius strains were determined by cultivation and gas analysis. Three strains (DSM 2542T, DSM 2543 and DSM 6285) were hydrogenogenic, while the fourth strain (DSM 21625) was not. Furthermore, in one strain (DSM 6285) H2 production commenced earlier in the cultivation than the other hydrogenogenic strains. Comparative genomic analysis of the four strains identified extensive differences in the protein complement encoded on the genomes, some of which are postulated to contribute to the different hydrogenogenic capacities of the strains. Furthermore, polymorphisms and deletions in the CODH-NiFe hydrogenase loci may also contribute towards this variable phenotype.<br><br>CONCLUSIONS: Disparities in the hydrogenogenic capacities of different P. thermoglucosidasius strains were identified, which may be correlated to variability in their global proteomes and genetic differences in their CODH-NiFe hydrogenase loci. The data from this study may contribute towards an improved understanding of WGS-catalysed hydrogenogenesis by P. thermoglucosidasius.}, }
@article {pmid30538275, year = {2018}, author = {Nicolás, C and Martin-Bertelsen, T and Floudas, D and Bentzer, J and Smits, M and Johansson, T and Troein, C and Persson, P and Tunlid, A}, title = {The soil organic matter decomposition mechanisms in ectomycorrhizal fungi are tuned for liberating soil organic nitrogen.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-018-0331-6}, pmid = {30538275}, issn = {1751-7370}, support = {2013.0073//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; }, abstract = {Many trees form ectomycorrhizal symbiosis with fungi. During symbiosis, the tree roots supply sugar to the fungi in exchange for nitrogen, and this process is critical for the nitrogen and carbon cycles in forest ecosystems. However, the extents to which ectomycorrhizal fungi can liberate nitrogen and modify the soil organic matter and the mechanisms by which they do so remain unclear since they have lost many enzymes for litter decomposition that were present in their free-living, saprotrophic ancestors. Using time-series spectroscopy and transcriptomics, we examined the ability of two ectomycorrhizal fungi from two independently evolved ectomycorrhizal lineages to mobilize soil organic nitrogen. Both species oxidized the organic matter and accessed the organic nitrogen. The expression of those events was controlled by the availability of glucose and inorganic nitrogen. Despite those similarities, the decomposition mechanisms, including the type of genes involved as well as the patterns of their expression, differed markedly between the two species. Our results suggest that in agreement with their diverse evolutionary origins, ectomycorrhizal fungi use different decomposition mechanisms to access organic nitrogen entrapped in soil organic matter. The timing and magnitude of the expression of the decomposition activity can be controlled by the below-ground nitrogen quality and the above-ground carbon supply.}, }
@article {pmid30536130, year = {2018}, author = {Wilpiszeski, RL and Zhang, Z and House, CH}, title = {Biogeography of thermophiles and predominance of Thermus scotoductus in domestic water heaters.}, journal = {Extremophiles : life under extreme conditions}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00792-018-1066-z}, pmid = {30536130}, issn = {1433-4909}, support = {NAI Cooperative agreement #NNA09DA76A//National Aeronautics and Space Administration/ ; }, abstract = {Built systems such as water heaters can harbor extremophiles similar to those residing in natural hot springs, but the extent of colonization is not well understood. To address this, we conducted a survey of thermophilic microorganisms in household water heaters across the United States. Filter samples and inoculated cultures were collected by citizen-scientists from 101 homes. Draft genomes were assembled from cultured isolates and 16S rRNA genes were sequenced from filter samples. 28% of households harbored communities with unambiguous DNA signatures of thermophilic organisms, 36% of households provided viable inocula, and 21% of households had both. All of the recovered cultures as well as the community sequencing results revealed Thermus scotoductus to be the dominant thermophile in domestic water heaters, with a minority of water heaters also containing Meiothermus species and a few containing Aquificae. Sequence distance comparisons show that allopatric speciation does not appear to be a strong control on T. scotoductus distribution. Our results demonstrate that thermophilic organisms are widespread in hot tap water, and that Thermus scotoductus preferentially colonizes water heaters at the expense of local environmental Thermus strains.}, }
@article {pmid30535916, year = {2018}, author = {Albecker, MA and Belden, LK and McCoy, MW}, title = {Comparative Analysis of Anuran Amphibian Skin Microbiomes Across Inland and Coastal Wetlands.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1295-9}, pmid = {30535916}, issn = {1432-184X}, support = {DEB 1136640//National Science Foundation/ ; Project No. 2014-R/14-HCE-3//North Carolina SeaGrant/ ; }, abstract = {Amphibians host a community of microbes on their skin that helps resist infectious disease via the dual influence of anti-pathogenic microbial species and emergent community dynamics. Many frogs rely on freshwater habitats, but salinization is rapidly increasing saltwater concentrations in wetlands around the globe, increasing the likelihood that frogs will come into contact with salt-contaminated habitats. Currently, we know little about how increased salt exposure will affect the symbiotic relationship between the skin microbes and frog hosts. To better understand how salt exposure in a natural context affects the frog skin microbiome, we use Hyla cinerea, a North American treefrog species that can inhabit brackish wetlands, to explore three questions. First, we determine the extent that microbial communities in the environment and on frog skin are similar across populations. Second, we assess the microbial species richness and relative abundance on frogs from habitats with different salinity levels to determine how salinity affects the microbiome. Third, we test whether the relative abundances of putatively pathogen-resistant bacterial species differ between frogs from inland and coastal environments. We found that the frog microbiome is more similar among frogs than to the microbial communities found in surface water and soil, but there is overlap between frog skin and the environmental samples. Skin microbial community richness did not differ among populations, but the relative abundances of microbes were different across populations and salinities. We found no differences in the relative abundances of the anti-fungal bacteria Janthinobacterium lividum, the genus Pseudomonas, and Serratia marcescens, suggesting that environmental exposure to saltwater has a limited influence on these putatively beneficial bacterial taxa.}, }
@article {pmid30535915, year = {2018}, author = {Chamizo, S and Adessi, A and Mugnai, G and Simiani, A and De Philippis, R}, title = {Soil Type and Cyanobacteria Species Influence the Macromolecular and Chemical Characteristics of the Polysaccharidic Matrix in Induced Biocrusts.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1305-y}, pmid = {30535915}, issn = {1432-184X}, support = {706351//H2020 Marie Skłodowska-Curie Actions/ ; }, abstract = {Inoculation of soils with cyanobacteria is proposed as a sustainable biotechnological technique for restoration of degraded areas in drylands due to the important role that cyanobacteria and their exopolysaccharides (EPS) play in the environment. So far, few studies have analyzed the macromolecular and chemical characteristics of the polysaccharidic matrix in induced cyanobacterial biocrusts and the scarce existing studies have mainly focused on sandy soil textures. However, the characteristics of the cyanobacterial polysaccharidic matrix may greatly depend on soil type. The objective of this study was to examine the macromolecular distribution and monosaccharidic composition of the polysaccharidic matrix induced by inoculation of two cyanobacterial species common in arid environments, Phormidium ambiguum (non N-fixing) and Scytonema javanicum (N-fixing) in different soil types. S. javanicum promoted a higher release in the soil of the more soluble and less condensed EPS fraction (i.e., the loosely bound EPS fraction, LB-EPS), while P. ambiguum showed a higher release of the less soluble and more condensed EPS fraction (i.e., the tightly bound EPS fraction, TB-EPS). LB-EPSs were mainly composed of low MW molecules (< 50 kDa), while TB-EPSs were mainly composed of high MW molecules (1100-2000 kDa). The two EPS fractions showed a complex monosaccharidic composition (from 11 to 12 different types of monosaccharides), with glucose as the most abundant monosaccharide, in particular in the poorer soils characterized by lower organic C contents. In more C-rich soils, high abundances of galactose, mannose, and xylose were also found. Low abundance of uronic acids and hydrophobic monosaccharides, such as fucose and rhamnose, was found in the EPS extracted from the inoculated soils. Our results point to the influence of soil type on the macromolecular distribution and monosaccharide composition of the polysaccharidic matrix in induced biocrusts, which is likely to affect biocrust development and their role in soil structure and nutrient cycling in restored dryland soils.}, }
@article {pmid30535914, year = {2018}, author = {Muthukrishnan, T and Al Khaburi, M and Abed, RMM}, title = {Fouling Microbial Communities on Plastics Compared with Wood and Steel: Are They Substrate- or Location-Specific?.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1303-0}, pmid = {30535914}, issn = {1432-184X}, support = {SQU-GCC/CL/17/02//Sultan Qaboos University/ ; }, abstract = {Although marine biofouling has been widely studied on different substrates, information on biofouling on plastics in the Arabian Gulf is limited. Substrate- and location-specific effects were investigated by comparing the microbial communities developed on polyethylene terephthalate (PET) and polyethylene (PE) with those on steel and wood, at two locations in the Sea of Oman. Total biomass was lower on PET and PE than on steel and wood. PET had the highest bacterial abundance at both locations, whereas chlorophyll a concentrations did not vary between substrates. MiSeq 16S ribosomal RNA sequencing revealed comparable operational taxonomic unit (OTU) richness on all substrates at one location but lower numbers on PET and PE at the other location. Non-metric multidimensional scaling (NMDS) showed distinct clusters of the bacterial communities based on substrate (analysis of similarity (ANOSIM), R = 0.45-0.97, p < 0.03) and location (ANOSIM, R = 0.56, p < 0.0001). The bacterial genera Microcystis and Hydrogenophaga and the diatoms Licmophora and Mastogloia were specifically detected on plastics. Desulfovibrio and Pseudomonas spp. exhibited their highest abundance on steel and Corynebacterium spp. on wood. Scanning electron microscopy (SEM) revealed fissure formation on PET and PE, indicating physical degradation. The presence of free radicals on PET and carbonyl bonds (C=O) on PE, as revealed by Fourier transform infrared (FTIR) spectroscopy, indicated abiotic degradation while hydroxyl groups and spectral peaks for proteins and polysaccharides on PE indicated biotic degradation. We conclude that fouling microbial communities are not only substrate-specific but also location-specific and microbes developing on plastics could potentially contribute to their degradation in the marine environment.}, }
@article {pmid30535652, year = {2018}, author = {Whittle, A and Amesbury, MJ and Charman, DJ and Hodgson, DA and Perren, BB and Roberts, SJ and Gallego-Sala, AV}, title = {Salt-Enrichment Impact on Biomass Production in a Natural Population of Peatland Dwelling Arcellinida and Euglyphida (Testate Amoebae).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1296-8}, pmid = {30535652}, issn = {1432-184X}, support = {NE/L002434/1//Natural Environment Research Council/ ; }, abstract = {Unicellular free-living microbial eukaryotes of the order Arcellinida (Tubulinea; Amoebozoa) and Euglyphida (Cercozoa; SAR), commonly termed testate amoebae, colonise almost every freshwater ecosystem on Earth. Patterns in the distribution and productivity of these organisms are strongly linked to abiotic conditions-particularly moisture availability and temperature-however, the ecological impacts of changes in salinity remain poorly documented. Here, we examine how variable salt concentrations affect a natural community of Arcellinida and Euglyphida on a freshwater sub-Antarctic peatland. We principally report that deposition of wind-blown oceanic salt-spray aerosols onto the peatland surface corresponds to a strong reduction in biomass and to an alteration in the taxonomic composition of communities in favour of generalist taxa. Our results suggest novel applications of this response as a sensitive tool to monitor salinisation of coastal soils and to detect salinity changes within peatland palaeoclimate archives. Specifically, we suggest that these relationships could be used to reconstruct millennial scale variability in salt-spray deposition-a proxy for changes in wind-conditions-from sub-fossil communities of Arcellinida and Euglyphida preserved in exposed coastal peatlands.}, }
@article {pmid30535561, year = {2018}, author = {Rydzanicz, K and Golab, E and Rozej-Bielicka, W and Masny, A}, title = {Screening of mosquitoes for filarioid helminths in urban areas in south western Poland-common patterns in European Setaria tundra xenomonitoring studies.}, journal = {Parasitology research}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00436-018-6134-x}, pmid = {30535561}, issn = {1432-1955}, abstract = {In recent years, numerous studies screening mosquitoes for filarioid helminths (xenomonitoring) have been performed in Europe. The entomological monitoring of filarial nematode infections in mosquitoes by molecular xenomonitoring might serve as the measure of the rate at which humans and animals expose mosquitoes to microfilariae and the rate at which animals and humans are exposed to the bites of the infected mosquitoes. We hypothesized that combining the data obtained from molecular xenomonitoring and phenological studies of mosquitoes in the urban environment would provide insights into the transmission risk of filarial diseases. In our search for Dirofilaria spp.-infected mosquitoes, we have found Setaria tundra-infected ones instead, as in many other European studies. We have observed that cross-reactivity in PCR assays for Dirofilaria repens, Dirofilaria immitis, and S. tundra COI gene detection was the rule rather than the exception. S. tundra infections were mainly found in Aedes mosquitoes. The differences in the diurnal rhythm of Aedes and Culex mosquitoes did not seem a likely explanation for the lack of S. tundra infections in Culex mosquitoes. The similarity of S. tundra COI gene sequences found in Aedes vexans and Aedes caspius mosquitoes and in roe deer in many European studies, supported by data on Ae. vexans biology, suggested host preference as the most likely cause of the mosquito genus-biased infections. High diversity of the COI gene sequences isolated in the city of Wroclaw in south western Poland and the presence of identical or almost identical sequences in mosquitoes and roe deer across Europe suggests that S. tundra has been established in most of Europe for a very long time.}, }
@article {pmid30534614, year = {2018}, author = {Rampelli, S and Guenther, K and Turroni, S and Wolters, M and Veidebaum, T and Kourides, Y and Molnár, D and Lissner, L and Benitez-Paez, A and Sanz, Y and Fraterman, A and Michels, N and Brigidi, P and Candela, M and Ahrens, W}, title = {Pre-obese children's dysbiotic gut microbiome and unhealthy diets may predict the development of obesity.}, journal = {Communications biology}, volume = {1}, number = {}, pages = {222}, doi = {10.1038/s42003-018-0221-5}, pmid = {30534614}, issn = {2399-3642}, abstract = {It is widely accepted that the intestinal microbiome is connected to obesity, as key mediator of the diet impact on the host metabolic and immunological status. To investigate whether the individual gut microbiome has a potential in predicting the onset and progression of diseases, here we characterized the faecal microbiota of 70 children in a two-time point prospective study, within a four-year window. All children had normal weight at the beginning of this study, but 36 of them gained excessive weight at the subsequent check-up. Microbiome data were analysed together with the hosts' diet information, physical activity, and inflammatory parameters. We find that the gut microbiota structures were stratified into a discrete number of groups, characterized by different biodiversity that correlates with inflammatory markers and dietary habits, regardless of age, gender, and body weight. Collectively, our data underscore the importance of the microbiome-host-diet configuration as a possible predictor of obesity.}, }
@article {pmid30534120, year = {2018}, author = {Heijboer, A and de Ruiter, PC and Bodelier, PLE and Kowalchuk, GA}, title = {Modulation of Litter Decomposition by the Soil Microbial Food Web Under Influence of Land Use Change.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2860}, doi = {10.3389/fmicb.2018.02860}, pmid = {30534120}, issn = {1664-302X}, abstract = {Soil microbial communities modulate soil organic matter (SOM) dynamics by catalyzing litter decomposition. However, our understanding of how litter-derived carbon (C) flows through the microbial portion of the soil food web is far from comprehensive. This information is necessary to facilitate reliable predictions of soil C cycling and sequestration in response to a changing environment such as land use change in the form of agricultural abandonment. To examine the flow of litter-derived C through the soil microbial food web and it's response to land use change, we carried out an incubation experiment with soils from six fields; three recently abandoned and three long term abandoned fields. In these soils, the fate of 13C-labeled plant litter was followed by analyzing phospholipid fatty acids (PLFA) over a period of 56 days. The litter-amended soils were sampled over time to measure 13CO2 and mineral N dynamics. Microbial 13C-incorporation patterns revealed a clear succession of microbial groups during litter decomposition. Fungi were first to incorporate 13C-label, followed by G- bacteria, G+ bacteria, actinomycetes and micro-fauna. The order in which various microbial groups responded to litter decomposition was similar across all the fields examined, with no clear distinction between recent and long-term abandoned soils. Although the microbial biomass was initially higher in long-term abandoned soils, the net amount of 13C-labeled litter that was incorporated by the soil microbial community was ultimately comparable between recent and long-term abandoned fields. In relative terms, this means there was a higher efficiency of litter-derived 13C-incorporation in recent abandoned soil microbial communities compared to long-term abandoned soils, most likely due to a net shift from SOM-derived C toward root-derived C input in the soil microbial food web following land-abandonment.}, }
@article {pmid30533919, year = {2018}, author = {Kim, SJ and Park, SJ and Kim, JG and Jung, MY and Gwak, JH and Rhee, SK}, title = {Draft Genome Sequence of &quot;Candidatus Izimaplasma sp.&quot; Strain ZiA1, Obtained from a Toluene-Degrading and Iron-Reducing Enrichment Culture.}, journal = {Microbiology resource announcements}, volume = {7}, number = {8}, pages = {}, doi = {10.1128/MRA.00861-18}, pmid = {30533919}, issn = {2576-098X}, abstract = {Here, we report the draft genome sequence of &quot;Candidatus Izimaplasma sp.&quot; strain ZiA1 (1.88 Mb and 29.6% G+C content). Strain ZiA1 was cocultured with iron-reducing and toluene-degrading bacteria in an enrichment culture from tidal flat sediment. Like the genomes of other strains of &quot;Ca. Izimaplasma,&quot; the ZiA1 genome contained genes required for anaerobic fermentation.}, }
@article {pmid30532746, year = {2018}, author = {Bachmann, J and Heimbach, T and Hassenrück, C and Kopprio, GA and Iversen, MH and Grossart, HP and Gärdes, A}, title = {Environmental Drivers of Free-Living vs. Particle-Attached Bacterial Community Composition in the Mauritania Upwelling System.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2836}, doi = {10.3389/fmicb.2018.02836}, pmid = {30532746}, issn = {1664-302X}, abstract = {Saharan dust input and seasonal upwelling along North-West Africa provide a model system for studying microbial processes related to the export and recycling of nutrients. This study offers the first molecular characterization of prokaryotic particle-attached (PA; >3.0 μm) and free-living (FL; 0.2-3.0 μm) players in this important ecosystem during August 2016. Environmental drivers for alpha-diversity, bacterial community composition, and differences between FL and PA fractions were identified. The ultra-oligotrophic waters off Senegal were dominated by Cyanobacteria while higher relative abundances of Alphaproteobacteria, Bacteroidetes, Verrucomicrobia, and Planctomycetes (known particle-degraders) occurred in the upwelling area. Temperature, proxy for different water masses, was the best predictor for changes in FL communities. PA community variation was best explained by temperature and ammonium. Bray Curtis dissimilarities between FL and PA were generally very high and correlated with temperature and salinity in surface waters. Greatest similarities between FL and PA occurred at the deep chlorophyll maximum, where bacterial substrate availability was likely highest. This indicates that environmental drivers do not only influence changes among FL and PA communities but also differences between them. This could provide an explanation for contradicting results obtained by different studies regarding the dissimilarity/similarity between FL and PA communities and their biogeochemical functions.}, }
@article {pmid30532651, year = {2018}, author = {Haruta, S and Yamamoto, K}, title = {Model Microbial Consortia as Tools for Understanding Complex Microbial Communities.}, journal = {Current genomics}, volume = {19}, number = {8}, pages = {723-733}, doi = {10.2174/1389202919666180911131206}, pmid = {30532651}, issn = {1389-2029}, abstract = {A major biological challenge in the postgenomic era has been untangling the composition and functions of microbes that inhabit complex communities or microbiomes. Multi-omics and modern bioinformatics have provided the tools to assay molecules across different cellular and community scales; however, mechanistic knowledge over microbial interactions often remains elusive. This is due to the immense diversity and the essentially undiminished volume of not-yet-cultured microbes. Simplified model communities hold some promise in enabling researchers to manage complexity so that they can mechanistically understand the emergent properties of microbial community interactions. In this review, we surveyed several approaches that have effectively used tractable model consortia to elucidate the complex behavior of microbial communities. We go further to provide some perspectives on the limitations and new opportunities with these approaches and highlight where these efforts are likely to lead as advances are made in molecular ecology and systems biology.}, }
@article {pmid30532562, year = {2018}, author = {Eze, EC and Chenia, HY and Zowalaty, MEE}, title = {Acinetobacter baumannii biofilms: effects of physicochemical factors, virulence, antibiotic resistance determinants, gene regulation, and future antimicrobial treatments.}, journal = {Infection and drug resistance}, volume = {11}, number = {}, pages = {2277-2299}, doi = {10.2147/IDR.S169894}, pmid = {30532562}, issn = {1178-6973}, abstract = {Acinetobacter baumannii is a leading cause of nosocomial infections due to its increased antibiotic resistance and virulence. The ability of A. baumannii to form biofilms contributes to its survival in adverse environmental conditions including hospital environments and medical devices. A. baumannii has undoubtedly propelled the interest of biomedical researchers due to its broad range of associated infections especially in hospital intensive care units. The interplay among microbial physicochemistry, alterations in the phenotype and genotypic determinants, and the impact of existing ecological niche and the chemistry of antimicrobial agents has led to enhanced biofilm formation resulting in limited access of drugs to their specific targets. Understanding the triggers to biofilm formation is a step towards limiting and containing biofilm-associated infections and development of biofilm-specific countermeasures. The present review therefore focused on explaining the impact of environmental factors, antimicrobial resistance, gene alteration and regulation, and the prevailing microbial ecology in A. baumannii biofilm formation and gives insights into prospective anti-infective treatments.}, }
@article {pmid30530153, year = {2018}, author = {Macintosh, KA and Chin, J and Jacobs, B and Cordell, D and McDowell, RW and Butler, P and Haygarth, PM and Williams, P and Quinn, JP and O'Flaherty, V and McGrath, JW}, title = {Transforming phosphorus use on the island of Ireland: A model for a sustainable system.}, journal = {The Science of the total environment}, volume = {656}, number = {}, pages = {852-861}, doi = {10.1016/j.scitotenv.2018.11.389}, pmid = {30530153}, issn = {1879-1026}, abstract = {Phosphorus is an essential part of the world food web and a non-substitutable nutrient in all biological systems. Losses of phosphorus occur along the food-supply chain and cause environmental degradation and eutrophication. A key global challenge is to meet rising worldwide food demand while protecting water and environmental quality, and seeking to manage uncertainty around potential future phosphorus price or supply shocks. This paper presents a stakeholder-generated conceptual model of potential transformative change for implementing phosphorus sustainability on the island of Ireland via an 'All-Island Phosphorus Sustainability' workshop. Key transition pathways identified by stakeholders included: incentivising phosphorus recovery, developing collaborative networks to facilitate change, developing markets and value chains for recovered products; implementing data-informed practices on-farm to prevent losses and increase efficiencies, and harmonisation of technologies with end-user needs. A comparable model was previously produced for the North American region. We describe consensus and differences around key priorities between the two regions' conceptual models, and assess how the model produced for the island of Ireland can effect system-wide change and policy moving forward. Many of the transitional pathways and future aspirations presented in both models resonate globally and are highly pertinent to other jurisdictions.}, }
@article {pmid30530129, year = {2018}, author = {Christiaens, MER and Udert, KM and Arends, JBA and Huysman, S and Vanhaecke, L and McAdam, E and Rabaey, K}, title = {Membrane stripping enables effective electrochemical ammonia recovery from urine while retaining microorganisms and micropollutants.}, journal = {Water research}, volume = {150}, number = {}, pages = {349-357}, doi = {10.1016/j.watres.2018.11.072}, pmid = {30530129}, issn = {1879-2448}, abstract = {Ammonia recovery from urine avoids the need for nitrogen removal through nitrification/denitrification and re-synthesis of ammonia (NH3) via the Haber-Bosch process. Previously, we coupled an alkalifying electrochemical cell to a stripping column, and achieved competitive nitrogen removal and energy efficiencies using only electricity as input, compared to other technologies such as conventional column stripping with air. Direct liquid-liquid extraction with a hydrophobic gas membrane could be an alternative to increase nitrogen recovery from urine into the absorbent while minimizing energy requirements, as well as ensuring microbial and micropollutant retention. Here we compared a column with a membrane stripping reactor, each coupled to an electrochemical cell, fed with source-separated urine and operated at 20 A m-2. Both systems achieved similar nitrogen removal rates, 0.34 ± 0.21 and 0.35 ± 0.08 mol N L-1 d-1, and removal efficiencies, 45.1 ± 18.4 and 49.0 ± 9.3%, for the column and membrane reactor, respectively. The membrane reactor improved nitrogen recovery to 0.27 ± 0.09 mol N L-1 d-1 (38.7 ± 13.5%) while lowering the operational (electrochemical and pumping) energy to 6.5 kWhe kg N-1 recovered, compared to the column reactor, which reached 0.15 ± 0.06 mol N L-1 d-1 (17.2 ± 8.1%) at 13.8 kWhe kg N-1. Increased cell concentrations of an autofluorescent E. coli MG1655 + prpsM spiked in the urine influent were observed in the absorbent of the column stripping reactor after 24 h, but not for the membrane stripping reactor. None of six selected micropollutants spiked in the urine were found in the absorbent of both technologies. Overall, the membrane stripping reactor is preferred as it improved nitrogen recovery with less energy input and generated an E. coli- and micropollutant-free product for potential safe reuse. Nitrogen removal rate and efficiency can be further optimized by increasing the NH3 vapor pressure gradient and/or membrane surface area.}, }
@article {pmid30529486, year = {2018}, author = {Labarthe, S and Polizzi, B and Phan, T and Goudon, T and Ribot, M and Laroche, B}, title = {A mathematical model to investigate the key drivers of the biogeography of the colon microbiota.}, journal = {Journal of theoretical biology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jtbi.2018.12.009}, pmid = {30529486}, issn = {1095-8541}, abstract = {The gut microbiota, mainly located in the colon, is engaged in a complex dialogue with the large intestinal epithelium through which important regulatory processes for the health and well-being of the host take place. Imbalances of the microbial populations, called dysbiosis, are related to several pathological status, emphasizing the importance of understanding the gut bacterial ecology. Among the ecological drivers of the microbiota, the spatial structure of the colon is of special interest: spatio-temporal mechanisms can lead to the constitution of spatial interactions among the bacterial populations and of environmental niches that impact the overall colonization of the colon. In the present study, we introduce a mathematical model of the colon microbiota in its fluid environment, based on the explicit coupling of a population dynamics model of microbial populations involved in fibre degradation with a fluid dynamics model of the luminal content. This modeling framework is used to study the main drivers of the spatial structure of the microbiota, specially focusing on the dietary fibre inflow, the epithelial motility, the microbial active swimming and viscosity gradients in the digestive track. We found 1) that the viscosity gradients allow the creation of favorable niches in the vicinity of the mucus layer; 2) that very low microbial active swimming in the radial direction is enough to promote bacterial growth, which sheds a new light on microbial motility in the colon and 3) that dietary fibres are the main driver of the spatial structure of the microbiota in the distal bowel whereas epithelial motility is preponderant for the colonization of the proximal colon; in the transverse colon, fibre levels and chemotaxis have the strongest impact on the distribution of the microbial communities.}, }
@article {pmid30521380, year = {2018}, author = {Calatayud, M and Dezutter, O and Hernandez-Sanabria, E and Hidalgo-Martinez, S and Meysman, FJR and Van de Wiele, T}, title = {Development of a host-microbiome model of the small intestine.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {}, number = {}, pages = {fj201801414R}, doi = {10.1096/fj.201801414R}, pmid = {30521380}, issn = {1530-6860}, abstract = {The intestinal epithelium plays an essential role in the balance between tolerant and protective immune responses to infectious agents. In vitro models do not typically consider the innate immune response and gut microbiome in detail, so these models do not fully mimic the physiologic aspects of the small intestine. We developed and characterized a long-term in vitro model containing enterocyte, goblet, and immune-like cells exposed to a synthetic microbial community representative of commensal inhabitants of the small intestine. This model showed differential responses toward a synthetic microbial community of commensal bacterial inhabitants of the small intestine in the absence or presence of LPS from Escherichia coli O111:B4. Simultaneous exposure to LPS and microbiota induced impaired epithelial barrier function; increased production of IL-8, IL-6, TNF-α, and C-X-C motif chemokine ligand 16; and augmented differentiation and adhesion of macrophage-like cells and the overexpression of dual oxidase 2 and TLR-2 and -4 mRNA. In addition, the model demonstrated the ability to assess the adhesion of specific bacterial strains from the synthetic microbial community-more specifically, Veillonella parvula-to the simulated epithelium. This novel in vitro model may assist in overcoming sampling and retrieval difficulties when studying host-microbiome interactions in the small intestine.-Calatayud, M., Dezutter, O., Hernandez-Sanabria, E., Hidalgo-Martinez, S., Meysman, F. J. R., Van de Wiele, T. Development of a host-microbiome model of the small intestine.}, }
@article {pmid30520189, year = {2018}, author = {Andeta, AF and Vandeweyer, D and Teffera, FE and Woldesenbet, F and Verreth, C and Crauwels, S and Lievens, B and Vancampenhout, K and Van Campenhout, L}, title = {Effect of fermentation system on the physicochemical and microbial community dynamics during enset (Ensete ventricosum) fermentation.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jam.14173}, pmid = {30520189}, issn = {1365-2672}, abstract = {AIMS: The present study was conducted to assess the effect of three different fermentation systems on fermentation of enset into kocho.<br><br>METHODS AND RESULTS: Nine enset plants were processed, mixed and fermented in either a pit, a bamboo basket or a Sauerkraut jar. Samples were taken on days 1, 7, 15, 31, 60 and 90. Moisture content and pH generally decreased and titratable acidity increased during fermentation. Total viable aerobic counts were generally high for all samples and Enterobacteriaceae counts were reduced to below the detectable level after day 1 for the pits and jars and after day 7 for the baskets. Illumina MiSeq sequencing of 16S ribosomal RNA genes revealed that Leuconostoc and Lactococcus spp. were the most abundant lactic acid bacteria in the initial phases of the fermentation. Later on, Lactobacillus, Weissella and Bifidobacterium dominated.<br><br>CONCLUSIONS: The type of fermentation system used had an effect on the microbial dynamics and the effect increased towards the end of fermentation.<br><br>Millions of people in Ethiopia daily consume kocho prepared in either a pit or a basket. These systems show practical problems, but this study shows that fermentation is also possible in a Sauerkraut jar. This article is protected by copyright. All rights reserved.}, }
@article {pmid30518818, year = {2018}, author = {Rosado, PM and Leite, DCA and Duarte, GAS and Chaloub, RM and Jospin, G and Nunes da Rocha, U and P Saraiva, J and Dini-Andreote, F and Eisen, JA and Bourne, DG and Peixoto, RS}, title = {Marine probiotics: increasing coral resistance to bleaching through microbiome manipulation.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-018-0323-6}, pmid = {30518818}, issn = {1751-7370}, abstract = {Although the early coral reef-bleaching warning system (NOAA/USA) is established, there is no feasible treatment that can minimize temperature bleaching and/or disease impacts on corals in the field. Here, we present the first attempts to extrapolate the widespread and well-established use of bacterial consortia to protect or improve health in other organisms (e.g., humans and plants) to corals. Manipulation of the coral-associated microbiome was facilitated through addition of a consortium of native (isolated from Pocillopora damicornis and surrounding seawater) putatively beneficial microorganisms for corals (pBMCs), including five Pseudoalteromonas sp., a Halomonas taeanensis and a Cobetia marina-related species strains. The results from a controlled aquarium experiment in two temperature regimes (26 °C and 30 °C) and four treatments (pBMC; pBMC with pathogen challenge - Vibrio coralliilyticus, VC; pathogen challenge, VC; and control) revealed the ability of the pBMC consortium to partially mitigate coral bleaching. Significantly reduced coral-bleaching metrics were observed in pBMC-inoculated corals, in contrast to controls without pBMC addition, especially challenged corals, which displayed strong bleaching signs as indicated by significantly lower photopigment contents and Fv/Fm ratios. The structure of the coral microbiome community also differed between treatments and specific bioindicators were correlated with corals inoculated with pBMC (e.g., Cobetia sp.) or VC (e.g., Ruegeria sp.). Our results indicate that the microbiome in corals can be manipulated to lessen the effect of bleaching, thus helping to alleviate pathogen and temperature stresses, with the addition of BMCs representing a promising novel approach for minimizing coral mortality in the face of increasing environmental impacts.}, }
@article {pmid30506480, year = {2018}, author = {Ascunce, MS and Shin, K and Huguet-Tapia, JC and Poudel, R and Garrett, KA and van Bruggen, AHC and Goss, EM}, title = {Penicillin Trunk Injection Affects Bacterial Community Structure in Citrus Trees.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1302-1}, pmid = {30506480}, issn = {1432-184X}, support = {N/A//Florida Department of Agriculture and Consumer Services/ ; N/A//Institute of Food and Agricultural Sciences/ ; N/A//Esther B. O'Keeffe Foundation/ ; }, abstract = {Huanglongbing (HLB), caused by Candidatus Liberibacter asiaticus (CLas), an uncultured α-proteobacterium, is the most destructive disease of citrus trees worldwide. In previous studies, trunk injections of penicillin reduced CLas titers and HLB symptoms in citrus. However, antibiotic effects on the whole plant microbial community, which include effects on taxa that interact with CLas, have not yet been addressed. In this study, we investigated the effects of penicillin injection (0, 1000, and 6000 mg L-1) on rhizospheric and endophytic bacterial communities of grapefruit trees in field and greenhouse experiments through culture-independent high-throughput sequencing. DNA extractions from petioles and roots were subjected to 16S rRNA high-throughput sequencing, and reads were clustered by sequence similarity into operational taxonomic units (OTUs). Principal coordinates analysis based on weighted-UniFrac distances did not reveal differences in bacterial communities among treatments in any of the sample sources. However, pairwise linear discriminant analysis indicated significant differences in relative abundance of some taxa (including CLas) among treatments. Network analysis showed that penicillin produced major changes in root bacterial community structure by affecting interspecific microbial associations. This study provides new knowledge of the effect of antimicrobial treatments on interspecific relationships in citrus microbial communities.}, }
@article {pmid30505703, year = {2018}, author = {Ellis, S and Ritz, K}, title = {A modified high-throughput analysis of PLFAs in soil.}, journal = {MethodsX}, volume = {5}, number = {}, pages = {1491-1497}, doi = {10.1016/j.mex.2018.10.022}, pmid = {30505703}, issn = {2215-0161}, abstract = {Microbial community profiling via phospholipid fatty-acid (PLFA) analysis is an insightful technique which elucidates the phenotypic structure of microbial assemblages within soil. Previous iterations of PLFA analysis have used large quantities of chemicals and can take extended periods of time to perform. Another barrier to the implementation of this method is the cost and availability of specialised machinery. We report on a high-throughput method which reduces both the time to extract PLFAs from soil and reduces the quantity of chemicals required.}, }
@article {pmid30504896, year = {2018}, author = {Aguilar-Trigueros, CA and Hempel, S and Powell, JR and Cornwell, WK and Rillig, MC}, title = {Bridging reproductive and microbial ecology: a case study in arbuscular mycorrhizal fungi.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-018-0314-7}, pmid = {30504896}, issn = {1751-7370}, abstract = {Offspring size is a key trait for understanding the reproductive ecology of species, yet studies addressing the ecological meaning of offspring size have so far been limited to macro-organisms. We consider this a missed opportunity in microbial ecology and provide what we believe is the first formal study of offspring-size variation in microbes using reproductive models developed for macro-organisms. We mapped the entire distribution of fungal spore size in the arbuscular mycorrhizal (AM) fungi (subphylum Glomeromycotina) and tested allometric expectations of this trait to offspring (spore) output and body size. Our results reveal a potential paradox in the reproductive ecology of AM fungi: while large spore-size variation is maintained through evolutionary time (independent of body size), increases in spore size trade off with spore output. That is, parental mycelia of large-spored species produce fewer spores and thus may have a fitness disadvantage compared to small-spored species. The persistence of the large-spore strategy, despite this apparent fitness disadvantage, suggests the existence of advantages to large-spored species that could manifest later in fungal life history. Thus, we consider that solving this paradox opens the door to fruitful future research establishing the relationship between offspring size and other AM life history traits.}, }
@article {pmid30503875, year = {2018}, author = {Gore, J}, title = {Simple organizing principles in microbial communities.}, journal = {Current opinion in microbiology}, volume = {45}, number = {}, pages = {195-202}, doi = {10.1016/j.mib.2018.11.007}, pmid = {30503875}, issn = {1879-0364}, abstract = {There is a great deal of interest in discovering the principles that organize microbial communities, to better understand the structure and diversity of these communities in the natural world. Recent conceptual and technical advances have shown how simple organizing principles can give rise to surprising diversity and complex patterns in these consortia. Understanding competition, cooperation, and communication among microbes has provided novel insights into the structure and behavior of microbial collectives, and the use of simple animal models has advanced our understanding of microbial ecology in the host. These multidisciplinary efforts to understand and predict the properties of microbial communities will be critical in the development of microbial ecology as an applied science.}, }
@article {pmid30502541, year = {2018}, author = {Pannekens, M and Kroll, L and Müller, H and Mbow, FT and Meckenstock, RU}, title = {Oil reservoirs, an exceptional habitat for microorganisms.}, journal = {New biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.nbt.2018.11.006}, pmid = {30502541}, issn = {1876-4347}, abstract = {Microorganisms are present in oil reservoirs around the world where they degrade oil and lead to changes in oil quality. Unfortunately, our knowledge about processes in deep oil reservoirs is limited due to the lack of undisturbed samples. In this review, we discuss the distribution of microorganisms at the oil-water transition zone as well as in water saturated parts of the oil leg and their possible physiological adaptations to abiotic and biotic ecological factors such as temperature, salinity and viruses. We show the importance of studying the water phase within the oil, because small water inclusions and pockets within the oil leg provide an exceptional habitat for microorganisms within a natural oil reservoir and concurrently enlarge the zone of oil biodegradation. Environmental factors such as temperature and salinity control oil biodegradation. Temperature determines the type of microorganisms which are able to inhabit the reservoir. Proteobacteria and Euryarchaeota, are ubiquitous in oil reservoirs over all temperature ranges, whereas some others are tied to specific temperatures. It is proposed that biofilm formation is the dominant way of life within oil reservoirs, enhancing nutrient uptake, syntrophic interactions and protection against environmental stress. Literature shows that viruses are abundant in oil reservoirs and the possible impact on microbial community composition due to control of microbial activity and function is discussed.}, }
@article {pmid30515182, year = {2018}, author = {Gil-Martínez, M and López-García, Á and Domínguez, MT and Navarro-Fernández, CM and Kjøller, R and Tibbett, M and Marañón, T}, title = {Ectomycorrhizal Fungal Communities and Their Functional Traits Mediate Plant-Soil Interactions in Trace Element Contaminated Soils.}, journal = {Frontiers in plant science}, volume = {9}, number = {}, pages = {1682}, doi = {10.3389/fpls.2018.01682}, pmid = {30515182}, issn = {1664-462X}, abstract = {There is an increasing consensus that microbial communities have an important role in mediating ecosystem processes. Trait-based ecology predicts that the impact of the microbial communities on ecosystem functions will be mediated by the expression of their traits at community level. The link between the response of microbial community traits to environmental conditions and its effect on plant functioning is a gap in most current microbial ecology studies. In this study, we analyzed functional traits of ectomycorrhizal fungal species in order to understand the importance of their community assembly for the soil-plant relationships in holm oak trees (Quercus ilex subsp. ballota) growing in a gradient of exposure to anthropogenic trace element (TE) contamination after a metalliferous tailings spill. Particularly, we addressed how the ectomycorrhizal composition and morphological traits at community level mediate plant response to TE contamination and its capacity for phytoremediation. Ectomycorrhizal fungal taxonomy and functional diversity explained a high proportion of variance of tree functional traits, both in roots and leaves. Trees where ectomycorrhizal fungal communities were dominated by the abundant taxa Hebeloma cavipes and Thelephora terrestris showed a conservative root economics spectrum, while trees colonized by rare taxa presented a resource acquisition strategy. Conservative roots presented ectomycorrhizal functional traits characterized by high rhizomorphs formation and low melanization which may be driven by resource limitation. Soil-to-root transfer of TEs was explained substantially by the ectomycorrhizal fungal species composition, with the highest transfer found in trees whose roots were colonized by Hebeloma cavipes. Leaf phosphorus was related to ectomycorrhizal species composition, specifically higher leaf phosphorus was related to the root colonization by Thelephora terrestris. These findings support that ectomycorrhizal fungal community composition and their functional traits mediate plant performance in metal-contaminated soils, and have a high influence on plant capacity for phytoremediation of contaminants. The study also corroborates the overall effects of ectomycorrhizal fungi on ecosystem functioning through their mediation over the plant economics spectrum.}, }
@article {pmid30514367, year = {2018}, author = {Marasco, R and Mosqueira, MJ and Fusi, M and Ramond, JB and Merlino, G and Booth, JM and Maggs-Kölling, G and Cowan, DA and Daffonchio, D}, title = {Rhizosheath microbial community assembly of sympatric desert speargrasses is independent of the plant host.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {215}, doi = {10.1186/s40168-018-0597-y}, pmid = {30514367}, issn = {2049-2618}, support = {95565//South African National Research Foundation/ ; }, abstract = {BACKGROUND: The rhizosheath-root system is an adaptive trait of sandy-desert speargrasses in response to unfavourable moisture and nutritional conditions. Under the deserts' polyextreme conditions, plants interact with edaphic microorganisms that positively affect their fitness and resistance. However, the trophic simplicity and environmental harshness of desert ecosystems have previously been shown to strongly influence soil microbial community assembly. We hypothesize that sand-driven ecological filtering constrains the microbial recruitment processes in the speargrass rhizosheath-root niche, prevailing over the plant-induced selection.<br><br>METHODS: Bacterial and fungal communities from the rhizosheath-root compartments (endosphere root tissues, rhizosheath and rhizosphere) of three Namib Desert speargrass species (Stipagrostis sabulicola, S. seelyae and Cladoraphis spinosa) along with bulk sand have been studied to test our hypothesis. To minimize the variability determined by edaphic and climatic factors, plants living in a single dune were studied. We assessed the role of plant species vs the sandy substrate on the recruitment and selection, phylogenetic diversity and co-occurrence microbial networks of the rhizosheath-root system microbial communities.<br><br>RESULTS: Microorganisms associated with the speargrass rhizosheath-root system were recruited from the surrounding bulk sand population and were significantly enriched in the rhizosheath compartments (105 and 104 of bacterial 16S rRNA and fungal ITS copies per gram of sand to up to 108 and 107 copies per gram, respectively). Furthermore, each rhizosheath-root system compartment hosted a specific microbial community demonstrating strong niche-partitioning. The rhizosheath-root systems of the three speargrass species studied were dominated by desert-adapted Actinobacteria and Alphaproteobacteria (e.g. Lechevalieria, Streptomyces and Microvirga) as well as saprophytic Ascomycota fungi (e.g. Curvularia, Aspergillus and Thielavia). Our results clearly showed a random phylogenetic turnover of rhizosheath-root system associated microbial communities, independent of the plant species, where stochastic factors drive neutral assembly. Co-occurrence network analyses also indicated that the bacterial and fungal community members of the rhizosheath-root systems established a higher number of interactions than those in the barren bulk sand, suggesting that the former are more stable and functional than the latter.<br><br>CONCLUSION: Our study demonstrates that the rhizosheath-root system microbial communities of desert dune speargrasses are stochastically assembled and host-independent. This finding supports the concept that the selection determined by the desert sand prevails over that imposed by the genotype of the different plant species.}, }
@article {pmid30512194, year = {2018}, author = {Petrovich, ML and Rosenthal, AF and Griffin, JS and Wells, GF}, title = {Spatially Resolved Abundances of Antibiotic Resistance Genes and intI1 in Wastewater Treatment Biofilms.}, journal = {Biotechnology and bioengineering}, volume = {}, number = {}, pages = {}, doi = {10.1002/bit.26887}, pmid = {30512194}, issn = {1097-0290}, abstract = {Attached growth bioprocesses that use biofilms to remove organic matter or nutrients from wastewater are known to harbor antibiotic resistance genes (ARGs). Biofilms in these processes are spatially heterogeneous, but little is known about depth stratification of ARGs in complex, mixed culture biofilms. To address this knowledge gap, we employed an experimental approach combining cryosectioning and qPCR to quantify spatial distribution of three ARGs (sul1, ermB, and qnrS) and the class 1 integron-integrase gene intI1 in biofilms from a lab-scale rotating annular reactor (RAR) fed with synthetic wastewater. We also employed high throughput 16S rRNA gene sequencing to characterize community structure with depth in biofilms. The ARG sul1 and the integron-integrase gene intI1 were found in higher abundances in upper layers of biofilm near the fluid-biofilm interface than in lower layers and exhibited significant correlations between distance from substratum and gene abundances. The genes ermB and qnrS were present in comparatively low relative abundances. Microbial community structure varied significantly by date of sampling and distance from substratum. These findings highlight the genetic and taxonomic heterogeneity with distance from substratum in wastewater treatment biofilms, and show that sul1 and intI1 are particularly abundant near fluid-biofilm interfaces where cells are most likely to detach and flow into downstream portions of treatment systems and can ultimately be released into the environment through effluent. This article is protected by copyright. All rights reserved.}, }
@article {pmid30502606, year = {2018}, author = {Xiong, Z and Hussain, A and Lee, J and Lee, HS}, title = {Food waste fermentation in a leach bed reactor: Reactor performance, and microbial ecology and dynamics.}, journal = {Bioresource technology}, volume = {274}, number = {}, pages = {153-161}, doi = {10.1016/j.biortech.2018.11.066}, pmid = {30502606}, issn = {1873-2976}, abstract = {Food waste fermentation was investigated in a leach bed reactor operated at acidic, neutral and alkaline conditions. Highest solids reduction of 87% was obtained at pH 7 in 14 days of reaction time with minimum mixing. The concentration of volatile fatty acids increased to 28.6 g COD/L under pH 7, while the highest butyric acid of 16 g COD/L was obtained at pH 6. Bacterial community structure was narrowed down to Bifidobacterium and Clostridium at pH 6, while Bacteroides and Dysgonomonas were identified as main players at both pH 7 and 8. Bacterial populations in the food residue generally reflected those in the leachate, but some bacteria were selectively enriched in the leachate or the food residue. Bacterial community dynamics suggested that biodegradable food waste was first fermented by one of dominant players (e.g., Clostridium) and the other degraded resistant dietary fibers later (e.g., Bifidobacterium, Bacteroides, Dysgonomonas).}, }
@article {pmid30500479, year = {2018}, author = {Kothamasi, D and Wannijn, J and Van Hees, M and Nauts, R and Van Gompel, A and Vanhoudt, N and Vandenhove, H}, title = {Exposure to ionizing radiation affects the growth of ectomycorrhizal fungi and induces increased melanin production and increased capacities of reactive oxygen species scavenging enzymes.}, journal = {Journal of environmental radioactivity}, volume = {197}, number = {}, pages = {16-22}, doi = {10.1016/j.jenvrad.2018.11.005}, pmid = {30500479}, issn = {1879-1700}, abstract = {Ectomycorrhizal (EM) fungi form symbioses with dominant tree families in boreal, temperate and tropical ecosystems and are important drivers of ecosystem function. EM fungal hyphae extend over a large area making them susceptible to enhanced radiation levels from naturally occurring or anthropogenically originating radioisotopes in the rhizosphere. In this study, the in-vitro effects of ionizing radiation on the growth and biomass of EM fungi Suillus luteus, S. bovinus and Rhizopogon luteolus were investigated. EM fungal cultures were exposed to gamma radiation from a 137Cs source for 137 h in darkness at 21 °C at dose rates of 404, 108.5 and 54.9 mGy h-1 resulting in total absorbed doses of 55.21, 14.82 and 7.50 Gy respectively. Cultures grown in the dark at 21 °C but not exposed to the 137Cs source served as the control. Our results show that EM fungi vary in their sensitivity to ionizing radiation. EM fungi used in this study produced melanin and reactive oxygen species scavenging enzymes such as catalase and superoxide dismutase as a response to ionizing radiation.}, }
@article {pmid30499007, year = {2018}, author = {Maillard, F and Leduc, V and Bach, C and de Moraes Gonçalves, JL and Androte, FD and Saint-André, L and Laclau, JP and Buée, M and Robin, A}, title = {Microbial Enzymatic Activities and Community-Level Physiological Profiles (CLPP) in Subsoil Layers Are Altered by Harvest Residue Management Practices in a Tropical Eucalyptus grandis Plantation.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1298-6}, pmid = {30499007}, issn = {1432-184X}, abstract = {Harvest residue management is a key issue for the sustainability of Eucalyptus plantations established on poor soils. Soil microbial communities contribute to soil fertility by the decomposition of the organic matter (OM), but little is known about the effect of whole-tree harvesting (WTH) in comparison to stem only harvesting (SOH) on soil microbial functional diversity in Eucalyptus plantations. We studied the effects of harvest residue management (branches, leaves, bark) of Eucalyptus grandis trees on soil enzymatic activities and community-level physiological profiles in a Brazilian plantation. We measured soil microbial enzymatic activities involved in OM decomposition and we compared the community level physiological profiles (CLPP) of the soil microbes in WTH and SOH plots. WTH decreased enzyme activities and catabolic potential of the soil microbial community. Furthermore, these negative effects on soil functional diversity were mainly observed below the 0-5 cm layer (5-10 and 10-20 cm), suggesting that WTH can be harmful to the soil health in these plantations.}, }
@article {pmid30498637, year = {2018}, author = {Honeyman, AS and Day, ML and Spear, JR}, title = {Regional fresh snowfall microbiology and chemistry are driven by geography in storm-tracked events, Colorado, USA.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e5961}, doi = {10.7717/peerj.5961}, pmid = {30498637}, issn = {2167-8359}, abstract = {Snowfall is a global phenomenon highly integrated with hydrology and ecology. Forays into studying bioaerosols and their dependence on aeolian movement are largely constrained to either precipitation-independent analyses or in silico models. Though snowpack and glacial microbiological studies have been conducted, little is known about the biological component of meteoric snow. Through culture-independent phylogenetic and geochemical analyses, we show that the geographical location at which snow precipitates determines snowfall's geochemical and microbiological composition. Storm-tracking, furthermore, can be used as a valuable environmental indicator to trace down what factors are influencing bioaerosols. We estimate annual aeolian snowfall deposits of up to ∼10 kg of bacterial/archaeal biomass per hectare along our study area of the eastern Front Range in Colorado. The dominant kinds of microbiota captured in an analysis of seven snow events at two different locations, one urban, one rural, across the winter of 2016/2017 included phyla Proteobacteria, Bacteroidetes, Firmicutes, and Acidobacteria, though a multitude of different kinds of organisms were found in both. Taxonomically, Bacteroidetes were more abundant in Golden (urban plain) snow while Proteobacteria were more common in Sunshine (rural mountain) samples. Chemically, Golden snowfall was positively correlated with some metals and anions. The work also hints at better informing the &quot;everything is everywhere&quot; hypotheses of the microbial world and that atmospheric transport of microbiota is not only common, but is capable of disseminating vast amounts of microbiota of different physiologies and genetics that then affect ecosystems globally. Snowfall, we conclude, is a significant repository of microbiological material with strong implications for both ecosystem genetic flux and general bio-aerosol theory.}, }
@article {pmid30498561, year = {2018}, author = {Sakoula, D and Nowka, B and Spieck, E and Daims, H and Lücker, S}, title = {The draft genome sequence of &quot;Nitrospira lenta&quot; strain BS10, a nitrite oxidizing bacterium isolated from activated sludge.}, journal = {Standards in genomic sciences}, volume = {13}, number = {}, pages = {32}, doi = {10.1186/s40793-018-0338-7}, pmid = {30498561}, issn = {1944-3277}, abstract = {The genus Nitrospira is considered to be the most widespread and abundant group of nitrite-oxidizing bacteria in many natural and man-made ecosystems. However, the ecophysiological versatility within this phylogenetic group remains highly understudied, mainly due to the lack of pure cultures and genomic data. To further expand our understanding of this biotechnologically important genus, we analyzed the high quality draft genome of &quot;Nitrospira lenta&quot; strain BS10, a sublineage II Nitrospira that was isolated from a municipal wastewater treatment plant in Hamburg, Germany. The genome of &quot;N. lenta&quot; has a size of 3,756,190 bp and contains 3968 genomic objects, of which 3907 are predicted protein-coding sequences. Thorough genome annotation allowed the reconstruction of the &quot;N. lenta&quot; core metabolism for energy conservation and carbon fixation. Comparative analyses indicated that most metabolic features are shared with N. moscoviensis and &quot;N. defluvii&quot;, despite their ecological niche differentiation and phylogenetic distance. In conclusion, the genome of &quot;N. lenta&quot; provides important insights into the genomic diversity of the genus Nitrospira and provides a foundation for future comparative genomic studies that will generate a better understanding of the nitrification process.}, }
@article {pmid30498480, year = {2018}, author = {Zäncker, B and Cunliffe, M and Engel, A}, title = {Bacterial Community Composition in the Sea Surface Microlayer Off the Peruvian Coast.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2699}, doi = {10.3389/fmicb.2018.02699}, pmid = {30498480}, issn = {1664-302X}, abstract = {The sea surface microlayer (SML) is located at the air-sea interface, with microorganisms and organic matter in the SML influencing air-sea exchange processes. Yet understanding of the SML bacterial (bacterioneuston) community composition and assembly remains limited. Availability of organic matter, UV radiation and wind speed have previously been suggested to influence the community composition of bacterioneuston. Another mechanism potentially controlling bacterioneuston dynamics is bacterioplankton attached to gel-like particles that ascend through the water column into the SML. We analyzed the bacterial community composition, Transparent Exopolymer Particles (TEP) abundance and nutrient concentrations in the surface waters of the Peruvian upwelling region. The bacterioneuston and bacterioplankton communities were similar, suggesting a close spatial coupling. Four Bacteroidetes families were significantly enriched in the SML, two of them, the Flavobacteriaceae and Cryomorphaceae, were found to comprise the majority of SML-enriched operational taxonomic units (OTUs). The enrichment of these families was controlled by a variety of environmental factors. The SML-enriched bacterial families were negatively correlated with water temperature and wind speed in the SML and positively correlated with nutrient concentrations, salinity and TEP in the underlying water (ULW). The correlations with nutrient concentrations and salinity suggest that the enriched bacterial families were more abundant at the upwelling stations.}, }
@article {pmid30497363, year = {2018}, author = {Sperlea, T and Füser, S and Boenigk, J and Heider, D}, title = {SEDE-GPS: socio-economic data enrichment based on GPS information.}, journal = {BMC bioinformatics}, volume = {19}, number = {Suppl 15}, pages = {440}, doi = {10.1186/s12859-018-2419-4}, pmid = {30497363}, issn = {1471-2105}, abstract = {BACKGROUND: Microbes are essentail components of all ecosystems because they drive many biochemical processes and act as primary producers. In freshwater ecosystems, the biodiversity in and the composition of microbial communities can be used as indicators for environmental quality. Recently, some environmental features have been identified that influence microbial ecosystems. However, the impact of human action on lake microbiomes is not well understood. This is, in part, due to the fact that environmental data is, albeit theoretically accessible, not easily available.<br><br>RESULTS: In this work, we present SEDE-GPS, a tool that gathers data that are relevant to the environment of an user-provided GPS coordinate. To this end, it accesses a list of public and corporate databases and aggregates the information in a single file, which can be used for further analysis. To showcase the use of SEDE-GPS, we enriched a lake microbial ecology sequencing dataset with around 18,000 socio-economic, climate, and geographic features. The sources of SEDE-GPS are public databases such as Eurostat, the Climate Data Center, and OpenStreetMap, as well as corporate sources such as Twitter. Using machine learning and feature selection methods, we were able to identify features in the data provided by SEDE-GPS that can be used to predict lake microbiome alpha diversity.<br><br>CONCLUSION: The results presented in this study show that SEDE-GPS is a handy and easy-to-use tool for comprehensive data enrichment for studies of ecology and other processes that are affected by environmental features. Furthermore, we present lists of environmental, socio-economic, and climate features that are predictive for microbial biodiversity in lake ecosystems. These lists indicate that human action has a major impact on lake microbiomes. SEDE-GPS and its source code is available for download at http://SEDE-GPS.heiderlab.de.}, }
@article {pmid30496195, year = {2018}, author = {Calderoli, PA and Espínola, FJ and Dionisi, HM and Gil, MN and Jansson, JK and Lozada, M}, title = {Predominance and high diversity of genes associated to denitrification in metagenomes of subantarctic coastal sediments exposed to urban pollution.}, journal = {PloS one}, volume = {13}, number = {11}, pages = {e0207606}, doi = {10.1371/journal.pone.0207606}, pmid = {30496195}, issn = {1932-6203}, abstract = {The aim of this work was to characterize the microbial nitrogen cycling potential in sediments from Ushuaia Bay, a subantarctic environment that has suffered a recent explosive demographic growth. Subtidal sediment samples were retrieved in triplicate from two urban points in the Bay, and analyzed through metagenomic shotgun sequencing. Sequences assigned to genes related to nitrification, nitrate reduction and denitrification were predominant in this environment with respect to metagenomes from other environments, including other marine sediments. The nosZ gene, responsible for nitrous oxide transformation into di-nitrogen, presented a high diversity. The majority of NosZ sequences were classified as Clade II (atypical) variants affiliated to different bacterial lineages such as Bacteroidetes, Chloroflexi, Firmicutes, Proteobacteria, Verrucomicrobia, as well as to Archaea. The analysis of a fosmid metagenomic library from the same site showed that the genomic context of atypical variants was variable, and was accompanied by distinct regulatory elements, suggesting the evolution of differential ecophysiological roles. This work increases our understanding of the microbial ecology of nitrogen transformations in cold coastal environments and provides evidence of an enhanced denitrification potential in impacted sediment microbial communities. In addition, it highlights the role of yet overlooked populations in the mitigation of environmentally harmful forms of nitrogen.}, }
@article {pmid30487782, year = {2018}, author = {Vadstein, O and Attramadal, KJK and Bakke, I and Olsen, Y}, title = {K-Selection as Microbial Community Management Strategy: A Method for Improved Viability of Larvae in Aquaculture.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2730}, doi = {10.3389/fmicb.2018.02730}, pmid = {30487782}, issn = {1664-302X}, abstract = {Aquaculture has the potential to become a major food supplier in a world with an increasing human population, and increased consumption of fish will likely have positive health implications. For marine aquaculture, the production of high quality juveniles is a bottleneck. Survival until the juvenile stage is typically as low as 10-15% for many species, which indicates suboptimal rearing conditions. Substantial evidence indicates that the poor performance and viability of larvae is largely due to detrimental larvae-microbiota interactions. This emphasises the need for microbial management strategies in the cultivation of marine fish larvae. Disinfection and probiotics are the most studied microbial management methods so far. However, most studies on these methods overlooked the role of mutualistic relationships between microbes and hosts, and have not proposed or examined methods steering toward such relationships. Based on ecological theory and a number of experiments, we find support for the hypothesis that current practise in aquaculture generally selects for r-strategic, opportunistic microbes, which results in detrimental host-microbiota interactions. Thus, the challenge is to develop technology and methods for microbial management at the ecosystem level that creates a K-selected microbial community, and by this mean select against r-strategic opportunists. Here we summarise experiments done during 25 years and with marine larvae of five different species showing that: (1) K-selection strategies result in different water microbiota with less opportunists, (2) this influences the microbiota of the fish larvae, and (3) the larvae cultivated in water inhabited by a K-selected microbiota perform better. Improved performance of larvae includes improved appetite, earlier onset of and faster growth, increased survival, and increased robustness to stress. K-selection as a method for management of the microbial community is a robust approach that allows steering of host-microbiota interactions in larviculture toward mutualism. It could also be applicable for young stages of other domesticated animals. Our review illustrates that a change from a &quot;beat-them&quot; to a &quot;join-them&quot; strategy for microbial management in larval rearing can lead to a more sustainable aquaculture industry.}, }
@article {pmid30483839, year = {2018}, author = {Zakharenko, AS and Galachyants, YP and Morozov, IV and Shubenkova, OV and Morozov, AA and Ivanov, VG and Pimenov, NV and Krasnopeev, AY and Zemskaya, TI}, title = {Bacterial Communities in Areas of Oil and Methane Seeps in Pelagic of Lake Baikal.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1299-5}, pmid = {30483839}, issn = {1432-184X}, support = {17-29-05040//ofi-m RFBR/ ; 0345-2016-0007//State Task for Limnological Institute SB RAS/ ; 18-34-00442//a-mol RFBR/ ; }, abstract = {We have assessed the diversity of bacteria near oil-methane (area I) and methane (area II) seeps in the pelagic zone of Lake Baikal using massive parallel sequencing of 16S rRNA, pmoA, and mxaF gene fragments amplified from total DNA. At depths from the surface to 100 m, sequences belonging to Cyanobacteria dominated. In the communities to a depth of 200 m of the studied areas, Proteobacteria dominated the deeper layers of the water column. Alphaproteobacteria sequences were predominant in the community near the oil-methane seep, while the community near the methane seep was characterized by the prevalence of Alpha- and Gammaproteobacteria. Among representatives of these classes, type I methanotrophs prevailed in the 16S rRNA gene libraries from the near-bottom area, and type II methanotrophs were detected in minor quantities at different depths. In the analysis of the libraries of the pmoA and mxaF functional genes, we observed the different taxonomic composition of methanotrophic bacteria in the surface and deep layers of the water column. All pmoA sequences from area I were type II methanotrophs and were detected at a depth of 300 m, while sequences of type I methanotrophs were the most abundant in deep layers of the water column of area II. All mxaF gene sequences belonged to Methylobacterium representatives. Based on comparative analyses of 16S rRNA, pmoA, and mxaF gene fragment libraries, we suggest that there must be a wider spectrum of functional genes facilitating methane oxidation that were not detected with the primers used.}, }
@article {pmid30482830, year = {2018}, author = {Espinoza, JL and Harkins, DM and Torralba, M and Gomez, A and Highlander, SK and Jones, MB and Leong, P and Saffery, R and Bockmann, M and Kuelbs, C and Inman, JM and Hughes, T and Craig, JM and Nelson, KE and Dupont, CL}, title = {Supragingival Plaque Microbiome Ecology and Functional Potential in the Context of Health and Disease.}, journal = {mBio}, volume = {9}, number = {6}, pages = {}, doi = {10.1128/mBio.01631-18}, pmid = {30482830}, issn = {2150-7511}, abstract = {To address the question of how microbial diversity and function in the oral cavities of children relates to caries diagnosis, we surveyed the supragingival plaque biofilm microbiome in 44 juvenile twin pairs. Using shotgun sequencing, we constructed a genome encyclopedia describing the core supragingival plaque microbiome. Caries phenotypes contained statistically significant enrichments in specific genome abundances and distinct community composition profiles, including strain-level changes. Metabolic pathways that are statistically associated with caries include several sugar-associated phosphotransferase systems, antimicrobial resistance, and metal transport. Numerous closely related previously uncharacterized microbes had substantial variation in central metabolism, including the loss of biosynthetic pathways resulting in auxotrophy, changing the ecological role. We also describe the first complete Gracilibacteria genomes from the human microbiome. Caries is a microbial community metabolic disorder that cannot be described by a single etiology, and our results provide the information needed for next-generation diagnostic tools and therapeutics for caries.IMPORTANCE Oral health has substantial economic importance, with over $100 billion spent on dental care in the United States annually. The microbiome plays a critical role in oral health, yet remains poorly classified. To address the question of how microbial diversity and function in the oral cavities of children relate to caries diagnosis, we surveyed the supragingival plaque biofilm microbiome in 44 juvenile twin pairs. Using shotgun sequencing, we constructed a genome encyclopedia describing the core supragingival plaque microbiome. This unveiled several new previously uncharacterized but ubiquitous microbial lineages in the oral microbiome. Caries is a microbial community metabolic disorder that cannot be described by a single etiology, and our results provide the information needed for next-generation diagnostic tools and therapeutics for caries.}, }
@article {pmid30481288, year = {2018}, author = {Khan, MAW and Bohannan, BJM and Nüsslein, K and Tiedje, JM and Tringe, SG and Parlade, E and Barberán, A and Rodrigues, JLM}, title = {Deforestation Impacts Network Co-occurrence Patterns of Microbial Communities in Amazon Soils.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiy230}, pmid = {30481288}, issn = {1574-6941}, abstract = {Co-occurrence networks allow for the identification of potential associations among species, which may be important for understanding community assembly and ecosystem functions. We employed this strategy to examine prokaryotic co-occurrence patterns in the Amazon soils and the response of these patterns to land use change to pasture, with the hypothesis that altered microbial composition due to deforestation will mirror the co-occurrence patterns across prokaryotic taxa. In this study, we calculated Spearman correlations between operational taxonomic units (OTUs) as determined by 16S rRNA gene sequencing, and only robust correlations were considered for network construction (-0.80 ≥ ρ ≥ 0.80, adjusted P <0.01). The constructed network represents distinct forest and pasture components, with altered compositional and topological features. A comparative analysis between two representative modules of these contrasting ecosystems revealed novel information regarding changes to metabolic pathways related to nitrogen cycling. Our results showed that soil physicochemical properties such as temperature, C/N and H++Al3+ had a significant impact on prokaryotic communities, with alterations to network topologies. Taken together, changes in co-occurrence patterns and physicochemical properties may contribute to ecosystem processes including nitrification and denitrification, two important biogeochemical processes occurring in tropical forest systems.}, }
@article {pmid30479328, year = {2018}, author = {de Bruijn, I and Verhoeven, KJF}, title = {Cross-species interference of gene expression.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {5019}, doi = {10.1038/s41467-018-07353-0}, pmid = {30479328}, issn = {2041-1723}, abstract = {Microbes can contribute to protection of animals and plants against diseases. A recent study reveals a mechanism by which a bacterium controls fungal infection in wheat, involving secretion of a metabolite that affects histone acetyltransferase activity of a plant pathogenic fungus.}, }
@article {pmid30478730, year = {2018}, author = {Dhaulaniya, AS and Balan, B and Kumar, M and Agrawal, PK and Singh, DK}, title = {Cold survival strategies for bacteria, recent advancement and potential industrial applications.}, journal = {Archives of microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00203-018-1602-3}, pmid = {30478730}, issn = {1432-072X}, support = {NASF/CA-6030/2017-18//National Agriculture Science Fund/ ; }, abstract = {Microorganisms have evolved themselves to thrive under various extreme environmental conditions such as extremely high or low temperature, alkalinity, and salinity. These microorganisms adapted several metabolic processes to survive and reproduce efficiently under such extreme environments. As the major proportion of earth is covered with the cold environment and is exploited by human beings, these sites are not pristine anymore. Human interventions are a great reason for disturbing the natural biogeochemical cycles in these regions. The survival strategies of these organisms have shown great potential for helping us to restore these pristine sites and the use of isolated cold-adapted enzymes from these organisms has also revolutionized various industrial products. This review gives you the insight of psychrophilic enzyme adaptations and their industrial applications.}, }
@article {pmid30478232, year = {2018}, author = {Liang, C and Huang, Y and Wang, H}, title = {A new functional marker gene of polycyclic aromatic hydrocarbons (PAHs) degrading bacteria: pahE.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.02399-18}, pmid = {30478232}, issn = {1098-5336}, abstract = {The characterization of native PAH-degrading bacteria is significant to understand the degradation process of PAHs in the natural environment and develop effective remediation technologies. Most previous investigations of PAH-degrading bacteria in environmental samples employ the pahAc, which encodes the α-subunit of PAH ring-hydroxylating dioxygenase, as a functional marker gene. However, the poor phylogenetic resolution and non-specificity of pahAc results in misestimating of PAH-degrading bacteria. Here we propose a PAH hydratase-aldolase encoding gene, pahE, as a superior biomarker for PAH-degrading bacteria. Comparative phylogenetic analysis of the key enzymes involved in the upper-pathway of PAH degradation indicated that pahE evolved dependently from a common ancestor. A phylogenetic tree constructed based on PahE is largely congruent with PahAc-based phylogenies, except the dispersion of several clades of other non-PAH-degrading aromatic hydrocarbon dioxygenases present in the PahAc tree. Analysis of pure strains by PCR confirmed that pahE can specifically distinguish PAH-degrading bacteria while pahAc cannot. Illumina sequencing of pahE and pahAc amplicons showed more genotypes, higher specificity and resolution of pahE Novel reads were also discovered among the pahE amplicons, suggesting the presence of novel PAH-degrading populations. These results suggest that pahE is a more powerful biomarker for exploring the ecological role and degradation potential of PAH-degrading bacteria in ecosystems, which is significant to the bioremediation of PAH pollution and environmental microbial ecology.IMPORTANCE PAHs contamination has become a worldwide environmental issue because of the potential toxic effects on natural ecosystems and human health. Biotransformation and biodegradation are considered the main natural elimination forms of PAHs from contaminated sites. Therefore, the knowledge of the degradation potential of the microbial community in contaminated sites is crucial for the PAHs pollution bioremediation. However, the non-specificity of pahAc as a functional marker of PAH-degrading bacteria has resulted in neither reliable prediction of PAH degradation potential nor an accurate assessment of degradation. Here, we introduced pahE encoding PAHs hydratase-aldolase as a new and better functional marker gene of PAH-degrading bacteria. This study provides a powerful molecular tool to more effectively explore the ecological role and degradation potential of PAH-degrading bacteria in ecosystems, which is significant to the bioremediation of PAH pollution.}, }
@article {pmid30477264, year = {2018}, author = {Almendras, K and García, J and Carú, M and Orlando, J}, title = {Nitrogen-Fixing Bacteria Associated with Peltigera Cyanolichens and Cladonia Chlorolichens.}, journal = {Molecules (Basel, Switzerland)}, volume = {23}, number = {12}, pages = {}, doi = {10.3390/molecules23123077}, pmid = {30477264}, issn = {1420-3049}, support = {11100381 and 1181510//Fondo Nacional de Desarrollo Científico y Tecnológico/ ; }, abstract = {Lichens have been extensively studied and described; however, recent evidence suggests that members of the bacterial community associated with them could contribute new functions to the symbiotic interaction. In this work, we compare the nitrogen-fixing guild associated with bipartite terricolous lichens with different types of photobiont: Peltigera cyanolichens and Cladonia chlorolichens. Since cyanobacteria contribute nitrogen to the symbiosis, we propose that chlorolichens have more diverse bacteria with the ability to fix nitrogen compared to cyanolichens. In addition, since part of these bacteria could be recruited from the substrate where lichens grow, we propose that thalli and substrates share some bacteria in common. The structure of the nitrogen-fixing guild in the lichen and substrate bacterial communities of both lichens was determined by terminal restriction fragment length polymorphism (TRFLP) of the nifH gene. Multivariate analyses showed that the nitrogen-fixing bacteria associated with both types of lichen were distinguishable from those present in their substrates. Likewise, the structure of the nitrogen-fixing bacteria present in the cyanolichens was different from that of chlorolichens. Finally, the diversity of this bacterial guild calculated using the Shannon index confirms the hypothesis that chlorolichens have a higher diversity of nitrogen-fixing bacteria than cyanolichens.}, }
@article {pmid30476032, year = {2018}, author = {Nierychlo, M and Milobedzka, A and Petriglieri, F and McIlroy, B and Nielsen, PH and McIlroy, SJ}, title = {The morphology and metabolic potential of the Chloroflexi in full-scale activated sludge wastewater treatment plants.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiy228}, pmid = {30476032}, issn = {1574-6941}, abstract = {Filamentous bacteria belonging to the phylum Chloroflexi have received considerable attention in wastewater treatment systems for their suggested role in the operational problem of impaired sludge settleability known as bulking. Their consistently high abundance in full-scale systems, even in the absence of bulking, indicates that they make a substantial contribution to the nutrient transformations during wastewater treatment. In this study, extensive 16S rRNA amplicon surveys of Danish wastewater treatment plants (WWTPs) with nutrient removal were screened to identify numerically important Chloroflexi genera. Fluorescence in situ hybridization probes were designed for their in situ characterization. All abundant Chloroflexi phylotypes were putatively identified as facultative anaerobic chemoorganotrophs involved in sugar fermentation. They were all filamentous but differed in their morphology and spatial arrangement. 'Candidatus Villigracilis' was predominantly located within the activated sludge flocs, where they possibly have structural importance, and their abundance was relatively stable. Conversely, the abundance of 'Candidatus Amarolinea' was highly dynamic, relative to other genera, sometimes reaching abundances in excess of 30% of the biovolume, suggesting their likely role in bulking episodes. This study gives an important insight into the role of Chloroflexi in WWTPs, thus contributing to the broader goal of understanding the ecology of these biotechnologically important systems.}, }
@article {pmid30474807, year = {2018}, author = {Wu, H and Chen, H and Jin, C and Tang, C and Zhang, Y}, title = {The chirality of imazethapyr herbicide selectively affects the bacterial community in soybean field soil.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, doi = {10.1007/s11356-018-3736-x}, pmid = {30474807}, issn = {1614-7499}, support = {41071314//National Natural Science Foundation of China/ ; }, abstract = {The chiral herbicide imazethapyr (IM) is frequently used to control weeds in soybean fields in northeast China. However, the impact of IM enantiomers on microbial communities in soil is still unknown. Genetic markers (16S rRNA V3-V4 regions) were used to characterize and evaluate the variation of the bacterial communities potentially effected by IM enantiomers. Globally, the bacterial community structure based on the OTU profiles in (-)-R-IM-treated soils was significantly different from those in (+)-S-IM-treated soils, and the differences were enlarged with the treatment dose increasing. Interestingly, the Rhizobiaceae family and several other beneficial bacteria, including Bradyrhizobium, Methylobacterium, and Paenibacillus, were strongly enriched in (-)-R-IM treatment compared to (+)-S-IM treatment. In contrast, the pathogenic bacteria, including Erwinia, Pseudomonas, Burkholderia, Streptomyces, and Agrobacterium, were suppressed in the presence of (-)-R-IM compared to (+)-S-IM. Furthermore, we also observed that the bacterial community structure in (-)-R-IM-treated soils was more quickly restored to its original state compared with those in (+)-S-IM-treated soils. These findings unveil a new role of chiral herbicide in the development of soil microbial ecology and provide theoretical support for the application of low-persistence, high-efficiency, and eco-friendly optical rotatory (-)-R-IM.}, }
@article {pmid30474731, year = {2018}, author = {Hosseinzadeh, S and Shams-Bakhsh, M and Mann, M and Fattah-Hosseini, S and Bagheri, A and Mehrabadi, M and Heck, M}, title = {Distribution and Variation of Bacterial Endosymbiont and &quot;Candidatus Liberibacter asiaticus&quot; Titer in the Huanglongbing Insect Vector, Diaphorina citri Kuwayama.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1290-1}, pmid = {30474731}, issn = {1432-184X}, support = {5300-163//California Citrus Research Board/ ; 2016-70016-24779//National Institute of Food and Agriculture/ ; 8062-22410-006-00-D//Agricultural Research Service/ ; }, abstract = {The Asian citrus psyllid (ACP), Diaphorina citri Kuwayama, is an economic insect pest in most citrus-growing regions and the vector of 'Candidatus Liberibacter asiaticus' (CLas), one of at least three known bacteria associated with Huanglongbing (HLB or citrus greening disease). D. citri harbors bacterial endosymbionts, including Wolbachia pipientis (strain Wolbachia wDi), 'Candidatus Carsonella ruddii,' and 'Candidatus Profftella armatura.' Many important functions of these bacteria can be inferred from their genome sequences, but their interactions with each other, CLas, and their D. citri host are poorly understood. In the present study, the titers of the endosymbionts in different tissues, in each sex, and in insects reared on healthy citrus (referred to as unexposed) and CLas-infected citrus (referred to as CLas-exposed) D. citri were investigated using real-time, quantitative PCR (qPCR) using two different quantitative approaches. Wolbachia and CLas were detected in all insect tissues. The titer of Wolbachia was higher in heads of CLas-exposed males as compared to unexposed males. In males and females, Wolbachia titer was highest in the Malpighian tubules. The highest titer of CLas was observed in the gut. Profftella and Carsonella titers were significantly reduced in the bacteriome of CLas-exposed males compared with that of unexposed males, but this effect was not observed in females. In ovaries of CLas-exposed females, the Profftella and Carsonella titers were increased as compared to non-exposed females. CLas appeared to influence the overall levels of the symbionts but did not drastically perturb the overall microbial community structure. In all the assessed tissues, CLas titer in males was significantly higher than that of females using absolute quantification. These data provide a better understanding of multi-trophic interactions regulating symbiont dynamics in the HLB pathosystem.}, }
@article {pmid30474730, year = {2018}, author = {Lima, BP and Hu, LI and Vreeman, GW and Weibel, DB and Lux, R}, title = {The Oral Bacterium Fusobacterium nucleatum Binds Staphylococcus aureus and Alters Expression of the Staphylococcal Accessory Regulator sarA.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1291-0}, pmid = {30474730}, issn = {1432-184X}, support = {DE021108//National Institute of Dental and Craniofacial Research/ ; DMR-1121288//National Science Foundation/ ; }, abstract = {Staphylococcus aureus, an opportunistic pathogen member of the nasal and skin microbiota, can also be found in human oral samples and has been linked to infectious diseases of the oral cavity. As the nasal and oral cavities are anatomically connected, it is currently unclear whether S. aureus can colonize the oral cavity and become part of the oral microbiota, or if its presence in the oral cavity is simply transient. To start addressing this question, we assessed S. aureus ability to directly bind selected members of the oral microbiota as well as its ability to integrate into a human-derived complex oral microbial community in vitro. Our data show that S. aureus forms aggregates with Fusobacterium nucleatum and Porphyromonas gingivalis and that it can incorporate into the human-derived in vitro oral community. Further analysis of the F. nucleatum-S. aureus interaction revealed that the outer-membrane adhesin RadD is partially involved in aggregate formation and that the RadD-mediated interaction leads to an increase in expression of the staphylococcal global regulator gene sarA. Our findings lend support to the notion that S. aureus can become part of the complex microbiota of the human mouth, which could serve as a reservoir for S. aureus. Furthermore, direct interaction with key members of the oral microbiota could affect S. aureus pathogenicity contributing to the development of several S. aureus associated oral infections.}, }
@article {pmid30474350, year = {2018}, author = {Cox, TL and Gan, HM and Moreau, JW}, title = {Seawater recirculation through subducting sediments sustains a deeply buried population of sulfate-reducing bacteria.}, journal = {Geobiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/gbi.12324}, pmid = {30474350}, issn = {1472-4669}, support = {//International Ocean Discovery Program (IODP)/ ; //Australia-New Zealand IODP Consortium (ANZIC)/ ; ARC DP110103668//Australian Research Council (ARC)/ ; }, abstract = {Subseafloor sulfate concentrations typically decrease with depth as this electron acceptor is consumed by respiring microorganisms. However, studies show that seawater can flow through hydraulically conductive basalt to deliver sulfate upwards into deeply buried overlying sediments. Our previous work on IODP Site C0012A (Nankai Trough, Japan) revealed that recirculation of sulfate through the subducting Philippine Sea Plate stimulated microbial activity near the sediment-basement interface (SBI). Here, we describe the microbial ecology, phylogeny, and energetic requirements of population of aero-tolerant sulfate-reducing bacteria in the deep subseafloor. We identified dissimilatory sulfite reductase gene (dsr) sequences 93% related to oxygen-tolerant Desulfovibrionales species across all reaction zones while no SRB were detected in drilling fluid control samples. Pore fluid chemistry revealed low concentrations of methane (<0.25 mM), while hydrogen levels were consistent with active bacterial sulfate reduction (0.51-1.52 nM). Solid phase total organic carbon (TOC) was also considerably low in these subseafloor sediments. Our results reveal the phylogenetic diversity, potential function, and physiological tolerance of a community of sulfate-reducing bacteria living at ~480 m below subducting seafloor.}, }
@article {pmid30471620, year = {2018}, author = {Gutiérrez, S and Zwart, MP}, title = {Population bottlenecks in multicomponent viruses: first forays into the uncharted territory of genome-formula drift.}, journal = {Current opinion in virology}, volume = {33}, number = {}, pages = {184-190}, doi = {10.1016/j.coviro.2018.09.001}, pmid = {30471620}, issn = {1879-6265}, abstract = {Multicomponent viral systems face specific challenges when enduring population bottlenecks. These systems can lose coding information due to the lack of co-encapsidation of all the genetic information, at least in a proportion of the capsids in a population. Moreover, bottlenecks can also impact one of the main potential advantages of multicomponent systems: the regulation of gene expression through changes in gene copy frequencies at the population level. How these systems cope with population bottlenecks is far from being clear. Here, two non-exclusive scenarios are described. In the first scenario, population bottlenecks during host infection allow for the isolation of within-host populations with different gene frequencies, leaving the door opened for the selection of populations with adaptive gene frequencies. The second scenario postulates that viruses could influence bottleneck size, at least at certain steps of their life cycle, to limit random changes in gene frequencies. Examples of viral mechanism impacting bottleneck size at cell infection are available and, intriguingly, they can lead to either increases or reductions in bottleneck size. This situation opens the way for putative trade-offs on both gene frequencies and bottleneck sizes that could differ among multicomponent systems.}, }
@article {pmid30470844, year = {2018}, author = {Lizoňová, Z and Zhai, M and Bojková, J and Horsák, M}, title = {Small-scale Variation of Testate Amoeba Assemblages: the Effect of Site Heterogeneity and Empty Shell Inclusion.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1292-z}, pmid = {30470844}, issn = {1432-184X}, support = {P505/16-03881S//Grantová Agentura České Republiky/ ; }, abstract = {Studies on testate amoeba species distribution at small scales (i.e., single peatland sites) are rare and mostly focus on bogs or mineral-poor Sphagnum fens, leaving spatial patterns within mineral-rich fens completely unexplored. In this study, two mineral-rich fen sites of contrasting groundwater chemistry and moss layer composition were selected for the analysis of testate amoeba compositional variance within a single site. At each study site, samples from 20 randomly chosen moss-dominated plots were collected with several environmental variables being measured at each sampling spot. We also distinguished between empty shells and living individuals to evaluate the effect of empty shell inclusion on recorded species distribution. At the heterogeneous-rich Sphagnum-fen, a clear composition turnover in testate amoebae between Sphagnum-dominated and brown moss-dominated samples was closely related to water pH, temperature and redox potential. We also found notable species composition variance within the homogeneous calcareous fen, yet it was not as high as for the former site and the likely drivers of community assembly remained unidentified. The exclusion of empty shells provided more accurate data on species distribution as well as their relationship with some environmental variables, particularly moisture. Small-scale variability in species composition of communities seems to be a worthwhile aspect in testate amoeba research and should be considered in future sampling strategies along with a possible empty shell bias for more precise understanding of testate amoeba ecology and paleoecology.}, }
@article {pmid30469475, year = {2018}, author = {Chi, H and Yang, L and Yang, W and Li, Y and Chen, Z and Huang, L and Chao, Y and Qiu, R and Wang, S}, title = {Variation of the Bacterial Community in the Rhizoplane Iron Plaque of the Wetland Plant Typha latifolia.}, journal = {International journal of environmental research and public health}, volume = {15}, number = {12}, pages = {}, doi = {10.3390/ijerph15122610}, pmid = {30469475}, issn = {1660-4601}, support = {2018YFD0800700//National Key R&amp;D Program of China/ ; 41671313//National Natural Science Foundation of China/ ; 2016A020221012; 2014A050503032; 2017B020216008//Science and Technology Planning Project of Guangdong Province, China/ ; B18060//the 111Project/ ; }, abstract = {The survival of wetland plants in iron, sulfur and heavy metals-rich mine tailing ponds has been commonly attributed to the iron plaque (IP) on the root surface that acts as a protective barrier. However, the contribution of bacteria potentially regulates the iron-sulfur cycle and heavy metal exclusion at the root surface has not been studied in depth, particularly from a microbial ecology perspective. In this study, a pot experiment using Typha latifolia, a typical wetland plant, in non-polluted soil (NP) and tailing soil (T) was conducted. Samples from four zones, comprising non-rhizosphere soil (NR), rhizosphere soil (R) and internal (I) and external (E) layers of iron plaque, were collected from the NP and T and analyzed by 16S rRNA sequencing. Simpson index of the genus level showed greater diversities of bacterial community in the NP and its I zone is the most important part of the rhizosphere. PICRUSt predicted that the I zones in both NP and T harbored most of the functional genes. Specifically, functional genes related to sulfur relay and metabolism occurred more in the I zone in the T, whereas those related to iron acquisition and carbon and nitrogen circulation occurred more in the I zone in the NP. Analysis of dominant bacterial communities at genus level showed highest abundance of heavy metal resistant genus Burkholderia in the E zones in both soils, indicating that heavy metal resistance of Typha latifolia driven by Burkholderia mainly occurred at the external layer of IP. Moreover, many bacterial genera, such as Acidithiobacillus, Ferritrophicum, Thiomonas, Metallibacterium and Sideroxydans, involved in iron and sulfur metabolisms were found in the T and most showed higher abundance in the I zone than in the other zones. This work, as the first endeavor to separate the iron plaque into external and internal layers and investigate the variations of the bacterial communities therein, can provide an insight for further understanding the survival strategy of wetland plants, e.g., Typha latifolia, in extreme environment.}, }
@article {pmid30467715, year = {2018}, author = {Lemmel, F and Maunoury-Danger, F and Fanesi, A and Leyval, C and Cébron, A}, title = {Soil Properties and Multi-Pollution Affect Taxonomic and Functional Bacterial Diversity in a Range of French Soils Displaying an Anthropisation Gradient.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1297-7}, pmid = {30467715}, issn = {1432-184X}, support = {ANR-13-JSV7-000701//Agence Nationale de la Recherche/ ; EC2CO- Biohefect/Ecodyn//Dril/MicrobiEen (EcobioS project)//Institut National des Sciences de l'Univers, Centre National de la Recherche Scientifique/ ; traitMic project//OSU-Otelo/ ; }, abstract = {The intensive industrial activities of the twentieth century have left behind highly contaminated wasteland soils. It is well known that soil parameters and the presence of pollutants shape microbial communities. But in such industrial waste sites, the soil multi-contamination with organic (polycyclic aromatic hydrocarbons, PAH) and metallic (Zn, Pb, Cd) pollutants and long-term exposure may induce a selection pressure on microbial communities that may modify soil functioning. The aim of our study was to evaluate the impact of long-term multi-contamination and soil characteristics on bacterial taxonomic and functional diversity as related to the carbon cycle. We worked on 10 soils from northeast of France distributed into three groups (low anthropised controls, slag heaps, and settling ponds) based on their physico-chemical properties (texture, C, N) and pollution level. We assessed bacterial taxonomic diversity by 16S rDNA Illumina sequencing, and functional diversity using Biolog® and MicroResp™ microtiter plate tools. Although taxonomic diversity at the phylum level was not different among the soil groups, many operational taxonomic units were influenced by metal or PAH pollution, and by soil texture and total nitrogen content. Functional diversity was not influenced by PAH contamination while metal pollution selected microbial communities with reduced metabolic functional diversity but more tolerant to zinc. Limited microbial utilisation of carbon substrates in metal-polluted soils was mainly due to the nitrogen content. Based on these two observations, we hypothesised that reduced microbial activity and lower carbon cycle-related functional diversity may have contributed to the accumulation of organic matter in the soils that exhibited the highest levels of metal pollution.}, }
@article {pmid30467714, year = {2018}, author = {Ellison, S and Rovito, S and Parra-Olea, G and Vásquez-Almazán, C and Flechas, SV and Bi, K and Vredenburg, VT}, title = {The Influence of Habitat and Phylogeny on the Skin Microbiome of Amphibians in Guatemala and Mexico.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1288-8}, pmid = {30467714}, issn = {1432-184X}, support = {IOS-1258133//National Science Foundation/ ; 1633948//National Science Foundation/ ; DEB-1026396//National Science Foundation/ ; ICER-1633948//National Science Foundation/ ; CN-13-614//University of California Institute for Mexico and the United States/ ; }, abstract = {Microbial symbionts are increasingly recognized as playing a critical role in organismal health across a wide range of hosts. Amphibians are unique hosts in that their skin helps to regulate the exchange of water, ions, and gases, and it plays an active role in defense against pathogens through the synthesis of anti-microbial peptides. The microbiome of amphibian skin includes a diverse community of bacteria known to defend against pathogens, including the global pandemic lineage of Batrachochytrium dendrobatidis associated with mass amphibian die-offs. The relative influence of host phylogeny and environment in determining the composition of the amphibian skin microbiome remains poorly understood. We collected skin swabs from montane amphibians in Mexico and Guatemala, focusing on two genera of plethodontid salamanders and one genus of frogs. We used high throughput sequencing to characterize the skin bacterial microbiome and tested the impact of phylogeny and habitat on bacterial diversity. Our results show that phylogenetic history strongly influences the diversity and community structure of the total bacterial microbiome at higher taxonomic levels (between orders), but on lower scales (within genera and species), the effect of habitat predominates. These results add to a growing consensus that habitat exerts a strong effect on microbiome structure and composition, particularly at shallow phylogenetic scales.}, }
@article {pmid30467713, year = {2018}, author = {Ribière, C and Hegarty, C and Stephenson, H and Whelan, P and O'Toole, PW}, title = {Gut and Whole-Body Microbiota of the Honey Bee Separate Thriving and Non-thriving Hives.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1287-9}, pmid = {30467713}, issn = {1432-184X}, support = {SFI/12/RC/2273//Science Foundation Ireland/Ireland ; }, abstract = {The recent worldwide decline of honey bee colonies is a major ecological problem which also threatens pollinated crop production. Several interacting stressors such as environmental pressures and pathogens are suspected. Recently, the gut microbiota has emerged as a critical factor affecting bee health and fitness. We profiled the bacterial communities associated with the gut and whole body of worker bees to assess whether non-thriving colonies could be separated from thriving hives based on their microbial signature. The microbiota of thriving colonies was characterised by higher diversity and higher relative abundance of bacterial taxa involved in sugar degradation that were previously associated with healthy bees (e.g. Commensalibacter sp. and Bartonella apis). In contrast, the microbiota of non-thriving bees was depleted in health-associated species (e.g. Lactobacillus apis), and bacterial taxa associated with disease states (e.g. Gilliamella apicola) and pollen degradation (e.g. G. apicola and Bifidobacterium asteroides) were present in higher abundance compared to thriving colonies. Gut and whole-body microbiota shared a similar dominant core but their comparison showed differences in composition and relative abundance. More differences in taxon relative abundance between gut and whole body were observed in non-thriving bees, suggesting that microbiota associated with other bee organs might also be different. Thus, microbiota profiling could be used as a diagnostic tool in beekeeping practices to predict hive health and guide hive management.}, }
@article {pmid30467310, year = {2018}, author = {Pollock, FJ and McMinds, R and Smith, S and Bourne, DG and Willis, BL and Medina, M and Thurber, RV and Zaneveld, JR}, title = {Coral-associated bacteria demonstrate phylosymbiosis and cophylogeny.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {4921}, doi = {10.1038/s41467-018-07275-x}, pmid = {30467310}, issn = {2041-1723}, abstract = {Scleractinian corals' microbial symbionts influence host health, yet how coral microbiomes assembled over evolution is not well understood. We survey bacterial and archaeal communities in phylogenetically diverse Australian corals representing more than 425 million years of diversification. We show that coral microbiomes are anatomically compartmentalized in both modern microbial ecology and evolutionary assembly. Coral mucus, tissue, and skeleton microbiomes differ in microbial community composition, richness, and response to host vs. environmental drivers. We also find evidence of coral-microbe phylosymbiosis, in which coral microbiome composition and richness reflect coral phylogeny. Surprisingly, the coral skeleton represents the most biodiverse coral microbiome, and also shows the strongest evidence of phylosymbiosis. Interactions between bacterial and coral phylogeny significantly influence the abundance of four groups of bacteria-including Endozoicomonas-like bacteria, which divide into host-generalist and host-specific subclades. Together these results trace microbial symbiosis across anatomy during the evolution of a basal animal lineage.}, }
@article {pmid30465731, year = {2018}, author = {Beji, O and Adouani, N and Poncin, S and Hamdi, M and Li, HZ}, title = {Mineral pollutants removal through immobilized microalgae-bacterial flocs in a multitrophic microreactor.}, journal = {Environmental technology}, volume = {}, number = {}, pages = {1-31}, doi = {10.1080/09593330.2018.1551939}, pmid = {30465731}, issn = {0959-3330}, abstract = {Microalgae-bacterial flocs (MaB-flocs) immobilization technique using polyvinyl alcohol (PVA) crosslinked with sodium alginate represent a novel approach for sustainable pollutants removal. The present work was performed to evaluate the performance of a multitrophic batch reactor at microscale for treating two synthetic wastewater solutions prepared with two different initial Chemical Oxygen Demand (COD): 200 mg.L-1 and 450 mg.L-1, respectively. Three MaB-flocs concentrations were entrapped into PVA-alginate beads: C1 (2%, v/v), C2 (5%, v/v) and C3 (10%, v/v), without O2 supply, during three periods 2, 4 and 6 days of batch incubation. PVA-alginate beads containing the highest concentration C3 of MaB-flocs improved the performance of the microreactor to remove significantly NH4+ and PO43- of about 61% and 82%, respectively, from wastewater more than two other concentrations used. This result confirms that C3 of MaB-flocs displays not only a good potential for nutrients removals but also the highest MaB-flocs morphological progression after 6 days of treatment with the highest COD of 450 mg.L-1. The feasibility of the PVA-alginate for cells immobilization, investigated through microscopy analysis, reveals that the evolution of multicellularity in MaB-flocs, for all experiments.}, }
@article {pmid30465068, year = {2018}, author = {Hubert, J and Nesvorna, M and Kopecky, J and Erban, T and Klimov, P}, title = {Population and Culture Age Influence the Microbiome Profiles of House Dust Mites.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1294-x}, pmid = {30465068}, issn = {1432-184X}, support = {17-12068S//Grantová Agentura České Republiky/ ; (No. 6.1933.2014/K Project Code 1933//Ministry of Education and Science of the Russian Federation/ ; No. 15-04-0s5185-a//the Russian Foundation for Basic Research/ ; }, abstract = {Interactions with microorganisms might enable house dust mites (HDMs) to derive nutrients from difficult-to-digest structural proteins and to flourish in human houses. We tested this hypothesis by investigating the effects of changes in the mite culture growth and population of two HDM species on HDM microbiome composition and fitness. Growing cultures of laboratory and industrial allergen-producing populations of Dermatophagoides farinae (DFL and DFT, respectively) and Dermatophagoides pteronyssinus (DPL and DPT, respectively) were sampled at four time points. The symbiotic microorganisms of the mites were characterized by DNA barcode sequencing and quantified by qPCR using universal/specific primers. The population growth of mites and nutrient contents of mite bodies were measured and correlated with the changes in bacteria in the HDM microbiome. The results showed that both the population and culture age significantly influenced the microbiome profiles. Cardinium formed 93% and 32% of the total sequences of the DFL and DFT bacterial microbiomes, respectively, but this bacterial species was less abundant in the DPL and DPT microbiomes. Staphylococcus abundance was positively correlated with increased glycogen contents in the bodies of mites, and increased abundances of Aspergillus, Candida, and Kocuria were correlated with increased lipid contents in the bodies of mites. The xerophilic fungus Wallemia accounted for 39% of the fungal sequences in the DPL microbiome, but its abundance was low in the DPT, DFL, and DFT microbiomes. With respect to the mite culture age, we made three important observations: the mite population growth from young cultures was 5-8-fold higher than that from old cultures; specimens from old cultures had greater abundances of fungi and bacteria in their bodies; and yeasts predominated in the gut contents of specimens from young cultures, whereas filamentous mycelium prevailed in specimens from old cultures. Our results are consistent with the hypothesis that mites derive nutrients through associations with microorganisms.}, }
@article {pmid30460544, year = {2018}, author = {Koosha, M and Vatandoost, H and Karimian, F and Choubdar, N and Oshaghi, MA}, title = {Delivery of a Genetically Marked Serratia AS1 to Medically Important Arthropods for Use in RNAi and Paratransgenic Control Strategies.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1289-7}, pmid = {30460544}, issn = {1432-184X}, support = {30353//Tehran University of Medical Sciences and Health Services/ ; 33613//Tehran University of Medical Sciences and Health Services/ ; }, abstract = {Understanding how arthropod vectors acquire their bacteria is essential for implementation of paratransgenic and RNAi strategies using genetically modified bacteria to control vector-borne diseases. In this study, a genetically marked Serratia AS1 strain expressing the mCherry fluorescent protein (mCherry-Serratia) was used to test various acquisition routes in six arthropod vectors including Anopheles stephensi, Culex pipiens, Cx. quinquefaciatus, Cx. theileri, Phlebotomus papatasi, and Hyalomma dromedarii. Depending on the species, the bacteria were delivered to (i) mosquito larval breeding water, (ii) host skin, (iii) sugar bait, and (iv) males (paratransgenic). The arthropods were screened for the bacteria in their guts or other tissues. All the hematophagous arthropods were able to take the bacteria from the skin of their hosts while taking blood meal. The mosquitoes were able to take up the bacteria from the water at larval stages and to transfer them transstadially to adults and finally to transfer them to the water they laid eggs in. The mosquitoes were also able to acquire the bacteria from male sperm. The level of bacterial acquisition was influenced by blood feeding time and strategies (pool or vessel feeding), dipping in water and resting time of newly emerged adult mosquitoes, and the disseminated tissue/organ. Transstadial, vertical, and venereal bacterial acquisition would increase the sustainability of the modified bacteria in vector populations and decrease the need for supplementary release experiments whereas release of paratransgenic males that do not bite has fewer ethical issues. Furthermore, this study is required to determine if the modified bacteria can be introduced to arthropods in the same routes in nature.}, }
@article {pmid30459201, year = {2018}, author = {Hannigan, GD and Duhaime, MB and Ruffin, MT and Koumpouras, CC and Schloss, PD}, title = {Diagnostic Potential and Interactive Dynamics of the Colorectal Cancer Virome.}, journal = {mBio}, volume = {9}, number = {6}, pages = {}, doi = {10.1128/mBio.02248-18}, pmid = {30459201}, issn = {2150-7511}, abstract = {Human viruses (those that infect human cells) have been associated with many cancers, largely due to their mutagenic and functionally manipulative abilities. Despite this, cancer microbiome studies have focused almost exclusively on bacteria instead of viruses. We began evaluating the cancer virome by focusing on colorectal cancer, a primary cause of morbidity and mortality throughout the world and a cancer linked to altered colonic bacterial community compositions but with an unknown association with the gut virome. We used 16S rRNA gene, whole shotgun metagenomic, and purified virus metagenomic sequencing of stool to evaluate the differences in human colorectal cancer virus and bacterial community composition. Through random forest modeling, we identified differences in the healthy and colorectal cancer viromes. The cancer-associated virome consisted primarily of temperate bacteriophages that were also predicted to be bacterium-virus community network hubs. These results provide foundational evidence that bacteriophage communities are associated with colorectal cancer and potentially impact cancer progression by altering the bacterial host communities.IMPORTANCE Colorectal cancer is a leading cause of cancer-related death in the United States and worldwide. Its risk and severity have been linked to colonic bacterial community composition. Although human-specific viruses have been linked to other cancers and diseases, little is known about colorectal cancer virus communities. We addressed this knowledge gap by identifying differences in colonic virus communities in the stool of colorectal cancer patients and how they compared to bacterial community differences. The results suggested an indirect role for the virome in impacting colorectal cancer by modulating the associated bacterial community. These findings both support the idea of a biological role for viruses in colorectal cancer and provide a new understanding of basic colorectal cancer etiology.}, }
@article {pmid30456756, year = {2018}, author = {Jung, MY and Kang, MS and Lee, KE and Lee, EY and Park, SJ}, title = {Paraburkholderia dokdonella sp. nov., isolated from a plant from the genus Campanula.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {}, number = {}, pages = {}, doi = {10.1007/s12275-019-8500-5}, pmid = {30456756}, issn = {1976-3794}, abstract = {The novel Gram-stain-negative, rod-shaped, aerobic bacterial strain DCR-13T was isolated from a native plant belonging to the genus Campanula on Dokdo, an island in the Republic of Korea. Comparative analysis of the 16S rRNA gene sequence indicated that this strain is closely related to Paraburkholderia peleae PP52-1T (98.43% 16S rRNA gene sequence similarity), Paraburkholderia oxyphila NBRC 105797T (98.42%), Paraburkholderia sacchari IPT 101T (98.28%), Paraburkholderia mimosarum NBRC 106338T (97.80%), Paraburkholderia denitrificans KIS30-44T (97.46%), and Paraburkholderia paradise WAT (97.45%). This analysis of the 16S rRNA gene sequence also suggested that DCR-13T and the six closely related strains formed a clade within the genus Paraburkholderia, but that DCR-13T was clearly separated from the established species. DCR-13T had ubiquinone 8 as its predominant respiratory quinone, and its genomic DNA G + C content was 63.9 mol%. The isolated strain grew at a pH of 6.0-8.0 (with an optimal pH of 6.5), 0-4% w/v NaCl (with an optimal level of 0%), and a temperature of 18-42°C (with an optimal temperature of 30°C). The predominant fatty acids were C16:0, summed feature 8 (C18:1ω7c/C18:1ω6c), C17:0 cyclo, C19:0 cyclo ω8c, summed feature 3 (C16:1ω6c/C16:1ω7c) and summed feature 2 (C12:0 aldehyde), and the major polar lipids were phosphatidylglycerol and phosphatidylethanolamine. On the basis of polyphasic evidence, it is proposed that strain DCR-13T (= KCTC 62811T = LMG 30889T) represents the type strain of a novel species, Paraburkholderia dokdonella sp. nov.}, }
@article {pmid30455213, year = {2018}, author = {Daru, BH and Bowman, EA and Pfister, DH and Arnold, AE}, title = {A novel proof of concept for capturing the diversity of endophytic fungi preserved in herbarium specimens.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {374}, number = {1763}, pages = {}, doi = {10.1098/rstb.2017.0395}, pmid = {30455213}, issn = {1471-2970}, abstract = {Herbarium specimens represent important records of morphological and genetic diversity of plants that inform questions relevant to global change, including species distributions, phenology and functional traits. It is increasingly appreciated that plant microbiomes can influence these aspects of plant biology, but little is known regarding the historic distribution of microbes associated with plants collected in the pre-molecular age. If microbiomes can be observed reliably in herbarium specimens, researchers will gain a new lens with which to examine microbial ecology, evolution, species interactions. Here, we describe a method for accessing historical plant microbiomes from preserved herbarium specimens, providing a proof of concept using two plant taxa from the imperiled boreal biome (Andromeda polifolia and Ledum palustre subsp. groenlandicum, Ericaceae). We focus on fungal endophytes, which occur within symptomless plant tissues such as leaves. Through a three-part approach (i.e. culturing, cloning and next-generation amplicon sequencing via the Illumina MiSeq platform, with extensive controls), we examined endophyte communities in dried, pressed leaves that had been processed as regular herbarium specimens and stored at room temperature in a herbarium for four years. We retrieved only one endophyte in culture, but cloning and especially the MiSeq analysis revealed a rich community of foliar endophytes. The phylogenetic distribution and diversity of endophyte assemblages, especially among the Ascomycota, resemble endophyte communities from fresh plants collected in the boreal biome. We could distinguish communities of endophytes in each plant species and differentiate likely endophytes from fungi that could be surface contaminants. Taxa found by cloning were observed in the larger MiSeq dataset, but species richness was greater when subsets of the same tissues were evaluated with the MiSeq approach. Our findings provide a proof of concept for capturing endophyte DNA from herbarium specimens, supporting the importance of herbarium records as roadmaps for understanding the dynamics of plant-associated microbial biodiversity in the Anthropocene.This article is part of the theme issue 'Biological collections for understanding biodiversity in the Anthropocene'.}, }
@article {pmid30453516, year = {2018}, author = {Sharma, L and Oliveira, I and Raimundo, F and Torres, L and Marques, G}, title = {Soil Chemical Properties Barely Perturb the Abundance of Entomopathogenic Fusarium oxysporum: A Case Study Using a Generalized Linear Mixed Model for Microbial Pathogen Occurrence Count Data.}, journal = {Pathogens (Basel, Switzerland)}, volume = {7}, number = {4}, pages = {}, doi = {10.3390/pathogens7040089}, pmid = {30453516}, issn = {2076-0817}, support = {UID/MULTI/04621/2013 ; UID/AGR/04033/2013 ; POCI-01-0145-FEDER-006958//National Funds by FCT - Portuguese Foundation for Science and Technology; EcoVitis project; FEDER/COMPETE/POCI - Operacional Competitiveness and Internationalization Programme/ ; }, abstract = {Fusarium oxysporum exhibits insect pathogenicity-however, generalized concerns of releasing phytopathogens within agroecosystems marred its entomopathogenicity-related investigations. In a previous study, soils were sampled from Douro vineyards and adjacent hedgerows. In this study, 80 of those soils were analyzed for their chemical properties and were subsequently co-related with the abundance of entomopathogenic F. oxysporum, after insect baiting of soils with Galleria mellonella and Tenebrio molitor larvae. The soil chemical properties studied were organic matter content; total organic carbon; total nitrogen; available potassium; available phosphorus; exchangeable cations, such as K⁺, Na⁺, Ca2+, and Mg2+; pH; total acidity; degree of base saturation; and effective cation exchange capacity. Entomopathogenic F. oxysporum was found in 48 soils, i.e., 60% ± 5.47%, of the total soil samples. Out of the 1280 insect larvae used, 93, i.e., 7.26% ± 0.72%, were found dead by entomopathogenic F. oxysporum. Stepwise deletion of non-significant variables using a generalized linear model was followed by a generalized linear mixed model (GLMM). A higher C:N (logarithmized) (p < 0.001) and lower exchangeable K⁺ (logarithmized) (p = 0.008) were found significant for higher fungal abundance. Overall, this study suggests that entomopathogenic F. oxysporum is robust with regard to agricultural changes, and GLMM is a useful statistical tool for count data in ecology.}, }
@article {pmid30451146, year = {2018}, author = {Matsuyama, M and Gomez-Arango, LF and Fukuma, NM and Morrison, M and Davies, PSW and Hill, RJ}, title = {Breastfeeding: a key modulator of gut microbiota characteristics in late infancy.}, journal = {Journal of developmental origins of health and disease}, volume = {}, number = {}, pages = {1-8}, doi = {10.1017/S2040174418000624}, pmid = {30451146}, issn = {2040-1752}, abstract = {The objective of this study was to investigate the impact of the most commonly cited factors that may have influenced infants' gut microbiota profiles at one year of age: mode of delivery, breastfeeding duration and antibiotic exposure. Barcoded V3/V4 amplicons of bacterial 16S-rRNA gene were prepared from the stool samples of 52 healthy 1-year-old Australian children and sequenced using the Illumina MiSeq platform. Following the quality checks, the data were processed using the Quantitative Insights Into Microbial Ecology pipeline and analysed using the Calypso package for microbiome data analysis. The stool microbiota profiles of children still breastfed were significantly different from that of children weaned earlier (P<0.05), independent of the age of solid food introduction. Among children still breastfed, Veillonella spp. abundance was higher. Children no longer breastfed possessed a more 'mature' microbiota, with notable increases of Firmicutes. The microbiota profiles of the children could not be differentiated by delivery mode or antibiotic exposure. Further analysis based on children's feeding patterns found children who were breastfed alongside solid food had significantly different microbiota profiles compared to that of children who were receiving both breastmilk and formula milk alongside solid food. This study provided evidence that breastfeeding continues to influence gut microbial community even at late infancy when these children are also consuming table foods. At this age, any impacts from mode of delivery or antibiotic exposure did not appear to be discernible imprints on the microbial community profiles of these healthy children.}, }
@article {pmid30450083, year = {2018}, author = {Meisner, A and de Boer, W}, title = {Strategies to Maintain Natural Biocontrol of Soil-Borne Crop Diseases During Severe Drought and Rainfall Events.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2279}, doi = {10.3389/fmicb.2018.02279}, pmid = {30450083}, issn = {1664-302X}, abstract = {In many parts of the world, agricultural ecosystems are increasingly exposed to severe drought, and rainfall events due to climate changes. This coincides with a higher vulnerability of crops to soil-borne diseases, which is mostly ascribed to decreased resistance to pathogen attacks. However, loss of the natural capacity of soil microbes to suppress soil-borne plant pathogens may also contribute to increased disease outbreaks. In this perspectives paper, we will discuss the effect of extreme weather events on pathogen-antagonist interactions during drought and rainfall events and upon recovery. We will focus on diseases caused by root-infecting fungi and oomycetes. In addition, we will explore factors that affect restoration of the balance between pathogens and other soil microbes. Finally, we will indicate potential future avenues to improve the resistance and/or recovery of natural biocontrol during, and after water stresses. As such, our perspective paper will highlight a knowledge gap that needs to be bridged to adapt agricultural ecosystems to changing climate scenarios.}, }
@article {pmid30449244, year = {2018}, author = {Sterlin, D and Fieschi, C and Malphettes, M and Larsen, M and Gorochov, G and Fadlallah, J}, title = {Immune/microbial interface perturbation in human IgA deficiency.}, journal = {Gut microbes}, volume = {}, number = {}, pages = {1-5}, doi = {10.1080/19490976.2018.1546520}, pmid = {30449244}, issn = {1949-0984}, abstract = {In a recently published article we report the metagenomic analysis of human gut microbiomes evolved in the absence of immunoglobulin A (IgA). We show that human IgA deficiency is not associated with massive quantitative perturbations of gut microbial ecology. While our study underlines a rather expected pathobiont expansion, we at the same time highlight a less expected depletion in some typically beneficial symbionts. We also show that IgM partially supply IgA deficiency, explaining the relatively mild clinical phenotype associated with the early steps of this condition. Microbiome studies in patients should consider potential issues such as cohort size, human genetic polymorphism and treatments. In this commentary, we discuss how such issues were taken into account in our own study.}, }
@article {pmid30448922, year = {2018}, author = {De Corte, D and Paredes, G and Yokokawa, T and Sintes, E and Herndl, GJ}, title = {Differential Response of Cafeteria roenbergensis to Different Bacterial and Archaeal Prey Characteristics.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1293-y}, pmid = {30448922}, issn = {1432-184X}, support = {P16085//Japan Society for the Promotion of Science/ ; Z194-B17//Austrian Science Fund/ ; P28781-B21//Austrian Science Fund/ ; P27696-B22//Austrian Science Fund/ ; PIEF-GA-2011-299860//FP7 People: Marie-Curie Actions/ ; 268595//European Research Council/International ; }, abstract = {In the marine environment, the abundance of Bacteria and Archaea is either controlled bottom-up via nutrient availability or top-down via grazing. Heterotrophic nanoflagellates (HNF) are mainly responsible for prokaryotic grazing losses besides viral lysis. However, the grazing specificity of HNF on specific bacterial and archaeal taxa is under debate. Bacteria and Archaea might have different nutritive values and surface properties affecting the growth rates of HNF. In this study, we offered different bacterial and archaeal strains with different morphologic and physiologic characteristics to Cafeteria roenbergensis, one of the most abundant and ubiquitous species of HNF in the ocean. Two Nitrosopumilus maritimus-related strains isolated from the northern Adriatic Sea (Nitrosopumilus adriaticus, Nitrosopumilus piranensis), two Nitrosococcus strains, and two fast growing marine Bacteria (Pseudoalteromonas sp. and Marinobacter sp.) were fed to Cafeteria cultures. Cafeteria roenbergensis exhibited high growth rates when feeding on Pseudoalteromonas sp., Marinobacter sp., and Nitrosopumilus adriaticus, while the addition of the other strains resulted in minimal growth. Taken together, our data suggest that the differences in growth of Cafeteria roenbergensis associated to grazing on different thaumarchaeal and bacterial strains are likely due to the subtle metabolic, cell size, and physiological differences between different bacterial and thaumarchaeal taxa. Moreover, Nitrosopumilus adriaticus experienced a similar grazing pressure by Cafeteria roenbergensis as compared to the other strains, suggesting that other HNF may also prey on Archaea which might have important consequences on the global biogeochemical cycles.}, }
@article {pmid30447886, year = {2018}, author = {Maayer, P and Aliyu, H and Cowan, DA}, title = {Reorganising the order Bacillales through phylogenomics.}, journal = {Systematic and applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.syapm.2018.10.007}, pmid = {30447886}, issn = {1618-0984}, abstract = {Bacterial classification at higher taxonomic ranks such as the order and family levels is currently reliant on phylogenetic analysis of 16S rRNA and the presence of shared phenotypic characteristics. However, these may not be reflective of the true genotypic and phenotypic relationships of taxa. This is evident in the order Bacillales, members of which are defined as aerobic, spore-forming and rod-shaped bacteria. However, some taxa are anaerobic, asporogenic and coccoid. 16S rRNA gene phylogeny is also unable to elucidate the taxonomic positions of several families incertae sedis within this order. Whole genome-based phylogenetic approaches may provide a more accurate means to resolve higher taxonomic levels. A suite of phylogenomic approaches were applied to re-evaluate the taxonomy of 80 representative taxa of eight families (and six family incertae sedis taxa) within the order Bacillales. This showed several anomalies in the current family and order level classifications including the existence of four Bacillaceae and two Paenibacillaceae &quot;family&quot; clades. Furthermore, the families Staphylococcaceae and Listeriaceae belong to the sister order Lactobacillales. Finally, we propose a consensus phylogenomic approach which may diminish algorithmic biases associated with single approaches and facilitate more accurate classification of a broad range of taxa at the higher taxonomic levels.}, }
@article {pmid30446738, year = {2018}, author = {Fernandez, VI and Yawata, Y and Stocker, R}, title = {A Foraging Mandala for Aquatic Microorganisms.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-018-0309-4}, pmid = {30446738}, issn = {1751-7370}, abstract = {Aquatic environments harbor a great diversity of microorganisms, which interact with the same patchy, particulate, or diffuse resources by means of a broad array of physiological and behavioral adaptations, resulting in substantially different life histories and ecological success. To date, efforts to uncover and understand this diversity have not been matched by equivalent efforts to identify unifying frameworks that can provide a degree of generality and thus serve as a stepping stone to scale up microscale dynamics to predict their ecosystem-level consequences. In particular, evaluating the ecological consequences of different resource landscapes and of different microbial adaptations has remained a major challenge in aquatic microbial ecology. Here, inspired by Ramon Margalef's mandala for phytoplankton, we propose a foraging mandala for microorganisms in aquatic environments, which accounts for both the local environment and individual adaptations. This biophysical framework distills resource acquisition into two fundamental parameters: the search time for a new resource and the growth return obtained from encounter with a resource. We illustrate the foraging mandala by considering a broad range of microbial adaptations and environmental characteristics. The broad applicability of the foraging mandala suggests that it could be a useful framework to compare disparate microbial strategies in aquatic environments and to reduce the vast complexity of microbe-environment interactions into a minimal number of fundamental parameters.}, }
@article {pmid30446737, year = {2018}, author = {Rath, KM and Fierer, N and Murphy, DV and Rousk, J}, title = {Linking bacterial community composition to soil salinity along environmental gradients.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-018-0313-8}, pmid = {30446737}, issn = {1751-7370}, support = {2015-04942//Vetenskapsrådet (Swedish Research Council)/ ; 942-2015-270//Svenska Forskningsrådet Formas (Swedish Research Council Formas)/ ; }, abstract = {Salinization is recognized as a threat to soil fertility worldwide. A challenge in understanding the effects of salinity on soil microbial communities is the fact that it can be difficult to disentangle the effects of salinity from those of other variables that may co-vary with salinity. Here we use a trait-based approach to identify direct effects of salinity on soil bacterial communities across two salinity gradients. Through dose-response relationships between salinity and bacterial growth, we quantified distributions of the trait salt tolerance within the communities. Community salt tolerance was closely correlated with soil salinity, indicating a strong filtering effect of salinity on the bacterial communities. Accompanying the increases in salt tolerance were consistent shifts in bacterial community composition. We identified specific bacterial taxa that increased in relative abundances with community salt tolerance, which could be used as bioindicators for high community salt tolerance. A strong filtering effect was also observed for pH across the gradients, with pH tolerance of bacterial communities correlated to soil pH. We propose phenotypic trait distributions aggregated at the community level as a useful approach to study the role of environmental factors as filters of microbial community composition.}, }
@article {pmid30445447, year = {2018}, author = {Philips, J and Monballyu, E and Georg, S and De Paepe, K and Prévoteau, A and Rabaey, K and Arends, JBA}, title = {An Acetobacterium strain isolated with metallic iron as electron donor enhances iron corrosion by a similar mechanism as Sporomusa sphaeroides.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiy222}, pmid = {30445447}, issn = {1574-6941}, abstract = {Sporomusa sphaeroides related strains are to date the only homoacetogens known to increase metallic iron corrosion. The goal of this work was to isolate additional homoacetogenic bacteria capable of using Fe(0) as electron donor and to explore their extracellular electron transfer mechanism. Enrichments were started from anoxic corrosion products and yielded Acetobacterium as main homoacetogenic genus. Isolations were performed with a new procedure using plates with a Fe(0) powder top layer. An Acetobacterium strain, closely related to A. malicum and A. wieringae, was isolated, in addition to a S. sphaeroides strain. The Acetobacterium isolate significantly increased Fe(0) corrosion ((1.44 ± 0.16)-fold) compared to abiotic controls. The increase of corrosion by type strains ranged from (1.28 ± 0.13)-fold for A. woodii to (2.03 ± 0.22)-fold for S. sphaeroides. Hydrogen mediated the electron uptake from Fe(0) by the acetogenic isolates and tested type strains. Exchange of the medium and SEM imaging suggested that cells were attached to Fe(0). The corrosion enhancement mechanism is for all tested strains likely related to free extracellular components catalyzing hydrogen formation on the Fe(0) surface, or to the maintenance of low hydrogen concentrations on the Fe(0) surface by attached cells thereby thermodynamically favoring hydrogen formation.}, }
@article {pmid30443991, year = {2018}, author = {Schneider, S and Schintlmeister, A and Becana, M and Wagner, M and Woebken, D and Wienkoop, S}, title = {Sulfate is transported at significant rates through the symbiosome membrane and is crucial for nitrogenase biosynthesis.}, journal = {Plant, cell &amp; environment}, volume = {}, number = {}, pages = {}, doi = {10.1111/pce.13481}, pmid = {30443991}, issn = {1365-3040}, abstract = {Legume-rhizobia symbioses play a major role in food production for an ever growing human population. In this symbiosis, dinitrogen is reduced ('fixed') to ammonia by the rhizobial nitrogenase enzyme complex and is secreted to the plant host cells, while dicarboxylic acids derived from photosynthetically-produced sucrose are transported into the symbiosomes and serve as respiratory substrates for the bacteroids. The symbiosome membrane contains high levels of SST1 protein, a sulfate transporter. Sulfate is an essential nutrient for all living organisms, but its importance for symbiotic nitrogen fixation and nodule metabolism has long been underestimated. Using chemical imaging, we demonstrate that the bacteroids take up 20-fold more sulfate than the nodule host cells. Furthermore, we show that nitrogenase biosynthesis relies on high levels of imported sulfate, making sulfur as essential as carbon for the regulation and functioning of symbiotic nitrogen fixation. Our findings thus establish the importance of sulfate and its active transport for the plant-microbe interaction that is most relevant for agriculture and soil fertility. This article provides a comprehensive explanation for the importance of the nodule specific sulfate transporter (SST1) and the role of sulfate by dissecting the sulfur distribution across the nodule tissue and directly linking sulfate incorporation to nitrogenase biosynthesis.}, }
@article {pmid30443603, year = {2018}, author = {Paver, SF and Muratore, D and Newton, RJ and Coleman, ML}, title = {Reevaluating the Salty Divide: Phylogenetic Specificity of Transitions between Marine and Freshwater Systems.}, journal = {mSystems}, volume = {3}, number = {6}, pages = {}, doi = {10.1128/mSystems.00232-18}, pmid = {30443603}, issn = {2379-5077}, abstract = {Marine and freshwater microbial communities are phylogenetically distinct, and transitions between habitat types are thought to be infrequent. We compared the phylogenetic diversity of marine and freshwater microorganisms and identified specific lineages exhibiting notably high or low similarity between marine and freshwater ecosystems using a meta-analysis of 16S rRNA gene tag-sequencing data sets. As expected, marine and freshwater microbial communities differed in the relative abundance of major phyla and contained habitat-specific lineages. At the same time, and contrary to expectations, many shared taxa were observed in both habitats. Based on several metrics, we found that Gammaproteobacteria, Alphaproteobacteria, Bacteroidetes, and Betaproteobacteria contained the highest number of closely related marine and freshwater sequences, suggesting comparatively recent habitat transitions in these groups. Using the abundant alphaproteobacterial group SAR11 as an example, we found evidence that new lineages, beyond the recognized LD12 clade, are detected in freshwater at low but reproducible abundances; this evidence extends beyond the 16S rRNA locus to core genes throughout the genome. Our results suggest that shared taxa are numerous, but tend to occur sporadically and at low relative abundance in one habitat type, leading to an underestimation of transition frequency between marine and freshwater habitats. Rare taxa with abundances near or below detection, including lineages that appear to have crossed the salty divide relatively recently, may possess adaptations enabling them to exploit opportunities for niche expansion when environments are disturbed or conditions change. IMPORTANCE The distribution of microbial diversity across environments yields insight into processes that create and maintain this diversity as well as potential to infer how communities will respond to future environmental changes. We integrated data sets from dozens of freshwater lake and marine samples to compare diversity across open water habitats differing in salinity. Our novel combination of sequence-based approaches revealed lineages that likely experienced a recent transition across habitat types. These taxa are promising targets for studying physiological constraints on salinity tolerance. Our findings contribute to understanding the ecological and evolutionary controls on microbial distributions, and open up new questions regarding the plasticity and adaptability of particular lineages.}, }
@article {pmid30442907, year = {2018}, author = {Zhou, W and Chow, KH and Fleming, E and Oh, J}, title = {Selective colonization ability of human fecal microbes in different mouse gut environments.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-018-0312-9}, pmid = {30442907}, issn = {1751-7370}, support = {DP2 GM126893/GM/NIGMS NIH HHS/United States ; K22 AI119231/AI/NIAID NIH HHS/United States ; 1 DP2 GM126893-01//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; ACS-RSG-16-255-01-MPC//American Cancer Society (American Cancer Society, Inc.)/ ; }, abstract = {Mammalian hosts constantly interact with diverse exogenous microbes, but only a subset of the microbes manage to colonize due to selective colonization resistance exerted by host genetic factors as well as the native microbiota of the host. An important question in microbial ecology and medical science is if such colonization resistance can discriminate closely related microbial species, or even closely related strains of the same species. Using human-mouse fecal microbiota transplantation and metagenomic shotgun sequencing, we reconstructed colonization patterns of human fecal microbes in mice with different genotypes (C57BL6/J vs. NSG) and with or without an intact gut microbiota. We found that mouse genotypes and the native mouse gut microbiota both exerted different selective pressures on exogenous colonizers: human fecal Bacteroides successfully established in the mice gut, however, different species of Bacteroides selectively enriched under different gut conditions, potentially due to a multitude of functional differences, ranging from versatility in nutrient acquisition to stress responses. Additionally, different clades of Bacteroides cellulosilyticus strains were selectively enriched in different gut conditions, suggesting that the fitness of conspecific microbial strains in a novel host environment could differ.}, }
@article {pmid30442070, year = {2018}, author = {Barnett, JA and Gibson, DL}, title = {H2Oh No! The importance of reporting your water source in your in vivo microbiome studies.}, journal = {Gut microbes}, volume = {}, number = {}, pages = {1-9}, doi = {10.1080/19490976.2018.1539599}, pmid = {30442070}, issn = {1949-0984}, abstract = {Water is a fundamental part of any in vivo microbiome experiment however, it is also one of the most overlooked and underreported variables within the literature. Currently there is no established standard for drinking water quality set by the Canadian Council on Animal Care. Most water treatment methods focus on inhibiting bacterial growth within the water while prolonging the shelf-life of bottles once poured. When reviewing the literature, it is clear that some water treatment methods, such as water acidification, alter the gut microbiome of experimental animals resulting in dramatic differences in disease phenotype progression. Furthermore, The Jackson Lab, one of the world's leading animal vendors, provides acidified water to their in-house animals and is often cited in the literature as having a dramatically different gut microbiome than animals acquired from either Charles River or Taconic. While we recognize that it is impossible to standardize water across all animal facilities currently conducting microbiome research, we hope that by drawing attention to the issue in this commentary, researchers will consider water source as an experimental variable and report their own water sources to facilitate experimental reproducibility. Moreover, researchers should be cognisant of potential phenotypic differences observed between commercial animal vendors due to changes in the gut microbiome as a result of various sources of water used.}, }
@article {pmid30430196, year = {2018}, author = {Wynants, E and Frooninckx, L and Crauwels, S and Verreth, C and De Smet, J and Sandrock, C and Wohlfahrt, J and Van Schelt, J and Depraetere, S and Lievens, B and Van Miert, S and Claes, J and Van Campenhout, L}, title = {Assessing the Microbiota of Black Soldier Fly Larvae (Hermetia illucens) Reared on Organic Waste Streams on Four Different Locations at Laboratory and Large Scale.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1286-x}, pmid = {30430196}, issn = {1432-184X}, support = {RT 15/9 EDINCO//FOD Volksgezondheid, Veiligheid van de Voedselketen en Leefmilieu/ ; }, abstract = {This study aimed to gain insight into the microbial quality, safety and bacterial community composition of black soldier fly larvae (Hermetia illucens) reared at different facilities on a variety of organic waste streams. For seven rearing cycles, both on laboratory-scale and in large-scale facilities at several locations, the microbiota of the larvae was studied. Also samples of the substrate used and the residue (= leftover substrate after rearing, existing of non-consumed substrate, exuviae and faeces) were investigated. Depending on the sample, it was subjected to plate counting, Illumina Miseq sequencing and/or detection of specific food pathogens. The results revealed that the substrates applied at the various locations differed substantially in microbial numbers as well as in the bacterial community composition. Furthermore, little similarity was observed between the microbiota of the substrate and that of the larvae reared on that substrate. Despite substantial differences between the microbiota of larvae reared at several locations, 48 species-level operational taxonomic units (OTUs) were shared by all larvae, among which most belonged to the phyla Firmicutes and Proteobacteria. Although the substrate is assumed to be an important source of bacteria, our results suggest that a variety of supposedly interacting factors-both abiotic and biotic-are likely to affect the microbiota in the larvae. In some larvae and/or residue samples, potential foodborne pathogens such as Salmonella and Bacillus cereus were detected, emphasising that decontamination technologies are required when the larvae are used in feed, just as for other feed ingredients, or eventually in food.}, }
@article {pmid30429840, year = {2018}, author = {Mas-Carrió, E and Dini-Andreote, F and Brossi, MJL and Salles, JF and Olff, H}, title = {Organic Amendment Under Increasing Agricultural Intensification: Effects on Soil Bacterial Communities and Plant Productivity.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2612}, doi = {10.3389/fmicb.2018.02612}, pmid = {30429840}, issn = {1664-302X}, abstract = {The soil microbiome is a complex living network that plays essential roles in agricultural systems, regardless of the level of intensification. However, the effects of agricultural management on the soil microbiome and the association with plant productivity remain largely unclear. Here, we studied the responses of three soil systems displaying distinct levels of agriculture intensiveness (i.e., natural, organic, and conventional soil management regimes) to experimentally manipulated organic farming amendments (i.e., dung and earthworms). We aimed at (i) identifying the effect on plant productivity and (ii) elucidating the degree of shifts in bacterial communities in response to the applied organic amendments. We found plant productivity to be lower with increasing agricultural intensification. Bacterial communities shifted distinctively for each soil management regime to the organic amendments applied. In brief, greater changes were observed in the Conventional management comparatively to the Organic and Natural management, an effect largely driven by dung addition. Moreover, we found evidence that the level of agricultural intensiveness also affects the timespan for these shifts. For instance, while the Natural system reached a relatively stable community composition before the end of the experiment, treatments on the conventional soil management regime did not. Random forest analyses further revealed an increasing impact of introduced taxa from dung addition aligned with increasing agricultural intensification. These analyses suggested that earthworms regulate the introduction of species from dung into the soil bacterial community. Collectively, our results contribute to a better understanding of the outcomes of organic amendments on soils under distinct levels of agriculture intensiveness, with implications for further development in soil restorations practices.}, }
@article {pmid30429832, year = {2018}, author = {Bruno, A and Sandionigi, A and Bernasconi, M and Panio, A and Labra, M and Casiraghi, M}, title = {Changes in the Drinking Water Microbiome: Effects of Water Treatments Along the Flow of Two Drinking Water Treatment Plants in a Urbanized Area, Milan (Italy).}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2557}, doi = {10.3389/fmicb.2018.02557}, pmid = {30429832}, issn = {1664-302X}, abstract = {While safe and of high quality, drinking water can host an astounding biodiversity of microorganisms, dismantling the belief of its &quot;biological simplicity.&quot; During the very few years, we are witnessing an exponential growth in scientific publications, exploring the ecology hidden in drinking water treatment plants (DWTPs) and drinking water distribution system (DWDS). We focused on what happens to the microbial communities from source water (groundwater) throughout the main steps of the potabilization process of a DWTP, located in an urbanized area in Northern Italy. Samples were processed by a stringent water filtration to retain even the smallest environmental bacteria and then analyzed with High-Throughput DNA Sequencing (HTS) techniques. We showed that carbon filters harbored a microbial community seeding and shaping water microbiota downstream, introducing a significant variation on incoming (groundwater) microbial community. Chlorination did not instantly affect the altered microbiota. We were also able to correctly predict (through machine learning analysis) samples belonging to groundwater (overall accuracy was 0.71), but the assignation was not reliable with carbon filter samples, which were incorrectly predicted as chlorination samples. The presence and abundance of specific microorganisms allowed us to hypothesize their role as indicators. In particular, Candidatus Adlerbacteria (Parcubacteria), together with microorganisms belonging to Alphaproteobacteria and Gammaproteobacteria, characterized treated water, but not raw water. An exception, confirming our hypothesis, is given by the samples downstream the filters renewal, which had a composition resembling groundwater. Volatility analysis illustrated how carbon filters represented an ecosystem that is stable over time, probably bearing the environmental conditions that promote the survival and growth of this peculiar microbial community.}, }
@article {pmid30429514, year = {2018}, author = {De Vrieze, J and Ijaz, UZ and Saunders, AM and Theuerl, S}, title = {Terminal restriction fragment length polymorphism is an &quot;old school&quot; reliable technique for swift microbial community screening in anaerobic digestion.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {16818}, doi = {10.1038/s41598-018-34921-7}, pmid = {30429514}, issn = {2045-2322}, abstract = {The microbial community in anaerobic digestion has been analysed through microbial fingerprinting techniques, such as terminal restriction fragment length polymorphism (TRFLP), for decades. In the last decade, high-throughput 16S rRNA gene amplicon sequencing has replaced these techniques, but the time-consuming and complex nature of high-throughput techniques is a potential bottleneck for full-scale anaerobic digestion application, when monitoring community dynamics. Here, the bacterial and archaeal TRFLP profiles were compared with 16S rRNA gene amplicon profiles (Illumina platform) of 25 full-scale anaerobic digestion plants. The α-diversity analysis revealed a higher richness based on Illumina data, compared with the TRFLP data. This coincided with a clear difference in community organisation, Pareto distribution, and co-occurrence network statistics, i.e., betweenness centrality and normalised degree. The β-diversity analysis showed a similar clustering profile for the Illumina, bacterial TRFLP and archaeal TRFLP data, based on different distance measures and independent of phylogenetic identification, with pH and temperature as the two key operational parameters determining microbial community composition. The combined knowledge of temporal dynamics and projected clustering in the β-diversity profile, based on the TRFLP data, distinctly showed that TRFLP is a reliable technique for swift microbial community dynamics screening in full-scale anaerobic digestion plants.}, }
@article {pmid30427665, year = {2018}, author = {Dang, H and Kanitkar, YH and Stedtfeld, RD and Hatzinger, PB and Hashsham, SA and Cupples, AM}, title = {Abundance of Chlorinated Solvent and 1,4-Dioxane Degrading Microorganisms at Five Chlorinated Solvent Contaminated Sites Determined via Shotgun Sequencing.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.8b04895}, pmid = {30427665}, issn = {1520-5851}, abstract = {Shotgun sequencing was used for the quantification of taxonomic and functional biomarkers associated with chlorinated solvent bioremediation in 20 groundwater samples (five sites), following bioaugmentation with SDC-9. The analysis determined the abundance of (1) genera associated with chlorinated solvent degradation, (2) reductive dehalogenase (RDases) genes, (3) genes associated with 1,4-dioxane removal, (4) genes associated with aerobic chlorinated solvent degradation, and (5) D. mccartyi genes associated with hydrogen and corrinoid metabolism. The taxonomic analysis revealed numerous genera previously linked to chlorinated solvent degradation, including Dehalococcoides, Desulfitobacterium, and Dehalogenimonas. The functional gene analysis indicated vcrA and tceA from D. mccartyi were the RDases with the highest relative abundance. Reads aligning with both aerobic and anaerobic biomarkers were observed across all sites. Aerobic solvent degradation genes, etnC or etnE, were detected in at least one sample from each site, as were pmoA and mmoX. The most abundant 1,4-dioxane biomarker detected was Methylosinus trichosporium OB3b mmoX. Reads aligning to thmA or Pseudonocardia were not found. The work illustrates the importance of shotgun sequencing to provide a more complete picture of the functional abilities of microbial communities. The approach is advantageous over current methods because an unlimited number of functional genes can be quantified.}, }
@article {pmid30426401, year = {2018}, author = {Ver Heul, A and Planer, J and Kau, AL}, title = {The Human Microbiota and Asthma.}, journal = {Clinical reviews in allergy &amp; immunology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s12016-018-8719-7}, pmid = {30426401}, issn = {1559-0267}, support = {K08AI113184//National Institute of Allergy and Infectious Diseases (US)/ ; 5T32DK077653-27//National Institute of Diabetes and Digestive and Kidney Diseases/ ; Faculty Development Award//AAAAI Foundation/ ; }, abstract = {Over the last few decades, advances in our understanding of microbial ecology have allowed us to appreciate the important role of microbial communities in maintaining human health. While much of this research has focused on gut microbes, microbial communities in other body sites and from the environment are increasingly recognized in human disease. Here, we discuss recent advances in our understanding of host-microbiota interactions in the development and manifestation of asthma focusing on three distinct microbial compartments. First, environmental microbes originating from house dust, pets, and farm animals have been linked to asthma pathogenesis, which is often connected to their production of bioactive molecules such as lipopolysaccharide. Second, respiratory microbial communities, including newly appreciated populations of microbes in the lung have been associated with allergic airway inflammation. Current evidence suggests that the presence of particular microbes, especially Streptococcus, Haemophilus, and Morexella species within the airway may shape local immune responses and alter the severity and manifestations of airway inflammation. Third, the gut microbiota has been implicated in both experimental models and clinical studies in predisposing to asthma. There appears to be a &quot;critical window&quot; of colonization that occurs during early infancy in which gut microbial communities shape immune maturation and confer susceptibility to allergic airway inflammation. The mechanisms by which gut microbial communities influence lung immune responses and physiology, the &quot;gut-lung axis,&quot; are still being defined but include the altered differentiation of immune cell populations important in asthma and the local production of metabolites that affect distal sites. Together, these findings suggest an intimate association of microbial communities with host immune development and the development of allergic airway inflammation. Improved understanding of these relationships raises the possibility of microbiota-directed therapies to improve or prevent asthma.}, }
@article {pmid30425147, year = {2018}, author = {Su, X and Jing, G and McDonald, D and Wang, H and Wang, Z and Gonzalez, A and Sun, Z and Huang, S and Navas, J and Knight, R and Xu, J}, title = {Identifying and Predicting Novelty in Microbiome Studies.}, journal = {mBio}, volume = {9}, number = {6}, pages = {}, doi = {10.1128/mBio.02099-18}, pmid = {30425147}, issn = {2150-7511}, abstract = {With the expansion of microbiome sequencing globally, a key challenge is to relate new microbiome samples to the existing space of microbiome samples. Here, we present Microbiome Search Engine (MSE), which enables the rapid search of query microbiome samples against a large, well-curated reference microbiome database organized by taxonomic similarity at the whole-microbiome level. Tracking the microbiome novelty score (MNS) over 8 years of microbiome depositions based on searching in more than 100,000 global 16S rRNA gene amplicon samples, we detected that the structural novelty of human microbiomes is approaching saturation and likely bounded, whereas that in environmental habitats remains 5 times higher. Via the microbiome focus index (MFI), which is derived from the MNS and microbiome attention score (MAS), we objectively track and compare the structural-novelty and attracted-attention scores of individual microbiome samples and projects, and we predict future trends in the field. For example, marine and indoor environments and mother-baby interactions are likely to receive disproportionate additional attention based on recent trends. Therefore, MNS, MAS, and MFI are proposed &quot;alt-metrics&quot; for evaluating a microbiome project or prospective developments in the microbiome field, both of which are done in the context of existing microbiome big data.IMPORTANCE We introduce two concepts to quantify the novelty of a microbiome. The first, the microbiome novelty score (MNS), allows identification of microbiomes that are especially different from what is already sequenced. The second, the microbiome attention score (MAS), allows identification of microbiomes that have many close neighbors, implying that considerable scientific attention is devoted to their study. By computing a microbiome focus index based on the MNS and MAS, we objectively track and compare the novelty and attention scores of individual microbiome samples and projects over time and predict future trends in the field; i.e., we work toward yielding fundamentally new microbiomes rather than filling in the details. Therefore, MNS, MAS, and MFI can serve as &quot;alt-metrics&quot; for evaluating a microbiome project or prospective developments in the microbiome field, both of which are done in the context of existing microbiome big data.}, }
@article {pmid30423502, year = {2018}, author = {Ntagia, E and Fiset, E and da Silva Lima, L and Pikaar, I and Zhang, X and Jeremiasse, AW and Prévoteau, A and Rabaey, K}, title = {Anode materials for sulfide oxidation in alkaline wastewater: An activity and stability performance comparison.}, journal = {Water research}, volume = {149}, number = {}, pages = {111-119}, doi = {10.1016/j.watres.2018.11.004}, pmid = {30423502}, issn = {1879-2448}, abstract = {Electrochemical sulfide removal can be attractive as a zero-chemical-input approach for treatment of waste streams such as spent caustics coupled to caustic recovery. A key concern is possible decline in catalytic activity, due to passivation from deposited elemental sulfur (S0) on the anode surface and stability limitation, due to sulfide oxidation under highly alkaline conditions. In this study, six commercially available electrode materials (Ir Mixed Metal Oxide (MMO), Ru MMO, Pt/IrOx, Pt, PbOx and TiO2/IrTaO2 coated titanium-based electrodes) were tested to investigate the impact of the electrocatalyst on the process efficiency in terms of sulfide removal and final product of sulfide oxidation, as well as to determine the stability of the electrocatalyst under high sulfide concentrations (50 mM Na2S) and high alkalinity (pH > 12). Short-term experiments showed that the catalyst type impacts the anode potential and the sulfide oxidation reaction products. Longer-term experiments under current densities up to 200 A m-2 showed a high differentiation in stability performance among the catalysts. Ru MMO was the most active towards sulfide oxidation with a coulombic efficiency of 63.2 ± 0.5% at an average anode potential of 0.92 ± 0.17 V vs SHE. Ir MMO was the most stable, preserving 100% of its original catalyst loading during the tests. The results demonstrated that Ru MMO and Ir MMO were the most suitable electrode materials for sulfide oxidation under highly alkaline conditions, while the need for establishing a good trade-off between activity, stability and cost still persists.}, }
@article {pmid30423115, year = {2018}, author = {Romano, S and Ansorge, R}, title = {Scientific communication strategies of microbiologists in the era of social media.}, journal = {FEMS microbiology letters}, volume = {365}, number = {23}, pages = {}, doi = {10.1093/femsle/fny264}, pmid = {30423115}, issn = {1574-6968}, abstract = {Over the last decades, the world of communication underwent drastic changes, and internet and social media emerged as essential vehicles for exchanging information. Following these trends, it is important that scientists adapt to changes and adopt optimal strategies to communicate with colleagues, lay people and institutions. We conducted an online survey to investigate the communication strategies of microbiologists and their colleagues from other disciplines. We collected data from 527 scholars from 57 countries, with ∼42% of them being microbiologists. We focused particularly on social media and found that >80% of participants used them for work, and that ∼50% of interviewed actively shared and gathered scientific contents from social media. Compared to colleagues from other fields, microbiologists were less averse to use social media for work and were also less accustomed to use pre-prints as a source and vehicle of information. However, a large proportion of microbiologists declared to have planned pre-print publications in the future. Surprisingly, our data revealed that age is a poor predictor of social media usage, but it is strongly associated with the type of social media used, the activity undertaken on them and the attitude towards pre-print publications. Considering the kaleidoscopic variety of scientific communication tools, our data might help to optimize the scientific promotion strategies among microbiologists.}, }
@article {pmid30421114, year = {2018}, author = {Chung, YA and Jumpponen, A and Rudgers, JA}, title = {Divergence in Diversity and Composition of Root-Associated Fungi Between Greenhouse and Field Studies in a Semiarid Grassland.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1277-y}, pmid = {30421114}, issn = {1432-184X}, support = {1601210//Division of Environmental Biology/ ; 1456955//Division of Environmental Biology/ ; 1748133//National Science Foundation/ ; 1440478//National Science Foundation/ ; }, abstract = {Investigations of plant-soil feedbacks (PSF) and plant-microbe interactions often rely exclusively on greenhouse experiments, yet we have little understanding of how, and when, results can be extrapolated to explain phenomena in nature. A systematic comparison of microbial communities using the same host species across study environments can inform the generalizability of such experiments. We used Illumina MiSeq sequencing to characterize the root-associated fungi of two foundation grasses from a greenhouse PSF experiment, a field PSF experiment, field monoculture stands, and naturally occurring resident plants in the field. A core community consisting < 10% of total fungal OTU richness but > 50% of total sequence abundance occurred in plants from all study types, demonstrating the ability of field and greenhouse experiments to capture the dominant component of natural communities. Fungal communities were plant species-specific across the study types, with the core community showing stronger host specificity than peripheral taxa. Roots from the greenhouse and field PSF experiments had lower among sample variability in community composition and higher diversity than those from naturally occurring, or planted monoculture plants from the field. Core and total fungal composition differed substantially across study types, and dissimilarity between fungal communities did not predict plant-soil feedbacks measured in experiments. These results suggest that rhizobiome assembly mechanisms in nature differ from the dynamics of short-term, inoculation studies. Our results validate the efficacy of common PSF experiment designs to test soil inoculum effects, and highlight the challenges of scaling the underlying microbial mechanisms of plant responses from whole-community inoculation experiments to natural ecosystems.}, }
@article {pmid30421109, year = {2018}, author = {La, A and Perré, P and Taidi, B}, title = {Process for symbiotic culture of Saccharomyces cerevisiae and Chlorella vulgaris for in situ CO2 mitigation.}, journal = {Applied microbiology and biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00253-018-9506-3}, pmid = {30421109}, issn = {1432-0614}, abstract = {Industrial biotechnology relies heavily on fermentation processes that release considerable amounts of CO2. Apart from the fact that this CO2 represents a considerable part of the organic substrate, it has a negative impact on the environment. Microalgae cultures have been suggested as potential means of capturing the CO2 with further applications in high-value compounds production or directly for feed applications. We developed a sustainable process based on a mixed co-dominant culture of Saccharomyces cerevisiae and Chlorella vulgaris where the CO2 production and utilization controlled the microbial ecology of the culture. By mixing yeast and microalga in the same culture, the CO2 is produced in dissolved form and is available to the microalga avoiding degassing and dissolution phenomena. With this process, the CO2 production and utilization rates were balanced and a mutual symbiosis between the yeast and the microalga was set up in the culture. In this study, the reutilization of CO2 and growth of C. vulgaris was demonstrated. The two organism populations were balanced at approximately 20 × 106 cells ml-1 and almost all the CO2 produced by yeast was reutilized by microalga within 168 h of culture. The C. vulgaris inoculum preparation played a key role in establishing co-dominance of the two organisms. Other key factors in establishing symbiosis were the inoculum ratio of the two organisms and the growth medium design. A new method allowed the independent enumeration of each organism in a mixed culture. This study could provide a basis for the development of green processes of low environmental impact.}, }
@article {pmid30419469, year = {2018}, author = {Miao, Y and Johnson, NW and Gedalanga, PB and Adamson, D and Newell, C and Mahendra, S}, title = {Response and recovery of microbial communities subjected to oxidative and biological treatments of 1,4-dioxane and co-contaminants.}, journal = {Water research}, volume = {149}, number = {}, pages = {74-85}, doi = {10.1016/j.watres.2018.10.070}, pmid = {30419469}, issn = {1879-2448}, abstract = {Microbial community dynamics were characterized following combined oxidation and biodegradation treatment trains for mixtures of 1,4-dioxane and chlorinated volatile organic compounds (CVOCs) in laboratory microcosms. Bioremediation is generally inhibited by co-contaminate CVOCs; with only a few specific bacterial taxa reported to metabolize or cometabolize 1,4-dioxane being unaffected. Chemical oxidation by hydrogen peroxide (H2O2) as a non-selective treatment demonstrated 50-80% 1,4-dioxane removal regardless of the initial CVOC concentrations. Post-oxidation bioaugmentation with 1,4-dioxane metabolizer Pseudonocardia dioxanivorans CB1190 removed the remaining 1,4-dioxane. The intrinsic microbial population, biodiversity, richness, and biomarker gene abundances decreased immediately after the brief oxidation phase, but recovery of cultivable microbiomes and a more diverse community were observed during the subsequent 9-week biodegradation phase. Results generated from the Illumina Miseq sequencing and bioinformatics analyses established that generally oxidative stress tolerant genus Ralstonia was abundant after the oxidation step, and Cupriavidus, Pseudolabrys, Afipia, and Sphingomonas were identified as dominant genera after aerobic incubation. Multidimensional analysis elucidated the separation of microbial populations as a function of time under all conditions, suggesting that temporal succession is a determining factor that is independent of 1,4-dioxane and CVOCs mixtures. Network analysis highlighted the potential interspecies competition or commensalism, and dynamics of microbiomes during the biodegradation phase, in line with the shifts of predominant genera and various developing directions during different steps of the treatment train. Collectively, this study demonstrated that chemical oxidation followed by bioaugmentation is effective for treating 1,4-dioxane, even in the presence of high levels of CVOC mixtures and residual peroxide, a disinfectant, and enhanced our understanding of microbial ecological impacts of the treatment train. These results will be valuable for predicting treatment synergies that lead to cost savings and improved remedial outcomes in short-term active remediation as well as long-term changes to the environmental microbial communities.}, }
@article {pmid30418580, year = {2018}, author = {Lekeux, G and Crowet, JM and Nouet, C and Joris, M and Jadoul, A and Bosman, B and Carnol, M and Motte, P and Lins, L and Galleni, M and Hanikenne, M}, title = {Homology modeling and in vivo functional characterization of the zinc permeation pathway in a heavy metal P-type ATPase.}, journal = {Journal of experimental botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/jxb/ery353}, pmid = {30418580}, issn = {1460-2431}, abstract = {The P1B ATPase heavy metal ATPase 4 (HMA4) is responsible for zinc and cadmium translocation from roots to shoots in Arabidopsis thaliana. It couples ATP hydrolysis to cytosolic domain movements, enabling metal transport across the membrane. The detailed mechanism of metal permeation by HMA4 through the membrane remains elusive. Here, homology modeling of the HMA4 transmembrane region was conducted based on the crystal structure of a ZntA bacterial homolog. The analysis highlighted amino acids forming a metal permeation pathway, whose importance was subsequently investigated functionally through mutagenesis and complementation experiments in plants. Although the zinc pathway displayed overall conservation among the two proteins, significant differences were observed, especially in the entrance area with altered electronegativity and the presence of a ionic interaction/hydrogen bond network. The analysis also newly identified amino acids whose mutation results in total or partial loss of the protein function. In addition, comparison of zinc and cadmium accumulation in shoots of A. thaliana complemented lines revealed a number of HMA4 mutants exhibiting different abilities in zinc and cadmium translocation. These observations could be instrumental to design low cadmium-accumulating crops, hence decreasing human cadmium exposure.}, }
@article {pmid30418043, year = {2018}, author = {Muleviciene, A and D'Amico, F and Turroni, S and Candela, M and Jankauskiene, A}, title = {Iron deficiency anemia-related gut microbiota dysbiosis in infants and young children: A pilot study.}, journal = {Acta microbiologica et immunologica Hungarica}, volume = {}, number = {}, pages = {1-14}, doi = {10.1556/030.65.2018.045}, pmid = {30418043}, issn = {1217-8950}, abstract = {Nutritional iron deficiency (ID) causes not only anemia but also malfunction of the entire human organism. Recently, a role of the gut microbiota has been hypothesized, but limited data are available especially in infants. Here, we performed a pilot study to explore the gut microbiota in 10 patients with iron deficiency anemia (IDA) and 10 healthy controls aged 6-34 months. Fresh stool samples were collected from diapers, and the fecal microbiota was profiled by next-generation sequencing of the V3-V4 hypervariable region of the 16S rRNA gene. Except for diet diversity, the breastfeeding status at the enrollment, the exclusive breastfeeding duration, and the introduction of complementary foods did not differ between groups. Distinct microbial signatures were found in IDA patients, with increased relative abundance of Enterobacteriaceae (mean relative abundance, patients vs. controls, 4.4% vs. 3.0%) and Veillonellaceae (13.7% vs. 3.6%), and reduced abundance of Coriobacteriaceae (3.5% vs. 8.8%) compared to healthy controls. A decreased Bifidobacteriaceae/Enterobacteriaceae ratio was observed in IDA patients. Notwithstanding the low sample size, our data highlight microbiota dysbalance in IDA worth for further investigations, aimed at unraveling the ID impact on the microbiome trajectory in early life, and the possible long-term consequences.}, }
@article {pmid30418019, year = {2018}, author = {Shan, Y and Harms, H and Wick, LY}, title = {Electric Field Effects on Bacterial Deposition and Transport in Porous Media.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.8b03648}, pmid = {30418019}, issn = {1520-5851}, abstract = {Bacterial deposition and transport are key to microbial ecology and biotechnological applications. We therefore tested whether electrokinetic forces (electroosmotic shear force (FEOF), electrophoretic drag force (FEP)) acting on bacteria may be used to control bacterial deposition during transport in laboratory percolation columns exposed to external direct current (DC) electric fields. For different bacteria, yet similar experimental conditions we observed that DC fields either enhanced or reduced bacterial deposition efficiencies (α) relative to DC-free controls. By calculating the DLVO force of colloidal interactions, FEOF, FEP, and the hydraulic shear forces acting on single cells at a collector surface we found that DC-induced changes of α correlated to | FEOF| to | FEP| ratios: If | FEOF| > | FEP|, α was clearly increased and if | FEOF| < | FEP| α was clearly decreased. Our findings allow for better prediction of the forces acting on a bacterium at collector surface and, hence, the electrokinetic control of microbial deposition in natural and manmade ecosystems.}, }
@article {pmid30417222, year = {2018}, author = {Zhang, FG and Bell, T and Zhang, QG}, title = {Experimental Testing of Dispersal Limitation in Soil Bacterial Communities with a Propagule Addition Approach.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1284-z}, pmid = {30417222}, issn = {1432-184X}, support = {31700434//National Natural Science Foundation of China/ ; 31725006 and 31670376//National Natural Science Foundation of China/ ; }, abstract = {The role of dispersal in the assembly of microbial communities remains contentious. This study tested the importance of dispersal limitation for the structuring of local soil bacterial communities using an experimental approach of propagule addition. Microbes extracted from soil pooled from samples collected at 20 localities across ~ 400 km in a temperate steppe were added to microcosms of local soils at three sites; the microcosms were then incubated in situ for 3 months. We then assessed the composition and diversity of bacterial taxa in the soils using 16S rRNA gene amplicon sequencing. The addition of the regional microbial pool did not cause significant changes in the overall composition or diversity of the total bacterial community, although a very small number of individual taxa may have been affected by the addition treatment. Our results suggest a negligible role of dispersal limitation in structuring soil bacterial communities in our study area.}, }
@article {pmid30417111, year = {2018}, author = {Minich, JJ and Humphrey, G and Benitez, RAS and Sanders, J and Swafford, A and Allen, EE and Knight, R}, title = {High-Throughput Miniaturized 16S rRNA Amplicon Library Preparation Reduces Costs while Preserving Microbiome Integrity.}, journal = {mSystems}, volume = {3}, number = {6}, pages = {}, doi = {10.1128/mSystems.00166-18}, pmid = {30417111}, issn = {2379-5077}, abstract = {Next-generation sequencing technologies have enabled many advances across biology, with microbial ecology benefiting primarily through expanded sample sizes. Although the cost of running sequencing instruments has decreased substantially over time, the price of library preparation methods has largely remained unchanged. In this study, we developed a low-cost miniaturized (5-µl volume) high-throughput (384-sample) amplicon library preparation method with the Echo 550 acoustic liquid handler. Our method reduces costs of library preparation to $1.42 per sample, a 58% reduction compared to existing automated methods and a 21-fold reduction from commercial kits, without compromising sequencing success or distorting the microbial community composition analysis. We further validated the optimized method by sampling five body sites from 46 Pacific chub mackerel fish caught across 16 sampling events over seven months from the Scripps Institution of Oceanography pier in La Jolla, CA. Fish microbiome samples were processed with the miniaturized 5-µl reaction volume with 0.2 µl of genomic DNA (gDNA) and the standard 25-µl reaction volume with 1 µl of gDNA. Between the two methods, alpha diversity was highly correlated (R2 > 0.95), while distances of technical replicates were much lower than within-body-site variation (P < 0.0001), further validating the method. The cost savings of implementing the miniaturized library preparation (going from triplicate 25-µl reactions to triplicate 5-µl reactions) are large enough to cover a MiSeq sequencing run for 768 samples while preserving accurate microbiome measurements. IMPORTANCE Reduced costs of sequencing have tremendously impacted the field of microbial ecology, allowing scientists to design more studies with larger sample sizes that often exceed 10,000 samples. Library preparation costs have not kept pace with sequencing prices, although automated liquid handling robots provide a unique opportunity to bridge this gap while also decreasing human error. Here, we take advantage of an acoustic liquid handling robot to develop a high-throughput miniaturized library preparation method of a highly cited and broadly used 16S rRNA gene amplicon reaction. We evaluate the potential negative effects of reducing the PCR volume along with varying the amount of gDNA going into the reaction. Our optimized method reduces sample-processing costs while continuing to generate a high-quality microbiome readout that is indistinguishable from the original method.}, }
@article {pmid30413836, year = {2018}, author = {Villegas-Plazas, M and Wos-Oxley, ML and Sanchez, JA and Pieper, DH and Thomas, OP and Junca, H}, title = {Variations in Microbial Diversity and Metabolite Profiles of the Tropical Marine Sponge Xestospongia muta with Season and Depth.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1285-y}, pmid = {30413836}, issn = {1432-184X}, support = {KBBE-2009-245226//MAGICPAH/ ; 652-2014//EcosNord-Colciencias/ ; JI-2012//Jóven Investigador - Colciencias/ ; MSc scholarship//Universidad de los Andes/ ; }, abstract = {Xestospongia muta is among the most emblematic sponge species inhabiting coral reefs of the Caribbean Sea. Besides being the largest sponge species growing in the Caribbean, it is also known to produce secondary metabolites. This study aimed to assess the effect of depth and season on the symbiotic bacterial dynamics and major metabolite profiles of specimens of X. muta thriving in a tropical marine biome (Portobelo Bay, Panamá), which allow us to determine whether variability patterns are similar to those reported for subtropical latitudes. The bacterial assemblages were characterized using Illumina deep-sequencing and metabolomic profiles using UHPLC-DAD-ELSD from five depths (ranging 9-28 m) across two seasons (spring and autumn). Diverse symbiotic communities, representing 24 phyla with a predominance of Proteobacteria and Chloroflexi, were found. Although several thousands of OTUs were determined, most of them belong to the rare biosphere and only 23 to a core community. There was a significant difference between the structure of the microbial communities in respect to season (autumn to spring), with a further significant difference between depths only in autumn. This was partially mirrored in the metabolome profile, where the overall metabolite composition did not differ between seasons, but a significant depth gradient was observed in autumn. At the phyla level, Cyanobacteria, Firmicutes, Actinobacteria, and Spirochaete showed a mild-moderate correlation with the metabolome profile. The metabolomic profiles were mainly characterized by known brominated polyunsaturated fatty acids. This work presents findings about the composition and dynamics of the microbial assemblages of X. muta expanding and confirming current knowledge about its remarkable diversity and geographic variability as observed in this tropical marine biome.}, }
@article {pmid30411190, year = {2018}, author = {Rossi, A and Bellone, A and Fokin, SI and Boscaro, V and Vannini, C}, title = {Detecting Associations Between Ciliated Protists and Prokaryotes with Culture-Independent Single-Cell Microbiomics: a Proof-of-Concept Study.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1279-9}, pmid = {30411190}, issn = {1432-184X}, support = {565-60%2016//University of Pisa/ ; 565-60%2017//University of Pisa/ ; 565-FFABR 2017//Ministero dell'Istruzione, dell'Università e della Ricerca/ ; }, abstract = {Symbioses between prokaryotes and microbial eukaryotes, particularly ciliated protists, have been studied for a long time. Nevertheless, researchers have focused only on a few host genera and species, mainly due to difficulties in cultivating the hosts, and usually have considered a single symbiont at a time. Here, we present a pilot study using a single-cell microbiomic approach to circumvent these issues. Unicellular ciliate isolation followed by simultaneous amplification of eukaryotic and prokaryotic markers was used. Our preliminary test gave reliable and satisfactory results both on samples collected from different habitats (marine and freshwater) and on ciliates belonging to different taxonomic groups. Results suggest that, as already assessed for many macro-organisms like plants and metazoans, ciliated protists harbor distinct microbiomes. The applied approach detected new potential symbionts as well as new hosts for previously described ones, with relatively low time and cost effort and without culturing. When further developed, single-cell microbiomics for ciliates could be applied to a large number of studies aiming to unravel the evolutionary and ecological meaning of these symbiotic systems.}, }
@article {pmid30411189, year = {2018}, author = {Dror, H and Novak, L and Evans, JS and López-Legentil, S and Shenkar, N}, title = {Core and Dynamic Microbial Communities of Two Invasive Ascidians: Can Host-Symbiont Dynamics Plasticity Affect Invasion Capacity?.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1276-z}, pmid = {30411189}, issn = {1432-184X}, support = {2014025//United States - Israel Binational Science Foundation/ ; 2014025//United States - Israel Binational Science Foundation/ ; }, abstract = {Ascidians (Chordata, Ascidiacea) are considered to be prominent marine invaders, able to tolerate highly polluted environments and fluctuations in salinity and temperature. Here, we examined the seasonal and spatial dynamics of the microbial communities in the inner-tunic of two invasive ascidians, Styela plicata (Lesueur 1823) and Herdmania momus (Savigny 1816), in order to investigate the changes that occur in the microbiome of non-indigenous ascidians in different environments. Microbial communities were characterized using next-generation sequencing of partial (V4) 16S rRNA gene sequences. A clear differentiation between the ascidian-associated microbiome and bacterioplankton was observed, and two distinct sets of operational taxonomic units (OTUs), one core and the other dynamic, were recovered from both species. The relative abundance of the dynamic OTUs in H. momus was higher than in S. plicata, for which core OTU structure was maintained independently of location. Ten and seventeen core OTUs were identified in S. plicata and H. momus, respectively, including taxa with reported capabilities of carbon fixing, ammonia oxidization, denitrification, and heavy-metal processing. The ascidian-sourced dynamic OTUs clustered in response to site and season but significantly differed from the bacterioplankton community structure. These findings suggest that the associations between invasive ascidians and their symbionts may enhance host functionality while maintaining host adaptability to changing environmental conditions.}, }
@article {pmid30411188, year = {2018}, author = {Liu, PY and Cheng, AC and Huang, SW and Chang, HW and Oshida, T and Yu, HT}, title = {Variations in Gut Microbiota of Siberian Flying Squirrels Correspond to Seasonal Phenological Changes in Their Hokkaido Subarctic Forest Ecosystem.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1278-x}, pmid = {30411188}, issn = {1432-184X}, support = {MOST 103-2311-B-002-001//Ministry of Science and Technology, Taiwan/ ; MOST 106-2633-B-006-004//Ministry of Science and Technology, Taiwan/ ; }, abstract = {Gut microbial communities of animals are influenced by diet and seasonal weather changes. Since foraging strategies of wild animals are affected by phenological changes, gut microbial communities would differ among seasons. However, interactions of plant-animal-microbiota with seasonal changes have not been well characterized. Here, we surveyed gut microbial diversity of Siberian flying squirrels (Pteromys volans orii) from a natural forest in Hokkaido during spring and summer of 2013 and 2014. Additionally, we compared microbial diversity to temperature changes and normalized difference vegetation index (NDVI). Changes in both seasonal temperature and phenology were significantly associated with alterations in gut microbiota. There were two clusters of OTUs, below and above 20 °C that were significantly correlated with low and high temperatures, respectively. Low-temperature cluster OTUs belonged to various phyla, whereas the high-temperature cluster was only constituted by Firmicutes. In conclusion, gut microbiota of Siberian flying squirrels varied with environmental changes on an ecological scale.}, }
@article {pmid30411009, year = {2018}, author = {Van den Abbeele, P and Kamil, A and Fleige, L and Chung, Y and De Chavez, P and Marzorati, M}, title = {Different Oat Ingredients Stimulate Specific Microbial Metabolites in the Gut Microbiome of Three Human Individuals in Vitro.}, journal = {ACS omega}, volume = {3}, number = {10}, pages = {12446-12456}, doi = {10.1021/acsomega.8b01360}, pmid = {30411009}, issn = {2470-1343}, abstract = {We used a standardized in vitro simulation of the intestinal environment of three human donors to investigate the effect of six oat ingredients, which were produced by the application of different processing techniques, on the gut microbial community. Fructooligosaccharide was used as the positive control. Consistent changes in pH and gas production, on average -0.4 pH units and +32 kPa, indicated the high fermentability of the oat ingredients, and the resulting increased production of metabolites that are considered as beneficial for human health. These metabolites included acetate and lactate, but mostly propionate (+13.6 mM on average). All oat ingredients resulted in increased bifidobacteria levels with an average increase of 0.73 log. Moreover, a decreased production of proteolytic markers was observed, including branched short-chain fatty acids and ammonium. The results were donor-specific and product-specific. The results suggested an association between the total amounts of dietary fiber and the prebiotic potentials of different ingredients. Furthermore, as mechanical processing of oat products has previously been linked to increased extractability of dietary fibers, the obtained results suggest that different processing techniques might have impacted the potential functional properties of the final ingredients.}, }
@article {pmid30405584, year = {2018}, author = {Godoy-Vitorino, F and Romaguera, J and Zhao, C and Vargas-Robles, D and Ortiz-Morales, G and Vázquez-Sánchez, F and Sanchez-Vázquez, M and de la Garza-Casillas, M and Martinez-Ferrer, M and White, JR and Bittinger, K and Dominguez-Bello, MG and Blaser, MJ}, title = {Cervicovaginal Fungi and Bacteria Associated With Cervical Intraepithelial Neoplasia and High-Risk Human Papillomavirus Infections in a Hispanic Population.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2533}, doi = {10.3389/fmicb.2018.02533}, pmid = {30405584}, issn = {1664-302X}, abstract = {The human cervicovaginal microbiota resides at an interface between the host and the environment and may affect susceptibility to disease. Puerto Rican women have high human papillomavirus (HPV) infection and cervical cancer rates. We hypothesized that the population structure of the cervicovaginal bacterial and fungal biota changed with cervical squamous intraepithelial lesions and HPV infections. DNA was extracted from cervix, introitus, and anal sites of 62 patients attending high-risk San Juan clinics. The 16S rRNA V4 region and ITS-2 fungal regions were amplified and sequenced using Illumina technology. HPV genotyping was determined by reverse hybridization with the HPV SPF10-LiPA25 kit. HPV prevalence was 84% of which ∼44% subjects were infected with high-risk HPV, ∼35% were co-infected with as many as 9 HPV types and ∼5% were infected with exclusively low-risk HPV types. HPV diversity did not change with cervical dysplasia. Cervical bacteria were more diverse in patients with CIN3 pre-cancerous lesions. We found enrichment of Atopobium vaginae and Gardnerella vaginalis in patients with CIN3 lesions. We found no significant bacterial biomarkers associated with HPV infections. Fungal diversity was significantly higher in cervical samples with high-risk HPV and introitus samples of patients with Atypical Squamous Cells of Undetermined Significance (ASCUS). Fungal biomarker signatures for vagina and cervix include Sporidiobolaceae and Sacharomyces for ASCUS, and Malassezia for high-risk HPV infections. Our combined data suggests that specific cervicovaginal bacterial and fungal populations are related to the host epithelial microenvironment, and could play roles in cervical dysplasia.}, }
@article {pmid30405571, year = {2018}, author = {Biagi, E and Aceti, A and Quercia, S and Beghetti, I and Rampelli, S and Turroni, S and Soverini, M and Zambrini, AV and Faldella, G and Candela, M and Corvaglia, L and Brigidi, P}, title = {Microbial Community Dynamics in Mother's Milk and Infant's Mouth and Gut in Moderately Preterm Infants.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2512}, doi = {10.3389/fmicb.2018.02512}, pmid = {30405571}, issn = {1664-302X}, abstract = {Mother's own milk represents the optimal source for preterm infant nutrition, as it promotes immune defenses and gastrointestinal function, protects against necrotizing enterocolitis, improves long-term clinical outcome and is hypothesized to drive gut microbiota assembly. Preterm infants at birth usually do not receive their mother's milk directly from the breast, because active suckling and coordination between suckling, swallowing and breathing do not develop until 32-34 weeks gestational age, but actual breastfeeding is usually possible as they grow older. Here, we enrolled moderately preterm infants (gestational age 32-34 weeks) to longitudinally characterize mothers' milk and infants' gut and oral microbiomes, up to more than 200 days after birth, through 16S rRNA sequencing. This peculiar population offers the chance to disentangle the differential contribution of human milk feeding per se vs. actual breastfeeding in the development of infant microbiomes, that have both been acknowledged as crucial contributors to short and long-term infant health status. In this cohort, the milk microbiome composition seemed to change following the infant's latching to the mother's breast, shifting toward a more diverse microbial community dominated by typical oral microbes, i.e., Streptococcus and Rothia. Even if all infants in the present study were fed human milk, features typical of healthy, full term, exclusively breastfed infants, i.e., high percentages of Bifidobacterium and low abundances of Pseudomonas in fecal and oral samples, respectively, were detected in samples taken after actual breastfeeding started. These findings underline the importance of encouraging not only human milk feeding, but also an early start of actual breastfeeding in preterm infants, since the infant's latching to the mother's breast might constitute an independent factor helping the health-promoting assembly of the infant gut microbiome.}, }
@article {pmid30405545, year = {2018}, author = {Mehner-Breitfeld, D and Rathmann, C and Riedel, T and Just, I and Gerhard, R and Overmann, J and Brüser, T}, title = {Evidence for an Adaptation of a Phage-Derived Holin/Endolysin System to Toxin Transport in Clostridioides difficile.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2446}, doi = {10.3389/fmicb.2018.02446}, pmid = {30405545}, issn = {1664-302X}, abstract = {The pathogenicity locus (PaLoc) of Clostridioides difficile usually comprises five genes (tcdR, tcdB, tcdE, tcdA, tcdC). While the proteins TcdA and TcdB represent the main toxins of this pathogen, TcdR and TcdC are involved in the regulation of their production. TcdE is a holin family protein, members of which are usually involved in the transport of cell wall-degrading enzymes (endolysins) for phage-induced lysis. In the past, TcdE has been shown to contribute to the release of TcdA and TcdB, but it is unclear whether it mediates a specific transport or rather a lysis of cells. TcdE of C. difficile strains analyzed so far can be produced in three isoforms that are initiated from distinct N-terminal ATG codons. When produced in Escherichia coli, we found that the longest TcdE isoform had a moderate effect on cell growth, whereas the shortest isoform strongly induced lysis. The effect of the longest isoform was inhibitory for cell lysis, implying a regulatory function of the N-terminal 24 residues. We analyzed the PaLoc sequence of 44 C. difficile isolates and found that four of these apparently encode only the short TcdE isoforms, and the most closely related holins from C. difficile phages only possess one of these initiation codons, indicating that an N-terminal extension of TcdE evolved in C. difficile. All PaLoc sequences comprised also a conserved gene encoding a short fragment of an endolysin remnant of a phage holin/endolysin pair. We could produce this peptide, which we named TcdL, and demonstrated by bacterial two-hybrid analysis a self-interaction and an interaction with TcdB that might serve to mediate TcdE-dependent transport.}, }
@article {pmid30405201, year = {2018}, author = {Wankhade, UD and Zhong, Y and Kang, P and Alfaro, M and Chintapalli, SV and Piccolo, BD and Mercer, KE and Andres, A and Thakali, KM and Shankar, K}, title = {Maternal High-Fat Diet Programs Offspring Liver Steatosis in a Sexually Dimorphic Manner in Association with Changes in Gut Microbial Ecology in Mice.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {16502}, doi = {10.1038/s41598-018-34453-0}, pmid = {30405201}, issn = {2045-2322}, support = {6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; }, abstract = {The contributions of maternal diet and obesity in shaping offspring microbiome remain unclear. Here we employed a mouse model of maternal diet-induced obesity via high-fat diet feeding (HFD, 45% fat calories) for 12 wk prior to conception on offspring gut microbial ecology. Male and female offspring were provided access to control or HFD from weaning until 17 wk of age. Maternal HFD-associated programming was sexually dimorphic, with male offspring from HFD dams showing hyper-responsive weight gain to postnatal HFD. Likewise, microbiome analysis of offspring cecal contents showed differences in α-diversity, β-diversity and higher Firmicutes in male compared to female mice. Weight gain in offspring was significantly associated with abundance of Lachnospiraceae and Clostridiaceae families and Adlercreutzia, Coprococcus and Lactococcus genera. Sex differences in metagenomic pathways relating to lipid metabolism, bile acid biosynthesis and immune response were also observed. HFD-fed male offspring from HFD dams also showed worse hepatic pathology, increased pro-inflammatory cytokines, altered expression of bile acid regulators (Cyp7a1, Cyp8b1 and Cyp39a1) and serum bile acid concentrations. These findings suggest that maternal HFD alters gut microbiota composition and weight gain of offspring in a sexually dimorphic manner, coincident with fatty liver and a pro-inflammatory state in male offspring.}, }
@article {pmid30402724, year = {2018}, author = {Veresoglou, SD and Verbruggen, E and Makarova, O and Mansour, I and Sen, R and Rillig, MC}, title = {Arbuscular Mycorrhizal Fungi Alter the Community Structure of Ammonia Oxidizers at High Fertility via Competition for Soil NH4.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1281-2}, pmid = {30402724}, issn = {1432-184X}, support = {300298//FP7 People: Marie-Curie Actions ()/ ; }, abstract = {Nitrification represents a central process in the cycling of nitrogen (N) which in high-fertility habitats can occasionally be undesirable. Here, we explore how arbuscular mycorrhiza (AM) impacts nitrification when N availability is not limiting to plant growth. We wanted to test which of the mechanisms that have been proposed in the literature best describes how AM influences nitrification. We manipulated the growth settings of Plantago lanceolata so that we could control the mycorrhizal state of our plants. AM induced no changes in the potential nitrification rates or the estimates of ammonium oxidizing (AO) bacteria. However, we could observe a moderate shift in the community of ammonia-oxidizers, which matched the shift we saw when comparing hyphosphere to rhizosphere soil samples and mirrored well changes in the availability of ammonium in soil. We interpret our results as support that it is competition for N that drives the interaction between AM and AO. Our experiment sheds light on an understudied interaction which is pertinent to typical management practices in agricultural systems.}, }
@article {pmid30397796, year = {2018}, author = {Kraus, C and Voegele, RT and Fischer, M}, title = {Temporal Development of the Culturable, Endophytic Fungal Community in Healthy Grapevine Branches and Occurrence of GTD-Associated Fungi.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1280-3}, pmid = {30397796}, issn = {1432-184X}, support = {FKZ 031A349D//Bundesministerium für Bildung und Forschung/ ; }, abstract = {Endophytic fungi play an important role in the life of grapevine, either as beneficial microorganisms or as pathogens. Many surveys concerning the fungal grapevine community have been conducted. Nevertheless, exactly how the fungal community arises within the plant and develops from young shoots to mature vines is still unknown. Therefore, it was the aim of this study to investigate the early development of endophytic fungal communities in healthy grapevine branches from 2 months to 8 years old. More than 3800 fungi belonging to 86 operational taxonomic units (OTUs) were isolated from wood samples and assigned to eight age groups. The community composition within the age groups changed and significant differences between young (≤ 1 year) and old (> 1 year) branches were found. The former were primarily dominated by ubiquitous, fast-growing fungi like Alternaria spp., Aureobasidium pullulans, Cladosporium spp., or Epicoccum nigrum, while communities of perennial branches additionally harbored many grapevine trunk disease (GTD)-associated fungi such as Diplodia seriata or Eutypa lata. This work gives an insight into the early development of fungal communities in grapevine, the nature and composition of primary settlers and core communities, as well as the emergence of GTD-associated fungi in perennial wood. This information may help grapevine growers to better estimate the risk in relation to the applied training system, producing mainly old branches or young shoots.}, }
@article {pmid30397795, year = {2018}, author = {Palacios, OA and Lopez, BR and Bashan, Y and de-Bashan, LE}, title = {Early Changes in Nutritional Conditions Affect Formation of Synthetic Mutualism Between Chlorella sorokiniana and the Bacterium Azospirillum brasilense.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1282-1}, pmid = {30397795}, issn = {1432-184X}, support = {251102//Consejo Nacional de Ciencia y Tecnología/ ; 284562//Consejo Nacional de Ciencia y Tecnología/ ; }, abstract = {The effect of three different nutritional conditions during the initial 12 h of interaction between the microalgae Chlorella sorokiniana UTEX 2714 and the plant growth-promoting bacterium Azospirillum brasilense Cd on formation of synthetic mutualism was assessed by changes in population growth, production of signal molecules tryptophan and indole-3-acetic acid, starch accumulation, and patterns of cell aggregation. When the interaction was supported by a nutrient-rich medium, production of both signal molecules was detected, but not when this interaction began with nitrogen-free (N-free) or carbon-free (C-free) media. Overall, populations of bacteria and microalgae were larger when co-immobilized. However, the highest starch production was measured in C. sorokiniana immobilized alone and growing continuously in a C-free mineral medium. In this interaction, the initial nutritional condition influenced the time at which the highest accumulation of starch occurred in Chlorella, where the N-free medium induced faster starch production and the richer medium delayed its accumulation. Formation of aggregates made of microalgae and bacteria occurred in all nutritional conditions, with maximum at 83 h in mineral medium, and coincided with declining starch content. This study demonstrates that synthetic mutualism between C. sorokiniana and A. brasilense can be modulated by the initial nutritional condition, mainly by the presence or absence of nitrogen and carbon in the medium in which they are interacting.}, }
@article {pmid30397794, year = {2018}, author = {Lau, NS and Zarkasi, KZ and Md Sah, ASR and Shu-Chien, AC}, title = {Diversity and Coding Potential of the Microbiota in the Photic and Aphotic Zones of Tropical Man-Made Lake with Intensive Aquaculture Activities: a Case Study on Temengor Lake, Malaysia.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1283-0}, pmid = {30397794}, issn = {1432-184X}, abstract = {Although freshwater biomes cover less than 1% of the Earth's surface, they have disproportionate ecological significances. Attempts to study the taxonomy and function of freshwater microbiota are currently limited to samples collected from temperate lakes. In this study, we investigated samples from the photic and aphotic of an aquaculture site (disturbed) of Temengor Lake, a tropical lake in comparison with the undisturbed site of the lake using 16S rRNA amplicon and shotgun metagenomic approaches. Vertical changes in bacterial community composition and function of the Temengor Lake metagenomes were observed. The photic water layer of Temengor Lake was dominated by typical freshwater assemblages consisting of Proteobacteria, Actinobacteria, Bacteroidetes, Verrucomicrobia, and Cyanobacteria lineages. On the other hand, the aphotic water featured in addition to Proteobacteria, Bacteroidetes, Verrucomicrobia, and two more abundant bacterial phyla that are typically ubiquitous in anoxic habitats (Chloroflexi and Firmicutes). The aphotic zone of Temengor Lake exhibited genetic potential for nitrogen and sulfur metabolisms for which terminal electron acceptors other than oxygen are used in the reactions. The aphotic water of the disturbed site also showed an overrepresentation of genes associated with the metabolism of carbohydrates, likely driven by the enrichment of nutrient resulting from aquaculture activities at the site. The results presented in this study can serve as a basis for understanding the structure and functional capacity of the microbial communities in the photic and aphotic zones/water layers of tropical man-made lakes.}, }
@article {pmid30397546, year = {2018}, author = {Md Zoqratt, MZH and Eng, WWH and Thai, BT and Austin, CM and Gan, HM}, title = {Microbiome analysis of Pacific white shrimp gut and rearing water from Malaysia and Vietnam: implications for aquaculture research and management.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e5826}, doi = {10.7717/peerj.5826}, pmid = {30397546}, issn = {2167-8359}, abstract = {Aquaculture production of the Pacific white shrimp is the largest in the world for crustacean species. Crucial to the sustainable global production of this important seafood species is a fundamental understanding of the shrimp gut microbiota and its relationship to the microbial ecology of shrimp pond. This is especially true, given the recently recognized role of beneficial microbes in promoting shrimp nutrient intake and in conferring resistance against pathogens. Unfortunately, aquaculture-related microbiome studies are scarce in Southeast Asia countries despite the severe impact of early mortality syndrome outbreaks on shrimp production in the region. In this study, we employed the 16S rRNA amplicon (V3-V4 region) sequencing and amplicon sequence variants (ASV) method to investigate the microbial diversity of shrimp guts and pond water samples collected from aquaculture farms located in Malaysia and Vietnam. Substantial differences in the pond microbiota were observed between countries with the presence and absence of several taxa extending to the family level. Microbial diversity of the shrimp gut was found to be generally lower than that of the pond environments with a few ubiquitous genera representing a majority of the shrimp gut microbial diversity such as Vibrio and Photobacterium, indicating host-specific selection of microbial species. Given the high sequence conservation of the 16S rRNA gene, we assessed its veracity at distinguishing Vibrio species based on nucleotide alignment against type strain reference sequences and demonstrated the utility of ASV approach in uncovering a wider diversity of Vibrio species compared to the conventional OTU clustering approach.}, }
@article {pmid30391860, year = {2019}, author = {van der Waals, MJ and Plugge, C and Meima-Franke, M and de Waard, P and Bodelier, PLE and Smidt, H and Gerritse, J}, title = {Ethyl tert-butyl ether (EtBE) degradation by an algal-bacterial culture obtained from contaminated groundwater.}, journal = {Water research}, volume = {148}, number = {}, pages = {314-323}, doi = {10.1016/j.watres.2018.10.050}, pmid = {30391860}, issn = {1879-2448}, abstract = {EtBE is a fuel oxygenate that is synthesized from (bio)ethanol and fossil-based isobutylene, and replaces the fossil-based MtBE. Biodegradation of EtBE to harmless metabolites or end products can reduce the environmental and human health risks after accidental release. In this study, an algal-bacterial culture enriched from contaminated groundwater was used to (i) assess the potential for EtBE degradation, (ii) resolve the EtBE degradation pathway and (iii) characterize the phylogenetic composition of the bacterial community involved in EtBE degradation in contaminated groundwater. In an unamended microcosm, algal growth was observed after eight weeks when exposed to a day-night light cycle. In the fed-batch reactor, oxygen produced by the algae Scenedesmus and Chlorella was used by bacteria to degrade 50 μM EtBE replenishments with a cumulative total of 1250 μM in a day/night cycle (650 lux), over a period of 913 days. The microbial community in the fed-batch reactor degraded EtBE, using a P450 monooxygenase and 2-hydroxyisobutyryl-CoA mutase, to tert-butyl alcohol (TBA), ethanol and CO2 as determined using 13C nuclear magnetic resonance spectroscopy (NMR) and gas chromatography. Stable isotope probing (SIP) with 13C6 labeled EtBE in a fed-batch vessel showed no significant difference in community profiles of the 13C and 12C enriched DNA fractions, with representatives of the families Halomonadaceae, Shewanellaceae, Rhodocyclaceae, Oxalobacteraceae, Comamonadaceae, Sphingomonadaceae, Hyphomicrobiaceae, Candidatus Moranbacteria, Omnitrophica, Anaerolineaceae, Nocardiaceae, and Blastocatellaceae. This is the first study describing micro-oxic degradation of EtBE by an algal-bacterial culture. This algal-bacterial culture has advantages compared with conventional aerobic treatments: (i) a lower risk of EtBE evaporation and (ii) no need for external oxygen supply in the presence of light. This study provides novel leads towards future possibilities to implement algal-bacterial consortia in field-scale groundwater or wastewater treatment.}, }
@article {pmid30390579, year = {2019}, author = {Gómez-Sagasti, MT and Epelde, L and Anza, M and Urra, J and Alkorta, I and Garbisu, C}, title = {The impact of nanoscale zero-valent iron particles on soil microbial communities is soil dependent.}, journal = {Journal of hazardous materials}, volume = {364}, number = {}, pages = {591-599}, doi = {10.1016/j.jhazmat.2018.10.034}, pmid = {30390579}, issn = {1873-3336}, abstract = {The application of nanoscale zero-valent iron particles (nZVI) for the remediation of contaminated sites is very promising. However, information concerning the ecotoxicity of nZVI on soil microbial communities and, hence, soil quality, is still scarce. We carried out a three-month experiment to evaluate the impact of the application of different concentrations of nZVI (from 1 to 20 mg g DW soil-1) on soil microbial properties in a clay-loam versus a sandy-loam soil. Data on microbial biomass (total bacteria and fungi by qPCR, microbial biomass carbon), activity (β-glucosidase, arylsulphatase and urease activities), and functional (Biolog Ecoplates™) and structural (ARISA, 16S rRNA amplicon sequencing) diversity evidenced that the sandy-loam soil was more vulnerable to the presence of nZVI than the clay-loam soil. In the sandy-loam soil, arylsulphatase activity and bacterial abundance, richness and diversity were susceptible to the presence of nZVI. The high content of clay and organic matter present in the clay-loam soil may explain the observed negligible effects of nZVI on soil microbial properties. It was concluded that the impact of nZVI on soil microbial communities and, hence, soil quality, is soil dependent.}, }
@article {pmid30388523, year = {2019}, author = {Zhang, Y and Hua, ZS and Lu, H and Oehmen, A and Guo, J}, title = {Elucidating functional microorganisms and metabolic mechanisms in a novel engineered ecosystem integrating C, N, P and S biotransformation by metagenomics.}, journal = {Water research}, volume = {148}, number = {}, pages = {219-230}, doi = {10.1016/j.watres.2018.10.061}, pmid = {30388523}, issn = {1879-2448}, abstract = {Denitrifying sulfur conversion-associated enhanced biological phosphorous removal (DS-EBPR) system is not only a novel wastewater treatment process, but also an ideal model for microbial ecology in a community context. However, it exists the knowledge gap on the roles and interactions of functional microorganisms in the DS-EBPR system for carbon (C), nitrogen (N), phosphorus (P) and sulfur (S) bioconversions. We use genome-resolved metagenomics to build up an ecological model of microbial communities in a lab-scale DS-EBPR system with stable operation for more than 400 days. Our results yield 11 near-complete draft genomes that represent a substantial portion of the microbial community (39.4%). Sulfate-reducing bacteria (SRB) and sulfide-oxidizing bacteria (SOB) promote complex metabolic processes and interactions for C, N, P and S conversions. Bins 1-4 and 10 are considered as new potential polyphosphate-accumulating organisms (PAOs), in which Bins 1-4 can be considered as S-related PAOs (S-PAOs) with no previously cultivated or reported members. Our findings give an insight into a new ecological system with C, N, P and S simultaneous bioconversions and improve the understanding of interactions among SRB, SOB, denitrifiers and PAOs within a community context.}, }
@article {pmid30387912, year = {2018}, author = {de Nijs, EA and Hicks, LC and Leizeaga, A and Tietema, A and Rousk, J}, title = {Soil microbial moisture dependences and responses to drying-rewetting: the legacy of 18 years drought.}, journal = {Global change biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/gcb.14508}, pmid = {30387912}, issn = {1365-2486}, abstract = {Climate change will alter precipitation patterns with consequences for soil C cycling. An understanding of how fluctuating soil moisture affects microbial processes is therefore critical to predict responses to future global change. We investigated how long-term experimental field drought influences microbial tolerance to lower moisture levels ('resistance') and ability to recover when rewetted after drought ('resilience'), using soils from a heathland which had been subjected to experimental precipitation reduction during the summer for 18 years. We tested whether drought could induce increased resistance, resilience, and changes in the balance between respiration and bacterial growth during perturbation events, by following a two-tiered approach. We first evaluated the effects of the long-term summer drought on microbial community functioning to drought and drying-rewetting (D/RW), and second tested the ability to alter resistance and resilience through additional perturbation cycles. A history of summer drought in the field selected for increased resilience but not resistance, suggesting that rewetting after drought, rather than low moisture levels during drought, was the selective pressure shaping the microbial community functions. Laboratory D/RW cycles also selected for communities with a higher resilience rather than increased resistance. The ratio of respiration to bacterial growth during D/RW perturbation was lower for the field drought-exposed communities and decreased for both field-treatments during the D/RW cycles. This suggests that cycles of D/RW also structure microbial communities to respond quickly and efficiently to rewetting after drought. Our findings imply that microbial communities can adapt to changing climatic conditions and that this might slow the rate of SOC loss predicted to be induced by future cyclic drought. This article is protected by copyright. All rights reserved.}, }
@article {pmid30386315, year = {2018}, author = {Florez, AM and Suarez-Barrera, MO and Morales, GM and Rivera, KV and Orduz, S and Ochoa, R and Guerra, D and Muskus, C}, title = {Toxic Activity, Molecular Modeling and Docking Simulations of Bacillus thuringiensis Cry11 Toxin Variants Obtained via DNA Shuffling.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2461}, doi = {10.3389/fmicb.2018.02461}, pmid = {30386315}, issn = {1664-302X}, abstract = {The Cry11 family belongs to a large group of δ-endotoxins that share three distinct structural domains. Among the dipteran-active toxins referred to as three-domain Cry11 toxins, the Cry11Aa protein from Bacillus thuringiensis subsp. israelensis (Bti) has been the most extensively studied. Despite the potential of Bti as an effective biological control agent, the understanding of Cry11 toxins remains incomplete. In this study, five Cry11 variants obtained via DNA shuffling displayed toxic activity against Aedes aegypti and Culex quinquefasciatus. Three of these Cry11 variants (8, 23, and 79) were characterized via 3D modeling and analysis of docking with ALP1. The relevant mutations in these variants, such as deletions, insertions and point mutations, are discussed in relation to their structural domains, toxic activities and toxin-receptor interactions. Importantly, deletion of the N-terminal segment in domain I was not associated with any change in toxic activity, and domain III exhibited higher sequence variability than domains I and II. Variant 8 exhibited up to 3.78- and 6.09-fold higher toxicity to A. aegypti than Cry11Bb and Cry11Aa, respectively. Importantly, variant 79 showed an α-helix conformation at the C-terminus and formed crystals retaining toxic activity. These findings indicate that five Cry11 variants were preferentially reassembled from the cry11Aa gene during DNA shuffling. The mutations described in loop 2 and loop 3 of domain II provide valuable information regarding the activity of Cry11 toxins against A. aegypti and C. quinquefasciatus larvae and reveal new insights into the application of directed evolution strategies to study the genetic variability of specific domains in cry11 family genes.}, }
@article {pmid30384950, year = {2018}, author = {Ihekweazu, FD and Versalovic, J}, title = {Development of the Pediatric Gut Microbiome: Impact on Health and Disease.}, journal = {The American journal of the medical sciences}, volume = {356}, number = {5}, pages = {413-423}, doi = {10.1016/j.amjms.2018.08.005}, pmid = {30384950}, issn = {1538-2990}, abstract = {The intestinal microbiota are important in human growth and development. Microbial composition may yield insights into the temporal development of microbial communities and vulnerabilities to disorders of microbial ecology such as recurrent Clostridium difficile infection. Discoveries of key microbiome features of carbohydrate and amino acid metabolism are lending new insights into possible therapies or preventative strategies for inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS). In this review, we summarize the current understanding of the development of the pediatric gastrointestinal microbiome, the influence of the microbiome on the developing brain through the gut-brain axis, and the impact of dysbiosis on disease development. Dysbiosis is explored in the context of pediatric allergy and asthma, recurrent C. difficile infection, IBD, IBS, and metabolic disorders. The central premise is that the human intestinal microbiome plays a vital role in health and disease, beginning in the prenatal period and extending throughout childhood.}, }
@article {pmid30379400, year = {2018}, author = {Van Hecke, T and De Vrieze, J and Boon, N and De Vos, WH and Vossen, E and De Smet, S}, title = {Combined Consumption of Beef-Based Cooked Mince and Sucrose Stimulates Oxidative Stress, Cardiac Hypertrophy, and Colonic Outgrowth of Desulfovibrionaceae in Rats.}, journal = {Molecular nutrition &amp; food research}, volume = {}, number = {}, pages = {e1800962}, doi = {10.1002/mnfr.201800962}, pmid = {30379400}, issn = {1613-4133}, support = {BOF grant PDO.2016.0021.01//Bijzonder Onderzoeksfonds/ ; //Fonds Wetenschappelijk Onderzoek (FWO)/ ; }, abstract = {SCOPE: High red meat and sucrose consumption increases the epidemiological risk for chronic diseases. Mechanistic hypotheses include alterations in oxidative status, gut microbiome, fat deposition, and low-grade inflammation.<br><br>METHODS AND RESULTS: For 2 weeks, 40 rats consumed a diet high in white or red meat (chicken-based or beef-based cooked mince, respectively), and containing corn starch or sucrose in a 2 × 2 factorial design. Lard was mixed with lean chicken or beef to obtain comparable dietary fatty acid profiles. Beef (vs chicken)-fed rats had higher lipid oxidation products (malondialdehyde, 4-hydroxy-2-nonenal, and hexanal) in stomach content and blood, and lower blood glutathione. Sucrose (vs corn starch)-fed rats showed increased blood lipid oxidation products and glutathione peroxidase activity, higher liver weight and malondialdehyde concentrations, and mesenterial and retroperitoneal fat accumulation. Beef-sucrose-fed rats had increased cardiac weight, suggesting pathophysiological effects on the cardiovascular system. The colonic microbiome of beef-sucrose-fed rats showed an outgrowth of the sulfate-reducing family of the Desulfovibrionaceae, and lower abundance of the Lactobacillus genus, indicating intestinal dysbiosis. Blood C-reactive protein, a marker for inflammation, was not different among groups.<br><br>CONCLUSIONS: Consumption of a cooked beef-based meat product with sucrose increased oxidative stress parameters and promoted cardiac hypertrophy and intestinal dysbiosis.}, }
@article {pmid30376889, year = {2018}, author = {Hale, VL and Jeraldo, P and Chen, J and Mundy, M and Yao, J and Priya, S and Keeney, G and Lyke, K and Ridlon, J and White, BA and French, AJ and Thibodeau, SN and Diener, C and Resendis-Antonio, O and Gransee, J and Dutta, T and Petterson, XM and Sung, J and Blekhman, R and Boardman, L and Larson, D and Nelson, H and Chia, N}, title = {Distinct microbes, metabolites, and ecologies define the microbiome in deficient and proficient mismatch repair colorectal cancers.}, journal = {Genome medicine}, volume = {10}, number = {1}, pages = {78}, doi = {10.1186/s13073-018-0586-6}, pmid = {30376889}, issn = {1756-994X}, support = {R01CA179243/NH/NIH HHS/United States ; R01CA170357/NH/NIH HHS/United States ; P30DK084567/DK/NIDDK NIH HHS/United States ; U24DK100469//Mayo Clinic Metabolomics Resource Core/International ; }, abstract = {BACKGROUND: Links between colorectal cancer (CRC) and the gut microbiome have been established, but the specific microbial species and their role in carcinogenesis remain an active area of inquiry. Our understanding would be enhanced by better accounting for tumor subtype, microbial community interactions, metabolism, and ecology.<br><br>METHODS: We collected paired colon tumor and normal-adjacent tissue and mucosa samples from 83 individuals who underwent partial or total colectomies for CRC. Mismatch repair (MMR) status was determined in each tumor sample and classified as either deficient MMR (dMMR) or proficient MMR (pMMR) tumor subtypes. Samples underwent 16S rRNA gene sequencing and a subset of samples from 50 individuals were submitted for targeted metabolomic analysis to quantify amino acids and short-chain fatty acids. A PERMANOVA was used to identify the biological variables that explained variance within the microbial communities. dMMR and pMMR microbial communities were then analyzed separately using a generalized linear mixed effects model that accounted for MMR status, sample location, intra-subject variability, and read depth. Genome-scale metabolic models were then used to generate microbial interaction networks for dMMR and pMMR microbial communities. We assessed global network properties as well as the metabolic influence of each microbe within the dMMR and pMMR networks.<br><br>RESULTS: We demonstrate distinct roles for microbes in dMMR and pMMR CRC. Bacteroides fragilis and sulfidogenic Fusobacterium nucleatum were significantly enriched in dMMR CRC, but not pMMR CRC. These findings were further supported by metabolic modeling and metabolomics indicating suppression of B. fragilis in pMMR CRC and increased production of amino acid proxies for hydrogen sulfide in dMMR CRC.<br><br>CONCLUSIONS: Integrating tumor biology and microbial ecology highlighted distinct microbial, metabolic, and ecological properties unique to dMMR and pMMR CRC. This approach could critically improve our ability to define, predict, prevent, and treat colorectal cancers.}, }
@article {pmid30375646, year = {2018}, author = {Philip, N and Walsh, L}, title = {The potential ecological effects of Casein Phosphopeptide-Amorphous Calcium Phosphate in dental caries prevention.}, journal = {Australian dental journal}, volume = {}, number = {}, pages = {}, doi = {10.1111/adj.12661}, pmid = {30375646}, issn = {1834-7819}, abstract = {Contemporary caries prevention protocols recommend not only effective remineralizing agents but also ecological measures to reverse the dental plaque dysbiosis responsible for the disease pathogenesis. There is a high-level of evidence supporting the remineralizing efficacy of Casein Phosphopeptide-Amorphous Calcium Phosphate (CPP-ACP) from studies around the world. There is now emerging evidence that CPP-ACP may also have a beneficial influence on the dental plaque microbial ecology and homeostasis. The ecological cariostatic effects of CPP-ACP are believed to be mediated predominantly through its anti-adhesion, buffering, and biofilm disrupting actions. This review principally discusses the ecological mechanisms of CPP-ACP and presents the current evidence for its effects on the oral microbiome ecology. This article is protected by copyright. All rights reserved.}, }
@article {pmid30374168, year = {2018}, author = {Reese, AT and Pereira, FC and Schintlmeister, A and Berry, D and Wagner, M and Hale, LP and Wu, A and Jiang, S and Durand, HK and Zhou, X and Premont, RT and Diehl, AM and O'Connell, TM and Alberts, SC and Kartzinel, TR and Pringle, RM and Dunn, RR and Wright, JP and David, LA}, title = {Microbial nitrogen limitation in the mammalian large intestine.}, journal = {Nature microbiology}, volume = {3}, number = {12}, pages = {1441-1450}, doi = {10.1038/s41564-018-0267-7}, pmid = {30374168}, issn = {2058-5276}, abstract = {Resource limitation is a fundamental factor governing the composition and function of ecological communities. However, the role of resource supply in structuring the intestinal microbiome has not been established and represents a challenge for mammals that rely on microbial symbionts for digestion: too little supply might starve the microbiome while too much might starve the host. We present evidence that microbiota occupy a habitat that is limited in total nitrogen supply within the large intestines of 30 mammal species. Lowering dietary protein levels in mice reduced their faecal concentrations of bacteria. A gradient of stoichiometry along the length of the gut was consistent with the hypothesis that intestinal nitrogen limitation results from host absorption of dietary nutrients. Nitrogen availability is also likely to be shaped by host-microbe interactions: levels of host-secreted nitrogen were altered in germ-free mice and when bacterial loads were reduced via experimental antibiotic treatment. Single-cell spectrometry revealed that members of the phylum Bacteroidetes consumed nitrogen in the large intestine more readily than other commensal taxa did. Our findings support a model where nitrogen limitation arises from preferential host use of dietary nutrients. We speculate that this resource limitation could enable hosts to regulate microbial communities in the large intestine. Commensal microbiota may have adapted to nitrogen-limited settings, suggesting one reason why excess dietary protein has been associated with degraded gut-microbial ecosystems.}, }
@article {pmid30372571, year = {2018}, author = {Nottingham, AT and Bååth, E and Reischke, S and Salinas, N and Meir, P}, title = {Adaptation of soil microbial growth to temperature: using a tropical elevation gradient to predict future changes.}, journal = {Global change biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/gcb.14502}, pmid = {30372571}, issn = {1365-2486}, abstract = {Terrestrial biogeochemical feedbacks to the climate are strongly modulated by the temperature response of soil microorganisms. Tropical forests, in particular, exert a major influence on global climate because they are the most productive terrestrial ecosystem. We used an elevation gradient across tropical forest in the Andes (a gradient of 20°C mean annual temperature, MAT), to test whether soil bacterial and fungal community growth responses are adapted to long-term temperature differences. We evaluated the temperature dependency of soil bacterial and fungal growth using the leucine- and acetate-incorporation methods, respectively, and determined indices for the temperature response of growth: Q10 and Tmin (the minimum temperature for growth). For both bacterial and fungal communities, increased MAT (decreased elevation) resulted in increases in Q10 and Tmin of growth. Across a MAT range from 6°C to 26°C, the Q10 and Tmin varied for bacterial growth (Q10-20 = 2.4 to 3.5; Tmin = -8°C to -1.5°C) and fungal growth (Q10-20 = 2.6 to 3.6; Tmin = -6°C to -1°C). Thus, bacteria and fungi did not differ in their growth temperature responses with changes in MAT. Our findings indicate that across natural temperature gradients, each increase in MAT by 1°C results in increases in Tmin of microbial growth by approximately 0.3°C and Q10-20 by 0.05, consistent with long-term temperature adaptation of soil microbial communities. A 2°C warming would increase microbial activity across a MAT gradient of 6°C to 26°C by 28% to 15%, respectively, and temperature adaptation of microbial communities would further increase activity by 1.2% to 0.3%. The impact of warming on microbial activity, and the related impact on soil carbon cycling, is thus greater in regions with lower MAT. These results can be used to predict future changes in the temperature response of microbial activity over different levels of warming and over large temperature ranges, extending to tropical regions. This article is protected by copyright. All rights reserved.}, }
@article {pmid30370317, year = {2018}, author = {Cooper, R and Tsimring, L and Hasty, J}, title = {Microfluidics-Based Analysis of Contact-dependent Bacterial Interactions.}, journal = {Bio-protocol}, volume = {8}, number = {16}, pages = {}, doi = {10.21769/BioProtoc.2970}, pmid = {30370317}, issn = {2331-8325}, support = {P50 GM085764/GM/NIGMS NIH HHS/United States ; }, abstract = {Bacteria in nature live in complex communities with multiple cell types and spatially-dependent interactions. Studying cells in well-mixed environments such as shaking culture tubes or flasks cannot capture these spatial dynamics, but cells growing in full-fledged biofilms are difficult to observe in real time. We present here a protocol for observing time-resolved, multi-species interactions at single-cell resolution. The protocol involves growing bacterial cells in a near monolayer in a microfluidic device. As a demonstration, we describe in particular observing the dynamic interactions between E. coli and Acinetobacter baylyi. In this case, the protocol is capable of observing both contact-dependent lysis of E. coli by A. baylyi via the Type VI Secretion System (T6SS) and subsequent functional horizontal gene transfer (HGT) of genes from E. coli to A. baylyi.}, }
@article {pmid30369284, year = {2018}, author = {Braga, RM and Padilla, G and Araújo, WL}, title = {The biotechnological potential of Epicoccum spp.: diversity of secondary metabolites.}, journal = {Critical reviews in microbiology}, volume = {}, number = {}, pages = {1-20}, doi = {10.1080/1040841X.2018.1514364}, pmid = {30369284}, issn = {1549-7828}, abstract = {Epicoccum is a genus of ubiquitous fungi typically found in air, in soil, and on decaying vegetation. They also commonly display an endophytic lifestyle and are isolated from diverse plant tissues. The fungi from the genus Epicoccum are mainly known for their use as biocontrol agents against phytopathogens and for their ability to produce many secondary metabolites with potential biotechnological applications, such as antioxidant, anticancer,r and antimicrobial compounds. Among the bioactive compounds produced by Epicoccum spp., epicocconone is a commercially available fluorophore, D8646-2-6 is a patented telomerase inhibitor, and taxol is an anticancer drug originally isolated from Taxus brevifolia. Epicoccum spp. also produces epicolactone, an antimicrobial compound with a unique and complex structure that has aroused considerable interest in the chemical-synthesis community. The main goal of the present review is to discuss the diversity of secondary metabolites produced by Epicoccum spp., their biotechnological applications, and proposed hypothetical biosynthesis. In addition, the use of Epicoccum spp. as biocontrol agents and the pigments produced by these fungi are also discussed.}, }
@article {pmid30368967, year = {2018}, author = {Feng, Y and Chen, R and Stegen, JC and Guo, Z and Zhang, J and Li, Z and Lin, X}, title = {Two key features influencing community assembly processes at regional scale: Initial state and degree of change in environmental conditions.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.14914}, pmid = {30368967}, issn = {1365-294X}, support = {//US Department of Energy/ ; 41430859//National Natural Science Foundation of China/ ; 41671267//National Natural Science Foundation of China/ ; KFZD-SW-112-03-04//CAS Strategic Priority Research Program/ ; XDB15010103//CAS Strategic Priority Research Program/ ; XDB15020103//CAS Strategic Priority Research Program/ ; 2014CB954500//National Basic Research Program/ ; 2016YFD0200306//National Key R&amp;D Program/ ; 2014271//Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; ISSASIP1639//Knowledge Innovation Program of Chinese Academy of Sciences/ ; //Subsurface Biogeochemical Research Program's Scientific Focus Area/ ; //Office of Biological and Environmental Research/ ; }, abstract = {Belowground microbial communities strongly influence ecosystem function such that predicting function may rely on understanding ecological processes that assemble communities. Uncertainty remains, however, in what governs the relative contributions of different ecological processes. To help fill this knowledge gap, we test the general hypothesis that both initial state and degree of change in environmental conditions govern the relative contributions of different ecological assembly processes. To do so, we leveraged regional-scale nutrient and organic matter addition experiments and used soil organic matter (SOM) as a proxy of integrated soil environmental conditions. Consistent with our hypothesis, we found that both the initial amount of SOM and the degree of change in SOM-in response to nutrient addition-influenced the relative contributions of different ecological assembly processes. These influences were most clearly observed at the regional scale, suggesting potential scale dependence. More specifically, nutrient additions homogenized bacterial community composition due to enhanced influences of homogenizing dispersal when SOM content was initially high. In contrast, nutrient additions led to divergence in community composition due to variable selection when initial SOM was low and/or when SOM increased significantly in response to nutrient additions. Our findings indicate important connections among initial conditions, degree of change in environmental variables and microbial community assembly processes that may influence ecosystem processes. These conceptual inferences highlight a need to strengthen connections between ecological theory and biogeochemical modelling.}, }
@article {pmid30368524, year = {2018}, author = {Li, X and Jousset, A and de Boer, W and Carrión, VJ and Zhang, T and Wang, X and Kuramae, EE}, title = {Legacy of land use history determines reprogramming of plant physiology by soil microbiome.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-018-0300-0}, pmid = {30368524}, issn = {1751-7370}, abstract = {Microorganisms associated with roots are thought to be part of the so-called extended plant phenotypes with roles in the acquisition of nutrients, production of growth hormones, and defense against diseases. Since the crops selectively enrich most rhizosphere microbes out of the bulk soil, we hypothesized that changes in the composition of bulk soil communities caused by agricultural management affect the extended plant phenotype. In the current study, we performed shotgun metagenome sequencing of the rhizosphere microbiome of the peanut (Arachis hypogaea) and metatranscriptome analysis of the roots of peanut plants grown in the soil with different management histories, peanut monocropping and crop rotation. We found that the past planting record had a significant effect on the assembly of the microbial community in the peanut rhizosphere, indicating a soil memory effect. Monocropping resulted in a reduction of the rhizosphere microbial diversity, an enrichment of several rare species, and a reduced representation of traits related to plant performance, such as nutrients metabolism and phytohormone biosynthesis. Furthermore, peanut plants in monocropped soil exhibited a significant reduction in growth coinciding with a down-regulation of genes related to hormone production, mainly auxin and cytokinin, and up-regulation of genes related to the abscisic acid, salicylic acid, jasmonic acid, and ethylene pathways. These findings suggest that land use history affects crop rhizosphere microbiomes and plant physiology.}, }
@article {pmid30367681, year = {2018}, author = {Lian, Y and Yang, J and Lian, Y and Xiao, C and Hu, X and Xu, H}, title = {DUXAP8, a pseudogene derived lncRNA, promotes growth of pancreatic carcinoma cells by epigenetically silencing CDKN1A and KLF2.}, journal = {Cancer communications (London, England)}, volume = {38}, number = {1}, pages = {64}, doi = {10.1186/s40880-018-0333-9}, pmid = {30367681}, issn = {2523-3548}, support = {81602052//the National Natural Science Foundation of China/International ; 8160100460//the National Natural Science Foundation of China/International ; 8157040399//the National Natural Science Foundation of China/International ; }, abstract = {BACKGROUND: Recent studies highlight pseudogene derived long non-coding RNAs (lncRNAs) as key regulators of cancer biology. However, few of them have been well characterized in pancreatic cancer. Here, we aimed to identify the association between pseudogene derived lncRNA DUXAP8 and growth of pancreatic cancer cells.<br><br>METHODS: We screened for pseudogene derived lncRNAs associated with human pancreatic cancer by comparative analysis of three independent datasets from GEO. Quantitative real-time reverse transcription polymerase chain reaction was used to assess the relative expression of DUXAP8 in pancreatic cancer tissues and cells. Loss-of-function approaches were used to investigate the potential functional roles of DUXAP8 in pancreatic cancer cell proliferation and apoptosis in vitro and in vivo. RNA immunoprecipitation, chromosome immunoprecipitation assay and rescue experiments were performed to analyze the association of DUXAP8 with target proteins and genes in pancreatic cancer cells.<br><br>RESULTS: Pancreatic cancer tissues had significantly higher DUXAP8 levels than paired adjacent normal tissues. High DUXAP8 expression was associated with a larger tumor size, advanced pathological stage and shorter overall survival of pancreatic cancer patients. Moreover, silencing DUXAP8 expression by siRNA or shRNA inhibited pancreatic cancer cell proliferation and promoted apoptosis in vitro and in vivo. Mechanistic analyses indicated that DUXAP8 regulates PC cell proliferation partly through downregulation of tumor suppressor CDKN1A and KLF2 expression.<br><br>CONCLUSION: Our results suggest that tumor expression of pseudogene derived lncRNA DUXAP8 plays an important role in pancreatic cancer progression. DUXAP8 may serve as a candidate biomarker and represent a novel therapeutic target of pancreatic cancer.}, }
@article {pmid30367007, year = {2018}, author = {Ren, L and Song, X and He, D and Wang, J and Tan, M and Xia, X and Li, G and Tan, Y and Wu, QL}, title = {Bacterioplankton metacommunity processes across thermal gradients: weaker species sorting but stronger niche segregation in summer than in winter subtropical bay.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.02088-18}, pmid = {30367007}, issn = {1098-5336}, abstract = {Thermal effluents from nuclear power plants greatly change the environmental and ecological conditions of the receiving marine water body, but knowledge about their impact on microbial ecology is limited. Here, we used high-throughput sequencing of 16S rRNA gene to examine marine bacterioplankton metacommunity assembly across thermal gradients in two representative seasons (i.e., winter and summer) in subtropical bay locating on the northern coast of the South China Sea. We found high heterogeneity in bacterioplankton community compositions (BCCs) across thermal gradients and between seasons. The spatially structured temperature gradient created by thermal effluents was the key determinant of BCC, but its influence differed by season. Using a metacommunity approach, we found that in the thermal discharge area, i.e., where water frequently exchanges with surrounding seawater and thermal effluent water, the BCC spatial patterns were shaped by species sorting rather than mass effects from surrounding seawater or dilution of thermal effluent water by surrounding seawater. However, this effect of species sorting was weaker in summer than in winter seawater. In both seasons, bacterioplankton community structure was predominately determined by niche sharing; however, the relative importance of niche segregation was enhanced in summer seawater. Our findings suggest that for the seasonal differences in metacommunity processes, BCCs of subtropical summer seawater were more sensitive to temperature and were more difficult to predict than those of winter seawater in face of different intensity of thermal impacts.IMPORTANCE Understanding the mechanisms of bacterial community assembly across environmental gradients is one of the major goals of marine microbial ecology. Thermal effluents off two nuclear power plants in subtropical Daya Bay have been present for more than 20 years and have generated a comparatively stable and long thermal gradient (a temperature increase from 0 to 10°C). The environment patches across thermal gradients are heterogeneous and very strongly interconnected on a microbial scale, thus it is a useful model to study metacommunity processes (i.e., patch dynamics, species sorting, mass effects, and neutral processes) that underlie marine bacterioplankton assembly. The significance of our research is to understand how environmental conditions and dispersal-related processes interact to influence bacterioplankton metacommunity processes and their seasonal differences across thermal gradients. Our results may advance the understanding of marine microbial ecology under future global warming.}, }
@article {pmid30367000, year = {2018}, author = {Šulčius, S and Šimoliūnas, E and Alzbutas, G and Gasiūnas, G and Jauniškis, V and Kuznecova, J and Miettinen, S and Nilsson, E and Meškys, R and Roine, E and Paškauskas, R and Holmfeldt, K}, title = {Genomic characterization of cyanophage vB_AphaS-CL131 infecting filamentous diazotrophic cyanobacterium Aphanizomenon flos-aquae reveals novel insights into virus-bacterium interactions.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.01311-18}, pmid = {30367000}, issn = {1098-5336}, abstract = {While filamentous cyanobacteria play a crucial role in food web dynamics and biogeochemical cycling of many aquatic ecosystems around the globe, the knowledge regarding phages infecting them is limited. Here we describe the complete genome of the virulent cyanophage vB_AphaS-CL131 (CL 131), a Siphoviridae phage that infects filamentous diazotrophic bloom forming cyanobacterium Aphanizomenon flos-aquae in the brackish Baltic Sea. CL 131 features a 112793 bp dsDNA genome, encompassing 149 putative open reading frames (ORFs), of which the majority (86%) lack sequence homology to genes with known functions in other bacteriophages or bacteria. Phylogenetic analysis revealed that CL 131 possibly represents a new evolutionary lineage within the group of cyanophages infecting filamentous cyanobacteria, which form a separate cluster compared to phages infecting unicellular cyanobacteria. CL 131 encodes a putative type V-U2 CRISPR-Cas system with one spacer (out of 10) targeting a DNA primase pseudogene in a cyanobacterium and a putative type II toxin-antitoxin system, consisting of GNAT family N-acetyltransferase and a protein of unknown function containing the PRK09726 domain (characteristic of HipB antitoxins). Comparison of CL 131 proteins to reads from Baltic Sea and other available fresh- and brackish-water metagenomes and analysis of CRISPR-Cas arrays in publicly available A. flos-aquae genomes demonstrated that phages similar to CL 131 are present and dynamic in the Baltic Sea and share common history with their hosts dating back at least several decades. In addition, different CRISPR-Cas systems within individual A. flos-aquae genomes targeted several sequences in the CL 131 genome, including genes related to virion structure and morphogenesis. Altogether, these findings revealed new genomic information for exploring viral diversity and provide a model system for investigation of virus-host interactions in filamentous cyanobacteria.Importance The genomic characterization of novel cyanophage vB_AphaS-CL131 and the analysis of its genomic features in the context of other viruses, metagenomic data and host CRISPR-Cas systems contribute toward better understanding of aquatic viral diversity and distribution in general and brackish water cyanophages infecting filamentous diazotrophic cyanobacteria in the Baltic Sea in particular. The results of this study revealed previously undescribed features of cyanophage genomes (e.g. self-excising intein-containing putative dCTP deaminase, putative cyanophage-encoded CRISPR-Cas and toxin-antitoxin systems) and can therefore be used to predict potential interactions between bloom-forming cyanobacteria and their cyanophages.}, }
@article {pmid30366996, year = {2018}, author = {De Filippis, F and La Storia, A and Villani, F and Ercolini, D}, title = {Strain-level diversity analysis of Pseudomonas fragi after in situ pangenome reconstruction shows distinctive spoilage-associated metabolic traits clearly selected by different storage conditions.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.02212-18}, pmid = {30366996}, issn = {1098-5336}, abstract = {Microbial spoilage of raw meat causes huge economic losses every year. Understanding the microbial ecology associated to the spoilage and its dynamics during refrigerated storage of meat can help in preventing and delaying the spoilage-related activities. Raw meat microbiota is usually complex but only few members will develop during storage and cause spoilage, upon the pressure of several external factors, such as temperature and oxygen availability. We characterized the metagenome of beef packed aerobically or under-vacuum during refrigerated storage to explore how different packaging conditions may influence microbial composition and potential spoilage-associated activities. Different population dynamics and spoilage-associated genomic repertoires occurred in beef stored in air or vacuum-packaging. Moreover, pangenomics of Pseudomonas fragi strains extracted from metagenomes was carried out. We demonstrated the presence of specific, storage-driven strain-level profiles of Pseudomonas fragi, characterized by a different gene repertoire, thus potentially able to act differently during meat spoilage. The results provide new knowledge on strain-level microbial ecology associated to meat spoilage and can be of value for future strategies of spoilage prevention and food waste reduction.IMPORTANCE This work provides insights on the mechanisms involved in raw beef spoilage during refrigerated storage and on the selective pressure exerted by the packaging conditions. We highlighted the presence of different microbial metagenomes during spoilage of beef packaged aerobically or under-vacuum. The packaging condition was able to select specific Pseudomonas fragi strains, with a distinctive genomic repertoire. This study may help in deciphering the behaviour of different biomes directly in-situ in food and in understanding the specific contribution of different strains to food spoilage.}, }
@article {pmid30366260, year = {2018}, author = {Sharma, S and Tripathi, P}, title = {Gut microbiome and type 2 diabetes: where we are and where to go?.}, journal = {The Journal of nutritional biochemistry}, volume = {63}, number = {}, pages = {101-108}, doi = {10.1016/j.jnutbio.2018.10.003}, pmid = {30366260}, issn = {1873-4847}, abstract = {Type 2 diabetes mellitus (T2D) is a highly prevalent metabolic disorder characterized by an imbalance in blood glucose level, altered lipid profile and high blood pressure. Genetic constituents, high-fat and high-energy dietary habits, and a sedentary lifestyle are three major factors that contribute to high risk of T2D. Several studies have reported gut microbiome dysbiosis as a factor in rapid progression of insulin resistance in T2D that accounts for about 90% of all diabetes cases worldwide. The gut microbiome dysbiosis may reshape intestinal barrier functions and host metabolic and signaling pathways, which are directly or indirectly related to the insulin resistance in T2D. Thousands of the metabolites derived from microbes interact with the epithelial, hepatic and cardiac cell receptors that modulate host physiology. Xenobiotics including dietary components, antibiotics and nonsteroidal anti-inflammatory drugs strongly affect the gut microbial composition and can promote dysbiosis. Any change in the gut microbiota can shift the host metabolism towards increased energy harvest during diabetes and obesity. However, the exact mechanisms behind the dynamics of gut microbes and their impact on host metabolism at the molecular level are yet to be deciphered. We reviewed the published literature for better understanding of the dynamics of gut microbiota, factors that potentially induce gut microbiome dysbiosis and their relation to the progression of T2D. Special emphasis was also given to understand the gut microbiome induced breaching of intestinal barriers and/or tight junctions and their relation to insulin resistance.}, }
@article {pmid30362214, year = {2018}, author = {Götz, F and Pjevac, P and Markert, S and McNichol, J and Becher, D and Schweder, T and Mussmann, M and Sievert, SM}, title = {Transcriptomic and proteomic insight into the mechanism of cyclooctasulfur- versus thiosulfate-oxidation by the chemolithoautotroph Sulfurimonas denitrificans.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14452}, pmid = {30362214}, issn = {1462-2920}, support = {OCE-1559198//NSF/ ; //The Investment in Science Fund at WHOI/ ; //Institute of Marine Biotechnology e.V./ ; }, abstract = {Chemoautotrophic bacteria belonging to the genus Sulfurimonas (class Campylobacteria) were previously identified as key players in the turnover of zero-valence sulfur, a central intermediate in the marine sulfur cycle. S. denitrificans was further shown to be able to oxidize cyclooctasulfur (S8). However, at present the mechanism of activation and metabolism of cyclooctasulfur is not known. Here, we assessed the transcriptome and proteome of S. denitrificans grown with either thiosulfate or S8 as the electron donor. While the overall expression profiles under the two growth conditions were rather similar, distinct differences were observed that could be attributed to the utilization of S8 . This included a higher abundance of expressed genes related to surface attachment in the presence of S8 , and the differential regulation of the sulfur-oxidation multienzyme complex (SOX), which in S. denitrificans is encoded in two gene clusters: soxABXY 1 Z 1 and soxCDY 2 Z 2 . While the proteins of both clusters were present with thiosulfate, only proteins of the soxCDY 2 Z 2 were detected at significant levels with S8 . Based on these findings a model for the oxidation of S8 is proposed. Our results have implications for interpreting metatranscriptomic and -proteomic data and for the observed high level of diversification of soxY 2 Z 2 among sulfur-oxidizing Campylobacteria.}, }
@article {pmid30362076, year = {2018}, author = {Almeida, OGG and De Martinis, ECP}, title = {Bioinformatics tools to assess metagenomic data for applied microbiology.}, journal = {Applied microbiology and biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00253-018-9464-9}, pmid = {30362076}, issn = {1432-0614}, support = {17/13759-6//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 6762/2006-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico (BR)/ ; }, abstract = {The reduction of the price of DNA sequencing has resulted in the emergence of large data sets to handle and analyze, especially in microbial ecosystems, which are characterized by high taxonomic and functional diversities. To assess the properties of these complex ecosystems, a conceptual background of the application of NGS technology and bioinformatics analysis to metagenomics is required. Accordingly, this article presents an overview of the evolution of knowledge of microbial ecology from traditional culture-dependent methods to culture-independent methods and the last frontier in knowledge, metagenomics. Topics that will be covered include sample preparation for NGS, starting with total DNA extraction and library preparation, followed by a brief discussion of the chemistry of NGS to help provide an understanding of which bioinformatics pipeline approach may be helpful for achieving a researcher's goals. The importance of selecting appropriate sequencing coverage and depth parameters to obtain a suitable measure of microbial diversity is discussed. As all DNA sequencing processes produce base-calling errors that compromise data analysis, including genome assembly and microbial functional analysis, dedicated software is presented and conceptually discussed with regard to potential applications in the general microbial ecology field.}, }
@article {pmid30359366, year = {2018}, author = {Bosmans, L and Pozo, MI and Verreth, C and Crauwels, S and Wilberts, L and Sobhy, IS and Wäckers, F and Jacquemyn, H and Lievens, B}, title = {Habitat-specific variation in gut microbial communities and pathogen prevalence in bumblebee queens (Bombus terrestris).}, journal = {PloS one}, volume = {13}, number = {10}, pages = {e0204612}, doi = {10.1371/journal.pone.0204612}, pmid = {30359366}, issn = {1932-6203}, abstract = {Gut microbial communities are critical for the health of many insect species. However, little is known about how gut microbial communities respond to anthropogenic changes and how such changes affect host-pathogen interactions. In this study, we used deep sequencing to investigate and compare the composition of gut microbial communities within the midgut and ileum (both bacteria and fungi) in Bombus terrestris queens collected from natural (forest) and urbanized habitats. Additionally, we investigated whether the variation in gut microbial communities under each habitat affected the prevalence of two important bumblebee pathogens that have recently been associated with Bombus declines (Crithidia bombi and Nosema bombi). Microbial community composition differed strongly among habitat types, both for fungi and bacteria. Fungi were almost exclusively associated with bumblebee queens from the forest habitats, and were not commonly detected in bumblebee queens from the urban sites. Further, gut bacterial communities of urban B. terrestris specimens were strongly dominated by bee-specific core bacteria like Snodgrassella (Betaproteobacteria) and Gilliamella (Gammaproteobacteria), whereas specimens from the forest sites contained a huge fraction of environmental bacteria. Pathogen infection was very low in urban populations and infection by Nosema was only observed in specimens collected from forest habitats. No significant relationship was found between pathogen prevalence and microbial gut diversity. However, there was a significant and negative relationship between prevalence of Nosema and relative abundance of the core resident Snodgrassella, supporting its role in pathogen defense. Overall, our results indicate that land-use change may lead to different microbial gut communities in bumblebees, which may have implications for bumblebee health, survival and overall fitness.}, }
@article {pmid30357428, year = {2018}, author = {Kamitani, M and Nagano, AJ and Honjo, MN and Kudoh, H}, title = {A Survey on Plant Viruses in Natural Brassicaceae Communities Using RNA-Seq.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1271-4}, pmid = {30357428}, issn = {1432-184X}, support = {JP26221106//KAKENHI/ ; 16H06171//KAKENHI/ ; JP16H01473//KAKENHI/ ; JPMJCR15O1//Core Research for Evolutional Science and Technology/ ; JPMJCR15O2//Core Research for Evolutional Science and Technology/ ; 15J00628//Grant-in-Aid for JSPS Fellows/ ; }, abstract = {Studies on plant viruses are biased towards crop diseases and little is known about viruses in natural vegetation. We conducted extensive surveys of plant viruses in wild Brassicaceae plants occurring in three local plant communities in central Japan. We applied RNA-Seq with selective depletion of rRNA, which allowed us to detect infections of all genome-reported viruses simultaneously. Infections of Turnip mosaic virus (TuMV), Cucumber mosaic virus (CMV), Brassica yellows virus, Pelargonium zonate spot virus, and Arabidopsis halleri partitivirus 1 were detected from the two perennial species, Arabidopsis halleri subsp. gemmifera and Rorippa indica. De novo assembly further detected partial sequences of a putative novel virus in Arabis fragellosa. Virus species composition and infection rate differed depending on site and plant species. Viruses were most frequently detected from the perennial clonal plant, A. halleri, in which a high clonal transmission rate of viruses across multiple years was confirmed. Phylogenetic analysis of TuMV and CMV showed that virus strains from wild Brassicaceae were included as a major clade of these viruses with other reported strains from crop plants, suggesting that viruses were shared among wild plants and crops. Our studies indicated that distribution of viruses in natural plant populations are determined by the combinations of life histories of viruses and hosts. Revealing viral distribution in the natural plant communities improves our knowledge on the ecology of plant viruses.}, }
@article {pmid30357425, year = {2018}, author = {Li, CX and Fan, YF and Luan, W and Dai, Y and Wang, MX and Wei, CM and Wang, Y and Tao, X and Mao, P and Ma, XR}, title = {Titanium Ions Inhibit the Bacteria in Vase Solutions of Freshly Cut Gerbera jamesonii and Extend the Flower Longevity.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1273-2}, pmid = {30357425}, issn = {1432-184X}, support = {2017YFD0201301//National Key Research and Development Program of China/ ; 2018NA0027//Key Research and Development Program of Sichuan/ ; }, abstract = {Titanium ions significantly promote plant growth, but the mechanism is still unclear. Cut flowers are ideal materials for the study of plant growth and senescence. In this study, freshly cut Gerbera jamesonii were used to study the effects of titanium ions (8 mg/L) on the flower longevity. Flowering observation showed that the gerbera vase life was significantly prolonged in the presence of titanium ions. Plate colony counts showed that the amounts of bacteria in the vase solution of the control group were approximately 1700 times more than that of titanium ion treatment group. High-throughput sequencing was used to determine the sequences of 16S rRNA gene V3-V4 variable regions of the vase solutions to analyze bacterial species, their average proportions, and absolute abundance. The results showed that the titanium ions reduced the entire bacterial counts as well as altered the absolute abundance of different bacterial species in the vase solution. The most prevalent bacteria were mainly Enterobacteriaceae, Pseudomonas veronii, Pseudomonas sp., Delftia sp., Agrobacterium sp., Sphingobacterium multivorum, Acinetobacter johnsonii, and Clostridiaceae. In combination with plate colony counts, we demonstrated that all the bacterial growths were significantly inhibited by titanium ions, regardless of their average proportions increased or decreased. These results showed that titanium ions could extend effectively the longevity of gerberas and possess the broad-spectrum antibacterial properties. This study provides a basis for further mechanism exploration of titanium ions action and its applications in cut flower preservation and agricultural production.}, }
@article {pmid30355963, year = {2018}, author = {Almendras, K and Leiva, D and Carú, M and Orlando, J}, title = {Carbon Consumption Patterns of Microbial Communities Associated with Peltigera Lichens from a Chilean Temperate Forest.}, journal = {Molecules (Basel, Switzerland)}, volume = {23}, number = {11}, pages = {}, doi = {10.3390/molecules23112746}, pmid = {30355963}, issn = {1420-3049}, support = {11100381 and 1181510//Fondo Nacional de Desarrollo Científico y Tecnológico/ ; }, abstract = {Lichens are a symbiotic association between a fungus and a green alga or a cyanobacterium, or both. They can grow in practically any terrestrial environment and play crucial roles in ecosystems, such as assisting in soil formation and degrading soil organic matter. In their thalli, they can host a wide diversity of non-photoautotrophic microorganisms, including bacteria, which play important functions and are considered key components of the lichens. In this work, using the BioLog® EcoPlate system, we studied the consumption kinetics of different carbon-sources by microbial communities associated with the thallus and the substrate of Peltigera lichens growing in a Chilean temperate rain forest dominated by Nothofagus pumilio. Based on the similarity of the consumption of 31 carbon-sources, three groups were formed. Among them, one group clustered the microbial metabolic profiles of almost all the substrates from one of the sampling sites, which exhibited the highest levels of consumption of the carbon-sources, and another group gathered the microbial metabolic profiles from the lichen thalli with the most abundant mycobiont haplotypes. These results suggest that the lichen thallus has a higher impact on the metabolism of its microbiome than on the microbial community of its substrate, with the latter being more diverse in terms of the metabolized sources and whose activity level is probably related to the availability of soil nutrients. However, although significant differences were detected in the microbial consumption of several carbon-sources when comparing the lichen thallus and the underlying substrate, d-mannitol, l-asparagine, and l-serine were intensively metabolized by both communities, suggesting that they share some microbial groups. Likewise, some communities showed high consumption of 2-hydroxybenzoic acid, d-galacturonic acid, and itaconic acid; these could serve as suitable sources of microorganisms as bioresources of novel bioactive compounds with biotechnological applications.}, }
@article {pmid30355662, year = {2018}, author = {Hird, SM and Ganz, H and Eisen, JA and Boyce, WM}, title = {The Cloacal Microbiome of Five Wild Duck Species Varies by Species and Influenza A Virus Infection Status.}, journal = {mSphere}, volume = {3}, number = {5}, pages = {}, doi = {10.1128/mSphere.00382-18}, pmid = {30355662}, issn = {2379-5042}, support = {HHSN266200700010C/AI/NIAID NIH HHS/United States ; HHSN272201400008C/AI/NIAID NIH HHS/United States ; }, abstract = {Waterfowl, especially ducks of the genus Anas, are natural reservoir species for influenza A virus (IAV). Duck populations contain nearly all the known diversity of IAVs, and the birds are asymptomatic to infection. Previous work established that IAV infection status is correlated with changes in the cloacal microbiome in juvenile mallards. Here, we analyze five Anas species to determine whether these duck species have similar IAV+ and IAV- cloacal microbiomes, or if the relationships among a host, influenza virus, and the microbiome are species specific. We assessed taxonomic composition of the microbiome, alpha diversity, and beta diversity and found very few patterns related to microbiome and infection status across species, while detecting strong differences within species. A host species-specific signal was stronger in IAV- ducks than IAV+ ducks, and the effect size of host species on the microbiome was three times higher in IAV- birds than IAV+ birds. The mallards and the northern shovelers, the species with highest sample sizes but also with differing feeding ecology, showed especially contrasting patterns in microbiome composition, alpha diversity, and beta diversity. Our results indicate that the microbiome may have a unique relationship with influenza virus infection at the species level.IMPORTANCE Waterfowl are natural reservoir species for influenza A virus (IAV). Thus, they maintain high levels of pathogen diversity, are asymptomatic to the infection, and also contribute to the risk of a global influenza pandemic. An individual's microbiome is a critical part in how a vertebrate manages pathogens and illness. Here, we describe the cloacal microbiome of 300 wild ducks, from five species (four with previously undescribed microbiomes), including both IAV-negative and IAV-positive individuals. We demonstrate that there is not one consistent &quot;flu-like&quot; microbiome or response to flu across species. Individual duck species appear to have unique relationships between their microbiomes and IAV, and IAV-negative birds have a stronger tie to host species than the IAV-positive birds. In a broad context, understanding the role of the microbiome in IAV reservoir species may have future implications for avian disease management.}, }
@article {pmid30355348, year = {2018}, author = {Tackmann, J and Arora, N and Schmidt, TSB and Rodrigues, JFM and von Mering, C}, title = {Ecologically informed microbial biomarkers and accurate classification of mixed and unmixed samples in an extensive cross-study of human body sites.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {192}, doi = {10.1186/s40168-018-0565-6}, pmid = {30355348}, issn = {2049-2618}, support = {31003A-160095//Swiss National Science Foundation/ ; }, abstract = {BACKGROUND: The identification of body site-specific microbial biomarkers and their use for classification tasks have promising applications in medicine, microbial ecology, and forensics. Previous studies have characterized site-specific microbiota and shown that sample origin can be accurately predicted by microbial content. However, these studies were usually restricted to single datasets with consistent experimental methods and conditions, as well as comparatively small sample numbers. The effects of study-specific biases and statistical power on classification performance and biomarker identification thus remain poorly understood. Furthermore, reliable detection in mixtures of different body sites or with noise from environmental contamination has rarely been investigated thus far. Finally, the impact of ecological associations between microbes on biomarker discovery was usually not considered in previous work.<br><br>RESULTS: Here we present the analysis of one of the largest cross-study sequencing datasets of microbial communities from human body sites (15,082 samples from 57 publicly available studies). We show that training a Random Forest Classifier on this aggregated dataset increases prediction performance for body sites by 35% compared to a single-study classifier. Using simulated datasets, we further demonstrate that the source of different microbial contributions in mixtures of different body sites or with soil can be detected starting at 1% of the total microbial community. We apply a biomarker selection method that excludes indirect environmental associations driven by microbe-microbe associations, yielding a parsimonious set of highly predictive taxa including novel biomarkers and excluding many previously reported taxa. We find a considerable fraction of unclassified biomarkers (&quot;microbial dark matter&quot;) and observe that negatively associated taxa have a surprisingly high impact on classification performance. We further detect a significant enrichment of rod-shaped, motile, and sporulating taxa for feces biomarkers, consistent with a highly competitive environment.<br><br>CONCLUSIONS: Our machine learning model shows strong body site classification performance, both in single-source samples and mixtures, making it promising for tasks requiring high accuracy, such as forensic applications. We report a core set of ecologically informed biomarkers, inferred across a wide range of experimental protocols and conditions, providing the most concise, general, and least biased overview of body site-associated microbes to date.}, }
@article {pmid30353678, year = {2018}, author = {Tan, CK and Natrah, I and Suyub, IB and Edward, MJ and Kaman, N and Samsudin, AA}, title = {Comparative study of gut microbiota in wild and captive Malaysian Mahseer (Tor tambroides).}, journal = {MicrobiologyOpen}, volume = {}, number = {}, pages = {e00734}, doi = {10.1002/mbo3.734}, pmid = {30353678}, issn = {2045-8827}, support = {FP0311B011//Ministry of Science, Technology and Innovation (MOSTI) of Malaysia/ ; }, abstract = {AIMS: The aim of this study was to identify and compare the gut microbial community of wild and captive Tor tambroides through 16S rDNA metagenetic sequencing followed by functions prediction.<br><br>METHODS AND RESULTS: The library of 16S rDNA V3-V4 hypervariable regions of gut microbiota was amplified and sequenced using Illumina MiSeq. The sequencing data were analyzed using Quantitative Insights into Microbial Ecology (QIIME) pipeline and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). The most abundant bacterial phyla in both wild and captive T. tambroides were Firmicutes, Proteobacteria, Fusobacteria and Bacteroidetes. Cetobacterium spp., Peptostreptococcaceae family, Bacteroides spp., Phosphate solubilizing bacteria PSB-M-3, and Vibrio spp. were five most abundant OTU in wild T. tambroides as compared to Cetobacterium spp., Citrobacter spp., Aeromonadaceae family, Peptostreptococcaceae family and Turicibacter spp. in captive T. tambroides.<br><br>CONCLUSION: In this study, the specimens of the wild T. tambroides contain more diverse gut microbiota than of the captive ones. The results suggested that Cetobacterium spp. is one of the core microbiota in guts of T. tambroides. Besides, high abundant Bacteroides spp., Citrobacter spp., Turicibacter spp., and Bacillus spp. may provide important functions in T. tambroides guts.<br><br>The results of this study provide significant information of T. tambroides gut microbiota for further understanding of their physiological functions including growth and disease resistance.}, }
@article {pmid30352731, year = {2018}, author = {De Vrieze, J and Colica, G and Pintucci, C and Sarli, J and Pedizzi, C and Willeghems, G and Bral, A and Varga, S and Prat, D and Peng, L and Spiller, M and Buysse, J and Colsen, J and Benito, O and Carballa, M and Vlaeminck, SE}, title = {Resource recovery from pig manure via an integrated approach: A technical and economic assessment for full-scale applications.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.biortech.2018.10.024}, pmid = {30352731}, issn = {1873-2976}, abstract = {Intensive livestock farming cannot be uncoupled from the massive production of manure, requiring adequate management to avoid environmental damage. The high carbon, nitrogen and phosphorus content of pig manure enables targeted resource recovery. Here, fifteen integrated scenarios for recovery of water, nutrients and energy are compared in terms of technical feasibility and economic viability. The recovery of refined nutrients with a higher market value and quality, i.e., (NH4)2SO4 for N and struvite for P, coincided with higher net costs, compared to basic composting. The inclusion of anaerobic digestion promoted nutrient recovery efficiency, and enabled energy recovery through electricity production. Co-digestion of the manure with carbon-rich waste streams increased electricity production, but did not result in lower process costs. Overall, key drivers for the selection of the optimal manure treatment scenario will include the market demand for more refined (vs. separated or concentrated) products, and the need for renewable electricity production.}, }
@article {pmid30352325, year = {2019}, author = {Christiaens, MER and De Vrieze, J and Clinckemaillie, L and Ganigué, R and Rabaey, K}, title = {Anaerobic ureolysis of source-separated urine for NH3 recovery enables direct removal of divalent ions at the toilet.}, journal = {Water research}, volume = {148}, number = {}, pages = {97-105}, doi = {10.1016/j.watres.2018.10.021}, pmid = {30352325}, issn = {1879-2448}, abstract = {Source-separated urine is of interest for nutrient recovery. Most nitrogen recovery technologies rely on ammonia (NH3) as input, which requires ureolysis. As urease positive bacteria are widespread, source-separated urine is unstable, not only leading to NH3 release but also loss, odor nuisance, and downstream scaling. Hence, ureolysis ideally occurs in a closed controlled environment close to the toilet. We characterized microbial-induced ureolysis, subsequent divalent cation precipitation, and fermentation in anaerobic sequencing batch reactors (SBRs) at 15 °C and 28 °C. Temperatures were a proxy for urine hydrolysis in a wet well at street level or in the toilet, respectively. The need for inoculation and the metabolic stability was assessed by inoculation with autofermented urine or a mixture of anaerobic digestion and fermentation sludge. The highest specific ureolysis rates in the SBRs were achieved at 28 °C: 2107 ± 395 and 1948 ± 1121 mg N g VSS-1 d-1, for the mixed and autofermented inoculum, respectively. For Ca2+ and Mg2+ precipitation, and organics fermentation, autofermented urine at 28 °C performed best with 47.9 ± 16.4 mg Ca2+ g VSS-1 d-1, 8.2 ± 4.6 mg Mg2+ g VSS-1 d-1, and 623 ± 129 mg VFA-COD g VSS-1 d-1, respectively. This indicates the hydrolysis reactor should be close to the toilet. The selected inoculum did not impact ureolysis, whereas both Ca2+ and Mg2+ precipitation and fermentation were better in the SBRs with autofermented urine. Ureolysis was identified as the only process significantly impacting the microbial community, indicating external inoculation would not be required. A urine hydrolysis reactor in the toilet without external inoculation could thus serve as a controlled environment to release NH3 and remove divalent cations to prevent scaling in downstream transport and processing. For practical implementation in a household toilet, the reactor should be designed for user-friendly precipitate discharge and odor control.}, }
@article {pmid30350953, year = {2018}, author = {Cabernard, L and Roscher, L and Lorenz, C and Gerdts, G and Primpke, S}, title = {Comparison of Raman and Fourier Transform Infrared Spectroscopy for the Quantification of Microplastics in the Aquatic Environment.}, journal = {Environmental science &amp; technology}, volume = {52}, number = {22}, pages = {13279-13288}, doi = {10.1021/acs.est.8b03438}, pmid = {30350953}, issn = {1520-5851}, abstract = {Microplastics (MPs, <5 mm) have been reported as emerging environmental contaminants, but reliable data are still lacking. We compared the two most promising techniques for MP analysis, namely, Raman and Fourier transform infrared (FTIR) spectroscopy, by analyzing MPs extracted from North Sea surface waters. Microplastics >500 μm were visually sorted and manually analyzed by μ-Raman and attenuated total reflection (ATR)-FTIR spectroscopy. Microplastics ≤500 μm were concentrated on gold-coated filters and analyzed by automated single-particle exploration coupled to μ-Raman (ASPEx-μ-Raman) and FTIR imaging (reflection mode). The number of identified MPs >500 μm was slightly higher for μ-Raman (+23%) than ATR-FTIR analysis. Concerning MPs ≤500 μm, ASPEx-μ-Raman quantified two-times higher MP numbers but required a four-times higher analysis time compared to FTIR imaging. Because ASPEx-μ-Raman revealed far higher MP concentrations (38-2621 particles m-3) compared to the results of previous water studies (0-559 particles m-3), the environmental concentration of MPs ≤500 μm may have been underestimated until now. This may be attributed to the exceptional increase in concentration with decreasing MP size found in this work. Our results demonstrate the need for further research to enable time-efficient routine application of ASPEx-μ-Raman for reliable MP counting down to 1 μm.}, }
@article {pmid30349964, year = {2018}, author = {Gonzalez-Escobedo, R and Briones-Roblero, CI and López, MF and Rivera-Orduña, FN and Zúñiga, G}, title = {Changes in the Microbial Community of Pinus arizonica Saplings After Being Colonized by the Bark Beetle Dendroctonus rhizophagus (Curculionidae: Scolytinae).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1274-1}, pmid = {30349964}, issn = {1432-184X}, support = {SIP 20180686//Secretaría de Investigación y Posgrado, Instituto Politécnico Nacional/ ; }, abstract = {The death of trees is an ecological process that promotes regeneration, organic matter recycling, and the structure of communities. However, diverse biotic and abiotic factors can disturb this process. Dendroctonus bark beetles (Curculionidae: Scolytinae) are natural inhabitants of pine forests, some of which produce periodic outbreaks, killing thousands of trees in the process. These insects spend almost their entire life cycle under tree bark, where they reproduce and feed on phloem. Tunneling and feeding of the beetles result in the death of the tree and an alteration of the resident microbiota as well as the introduction of microbes that the beetles vector. To understand how microbial communities in subcortical tissues of pines change after they are colonized by the bark beetle Dendroctonus rhizophagus, we compare both the bacterial and fungal community structures in two colonization stages of Pinus arizonica (Arizona pine) employing Illumina MiSeq. Our findings showed significant differences in diversity and the dominance of bacterial community in the two colonization stages with Shannon (P = 0.004) and Simpson (P = 0.0006) indices, respectively, but not in species richness with Chao1 (P = 0.19). In contrast, fungal communities in both stages showed significant differences in species richness with Chao1 (P = 0.0003) and a diversity with Shannon index (P = 0.038), but not in the dominance with the Simpson index (P = 0.12). The β-diversity also showed significant changes in the structure of bacterial and fungal communities along the colonization stages, maintaining the dominant members in both cases. Our results suggest that microbial communities present in the Arizona pine at the tree early colonization stage by bark beetle change predictably over time.}, }
@article {pmid30348833, year = {2018}, author = {Zeng, L and Burne, RA}, title = {Essential Roles of the sppRA Fructose-Phosphate Phosphohydrolase Operon in Carbohydrate Metabolism and Virulence Expression by Streptococcus mutans.}, journal = {Journal of bacteriology}, volume = {}, number = {}, pages = {}, doi = {10.1128/JB.00586-18}, pmid = {30348833}, issn = {1098-5530}, abstract = {The dental caries pathogen Streptococcus mutans can ferment a variety of sugars to produce organic acids. Exposure of S. mutans to certain non-metabolizable carbohydrates such as xylitol impairs growth and can cause cell death. Recently, the presence of a sugar-phosphate stress in S. mutans was demonstrated using a mutant lacking 1-phosphofructokinase (FruK) that accumulates fructose-1-phosphate (F-1-P). Here we studied an operon in S. mutans, sppRA, which was highly expressed in the fruK mutant. Biochemical characterization of a recombinant SppA protein indicated that it possessed hexose-phosphate phosphohydrolase activity, with preferences for F-1-P and, to a lesser degree, fructose-6-phosphate (F-6-P). SppA activity was stimulated by Mg2+ and Mn2+, but inhibited by NaF. SppR, a DeoR-family regulator, repressed the expression of the sppRA operon to minimum levels in the absence of the fructose-derived metabolites, F-1-P and likely also F-6-P. Accumulation of F-1-P, as a result of growth on fructose, not only induced sppA expression, it significantly altered biofilm maturation through increased cell lysis and enhanced extracellular DNA release. Constitutive expression of sppA, via a plasmid or by deleting sppR, greatly alleviated fructose-induced stress in a fruK mutant, enhanced resistance to xylitol, and reversed effects of fructose on biofilm formation. Finally, by identifying three additional putative phosphatases that are capable of promoting sugar-phosphate tolerance, we show that S. mutans is capable of mounting a sugar-phosphate stress response by modulating the levels of certain glycolytic intermediates, functions that are interconnected with the ability of the organism to manifest key virulence behaviors.IMPORTANCEStreptococcus mutans is a major etiologic agent for dental caries, primarily due to its ability to form biofilms on tooth surface and to convert carbohydrates into organic acids. We have discovered a two-gene operon in S. mutans that regulates fructose metabolism by controlling the levels of fructose-1-phosphate, a potential signaling compound that affects bacterial behaviors. With fructose becoming increasingly common and abundant in the human diet, we reveal the ways fructose may alter bacterial development, stress tolerance, and microbial ecology in the oral cavity to promote oral diseases.}, }
@article {pmid30344635, year = {2018}, author = {Lavoie, C and Courcelle, M and Redivo, B and Derome, N}, title = {Structural and compositional mismatch between captive and wild Atlantic salmon (Salmo salar) parrs' gut microbiota highlights the relevance of integrating molecular ecology for management and conservation methods.}, journal = {Evolutionary applications}, volume = {11}, number = {9}, pages = {1671-1685}, doi = {10.1111/eva.12658}, pmid = {30344635}, issn = {1752-4571}, abstract = {Stocking methods are used in the Province of Quebec to restore Salmo salar populations. However, Atlantic salmon stocked juveniles show higher mortality rates than wild ones when introduced into nature. Hatchery environment, which greatly differs from the natural environment, is identified as the main driver of the phenotypic mismatch between captive and wild parrs. The latter is also suspected to impact the gut microbiota composition, which can be associated with essential metabolic functions for their host. We hypothesized that hatchery-raised parrs potentially recruit gut microbial communities that are different from those recruited in the wild. This study evaluated the impacts of artificial rearing on gut microbiota composition in 0+ parrs meant for stocking in two distinct Canadian rivers: Rimouski and Malbaie (Quebec, Canada). Striking differences between hatchery and wild-born parrs' gut microbiota suggest that microbiota could be another factor that could impact their survival in the targeted river, because the microbiome is narrowly related to host physiology. For instance, major commensals belonging to Enterobacteriaceae and Clostridiacea from wild parrs' gut microbiota were substituted in captive parrs by lactic acid bacteria from the Lactobacillaceae family. Overall, captive parrs host a generalist bacterial community whereas wild parrs' microbiota is much more specialized. This is the very first study demonstrating extensive impact of captive rearing on intestinal microbiota composition in Atlantic salmon intended for wild population stocking. Our results strongly suggest the need to implement microbial ecology concepts into conservation management of endangered salmon stocks supplemented with hatchery-reared parrs.}, }
@article {pmid30343437, year = {2018}, author = {Li, T and Qi, M and Gatesoupe, FJ and Tian, D and Jin, W and Li, J and Lin, Q and Wu, S and Li, H}, title = {Adaptation to Fasting in Crucian Carp (Carassius auratus): Gut Microbiota and Its Correlative Relationship with Immune Function.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1275-0}, pmid = {30343437}, issn = {1432-184X}, support = {lzujbky-2018-68//Fundamental Research Funds for the Central Universities/ ; LY18E090010//Zhejiang Provincial Natural Science Foundation of China/ ; }, abstract = {Fasting influences the overall physiology of fish, and the knowledge how the gut microbiota, growth performances, and immune function in response to intermittent and long-term fasting is still insufficient. Here, we characterized the effects of fasting on the host-gut microbiota in crucian carp, which would enhance our insight into physiological adaptation to fasting. To achieve this, we investigated the gut microbial communities of crucian carp with different fasting stress, and corresponding immune and growth parameters. The gut microbial communities were structured into four clusters according to different fasting stress, namely one control group (feed regularly), two intermittent fasting groups (fasting period and re-feeding period, respectively), and one long-term fasting group. Intermittent fasting significantly improved the activity of superoxide dismutase (SOD) and lysozyme (LZM) (ANOVA, p < 0.05) and significantly increased alpha diversity and ecosystem stability of gut microbiota (ANOVA, p < 0.05). Gut length (GL) and condition factor (CF) showed no significant difference between the control group (CG) and intermittent fasting group under re-feeding period (RIF) (ANOVA, p = 0.11), but relative gut length (RGL) in group RIF was higher than that in the CG (ANOVA, p = 0.00). The bacterial genera Bacteroides, Akkermansia, and Erysipelotrichaceae were enriched in fishes under intermittent fasting. Two Bacteroides OTUs (OTU50 and OTU1292) correlated positively with immune (SOD, complement, and LZM) and growth (GL and RGL) parameters. These results highlight the possible interplay between growth performances, immune function, and gut microbiota in response to fasting.}, }
@article {pmid30342721, year = {2018}, author = {Free, A and McDonald, MA and Pagaling, E}, title = {Diversity-Function Relationships in Natural, Applied, and Engineered Microbial Ecosystems.}, journal = {Advances in applied microbiology}, volume = {105}, number = {}, pages = {131-189}, doi = {10.1016/bs.aambs.2018.07.002}, pmid = {30342721}, issn = {0065-2164}, abstract = {The connection between ecosystem function and taxonomic diversity has been of interest and relevance to macroecologists for decades. After many years of lagging behind due to the difficulty of assigning both taxonomy and function to poorly distinguishable microscopic cells, microbial ecology now has access to a suite of powerful molecular tools which allow its practitioners to generate data relating to diversity and function of a microbial community on an unprecedented scale. Instead, the problem facing today's microbial ecologists is coupling the ease of generation of these datasets with the formulation and testing of workable hypotheses relating the diversity and function of environmental, host-associated, and engineered microbial communities. Here, we review the current state of knowledge regarding the links between taxonomic alpha- and beta-diversity and ecosystem function, comparing our knowledge in this area to that obtained by macroecologists who use more traditional techniques. We consider the methodologies that can be applied to study these properties and how successful they are at linking function to diversity, using examples from the study of model microbial ecosystems, methanogenic bioreactors (anaerobic digesters), and host-associated microbiota. Finally, we assess ways in which our newly acquired understanding might be used to manipulate diversity in ecosystems of interest in order to improve function for the benefit of us or the environment in general through the provision of ecosystem services.}, }
@article {pmid30341500, year = {2018}, author = {Deja-Sikora, E and Gołębiewski, M and Kalwasińska, A and Krawiec, A and Kosobucki, P and Walczak, M}, title = {Comamonadaceae OTU as a Remnant of an Ancient Microbial Community in Sulfidic Waters.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1270-5}, pmid = {30341500}, issn = {1432-184X}, support = {1919-B//Uniwersytet Mikolaja Kopernika w Toruniu/ ; }, abstract = {Intraterrestrial waters harbor microbial communities being extensively studied to understand microbial processes underlying subsurface ecosystem functioning. This paper provides the results of an investigation on the microbiomes of unique, subsurface sulfidic waters associated with Upper Jurassic, Cretaceous, and Miocene sediments. We used high-throughput 16S rDNA amplicon sequencing to reveal the structure of bacterial and archaeal communities in water samples differing in sulfide content (20-960 mg/dm3), salinity (1.3-3.2%), and depth of extraction (60-660 m below ground level). Composition of the bacterial communities strongly varied across the samples; however, the bacteria participating in the sulfur cycle were common in all sulfidic waters. The shallowest borehole water (60 m bgl) was dominated by sulfur-oxidizing Epsilonproteobacteria (Sulfurimonas, Sulfurovum). In the waters collected from greater depths (148-300 m bgl), the prevalence of Betaproteobacteria (Comamonadaceae) and sulfate/sulfur-reducing Deltaproteobacteria (Desulfopila, Desulfomicrobium, MSBL7) was observed. Sulfate reducers (members of Clostridia: Candidatus Desulforudis) were the most abundant bacteria in the deepest borehole water (660 m bgl). Out of 850 bacterial OTUs, only one, affiliated with the Comamonadaceae family, was found abundant (> 1% of total bacterial sequences) in all samples. Contribution of Archaea to the whole microbial communities was lower than 0.5%. Archaeal communities did not differ across the samples and they consisted of Halobacteriaceae. Out of 372 archaeal OTUs, five, belonging to the four genera Natronomonas, Halorubrum, Halobellus, and Halorhabdus, were the most numerous.}, }
@article {pmid30341452, year = {2018}, author = {Amberkar, U and Khandeparker, R and Parab, P}, title = {Nitrate Reductase Gene Expression in Idiomarina Strain cos21 Obtained from Oxygen Minimum Zone of Arabian Sea.}, journal = {Current microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00284-018-1585-y}, pmid = {30341452}, issn = {1432-0991}, abstract = {This study analyses the induction and repression of nitrate reduction activity in a batch culture of Idiomarina strain cos21. On a change from aerobic to anaerobic respiration, the culture entered a stationary phase. The onset of this phase showed 3.75 fold increase in mRNA levels for the nitrate reductase enzyme. mRNA accumulated very rapidly during a short period, after which its overall concentration declined to reach a lower value. The level of nitrite reductase protein reached a maximum value at 36 h of growth when the oxygen concentration dropped below 10 µM. The data set provided here confer new insights into the understanding of the physiological response of Idiomarina strain cos21 to change in oxygen concentration allowing the bacterium to survive and adapt to a new environment by dissimilatory reduction of nitrate to nitrite, which serves to provide energy as the bacteria adapt to anaerobiosis. Main strategy used here is to induce, measure, and track the expression of microbial genes, while they grow in culture conditions to better mimic interaction in a natural environment. This study will help us with a better understanding of the nitrate reduction process in the oxygen minimum zone.}, }
@article {pmid30340417, year = {2018}, author = {Van Houdt, R and Provoost, A and Van Assche, A and Leys, N and Lievens, B and Mijnendonckx, K and Monsieurs, P}, title = {Cupriavidus metallidurans Strains with Different Mobilomes and from Distinct Environments Have Comparable Phenomes.}, journal = {Genes}, volume = {9}, number = {10}, pages = {}, doi = {10.3390/genes9100507}, pmid = {30340417}, issn = {2073-4425}, support = {C90356//Federaal Wetenschapsbeleid/ ; }, abstract = {Cupriavidus metallidurans has been mostly studied because of its resistance to numerous heavy metals and is increasingly being recovered from other environments not typified by metal contamination. They host a large and diverse mobile gene pool, next to their native megaplasmids. Here, we used comparative genomics and global metabolic comparison to assess the impact of the mobilome on growth capabilities, nutrient utilization, and sensitivity to chemicals of type strain CH34 and three isolates (NA1, NA4 and H1130). The latter were isolated from water sources aboard the International Space Station (NA1 and NA4) and from an invasive human infection (H1130). The mobilome was expanded as prophages were predicted in NA4 and H1130, and a genomic island putatively involved in abietane diterpenoids metabolism was identified in H1130. An active CRISPR-Cas system was identified in strain NA4, providing immunity to a plasmid that integrated in CH34 and NA1. No correlation between the mobilome and isolation environment was found. In addition, our comparison indicated that the metal resistance determinants and properties are conserved among these strains and thus maintained in these environments. Furthermore, all strains were highly resistant to a wide variety of chemicals, much broader than metals. Only minor differences were observed in the phenomes (measured by phenotype microarrays), despite the large difference in mobilomes and the variable (shared by two or three strains) and strain-specific genomes.}, }
@article {pmid30327827, year = {2018}, author = {Kowalec, M and Szewczyk, T and Welc-Falęciak, R and Siński, E and Karbowiak, G and Bajer, A}, title = {Rickettsiales Occurrence and Co-occurrence in Ixodes ricinus Ticks in Natural and Urban Areas.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1269-y}, pmid = {30327827}, issn = {1432-184X}, support = {NN404795240//Ministerstwo Nauki i Szkolnictwa Wyższego/ ; The study was financially supported by the Ministry of Science and Higher Education through the Faculty of Biology, University of Warsaw intramural grant DSM #501/86 - 104911//Ministerstwo Nauki i Szkolnictwa Wyższego/ ; The study was financially supported by the Ministry of Science and Higher Education through the Faculty of Biology, University of Warsaw intramural grant DSM #501/86 - 107422//Ministerstwo Nauki i Szkolnictwa Wyższego/ ; }, abstract = {Bacteria of Rickettsiaceae and Anaplasmataceae families include disease agents spread by Ixodes ricinus ticks, the most common tick vector in Europe. The aim of the study was to compare the prevalence and co-infection prevalence of particular tick-transmitted Rickettsiales members: Rickettsia spp. (further referred as Rs), Anaplasma phagocytophilum (Ap), and &quot;Candidatus Neoehrlichia mikurensis&quot; (CNM) in I. ricinus ticks in two types of areas, different in terms of human impact: natural and urban. Using additional data, we aimed at investigating co-occurrence of these Rickettsiales with Borreliella spp. A total of 4189 tick specimens, 2363 from the urban area (Warsaw park and forests) and 1826 from the natural area (forests and park in the vicinity of National Parks), were tested for the presence of Rickettsiales DNA by PCRs. The prevalence of selected Rickettsiales was twice higher in urban than natural areas (13.2% vs. 6.9%, respectively). In total ticks, the prevalence of Rs, Ap, and CNM was 6.5%, 5.3%, and 3.6% in urban areas vs. 4.4%, 1.1%, and 2.1% in natural areas, respectively. Co-infections of Rickettsiales were also more prevalent in urban areas (2.6% vs. 0.3%, respectively). The most common Rs was R. helvetica; also R. monacensis and novel &quot;Candidatus Rickettsia mendelii&quot; were detected. Positive association between Ap and CNM infections was discovered. Rickettsiales bacteria occurrence was not associated with Borreliella occurrence, but co-infections with these two groups were more common in ticks in urban areas. In conclusion, three groups of Rickettsiales constituted the important part of the tick pathogen community in Poland, especially in the urbanized central Poland (Mazovia). In the Warsaw agglomeration, there is a greater risk of encountering the I. ricinus tick infected with Rickettsiales and co-infected with Lyme spirochaetes, in comparison to natural areas. This finding raises the question whether cities might in fact be the hot spots for TBDs.}, }
@article {pmid30326440, year = {2019}, author = {Van Winckel, T and Liu, X and Vlaeminck, SE and Takács, I and Al-Omari, A and Sturm, B and Kjellerup, BV and Murthy, SN and De Clippeleir, H}, title = {Overcoming floc formation limitations in high-rate activated sludge systems.}, journal = {Chemosphere}, volume = {215}, number = {}, pages = {342-352}, doi = {10.1016/j.chemosphere.2018.09.169}, pmid = {30326440}, issn = {1879-1298}, abstract = {High-rate activated sludge (HRAS) is an essential cornerstone of the pursuit towards energy positive sewage treatment through maximizing capture of organics. The capture efficiency heavily relies on the degree of solid separation achieved in the clarifiers. Limitations in the floc formation process commonly emerge in HRAS systems, with detrimental consequences for the capture of organics. This study pinpointed and overcame floc formation limitations present in full-scale HRAS reactors. Orthokinetic flocculation tests were performed with varying shear, sludge concentration, and coagulant or flocculant addition. These were analyzed with traditional and novel settling parameters and extracellular polymeric substances (EPS) measurements. HRAS was limited by insufficient collision efficiency and occurred because the solids retention time (SRT) was short and colloid loading was high. The limitation was predominantly caused by impaired flocculation rather than coagulation. In addition, the collision efficiency limitation was driven by EPS composition (low protein over polysaccharide ratio) instead of total EPS amount. Collision efficiency limitation was successfully overcome by bio-augmenting sludge from a biological nutrient removal reactor operating at long SRT which did not show any floc formation limitations. However, this action brought up a floc strength limitation. The latter was not correlated with EPS composition, but rather EPS amount and hindered settling parameters, which determined floc morphology. With this, an analysis toolkit was proposed that will enable design engineers and operators to tackle activated solid separation challenges found in HRAS systems and maximize the recovery potential of the process.}, }
@article {pmid30325958, year = {2018}, author = {Lee, YM and Kor, CT and Zhou, D and Lai, HC and Chang, CC and Ma, WL}, title = {Impact of age at appendectomy on development of type 2 diabetes: A population-based cohort study.}, journal = {PloS one}, volume = {13}, number = {10}, pages = {e0205502}, doi = {10.1371/journal.pone.0205502}, pmid = {30325958}, issn = {1932-6203}, abstract = {AIM: Diabetes is a complex metabolic disease characterized by chronic low-grade inflammation in which genetic and environmental factors are involved. Growing evidence implicates that alterations of the gut microbiota potentially contribute to the emergence of metabolic diseases. The human appendix has more recently been recognized as a microbial reservoir for repopulating the gastrointestinal tract and an important part of the immune system. Thus, appendectomy may influence microbial ecology and immune function. This study investigated the association between appendectomy and type 2 diabetes risk.<br><br>METHODS: We analyzed a cohort of 10954 patients who underwent appendectomy between 1998 and 2013 based on the Taiwan National Health Insurance Program database. A comparison cohort of 43815 persons without appendectomy was selected randomly and matched by sex, age, comorbidities, and index year. To ensure reliability of the results, a sensitivity analysis using a propensity score-matched study was performed. We observed the subsequent development of type 2 diabetes in both cohorts.<br><br>RESULTS: Although the overall incidence of type 2 diabetes in the appendectomy patients was 7.9% higher than that in the non-appendectomy patients, it was not statistically significant (95% confidence interval [CI], 0.997-1.168) after the adjustment of confounding factors. Multivariate regression analysis revealed that the adjusted hazard ratio (HR) of type 2 diabetes was 1.347 for appendectomy patients < 30 years of age (95% CI, 1.009-1.798) compared to non-appendectomy patients. The incidence of type 2 diabetes was higher within 3 years of post-appendectomy follow-up than for non-appendectomy patients (HR, 2.017; 95% CI, 1.07-3.802). Age impacted the association between appendectomy and type 2 diabetes risk (Pinteraction = 0.002); in contrast, sex did not affect the association between appendectomy and type 2 diabetes risk (Pinteraction = 0.88).<br><br>CONCLUSIONS: Our study results suggest that appendectomy increases type 2 diabetes risk, particularly when performed prior to middle age.}, }
@article {pmid30324255, year = {2018}, author = {Szczepańska, A and Kiewra, D and Guz-Regner, K}, title = {Sensitivity of Ixodes ricinus (L., 1758) and Dermacentor reticulatus (Fabr., 1794) ticks to Bacillus thuringiensis isolates: preliminary study.}, journal = {Parasitology research}, volume = {117}, number = {12}, pages = {3897-3902}, doi = {10.1007/s00436-018-6096-z}, pmid = {30324255}, issn = {1432-1955}, support = {0420/2308/17//Uniwersytet Wrocławski/ ; }, abstract = {Bacillus thuringiensis is a highly specific entomopathogenic microorganism. Although defined as having properties which work against insects, its role in the control of tick populations is still insufficiently known. In our bioassay, four environmental strains of B. thuringiensis, along with one commercially available product (Vectobac), have been used against ticks. Vectobac turned out to be ineffective in the biocontrol of ticks; however, two of environmental B. thuringiensis strains proved to be efficient against both Ixodes ricinus and Dermacentor reticulatus. In those cases, the mortality rate for ticks was assessed as being up to 80%, and LC50 ranged between 9.1 × 106 and 1.3 × 1015 (cfu/ml). Dermacentor reticulatus males were the most sensitive to bacteria. The similarity between the most and least efficient B. thuringiensis strains in enzymatic profiles-including lipases, phosphatases, proteases, and chitinases-may indicate a limited role of detected enzymes in the pathogenicity profile of bacterial strains against ticks.}, }
@article {pmid30321727, year = {2019}, author = {Liu, K and Liu, Y and Han, BP and Xu, B and Zhu, L and Ju, J and Jiao, N and Xiong, J}, title = {Bacterial community changes in a glacial-fed Tibetan lake are correlated with glacial melting.}, journal = {The Science of the total environment}, volume = {651}, number = {Pt 2}, pages = {2059-2067}, doi = {10.1016/j.scitotenv.2018.10.104}, pmid = {30321727}, issn = {1879-1026}, abstract = {Climate change-induced glacial melting is a global phenomenon. The effects of climate change-induced melting on the microbial ecology in different glacial-fed aquatic systems have been well illuminated, but the resolution of seasonal dynamics was still limited. Here, we studied bacterial community composition and diversity in a glacial-fed Tibetan lake, Lake Ranwu, to elucidate how glacial-fed aquatic ecosystems respond to the seasonal glacial melting. Obvious seasonal variations of bacterial dominant groups were found in Lake Ranwu and inlet rivers. In April, the majority of OTUs belonged to the Bacteroidetes, Actinobacteria and Proteobacteria. The Proteobacteria increased to the most abundant phylum in July and November, while the Bacteroidetes and Actinobacteria decreased about 50% over seasons. Most key discriminant taxa of each season's community strongly associated with specific environmental variables, suggesting their adaptation to seasonal environments. Bacterial alpha diversity varied among seasons and exhibited strongly negative correlations with conductivity. Conductivity was the major driving force in determining the seasonal variation of bacterial community composition. Fluctuated conductivity was one of the consequences of seasonal melting of glaciers. This study offered evidence for the unique seasonal dynamics pattern of bacterial communities responding to glacial melting. Moreover, this study may provide a reference for assessing the long-term effects of glacial retreat on glacial-fed aquatic ecosystems.}, }
@article {pmid30320221, year = {2018}, author = {Stegen, JC and Goldman, AE}, title = {WHONDRS: a Community Resource for Studying Dynamic River Corridors.}, journal = {mSystems}, volume = {3}, number = {5}, pages = {}, doi = {10.1128/mSystems.00151-18}, pmid = {30320221}, issn = {2379-5077}, abstract = {The Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS) aims to galvanize a global community to provide the scientific basis for improved management of dynamic river corridors. WHONDRS is a global research consortium working to understand connections among dynamic hydrology, biogeochemistry, and microbiology in river corridors from local to global scales. WHONDRS ascribes to the perspective that resources, knowledge, and data belong to the community as a whole and that science advances more rapidly and more robustly through community ownership. As such, WHONDRS provides free access to novel instrumentation, molecular analysis, and well-curated data associated with river corridor hydrology, biogeochemistry, and microbiology. There are a number of ways to be involved in WHONDRS, ranging from one-time surface water sampling to installation of WHONDRS-developed multiparameter sensors for continuous monitoring. WHONDRS hinges on broad involvement, and we encourage all interested parties to contact us and become part of the consortium.}, }
@article {pmid30320215, year = {2018}, author = {Trubl, G and Jang, HB and Roux, S and Emerson, JB and Solonenko, N and Vik, DR and Solden, L and Ellenbogen, J and Runyon, AT and Bolduc, B and Woodcroft, BJ and Saleska, SR and Tyson, GW and Wrighton, KC and Sullivan, MB and Rich, VI}, title = {Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing.}, journal = {mSystems}, volume = {3}, number = {5}, pages = {}, doi = {10.1128/mSystems.00076-18}, pmid = {30320215}, issn = {2379-5077}, abstract = {Rapidly thawing permafrost harbors ∼30 to 50% of global soil carbon, and the fate of this carbon remains unknown. Microorganisms will play a central role in its fate, and their viruses could modulate that impact via induced mortality and metabolic controls. Because of the challenges of recovering viruses from soils, little is known about soil viruses or their role(s) in microbial biogeochemical cycling. Here, we describe 53 viral populations (viral operational taxonomic units [vOTUs]) recovered from seven quantitatively derived (i.e., not multiple-displacement-amplified) viral-particle metagenomes (viromes) along a permafrost thaw gradient at the Stordalen Mire field site in northern Sweden. Only 15% of these vOTUs had genetic similarity to publicly available viruses in the RefSeq database, and ∼30% of the genes could be annotated, supporting the concept of soils as reservoirs of substantial undescribed viral genetic diversity. The vOTUs exhibited distinct ecology, with different distributions along the thaw gradient habitats, and a shift from soil-virus-like assemblages in the dry palsas to aquatic-virus-like assemblages in the inundated fen. Seventeen vOTUs were linked to microbial hosts (in silico), implicating viruses in infecting abundant microbial lineages from Acidobacteria, Verrucomicrobia, and Deltaproteobacteria, including those encoding key biogeochemical functions such as organic matter degradation. Thirty auxiliary metabolic genes (AMGs) were identified and suggested virus-mediated modulation of central carbon metabolism, soil organic matter degradation, polysaccharide binding, and regulation of sporulation. Together, these findings suggest that these soil viruses have distinct ecology, impact host-mediated biogeochemistry, and likely impact ecosystem function in the rapidly changing Arctic. IMPORTANCE This work is part of a 10-year project to examine thawing permafrost peatlands and is the first virome-particle-based approach to characterize viruses in these systems. This method yielded >2-fold-more viral populations (vOTUs) per gigabase of metagenome than vOTUs derived from bulk-soil metagenomes from the same site (J. B. Emerson, S. Roux, J. R. Brum, B. Bolduc, et al., Nat Microbiol 3:870-880, 2018, https://doi.org/10.1038/s41564-018-0190-y). We compared the ecology of the recovered vOTUs along a permafrost thaw gradient and found (i) habitat specificity, (ii) a shift in viral community identity from soil-like to aquatic-like viruses, (iii) infection of dominant microbial hosts, and (iv) carriage of host metabolic genes. These vOTUs can impact ecosystem carbon processing via top-down (inferred from lysing dominant microbial hosts) and bottom-up (inferred from carriage of auxiliary metabolic genes) controls. This work serves as a foundation which future studies can build upon to increase our understanding of the soil virosphere and how viruses affect soil ecosystem services.}, }
@article {pmid30320131, year = {2018}, author = {Ziadi, M and Bouzaiene, T and M'Hir, S and Zaafouri, K and Mokhtar, F and Hamdi, M and Boisset-Helbert, C}, title = {Evaluation of the Efficiency of Ethanol Precipitation and Ultrafiltration on the Purification and Characteristics of Exopolysaccharides Produced by Three Lactic Acid Bacteria.}, journal = {BioMed research international}, volume = {2018}, number = {}, pages = {1896240}, doi = {10.1155/2018/1896240}, pmid = {30320131}, issn = {2314-6141}, abstract = {Exopolysaccharides (EPS) produced by three Lactic Acid Bacteria strains, Lactococcus lactis SLT10, Lactobacillus plantarum C7, and Leuconostoc mesenteroides B3, were isolated using two methods: ethanol precipitation (EPS-ETOH) and ultrafiltration (EPS-UF) through a 10 KDa cut-off membrane. EPS recovery by ultrafiltration was higher than ethanol precipitation for Lactococcus lactis SLT10 and Lactobacillus plantarum C7. However, it was similar with both methods for Leuconostoc mesenteroides B3. The monomer composition of the EPS fractions revealed differences in structures and molar ratios between the two studied methods. EPS isolated from Lactococcus lactis SLT10 are composed of glucose and mannose for EPS-ETOH against glucose, mannose, and rhamnose for EPS-UF. EPS extracted from Lactobacillus plantarum C7 and Leuconostoc mesenteroides B3 showed similar composition (glucose and mannose) but different molar ratios. The molecular weights of the different EPS fractions ranged from 11.6±1.83 to 62.4±2.94 kDa. Molecular weights of EPS-ETOH fractions were higher than those of EPS-UF fractions. Fourier transform infrared (FTIR) analysis revealed a similarity in the distribution of the functional groups (O-H, C-H, C=O, -COO, and C-O-C) between the EPS isolated from the three strains.}, }
@article {pmid30319569, year = {2018}, author = {D'Amico, F and Candela, M and Turroni, S and Biagi, E and Brigidi, P and Bega, A and Vancini, D and Rampelli, S}, title = {The Rootstock Regulates Microbiome Diversity in Root and Rhizosphere Compartments of Vitis vinifera Cultivar Lambrusco.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2240}, doi = {10.3389/fmicb.2018.02240}, pmid = {30319569}, issn = {1664-302X}, abstract = {Plants belonging to Vitis vinifera varieties are usually grafted on different rootstocks to enhance the plant defenses against pathogens and increase productivity under harsh environmental conditions. Particularly, in Emilia-Romagna region (Italy), Vitis vinifera cultivar Lambrusco can be grafted on a hybrid of V. berlandieri × V. riparia (5BB) or V. berlandieri × V. rupestris (1103P). However, the latter shows potassium absorption problems, with a consequent reduction in grapevine production. Since it has recently been demonstrated that the rootstock has the potential to select for different microorganisms at the root-soil interface, here we hypothesized that the potassium deficiency of 1103P could be partially accounted for by the peculiarities of the rootstock microbiome. We thus employed 16S rRNA sequencing to compare root and rhizosphere microbiomes in plants of V. vinifera cultivar Lambrusco grafted on the two aforementioned rootstocks. According to our findings, 1103P shows a reduced diversity in root and rhizosphere microbiomes, including members of potassium-solubilizing microorganisms, possibly explaining the inadequate potassium absorption of this hybrid. Besides confirming the importance of the rootstock as a determinant of the composition of plant microbiomes, our data indicate the relevance of rootstock-selected microbiomes as possible regulators of potassium absorption by V. vinifera.}, }
@article {pmid30318762, year = {2018}, author = {Van Assche, A and Crauwels, S and De Brabanter, J and Willems, KA and Lievens, B}, title = {Characterization of the bacterial community composition in water of drinking water production and distribution systems in Flanders, Belgium.}, journal = {MicrobiologyOpen}, volume = {}, number = {}, pages = {e726}, doi = {10.1002/mbo3.726}, pmid = {30318762}, issn = {2045-8827}, support = {L2010S0013X//Vlaamse Instelling voor Technologisch Onderzoek/ ; L2010S0013X//Flemish Environment Agency/ ; }, abstract = {The quality of drinking water is influenced by its chemical and microbial composition which in turn may be affected by the source water and the different processes applied in drinking water purification systems. In this study, we investigated the bacterial diversity in different water samples from the production and distribution chain of thirteen drinking water production and distribution systems from Flanders (Belgium) that use surface water or groundwater as source water. Water samples were collected over two seasons from the source water, the processed drinking water within the production facility and out of the tap in houses along its distribution network. 454-pyrosequencing of 16S ribosomal RNA gene sequences revealed a total of 1,570 species-level bacterial operational taxonomic units. Strong differences in community composition were found between processed drinking water samples originating from companies that use surface water and other that use groundwater as source water. Proteobacteria was the most abundant phylum in all samples. Yet, several phyla including Actinobacteria were significantly more abundant in surface water while Cyanobacteria were more abundant in surface water and processed water originating from surface water. Gallionella, Acinetobacter, and Pseudomonas were the three most abundant genera detected. Members of the Acinetobacter genus were even found at a relative read abundance of up to 47.5% in processed water samples, indicating a general occurrence of Acinetobacter in drinking water (systems).}, }
@article {pmid30318710, year = {2018}, author = {Liu, Y and Qin, Q and Defoirdt, T}, title = {Does quorum sensing interference affect the fitness of bacterial pathogens in the real world?.}, journal = {Environmental microbiology}, volume = {20}, number = {11}, pages = {3918-3926}, doi = {10.1111/1462-2920.14446}, pmid = {30318710}, issn = {1462-2920}, support = {//Special Research Fund of Ghent University/ ; 218043//Scientific Research Startup Fund of South China Agricultural University/ ; }, abstract = {Many bacterial pathogens rely on quorum sensing to control virulence gene expression. Based on numerous experiments conducted under well-defined conditions, quorum sensing interference is considered as a promising strategy to tackle infections and thus might have the potential to (partially) replace antibiotics. Despite the promising results in well-defined (artificial) laboratory experiments, there still is a lack of knowledge with respect to the impact of quorum sensing interference on the fitness of pathogens in more realistic scenarios, including interactions with a host, the external environment and complex microbial communities. In this article, we critically evaluate the current knowledge with respect to these three facets of the real world that can affect the fitness of quorum sensing bacterial pathogens. We argue that further research is needed in order to determine how these factors interplay with quorum sensing and to what extent they can influence the selective pressure that might be exerted by quorum sensing interference (and thus determine the risk of resistance development against quorum sensing interference). This kind of information is indispensable in order to optimize quorum sensing interference-based therapeutic strategies.}, }
@article {pmid30317429, year = {2018}, author = {Mania, I and Gorra, R and Colombo, N and Freppaz, M and Martin, M and Anesio, AM}, title = {Prokaryotic Diversity and Distribution in Different Habitats of an Alpine Rock Glacier-Pond System.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1272-3}, pmid = {30317429}, issn = {1432-184X}, support = {NE/J02399X/1//Natural Environment Research Council/ ; }, abstract = {Rock glaciers (RG) are assumed to influence the biogeochemistry of downstream ecosystems because of the high ratio of rock:water in those systems, but no studies have considered the effects of a RG inflow on the microbial ecology of sediments in a downstream pond. An alpine RG-pond system, located in the NW Italian Alps has been chosen as a model, and Bacteria and Archaea 16S rRNA genes abundance, distribution and diversity have been assessed by qPCR and Illumina sequencing, coupled with geochemical analyses on sediments collected along a distance gradient from the RG inflow. RG surface material and neighbouring soil have been included in the analysis to better elucidate relationships among different habitats.Our results showed that different habitats harboured different, well-separated microbial assemblages. Across the pond, the main variations in community composition (e.g. Thaumarchaeota and Cyanobacteria relative abundance) and porewater geochemistry (pH, DOC, TDN and NH4+) were not directly linked to RG proximity, but to differences in water depth. Some microbial markers potentially linked to the presence of meltwater inputs from the RG have been recognised, although the RG seems to have a greater influence on the pond microbial communities due to its contribution in terms of sedimentary material.}, }
@article {pmid30314008, year = {2018}, author = {Sen, A and Saha, R and Sivakumar, K and Bhadury, P}, title = {Inventorizing the modern benthic foraminiferal assemblage from marginal marine environments across the North West coast of Bay of Bengal.}, journal = {Zootaxa}, volume = {4441}, number = {2}, pages = {245-260}, doi = {10.11646/zootaxa.4441.2.3}, pmid = {30314008}, issn = {1175-5334}, abstract = {Modern benthic foraminiferal assemblages are instrumental in providing information regarding changes in relative sea level as well as prevailing environmental conditions in marine environments. Marginal marine environments are coastal environments that are in most cases characterized by high influx of terrestrially originated nutrients. Inventorizing of modern benthic foraminiferal assemblages from such habitats can act as biotic indicators of water quality variations along with any changes in relative sea level. The present study documents the modern benthic foraminiferal assemblage from three major marginal marine habitats located along the North West coast of Bay of Bengal, in the Indian Ocean. Sediment samples for the purpose were thus collected from the Indian Sundarbans Delta, Chilika lagoon and the Gautami Godavari estuarine zone which encompasses the Kakinada bay. A total of 32 species of benthic foraminifera were documented during the study. The present observations were compared with previous reports of benthic foraminiferal diversity from these habitats and exhibited variability.}, }
@article {pmid30312413, year = {2018}, author = {Van Geel, M and Yu, K and Ceulemans, T and Peeters, G and van Acker, K and Geerts, W and Ramos, MA and Serafim, C and Kastendeuch, P and Najjar, G and Ameglio, T and Ngao, J and Saudreau, M and Waud, M and Lievens, B and Castro, PM and Somers, B and Honnay, O}, title = {Variation in ectomycorrhizal fungal communities associated with Silver linden (Tilia tomentosa) within and across urban areas.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {12}, pages = {}, doi = {10.1093/femsec/fiy207}, pmid = {30312413}, issn = {1574-6941}, abstract = {Trees in urban areas face harsh environmental conditions. Ectomycorrhizal fungi (EcM) form a symbiosis with many tree species and provide a range of benefits to their host through their extraradical hyphal network. Although our understanding of the environmental drivers and large scale geographical variation of EcM communities in natural ecosystems is growing, our knowledge of EcM communities within and across urban areas is still limited. Here, we characterized EcM communities using Illumina miseq sequencing on 175 root samples of the urban tree Tilia tomentosa from three European cities, namely Leuven (Belgium), Strasbourg (France) and Porto (Portugal). We found strong differences in EcM richness and community composition between cities. Soil acidity, organic matter and moisture content were significantly associated with EcM community composition. In agreement, the explained variability in EcM communities was mostly attributed to general soil characteristics, whereas very little variation was explained by city and heavy metal pollution. Overall, our results suggest that EcM communities in urban areas are significantly associated with soil characteristics, while heavy metal pollution and biogeography had little or no impact. These findings deliver new insights into EcM distribution patterns in urban areas and contribute to specific inoculation strategies to improve urban tree vitality.}, }
@article {pmid30310241, year = {2017}, author = {Eisenhauer, N and Powell, JR}, title = {Plant trait effects on soil organisms and functions.}, journal = {Pedobiologia}, volume = {65}, number = {}, pages = {1-4}, doi = {10.1016/j.pedobi.2017.11.001}, pmid = {30310241}, issn = {0031-4056}, support = {677232//European Research Council/International ; }, abstract = {Global change alters the composition and functioning of ecosystems by creating novel environmental conditions and thereby selecting for specific traits of organisms. Thus, trait-based approaches are promising tools to more mechanistically understand compositional and functional shifts in ecological communities as well as the dependency of response and effect traits upon global change. Such approaches have been particularly successful for the study of plant communities in terrestrial ecosystems. However, given the intimate linkages between aboveground and belowground compartments as well as the significance of plants as integrating organisms across those compartments, the role of plant traits in affecting soils communities has been understudied. This special issue contains empirical studies and reviews of plant trait effects on soil organisms and functions. Based on those contributions, we discuss here plasticity in trait expression, the context-dependency of plant trait effects, time lags in soil biotic responses to trait expression, and limitations of measured plant traits. We conclude that plant trait-based approaches are an important tool to advance soil ecological research, but also identify critical limitations and next steps.}, }
@article {pmid30310127, year = {2018}, author = {Cuer, CA and Rodrigues, RAR and Balieiro, FC and Jesus, J and Silva, EP and Alves, BJR and Rachid, CTCC}, title = {Short-term effect of Eucalyptus plantations on soil microbial communities and soil-atmosphere methane and nitrous oxide exchange.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {15133}, doi = {10.1038/s41598-018-33594-6}, pmid = {30310127}, issn = {2045-2322}, abstract = {Soil greenhouse gas (GHG) emissions are a significant environmental problem resulting from microbially-mediated nitrogen (N) and carbon (C) cycling. This study aimed to investigate the impact of Eucalyptus plantations on the structure and function of a soil microbial community, and how resulting alterations may be linked to GHG fluxes. We sampled and monitored two adjacent Eucalyptus plantations-a recently logged site that harbored new seedlings and an adult plantation-and compared them to a site hosting native vegetation. We used 16S rRNA gene sequencing and qPCR amplifications of key nitrogen and methane cycle genes to characterize microbial structure and functional gene abundance and compared our data with soil parameters and GHG fluxes. Both microbial community attributes were significantly affected by land use and logging of Eucalyptus plantations. The genes nosZ and archaeal amoA were significantly more abundant in native forest than in either young or old Eucalyptus plantations. Statistical analyses suggest that land use type has a greater impact on microbial community structure and functional gene abundance than Eucalyptus rotation. There was no correlation between GHG fluxes and shifts in microbial community, suggesting that microbial community structure and functional gene abundance are not the main drivers of GHG fluxes in this system.}, }
@article {pmid30308860, year = {2019}, author = {Karmakar, R and Bindiya, S and Hariprasad, P}, title = {Convergent evolution in bacteria from multiple origins under antibiotic and heavy metal stress, and endophytic conditions of host plant.}, journal = {The Science of the total environment}, volume = {650}, number = {Pt 1}, pages = {858-867}, doi = {10.1016/j.scitotenv.2018.09.078}, pmid = {30308860}, issn = {1879-1026}, mesh = {Adaptation, Physiological/physiology ; Anti-Bacterial Agents/*toxicity ; Bacteria/*genetics ; *Biological Evolution ; Endophytes ; Integrons ; Metals, Heavy/*toxicity ; Plants/*microbiology ; Soil Pollutants/*toxicity ; }, abstract = {The focus of this work is to study the convergent evolution in bacteria from multiple origins under antibiotic and heavy metal stress, and endophytic conditions of host plant cultivated on the Yamuna river bank. Forty-one endophytic bacteria (EB) were isolated from green leafy vegetables (GLV's) and were found to be resistant to a wide range of antibiotics (AB) and heavy metals (HM) tested. Further, they showed susceptibility to Quinolones group of antibiotics, and the HM, Cadmium, Chromium, and Mercury. Twenty-seven percent of these bacteria endowed with Class I integron. The probability of co-existence of HM resistance with β‑lactams was higher, whereas quinolones group of AB recorded lesser values. These EB owned a wide array of beneficial traits, through which they improved the plant health under HM and salt stress conditions. Bacterial identity revealed the association of both plant beneficial and human pathogenic bacteria as an endophyte with GLV's. Principal component analysis showed a pattern of convergent evolution irrespective of their origin. In conclusion, under the selection pressure of AB and HM, the susceptible EB population may reduce with time and the resistant native/introduced bacteria might survive. The vertical and horizontal gene transfer between introduced and native bacteria is the crucial factor in enhancing their fitness along with the host plant to survive under abiotic stress conditions.}, }
@article {pmid30308834, year = {2019}, author = {Lourenço, KS and Rossetto, R and Vitti, AC and Montezano, ZF and Soares, JR and Sousa, RM and do Carmo, JB and Kuramae, EE and Cantarella, H}, title = {Strategies to mitigate the nitrous oxide emissions from nitrogen fertilizer applied with organic fertilizers in sugarcane.}, journal = {The Science of the total environment}, volume = {650}, number = {Pt 1}, pages = {1476-1486}, doi = {10.1016/j.scitotenv.2018.09.037}, pmid = {30308834}, issn = {1879-1026}, abstract = {Vinasse is a major byproduct of the sugarcane biofuel industry, recycled in the fields. However, there is evidence that the application of vinasse with mineral nitrogen (N) fertilizers in sugarcane enhances the emission of greenhouse gases (GHGs). Therefore, strategies are needed to decrease the environmental impacts caused by both inputs. We carried out three sugarcane field experiments by applying N fertilizer (ammonium nitrate) with types of vinasses (concentrated-CV and standard-V) in different combinations (vinasses with N fertilizer and vinasses one month before or after mineral N fertilization). The gases nitrous oxide (N2O), carbon dioxide (CO2), and methane (CH4) were measured in one experiment fertilized in the beginning (fall/winter = dry season) and two experiments fertilized in the end (spring = rainy season) of the harvest season. Sugarcane fields were sinks rather than sources of CH4, while total carbon emitted as CO2 was similar between seasons and treatments. The effect of mineral fertilization and vinasses (CV and V) on N2O emissions was highly dependent on soil moisture (rain events). The N2O-N fertilizer emission factor (EF) varied from 0.07% to 0.51%, whereas the average EF of V and CV were 0.66% and 0.34%, respectively. On average across the three experiments, the combination of vinasse (CV or V) with N fertilizer increased the N2O emissions 2.9-fold compared to that of N fertilizer alone. For CV + N, the EF was 0.94% of the applied N and 0.23% of the ammonium nitrate-N, and for V + N (EF = 0.47%), increased emissions were observed in two out of three experiments. The strategy of anticipating or postponing vinasse application by one month with respect to mineral N reduced the N2O emissions by 51% for CV, but not for V. Therefore, to avoid boosting N2O emissions, we suggest applying vinasses (CV and V) before or after mineral N fertilization.}, }
@article {pmid30308248, year = {2018}, author = {Hessler, T and Harrison, STL and Huddy, RJ}, title = {Stratification of microbial communities throughout a biological sulphate reducing up-flow anaerobic packed bed reactor, revealed through 16S metagenomics.}, journal = {Research in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.resmic.2018.09.003}, pmid = {30308248}, issn = {1769-7123}, abstract = {Biological sulphate reduction (BSR) is a promising low-cost treatment of acid rock drainage effluents. In this paper, the system performance and microbial ecology of a lactate supplemented BSR up-flow anaerobic packed bed reactor (UAPBR) are evaluated across reactor height and compared to a continuous stirred tank reactor (CSTR). The biomass concentrations of planktonic and biofilm communities were quantified and subsequently characterised by 16S rRNA gene amplicon sequencing. The defined microbial communities were shown to correlate with differing availability of lactate, volatile fatty acids produced from lactate degradation and sulphate concentration. The UAPBR was able to achieve near complete sulphate conversion at a 4-day hydraulic residence time (HRT) at a sulphate feed concentration of 10.41 mM (1 g/L). The high volumetric sulphate reduction rate of 0.184 mM/L.h achieved in the first third of the reactor was attributed to OTUs present in the planktonic and biofilm communities. While the scavenging of sulphate within the final third of the UAPBR was attributed to an acetate oxidising genus of SRB which was not detected in the lactate-fed CSTR. The detailed analyses of the microbial communities throughout the UAPBR and CSTR contribute to the growing understanding of the impact of the microbial communities of BSR reactors on system performance.}, }
@article {pmid30305843, year = {2018}, author = {Cassman, NA and Lourenço, KS and do Carmo, JB and Cantarella, H and Kuramae, EE}, title = {Correction to: Genome-resolved metagenomics of sugarcane vinasse bacteria.}, journal = {Biotechnology for biofuels}, volume = {11}, number = {}, pages = {270}, doi = {10.1186/s13068-018-1254-1}, pmid = {30305843}, issn = {1754-6834}, abstract = {[This corrects the article DOI: 10.1186/s13068-018-1036-9.].}, }
@article {pmid30303297, year = {2018}, author = {Ghosh, A and Bhadury, P}, title = {Exploring biogeographic patterns of bacterioplankton communities across global estuaries.}, journal = {MicrobiologyOpen}, volume = {}, number = {}, pages = {e741}, doi = {10.1002/mbo3.741}, pmid = {30303297}, issn = {2045-8827}, support = {//IISER Kolkata/ ; }, abstract = {Estuaries provide an ideal niche to study structure and function of bacterioplankton communities owing to the presence of a multitude of environmental stressors. Bacterioplankton community structures from nine global estuaries were compared to understand their broad-scale biogeographic patterns. Bacterioplankton community structure from four estuaries of Sundarbans, namely Mooriganga, Thakuran, Matla, and Harinbhanga, was elucidated using Illumina sequencing. Bacterioplankton communities from these estuaries were compared against available bacterioplankton sequence data from Columbia, Delaware, Jiulong, Pearl, and Hangzhou estuaries. All nine estuaries were dominated by Proteobacteria. Other abundant phyla included Bacteroidetes, Firmicutes, Acidobacteria, Actinobacteria, Cyanobacteria, Planctomycetes, and Verrucomicrobia. The abundant bacterial phyla showed a ubiquitous presence across the estuaries. At class level, the overwhelming abundance of Gammaproteobacteria in the estuaries of Sundarbans and Columbia estuary clearly stood out amidst high abundance of Alphaproteobacteria observed in the other estuaries. Abundant bacterial families including Rhodobacteriaceae, Shingomonadaceae, Acidobacteriaceae, Vibrionaceae, and Xanthomondaceae also showed ubiquitous presence in the studied estuaries. However, rare taxa including Chloroflexi, Tenericutes, Nitrospirae, and Deinococcus-Thermus showed clear site-specific distribution patterns. Such distribution patterns were also reinstated by nMDS ordination plots. Such clustering patterns could hint toward the potential role of environmental parameters and substrate specificity which could result in distinct bacterioplankton communities at specific sites. The ubiquitous presence of abundant bacterioplankton groups along with their strong correlation with surface water temperature and dissolved nutrient concentrations indicates the role of such environmental parameters in shaping bacterioplankton community structure in estuaries. Overall, studies on biogeographic patters of bacterioplankton communities can provide interesting insights into ecosystem functioning and health of global estuaries.}, }
@article {pmid30301807, year = {2018}, author = {Weber, Y and Sinninghe Damsté, JS and Zopfi, J and De Jonge, C and Gilli, A and Schubert, CJ and Lepori, F and Lehmann, MF and Niemann, H}, title = {Redox-dependent niche differentiation provides evidence for multiple bacterial sources of glycerol tetraether lipids in lakes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {43}, pages = {10926-10931}, doi = {10.1073/pnas.1805186115}, pmid = {30301807}, issn = {1091-6490}, abstract = {Terrestrial paleoclimate archives such as lake sediments are essential for our understanding of the continental climate system and for the modeling of future climate scenarios. However, quantitative proxies for the determination of paleotemperatures are sparse. The relative abundances of certain bacterial lipids, i.e., branched glycerol dialkyl glycerol tetraethers (brGDGTs), respond to changes in environmental temperature, and thus have great potential for climate reconstruction. Their application to lake deposits, however, is hampered by the lack of fundamental knowledge on the ecology of brGDGT-producing microbes in lakes. Here, we show that brGDGTs are synthesized by multiple groups of bacteria thriving under contrasting redox regimes in a deep meromictic Swiss lake (Lake Lugano). This niche partitioning is evidenced by highly distinct brGDGT inventories in oxic vs. anoxic water masses, and corresponding vertical patterns in bacterial 16S rRNA gene abundances, implying that sedimentary brGDGT records are affected by temperature-independent changes in the community composition of their microbial producers. Furthermore, the stable carbon isotope composition (δ13C) of brGDGTs in Lake Lugano and 34 other (peri-)Alpine lakes attests to the widespread heterotrophic incorporation of 13C-depleted, methane-derived biomass at the redox transition zone of mesotrophic to eutrophic lake systems. The brGDGTs produced under such hypoxic/methanotrophic conditions reflect near-bottom water temperatures, and are characterized by comparatively low δ13C values. Depending on climate zone and water depth, lake sediment archives predominated by deeper water/low-13C brGDGTs may provide more reliable records of climate variability than those where brGDGTs derive from terrestrial and/or aquatic sources with distinct temperature imprints.}, }
@article {pmid30298251, year = {2018}, author = {Hall, M and Beiko, RG}, title = {16S rRNA Gene Analysis with QIIME2.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1849}, number = {}, pages = {113-129}, doi = {10.1007/978-1-4939-8728-3_8}, pmid = {30298251}, issn = {1940-6029}, abstract = {Microbial marker-gene sequence data can be used to generate comprehensive taxonomic profiles of the microorganisms present in a given community and for other community diversity analyses. The process of going from raw gene sequences to taxonomic profiles or diversity measures involves a series of data transformations performed by numerous computational tools. This includes tools for sequence quality checking, denoising, taxonomic classification, alignment, and phylogenetic tree building. In this chapter, we demonstrate how the Quantitative Insights Into Microbial Ecology version 2 (QIIME2) software suite can simplify 16S rRNA marker-gene analysis. We walk through an example data set extracted from the guts of bumblebees in order to show how QIIME2 can transform raw sequences into taxonomic bar plots, phylogenetic trees, principal co-ordinates analyses, and other visualizations of microbial diversity.}, }
@article {pmid30297403, year = {2018}, author = {García, FC and Bestion, E and Warfield, R and Yvon-Durocher, G}, title = {Changes in temperature alter the relationship between biodiversity and ecosystem functioning.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {43}, pages = {10989-10994}, doi = {10.1073/pnas.1805518115}, pmid = {30297403}, issn = {1091-6490}, abstract = {Global warming and the loss of biodiversity through human activities (e.g., land-use change, pollution, invasive species) are two of the most profound threats to the functional integrity of the Earth's ecosystems. These factors are, however, most frequently investigated separately, ignoring the potential for synergistic effects of biodiversity loss and environmental warming on ecosystem functioning. Here we use high-throughput experiments with microbial communities to investigate how changes in temperature affect the relationship between biodiversity and ecosystem functioning. We found that changes in temperature systematically altered the relationship between biodiversity and ecosystem functioning. As temperatures departed from ambient conditions the exponent of the diversity-functioning relationship increased, meaning that more species were required to maintain ecosystem functioning under thermal stress. This key result was driven by two processes linked to variability in the thermal tolerance curves of taxa. First, more diverse communities had a greater chance of including species with thermal traits that enabled them to maintain productivity as temperatures shifted from ambient conditions. Second, we found a pronounced increase in the contribution of complementarity to the net biodiversity effect at high and low temperatures, indicating that changes in species interactions played a critical role in mediating the impacts of temperature change on the relationship between biodiversity and ecosystem functioning. Our results highlight that if biodiversity loss occurs independently of species' thermal tolerance traits, then the additional impacts of environmental warming will result in sharp declines in ecosystem function.}, }
@article {pmid30297041, year = {2019}, author = {Ssepuuya, G and Wynants, E and Verreth, C and Crauwels, S and Lievens, B and Claes, J and Nakimbugwe, D and Van Campenhout, L}, title = {Microbial characterisation of the edible grasshopper Ruspolia differens in raw condition after wild-harvesting in Uganda.}, journal = {Food microbiology}, volume = {77}, number = {}, pages = {106-117}, doi = {10.1016/j.fm.2018.09.005}, pmid = {30297041}, issn = {1095-9998}, abstract = {This research aimed at establishing the chemical intrinsic properties and the microbial quality of an edible grasshopper Ruspolia differens and the effect of its source (geographical area) in Uganda, trading point, swarming season and plucking on these parameters. The intrinsic properties of the grasshopper can support the growth of a wide variety of microorganisms. High counts of total aerobic microbes, Enterobacteriaceae, lactic acid bacteria, total aerobic spores, and yeasts and moulds were obtained. Metagenetic analyses yielded 1793 Operational Taxonomic Units (OTUs) belonging to 24 phyla. Actinobacteria, Bacteroidetes, Firmicutes, Fusobacteria and Proteobacteria were the most abundant phyla, while members of the genera Acinetobacter, Buttiauxella, Lactococcus, Staphylococcus and Undibacterium were the most abundant OTUs. A number of genera harbouring potential pathogens (Acinetobacter, Bacillus, Buttiauxella, Campylobacter, Clostridium, Staphylococcus, Pseudomonas and Neisseria) were identified. The geographical area, trading point, swarming season and plucking significantly influenced microbial counts and bacterial diversity. The high microbial counts predispose R. differens to fast microbial spoilage, while the presence of Clostridium and Campylobacter makes this grasshopper a potential source of food borne diseases. Further research should identify the specific spoilage microorganisms of R. differens and assess the characteristics of this grasshopper that support growth of food pathogens.}, }
@article {pmid30294625, year = {2018}, author = {Urra, J and Alkorta, I and Mijangos, I and Garbisu, C}, title = {Data on links between structural and functional prokaryotic diversity in long-term sewage sludge amended soil.}, journal = {Data in brief}, volume = {20}, number = {}, pages = {1787-1796}, doi = {10.1016/j.dib.2018.09.025}, pmid = {30294625}, issn = {2352-3409}, abstract = {The application of sewage sludge to agricultural soil induces co-exposure of prokaryotic populations to antibiotics and heavy metals, thus exerting a selection pressure that may lead to the development of antibiotic resistance. Here, soil samples from a long-term factorial field experiment in which sewage sludge was applied to agricultural soil, at different rates (40 and 80 t ha-1) and frequencies (every 1, 2 and 4 years) of application, were studied to assess: (i) the effect of sewage sludge application on prokaryotic community composition, (ii) the links between prokaryotic community composition and antibiotic resistance profiles, and (iii) the links between antibiotic resistance and metal(oid) concentrations in amended soil. We found no significant impact of sewage sludge on prokaryotic community composition. Some antibiotic resistance genes (ARGs) correlated positively with particular prokaryotic taxa, being Gemmatimonadetes the taxon with the greatest number of positive correlations at phylum level. No positive correlation was found between prokaryotic taxa and genes encoding resistance to sulfonamides and FCA. All metal(oid)s showed positive correlations with, at least, one ARG. Metal(oid) concentrations in soil also showed positive correlations with mobile genetic element genes, particularly with the gene tnpA-07. These data provide useful information on the links between soil prokaryotic composition and resistome profiles, and between antibiotic resistance and metal(oid) concentrations, in agricultural soils amended with sewage sludge.}, }
@article {pmid30294306, year = {2018}, author = {Purahong, W and Wubet, T and Lentendu, G and Hoppe, B and Jariyavidyanont, K and Arnstadt, T and Baber, K and Otto, P and Kellner, H and Hofrichter, M and Bauhus, J and Weisser, WW and Krüger, D and Schulze, ED and Kahl, T and Buscot, F}, title = {Determinants of Deadwood-Inhabiting Fungal Communities in Temperate Forests: Molecular Evidence From a Large Scale Deadwood Decomposition Experiment.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2120}, doi = {10.3389/fmicb.2018.02120}, pmid = {30294306}, issn = {1664-302X}, abstract = {Despite the important role of wood-inhabiting fungi (WIF) in deadwood decomposition, our knowledge of the factors shaping the dynamics of their species richness and community composition is scarce. This is due to limitations regarding the resolution of classical methods used for characterizing WIF communities and to a lack of well-replicated long-term experiments with sufficient numbers of tree species. Here, we used a large scale experiment with logs of 11 tree species at an early stage of decomposition, distributed across three regions of Germany, to identify the factors shaping WIF community composition and Operational Taxonomic Unit (OTU) richness using next generation sequencing. We found that tree species identity was the most significant factor, corresponding to (P < 0.001) and explaining 10% (representing 48% of the explainable variance) of the overall WIF community composition. The next important group of variables were wood-physicochemical properties, of which wood pH was the only factor that consistently corresponded to WIF community composition. For overall WIF richness patterns, we found that approximately 20% of the total variance was explained by wood N content, location, tree species identity and wood density. It is noteworthy that the importance of determinants of WIF community composition and richness appeared to depend greatly on tree species group (broadleaved vs. coniferous) and it differed between the fungal phyla Ascomycota and Basidiomycota.}, }
@article {pmid30290356, year = {2019}, author = {Cipullo, S and Negrin, I and Claveau, L and Snapir, B and Tardif, S and Pulleyblank, C and Prpich, G and Campo, P and Coulon, F}, title = {Linking bioavailability and toxicity changes of complex chemicals mixture to support decision making for remediation endpoint of contaminated soils.}, journal = {The Science of the total environment}, volume = {650}, number = {Pt 2}, pages = {2150-2163}, doi = {10.1016/j.scitotenv.2018.09.339}, pmid = {30290356}, issn = {1879-1026}, abstract = {A six-month laboratory scale study was carried out to investigate the effect of biochar and compost amendments on complex chemical mixtures of tar, heavy metals and metalloids in two genuine contaminated soils. An integrated approach, where organic and inorganic contaminants bioavailability and distribution changes, along with a range of microbiological indicators and ecotoxicological bioassays, was used to provide multiple lines of evidence to support the risk characterisation and assess the remediation end-point. Both compost and biochar amendment (p = 0.005) as well as incubation time (p = 0.001) significantly affected the total and bioavailable concentrations of the total petroleum hydrocarbons (TPH) in the two soils. Specifically, TPH concentration decreased by 46% and 30% in Soil 1 and Soil 2 amended with compost. These decreases were accompanied by a reduction of 78% (Soil 1) and 6% (Soil 2) of the bioavailable hydrocarbons and the most significant decrease was observed for the medium to long chain aliphatic compounds (EC16-35) and medium molecular weight aromatic compounds (EC16-21). Compost amendment enhanced the degradation of both the aliphatic and aromatic fractions in the two soils, while biochar contributed to lock the hydrocarbons in the contaminated soils. Neither compost nor biochar affected the distribution and behaviour of the heavy metals (HM) and metalloids in the different soil phases, suggesting that the co-presence of heavy metals and metalloids posed a low risk. Strong negative correlations were observed between the bioavailable hydrocarbon fractions and the ecotoxicological assays suggesting that when bioavailable concentrations decreased, the toxicity also decreased. This study showed that adopting a combined diagnostic approach can significantly help to identify optimal remediation strategies and contribute to change the over-conservative nature of the current risk assessments thus reducing the costs associated with remediation endpoint.}, }
@article {pmid30288545, year = {2018}, author = {Benucci, GMN and Bonito, V and Bonito, G}, title = {Fungal, Bacterial, and Archaeal Diversity in Soils Beneath Native and Introduced Plants in Fiji, South Pacific.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1266-1}, pmid = {30288545}, issn = {1432-184X}, support = {project MICL02416//Michigan State University AgBioResearch NIFA/ ; DEB1737898//National Science Foundation/ ; }, abstract = {The Fiji Islands is an archipelago of more than 330 islands located in the tropics of the South Pacific Ocean. Microbial diversity and biogeography in this region is still not understood. Here, we present the first molecular characterization of fungal, bacterial, and archaeal communities in soils from different habitats within the largest Fijian island, Viti Levu. Soil samples were collected from under native vegetation in maritime-, forest-, stream-, grassland-, and casuarina-dominated habitats, as well as from under the introduced agricultural crops sugarcane, cassava, pine, and mahogany. Soil microbial diversity was analyzed through MiSeq amplicon sequencing of 16S (for prokaryotes), ITS, LSU ribosomal DNA (for fungi). Prokaryotic communities were dominated by Proteobacteria (~ 25%), Acidobacteria (~ 19%), and Actinobacteria (~ 17%), and there were no indicator species associated with particular habitats. ITS and LSU were congruent in β-diversity patterns of fungi, and fungal communities were dominated by Ascomycota (~ 57-64%), followed by Basidiomycota (~ 20-23%) and Mucoromycota (~ 10%) according to ITS, or Chytridiomycota (~ 9%) according to LSU. Indicator species analysis of fungi found statistical associations of Cenococcum, Wilcoxina, and Rhizopogon to Pinus caribaea. We hypothesize these obligate biotrophic fungi were co-introduced with their host plant. Entoloma was statistically associated with grassland soils, and Fusarium and Lecythophora with soils under cassava. Observed richness varied from 65 (casuarina) to 404 OTUs (cassava) for fungi according to ITS region, and from 1268 (pine) to 2931 OTUs (cassava) for bacteria and archaea. A major finding of this research is that nearly 25% of the fungal OTUs are poorly classified, indicative of novel biodiversity in this region. This preliminary survey provides important baseline data on fungal, bacterial, and archaeal diversity and biogeography in the Fiji Islands.}, }
@article {pmid30288544, year = {2018}, author = {Peters, MJ and Suwannapong, G and Pelin, A and Corradi, N}, title = {Genetic and Genome Analyses Reveal Genetically Distinct Populations of the Bee Pathogen Nosema ceranae from Thailand.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1268-z}, pmid = {30288544}, issn = {1432-184X}, support = {ER13-09-190//Ministry of Research, Innovation and Science/ ; }, abstract = {The recent global decline in Western honeybee (Apis mellifera) populations is of great concern for pollination and honey production worldwide. Declining honeybee populations are frequently infected by the microsporidian pathogen Nosema ceranae. This species was originally described in the Asiatic honeybee (Apis cerana), and its identification in global A. mellifera hives could result from a recent host transfer. Recent genome studies have found that global populations of this parasite are polyploid and that humans may have fueled their global expansion. To better understand N. ceranae biology, we investigated its genetic diversity within part of their native range (Thailand) and among different hosts (A. mellifera, A. cerana) using both PCR and genome-based methods. We find that Thai N. ceranae populations share many SNPs with other global populations and appear to be clonal. However, in stark contrast with previous studies, we found that these populations also carry many SNPs not found elsewhere, indicating that these populations have evolved in their current geographic location for some time. Our genome analyses also indicate the potential presence of diploidy within Thai populations of N. ceranae.}, }
@article {pmid30288176, year = {2018}, author = {Walker, TWN and Kaiser, C and Strasser, F and Herbold, CW and Leblans, NIW and Woebken, D and Janssens, IA and Sigurdsson, BD and Richter, A}, title = {Microbial temperature sensitivity and biomass change explain soil carbon loss with warming.}, journal = {Nature climate change}, volume = {8}, number = {10}, pages = {885-889}, doi = {10.1038/s41558-018-0259-x}, pmid = {30288176}, issn = {1758-678X}, support = {294343//European Research Council/International ; 610028//European Research Council/International ; 636928//European Research Council/International ; }, abstract = {Soil microorganisms control carbon losses from soils to the atmosphere1-3, yet their responses to climate warming are often short-lived and unpredictable4-7. Two mechanisms, microbial acclimation and substrate depletion, have been proposed to explain temporary warming effects on soil microbial activity8-10. However, empirical support for either mechanism is unconvincing. Here we used geothermal temperature gradients (> 50 years of field warming)11 and a short-term experiment to show that microbial activity (gross rates of growth, turnover, respiration and carbon uptake) is intrinsically temperature sensitive and does not acclimate to warming (+ 6 ºC) over weeks or decades. Permanently accelerated microbial activity caused carbon loss from soil. However, soil carbon loss was temporary because substrate depletion reduced microbial biomass and constrained the influence of microbes over the ecosystem. A microbial biogeochemical model12-14 showed that these observations are reproducible through a modest, but permanent, acceleration in microbial physiology. These findings reveal a mechanism by which intrinsic microbial temperature sensitivity and substrate depletion together dictate warming effects on soil carbon loss via their control over microbial biomass. We thus provide a framework for interpreting the links between temperature, microbial activity and soil carbon loss on timescales relevant to Earth's climate system.}, }
@article {pmid30287354, year = {2018}, author = {Staley, C and Sadowsky, MJ}, title = {Practical considerations for sampling and data analysis in contemporary metagenomics-based environmental studies.}, journal = {Journal of microbiological methods}, volume = {154}, number = {}, pages = {14-18}, doi = {10.1016/j.mimet.2018.09.020}, pmid = {30287354}, issn = {1872-8359}, abstract = {Recent advancements in metagenomic-based studies, especially analyses of amplicon-based DNA sequencing targeting taxonomic marker genes, has led to an unprecedented characterization of microbial communities from diverse ecosystems around the world. While originally constrained by a lack of appropriate analytical tools and sequencing depth, new technologies and computational and statistical algorithms have been developed to handle highly dimensional, next-generation sequencing datasets. Both these tools allow for the robust analysis of structural and distributional patterns of microbiota essential for the understanding of microbial ecology and biogeography. Furthermore, consortia of individual laboratories working on large interdisciplinary research programs, like the Human and Earth Microbiome Projects, have developed standardized protocols for DNA extraction, sequencing pipelines, and bioinformatics. These approaches provide large repositories of publicly available data to serve as references for on-going and future, hypothesis-driven studies to better characterize the roles of microbial communities in diverse ecosystems. In this review, we outline the currently available statistical approaches and tools to aid in statistically powered study designs and analyses. Given what is now known about the enormous diversity and variability of the microbial communities in aquatic and terrestrial habitats, we also discuss practical considerations for sample collection. Due to the extensive advances made in the field of metagenomics over the last decade, rigorous, well replicated, hypothesis-driven studies are: 1) needed, 2) now possible, and 3) essential to make best use of sequencing-based technologies to characterize the roles of microbial communities in the structure and function of diverse ecosystems.}, }
@article {pmid30285851, year = {2018}, author = {Mehrshad, M and Salcher, MM and Okazaki, Y and Nakano, SI and Šimek, K and Andrei, AS and Ghai, R}, title = {Hidden in plain sight-highly abundant and diverse planktonic freshwater Chloroflexi.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {176}, doi = {10.1186/s40168-018-0563-8}, pmid = {30285851}, issn = {2049-2618}, abstract = {BACKGROUND: Representatives of the phylum Chloroflexi, though reportedly highly abundant in the extensive deep water habitats of both marine (SAR202 up to 30% of total prokaryotes) and freshwater (CL500-11 up to 26% of total prokaryotes), remain uncultivated and uncharacterized. There are few metagenomic studies on marine Chloroflexi representatives, while the pelagic freshwater Chloroflexi community is largely unknown except for a single metagenome-assembled genome of CL500-11.<br><br>RESULTS: Here, we provide the first extensive examination of the community composition of this cosmopolitan phylum in a range of pelagic habitats (176 datasets) and highlight the impact of salinity and depth on their phylogenomic composition. Reconstructed genomes (53 in total) provide a perspective on the phylogeny, metabolism, and distribution of three novel classes and two family-level taxa within the phylum Chloroflexi. We unraveled a remarkable genomic diversity of pelagic freshwater Chloroflexi representatives that thrive not only in the hypolimnion as previously suspected, but also in the epilimnion. Our results suggest that the lake hypolimnion provides a globally stable habitat reflected in lower species diversity among hypolimnion-specific CL500-11 and TK10 clusters in distantly related lakes compared to a higher species diversity of the epilimnion-specific SL56 cluster. Cell volume analyses show that the CL500-11 are among the largest prokaryotic cells in the water column of deep lakes and with a biomass to abundance ratio of two they significantly contribute to the deep lake carbon flow. Metabolic insights indicate participation of JG30-KF-CM66 representatives in the global cobalamin production via cobinamide to cobalamin salvage pathway.<br><br>CONCLUSIONS: Extending phylogenomic comparisons to brackish and marine habitats suggests salinity as the major influencer of the community composition of the deep-dwelling Chloroflexi in marine (SAR202) and freshwater (CL500-11) habitats as both counterparts thrive in intermediate brackish salinity; however, freshwater habitats harbor the most phylogenetically diverse community of pelagic Chloroflexi representatives that reside both in epi- and hypolimnion.}, }
@article {pmid30285747, year = {2018}, author = {Lebre, PH and Aliyu, H and De Maayer, P and Cowan, DA}, title = {In silico characterization of the global Geobacillus and Parageobacillus secretome.}, journal = {Microbial cell factories}, volume = {17}, number = {1}, pages = {156}, doi = {10.1186/s12934-018-1005-9}, pmid = {30285747}, issn = {1475-2859}, abstract = {BACKGROUND: Geobacillus and Parageobacillus are two ecologically diverse thermophilic genera within the phylum Firmicutes. These taxa have long been of biotechnological interest due to their ability to secrete thermostable enzymes and other biomolecules that have direct applications in various industrial and clinical fields. Despite the commercial and industrial interest in these microorganisms, the full scope of the secreted protein, i.e. the secretome, of Geobacillus and Parageobacillus species remains largely unexplored, with most studies focusing on single enzymes. A genome-wide exploration of the global secretome can provide a platform for understanding the extracellular functional &quot;protein cloud&quot; and the roles that secreted proteins play in the survival and adaptation of these biotechnologically relevant organisms.<br><br>RESULTS: In the present study, the global secretion profile of 64 Geobacillus and Parageobacillus strains, comprising 772 distinct proteins, was predicted using comparative genomic approaches. Thirty-one of these proteins are shared across all strains used in this study and function in cell-wall/membrane biogenesis as well as transport and metabolism of carbohydrates, amino acids and inorganic ions. An analysis of the clustering patterns of the secretomes of the 64 strains according to shared functional orthology revealed a correlation between the secreted profiles of different strains and their phylogeny, with Geobacillus and Parageobacillus species forming two distinct functional clades.<br><br>CONCLUSIONS: The in silico characterization of the global secretome revealed a metabolically diverse set of secreted proteins, which include proteases, glycoside hydrolases, nutrient binding proteins and toxins.}, }
@article {pmid30284602, year = {2018}, author = {Lin, X and Hetharua, B and Lin, L and Xu, H and Zheng, T and He, Z and Tian, Y}, title = {Mangrove Sediment Microbiome: Adaptive Microbial Assemblages and Their Routed Biogeochemical Processes in Yunxiao Mangrove National Nature Reserve, China.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1261-6}, pmid = {30284602}, issn = {1432-184X}, support = {2017YFC05061001//National Key Research and Development Program of China/ ; }, abstract = {Microorganisms play important roles in mangrove ecosystems. However, we know little about the ecological implications of mangrove microbiomes for high productivity and the efficient circulation of elements in mangrove ecosystems. Here, we focused on mangrove sediments located at the Yunxiao National Mangrove Reserve in southeast China, uncovering the mangrove microbiome using the 16S rRNA gene and shotgun metagenome sequencing approaches. Physicochemical assays characterized the Yunxiao mangrove sediments as carbon (C)-rich, sulfur (S)-rich, and nitrogen (N)-limited environment. Then phylogenetic analysis profiling a distinctive microbiome with an unexpected high frequency of Chloroflexi and Nitrospirae appeared to be an adaptive characteristic of microbial structure in S-rich habitat. Metagenome sequencing analysis revealed that the metabolic pathways of N and S cycling at the community-level were routed through ammonification and dissimilatory nitrate reduction to ammonium for N conservation in this N-limited habitat, and dissimilatory sulfate reduction along with polysulfide formation for generating bioavailable S resource avoiding the biotoxicity of sulfide in mangrove sediments. In addition, methane metabolism acted as a bridge to connect C cycling to N and S cycling. Further identification of possible biogeochemical linkers suggested Syntrophobacter, Sulfurovum, Nitrospira, and Anaerolinea potentially drive the coupling of C, N, and S cycling. These results highlighting the adaptive routed metabolism flow, a previously undescribed property of mangrove sediment microbiome, appears to be a defining characteristic of this habitat and may significantly contribute to the high productivity of mangrove ecosystems, which could be used as indicators for the health and biodiversity of mangrove ecosystems.}, }
@article {pmid30283424, year = {2018}, author = {El-Chakhtoura, J and Saikaly, PE and van Loosdrecht, MCM and Vrouwenvelder, JS}, title = {Impact of Distribution and Network Flushing on the Drinking Water Microbiome.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2205}, doi = {10.3389/fmicb.2018.02205}, pmid = {30283424}, issn = {1664-302X}, abstract = {We sampled the tap water of seven unique, full-scale drinking water distribution systems at different locations as well as the corresponding treatment plant effluents to evaluate the impact of distribution and the potential presence of a core drinking water microbiome. The water was also sampled during network flushing to examine its effect on the microbial ecology. While a core microbiome dominated by Gammaproteobacteria was found using 16S rRNA gene pyrosequencing, an increase in biomass was detected in the networks, especially during flushing. Water age did not significantly impact the microbiology. Irrespective of differences in treatment plants, tap water bacterial communities in the distinct networks converged and highly resembled the flushed water communities. Piping biofilm and sediment communities therefore largely determine the final tap water microbial quality, attenuating the impact of water source and treatment strategy and highlighting the fundamental role of local physicochemical conditions and microbial processes within infrastructure micro-niches.}, }
@article {pmid30283421, year = {2018}, author = {Durán, P and Tortella, G and Viscardi, S and Barra, PJ and Carrión, VJ and Mora, ML and Pozo, MJ}, title = {Microbial Community Composition in Take-All Suppressive Soils.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2198}, doi = {10.3389/fmicb.2018.02198}, pmid = {30283421}, issn = {1664-302X}, abstract = {Gaeumannomyces graminis var. tritici (Ggt) is the main soilborne factor that affects wheat production around the world. Recently we reported the occurrence of six suppressive soils in monoculture areas from indigenous &quot;Mapuche&quot; communities, and evidenced that the suppression relied on the biotic component of those soils. Here, we compare the rhizosphere and endosphere microbial community structure (total bacteria, actinomycetes, total fungi, and ascomycetes) of wheat plants grown in suppressive and conducive soils. Our results suggested that Ggt suppression could be mediated mostly by bacterial endophytes, rather than rhizosphere microorganisms, since the community structure was similar in all suppressive soils as compared with conducive. Interestingly, we found that despite the lower incidence of take-all disease in suppressive soils, the Ggt concentration in roots was not significantly reduced in all suppressive soils compared to those growing in conducive soil. Therefore, the disease suppression is not always related to a reduction of the pathogen biomass. Furthermore, we isolated endophytic bacteria from wheat roots growing in suppressive soils. Among them we identified Serratia spp. and Enterobacter spp. able to inhibit Ggt growth in vitro. Since the disease, but not always pathogen amount, was reduced in the suppressive soils, we propose that take all disease suppressiveness is not only related to direct antagonism to the pathogen.}, }
@article {pmid30283052, year = {2018}, author = {Boers, SA and Prest, EI and Taučer-Kapteijn, M and Knezev, A and Schaap, PG and Hays, JP and Jansen, R}, title = {Monitoring of microbial dynamics in a drinking water distribution system using the culture-free, user-friendly, MYcrobiota platform.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {14727}, doi = {10.1038/s41598-018-32987-x}, pmid = {30283052}, issn = {2045-2322}, abstract = {Drinking water utilities currently rely on a range of microbiological detection techniques to evaluate the quality of their drinking water (DW). However, microbiota profiling using culture-free 16S rRNA gene next-generation sequencing (NGS) provides an opportunity for improved monitoring of the microbial ecology and quality of DW. Here, we evaluated the utility of a previously validated microbiota profiling platform (MYcrobiota) to investigate the microbial dynamics of a full-scale, non-chlorinated DW distribution system (DWDS). In contrast to conventional methods, we observed spatial and temporal bacterial genus changes (expressed as operational taxonomic units - OTUs) within the DWDS. Further, a small subset of bacterial OTUs dominated with abundances that shifted across the length of the DWDS, and were particularly affected by a post-disinfection step. We also found seasonal variation in OTUs within the DWDS and that many OTUs could not be identified, even though MYcrobiota is specifically designed to reduce potential PCR sequencing artefacts. This suggests that our current knowledge about the microbial ecology of DW communities is limited. Our findings demonstrate that the user-friendly MYcrobiota platform facilitates culture-free, standardized microbial dynamics monitoring and has the capacity to facilitate the introduction of microbiota profiling into the management of drinking water quality.}, }
@article {pmid30281902, year = {2018}, author = {Sollai, M and Villanueva, L and Hopmans, EC and Reichart, GJ and Sinninghe Damsté, JS}, title = {A combined lipidomic and 16S rRNA gene amplicon sequencing approach reveals archaeal sources of intact polar lipids in the stratified Black Sea water column.}, journal = {Geobiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/gbi.12316}, pmid = {30281902}, issn = {1472-4669}, support = {024.002.002//Nederlandse Organisatie voor Wetenschappelijk Onderzoek - Soehngen Institute for Anaerobic Microbiology (SIAM)/ ; 024.002.001//Nederlandse Organisatie voor Wetenschappelijk Onderzoek - Netherlands Earth System Science Center (NESSC)/ ; 3012//Darwin Center for Biogeosciences/ ; 822.01013//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; }, abstract = {Archaea are important players in marine biogeochemical cycles, and their membrane lipids are useful biomarkers in environmental and geobiological studies. However, many archaeal groups remain uncultured and their lipid composition unknown. Here, we aim to expand the knowledge on archaeal lipid biomarkers and determine the potential sources of those lipids in the water column of the euxinic Black Sea. The archaeal community was evaluated by 16S rRNA gene amplicon sequencing and by quantitative PCR. The archaeal intact polar lipids (IPLs) were investigated by ultra-high-pressure liquid chromatography coupled to high-resolution mass spectrometry. Our study revealed both a complex archaeal community and large changes with water depth in the IPL assemblages. In the oxic/upper suboxic waters (<105 m), the archaeal community was dominated by marine group (MG) I Thaumarchaeota, coinciding with a higher relative abundance of hexose phosphohexose crenarchaeol, a known marker for Thaumarchaeota. In the suboxic waters (80-110 m), MGI Nitrosopumilus sp. dominated and produced predominantly monohexose glycerol dibiphytanyl glycerol tetraethers (GDGTs) and hydroxy-GDGTs. Two clades of MGII Euryarchaeota were present in the oxic and upper suboxic zones in much lower abundances, preventing the detection of their specific IPLs. In the deep sulfidic waters (>110 m), archaea belonging to the DPANN Woesearchaeota, Bathyarchaeota, and ANME-1b clades dominated. Correlation analyses suggest that the IPLs GDGT-0, GDGT-1, and GDGT-2 with two phosphatidylglycerol (PG) head groups and archaeol with a PG, phosphatidylethanolamine, and phosphatidylserine head groups were produced by ANME-1b archaea. Bathyarchaeota represented 55% of the archaea in the deeper part of the euxinic zone and likely produces archaeol with phospho-dihexose and hexose-glucuronic acid head groups.}, }
@article {pmid30280234, year = {2018}, author = {Boixel, AL and Delestre, G and Legeay, J and Chelle, M and Suffert, F}, title = {Phenotyping Thermal Responses of Yeasts and Yeast-like Microorganisms at the Individual and Population Levels: Proof-of-Concept, Development and Application of an Experimental Framework to a Plant Pathogen.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1253-6}, pmid = {30280234}, issn = {1432-184X}, support = {ANR-11-LABX-0034//Agence Nationale de la Recherche/ ; }, abstract = {Deciphering the responses of microbial populations to spatiotemporal changes in their thermal environment is instrumental in improving our understanding of their eco-evolutionary dynamics. Recent studies have shown that current phenotyping protocols do not adequately address all dimensions of phenotype expression. Therefore, these methods can give biased assessments of sensitivity to temperature, leading to misunderstandings concerning the ecological processes underlying thermal plasticity. We describe here a new robust and versatile experimental framework for the accurate investigation of thermal performance and phenotypic diversity in yeasts and yeast-like microorganisms, at the individual and population levels. In addition to proof-of-concept, the application of this framework to the fungal wheat pathogen Zymoseptoria tritici resulted in detailed characterisations for this yeast-like microorganism of (i) the patterns of temperature-dependent changes in performance for four fitness traits; (ii) the consistency in thermal sensitivity rankings of strains between in planta and in vitro growth assessments; (iii) significant interindividual variation in thermal responses, with four principal thermotypes detected in a sample of 66 strains; and (iv) the ecological consequences of this diversity for population-level processes through pairwise competition experiments highlighting temperature-dependent outcomes. These findings extend our knowledge and ability to quantify and categorise the phenotypic heterogeneity of thermal responses. As such, they lay the foundations for further studies elucidating local adaptation patterns and the effects of temperature variations on eco-evolutionary and epidemiological processes.}, }
@article {pmid30280026, year = {2018}, author = {Li, J and Lin, J and Pei, C and Lai, K and Jeffries, TC and Tang, G}, title = {Variation of soil bacterial communities along a chronosequence of Eucalyptus plantation.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e5648}, doi = {10.7717/peerj.5648}, pmid = {30280026}, issn = {2167-8359}, abstract = {Eucalyptus is harvested for wood and fiber production in many tropical and sub-tropical habitats globally. Plantation has been controversial because of its influence on the surrounding environment, however, the influence of massive Eucalyptus planting on soil microbial communities is unclear. Here we applied high-throughput sequencing of the 16S rRNA gene to assess the microbial community composition and diversity of planting chronosequences, involving two, five and ten years of Eucalyptus plantation, comparing to that of secondary-forest in South China. We found that significant changes in the composition of soil bacteria occurred when the forests were converted from secondary-forest to Eucalyptus. The bacterial community structure was clearly distinct from control and five year samples after Eucalyptus was grown for 2 and 10 years, highlighting the influence of this plantation on local soil microbial communities. These groupings indicated a cycle of impact (2 and 10 year plantations) and low impact (5-year plantations) in this chronosequence of Eucalyptus plantation. Community patterns were underpinned by shifts in soil properties such as pH and phosphorus concentration. Concurrently, key soil taxonomic groups such as Actinobacteria showed abundance shifts, increasing in impacted plantations and decreasing in low impacted samples. Shifts in taxonomy were reflected in a shift in metabolic potential, including pathways for nutrient cycles such as carbon fixation, which changed in abundance over time following Eucalyptus plantation. Combined these results confirm that Eucalyptus plantation can change the community structure and diversity of soil microorganisms with strong implications for land-management and maintaining the health of these ecosystems.}, }
@article {pmid30279438, year = {2018}, author = {Quintanilla, E and Ramírez-Portilla, C and Adu-Oppong, B and Walljasper, G and Glaeser, SP and Wilke, T and Muñoz, AR and Sánchez, JA}, title = {Local confinement of disease-related microbiome facilitates recovery of gorgonian sea fans from necrotic-patch disease.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {14636}, doi = {10.1038/s41598-018-33007-8}, pmid = {30279438}, issn = {2045-2322}, abstract = {Microbiome disruptions triggering disease outbreaks are increasingly threatening corals worldwide. In the Tropical Eastern Pacific, a necrotic-patch disease affecting gorgonian corals (sea fans, Pacifigorgia spp.) has been observed in recent years. However, the composition of the microbiome and its disease-related disruptions remain unknown in these gorgonian corals. Therefore, we analysed 16S rRNA gene amplicons from tissues of healthy colonies (n = 19) and from symptomatic-asymptomatic tissues of diseased colonies (n = 19) of Pacifigorgia cairnsi (Gorgoniidae: Octocorallia) in order to test for disease-related changes in the bacterial microbiome. We found that potential endosymbionts (mostly Endozoicomonas spp.) dominate the core microbiome in healthy colonies. Moreover, healthy tissues differed in community composition and functional profile from those of the symptomatic tissues but did not show differences to asymptomatic tissues of the diseased colonies. A more diverse set of bacteria was observed in symptomatic tissues, together with the decline in abundance of the potential endosymbionts from the healthy core microbiome. Furthermore, according to a comparative taxonomy-based functional profiling, these symptomatic tissues were characterized by the increase in heterotrophic, ammonia oxidizer and dehalogenating bacteria and by the depletion of nitrite and sulphate reducers. Overall, our results suggest that the bacterial microbiome associated with the disease behaves opportunistically and is likely in a state of microbial dysbiosis. We also conclude that the confinement of the disease-related consortium to symptomatic tissues may facilitate colony recovery.}, }
@article {pmid30276419, year = {2018}, author = {Renoz, F and Pons, I and Vanderpoorten, A and Bataille, G and Noël, C and Foray, V and Pierson, V and Hance, T}, title = {Evidence for Gut-Associated Serratia symbiotica in Wild Aphids and Ants Provides New Perspectives on the Evolution of Bacterial Mutualism in Insects.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1265-2}, pmid = {30276419}, issn = {1432-184X}, support = {1.E074.14//Fonds pour la Formation à la Recherche dans l'Industrie et dans l'Agriculture/ ; }, abstract = {Many insects engage in symbiotic associations with diverse assemblages of bacterial symbionts that can deeply impact on their ecology and evolution. The intraspecific variation of symbionts remains poorly assessed while phenotypic effects and transmission behaviors, which are key processes for the persistence and evolution of symbioses, may differ widely depending on the symbiont strains. Serratia symbiotica is one of the most frequent symbiont species in aphids and a valuable model to assess this intraspecific variation since it includes both facultative and obligate symbiotic strains. Despite evidence that some facultative S. symbiotica strains exhibit a free-living capacity, the presence of these strains in wild aphid populations, as well as in insects with which they maintain regular contact, has never been demonstrated. Here, we examined the prevalence, diversity, and tissue tropism of S. symbiotica in wild aphids and associated ants. We found a high occurrence of S. symbiotica infection in ant populations, especially when having tended infected aphid colonies. We also found that the S. symbiotica diversity includes strains found located within the gut of aphids and ants. In the latter, this tissue tropism was found restricted to the proventriculus. Altogether, these findings highlight the extraordinary diversity and versatility of an insect symbiont and suggest the existence of novel routes for symbiont acquisition in insects.}, }
@article {pmid30274898, year = {2018}, author = {Blachier, F and Beaumont, M and Portune, KJ and Steuer, N and Lan, A and Audebert, M and Khodorova, N and Andriamihaja, M and Airinei, G and Benamouzig, R and Davila, AM and Armand, L and Rampelli, S and Brigidi, P and Tomé, D and Claus, SP and Sanz, Y}, title = {High-protein diets for weight management: Interactions with the intestinal microbiota and consequences for gut health. A position paper by the my new gut study group.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.clnu.2018.09.016}, pmid = {30274898}, issn = {1532-1983}, abstract = {BACKGROUND &amp; AIMS: This review examines to what extent high-protein diets (HPD), which may favor body weight loss and improve metabolic outcomes in overweight and obese individuals, may also impact the gut environment, shaping the microbiota and the host-microbe (co)metabolic pathways and products, possibly affecting large intestine mucosa homeostasis.<br><br>METHODS: PubMed-referenced publications were analyzed with an emphasis on dietary intervention studies involving human volunteers in order to clarify the beneficial vs. deleterious effects of HPD in terms of both metabolic and gut-related health parameters; taking into account the interactions with the gut microbiota.<br><br>RESULTS: HPD generally decrease body weight and improve blood metabolic parameters, but also modify the fecal and urinary contents in various bacterial metabolites and co-metabolites. The effects of HPD on the intestinal microbiota composition appear rather heterogeneous depending on the type of dietary intervention. Recently, HPD consumption was shown to modify the expression of genes playing key roles in homeostatic processes in the rectal mucosa, without evidence of intestinal inflammation. Importantly, the effects of HPD on the gut were dependent on the protein source (i.e. from plant or animal sources), a result which should be considered for further investigations.<br><br>CONCLUSION: Although HPD appear to be efficient for weight loss, the effects of HPD on microbiota-derived metabolites and gene expression in the gut raise new questions on the impact of HPD on the large intestine mucosa homeostasis leading the authors to recommend some caution regarding the utilization of HPD, notably in a recurrent and/or long-term ways.}, }
@article {pmid30273809, year = {2018}, author = {De Vrieze, J and Arends, JBA and Verbeeck, K and Gildemyn, S and Rabaey, K}, title = {Interfacing anaerobic digestion with (bio)electrochemical systems: Potentials and challenges.}, journal = {Water research}, volume = {146}, number = {}, pages = {244-255}, doi = {10.1016/j.watres.2018.08.045}, pmid = {30273809}, issn = {1879-2448}, abstract = {For over a century, anaerobic digestion has been a key technology in stabilizing organic waste streams, while at the same time enabling the recovery of energy. The anticipated transition to a bio-based economy will only increase the quantity and diversity of organic waste streams to be treated, and, at the same time, increase the demand for additional and effective resource recovery schemes for nutrients and organic matter. The performance of anaerobic digestion can be supported and enhanced by (bio)electrochemical systems in a wide variety of hybrid technologies. Here, the possible benefits of combining anaerobic digestion with (bio)electrochemical systems were reviewed in terms of (1) process monitoring, control, and stabilization, (2) nutrient recovery, (3) effluent polishing, and (4) biogas upgrading. The interaction between microorganisms and electrodes with respect to niche creation is discussed, and the potential impact of this interaction on process performance is evaluated. The strength of combining anaerobic digestion with (bio)electrochemical technologies resides in the complementary character of both technologies, and this perspective was used to distinguish transient trends from schemes with potential for full-scale application. This is supported by an operational costs assessment, showing that the economic potential of combining anaerobic digestion with a (bio)electrochemical system is highly case-specific, and strongly depends on engineering challenges with respect to full-scale applications.}, }
@article {pmid30273364, year = {2018}, author = {Tam, J and Hoffmann, T and Fischer, S and Bornstein, S and Gräßler, J and Noack, B}, title = {Obesity alters composition and diversity of the oral microbiota in patients with type 2 diabetes mellitus independently of glycemic control.}, journal = {PloS one}, volume = {13}, number = {10}, pages = {e0204724}, doi = {10.1371/journal.pone.0204724}, pmid = {30273364}, issn = {1932-6203}, abstract = {BACKGROUND AND OBJECTIVE: The involvement of the oral microbiota as a possible link between periodontitis, type 2 diabetes mellitus and obesity is still not well understood. The objective of the study was to investigate if glycemic control and obesity play a role in modulating the composition and diversity of the oral microbial ecology.<br><br>MATERIAL AND METHODS: A cohort of patients with type 2 diabetes mellitus (n = 18) was recruited. Participants demonstrating improved glycemic control after 3 months (n = 6) were included in a second examination. A full mouth examination was performed to estimate periodontitis severity followed by sample collection (subgingival plaque and saliva). Generation of large sequence libraries was performed using the high-throughput Illumina MiSeq sequencing platform.<br><br>RESULTS: The majority of participants (94.4%, n = 17) presented with moderate or severe forms of periodontitis. Differences in microbial composition and diversity between obese (BMI ≥ 30 kg/m2) and non-obese (BMI < 30 kg/m2) groups were statistically significant. Cross-sectional and longitudinal approaches failed to reveal statistically significant associations between HbA1c level and species composition or diversity.<br><br>CONCLUSIONS: Obesity was significantly associated with the oral microbial composition. The impact of glycemic control on oral microbiota, however, could not be assured statistically.}, }
@article {pmid30272014, year = {2018}, author = {de Araujo, ASF and Mendes, LW and Lemos, LN and Antunes, JEL and Beserra, JEA and de Lyra, MDCCP and Figueiredo, MDVB and Lopes, ÂCA and Gomes, RLF and Bezerra, WM and Melo, VMM and de Araujo, FF and Geisen, S}, title = {Protist species richness and soil microbiome complexity increase towards climax vegetation in the Brazilian Cerrado.}, journal = {Communications biology}, volume = {1}, number = {}, pages = {135}, doi = {10.1038/s42003-018-0129-0}, pmid = {30272014}, issn = {2399-3642}, abstract = {Biodiversity underlies ecosystem functioning. While aboveground biodiversity is often well studied, the belowground microbiome, in particular protists, remains largely unknown. Indeed, holistic insights into soil microbiome structures in natural soils, especially in hyperdiverse biomes such as the Brazilian Cerrado, remain unexplored. Here, we study the soil microbiome across four major vegetation zones of the Cerrado, ranging from grass-dominated to tree-dominated vegetation with a focus on protists. We show that protist taxon richness increases towards the tree-dominated climax vegetation. Early successional habitats consisting of primary grass vegetation host most potential plant pathogens and least animal parasites. Using network analyses combining protist with prokaryotic and fungal sequences, we show that microbiome complexity increases towards climax vegetation. Together, this suggests that protists are key microbiome components and that vegetation succession towards climax vegetation is stimulated by higher loads of animal and plant pathogens. At the same time, an increase in microbiome complexity towards climax vegetation might enhance system stability.}, }
@article {pmid30269410, year = {2018}, author = {Bovio, P and Cabezas, A and Etchebehere, C}, title = {Preliminary analysis of Chloroflexi populations in full scale UASB methanogenic reactors.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jam.14115}, pmid = {30269410}, issn = {1365-2672}, abstract = {AIMS: The phylum Chloroflexi is frequently found in high abundance in methanogenic reactors, but, their role is still unclear as most of them remain uncultured and understudied. Hence, a detailed analysis was performed in samples from five Up-flow anaerobic sludge blanket (UASB) full-scale reactors fed with different industrial wastewaters.<br><br>METHODS AND RESULTS: Quantitative PCR show that the phylum Chloroflexi was abundant in all UASB methanogenic reactors, with higher abundance in the reactors operated for a long period of time, which presented granular biomass. Both T-RFLP and 16S rRNA gene amplicon sequencing revealed diverse Chloroflexi populations apparently determined by the different inocula. According to the phylogenetic analysis the sequences from the dominant Chloroflexi were positioned in branches where no sequences of the cultured representative strains is placed. FISH analysis performed in two of the reactors showed filamentous morphology of the hybridizing cells.<br><br>CONCLUSIONS: While members of the Anaerolineae class within phylum Chloroflexi were predominant, their diversity is still poorly described in anaerobic reactors. Due to their filamentous morphology, Chloroflexi may have a key role in the granulation in methanogenic UASB reactors.<br><br>Our results bring new insights about the diversity, stability, dynamics and abundance of this phylum in full scale UASB reactors which aid in understanding their function within the reactor biomass. However, new methodological approaches and analysis of bulking biomass is needed to completely unravel their role in these reactors. Combining all this knowledge with reactor operational parameters will allow to understand their participation in granulation and bulking episodes and design strategies to prevent Chloroflexi overgrowth. This article is protected by copyright. All rights reserved.}, }
@article {pmid30267172, year = {2018}, author = {Staley, C and Kaiser, T and Khoruts, A}, title = {Clinician Guide to Microbiome Testing.}, journal = {Digestive diseases and sciences}, volume = {63}, number = {12}, pages = {3167-3177}, doi = {10.1007/s10620-018-5299-6}, pmid = {30267172}, issn = {1573-2568}, abstract = {Recent recognition that the intestinal microbiome plays potential roles in the pathogenesis of multiple common diseases has led to a growing interest in personalized microbiome analysis among clinical investigators and patients. Permissibility of direct access testing has allowed the emergence of commercial companies offering microbiome analysis to patients seeking to gain a better understanding of their symptoms and disease conditions. In turn, physicians are often asked to help with interpretation of such tests or even requested by their patients to order them. Therefore, physicians need to have a basic understanding of the current state of microbiome science. This review examines how the perspective of microbial ecology, which is fundamental to understanding the microbiome, updates the classical version of the germ theory of disease. We provide the essential vocabulary of microbiome science and describe its current limitations. We look forward to the future when microbiome diagnostics may live up to its potential of becoming integral to clinical care that will become increasingly individualized, and microbiome analysis may become incorporated into that future paradigm. However, we caution patients and providers that the current microbiome tests, given the state of knowledge and technology, do not provide much value in clinical decisions. Considerable research remains to be carried out to make this objective a reality.}, }
@article {pmid30267129, year = {2018}, author = {Miller, SR and Carvey, D}, title = {Ecological Divergence with Gene Flow in a Thermophilic Cyanobacterium.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1267-0}, pmid = {30267129}, issn = {1432-184X}, support = {EF-0801999//National Science Foundation/ ; }, abstract = {How ecological diversity is maintained and distributed within populations is a longstanding question in microbial ecology. In the thermophilic cyanobacterium Synechococcus B', high observed levels of recombination are predicted to maintain ecological variation despite the simultaneous action of diverse selective pressures on different regions of the genome. To investigate ecological diversity in these bacteria, we directly isolated laboratory strains of Synechococcus B' from samples collected along the thermal gradients of two geothermal environments in Yellowstone National Park. Extensive recombination was evident for a multi-locus sequence data set, and, consequently, our sample did not exhibit the sequence clustering expected for distinct ecotypes evolving by periodic clonal selection. Evidence for local selective sweeps at specific loci suggests that sweeps may be common but that recombination is effective for maintaining diversity of unlinked genomic regions. Thermal performance for strain growth was positively associated with the temperature of the environment, indicating that Synechococcus B' populations consist of locally adapted ecological specialists that occupy specific thermal niches. Because this ecological differentiation is observed despite the absence of dispersal barriers among sites, we conclude that these bacteria may freely exchange much of the genome but that barriers to gene flow exist for loci under direct temperature selection.}, }
@article {pmid30266729, year = {2018}, author = {Vital, M and Howe, A and Bergeron, N and Krauss, RM and Jansson, JK and Tiedje, JM}, title = {Metagenomic Insights into the Degradation of Resistant Starch by Human Gut Microbiota.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {23}, pages = {}, doi = {10.1128/AEM.01562-18}, pmid = {30266729}, issn = {1098-5336}, abstract = {Several studies monitoring alterations in the community structure upon resistant starch (RS) interventions are available, although comprehensive function-based analyses are lacking. Recently, a multiomics approach based on 16S rRNA gene sequencing, metaproteomics, and metabolomics on fecal samples from individuals subjected to high and low doses of type 2 RS (RS2; 48 g and 3 g/2,500 kcal, respectively, daily for 2 weeks) in a crossover intervention experiment was performed. In the present study, we did pathway-based metagenomic analyses on samples from a subset of individuals (n = 12) from that study to obtain additional detailed insights into the functional structure at high resolution during RS2 intervention. A mechanistic framework based on obtained results is proposed where primary degradation was governed by Firmicutes, with Ruminococcus bromii as a major taxon involved, providing fermentation substrates and increased acetate concentrations for the growth of various major butyrate producers exhibiting the enzyme butyryl-coenzyme A (CoA):acetate CoA-transferase. H2-scavenging sulfite reducers and acetogens concurrently increased. Individual responses of gut microbiota were noted, where seven of the 12 participants displayed all features of the outlined pattern, whereas four individuals showed mixed behavior and one subject was unresponsive. Intervention order did not affect the outcome, emphasizing a constant substrate supply for maintaining specific functional communities.IMPORTANCE Manipulation of gut microbiota is increasingly recognized as a promising approach to reduce various noncommunicable diseases, such as obesity and type 2 diabetes. Specific dietary supplements, including resistant starches (RS), are often a focus, yet comprehensive insights into functional responses of microbiota are largely lacking. Furthermore, unresponsiveness in certain individuals is poorly understood. Our data indicate that distinct parts of microbiota work jointly to degrade RS and successively form health-promoting fermentation end products. It highlights the need to consider both primary degraders and specific more-downstream-acting bacterial groups in order to achieve desired intervention outcomes. The gained insights will assist the design of personalized treatment strategies based on an individual's microbiota.}, }
@article {pmid30266244, year = {2018}, author = {Miller, ET and Svanbäck, R and Bohannan, BJM}, title = {Microbiomes as Metacommunities: Understanding Host-Associated Microbes through Metacommunity Ecology.}, journal = {Trends in ecology &amp; evolution}, volume = {33}, number = {12}, pages = {926-935}, doi = {10.1016/j.tree.2018.09.002}, pmid = {30266244}, issn = {1872-8383}, abstract = {Interest in host-associated microbiomes has skyrocketed recently, yet our ability to explain microbiome variation has remained stubbornly low. Considering scales of interaction beyond the level of the individual host could lead to new insights. Metacommunity theory has many of the tools necessary for modeling multiscale processes and has been successfully applied to host microbiomes. However, the biotic nature of the host requires an expansion of theory to incorporate feedback between the habitat patch (host) and their local (microbial) community. This feedback can have unexpected effects, is predicted to be common, and can arise through a variety of mechanisms, including developmental, ecological, and evolutionary processes. We propose a new way forward for both metacommunity theory and host microbiome research that incorporates this feedback.}, }
@article {pmid30265892, year = {2018}, author = {Fiorentino, A and Cucciniello, R and Di Cesare, A and Fontaneto, D and Prete, P and Rizzo, L and Corno, G and Proto, A}, title = {Disinfection of urban wastewater by a new photo-Fenton like process using Cu-iminodisuccinic acid complex as catalyst at neutral pH.}, journal = {Water research}, volume = {146}, number = {}, pages = {206-215}, doi = {10.1016/j.watres.2018.08.024}, pmid = {30265892}, issn = {1879-2448}, abstract = {Photo-Fenton process is among the most effective advanced oxidation processes (AOPs) in urban wastewater treatment and disinfection, but its application as tertiary treatment at full scale has not been a feasible/attractive option so far because optimum conditions are typically achieved under acidic pH. In this work a new photo Fenton like process (UV-C/H2O2/IDS-Cu) using iminodisuccinic acid (IDS)-Cu complex as catalyst, was compared to other processes (UV-C/H2O2/Cu, UV-C/H2O2/Fe, H2O2 and UV-C) in urban wastewater disinfection. Since this is the first time that IDS-Cu complex was isolated and used as catalyst, preliminary tests to evaluate the mineralization of a model compound (phenol, 25 mg L-1 initial concentration) in water by UV-C/H2O2/IDS-Cu were carried out. Almost complete mineralization of phenol (95%) was observed after 60 min treatment, being the process more effective than all other investigated AOPs (Fenton and photo-Fenton processes). This process was also proven to be more effective in the inactivation of E. coli (complete inactivation (3.5 log units) in 10 min) at natural pH (7.8 ± 0.5) in real wastewater, than the other processes investigated. Unlike of what observed for E. coli inactivation, the investigated processes only partially inactivated total bacterial population (from 18% for UV-C to 43% for UV-C/H2O2/Cu), according to flow cytometry measurements. In particular, Cu based photo-Fenton processes resulted in the higher percentage of inactivated total cells, thus being consistent with the results of E. coli inactivation. It is worthy to note that, as H2O2 was decreased, UV-C/H2O2/Cu-IDS was more effective than UV-C/H2O2/Cu process. Moreover, the formation of small and large clusters decreased in the presence of Cu and Cu-IDS complex, and process efficiency improved accordingly; these results show that Cu based AOPs can more effectively disaggregate clusters, thus making disinfection process more effective than Fe based AOPs.}, }
@article {pmid30262203, year = {2018}, author = {Tomuschat, C and Virbel, CR and O'Donnell, AM and Puri, P}, title = {Reduced expression of the NLRP6 inflammasome in the colon of patients with Hirschsprung's disease.}, journal = {Journal of pediatric surgery}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jpedsurg.2018.08.059}, pmid = {30262203}, issn = {1531-5037}, abstract = {PURPOSE: Hirschsprung's associated enterocolitis (HAEC) is the most common cause of morbidity and mortality in Hirschsprung's Disease (HSCR). The pathogenesis of HAEC remains unsatisfactorily understood. Mounting evidence of an altered microbiome in patients with HSCR adds a new angle to the pathogenesis of HAEC. NLRP6 is a member of the nucleotide-binding domain, leucine-rich-repeat-containing (NLR) innate immune receptor family, a multiprotein complex that functions as a sensor of damage-associated molecular patterns. Known as inflammasomes they have been implicated in the regulation of colonic microbial ecology and by alteration, regulators of inflammation. We designed this study to test the hypothesis that NLRP6 expression is altered in the colon of patients with HSCR.<br><br>METHODS: We investigated NLPR6 protein expression in both the aganglionic and ganglionic regions of HSCR patients (n = 10) versus healthy control colon (n = 10). Protein distribution was assessed by using immunofluorescence and confocal microscopy. Gene and protein expressions were quantified using quantitative real-time polymerase chain reaction (qPCR), Western blot analysis, and densitometry.<br><br>MAIN RESULTS: qPCR and Western blot analysis revealed that NLRP6 is expressed in the colon of patients with HSCR. NLRP6 expression was significantly decreased (p < 0.003) in the ganglionic and aganglionic bowel in HSCR compared to controls. Confocal microscopy revealed that NLRP6 expression in colonic epithelium was markedly decreased in HSCR specimens compared to controls.<br><br>CONCLUSION: We demonstrate for the first time the expression and distribution of NLRP6 in patients with HSCR. The observed decreased expression of NLRP6 may contribute to an altered colonic microbiome in patients with HSCR and increases the susceptibility to develop HAEC.}, }
@article {pmid30261358, year = {2018}, author = {Friedman, L and Mamane, H and Avisar, D and Chandran, K}, title = {The role of influent organic carbon-to-nitrogen (COD/N) ratio in removal rates and shaping microbial ecology in soil aquifer treatment (SAT).}, journal = {Water research}, volume = {146}, number = {}, pages = {197-205}, doi = {10.1016/j.watres.2018.09.014}, pmid = {30261358}, issn = {1879-2448}, abstract = {Soil columns simulating soil aquifer treatment (SAT), fed with synthetic secondary effluent by intermittent infiltration of flooding/drying cycles, were characterized for nitrogen and organic carbon removal, and microbial ecology and biokinetics. The columns differed in the concentration ratio of chemical oxygen demand (COD) to the summed NH4+, NO2- and organic nitrogen-2 (C/N2) or 5 (C/N5). Chemical profiles along the column demonstrated a preference for COD oxidation over nitrification and coupled denitrification, with higher nitrogen loss (57% vs. 16%) in the C/N5 column. Unexpectedly, significant dominance of the genus Nitrospira over the genus Nitrobacter and ammonia-oxidizing bacteria (AOB) was strongly correlated at column depths where NH4+ removal occurred. Moreover, the Nitrospira profile had the strongest correlation to the profile of NH4+ (positive) and NO3- (negative), strongly indicating complete ammonia oxidation. 16S sequencing analysis of the topsoil in C/N2 vs. C/N5 columns revealed double the abundance of microbial aerobic potential (64% vs. 32%) vs. one-third the denitrification potential (13% vs. 31%). The concentrations and degradability levels of organic carbon were the most influential parameters shaping community structure. Niche differentiation within the biofilm attached to the soil is suggested to have an important role in the process's anoxic activity and nitrogen removal.}, }
@article {pmid30259511, year = {2018}, author = {Pimentel, SP and Fontes, M and Ribeiro, FV and Corrêa, MG and Nishii, D and Cirano, FR and Casati, MZ and Casarin, RCV}, title = {Smoking habit modulates peri-implant microbiome: A case-control study.}, journal = {Journal of periodontal research}, volume = {53}, number = {6}, pages = {983-991}, doi = {10.1111/jre.12597}, pmid = {30259511}, issn = {1600-0765}, abstract = {BACKGROUND AND OBJECTIVE: Smoking is a recognized risk factor for peri-implant disease and leads to microbiological changes in mucositis and peri-implantitis. However, there is no knowledge about the impact of smoking in healthy peri-implant tissue. The aim of the study was to evaluate the microbiome in a peri-implant environment in smokers with healthy peri-implant conditions.<br><br>METHODS: Peri-implant biofilm was collected around single clinically healthy, screwed-retained, teeth-surrounded implants in 12 non-smoker (NSMK) and 12 smoker (SMK) non-periodontitis subjects (no bleeding and probing depth <4 mm). Bacterial DNA was isolated and 16S ribosomal RNA gene libraries were sequenced using pyrosequencing, targeting the V3-V4 region. Datasets were processed using the Quantitative Insights into Microbial Ecology, Greengenes and the Human Oral Microbiome Database databases.<br><br>RESULTS: An evident difference in the SMK peri-implant microbiome was observed compared to the NSMK microbiome, with a large abundance of species, even with a healthy peri-implant. The SMK core-microbiome showed an abundance of Fusobacterium, Tannerella and Mogibacterium, while the NSMK core revealed an abundance of Actinomyces, Capnocytophaga and Streptococcus, genera that are usually related to periodontal health. The microbiome inter-relationship was shown to be more inter-generic in SMK then in NSMK, indicating different microbiome cohesion.<br><br>CONCLUSION: Smoking negatively affected the peri-implant microbiome, leading to a disease-associated state, even in clinically healthy individuals.}, }
@article {pmid30259168, year = {2018}, author = {Cardinale, M and Suarez, C and Steffens, D and Ratering, S and Schnell, S}, title = {Effect of Different Soil Phosphate Sources on the Active Bacterial Microbiota Is Greater in the Rhizosphere than in the Endorhiza of Barley (Hordeum vulgare L.).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1264-3}, pmid = {30259168}, issn = {1432-184X}, abstract = {Phosphate is a macronutrient and often the limiting growing factor of many ecosystems. The aim of this work was to assess the effect of various phosphate sources on the active bacterial microbiota of barley rhizosphere and endorhiza. Barley was grown on poor soil supplemented with either Ca(H2PO4)2 (CaP), Gafsa rock phosphate (Gafsa), sodium hexaphytate (NaHex), or not amended (P0). RNA was extracted and cDNA synthesized via reverse transcription from both rhizosphere and endorhiza of barley roots; the obtained 16S rRNA cDNA was sequenced by Ion Torrent and analyzed with QIIME and co-occurrence network analysis. Phosphatase activity was measured in the rhizosphere. The phosphate source significantly affected alpha- and beta-diversities of the active microbiota, especially in the rhizosphere. CaP enriched the relative abundance of a broad range of taxa, while NaHex and Gafsa specifically enriched one dominant Massilia-related OTU. Co-occurrence network analysis showed that the most abundant OTUs were affected by phosphate source and, at the same time, were low connected to other OTUs (thus they were relatively &quot;independent&quot; from other bacteria); this indicates a successful adaptation to the specific abiotic conditions. In the rhizosphere, the phosphatase activities were correlated to several OTUs. Moreover, the phosphodiesterase/alk. phosphomonoesterase ratio was highly correlated to the dominance index of the microbiota and to the relative abundance of the dominant Massilia OTU. This study shows the differential response of the rhizosphere- and endorhiza bacterial microbiota of barley to various phosphate sources in soil, thus providing insights onto this largely unknown aspect of the soil microbiome ecology and plant-microbe interactions.}, }
@article {pmid30258074, year = {2018}, author = {Cheung, MK and Wong, CK and Chu, KH and Kwan, HS}, title = {Community Structure, Dynamics and Interactions of Bacteria, Archaea and Fungi in Subtropical Coastal Wetland Sediments.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {14397}, doi = {10.1038/s41598-018-32529-5}, pmid = {30258074}, issn = {2045-2322}, abstract = {Bacteria, archaea and fungi play crucial roles in wetland biogeochemical processes. However, little is known about their community structure, dynamics and interactions in subtropical coastal wetlands. Here, we examined communities of the three kingdoms in mangrove and mudflat sediments of a subtropical coastal wetland using Ion Torrent amplicon sequencing and co-occurrence network analysis. Bacterial, archaeal and fungal communities comprised mainly of members from the phyla Proteobacteria and Bacteroidetes, Bathyarchaeota and Euryarchaeota, and Ascomycota, respectively. Species richness and Shannon diversity were highest in bacteria, followed by archaea and were lowest in fungi. Distinct spatiotemporal patterns were observed, with bacterial and fungal communities varying, to different extent, between wet and dry seasons and between mangrove and mudflat, and archaeal community remaining relatively stable between seasons and regions. Redundancy analysis revealed temperature as the major driver of the seasonal patterns of bacterial and fungal communities but also highlighted the importance of interkingdom biotic factors in shaping the community structure of all three kingdoms. Potential ecological interactions and putative keystone taxa were identified based on co-occurrence network analysis. These findings facilitate current understanding of the microbial ecology of subtropical coastal wetlands and provide a basis for better modelling of ecological processes in this important ecosystem.}, }
@article {pmid30255115, year = {2018}, author = {Anza, M and Salazar, O and Epelde, L and Garbisu, C}, title = {Data on the selection of biostimulating agents for the bioremediation of soil simultaneously contaminated with lindane and zinc.}, journal = {Data in brief}, volume = {20}, number = {}, pages = {1371-1377}, doi = {10.1016/j.dib.2018.08.203}, pmid = {30255115}, issn = {2352-3409}, abstract = {The bioremediation of contaminated soil often involves the addition of organic/inorganic amendments and mobilizing agents (e.g. surfactants, detergents), in order to stimulate the growth and degrading activity of soil microbial populations and increase contaminant bioavailability. For this data article we carried out an experiment to select biostimulating agents for the bioremediation of soil simultaneously contaminated with lindane (HCH, 10 mg kg-1 DW soil) and Zinc (Zn, 1500 mg kg-1 DW soil). To this purpose, a factorial design was used to test the effect of three organic amendments (i.e. hen manure, composted horse manure, cow slurry) and three mobilizing agents (i.e. sodium dodecylbenzenesulfonate (SDS), rhamnolipids and Tween-80) on the reduction of total HCH and bioavailable Zn concentration in soil. Similarly, the effect of the addition of cyclohexane, as chemical inducer of HCH degradation, was also studied. The addition of SDS, rhamnolipids and Tween-80 significantly reduced HCH concentration in soil, regardless of the presence of other biostimulating agents. When added individually, the three organic amendments (hen manure, composted horse manure, cow slurry) significantly reduced bioavailable Zn concentration in soil. These data provide useful information for the bioremediation, through biostimulation, of soils simultaneously contaminated with HCH and Zn.}, }
@article {pmid30254509, year = {2018}, author = {Krzmarzick, MJ and Taylor, DK and Fu, X and McCutchan, AL}, title = {Diversity and Niche of Archaea in Bioremediation.}, journal = {Archaea (Vancouver, B.C.)}, volume = {2018}, number = {}, pages = {3194108}, doi = {10.1155/2018/3194108}, pmid = {30254509}, issn = {1472-3654}, abstract = {Bioremediation is the use of microorganisms for the degradation or removal of contaminants. Most bioremediation research has focused on processes performed by the domain Bacteria; however, Archaea are known to play important roles in many situations. In extreme conditions, such as halophilic or acidophilic environments, Archaea are well suited for bioremediation. In other conditions, Archaea collaboratively work alongside Bacteria during biodegradation. In this review, the various roles that Archaea have in bioremediation is covered, including halophilic hydrocarbon degradation, acidophilic hydrocarbon degradation, hydrocarbon degradation in nonextreme environments such as soils and oceans, metal remediation, acid mine drainage, and dehalogenation. Research needs are addressed in these areas. Beyond bioremediation, these processes are important for wastewater treatment (particularly industrial wastewater treatment) and help in the understanding of the natural microbial ecology of several Archaea genera.}, }
@article {pmid30252869, year = {2018}, author = {Chen, X and Liu, X and Du, Y and Wang, B and Zhao, N and Geng, Z}, title = {Green forage and fattening duration differentially modulate cecal microbiome of Wanxi white geese.}, journal = {PloS one}, volume = {13}, number = {9}, pages = {e0204210}, doi = {10.1371/journal.pone.0204210}, pmid = {30252869}, issn = {1932-6203}, abstract = {Gut microbial ecology is responsible for fatty acid metabolism in ruminants. The cecal microbiota composition of geese and their adaptation to fiber inclusion and feeding timeswere investigated in this study. A total of 116 Wanxi white geese were randomly selected at 70 days old. Eight geese were subjected to cecal sampling at 70 d of age, and the remaining 108 geese were divided into four groups with three replicates each (9 geese in each replicate). The geese in the four groups were fed 0, 15, 30, and 45% green forage (relative to dry matter), respectively. Three birds from each replicate were selected for cecal sampling at 80, 90, and 100 days old. All samples were subjected to 16S rRNA gene sequencing using the Illumina Ion Personal Genome Machine platform. Bacterial abundance was analyzed using two-way ANOVA analysis, and the relationship between the relative abundance of bacteria (phylum level) and fatty acids was analyzed using acanonical correspondence analysis. Cecal microbiota in geese were mainly composed of Bacteroidetes (68.46%), Firmicutes (20.04%), and Proteobacteria (7.89%). Dietary treatments had no significant effect on the α-diversity indices of the cecal bacterial community (P > 0.05), but a numerical increase occurred with increased fattening duration and green forage inclusion. The Selenomonadales order (P = 0.024), Negativicutes class (P = 0.026), and Megamonas (P = 0.012) and Oscillospira (P = 0.042) genera were affected by green forageinclusion level, and microflora abundance was mainly influenced by the fattening duration. Bacteria phyla were mostly set along the line of linolenic acid and oleic acid. Finally, Bacteroidales might be an intestinal promoter that improves unsaturated fatty acid synthesis in geese.}, }
@article {pmid30251120, year = {2018}, author = {Oh, S and Choi, D}, title = {Microbial Community Enhances Biodegradation of Bisphenol A Through Selection of Sphingomonadaceae.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1263-4}, pmid = {30251120}, issn = {1432-184X}, support = {NRF-2017R1C1B5076367//National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIP; Ministry of Science, ICT &amp; Future Planning)/ ; }, abstract = {Bisphenol A (BPA) is a common ingredient in plastic wares and epoxy resins that are essential for our daily life. Despite the obvious benefits, BPA may act as an environmental endocrine disruptor, causing metabolic, reproductive, and/or developmental consequences and diseases in humans and other organisms. Although previous studies have yielded progress toward the microbial breakdown of BPA, the work has primarily been focused on pure cultures rather than complex microbial communities. In this study, we examined microbial communities in bioreactors that control the fate of BPA at various levels (up to 5000 μg L-1). Microbial communities rapidly increased removal rates of 500-5000 μg L-1 BPA from 23-29 to 89-99% during the first 2 weeks of the acclimation period, after which > 90% stable removal rates were maintained over 3 months. Biochemical assays demonstrated that BPA was removed by biodegradation, rather than other abiotic removal routes (e.g., adsorption and volatilization). The 16S rRNA gene-based community analysis revealed that 50-5000 μg L-1 of BPA exposure systematically selected for three Sphingomonadaceae species (Sphingobium, Novosphingobium, and Sphingopyxis). The Sphingomonadaceae-enriched communities acclimated to BPA showed a 7.0-L gVSS-1 day-1 BPA degradation rate constant, which is comparable to that (4.1-6.3) of Sphingomonadaceae isolates and is higher than other potential BPA degraders. Taken together, our results advanced the understanding of how microbial communities acclimate to environmentally relevant levels of BPA, gradually enhancing BPA degradation via selective enrichment of a few Sphingomonadaceae populations with higher BPA metabolic activity.}, }
@article {pmid30251018, year = {2018}, author = {Sanchis-Chordà, J and Del Pulgar, EMG and Carrasco-Luna, J and Benítez-Páez, A and Sanz, Y and Codoñer-Franch, P}, title = {Bifidobacterium pseudocatenulatum CECT 7765 supplementation improves inflammatory status in insulin-resistant obese children.}, journal = {European journal of nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00394-018-1828-5}, pmid = {30251018}, issn = {1436-6215}, support = {AGL2014-52101-P//Spanish Ministry of Economy and Competitiveness/ ; FPU13/03753//Spanish Training University Lecturers Programme/ ; No. 613979//EU Project MyNewGut/ ; }, abstract = {PURPOSE: The relationships between gut microbiota and obesity-related co-morbidities have been increasingly recognized. Low-grade inflammation may be the main factor in the pathogenesis of such disorders. We investigated the effect of the potential probiotic Bifidobacterium pseudocatenulatum CECT 7765 on cardiometabolic risk factors, inflammatory cytokines and gut microbiota composition in obese children with insulin resistance.<br><br>METHODS: The study included 48 obese children (10-15 years old) with insulin resistance. They received dietary advice and were assigned to take the capsules with or without probiotic (109-10 CFU) daily for 13 weeks. Clinical, biochemical and gut microbiome measurements were made at baseline and at the end of the intervention.<br><br>RESULTS: There was a significant improvement in body mass index in all children after the intervention, suggesting that weight changes are related to the dietary advice. A significant decrease in circulating high-sensitive C-reactive protein (P = 0.026) and monocyte chemoattractant protein-1 (P = 0.032) and an increase in high-density lipoprotein cholesterol (P = 0.035) and omentin-1 (P = 0.023) in children receiving probiotic supplementation were observed compared to the control group. Regarding gut microbiota, probiotic administration significantly increased the proportion of the Rikenellaceae family members, particularly of the Alistipes genus.<br><br>CONCLUSIONS: The beneficial effects of the intervention on inflammatory markers and lipid profile suggest that B. pseudocatenulatum CECT 7765 intake together with dietary recommendations can improve inflammatory status in children with obesity and insulin resistance. These effects are parallel to increases in bacterial groups associated with a lean phenotype. The modulation of gut microbiota with probiotic supplementation can be considered an effective tool to ameliorate some obesity-related disorders in children.}, }
@article {pmid30250249, year = {2018}, author = {Takano, Y and Chikaraishi, Y and Imachi, H and Miyairi, Y and Ogawa, NO and Kaneko, M and Yokoyama, Y and Krüger, M and Ohkouchi, N}, title = {Insight into anaerobic methanotrophy from 13C/12C- amino acids and 14C/12C-ANME cells in seafloor microbial ecology.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {14070}, doi = {10.1038/s41598-018-31004-5}, pmid = {30250249}, issn = {2045-2322}, abstract = {Oceanic methane from global deep-sea sediment is largely consumed through microbially mediated sulfate-coupled oxidation, resulting in 13C-depleted cell biomass of anaerobic methanotrophic archaea (ANME). The general ecological importance of subseafloor ANME has been well recognized in the last two decades. However, the crucial biochemical pathways for the overall anaerobic oxidation of methane (AOM) still remain enigmatic. Here, methanotrophic pathways were analyzed to trace 13C-depleted amino acid biosynthesis in two clades of ANME (ANME-1 and ANME-2) from the Black Sea. Compound-specific analysis of ANME-dominated microbial mats showed a significant 13C-depletion trend in association with increasing carbon numbers in protein-derived amino acid families (e.g., the pyruvate family in the order of alanine, valine, isoleucine and leucine was down to -114‰). This result indicates a stepwise elongation of 13C-depleted carbon during amino acid biosynthesis. The overall results suggest that intracellular protein amino acids and the most 13C-depleted signature of leucine, which has a specific branched-chain structure, are potentially propagated as isoprenoid precursor molecules into archaeal biosynthesis, resulting in the extremely 13C- and 14C-depleted nature of ANME cells in the deep microbial oasis.}, }
@article {pmid30250138, year = {2018}, author = {Ventorino, V and Pascale, A and Adamo, P and Rocco, C and Fiorentino, N and Mori, M and Faraco, V and Pepe, O and Fagnano, M}, title = {Comparative assessment of autochthonous bacterial and fungal communities and microbial biomarkers of polluted agricultural soils of the Terra dei Fuochi.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {14281}, doi = {10.1038/s41598-018-32688-5}, pmid = {30250138}, issn = {2045-2322}, support = {LIFE11/ENV/IT/275//European Commission (EC)/ ; LIFE11/ENV/IT/275//European Commission (EC)/ ; LIFE11/ENV/IT/275//European Commission (EC)/ ; LIFE11/ENV/IT/275//European Commission (EC)/ ; LIFE11/ENV/IT/275//European Commission (EC)/ ; LIFE11/ENV/IT/275//European Commission (EC)/ ; LIFE11/ENV/IT/275//European Commission (EC)/ ; LIFE11/ENV/IT/275//European Commission (EC)/ ; LIFE11/ENV/IT/275//European Commission (EC)/ ; }, abstract = {Organic and inorganic xenobiotic compounds can affect the potential ecological function of the soil, altering its biodiversity. Therefore, the response of microbial communities to environmental pollution is a critical issue in soil ecology. Here, a high-throughput sequencing approach was used to investigate the indigenous bacterial and fungal community structure as well as the impact of pollutants on their diversity and richness in contaminated and noncontaminated soils of a National Interest Priority Site of Campania Region (Italy) called &quot;Terra dei Fuochi&quot;. The microbial populations shifted in the polluted soils via their mechanism of adaptation to contamination, establishing a new balance among prokaryotic and eukaryotic populations. Statistical analyses showed that the indigenous microbial communities were most strongly affected by contamination rather than by site of origin. Overabundant taxa and Actinobacteria were identified as sensitive biomarkers for assessing soil pollution and could provide general information on the health of the environment. This study has important implications for microbial ecology in contaminated environments, increasing our knowledge of the capacity of natural ecosystems to develop microbiota adapted to polluted soil in sites with high agricultural potential and providing a possible approach for modeling pollution indicators for bioremediation purposes.}, }
@article {pmid30249184, year = {2018}, author = {Byloos, B and Monsieurs, P and Mysara, M and Leys, N and Boon, N and Van Houdt, R}, title = {Characterization of the bacterial communities on recent Icelandic volcanic deposits of different ages.}, journal = {BMC microbiology}, volume = {18}, number = {1}, pages = {122}, doi = {10.1186/s12866-018-1262-0}, pmid = {30249184}, issn = {1471-2180}, support = {E-GEM/BIOROCK//Federaal Wetenschapsbeleid/ ; TD1308//European Cooperation in Science and Technology/ ; IUAP 305 P7/25//Federaal Wetenschapsbeleid (BE)/ ; }, abstract = {BACKGROUND: Basalt is the most common igneous rock on the Earth's surface covering. Basalt-associated microorganisms drive the cycling and sequestration of different elements such as nitrogen, carbon and other nutrients, which facilitate subsequent pioneer and plant development, impacting long-term regulation of the Earth's temperature and biosphere. The initial processes of colonization and subsequent rock weathering by microbial communities are still poorly understood and relatively few data are available on the diversity and richness of the communities inhabiting successive and chronological lava flows. In this study, the bacterial communities present on lava deposits from different eruptions of the 1975-84 Krafla Fires (32-, 35- and 39-year old, respectively) at the Krafla, Iceland, were determined.<br><br>RESULTS: Three sites were sampled for each deposit (32-, 35- and 39-year old), two proximal sites (at 10 m distance) and one more distant site (at 100 m from the two other sites). The determined chemical composition and metal concentrations were similar for the three basalt deposits. No significant differences were observed in the total number of cells in each flow. 16S rRNA gene amplicon sequencing showed that the most abundant classified phylum across the 3 flows was Proteobacteria, although predominance of Acidobacteria, Actinobacteria and Firmicutes was observed for some sampling sites. In addition, a considerable fraction of the operational taxonomic units remained unclassified. Alpha diversity (Shannon, inverse Simpson and Chao), HOMOVA and AMOVA only showed a significant difference for Shannon between the 32- and 39-year old flow (p < 0.05). Nonmetric multidimensional scaling (NMDS) analysis showed that age significantly (p = 0.026) influenced the leftward movement along NMDS axis 1.<br><br>CONCLUSIONS: Although NMDS indicated that the (relatively small) age difference of the deposits appeared to impact the bacterial community, this analysis was not consistent with AMOVA and HOMOVA, indicating no significant difference in community structure. The combined results drive us to conclude that the (relatively small) age differences of the deposits do not appear to be the main factor shaping the microbial communities. Probably other factors such as spatial heterogeneity, associated carbon content, exogenous rain precipitations and wind also affect the diversity and dynamics.}, }
@article {pmid30249049, year = {2018}, author = {Sivakumar, G and Uccella, NA and Gentile, L}, title = {Probing Downstream Olive Biophenol Secoiridoids.}, journal = {International journal of molecular sciences}, volume = {19}, number = {10}, pages = {}, doi = {10.3390/ijms19102892}, pmid = {30249049}, issn = {1422-0067}, abstract = {Numerous bioactive biophenol secoiridoids (BPsecos) are found in the fruit, leaves, and oil of olives. These BPsecos play important roles in both the taste of food and human health. The main BPseco bioactive from green olive fruits, leaves, and table olives is oleuropein, while olive oil is rich in oleuropein downstream pathway molecules. The aim of this study was to probe olive BPseco downstream molecular pathways that are alike in biological and olive processing systems at different pHs and reaction times. The downstream molecular pathway were analyzed by high performance liquid chromatography coupled with electrospray ionization mass spectrometry (HPLC-ESI/MS) and typed neglected of different overlap (TNDO) computational methods. Our study showed oleuropein highest occupied molecular orbital (HOMO) and HOMO-1 triggered the free radical processes, while HOMO-2 and lowest unoccupied molecular orbital (LUMO) were polar reactions of glucoside and ester groups. Olive BPsecos were found to be stable under acid and base catalylic experiments. Oleuropein aglycone opened to diales and rearranged to hydroxytyrosil-elenolate under strong reaction conditions. The results suggest that competition among olive BPseco HOMOs could induce glucoside hydrolysis during olive milling due to native olive β-glucosidases. The underlined olive BPsecos downstream molecular mechanism herein could provide new insights into the olive milling process to improve BPseco bioactives in olive oil and table olives, which would enhance both the functional food and the nutraceuticals that are produced from olives.}, }
@article {pmid30248830, year = {2018}, author = {Qi, Y and Yang, X and Pelaez, AM and Huerta Lwanga, E and Beriot, N and Gertsen, H and Garbeva, P and Geissen, V}, title = {Macro- and micro- plastics in soil-plant system: Effects of plastic mulch film residues on wheat (Triticum aestivum) growth.}, journal = {The Science of the total environment}, volume = {645}, number = {}, pages = {1048-1056}, doi = {10.1016/j.scitotenv.2018.07.229}, pmid = {30248830}, issn = {1879-1026}, abstract = {Plastic residues have become a serious environmental problem in the regions with intensive use of plastic mulching. Even though plastic mulch is widely used, the effects of macro- and micro- plastic residues on the soil-plant system and the agroecosystem are largely unknown. In this study, low density polyethylene and one type of starch-based biodegradable plastic mulch film were selected and used as examples of macro- and micro- sized plastic residues. A pot experiment was performed in a climate chamber to determine what effect mixing 1% concentration of residues of these plastics with sandy soil would have on wheat growth in the presence and absence of earthworms. The results showed that macro- and micro- plastic residues affected both above-ground and below-ground parts of the wheat plant during both vegetative and reproductive growth. The type of plastic mulch films used had a strong effect on wheat growth with the biodegradable plastic mulch showing stronger negative effects as compared to polyethylene. The presence of earthworms had an overall positive effect on the wheat growth and chiefly alleviated the impairments made by plastic residues.}, }
@article {pmid30247566, year = {2018}, author = {Otte, JM and Blackwell, N and Soos, V and Rughöft, S and Maisch, M and Kappler, A and Kleindienst, S and Schmidt, C}, title = {Sterilization impacts on marine sediment---Are we able to inactivate microorganisms in environmental samples?.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {12}, pages = {}, doi = {10.1093/femsec/fiy189}, pmid = {30247566}, issn = {1574-6941}, abstract = {To distinguish between biotic and abiotic processes in laboratory experiments with environmental samples, an effective sterilization method is required that prevents biological activity but does not change physico-geochemical properties of samples. We compared standard sterilization methods with respect to their impact on microbial abundance and activity. We exposed marine sediment to (i) autoclaving, (ii) gamma-radiation or (iii) sodium azide (NaN3) and determined how nucleic acids, microbial productivity, colony forming units (CFUs) and community composition of microorganisms, fungi, unicellular protists and protozoa were affected. In autoclaved and gamma-sterilized sediments, only few colonies formed within 16 days. After addition of NaN3 to the sediment, numerous CFUs (>50) but lower 3H-leucine incorporation rates, i.e. lower protein biosynthesis rates, were found compared to the other two sterilization techniques. Extractable RNA was detected immediately after all sterilization treatments (0.2-17.9 ng/g dry sediment) but decreased substantially by 84%-98% after 16 days of incubation. The total organic carbon content increased from 18 mg L-1 to 220 mg L-1 (autoclaving) and 150 mg L-1 (gamma-radiation) after sterilization. We compare advantages and disadvantages for each tested sterilization method and provide a helpful decision-making resource for choosing the appropriate sterilization technique for environmental studies, particularly for marine sediments.}, }
@article {pmid30247563, year = {2018}, author = {Cieplak, T and Wiese, M and Nielsen, S and Van de Wiele, T and van den Berg, F and Nielsen, DS}, title = {The Smallest Intestine (TSI)-a low volume in vitro model of the small intestine with increased throughput.}, journal = {FEMS microbiology letters}, volume = {365}, number = {21}, pages = {}, doi = {10.1093/femsle/fny231}, pmid = {30247563}, issn = {1574-6968}, abstract = {There is a growing interest in understanding the fate and behaviour of probiotic microorganisms and bioactive compounds during passage of the human gastrointestinal tract (GIT). Here, we report the development of a small volume in vitro model called The smallest Intestine (TSI) with increased throughput focusing on simulating passage through the stomach and small intestine (SI). The basic TSI module consists of five reactors, with a working volume of 12 ml each. During the simulated passage through the SI, bile is absorbed and pH is adjusted to physiologically relevant values for duodenum, jejunum and ileum. A consortium of seven representative bacterial members of the ileum microbiota is included in the ileal stage of the model. The behaviour of three putative probiotic Lactobacillus strains during in vitro simulated upper GIT passage was tested in the model and results were compared to previous studies describing probiotic survival. It was found, that probiotic persistence is strongly related to whether food was ingested, but also to presence of the ileal microbiota, which significantly impacted probiotic survival. In conclusion, TSI allows testing a substantial number of samples, at low cost and short time, and is thus suitable as an in vitro screening platform.}, }
@article {pmid30245683, year = {2018}, author = {Hernandez-Agreda, A and Leggat, W and Ainsworth, TD}, title = {A Comparative Analysis of Microbial DNA Preparation Methods for Use With Massive and Branching Coral Growth Forms.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2146}, doi = {10.3389/fmicb.2018.02146}, pmid = {30245683}, issn = {1664-302X}, abstract = {In the last two decades, over 100 studies have investigated the structure of the coral microbiome. However, as yet there are no standardized methods applied to sample preservation and preparation, with different studies using distinct methods. There have also been several comparisons made of microbiome data generated across different studies, which have not addressed the influence of the methodology employed over each of the microbiome datasets. Here, we assess three different preservation methods; salt saturated dimethyl sulfoxide (DMSO) - EDTA, snap freezing with liquid nitrogen and 4% paraformaldehyde solution, and two different preparation methodologies; bead beating and crushing, that have been applied to study the coral microbiome. We compare the resultant bacterial assemblage data for two coral growth forms, the massive coral Goniastrea edwardsi and the branching coral Isopora palifera. We show that microbiome datasets generated from differing preservation and processing protocols are comparable in composition (presence/absence). Significant discrepancies between preservation and homogenization methods are observed in structure (relative abundance), and in the occurrence and dominance of taxa, with rare (low abundance and low occurrence) phylotypes being the most variable fraction of the microbial community. Finally, we provide evidence to support chemical preservation with DMSO as effective as snap freezing samples for generating reliable and robust microbiome datasets. In conclusion, we recommend where possible a standardized preservation and extraction method be taken up by the field to provide the best possible practices for detailed assessments of symbiotic and conserved bacterial associations.}, }
@article {pmid30245425, year = {2019}, author = {Li, B and Cao, Y and Guan, X and Li, Y and Hao, Z and Hu, W and Chen, L}, title = {Microbial assessments of soil with a 40-year history of reclaimed wastewater irrigation.}, journal = {The Science of the total environment}, volume = {651}, number = {Pt 1}, pages = {696-705}, doi = {10.1016/j.scitotenv.2018.09.193}, pmid = {30245425}, issn = {1879-1026}, abstract = {The long-term effects on soil microorganisms from 40 years of irrigating soil with reclaimed wastewater was investigated by determining the quantity, composition, and inter-species connection of microorganisms. No significant difference in microbial quantity and composition were identified in the reclaimed wastewater- and groundwater-irrigated soils. The dominant bacterial phylum in both irrigation water sources and soils was Proteobacteria, which commonly exists in soil. From the analysis of four (4) alpha diversity metrics, including the observed number of operational taxonomic units (OTUs), Chao1, and the Shannon and Simpson diversity, there was no significant difference between the reclaimed wastewater- and groundwater-irrigated soils. Three zones (shallow, medium and deep) were identified in the reclaimed wastewater- and groundwater-irrigated soils based on the taxonomic networks and clusters generated by graphical lasso and random walk algorithm. The cluster profiles (shallow, medium and deep zones) appear to be different in the reclaimed wastewater- and groundwater-irrigated soils. Soil irrigated with reclaimed wastewater showed less depth of clustered profile in medium zone than that in soil irrigated with groundwater (20-60 cm of reclaimed wastewater-irrigated soil compared to 20-100 cm of groundwater-irrigated soil), although the significance of such a variance (the depth of medium zone of reclaimed wastewater-irrigated soil decreased 40 cm than that of groundwater-irrigated soil) is not clear at this time. Positive influence has been identified in the growth and yield of eggplant, tomato and cucumber between the reclaimed wastewater- and groundwater-irrigated soils, suggesting that reclaimed wastewater irrigation can potentially substitute groundwater irrigation, despite the variance in inter-species clustering profiles in soil microbes in certain soil zones. Nevertheless, the possible negative influence of pathogens, organic compounds and pharmaceuticals should be seriously considered during the reclaimed wastewater irrigation.}, }
@article {pmid30244277, year = {2018}, author = {Shteindel, N and Yankelev, D and Gerchman, Y}, title = {High-Throughput Quantitative Measurement of Bacterial Attachment Kinetics on Seconds Time Scale.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1254-5}, pmid = {30244277}, issn = {1432-184X}, abstract = {Surface attachment is an important factor in the life of many microbial species. Late stages of attachment (i.e., mature biofilms) are rigorously studied, but data on the very early stages is scarce. The lack of robust research methods may go a long way in explaining this situation. We have developed a method that allows the rapid kinetic measurement of bacterial attachment, with seconds to minute's temporal resolution, in a high-throughput setting. The method requires the use of a commercially available microtiter plate reader capable of fluorescence measurement from the bottom, standard microtiter plates, fluorescently tagged bacteria, and a common dye. The high temporal resolution reveals nuanced, fast, and dynamic behaviors in the very early phases of attachment. To demonstrate potential applications, we tested the effect of various conditions on attachment kinetics-specie, substratum, salt concentration, and culture density. Results are in good agreement with crystal violet staining (correlation R2 > 0.95 in all cases) and reproducing published data but show much greater detail and fidelity.}, }
@article {pmid30244124, year = {2018}, author = {Podduturi, R and Jørgensen, NOG}, title = {Conidia-based fluorescence quantification of Streptomyces.}, journal = {Journal of microbiological methods}, volume = {153}, number = {}, pages = {104-107}, doi = {10.1016/j.mimet.2018.09.010}, pmid = {30244124}, issn = {1872-8359}, abstract = {Determination of cell numbers in filamentous bacteria, such as Streptomyces, is challenging due to the tangled and twisted structure of the filaments and formation of cell clumps in liquid cultures. Here, we developed a conidia-based approach, in which fluorescence of conidia, after staining with the DNA-binding stain SYBR Green 1, was related to SYBR Green 1 fluorescence of DNA in Streptomyces. When cell number in Streptomyces filaments, determined by the conidia assay, was compared to number obtained by a qPCR assay, 34 to 62% of cells in the Streptomyces filaments were recovered. The difference in numbers probably reflects an insufficient extraction of DNA from the Gram-positive bacteria, rather than underestimation of the actual cell number by the conidia-based determination. The conidia-based approach appears to be a fast and reliable procedure for counting cell numbers in Streptomyces filaments but it can also be used for other filamentous bacteria, if proper standard curves can be made.}, }
@article {pmid30243206, year = {2018}, author = {Wen, D and Chang, NB and Wanielista, MP}, title = {Comparative copper toxicity impact and enzymatic cascade effect on Biosorption Activated Media and woodchips for nutrient removal in stormwater treatment.}, journal = {Chemosphere}, volume = {213}, number = {}, pages = {403-413}, doi = {10.1016/j.chemosphere.2018.09.062}, pmid = {30243206}, issn = {1879-1298}, abstract = {Copper, a commonly occurring heavy metal in stormwater runoff, was tested for its inhibitory effects on key nitrogen cycle bacteria in Biosorption Activated Media (BAM) and woodchip. The information in this paper is used to show that copper can enhance the denitrification process through enzyme cascade reactions since nitrous reductase is the enzyme responsible for the last step of denitrification and is largely dependent on copper as its cofactor. However, media characteristics are critical for assessing multi-enzymatic cascade reactions from the microbial ecology point of view. Moreover, both media showed significant copper removal through various mechanisms at 30 cm depth. The bioactivity evaluation indicates that other bacteria (fermentative bacteria, etc.) can be largely depressed with the presence of copper, hence the biofilm structure would be more vulnerable under shearing effects, which may result in holistic depression on the microbial community.}, }
@article {pmid30241680, year = {2018}, author = {Mergoni, G and Percudani, D and Lodi, G and Bertani, P and Manfredi, M}, title = {Prevalence of Candida Species in Endodontic Infections: Systematic Review and Meta-analysis.}, journal = {Journal of endodontics}, volume = {44}, number = {11}, pages = {1616-1625.e9}, doi = {10.1016/j.joen.2018.07.016}, pmid = {30241680}, issn = {1878-3554}, abstract = {INTRODUCTION: Candida in endodontic infections has been investigated in a large number of studies, but its role as an endodontic pathogen is still debatable. The aim of this study was to systematically review the literature on the prevalence of Candida species in root canal infections.<br><br>METHODS: Extensive literature research was performed in the most important electronic biomedical databases, and additional studies have been identified from references from relevant articles. Studies were critically appraised using a modified version of the Joanna Briggs Institute Critical Appraisal Checklist.<br><br>RESULTS: From 2225 unique records, 2118 were excluded on the basis of title and abstract. Of the remaining 107 studies, 50 were excluded after full-text review, and 57 were included for qualitative and quantitative analysis. The overall prevalence of Candida spp. in root canal infections was 8.20% (95% confidence interval, 5.56%-11.21%). Candida albicans was the most frequently isolated species. Significant heterogeneity among studies was observed (P < .001, I2 = 86.07%). Subgroup analyses revealed a higher prevalence of Candida spp. from African samples. All studies considered, a high or unclear risk of bias was prevalent regarding 6 out of the 8 items considered in the critical appraisal.<br><br>CONCLUSIONS: Candida spp. occurred in a small proportion of root canal infections. Further and better designed research is needed to investigate the real contribution of Candida spp. to the microbial ecology in infected root canals.}, }
@article {pmid30239657, year = {2018}, author = {Van Herreweghen, F and De Paepe, K and Roume, H and Kerckhof, FM and Van de Wiele, T}, title = {Mucin degradation niche as a driver of microbiome composition and Akkermansia muciniphila abundance in a dynamic gut model is donor independent.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {12}, pages = {}, doi = {10.1093/femsec/fiy186}, pmid = {30239657}, issn = {1574-6941}, abstract = {Akkermansia muciniphila, an abundant mucin degrading intestinal bacterium, has been correlated with human health in various studies. The in vitro SHIME model was used to reach a mechanistic understanding of A. muciniphila's colonization preferences and its response to environmental parameters such as colon pH and mucins. These insight can help to identify the optimal conditions for successful in vivo application. After a period of mucin deprivation, we found that mucin supplementation resulted in significantly different microbial communities, with more Akkermansia, Bacteroides and Ruminococcus. Mucin treatment accounted for 26% of the observed variation in the microbial community at OTU level (P = 0.001), whereas the donor effect was limited (8%) (P = 0.035), indicating mucins to constitute an important ecological niche shaping the microbiota composition. The effect of colonic pH had a less profound impact on the microbiome with both pH and donor origin explaining around 10% of the variability in the dataset. Yet, higher simulated colonic pH had a positive impact on Akkermansia abundance while short chain fatty acid analysis displayed a preference for propionate production with higher colonic pH. Our results show that mucins as nutritional resource are a more important modulator of the gut microbiome than colon pH as environmental factor.}, }
@article {pmid30238141, year = {2018}, author = {Roussel, C and Galia, W and Leriche, F and Chalancon, S and Denis, S and Van de Wiele, T and Blanquet-Diot, S}, title = {Comparison of conventional plating, PMA-qPCR, and flow cytometry for the determination of viable enterotoxigenic Escherichia coli along a gastrointestinal in vitro model.}, journal = {Applied microbiology and biotechnology}, volume = {102}, number = {22}, pages = {9793-9802}, doi = {10.1007/s00253-018-9380-z}, pmid = {30238141}, issn = {1432-0614}, abstract = {Recent technological advances for bacterial viability assessment using molecular methods or flow cytometry can provide meaningful interest for the demarcation between live and dead microorganisms. Nonetheless, these methods have been scarcely applied to foodborne pathogens and never for directly assessing their viability within the human digestive environment. The purpose of this study was to compare two methods based on membrane integrity (propidium monoazide (PMA) q-PCR and Live/Dead flow cytometry) and the classical plate-count method to determine the viability of a common foodborne pathogen, enterotoxigenic Escherichia coli (ETEC), during its transit trough simulated human gastrointestinal environment. Viable ETEC counts in the gastric and small intestinal compartments of the gastrointestinal TIM model indicated a consensus between the three tested methods (PMA-qPCR, flow cytometry, and plate counts). In a further step, flow cytometry analysis appeared as the preferred method to elucidate ETEC physiological states in the in vitro digestive environment by discriminating four subpopulations, while PMA-qPCR can only distinguish two. The defined viable/altered ETEC population was found during all in vitro digestions, but mainly in the gastric compartment. Being able to discriminate the particular physiological states of pathogenic microorganisms in the digestive environment is of high interest, because if some cells are not observable on culture media, they might keep their ability to express virulence functions.}, }
@article {pmid30237506, year = {2018}, author = {Erşan, YÇ and Van Tittelboom, K and Boon, N and De Belie, N}, title = {Nitrite producing bacteria inhibit reinforcement bar corrosion in cementitious materials.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {14092}, doi = {10.1038/s41598-018-32463-6}, pmid = {30237506}, issn = {2045-2322}, abstract = {Chemicals and synthetic coatings are widely used to protect steel against corrosion. Bio-based corrosion inhibition strategies can be an alternative in the arising bioeconomy era. To maintain the good state of steel reinforcement in cracked concrete, microbe-based self-healing cementitious composites (MSCC) have been developed. Yet, proposed strategies involve reasonably slow crack filling by biomineralization and thus risk the possible rebar corrosion during crack healing. Here we upgrade the rebar protection to a higher level by combining MSCC with microbial induced corrosion inhibition. Presented NO3- reducing bacterial granules inhibit rebar corrosion by producing the anodic corrosion inhibitor NO2- and meanwhile heal a 300-µm-wide crack in 28 days. During 120 days exposure to 0.5 M Cl- solution, the rebars in cracked MSCC keep showing open circuit potentials above the critical value of -250 mV and they lose less than 2% of the total rebar material which corresponds to half the material loss in cracked plain mortar. Overall, the obtained rebar protection performance is comparable with that of uncracked mortar and mortar containing chemical inhibitor, hence the microbe-based system becomes an alternative to the traditional methods.}, }
@article {pmid30235606, year = {2019}, author = {Fiorentino, A and Di Cesare, A and Eckert, EM and Rizzo, L and Fontaneto, D and Yang, Y and Corno, G}, title = {Impact of industrial wastewater on the dynamics of antibiotic resistance genes in a full-scale urban wastewater treatment plant.}, journal = {The Science of the total environment}, volume = {646}, number = {}, pages = {1204-1210}, doi = {10.1016/j.scitotenv.2018.07.370}, pmid = {30235606}, issn = {1879-1026}, abstract = {Urban Wastewater Treatment Plants (UWTPs) treating mixed urban sewage and industrial wastewater are among the major hotspots for the spread of Antibiotic Resistance Genes (ARGs) into the environment. This study addresses the impact of the wastewater origin on ARG dynamics in a full-scale UWTP (15,000 Population Equivalent, PE) by operating the plant with and without industrial wastewater. Composite samples (4 L) from different treatment points were characterized for their chemical composition, bacterial abundance and for the abundance of four resistance genes against tetracycline, sulfonamides, erythromycin, and quinolones (tetA, sul2, ermB, and qnrS), and of the class 1 integrons (intI1). Although the chemical composition of the outflow significantly differed when the plant operated with or without industrial wastewater, the system efficiency in the removal of bacterial cells, ARGs, and intI1 was constant. The final disinfection by peracetic acid (PAA) did not affect the removal of ARGs, independently of the wastewater origin and the chemical characteristics of the inflows. Our results demonstrated that a well-functioning small size UWTP could treat a significant amount of industrial wastewater mixed in the urban sewage without affecting the overall ARGs and class 1 integrons released into the environment.}, }
@article {pmid30234420, year = {2018}, author = {De Mulder, T and Rasschaert, G and Van Coillie, E and Van den Meersche, T and Haegeman, A and Ruttink, T and de Wiele, TV and Heyndrickx, M}, title = {Impact of Cross-Contamination Concentrations of Doxycycline Hyclate on the Microbial Ecosystem in an Ex Vivo Model of the Pig's Cecum.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {}, number = {}, pages = {}, doi = {10.1089/mdr.2018.0034}, pmid = {30234420}, issn = {1931-8448}, abstract = {AIMS: Cross-contamination of feed with antibiotics causes pigs to become unintentionally exposed to low concentrations of antibiotics. This study investigates the effect of residues of doxycycline hyclate (DOX) in an ex vivo model of the intestinal tract of pigs, focusing on the microbial community, microbial activity, and the enrichment of resistant bacteria and resistance genes.<br><br>RESULTS: The effect of three concentrations DOX were tested; 1 and 4 mg/L correspond to the intestinal concentrations when pigs are fed a compound feed containing 3% of a therapeutic dose, and a reference concentration of 16 mg/L. These were continuously administered to a chemostat, simulating the microbial ecosystem of the pig cecum and inoculated with cecal content of organically grown pigs. The administration of even the lowest DOX concentration caused a significant decrease in bacterial activity, while the microbial community profile appeared to remain unaffected by any of the concentrations. A concentration of 1 mg/L DOX caused minor selection pressure for tetracycline-resistant Escherichia coli but no other groups enumerated with plate cultivation, while 4 mg/L induced major enrichment of tetracycline-resistant E. coli, Enterobacteriaceae and total anaerobes. High abundances of tet(Q), tet(M), tet(W), tet(O), and tet(B) were detected in the inoculum and also before antibiotic administration in the chemostat and did not significantly increase during administration of 1 and 4 mg/L DOX. Only 16 mg/L DOX caused minor enrichments.<br><br>CONCLUSIONS: Cross-contamination concentrations of doxycycline, as a result of cross-contamination, cause a selection pressure for resistant bacteria and negatively affect microbial activity.}, }
@article {pmid30233537, year = {2018}, author = {Teurlincx, S and Heijboer, A and Veraart, AJ and Kowalchuk, GA and Declerck, SAJ}, title = {Local Functioning, Landscape Structuring: Drivers of Soil Microbial Community Structure and Function in Peatlands.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2060}, doi = {10.3389/fmicb.2018.02060}, pmid = {30233537}, issn = {1664-302X}, abstract = {Agricultural peatlands are essential for a myriad of ecosystem functions and play an important role in the global carbon (C) cycle through C sequestration. Management of these agricultural peatlands takes place at different spatial scales, ranging from local to landscape management, and drivers of soil microbial community structure and function may be scale-dependent. Effective management for an optimal biogeochemical functioning thus requires knowledge of the drivers on soil microbial community structure and functioning, as well as the spatial scales upon which they are influenced. During two field campaigns, we examined the importance of different drivers (i.e., soil characteristics, nutrient management, vegetation composition) at two spatial scales (local vs. landscape) for, respectively, the soil microbial community structure (determined by PLFA) and soil microbial community functional capacity (as assessed by CLPP) in agricultural peatlands. First, we show by an analysis of PLFA profiles that the total microbial biomass changes with soil moisture and relative C:P nutrient availability. Secondly, we showed that soil communities are controlled by a distinct set of drivers at the local, as opposed to landscape, scale. Community structure was found to be markedly different between areas, in contrast to community function which showed high variability within areas. We further found that microbial structure appears to be controlled more at a landscape scale by nutrient-related variables, whereas microbial functional capacity is driven locally through plant community feedbacks. Optimal management strategies within such peatlands should therefore consider the scale-dependent action of soil microbial community drivers, for example by first optimizing microbial structure at the landscape scale by targeted areal management, and then optimizing soil microbial function by local vegetation management.}, }
@article {pmid30232167, year = {2018}, author = {Ingala, MR and Simmons, NB and Perkins, SL}, title = {Bats Are an Untapped System for Understanding Microbiome Evolution in Mammals.}, journal = {mSphere}, volume = {3}, number = {5}, pages = {}, doi = {10.1128/mSphere.00397-18}, pmid = {30232167}, issn = {2379-5042}, abstract = {Mammals evolved in a microbial world, and consequently, microbial symbionts have played a role in their evolution. An exciting new subdiscipline of metagenomics considers the ways in which microbes, particularly those found in the gut, have facilitated the ecological and phylogenetic radiation of mammals. However, the vast majority of such studies focus on domestic animals, laboratory models, or charismatic megafauna (e.g., pandas and chimpanzees). The result is a plethora of studies covering few taxa across the mammal tree of life, leaving broad patterns of microbiome function and evolution unclear. Wildlife microbiome research urgently needs a model system in which to test hypotheses about metagenomic involvement in host ecology and evolution. We propose that bats (Order: Chiroptera) represent a model system ideal for comparative microbiome research, affording opportunities to examine host phylogeny, diet, and other natural history characteristics in relation to the evolution of the gut microbiome.}, }
@article {pmid30231985, year = {2018}, author = {Malik, A and Sharma, D and Malireddi, RKS and Guy, CS and Chang, TC and Olsen, SR and Neale, G and Vogel, P and Kanneganti, TD}, title = {SYK-CARD9 Signaling Axis Promotes Gut Fungi-Mediated Inflammasome Activation to Restrict Colitis and Colon Cancer.}, journal = {Immunity}, volume = {49}, number = {3}, pages = {515-530.e5}, doi = {10.1016/j.immuni.2018.08.024}, pmid = {30231985}, issn = {1097-4180}, abstract = {Fungi represent a significant proportion of the gut microbiota. Aberrant immune responses to fungi are frequently observed in inflammatory bowel diseases (IBD) and colorectal cancer (CRC), and mutations in the fungal-sensing pathways are associated with the pathogenesis of IBD. Fungal recognition receptors trigger downstream signaling via the common adaptor protein CARD9 and the kinase SYK. Here we found that commensal gut fungi promoted inflammasome activation during AOM-DSS-induced colitis. Myeloid cell-specific deletion of Card9 or Syk reduced inflammasome activation and interleukin (IL)-18 maturation and increased susceptibility to colitis and CRC. IL-18 promoted epithelial barrier restitution and interferon-γ production by intestinal CD8+ T cells. Supplementation of IL-18 or transfer of wild-type myeloid cells reduced tumor burden in AOM-DSS-treated Card9-/- and Sykfl/flLysMCre/+ mice, whereas treatment with anti-fungal agents exacerbated colitis and CRC. CARD9 deletion changes the gut microbial landscape, suggesting that SYK-CARD9 signaling maintains a microbial ecology that promotes inflammasome activation and thereby restrains colitis and colon tumorigenesis.}, }
@article {pmid30231921, year = {2018}, author = {Vavourakis, CD and Andrei, AS and Mehrshad, M and Ghai, R and Sorokin, DY and Muyzer, G}, title = {A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {168}, doi = {10.1186/s40168-018-0548-7}, pmid = {30231921}, issn = {2049-2618}, support = {322551//European Research Council/International ; 322551//European Research Council/International ; L200961651//Czech Academy of Science/ ; 16-14-00121//Russian Science Support Foundation/ ; 24002002//Dutch Ministry of Education and Science/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; 17-04828S//Grant Agency of the Czech Republic/ ; 17-04828S//Grant Agency of the Czech Republic/ ; }, abstract = {BACKGROUND: Hypersaline soda lakes are characterized by extreme high soluble carbonate alkalinity. Despite the high pH and salt content, highly diverse microbial communities are known to be present in soda lake brines but the microbiome of soda lake sediments received much less attention of microbiologists. Here, we performed metagenomic sequencing on soda lake sediments to give the first extensive overview of the taxonomic diversity found in these complex, extreme environments and to gain novel physiological insights into the most abundant, uncultured prokaryote lineages.<br><br>RESULTS: We sequenced five metagenomes obtained from four surface sediments of Siberian soda lakes with a pH 10 and a salt content between 70 and 400 g L-1. The recovered 16S rRNA gene sequences were mostly from Bacteria, even in the salt-saturated lakes. Most OTUs were assigned to uncultured families. We reconstructed 871 metagenome-assembled genomes (MAGs) spanning more than 45 phyla and discovered the first extremophilic members of the Candidate Phyla Radiation (CPR). Five new species of CPR were among the most dominant community members. Novel dominant lineages were found within previously well-characterized functional groups involved in carbon, sulfur, and nitrogen cycling. Moreover, key enzymes of the Wood-Ljungdahl pathway were encoded within at least four bacterial phyla never previously associated with this ancient anaerobic pathway for carbon fixation and dissimilation, including the Actinobacteria.<br><br>CONCLUSIONS: Our first sequencing effort of hypersaline soda lake sediment metagenomes led to two important advances. First, we showed the existence and obtained the first genomes of haloalkaliphilic members of the CPR and several hundred other novel prokaryote lineages. The soda lake CPR is a functionally diverse group, but the most abundant organisms in this study are likely fermenters with a possible role in primary carbon degradation. Second, we found evidence for the presence of the Wood-Ljungdahl pathway in many more taxonomic groups than those encompassing known homo-acetogens, sulfate-reducers, and methanogens. Since only few environmental metagenomics studies have targeted sediment microbial communities and never to this extent, we expect that our findings are relevant not only for the understanding of haloalkaline environments but can also be used to set targets for future studies on marine and freshwater sediments.}, }
@article {pmid30231187, year = {2018}, author = {Wu, T and Grootaert, C and Pitart, J and Vidovic, NK and Kamiloglu, S and Possemiers, S and Glibetic, M and Smagghe, G and Raes, K and Van de Wiele, T and Van Camp, J}, title = {Aronia (Aronia melanocarpa) Polyphenols Modulate the Microbial Community in a Simulator of the Human Intestinal Microbial Ecosystem (SHIME) and Decrease Secretion of Proinflammatory Markers in a Caco-2/endothelial Cell Coculture Model.}, journal = {Molecular nutrition &amp; food research}, volume = {62}, number = {22}, pages = {e1800607}, doi = {10.1002/mnfr.201800607}, pmid = {30231187}, issn = {1613-4133}, support = {//China Scholarship Council (CSC)/ ; //Ghent University/ ; 01B04212//BOF/ ; FP7/2007-2013//Project BACCHUS/ ; 312090//Project BACCHUS/ ; }, abstract = {SCOPE: To explore the mechanisms behind the health effects of Aronia (Aronia melanocarpa), the microbial community modulating and anti-inflammatory effects of Aronia polyphenols are investigated by combining the similutor of the human intestinal microbial ecosystem (SHIME) with a coculture of intestinal and endothelial cells.<br><br>RESULTS: Administration of Aronia juice (6.5g L-1) to the SHIME for 2 weeks increases the abundance of firmicutes to 92% in the ascending colon (AC), 85% in the transverse colon (TC), and 82% in the descending colon (DC; p < 0.001), proteobacteria (6.7% in AC, p < 0.001), and Akkermansia (14% in TC and 18% in DC, p < 0.001) and decreases the abundance of Bifidobacterium species, associated with a decrease of acetate and increase of propionate and butyrate, whereas no significant difference is observed upon placebo juice treatment. After addition of the digests to TNF-α challenged Caco-2/endothelial cocultures, intercellular adhesion molecule (ICAM)-1, IL-8, and monocyte chemoattractant protein-1 levels are significantly downregulated. Interestingly, Aronia juice treats digests from each colon compartment resulting in a stronger decrease of the ICAM-1 secretion (up to 73%, p < 0.001) compared to their corresponding placebo treated digests, thereby pointing to a polyphenol-dependent effect.<br><br>CONCLUSIONS: Aronia polyphenols modulate intestinal microbial composition, induce beneficial short chain fatty acid production, and prevent inflammatory stress in endothelial cells. This opens perspectives for the use of Aronia polyphenols as prebiotics in the context of intestinal and cardiovascular health.}, }
@article {pmid30229264, year = {2018}, author = {Ziller, A and Fraissinet-Tachet, L}, title = {Metallothionein diversity and distribution in the tree of life: a multifunctional protein.}, journal = {Metallomics : integrated biometal science}, volume = {10}, number = {11}, pages = {1549-1559}, doi = {10.1039/c8mt00165k}, pmid = {30229264}, issn = {1756-591X}, abstract = {MTs are small cysteine-rich proteins that chelate metal ions such as Cu+ and Zn2+, and are widely distributed in several life domains, in particular the eukaryotic one. They are present in the following phyla: Opisthokonta (mainly Fungi and Metazoa), Chloroplastida, Alveolata (ciliates) and Excavata (Trichomonas) for Eukaryota and Cyanobacteria, Actinobacteria, Proteobacteria and Firmicutes for Bacteria. However, their absence in some phyla underlines that MTs are far from being fully known. The MT amino acid sequences show a great diversity of sizes and structures both in terms of cysteine motifs and organization of these motifs. This review also highlights the different oxidized, apoprotein and metalated forms of MTs, the diversity of interactions they can establish with different molecules and their central and multifunctional cellular role. We present MTs as a protein system that could be a hub in molecular interaction networks. Studying MTs as a hub in cellular interaction networks should provide new insights for a better understanding of MT functioning and cellular processes.}, }
@article {pmid30228802, year = {2018}, author = {Gacesa, R and Baranasic, D and Starcevic, A and Diminic, J and Korlević, M and Najdek, M and Blažina, M and Oršolić, D and Kolesarić, D and Long, PF and Cullum, J and Hranueli, D and Orlic, S and Zucko, J}, title = {Bioprospecting for Genes Encoding Hydrocarbon-Degrading Enzymes from Metagenomic Samples Isolated from 
Northern Adriatic Sea Sediments.}, journal = {Food technology and biotechnology}, volume = {56}, number = {2}, pages = {270-277}, doi = {10.17113/ftb.56.02.18.5393}, pmid = {30228802}, issn = {1330-9862}, abstract = {Three metagenomic libraries were constructed using surface sediment samples from the northern Adriatic Sea. Two of the samples were taken from a highly polluted and an unpolluted site respectively. The third sample from a polluted site had been enriched using crude oil. The results of the metagenome analyses were incorporated in the REDPET relational database (http://redpet.bioinfo.pbf.hr/REDPET), which was generated using the previously developed MEGGASENSE platform. The database includes taxonomic data to allow the assessment of the biodiversity of metagenomic libraries and a general functional analysis of genes using hidden Markov model (HMM) profiles based on the KEGG database. A set of 22 specialised HMM profiles was developed to detect putative genes for hydrocarbon-degrading enzymes. Use of these profiles showed that the metagenomic library generated after selection on crude oil had enriched genes for aerobic n-alkane degradation. The use of this system for bioprospecting was exemplified using potential alkB and almA genes from this library.}, }
@article {pmid30228389, year = {2018}, author = {Mechmeche, M and Kachouri, F and Ksontini, H and Setti, K and Hamdi, M}, title = {Bioprocess development and preservation of functional food from tomato seed isolate fermented by kefir culture mixture.}, journal = {Journal of food science and technology}, volume = {55}, number = {10}, pages = {3911-3921}, doi = {10.1007/s13197-018-3315-7}, pmid = {30228389}, issn = {0022-1155}, abstract = {The aim of this work was to explore the use of protein isolate from tomato seed enriched with the sucrose and the ascorbic acid as a medium for the growth of kefir mixture culture to develop a new non-dairy functional food. Unstructured mathematical and logistic models were proposed to describe cell growth, kefiran production, nutriment consumption and antioxidant activity. It was found that the maximal cell mass in the culture reached 8.38 g L-1 after 24 h of fermentation. A significant amount of kefiran was also produced (0.65 g L-1). The kefir culture growth significantly decreased protein content and enhanced the antioxidant activity during varied fermentation through the production of bio active peptides. After 24 h of fermentation, IC50 value for protein isolate was estimated to be about 10.48 µg mL-1. The proposed models adequately described the changes during fermentation and as observed as a promising approach for the formulation of tomato seed-based functional foods. The preservation of the isolate was also investigated through a spray-drying process. The effect of spray-drying on the viability of lactic acid bacteria and stability of protein content and the antioxidant activity of the powder was also carried out. Results showed that the spray-drying method has great potential for the synthesis of powder from the fermented isolate that are rich in desirable properties. However, it was appropriate to preserve the powder for 10 days at 37 °C for the preservation of protein functionality.}, }
@article {pmid30223892, year = {2018}, author = {Sitaraman, R}, title = {Prokaryotic horizontal gene transfer within the human holobiont: ecological-evolutionary inferences, implications and possibilities.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {163}, doi = {10.1186/s40168-018-0551-z}, pmid = {30223892}, issn = {2049-2618}, abstract = {The ubiquity of horizontal gene transfer in the living world, especially among prokaryotes, raises interesting and important scientific questions regarding its effects on the human holobiont i.e., the human and its resident bacterial communities considered together as a unit of selection. Specifically, it would be interesting to determine how particular gene transfer events have influenced holobiont phenotypes in particular ecological niches and, conversely, how specific holobiont phenotypes have influenced gene transfer events. In this synthetic review, we list some notable and recent discoveries of horizontal gene transfer among the prokaryotic component of the human microbiota, and analyze their potential impact on the holobiont from an ecological-evolutionary viewpoint. Finally, the human-Helicobacter pylori association is presented as an illustration of these considerations, followed by a delineation of unresolved questions and avenues for future research.}, }
@article {pmid30218926, year = {2018}, author = {Zhang, X and Prévoteau, A and Louro, RO and Paquete, CM and Rabaey, K}, title = {Periodic polarization of electroactive biofilms increases current density and charge carriers concentration while modifying biofilm structure.}, journal = {Biosensors &amp; bioelectronics}, volume = {121}, number = {}, pages = {183-191}, doi = {10.1016/j.bios.2018.08.045}, pmid = {30218926}, issn = {1873-4235}, abstract = {Anodic electroactive biofilms (EABs) need to overcome low current densities for applications such as microbial fuel cells or biosensors. EABs can store charge in self-produced redox proteins when temporarily left in open circuit, and discharge them once the electrode is appropriately repolarized, thus behaving as pseudocapacitors. Here we investigated the effect of such periodic polarization on the intrinsic nature of the EABs during their entire growth (i.e. starting from inoculation and for 10 days) on glassy carbon electrodes. An optimal periodic polarization (half-period of 10 s) greatly increased the maximum steady-state current density delivered by the Geobacter-dominated EABs (up to 1.10 ± 0.02 mA cm-2, n = 3 electrodes) when compared to continuously polarized EABs (0.41 ± 0.04 mA cm-2); and increased the amount of electric charges produced per hour by 69 ± 17% even taking into account the half-periods of open circuit. This enhancement was highly correlated with a substantial increase in charge carriers concentration (10.6 ± 0.5 mMe- vs. 2.9 ± 0.6 mMe-), allowing higher charge storage capacity and higher electron mobility across the EABs. Our results suggest that appropriate periodic polarizations may upregulate the expression of heme-containing redox proteins associated with the matrix, such as c-type cytochromes. The EABs grown under periodic polarization presented mushroom-like structures on their top layers, while EABs grown under continuous polarization were flat.}, }
@article {pmid30218130, year = {2018}, author = {Bernasconi, R and Stat, M and Koenders, A and Huggett, MJ}, title = {Global Networks of Symbiodinium-Bacteria Within the Coral Holobiont.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1255-4}, pmid = {30218130}, issn = {1432-184X}, abstract = {Scleractinian corals form the framework of coral reefs and host abundant and diverse microbial communities that are fundamental to their success. A very limited number of studies have examined the co-occurrence of multiple partners within the coral 'holobiont' and their pattern of specificity over different geographical scales. In this study, we explored two molecular sequence datasets representing associations between corals and dinoflagellates in the genus Symbiodinium and between corals and bacteria, across the globe. Through a network theory approach, we characterised patterns of co-occurrences between bacteria and Symbiodinium with 13 coral genera across six water basins. The majority of the bacteria-Symbiodinium co-occurrences were specific to either a coral genus or water basin, emphasising both coral host and environment as important factors driving the diversity of coral assemblages. Yet, results also identified bacteria and Symbiodinium that were shared by multiple coral genera across several water basins. The analyses indicate that shared co-occurrences are independent of the phylogenetic and biogeographic relationship of coral hosts.}, }
@article {pmid30218129, year = {2018}, author = {Biswas, S and Mukherjee, P and Manna, T and Dutta, K and Guchhait, KC and Karmakar, A and Karmakar, M and Dua, P and Panda, AK and Ghosh, C}, title = {Quorum Sensing Autoinducer(s) and Flagellum Independently Mediate EPS Signaling in Vibrio cholerae Through LuxO-Independent Mechanism.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1262-5}, pmid = {30218129}, issn = {1432-184X}, support = {SR/SO/HS-43/2006//Department of Science and Technology/ ; BT/PR3802/BRB/10/981/2011//Department of Biotechnology , Ministry of Science and Technology/ ; }, abstract = {Vibrio cholerae, the Gram-negative bacterium causing lethal diarrheal disease cholera, forms biofilm on solid surfaces to gain adaptive advantage for successful survival in aquatic reservoirs. Expression of exopolysaccharide (EPS), an extracellular matrix material, has been found critical for biofilm-based environmental persistence. In a subset of epidemic-causing V. cholerae, absence of flagellum but not motility was identified to induce elevated exopolysaccharide expression. Identification of the role played by quorum sensing autoinducer molecules, i.e., cholera autoinducer 1 (CAI-1) and autoinducer 2 (AI-2) as well as central regulator LuxO on EPS expression in the subset was explored. Deletion mutations were introduced in vital genes responsible for synthesizing CAI-1 (cqsA), AI-2 (luxS), flagellum (flaA), LuxO (luxO), flagellar motor (motX), and VpsR (vpsR) in the model strain MO10. Subsequent phenotypic alterations in terms of colony morphology, EPS expression, biofilm formation, and transcription level of relevant genes were analyzed. Autoinducer cross-feeding experiment confirmed the role of autoinducers in EPS signaling. Results reveal that autoinducers and flagellum are the two major EPS signaling units in this subset where one unit becomes predominant for EPS production in absence of the other. Moreover, either unit exerts negative influence on EPS induction by the other. Both the EPS signaling cascades are independent of LuxO contribution and essentially involve sodium-driven flagellar motor and VpsR. A cell density and flagellum-mediated, but LuxO-independent, EPS signaling mechanism is considered to be functional in these organisms that confers their survival fitness.}, }
@article {pmid30217851, year = {2018}, author = {Stough, JMA and Kolton, M and Kostka, JE and Weston, DJ and Pelletier, DA and Wilhelm, SW}, title = {Diversity of Active Viral Infections within the Sphagnum Microbiome.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {23}, pages = {}, doi = {10.1128/AEM.01124-18}, pmid = {30217851}, issn = {1098-5336}, abstract = {Sphagnum-dominated peatlands play an important role in global carbon storage and represent significant sources of economic and ecological value. While recent efforts to describe microbial diversity and metabolic potential of the Sphagnum microbiome have demonstrated the importance of its microbial community, little is known about the viral constituents. We used metatranscriptomics to describe the diversity and activity of viruses infecting microbes within the Sphagnum peat bog. The vegetative portions of six Sphagnum plants were obtained from a peatland in northern Minnesota, and the total RNA was extracted and sequenced. Metatranscriptomes were assembled and contigs were screened for the presence of conserved virus marker genes. Using bacteriophage capsid protein gp23 as a marker for phage diversity, we identified 33 contigs representing undocumented phages that were active in the community at the time of sampling. Similarly, RNA-dependent RNA polymerase and the nucleocytoplasmic large DNA virus (NCLDV) major capsid protein were used as markers for single-stranded RNA (ssRNA) viruses and NCLDV, respectively. In total, 114 contigs were identified as originating from undescribed ssRNA viruses, 22 of which represent nearly complete genomes. An additional 64 contigs were identified as being from NCLDVs. Finally, 7 contigs were identified as putative virophage or polinton-like viruses. We developed co-occurrence networks with these markers in relation to the expression of potential-host housekeeping gene rpb1 to predict virus-host relationships, identifying 13 groups. Together, our approach offers new tools for the identification of virus diversity and interactions in understudied clades and suggests that viruses may play a considerable role in the ecology of the Sphagnum microbiome.IMPORTANCESphagnum-dominated peatlands play an important role in maintaining atmospheric carbon dioxide levels by modifying conditions in the surrounding soil to favor the growth of Sphagnum over that of other plant species. This lowers the rate of decomposition and facilitates the accumulation of fixed carbon in the form of partially decomposed biomass. The unique environment produced by Sphagnum enriches for the growth of a diverse microbial consortia that benefit from and support the moss's growth, while also maintaining the hostile soil conditions. While a growing body of research has begun to characterize the microbial groups that colonize Sphagnum, little is currently known about the ecological factors that constrain community structure and define ecosystem function. Top-down population control by viruses is almost completely undescribed. This study provides insight into the significant viral influence on the Sphagnum microbiome and identifies new potential model systems to study virus-host interactions in the peatland ecosystem.}, }
@article {pmid30217848, year = {2018}, author = {Mbareche, H and Veillette, M and Bilodeau, GJ and Duchaine, C}, title = {Bioaerosol Sampler Choice Should Consider Efficiency and Ability of Samplers to Cover Microbial Diversity.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.01589-18}, pmid = {30217848}, issn = {1098-5336}, abstract = {Bioaerosol studies tend to describe the microbial content and understand the aerosolization processes linked to diseases. Air samplers are used to collect, identify and quantify bioaerosols. Studies comparing the performance of air samplers have typically used a culture approach or have targeted a specific microorganism in laboratory settings. The objective of this study was to use environmental field samples to compare the efficiency of 3 high airflow rate samplers for describing bioaerosol diversity using a next-generation sequencing approach. Two liquid cyclonic impactors and one electrostatic filter dry sampler were used in four wastewater treatment plants to target bacterial diversity and in five dairy farms to target fungal diversity. The dry electrostatic sampler was consistently more powerful in collecting more fungal and bacterial OTUs. Substantial differences in OTU abundance between liquid and dry sampling were revealed. The majority of the diversity revealed by dry electrostatic sampling was not identified using the cyclonic liquid impactors. The findings on this work suggest that the choice of a bioaerosol sampler should include information about the efficiency and ability of samplers to cover microbial diversity. Although these results suggest that electrostatic filters result in better coverage of the microbial diversity amongst the tested air samplers, further studies are needed to confirm this hypothesis. While it is difficult to determine a single universally optimal air sampler, this work provides an in-depth look at some of the considerations that are essential when choosing an air sampler for studying the microbial ecology of bioaerosols.Importance Associating bioaerosol exposure and health problems is challenging and adequate exposure monitoring is a priority for scientist in the field. Conclusions that can be drawn from bioaerosol exposure studies are highly dependent on the design of the study and the methodologies used. The air sampling strategy is the first methodological step leading to an accurate interpretation of what is present in the air. Applying new molecular approaches to evaluate the efficiency of the different types of samplers used in the field is a necessary work around the traditional approaches and the biases they introduce to such studies. The results and conclusions provided in this manuscript should be taken in considerations when conducting a bioaerosol study.}, }
@article {pmid30214003, year = {2018}, author = {Lindeboom, REF and Ilgrande, C and Carvajal-Arroyo, JM and Coninx, I and Van Hoey, O and Roume, H and Morozova, J and Udert, KM and Sas, B and Paille, C and Lasseur, C and Ilyin, V and Clauwaert, P and Leys, N and Vlaeminck, SE}, title = {Nitrogen cycle microorganisms can be reactivated after Space exposure.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {13783}, doi = {10.1038/s41598-018-32055-4}, pmid = {30214003}, issn = {2045-2322}, abstract = {Long-term human Space missions depend on regenerative life support systems (RLSS) to produce food, water and oxygen from waste and metabolic products. Microbial biotechnology is efficient for nitrogen conversion, with nitrate or nitrogen gas as desirable products. A prerequisite to bioreactor operation in Space is the feasibility to reactivate cells exposed to microgravity and radiation. In this study, microorganisms capable of essential nitrogen cycle conversions were sent on a 44-days FOTON-M4 flight to Low Earth Orbit (LEO) and exposed to 10-3-10-4 g (gravitational constant) and 687 ± 170 µGy (Gray) d-1 (20 ± 4 °C), about the double of the radiation prevailing in the International Space Station (ISS). After return to Earth, axenic cultures, defined and reactor communities of ureolytic bacteria, ammonia oxidizing archaea and bacteria, nitrite oxidizing bacteria, denitrifiers and anammox bacteria could all be reactivated. Space exposure generally yielded similar or even higher nitrogen conversion rates as terrestrial preservation at a similar temperature, while terrestrial storage at 4 °C mostly resulted in the highest rates. Refrigerated Space exposure is proposed as a strategy to maximize the reactivation potential. For the first time, the combined potential of ureolysis, nitritation, nitratation, denitrification (nitrate reducing activity) and anammox is demonstrated as key enabler for resource recovery in human Space exploration.}, }
@article {pmid30213542, year = {2018}, author = {Lee, K and Yu, H and Zhang, X and Choo, KH}, title = {Quorum sensing and quenching in membrane bioreactors: Opportunities and challenges for biofouling control.}, journal = {Bioresource technology}, volume = {270}, number = {}, pages = {656-668}, doi = {10.1016/j.biortech.2018.09.019}, pmid = {30213542}, issn = {1873-2976}, abstract = {Membrane biofouling, due to biofilm growth after planktonic bacteria attachment to a membrane, is a major bottleneck limiting the energy-efficient operation and maintenance of membrane bioreactors (MBRs). Microbial communications, known as quorum sensing (QS), are responsible for this biofouling behavior. Novel strategies for stopping this communication, known as quorum quenching (QQ), appear to be successful for biofouling control in MBRs used for wastewater treatment. This review describes recent information regarding the signal molecules and mechanisms responsible for QS behaviors, promising approaches for QQ (enzymatic, bacterial, fungal, photocatalytic, mimicking, and biostimulating methods), and efficient fabrication and use of QQ media for MBR applications. We discuss the opportunities and challenges of QQ techniques for their further improvement and practical use in MBRs.}, }
@article {pmid30210468, year = {2018}, author = {Nguyen, NL and Yu, WJ and Gwak, JH and Kim, SJ and Park, SJ and Herbold, CW and Kim, JG and Jung, MY and Rhee, SK}, title = {Genomic Insights Into the Acid Adaptation of Novel Methanotrophs Enriched From Acidic Forest Soils.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1982}, doi = {10.3389/fmicb.2018.01982}, pmid = {30210468}, issn = {1664-302X}, abstract = {Soil acidification is accelerated by anthropogenic and agricultural activities, which could significantly affect global methane cycles. However, detailed knowledge of the genomic properties of methanotrophs adapted to acidic soils remains scarce. Using metagenomic approaches, we analyzed methane-utilizing communities enriched from acidic forest soils with pH 3 and 4, and recovered near-complete genomes of proteobacterial methanotrophs. Novel methanotroph genomes designated KS32 and KS41, belonging to two representative clades of methanotrophs (Methylocystis of Alphaproteobacteria and Methylobacter of Gammaproteobacteria), were dominant. Comparative genomic analysis revealed diverse systems of membrane transporters for ensuring pH homeostasis and defense against toxic chemicals. Various potassium transporter systems, sodium/proton antiporters, and two copies of proton-translocating F1F0-type ATP synthase genes were identified, which might participate in the key pH homeostasis mechanisms in KS32. In addition, the V-type ATP synthase and urea assimilation genes might be used for pH homeostasis in KS41. Genes involved in the modification of membranes by incorporation of cyclopropane fatty acids and hopanoid lipids might be used for reducing proton influx into cells. The two methanotroph genomes possess genes for elaborate heavy metal efflux pumping systems, possibly owing to increased heavy metal toxicity in acidic conditions. Phylogenies of key genes involved in acid adaptation, methane oxidation, and antiviral defense in KS41 were incongruent with that of 16S rRNA. Thus, the detailed analysis of the genome sequences provides new insights into the ecology of methanotrophs responding to soil acidification.}, }
@article {pmid30209587, year = {2018}, author = {Hernández-Gómez, O and Briggler, JT and Williams, RN}, title = {Captivity-Induced Changes in the Skin Microbial Communities of Hellbenders (Cryptobranchus alleganiensis).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1258-1}, pmid = {30209587}, issn = {1432-184X}, abstract = {Variation in environmental conditions can result in disparate associations between hosts and microbial symbionts. As such, it is imperative to evaluate how environmental variables (e.g., habitat quality) can influence host-associated microbiome composition. Within wildlife conservation programs, captive conditions can negatively influence the establishment and maintenance of &quot;wild-type&quot; microbiotas within a host. Alternative microbial communities can result in the proliferation of disease among captive stock or upon reintroduction. Hellbenders (Cryptobranchus alleganiensis) are a threatened salamander for which extensive captive management is currently employed. Using metabarcoding, we characterized the skin microbiota of wild and captive hellbenders from two subspecies in the state of Missouri, the eastern (C. a. alleganiensis) and the Ozark hellbender (C. a. bishopi). Both subspecies in our study included wild adults and captive juveniles that were collected from the wild as eggs. Our objectives were to investigate differences in the skin microbial communities' richness/diversity, composition, and functional profiles of microbes between wild and captive individuals. Captive eastern hellbenders possessed richer communities than wild cohorts, whereas the opposite pattern was observed within the Ozark subspecies. We found significant microbial community structure between wild and captive populations of both subspecies. Microbiota structure translated into differences in the predicted metagenome of wild and captive individuals as well. As such, we can expect captive hellbenders to experience alternative microbial structure and function upon reintroduction into the wild. Our study provides a baseline for the effect of captivity on the skin microbial communities of hellbenders, and highlights the need to incorporate microbiota management in current captive-rearing programs.}, }
@article {pmid30209586, year = {2018}, author = {Manjunatha, BS and Paul, S and Aggarwal, C and Bandeppa, S and Govindasamy, V and Dukare, AS and Rathi, MS and Satyavathi, CT and Annapurna, K}, title = {Diversity and Tissue Preference of Osmotolerant Bacterial Endophytes Associated with Pearl Millet Genotypes Having Differential Drought Susceptibilities.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1257-2}, pmid = {30209586}, issn = {1432-184X}, abstract = {Genetic and functional diversity of osmotolerant bacterial endophytes colonizing the root, stem, and leaf tissues of pearl millet genotypes differing in their drought susceptibility was assessed. Two genotypes of pearl millet, viz., the drought tolerant genotype TT-1 and the drought susceptible genotype PPMI-69, were used in the present study. Diazotrophs were found to be the predominant colonizers, followed by the Gram positive bacteria in most of the tissues of both the genotypes. Higher proportion of bacterial endophytes obtained from the drought tolerant genotype was found to be osmotolerant. Results of 16S rRNA gene-ARDRA analysis grouped 50 of the highly osmotolerant isolates into 16 clusters, out of which nine clusters had only one isolate each, indicating their uniqueness. One cluster had 21 isolates and remaining clusters were represented by isolates ranging from two to four. The representative isolates from each cluster were identified, and Bacillus was found to be the most prevalent osmotolerant genera with many different species. Other endophytic bacteria belonged to Pseudomonas sp., Stenotrophomonas sp., and Macrococcus caseolyticus. High phylogenetic diversity was observed in the roots of the drought tolerant genotype while different tissues of the drought susceptible genotype showed less diversity. Isolates of Bacillus axarquiensis were present in all the tissues of both the genotypes of pearl millet. However, most of the other endophytic bacteria showed tissue/genotype specificity. With the exception of B. axarquiensis and B. thuringiensis, rest all the species of Bacillus were found colonizing only the drought-tolerant genotype; while M. caseolyticus colonized all the tissues of only the drought susceptible genotype. There was high incidence of IAA producers and low incidence of ACC deaminase producers among the isolates from the root tissues of the drought-tolerant genotype while reverse was the case for the drought-susceptible genotype. Thus, host played an important role in the selection of endophytes based on both phylogenetic and functional traits.}, }
@article {pmid30209585, year = {2018}, author = {Houfani, AA and Větrovský, T and Navarrete, OU and Štursová, M and Tláskal, V and Beiko, RG and Boucherba, N and Baldrian, P and Benallaoua, S and Jorquera, MA}, title = {Cellulase-Hemicellulase Activities and Bacterial Community Composition of Different Soils from Algerian Ecosystems.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1251-8}, pmid = {30209585}, issn = {1432-184X}, support = {LM2015055//Ministry of Education, Youth and Sports of the Czech Republic/ ; 1160302//Fondo Nacional de Desarrollo Científico y Tecnológico/ ; }, abstract = {Soil microorganisms are important mediators of carbon cycling in nature. Although cellulose- and hemicellulose-degrading bacteria have been isolated from Algerian ecosystems, the information on the composition of soil bacterial communities and thus the potential of their members to decompose plant residues is still limited. The objective of the present study was to describe and compare the bacterial community composition in Algerian soils (crop, forest, garden, and desert) and the activity of cellulose- and hemicellulose-degrading enzymes. Bacterial communities were characterized by high-throughput 16S amplicon sequencing followed by the in silico prediction of their functional potential. The highest lignocellulolytic activity was recorded in forest and garden soils whereas activities in the agricultural and desert soils were typically low. The bacterial phyla Proteobacteria (in particular classes α-proteobacteria, δ-proteobacteria, and γ-proteobacteria), Firmicutes, and Actinobacteria dominated in all soils. Forest and garden soils exhibited higher diversity than agricultural and desert soils. Endocellulase activity was elevated in forest and garden soils. In silico analysis predicted higher share of genes assigned to general metabolism in forest and garden soils compared with agricultural and arid soils, particularly in carbohydrate metabolism. The highest potential of lignocellulose decomposition was predicted for forest soils, which is in agreement with the highest activity of corresponding enzymes.}, }
@article {pmid30209011, year = {2018}, author = {Shade, A and Dunn, RR and Blowes, SA and Keil, P and Bohannan, BJM and Herrmann, M and Küsel, K and Lennon, JT and Sanders, NJ and Storch, D and Chase, J}, title = {Macroecology to Unite All Life, Large and Small.}, journal = {Trends in ecology &amp; evolution}, volume = {33}, number = {10}, pages = {731-744}, doi = {10.1016/j.tree.2018.08.005}, pmid = {30209011}, issn = {1872-8383}, abstract = {Macroecology is the study of the mechanisms underlying general patterns of ecology across scales. Research in microbial ecology and macroecology have long been detached. Here, we argue that it is time to bridge the gap, as they share a common currency of species and individuals, and a common goal of understanding the causes and consequences of changes in biodiversity. Microbial ecology and macroecology will mutually benefit from a unified research agenda and shared datasets that span the entirety of the biodiversity of life and the geographic expanse of the Earth.}, }
@article {pmid30206025, year = {2018}, author = {Kispal, ZF and Vajda, P and Kardos, D and Klymiuk, I and Moissl-Eichinger, C and Castellani, C and Singer, G and Till, H}, title = {The local microbiome after pediatric bladder augmentation: intestinal segments and the native urinary bladder host similar mucosal microbiota.}, journal = {Journal of pediatric urology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jpurol.2018.07.028}, pmid = {30206025}, issn = {1873-4898}, abstract = {INTRODUCTION: Next-generation sequencing (NGS) techniques have provided novel insights into the microbiome of the urinary bladder (UB). In children after bladder augmentation using either ileum (ileocystoplasty, ICP) or colon (colocystoplasty, CCP), the fate of the mucosal microbiome introduced into the urinary tract remains unknown.<br><br>OBJECTIVE: The aim was to compare the mucosal microbiome of the native UB vs the augmented intestinal segment (IS) using NGS.<br><br>STUDY DESIGN: Twelve children after bladder augmentation (ICP n = 6, CCP n = 6) were included. Biopsies were taken during routine postoperative cystoscopy from the native UB and the IS. Specimens underwent whole-genome DNA extraction, 16S rRNA gene amplification, NGS, and Quantitative Insights Into Microbial Ecology (QIIME) data analysis. Downstream statistical data analyses were performed in Calypso.<br><br>RESULTS: Patients' median age at the time of surgery was 11 years (6-17 years), and the median interval between augmentation and sampling was 7 years (4-13 years). α-Diversity (Shannon diversity index) was not significantly different between IS vs UB, ICP vs CCP, and male vs female. No general differences in the overall bacterial pattern (β-diversity) were found between IS, UB, ICP, and CCP groups. The groups overlapped in principal coordinate analysis (PCoA) and non-metric multidimensional scaling (NMDS) analysis (Figure). Age at sampling had a statistically significant influence on β-diversity at the genus level. Corynebacterium, Pseudoxanthomonas, Lactobacillus, Flavobacterium, and Micrococcus were the most dominating taxa detected over all samples. There was an obvious dominance of the genus Corynebacterium in the samples taken from the UB and IS in both ICP and CCP patients. Limitations of this study include the relatively small number of patients.<br><br>CONCLUSION: After bladder augmentation, the native UB and augmented ISs (ICP and CCP) host similar microbiota despite their distinct differences of originating mucosal anatomy.}, }
@article {pmid30204767, year = {2018}, author = {Lee, JZ and Everroad, RC and Karaoz, U and Detweiler, AM and Pett-Ridge, J and Weber, PK and Prufert-Bebout, L and Bebout, BM}, title = {Metagenomics reveals niche partitioning within the phototrophic zone of a microbial mat.}, journal = {PloS one}, volume = {13}, number = {9}, pages = {e0202792}, doi = {10.1371/journal.pone.0202792}, pmid = {30204767}, issn = {1932-6203}, abstract = {Hypersaline photosynthetic microbial mats are stratified microbial communities known for their taxonomic and metabolic diversity and strong light-driven day-night environmental gradients. In this study of the upper photosynthetic zone of hypersaline microbial mats of Elkhorn Slough, California (USA), we show how metagenome sequencing can be used to meaningfully assess microbial ecology and genetic partitioning in these complex microbial systems. Mapping of metagenome reads to the dominant Cyanobacteria observed in the system, Coleofasciculus (Microcoleus) chthonoplastes, was used to examine strain variants within these metagenomes. Highly conserved gene subsystems indicated a core genome for the species, and a number of variant genes and subsystems suggested strain level differentiation, especially for nutrient utilization and stress response. Metagenome sequence coverage binning was used to assess ecosystem partitioning of remaining microbes to both reconstruct the model organisms in silico and identify their ecosystem functions as well as to identify novel clades and propose their role in the biogeochemical cycling of mats. Functional gene annotation of these bins (primarily of Proteobacteria, Bacteroidetes, and Cyanobacteria) recapitulated the known biogeochemical functions in microbial mats using a genetic basis, and revealed significant diversity in the Bacteroidetes, presumably in heterotrophic cycling. This analysis also revealed evidence of putative phototrophs within the Gemmatimonadetes and Gammaproteobacteria residing in microbial mats. This study shows that metagenomic analysis can produce insights into the systems biology of microbial ecosystems from a genetic perspective and to suggest further studies of novel microbes.}, }
@article {pmid30199845, year = {2018}, author = {Dolan, JR}, title = {The Villefranche Strombidium sulcatum: A review.}, journal = {European journal of protistology}, volume = {66}, number = {}, pages = {68-76}, doi = {10.1016/j.ejop.2018.08.002}, pmid = {30199845}, issn = {1618-0429}, abstract = {The marine oligotrich ciliate Strombidium sulcatum, the best known marine oligotrich of the marine microozoplankton, was first cultured in Villefranche-sur-Mer 35 years ago. Cultures were maintained from 1983 to 2003 and used in 22 studies investigating a very wide variety of questions. Here we review the major findings of these studies and underline their contributions to our knowledge of planktonic ciliate ecology and microbial ecology in general. We conclude with the observation that while ecophysiology has apparently fallen out of fashion, culture work will likely return as an invaluable resource in our present 'omics' era.}, }
@article {pmid30199026, year = {2018}, author = {Couper, L and Swei, A}, title = {Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {138}, pages = {}, doi = {10.3791/58239}, pmid = {30199026}, issn = {1940-087X}, abstract = {In recent decades, vector-borne diseases have re-emerged and expanded at alarming rates, causing considerable morbidity and mortality worldwide. Effective and widely available vaccines are lacking for a majority of these diseases, necessitating the development of novel disease mitigation strategies. To this end, a promising avenue of disease control involves targeting the vector microbiome, the community of microbes inhabiting the vector. The vector microbiome plays a pivotal role in pathogen dynamics, and manipulations of the microbiome have led to reduced vector abundance or pathogen transmission for a handful of vector-borne diseases. However, translating these findings into disease control applications requires a thorough understanding of vector microbial ecology, historically limited by insufficient technology in this field. The advent of next-generation sequencing approaches has enabled rapid, highly parallel sequencing of diverse microbial communities. Targeting the highly-conserved 16S rRNA gene has facilitated characterizations of microbes present within vectors under varying ecological and experimental conditions. This technique involves amplification of the 16S rRNA gene, sample barcoding via PCR, loading samples onto a flow cell for sequencing, and bioinformatics approaches to match sequence data with phylogenetic information. Species or genus-level identification for a high number of replicates can typically be achieved through this approach, thus circumventing challenges of low detection, resolution, and output from traditional culturing, microscopy, or histological staining techniques. Therefore, this method is well-suited for characterizing vector microbes under diverse conditions but cannot currently provide information on microbial function, location within the vector, or response to antibiotic treatment. Overall, 16S next-generation sequencing is a powerful technique for better understanding the identity and role of vector microbes in disease dynamics.}, }
@article {pmid30197411, year = {2018}, author = {Mise, K and Fujita, K and Kunito, T and Senoo, K and Otsuka, S}, title = {Phosphorus-mineralizing Communities Reflect Nutrient-Rich Characteristics in Japanese Arable Andisols.}, journal = {Microbes and environments}, volume = {33}, number = {3}, pages = {282-289}, doi = {10.1264/jsme2.ME18043}, pmid = {30197411}, issn = {1347-4405}, mesh = {Alkaline Phosphatase/*genetics/metabolism ; Bacteria/classification/enzymology/genetics/*metabolism ; Bacterial Proteins/*genetics/metabolism ; Biodiversity ; Computational Biology ; DNA, Bacterial/genetics ; Genes, Bacterial/genetics ; Geography ; Japan ; Metagenome/genetics ; Phosphorus/analysis/*metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Elucidating the soil phosphorus cycle driven by soil microbes is a vital question in soil microbial ecology. The Japanese arable Andisols, occupying half of the Japanese cropland, are known for their high phosphorus sorption capacity. However, limited information is currently available on microbially driven phosphorus mineralization in arable Andisols. We herein report that the phosphorus-mineralizing community in the Japanese arable Andisols showed characteristic distribution and composition patterns, from those in other types of soils. We performed a chemical analysis and microbial community analysis of 43 arable Andisols along the Japanese archipelago. Soil phosphomonoesterase activities measured at pH 11 were approximately 70% of those at pH 6.5, which indicates that alkaline phosphatase contributes to phosphorus cycling, although most soil samples were acidic. Functional gene predictions based on 16S rRNA gene sequencing indicated that the alkaline phosphatase gene phoD was more abundant than other alkaline phosphatase genes and, thus, plays major roles. Hence, amplicon sequencing targeting phoD was performed and the results obtained showed that alphaproteobacterial phoD was dominant. This is in contrast to previously reported phoD compositions in other soils and may be attributed to the nutrient conditions in arable Andisols, which favor copiotrophic Alphaproteobacteria. Furthermore, the composition of phoD correlated with soil pH and bioavailable phosphorus concentrations rather than carbon or nitrogen concentrations. These results were partly different from previous findings, varying in the soil types and geographic ranges of sampling sites. Collectively, the present results indicate that the phosphorus-mineralizing community in the Japanese arable Andisols is regulated differently from those in other soil types.}, }
@article {pmid30196926, year = {2018}, author = {Šulčius, S and Mazur-Marzec, H and Vitonytė, I and Kvederavičiūtė, K and Kuznecova, J and Šimoliūnas, E and Holmfeldt, K}, title = {Insights into cyanophage-mediated dynamics of nodularin and other non-ribosomal peptides in Nodularia spumigena.}, journal = {Harmful algae}, volume = {78}, number = {}, pages = {69-74}, doi = {10.1016/j.hal.2018.07.004}, pmid = {30196926}, issn = {1878-1470}, abstract = {The effect of cyanophage infection and lysis on the dynamics of the hepatotoxin nodularin (NOD) and other non-ribosomal peptides (NRPs) produced by cyanobacteria is poorly understood. In this study, changes in concentration of NOD and other NRPs during cyanophage infection of the filamentous cyanobacteria Nodularia spumigena were assessed using incubation experiments. Viral infection and lysis were associated with a significant reduction (93% at the 96 h post infection) of N. spumigena cell density. While no correlation between N. spumigena abundance and total concentration of NOD (ng mL-1) within the infected cells was observed, cellular NOD quota (ng cell-1) gradually increased in the remaining cyanophage resistant N. spumigena subpopulation. Lysis of N. spumigena cells resulted in a substantial increase (>57 times) of dissolved NOD concentration in the culture medium. The relative concentration of other cyclic (anabaenopeptins) and linear (aeruginosins, spumigins) NRPs produced by N. spumigena also increased in response to cyanophage addition. This study highlights the importance of cyanophage infection on the population toxicity of filamentous cyanobacteria and demonstrates a significant contribution of virus-mediated cell lysis on the conversion of NOD from the particulate to dissolved phase.}, }
@article {pmid30196314, year = {2018}, author = {Ullah, A and Akbar, A and Luo, Q and Khan, AH and Manghwar, H and Shaban, M and Yang, X}, title = {Microbiome Diversity in Cotton Rhizosphere Under Normal and Drought Conditions.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1260-7}, pmid = {30196314}, issn = {1432-184X}, support = {2016YFD0101006//National Key Project of Research and Development Plan/ ; 2016ZX08005-004-002//Transgenic Crops of Transgenic Crops of Ministry of Science and Technology of China/ ; }, abstract = {Climate change contributes to drought stress and subsequently affects crop growth, development, and yield. The microbial community, such as fungi and bacteria in the rhizosphere, is of special importance to plant productivity. In this study, soil collected from a cotton research field was used to grow cotton plants (Gossypium hirsutum cv. Jin668) under controlled environment conditions. Drought stress was applied at flowering stage, while control plants were regularly watered. At the same time, the soil without plants was also subjected to drought, while control pots were regularly watered. The soil was collected in sterilized tubes and microbial DNA was isolated and high-throughput sequencing of 16S rRNA genes was carried out. The alpha diversity of bacteria community significantly increased in the soil with cotton plants compared to the soil without cotton plants. Taxonomic analysis revealed that the bacterial community structure of the cotton rhizosphere predominantly consisted of the phyla Proteobacteria (31.7%), Actinobacteria (29.6%), Gemmatimonadetes (9.8%), Chloroflexi (9%), Cyanobacteria (5.6%), and Acidobacteria. In the drought-treated rhizosphere, Chloroflexi and Gemmatimonadetes were the dominant phyla. This study reveals that the cotton rhizosphere has a rich pool of bacterial communities even under drought stress, and which may improve drought tolerance in plants. These data will underpin future improvement of drought tolerance of cotton via the soil microbial community.}, }
@article {pmid30195549, year = {2018}, author = {Jamar, G and Santamarina, AB and Dias, GC and Masquio, DCL and de Rosso, VV and Pisani, LP}, title = {Relationship between fatty acids intake and Clostridium coccoides in obese individuals with metabolic syndrome.}, journal = {Food research international (Ottawa, Ont.)}, volume = {113}, number = {}, pages = {86-92}, doi = {10.1016/j.foodres.2018.07.002}, pmid = {30195549}, issn = {1873-7145}, abstract = {Dietary habits exert a strong influence on gut microbial composition and may result in an imbalance of gut microbes, representing a predisposition to obesity and metabolic disorders. We aimed to investigate a potential relationship between gut bacterial species and metabolic parameters and dietary intake. Bacterial DNA was extracted from feces of 34 obese subjects with and without metabolic syndrome (MS and n-MS group, respectively). We then used real-time polymerase chain reaction (qPCR) for quantifying specific sequences to Akkermansia muciniphila, Bifidobacterium spp., Clostridium coccoides, and Lactobacillus spp. and analyzed them with respect to clinical characteristics. Our data showed that the MS group had a 6.7-fold higher level of C. coccoides in their stool samples than the n-MS group. The abundance of C. coccoides was positively correlated with a high intake of monounsaturated fatty acids (MUFA) and polyunsaturated fatty acids. Furthermore, an excessive dietary level of MUFA was identified as a predictor of C. coccoides abundance. Alterations in the gut microbial ecology were positively correlated with levels of triacylglycerol in obese individuals. Therefore, the type and quantity of dietary fat may alter the gut microbial ecology in obese individuals with MS and may predispose them to dyslipidemia.}, }
@article {pmid30195522, year = {2018}, author = {Nash, V and Ranadheera, CS and Georgousopoulou, EN and Mellor, DD and Panagiotakos, DB and McKune, AJ and Kellett, J and Naumovski, N}, title = {The effects of grape and red wine polyphenols on gut microbiota - A systematic review.}, journal = {Food research international (Ottawa, Ont.)}, volume = {113}, number = {}, pages = {277-287}, doi = {10.1016/j.foodres.2018.07.019}, pmid = {30195522}, issn = {1873-7145}, abstract = {There is a growing body of evidence implicating the gut 'microbiome' role in overall human health. Bacterial species belonging to the genera Lactobacillus and Bifidobacterium are generally considered to be beneficial and are commonly used in probiotic applications, whereas increases in some genera including Clostridum, Eubacterium and Bacteroides are implicated in negative health outcomes. Dietary polyphenols are bioactive compounds that have been found to increase the numbers of beneficial bacteria and antimicrobial actions against pathogenic bacteria, however most studies have been conducted in animal models or in-vitro colonic models. The aim of this systematic review was to provide an overview of recent trials on the effect of dietary grape and red wine polyphenols on the gut microbiota in humans. Following PRISMA guidelines, a systematic review was conducted of electronic databases (PubMed, CINAHL, Cochrane Library, Wed of Science and Scopus) to identify human intervention trials examining the effect of grape or wine polyphenols on gut microbiota. Seven trials met the inclusion criteria. One study looked at changes in gut microbiota following the ingestion of de-alcoholised red wine or red wine, and six studies referred to gut microbiota as intermediates in formation of phenolic metabolites. All studies confirmed that ingested polyphenols from grape and red wine, were modulated by gut microbiota, increasing numbers of polyphenolic metabolites which were found in blood, urine, ileal fluid and faeces. Intake of polyphenols derived from grape and red wine can modulate gut microbiota and contribute to beneficial microbial ecology that can enhance human health benefits. Additionally, grape and red wine polyphenols were modulated by the gut microbiota and there is a potential for a two-way relationship between the gut microbiota and polyphenolic compounds. Nevertheless, additional research is required to fully understand the complex relationship between gut microbiota and dietary polyphenols before any health claims can be made in relation to human health.}, }
@article {pmid30195437, year = {2018}, author = {Medlock, GL and Carey, MA and McDuffie, DG and Mundy, MB and Giallourou, N and Swann, JR and Kolling, GL and Papin, JA}, title = {Inferring Metabolic Mechanisms of Interaction within a Defined Gut Microbiota.}, journal = {Cell systems}, volume = {7}, number = {3}, pages = {245-257.e7}, doi = {10.1016/j.cels.2018.08.003}, pmid = {30195437}, issn = {2405-4712}, support = {R01 GM108501/GM/NIGMS NIH HHS/United States ; T32 GM008136/GM/NIGMS NIH HHS/United States ; T32 LM012416/LM/NLM NIH HHS/United States ; }, abstract = {The diversity and number of species present within microbial communities create the potential for a multitude of interspecies metabolic interactions. Here, we develop, apply, and experimentally test a framework for inferring metabolic mechanisms associated with interspecies interactions. We perform pairwise growth and metabolome profiling of co-cultures of strains from a model mouse microbiota. We then apply our framework to dissect emergent metabolic behaviors that occur in co-culture. Based on one of the inferences from this framework, we identify and interrogate an amino acid cross-feeding interaction and validate that the proposed interaction leads to a growth benefit in vitro. Our results reveal the type and extent of emergent metabolic behavior in microbial communities composed of gut microbes. We focus on growth-modulating interactions, but the framework can be applied to interspecies interactions that modulate any phenotype of interest within microbial communities.}, }
@article {pmid30194506, year = {2018}, author = {da Silveira, APD and Iório, RPF and Marcos, FCC and Fernandes, AO and de Souza, SACD and Kuramae, EE and Cipriano, MAP}, title = {Exploitation of new endophytic bacteria and their ability to promote sugarcane growth and nitrogen nutrition.}, journal = {Antonie van Leeuwenhoek}, volume = {}, number = {}, pages = {}, doi = {10.1007/s10482-018-1157-y}, pmid = {30194506}, issn = {1572-9699}, support = {2008/56147-1//FAPESP/ ; 456420/2013-4//CNPq/NWO/ ; 729.004.013//NWO/ ; }, abstract = {Few studies have evaluated endophytic bacteria in relation to plant growth promotion, nitrogen uptake and biological control. The aim of this study was to molecularly and physiologically characterize thirteen endophytic bacteria strains, evaluate their biological control properties and their ability to promote plant growth and plant N nutrition. All the strains produced indole acetic acid and promoted increase of plant biomass, N accumulative amount and N-use efficiency index. None of the strains carries the nifH gene. Four strains stimulated plant nitrate reductase activity, four solubilized phosphate, nine produced siderophores and none produced HCN. Seven strains inhibited Bipolaris sacchari growth and one was antagonistic to Ceratocystis paradoxa. The pathogens were inhibited by the production of diffusible and volatile metabolites by the bacterial strains. Moreover, this is the first study to demonstrate the effect of Delftia acidovorans on sugarcane plant growth, nitrogen metabolism improvement and antagonism to B. sacchari. The most efficient strains in promoting plant growth and exhibiting antagonistic activities towards fungal pathogens were Herbaspirillum frinsingense (IAC-BECa-152) and three Pantoea dispersa strains (IAC-BECa-128, IAC-BECa-129, and IAC-BECa-132). These bacteria show potential to be used as inoculants for sustainable agricultural management, mainly at the seedling production phase.}, }
@article {pmid30194484, year = {2018}, author = {Szubert-Kruszyńska, A and Stańczak, J and Cieniuch, S and Podsiadły, E and Postawa, T and Michalik, J}, title = {Correction to: Bartonella and Rickettsia Infections in Haematophagous Spinturnix myoti Mites (Acari: Mesostigmata) and their Bat Host, Myotis myotis (Yangochiroptera: Vespertilionidae), from Poland.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1259-0}, pmid = {30194484}, issn = {1432-184X}, abstract = {The original version of this article published online (27 August 2018) unfortunately contained a mistake regarding an affiliation of Dr. Edyta Podsiadły, one of the authors.}, }
@article {pmid30194483, year = {2018}, author = {Eichmeier, A and Kiss, T and Necas, T and Penazova, E and Tekielska, D and Bohunicka, M and Valentova, L and Cmejla, R and Morais, D and Baldrian, P}, title = {High-Throughput Sequencing Analysis of the Bacterial Community in Stone Fruit Phloem Tissues Infected by &quot;Candidatus Phytoplasma prunorum&quot;.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1250-9}, pmid = {30194483}, issn = {1432-184X}, support = {QJ1510352//Ministry of Agriculture of the Czech Republic/ ; CZ.02.1.01/0.0/0.0/16_025/0007314//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; LM2015042//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; }, abstract = {&quot;Candidatus Phytoplasma prunorum&quot; (CPp) is a highly destructive phytopathogenic agent in many stone fruit-growing regions in Europe and the surrounding countries. In this work, we focused on documenting entire bacterial community in the phloem tissues of 60 stone fruit trees. Nested PCR and two real-time PCR assays were used to select CPp-positive (group A) and CPp-negative samples (group B). Afterwards, high-throughput amplicon sequencing was performed to assess bacterial community compositions in phloem tissues. The bacterial composition in phloem tissue consisted of 118 distinct genera, represented mainly by Pseudomonas, Acinetobacter, Methylobacterium, Sphingomonas, and Rhizobium. Statistics showed that CPp influenced the bacterial composition of infected plants (group A) and that the bacterial community depended on the geographical origin of the sample. This is the first work focusing on an analysis of the influence of CPp on the bacteria coexisting in the phloem tissues of stone fruit trees.}, }
@article {pmid30194105, year = {2018}, author = {Cordovez, V and Schop, S and Hordijk, K and Dupré de Boulois, H and Coppens, F and Hanssen, I and Raaijmakers, JM and Carrión, VJ}, title = {Priming of Plant Growth Promotion by Volatiles of Root-Associated Microbacterium spp.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {22}, pages = {}, doi = {10.1128/AEM.01865-18}, pmid = {30194105}, issn = {1098-5336}, abstract = {Volatile compounds produced by plant-associated microorganisms represent a diverse resource to promote plant growth and health. Here, we investigated the effect of volatiles from root-associated Microbacterium species on plant growth and development. Volatiles of eight strains induced significant increases in shoot and root biomass of Arabidopsis but differed in their effects on root architecture. Microbacterium strain EC8 also enhanced root and shoot biomass of lettuce and tomato. Biomass increases were also observed for plants exposed only briefly to volatiles from EC8 prior to transplantation of the seedlings to soil. These results indicate that volatiles from EC8 can prime plants for growth promotion without direct and prolonged contact. We further showed that the induction of plant growth promotion is tissue specific; that is, exposure of roots to volatiles from EC8 led to an increase in plant biomass, whereas shoot exposure resulted in no or less growth promotion. Gas chromatography-quadrupole time of flight mass spectometry (GC-QTOF-MS) analysis revealed that EC8 produces a wide array of sulfur-containing compounds, as well as ketones. Bioassays with synthetic sulfur volatile compounds revealed that the plant growth response to dimethyl trisulfide was concentration-dependent, with a significant increase in shoot weight at 1 μM and negative effects on plant biomass at concentrations higher than 1 mM. Genome-wide transcriptome analysis of volatile-exposed Arabidopsis seedlings showed upregulation of genes involved in assimilation and transport of sulfate and nitrate. Collectively, these results show that root-associated Microbacterium primes plants, via the roots, for growth promotion, most likely via modulation of sulfur and nitrogen metabolism.IMPORTANCE In the past decade, various studies have described the effects of microbial volatiles on other (micro)organisms in vitro, but their broad-spectrum activity in vivo and the mechanisms underlying volatile-mediated plant growth promotion have not been addressed in detail. Here, we revealed that volatiles from root-associated bacteria of the genus Microbacterium can enhance the growth of different plant species and can prime plants for growth promotion without direct and prolonged contact between the bacterium and the plant. Collectively, these results provide new opportunities for sustainable agriculture and horticulture by exposing roots of plants only briefly to a specific blend of microbial volatile compounds prior to transplantation of the seedlings to the greenhouse or field. This strategy has no need for large-scale introduction or root colonization and survival of the microbial inoculant.}, }
@article {pmid30192223, year = {2018}, author = {Borel, N and Bavoil, P and Greub, G and Horn, M}, title = {International Committee on Systematics of Prokaryotes Subcommittee on the taxonomy of Chlamydiae. Minutes of the closed meeting, 9 April 2017, Charlotte, USA.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {68}, number = {1}, pages = {3369-3370}, doi = {10.1099/ijsem.0.003010}, pmid = {30192223}, issn = {1466-5034}, }
@article {pmid30191255, year = {2018}, author = {Tarnecki, AM and Brennan, NP and Schloesser, RW and Rhody, NR}, title = {Shifts in the Skin-Associated Microbiota of Hatchery-Reared Common Snook Centropomus undecimalis During Acclimation to the Wild.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1252-7}, pmid = {30191255}, issn = {1432-184X}, support = {R/LR-A-54//Florida Sea Grant, University of Florida/ ; }, abstract = {The skin-associated microbiota of fish competes against pathogens for space and nutrients, preventing colonization by harmful bacteria encountered during environmental transitions such as those faced during stock enhancement. Thus, alterations in bacterial community structure during release of cultured fish have important implications for health of these individuals. This study investigated microbiota structure during acclimation of juvenile hatchery-reared common snook Centropomus undecimalis to the wild by comparing skin-associated microflora among snook in captivity, after 48 h of acclimation at release sites, and from the wild. After two days of acclimation, the microbiota of hatchery-reared snook mirrored that observed on wild snook. Relative abundances of potential pathogens were higher in captive fish, whereas acclimated and wild fish harbored bacterial taxa influenced by geographical factors and water quality at release sites. Predicted microbiota function of acclimated and wild fish showed higher production of protective amino acids and antimicrobials, identifying a mechanism for microbial supplementation of the immune defense of these fish. The two-day transition to wild-type microbiota suggests a temporal scale of hours associated with bacterial succession indicating that the microbiota, whose structure is vital to fish health, aids in acclimation of fish to new environments during stock enhancement efforts.}, }
@article {pmid30190715, year = {2018}, author = {Safonov, AV and Babich, TL and Sokolova, DS and Grouzdev, DS and Tourova, TP and Poltaraus, AB and Zakharova, EV and Merkel, AY and Novikov, AP and Nazina, TN}, title = {Microbial Community and in situ Bioremediation of Groundwater by Nitrate Removal in the Zone of a Radioactive Waste Surface Repository.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1985}, doi = {10.3389/fmicb.2018.01985}, pmid = {30190715}, issn = {1664-302X}, abstract = {The goal of the present work was to investigate the physicochemical and radiochemical conditions and the composition of the microbial community in the groundwater of a suspended surface repository for radioactive waste (Russia) and to determine the possibility of in situ groundwater bioremediation by removal of nitrate ions. Groundwater in the repository area (10-m depth) had elevated concentrations of strontium, tritium, nitrate, sulfate, and bicarbonate ions. High-throughput sequencing of the V3-V4/V4 region of the 16S rRNA gene revealed the presence of members of the phyla Proteobacteria (genera Acidovorax, Simplicispira, Thermomonas, Thiobacillus, Pseudomonas, Brevundimonas, and uncultured Oxalobacteraceae), Firmicutes (genera Bacillus and Paenibacillus), and Actinobacteria (Candidatus Planktophila, Gaiella). Canonical correspondence analysis suggested that major contaminant - nitrate, uranium, and sulfate shaped the composition of groundwater microbial community. Groundwater samples contained culturable aerobic organotrophic, as well as anaerobic fermenting, iron-reducing, and denitrifying bacteria. Pure cultures of 33 bacterial strains belonging to 15 genera were isolated. Members of the genera Pseudomonas, Rhizobium, Cupriavidus, Shewanella, Ensifer, and Thermomonas reduced nitrate to nitrite and/or dinitrogen. Application of specific primers revealed the nirS and nirK genes encoding nitrite reductases in bacteria of the genera Pseudomonas, Rhizobium, and Ensifer. Nitrate reduction by pure bacterial cultures resulted in decreased ambient Eh. Among the organic substrates tested, sodium acetate and milk whey were the best for stimulation of denitrification by the microcosms with groundwater microorganisms. Injection of these substrates into the subterranean horizon (single-well push-pull test) resulted in temporary removal of nitrate ions in the area of the suspended radioactive waste repository and confirmed the possibility for in situ application of this method for bioremediation.}, }
@article {pmid30190707, year = {2018}, author = {Hicks, N and Liu, X and Gregory, R and Kenny, J and Lucaci, A and Lenzi, L and Paterson, DM and Duncan, KR}, title = {Temperature Driven Changes in Benthic Bacterial Diversity Influences Biogeochemical Cycling in Coastal Sediments.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1730}, doi = {10.3389/fmicb.2018.01730}, pmid = {30190707}, issn = {1664-302X}, abstract = {Marine sediments are important sites for global biogeochemical cycling, mediated by macrofauna and microalgae. However, it is the microorganisms that drive these key processes. There is strong evidence that coastal benthic habitats will be affected by changing environmental variables (rising temperature, elevated CO2), and research has generally focused on the impact on macrofaunal biodiversity and ecosystem services. Despite their importance, there is less understanding of how microbial community assemblages will respond to environmental changes. In this study, a manipulative mesocosm experiment was employed, using next-generation sequencing to assess changes in microbial communities under future environmental change scenarios. Illumina sequencing generated over 11 million 16S rRNA gene sequences (using a primer set biased toward bacteria) and revealed Bacteroidetes and Proteobacteria dominated the total bacterial community of sediment samples. In this study, the sequencing coverage and depth revealed clear changes in species abundance within some phyla. Bacterial community composition was correlated with simulated environmental conditions, and species level community composition was significantly influenced by the mean temperature of the environmental regime (p = 0.002), but not by variation in CO2 or diurnal temperature variation. Species level changes with increasing mean temperature corresponded with changes in NH4 concentration, suggesting there is no functional redundancy in microbial communities for nitrogen cycling. Marine coastal biogeochemical cycling under future environmental conditions is likely to be driven by changes in nutrient availability as a direct result of microbial activity.}, }
@article {pmid30188995, year = {2018}, author = {Shibl, AA and Ngugi, DK and Talarmin, A and Thompson, LR and Blom, J and Stingl, U}, title = {The genome of a novel isolate of Prochlorococcus from the Red Sea contains transcribed genes for compatible solute biosynthesis.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {12}, pages = {}, doi = {10.1093/femsec/fiy182}, pmid = {30188995}, issn = {1574-6941}, abstract = {Marine microbes possess genomic and physiological adaptations to cope with varying environmental conditions. So far, the effects of high salinity on the most abundant marine photoautotrophic organism, Prochlorococcus, in marine oligotrophic environments, are mostly unknown. Here, we report the isolation of a new Prochlorococcus strain (RSP50) belonging to high-light (HL) clade II from the Red Sea, one of the warmest and most saline bodies of water in the global oceans. A comparative genomic analysis identified a set of 59 genes that were exclusive to RSP50 relative to currently available Prochlorococcus genomes, the majority of which (70%) encode for hypothetical proteins of unknown function. However, three of the unique genes encode for a complete pathway for the biosynthesis of the compatible solute glucosylglycerol, and are homologous to enzymes found in the sister lineage Synechococcus. Metatranscriptomic analyses of this metabolic pathway in the water column of the Red Sea revealed that the corresponding genes were constitutively transcribed, independent of depth and light, suggesting that osmoregulation using glucosylglycerol is a general feature of HL II Prochlorococcus in the Red Sea.}, }
@article {pmid30188282, year = {2018}, author = {Coats, ER and Eyre, K and Bryant, C and Woodland, T and Brinkman, CK}, title = {Assessing the Effects of RAS Fermentation on EBPR Performance and Associated Microbial Ecology.}, journal = {Water environment research : a research publication of the Water Environment Federation}, volume = {90}, number = {7}, pages = {659-671}, doi = {10.2175/106143017X15131012153130}, pmid = {30188282}, issn = {1061-4303}, mesh = {Anaerobiosis ; Carbon/metabolism ; Fatty Acids, Volatile/metabolism ; Fermentation ; Glycogen/metabolism ; Nitrates/metabolism ; Phosphorus/*metabolism ; Sewage/chemistry/*microbiology ; Waste Disposal, Fluid/*methods ; }, abstract = {Enhanced biological phosphorus removal (EBPR) is an engineered water resource recovery facility (WRRF) process configuration that can produce effluent P < 0.5 mg/L. To consistently achieve low effluent P concentrations, EBPR requires volatile fatty acids (VFAs) to induce requisite biochemical reactions. Moreover, returned activated sludge (RAS) nitrate concentrations must be minimized. Returned activated sludge fermentation can potentially address process needs. However, research detailed herein highlights concerns with RAS fermentation integrated with EBPR. Under 2 and 4 hours of RAS fermentation periods, no consequential VFA production was observed; similar results were observed in batch tests with RAS from a full-scale EBPR WRRF. More critically, EBPR performance was poor, with average effluent concentrations of 1.0 to 2.4 mg/L. Furthermore, the glycogen accumulating organism (GAO) fraction under RAS fermentation was 4.3 to 8.7 times higher than in a conventional EBPR mixed microbial consortium (MMC). Integrated RAS fermentation-EBPR only performed well under &quot;high&quot; RAS nitrate; thus, should RAS fermentation be implemented, careful control to prevent anaerobic conditions in the fermentation zone is required.}, }
@article {pmid30187987, year = {2018}, author = {Hooper, R and Brealey, JC and van der Valk, T and Alberdi, A and Durban, JW and Fearnbach, H and Robertson, KM and Baird, RW and Bradley Hanson, M and Wade, P and Gilbert, MTP and Morin, PA and Wolf, JBW and Foote, AD and Guschanski, K}, title = {Host-derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.14860}, pmid = {30187987}, issn = {1365-294X}, support = {//Lindblad Expeditions/National Geographic Conservation Fund/ ; ERCStG-336536//European Research Council/International ; DNRF94//Danish National Research Foundation/ ; //Antarctic Science Bursary/ ; //Welsh Government and Higher Education Funding Council for Wales through the Sêr Cymru National Research Network for Low Carbon, Energy and Environment/ ; 663830//European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie/ ; SR17/1227//British Ecological Society/ ; 2016-00835//FORMAS/ ; 5051-00033//Danish Council for Independent Research-DFF/ ; R250-2017-1351//Lundbeckfonden/ ; }, abstract = {Recent exploration into the interactions and relationship between hosts and their microbiota has revealed a connection between many aspects of the host's biology, health and associated micro-organisms. Whereas amplicon sequencing has traditionally been used to characterize the microbiome, the increasing number of published population genomics data sets offers an underexploited opportunity to study microbial profiles from the host shotgun sequencing data. Here, we use sequence data originally generated from killer whale Orcinus orca skin biopsies for population genomics, to characterize the skin microbiome and investigate how host social and geographical factors influence the microbial community composition. Having identified 845 microbial taxa from 2.4 million reads that did not map to the killer whale reference genome, we found that both ecotypic and geographical factors influence community composition of killer whale skin microbiomes. Furthermore, we uncovered key taxa that drive the microbiome community composition and showed that they are embedded in unique networks, one of which is tentatively linked to diatom presence and poor skin condition. Community composition differed between Antarctic killer whales with and without diatom coverage, suggesting that the previously reported episodic migrations of Antarctic killer whales to warmer waters associated with skin turnover may control the effects of potentially pathogenic bacteria such as Tenacibaculum dicentrarchi. Our work demonstrates the feasibility of microbiome studies from host shotgun sequencing data and highlights the importance of metagenomics in understanding the relationship between host and microbial ecology.}, }
@article {pmid30187089, year = {2018}, author = {Chan, YF and Chiang, KP and Ku, Y and Gong, GC}, title = {Abiotic and Biotic Factors Affecting the Ingestion Rates of Mixotrophic Nanoflagellates (Haptophyta).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1249-2}, pmid = {30187089}, issn = {1432-184X}, abstract = {Mixotrophic haptophytes comprise one of several important groups of mixotrophic nanoflagellates in the pelagic environment. This study aimed to investigate if phagotrophy in mixotrophic haptophytes is regulated by light or other factors in the surface (SE) and bottom (BE) of the euphotic zone in the subtropical northwestern Pacific Ocean. We estimated the rates of bacterial ingestion by haptophytes using fluorescently labeled bacteria (FLBs) and fluorescence in situ hybridization. Haptophyte diversity and abundance were also investigated in the same sampling area. The annual mean abundance of haptophytes was 419 ± 85.6 cells mL-1 in both SE and BE. Cells 3-5 μm in size were the dominant group in all haptophytes and accounted for majority of bacteria standing stock removed by haptophytes (53%). Most haptophyte ingestion rates (IRs) were not significantly different between the two layers (average SE ingestion rate: 12.5 ± 2.29 bac Hap-1 h-1; BE: 14.7 ± 3.03 bac Hap-1 h-1). Furthermore, the haptophyte IRs were negatively correlated with nitrate concentrations in the SE and positively correlated with bacterial abundances in the BE, which accounts for the significantly high IRs in August 2012 and 2013. These findings imply that mixotrophic haptophytes in this region had different factors affecting phagotrophy to adapt to the ambient light intensity alterations between SE and BE.}, }
@article {pmid30187088, year = {2018}, author = {Vallesi, A and Sjödin, A and Petrelli, D and Luporini, P and Taddei, AR and Thelaus, J and Öhrman, C and Nilsson, E and Di Giuseppe, G and Gutiérrez, G and Villalobo, E}, title = {A New Species of the γ-Proteobacterium Francisella, F. adeliensis Sp. Nov., Endocytobiont in an Antarctic Marine Ciliate and Potential Evolutionary Forerunner of Pathogenic Species.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1256-3}, pmid = {30187088}, issn = {1432-184X}, abstract = {The study of the draft genome of an Antarctic marine ciliate, Euplotes petzi, revealed foreign sequences of bacterial origin belonging to the γ-proteobacterium Francisella that includes pathogenic and environmental species. TEM and FISH analyses confirmed the presence of a Francisella endocytobiont in E. petzi. This endocytobiont was isolated and found to be a new species, named F. adeliensis sp. nov.. F. adeliensis grows well at wide ranges of temperature, salinity, and carbon dioxide concentrations implying that it may colonize new organisms living in deeply diversified habitats. The F. adeliensis genome includes the igl and pdp gene sets (pdpC and pdpE excepted) of the Francisella pathogenicity island needed for intracellular growth. Consistently with an F. adeliensis ancient symbiotic lifestyle, it also contains a single insertion-sequence element. Instead, it lacks genes for the biosynthesis of essential amino acids such as cysteine, lysine, methionine, and tyrosine. In a genome-based phylogenetic tree, F. adeliensis forms a new early branching clade, basal to the evolution of pathogenic species. The correlations of this clade with the other clades raise doubts about a genuine free-living nature of the environmental Francisella species isolated from natural and man-made environments, and suggest to look at F. adeliensis as a pioneer in the Francisella colonization of eukaryotic organisms.}, }
@article {pmid30186247, year = {2018}, author = {Olivares, M and Schüppel, V and Hassan, AM and Beaumont, M and Neyrinck, AM and Bindels, LB and Benítez-Páez, A and Sanz, Y and Haller, D and Holzer, P and Delzenne, NM}, title = {The Potential Role of the Dipeptidyl Peptidase-4-Like Activity From the Gut Microbiota on the Host Health.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1900}, doi = {10.3389/fmicb.2018.01900}, pmid = {30186247}, issn = {1664-302X}, abstract = {The Dipeptidyl peptidase-4 (DPP-4) activity influences metabolic, behavioral and intestinal disorders through the cleavage of key hormones and peptides. Some studies describe the existence of human DPP-4 homologs in commensal bacteria, for instance in Prevotella or Lactobacillus. However, the role of the gut microbiota as a source of DPP-4-like activity has never been investigated. Through the comparison of the DPP-4 activity in the cecal content of germ-free mice (GFM) and gnotobiotic mice colonized with the gut microbiota of a healthy subject, we bring the proof of concept that a significant DPP-4-like activity occurs in the microbiota. By analyzing the existing literature, we propose that DPP-4-like activity encoded by the intestinal microbiome could constitute a novel mechanism to modulate protein digestion as well as host metabolism and behavior.}, }
@article {pmid30185512, year = {2018}, author = {Rohwer, RR and Hamilton, JJ and Newton, RJ and McMahon, KD}, title = {TaxAss: Leveraging a Custom Freshwater Database Achieves Fine-Scale Taxonomic Resolution.}, journal = {mSphere}, volume = {3}, number = {5}, pages = {}, doi = {10.1128/mSphere.00327-18}, pmid = {30185512}, issn = {2379-5042}, abstract = {Taxonomy assignment of freshwater microbial communities is limited by the minimally curated phylogenies used for large taxonomy databases. Here we introduce TaxAss, a taxonomy assignment workflow that classifies 16S rRNA gene amplicon data using two taxonomy reference databases: a large comprehensive database and a small ecosystem-specific database rigorously curated by scientists within a field. We applied TaxAss to five different freshwater data sets using the comprehensive SILVA database and the freshwater-specific FreshTrain database. TaxAss increased the percentage of the data set classified compared to using only SILVA, especially at fine-resolution family to species taxon levels, while across the freshwater test data sets classifications increased by as much as 11 to 40% of total reads. A similar increase in classifications was not observed in a control mouse gut data set, which was not expected to contain freshwater bacteria. TaxAss also maintained taxonomic richness compared to using only the FreshTrain across all taxon levels from phylum to species. Without TaxAss, most organisms not represented in the FreshTrain were unclassified, but at fine taxon levels, incorrect classifications became significant. We validated TaxAss using simulated amplicon data derived from full-length clone libraries and found that 96 to 99% of test sequences were correctly classified at fine resolution. TaxAss splits a data set's sequences into two groups based on their percent identity to reference sequences in the ecosystem-specific database. Sequences with high similarity to sequences in the ecosystem-specific database are classified using that database, and the others are classified using the comprehensive database. TaxAss is free and open source and is available at https://www.github.com/McMahonLab/TaxAssIMPORTANCE Microbial communities drive ecosystem processes, but microbial community composition analyses using 16S rRNA gene amplicon data sets are limited by the lack of fine-resolution taxonomy classifications. Coarse taxonomic groupings at the phylum, class, and order levels lump ecologically distinct organisms together. To avoid this, many researchers define operational taxonomic units (OTUs) based on clustered sequences, sequence variants, or unique sequences. These fine-resolution groupings are more ecologically relevant, but OTU definitions are data set dependent and cannot be compared between data sets. Microbial ecologists studying freshwater have curated a small, ecosystem-specific taxonomy database to provide consistent and up-to-date terminology. We created TaxAss, a workflow that leverages this database to assign taxonomy. We found that TaxAss improves fine-resolution taxonomic classifications (family, genus, and species). Fine taxonomic groupings are more ecologically relevant, so they provide an alternative to OTU-based analyses that is consistent and comparable between data sets.}, }
@article {pmid30184128, year = {2018}, author = {Mangin, I and Dossou-Yovo, F and Lévêque, C and Dessoy, MV and Sawoo, O and Suau, A and Pochart, P}, title = {Oral administration of viable Bifidobacterium pseudolongum strain Patronus modified colonic microbiota and increased mucus layer thickness in rat.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {11}, pages = {}, doi = {10.1093/femsec/fiy177}, pmid = {30184128}, issn = {1574-6941}, abstract = {This study aimed at evaluating the alteration of the colonic microbiota and the changes in the mucus layer thickness induced by oral administration of living bifidobacteria in rats. The study was performed on rats fed with Bifidobacterium pseudolongum strain Patronus (1010 bacteria per day for 7 days). This bacterial administration led to a large increase of mucus thickness (57%, P < 0.05). Both quantitative PCR and high-throughput sequencing of bacterial 16S rRNA gene revealed a significant increase of the amount of the Bifidobacterium genus in the microbiota of rats fed with the strain Patronus, associated with a decrease of Akkermansia muciniphila. The increase in mucus thickness could be due to an increase of the bifidobacteria per se or via the decrease of A. muciniphila, a major mucin-degrading species. As the mucus layer plays an essential role in gut protection, our data enlighten the importance of studying mucus-degrading bacteria for understanding the underlying etiology of diseases such as intestinal bowel diseases and to implement new therapeutic strategies.}, }
@article {pmid30181663, year = {2018}, author = {Castelle, CJ and Brown, CT and Anantharaman, K and Probst, AJ and Huang, RH and Banfield, JF}, title = {Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations.}, journal = {Nature reviews. Microbiology}, volume = {16}, number = {10}, pages = {629-645}, doi = {10.1038/s41579-018-0076-2}, pmid = {30181663}, issn = {1740-1534}, abstract = {Candidate phyla radiation (CPR) bacteria and DPANN (an acronym of the names of the first included phyla) archaea are massive radiations of organisms that are widely distributed across Earth's environments, yet we know little about them. Initial indications are that they are consistently distinct from essentially all other bacteria and archaea owing to their small cell and genome sizes, limited metabolic capacities and often episymbiotic associations with other bacteria and archaea. In this Analysis, we investigate their biology and variations in metabolic capacities by analysis of approximately 1,000 genomes reconstructed from several metagenomics-based studies. We find that they are not monolithic in terms of metabolism but rather harbour a diversity of capacities consistent with a range of lifestyles and degrees of dependence on other organisms. Notably, however, certain CPR and DPANN groups seem to have exceedingly minimal biosynthetic capacities, whereas others could potentially be free living. Understanding of these microorganisms is important from the perspective of evolutionary studies and because their interactions with other organisms are likely to shape natural microbiome function.}, }
@article {pmid30180359, year = {2019}, author = {Evans, SE and Dueker, ME and Logan, JR and Weathers, KC}, title = {The biology of fog: results from coastal Maine and Namib Desert reveal common drivers of fog microbial composition.}, journal = {The Science of the total environment}, volume = {647}, number = {}, pages = {1547-1556}, doi = {10.1016/j.scitotenv.2018.08.045}, pmid = {30180359}, issn = {1879-1026}, abstract = {Fog supplies water and nutrients to systems ranging from coastal forests to inland deserts. Fog droplets can also contain bacterial and fungal aerosols, but our understanding of fog biology is limited. Using metagenomic tools and culturing, we provide a unique look at fungal and bacterial communities in fog at two fog-dominated sites: coastal Maine (USA) and the Namib Desert (Namibia). Microbial communities in the fog at both sites were diverse, distinct from clear aerosols, and influenced by both soil and marine sources. Fog from both sites contained Actinobacteria and Firmicutes, commonly soil- and air-associated phyla, but also contained bacterial taxa associated with marine environments including Cyanobacteria, Oceanospirillales, Novosphingobium, Pseudoalteromonas, and Bradyrhizobiaceae. Marine influence on fog communities was greatest near the coast, but still evident in Namib fogs 50 km inland. In both systems, differences between pre- and post-fog aerosol communities suggest that fog events can significantly alter microbial aerosol diversity and composition. Fog is likely to enhance viability of transported microbes and facilitate their deposition, making fog biology ecologically important in fog-dominated environments. Fog may introduce novel species to terrestrial ecosystems, including human and plant pathogens, warranting further work on the drivers of this important and underrecognized aerobiological transfer between marine and terrestrial systems.}, }
@article {pmid30180347, year = {2019}, author = {Urra, J and Alkorta, I and Mijangos, I and Epelde, L and Garbisu, C}, title = {Application of sewage sludge to agricultural soil increases the abundance of antibiotic resistance genes without altering the composition of prokaryotic communities.}, journal = {The Science of the total environment}, volume = {647}, number = {}, pages = {1410-1420}, doi = {10.1016/j.scitotenv.2018.08.092}, pmid = {30180347}, issn = {1879-1026}, abstract = {The application of sewage sludge as soil amendment is a common agricultural practice. However, wastewater treatment plants, sewage sludge and sewage sludge-amended soils have been reported as hotspots for the appearance and dissemination of antibiotic resistance, driven, among other factors, by selection pressure exerted by co-exposure to antibiotics and heavy metals. To address this threat to environmental and human health, soil samples from a long-term (24 years) field experiment, carried out to study the impact of thermally dried and anaerobically digested sewage sludge (at different doses and frequencies of application) on agricultural soil quality, were investigated for the presence of genes encoding antibiotic resistance (ARGs) and mobile genetic elements (MGEs). Sewage sludge-induced changes in specific soil physicochemical and microbial properties, as indicators of soil quality, were also investigated. The application of sewage sludge increased the total concentration of copper and zinc in amended soils, but without affecting the bioavailability of these metals, possibly due to the high values of soil pH and organic matter content. Soil microbal quality, as reflected by the value of the Soil Quality Index, was higher in sewage sludge-amended soils. Similarly, the application of sewage sludge increased soil microbial activity and biomass, as well as the abundance of ARGs and MGE genes, posing a risk of dissemination of antibiotic resistance. In contrast, the composition of soil prokaryotic communities was not significantly altered by the application of sewage sludge. We found correlation between soil Cu and Zn concentrations and the abundance of ARGs and MGE genes. It was concluded that sewage sludge-derived amendments must be properly treated and managed if they are to be applied to agricultural soil.}, }
@article {pmid30179784, year = {2018}, author = {Perez, S and Czerner, M and Patat, ML and Zaritzky, NE and Murialdo, SE and Yeannes, MI}, title = {Monitoring the characteristics of cultivable halophilic microbial community during salted-ripened anchovy (Engraulis anchoita) production.}, journal = {International journal of food microbiology}, volume = {286}, number = {}, pages = {179-189}, doi = {10.1016/j.ijfoodmicro.2018.08.013}, pmid = {30179784}, issn = {1879-3460}, abstract = {The halophilic microbial community of the salted-ripened anchovy process was studied. Samples from raw materials (salt and fresh anchovies) and from the stages of brining and ripening were collected and analyzed for their bacterial counts at 15 and 20% NaCl. No halophilic colonies were found in fresh anchovy and counts of about 103 CFU/g were determined in salt samples. A fluctuation of bacterial counts during the process was found. At the end of brining, ~104 CFU/g were determined in anchovy samples and this value was reduced to not detectable counts at the beginning of the ripening stage. After one month, counts increased to ~104 CFU/g and remained stable until the end of the process. From each sample, colonies having different morphotypes were isolated and submitted to a macro and microscopic characterization, a study of salt requirement for growth, and biochemical and phenotypic tests. The results were submitted to Univariate, Bivariate and Multiple Correspondence Factorial Analysis (MCFA). A total of 79 colonies were isolated during the salting-ripening anchovy process. Among the isolates, about 40-50% was positive for indole production and lipolytic activity and a 25% showed ability to produce H2S and proteolytic capacity. Proteolytic and lipolytic activities were well balanced along the process and resulted independent from the isolation stage, which is a desirable condition due to the contribution of microbial proteolysis and lipolysis to the development of texture and final aroma, respectively. H2S and indole producers practically were not detected during ripening. This fact is important because indole and H2S are associated with the development of off-flavors and spoilage in salted fish products. MFCA and Cluster Analyses complemented the Bivariate Analyses. The factor map showed proximity between the isolates from salt samples and from ripening. Isolates were statistically clustered in two groups. Cluster 1 grouped non-desirable activities (H2S and indole production) with cultures proceeding from brining whereas Cluster 2 related isolates mainly from salt samples and during ripening with some desirable microbial capacities (Cytochrome oxidase activity and non-H2S and non-indole production). These results would indicate that during the ripening process of salted anchovies, a natural selection of beneficial microorganisms for the development of the typical product sensory attributes occurred.}, }
@article {pmid30179231, year = {2018}, author = {Berube, PM and Biller, SJ and Hackl, T and Hogle, SL and Satinsky, BM and Becker, JW and Braakman, R and Collins, SB and Kelly, L and Berta-Thompson, J and Coe, A and Bergauer, K and Bouman, HA and Browning, TJ and De Corte, D and Hassler, C and Hulata, Y and Jacquot, JE and Maas, EW and Reinthaler, T and Sintes, E and Yokokawa, T and Lindell, D and Stepanauskas, R and Chisholm, SW}, title = {Single cell genomes of Prochlorococcus, Synechococcus, and sympatric microbes from diverse marine environments.}, journal = {Scientific data}, volume = {5}, number = {}, pages = {180154}, doi = {10.1038/sdata.2018.154}, pmid = {30179231}, issn = {2052-4463}, abstract = {Prochlorococcus and Synechococcus are the dominant primary producers in marine ecosystems and perform a significant fraction of ocean carbon fixation. These cyanobacteria interact with a diverse microbial community that coexists with them. Comparative genomics of cultivated isolates has helped address questions regarding patterns of evolution and diversity among microbes, but the fraction that can be cultivated is miniscule compared to the diversity in the wild. To further probe the diversity of these groups and extend the utility of reference sequence databases, we report a data set of single cell genomes for 489 Prochlorococcus, 50 Synechococcus, 9 extracellular virus particles, and 190 additional microorganisms from a diverse range of bacterial, archaeal, and viral groups. Many of these uncultivated single cell genomes are derived from samples obtained on GEOTRACES cruises and at well-studied oceanographic stations, each with extensive suites of physical, chemical, and biological measurements. The genomic data reported here greatly increases the number of available Prochlorococcus genomes and will facilitate studies on evolutionary biology, microbial ecology, and biological oceanography.}, }
@article {pmid30178561, year = {2018}, author = {Kilian, M}, title = {The oral microbiome - friend or foe?.}, journal = {European journal of oral sciences}, volume = {126 Suppl 1}, number = {}, pages = {5-12}, doi = {10.1111/eos.12527}, pmid = {30178561}, issn = {1600-0722}, abstract = {The microbiome and the human body constitute an integrated superorganism, which is the result of millions of years of coevolution with mutual adaptation and functional integration, and confers significant benefits for both parties. This evolutionary process has resulted in a highly diverse oral microbiome, which covers the full spectrum of acidogenic, aciduric, inflammatory, and anti-inflammatory properties. The relative proportions of members of the microbiome are affected by factors associated with modern life, such as general diet patterns, sugar consumption, tobacco smoking, oral hygiene, use of antibiotics and other antimicrobials, and vaccines. A perturbed balance in the oral microbiome may result in caries, periodontal disease, or candidiasis, and oral bacteria passively transferred to normally sterile parts of the body may cause extra-oral infections. Nevertheless, it should never be our goal to eliminate the oral microbiome, but rather we have to develop ways to re-establish a harmonious coexistence that is lost because of the modern lifestyle. With regard to oral diseases, this goal can normally be achieved by optimal oral hygiene, exposure to fluoride, reduction of sucrose consumption, stimulation of our innate immune defense, smoking cessation, and control of diabetes.}, }
@article {pmid30178387, year = {2018}, author = {Xu, WF and Ren, HS and Ou, T and Lei, T and Wei, JH and Huang, CS and Li, T and Strobel, G and Zhou, ZY and Xie, J}, title = {Genomic and Functional Characterization of the Endophytic Bacillus subtilis 7PJ-16 Strain, a Potential Biocontrol Agent of Mulberry Fruit Sclerotiniose.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1247-4}, pmid = {30178387}, issn = {1432-184X}, support = {31601678//National Natural Science Foundation of China/ ; XDJK2018D020//Fundamental Research Funds for the Central Universities/ ; cstc2015jcyjys80001//Natural Science Foundation of Chongqing/ ; }, abstract = {Bacillus sp. 7PJ-16, an endophytic bacterium isolated from a healthy mulberry stem and previously identified as Bacillus tequilensis 7PJ-16, exhibits strong antifungal activity and has the capacity to promote plant growth. This strain was studied for its effectiveness as a biocontrol agent to reduce mulberry fruit sclerotiniose in the field and as a growth-promoting agent for mulberry in the greenhouse. In field studies, the cell suspension and supernatant of strain 7PJ-16 exhibited biocontrol efficacy and the lowest disease incidence was reduced down to only 0.80%. In greenhouse experiments, the cell suspension (1.0 × 106 and 1.0 × 105 CFU/mL) and the cell-free supernatant (100-fold and 1000-fold dilution) stimulated mulberry seed germination and promoted mulberry seedling growth. In addition, to accurately identify the 7PJ-16 strain and further explore the mechanisms of its antifungal and growth-promoting properties, the complete genome of this strain was sequenced and annotated. The 7PJ-16 genome is comprised of two circular plasmids and a 4,209,045-bp circular chromosome, containing 4492 protein-coding genes and 116 RNA genes. This strain was ultimately designed as Bacillus subtilis based on core genome sequence analyses using a phylogenomic approach. In this genome, we identified a series of gene clusters that function in the synthesis of non-ribosomal peptides (surfactin, fengycin, bacillibactin, and bacilysin) as well as the ribosome-dependent synthesis of tasA and bacteriocins (subtilin, subtilosin A), which are responsible for the biosynthesis of numerous antimicrobial metabolites. Additionally, several genes with function that promote plant growth, such as indole-3-acetic acid biosynthesis, the production of volatile substances, and siderophores synthesis, were also identified. The information described in this study has established a good foundation for understanding the beneficial interactions between endophytes and host plants, and facilitates the further application of B. subtilis 7PJ-16 as an agricultural biofertilizer and biocontrol agent.}, }
@article {pmid30175237, year = {2018}, author = {Coenen, AR and Weitz, JS}, title = {Limitations of Correlation-Based Inference in Complex Virus-Microbe Communities.}, journal = {mSystems}, volume = {3}, number = {4}, pages = {}, doi = {10.1128/mSystems.00084-18}, pmid = {30175237}, issn = {2379-5077}, abstract = {Microbes are present in high abundances in the environment and in human-associated microbiomes, often exceeding 1 million per ml. Viruses of microbes are present in even higher abundances and are important in shaping microbial populations, communities, and ecosystems. Given the relative specificity of viral infection, it is essential to identify the functional linkages between viruses and their microbial hosts, particularly given dynamic changes in virus and host abundances. Multiple approaches have been proposed to infer infection networks from time series of in situ communities, among which correlation-based approaches have emerged as the de facto standard. In this work, we evaluate the accuracy of correlation-based inference methods using an in silico approach. In doing so, we compare predicted networks to actual networks to assess the self-consistency of correlation-based inference. At odds with assumptions underlying its widespread use, we find that correlation is a poor predictor of interactions in the context of viral infection and lysis of microbial hosts. The failure to predict interactions holds for methods that leverage product-moment, time-lagged, and relative-abundance-based correlations. In closing, we discuss alternative inference methods, particularly model-based methods, as a means to infer interactions in complex microbial communities with viruses. IMPORTANCE Inferring interactions from population time series is an active and ongoing area of research. It is relevant across many biological systems-particularly in virus-microbe communities, but also in gene regulatory networks, neural networks, and ecological communities broadly. Correlation-based inference-using correlations to predict interactions-is widespread. However, it is well-known that &quot;correlation does not imply causation.&quot; Despite this, many studies apply correlation-based inference methods to experimental time series without first assessing the potential scope for accurate inference. Here, we find that several correlation-based inference methods fail to recover interactions within in silico virus-microbe communities, raising questions on their relevance when applied in situ.}, }
@article {pmid30175122, year = {2018}, author = {Asses, N and Ayed, L and Hkiri, N and Hamdi, M}, title = {Congo Red Decolorization and Detoxification by Aspergillus niger: Removal Mechanisms and Dye Degradation Pathway.}, journal = {BioMed research international}, volume = {2018}, number = {}, pages = {3049686}, doi = {10.1155/2018/3049686}, pmid = {30175122}, issn = {2314-6141}, mesh = {*Aspergillus niger ; Azo Compounds ; *Biodegradation, Environmental ; Coloring Agents ; Congo Red/*metabolism ; Water Purification ; }, abstract = {Congo red is one of the best known and used azo dyes which has two azo bonds (-N=N-) chromophore in its molecular structure. Its structural stability makes it highly toxic and resistant to biodegradation. The objective of this study was to assess the congo red biodegradation and detoxification by Aspergillus niger. The effects of pH, initial dye concentration, temperature, and shaking speed on the decolorization rate and enzymes production were studied. The maximum decolorization was correlated with lignin peroxidase and manganese peroxidase production. Above 97% were obtained when 2 g mycelia were incubated at pH 5, in presence of 200 mg/L of dye during 6 days at 28°C and under 120 to 150 rpm shaking speed. The degraded metabolites were characterized by using LC-MS/MS analyses and the biodegradation mechanism was also studied. Congo red bioconversion formed degradation metabolites mainly by peroxidases activities, i.e., the sodium naphthalene sulfonate (m/z = 227) and the cycloheptadienylium (m/z = 91). Phytotoxicity and microtoxicity tests confirmed that degradation metabolites were less toxic than original dye.}, }
@article {pmid30175029, year = {2018}, author = {Li, Y and Jiang, W and Gao, R and Cai, Y and Guan, Z and Liao, X}, title = {Fe(III)-based immobilized metal-affinity chromatography (IMAC) method for the separation of the catechol siderophore from Bacillus tequilensis CD36.}, journal = {3 Biotech}, volume = {8}, number = {9}, pages = {392}, doi = {10.1007/s13205-018-1396-7}, pmid = {30175029}, issn = {2190-572X}, abstract = {Catechol siderophore plays an important role in microbial ecology, agriculture, and medicine, but its research is often limited by the difficulty in acquisition of it in large quantities. Based on evidence from the coordination chemistry and chemical biology, catechol siderophore could chelate Fe3+ with high affinity. Therefore, Fe(III)-based immobilized metal-affinity chromatography (IMAC) was applied to capture siderophore from the culture filtrate of Bacillus tequilensis CD36. The ethanol-precipitated sample and the separated sample from Fe(III)-based IMAC were analyzed by liquid chromatography-mass spectrometry. According to the result, the pure siderophore DHB-Gly-Thr could be extracted from the ethanol-precipitated sample. Compared with other purifications, Fe(III)-based IMAC was convenient and had fewer steps. In addition, it also reduced the use of toxic chemical solvents in some traditional extraction process, such as extraction and ion exchange chromatography. Fe(III)-based IMAC was successfully used in separation of the catechol siderophore from B. tequilensis CD36. The results revealed that Fe(III)-based IMAC was an efficient and environmentally friendly method for the separation and purification of catechol siderophore.}, }
@article {pmid30172443, year = {2018}, author = {Gänzle, MG and Zheng, J}, title = {Lifestyles of sourdough lactobacilli - Do they matter for microbial ecology and bread quality?.}, journal = {International journal of food microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ijfoodmicro.2018.08.019}, pmid = {30172443}, issn = {1879-3460}, abstract = {Sourdough is used in production of (steamed) bread as leavening agent (type I sourdoughs) or as baking improver to enhance flavour, texture, and shelf life of bread (type II sourdoughs). The long-term propagation of sourdoughs eliminates dispersal limitation and consistently leads to sourdough microbiota that are composed of host adapted lactobacilli. In contrast, community assembly in spontaneous cereal fermentations is limited by dispersal and nomadic or environmental lactic acid bacteria are the first colonizers of these sourdoughs. Propagation of sourdoughs for use as sole leavening agent (type I sourdoughs) dictates fermentation conditions that select for rapid growth. Type I wheat- and rye sourdoughs are consistently populated by insect-adapted lactobacilli, particularly Lactobacillus sanfranciscensis, which is characterized by a small genome size and a restricted metabolic potential. The diverse fermentation conditions employed in industrial or artisanal Type II sourdough fermentation processes also result in a more diverse microbiota. Nevertheless, type II sourdoughs are typically populated by vertebrate host adapted lactobacilli of the L. delbrueckii and L. reuteri groups. Metabolic traits of host-adapted lactobacilli that enhance competitiveness in intestinal ecosystems also provide technological functionality in bread making. Examples include formation of exopolysaccharides, arginine-, glutamine- and glutamate based mechanisms of acid resistance, and glycosyl hydrolases that reduce FODMAP levels in sourdough and sourdough bread. In conclusion, consideration of the lifestyle of sourdough lactobacilli facilitates the selection of competitive and functional sourdough starter cultures.}, }
@article {pmid30172137, year = {2019}, author = {Macintosh, KA and Doody, DG and Withers, PJA and McDowell, RW and Smith, DR and Johnson, LT and Bruulsema, TW and O'Flaherty, V and McGrath, JW}, title = {Transforming soil phosphorus fertility management strategies to support the delivery of multiple ecosystem services from agricultural systems.}, journal = {The Science of the total environment}, volume = {649}, number = {}, pages = {90-98}, doi = {10.1016/j.scitotenv.2018.08.272}, pmid = {30172137}, issn = {1879-1026}, abstract = {Despite greater emphasis on holistic phosphorus (P) management, current nutrient advice delivered at farm-scale still focuses almost exclusively on agricultural production. This limits our ability to address national and international strategies for the delivery of multiple ecosystem services (ES). Currently there is no operational framework in place to manage P fertility for multiple ES delivery and to identify the costs of potentially sacrificing crop yield and/or quality. As soil P fertility plays a central role in ES delivery, we argue that soil test phosphorus (STP) concentration provides a suitable common unit of measure by which delivering multiple ES can be economically valued relative to maximum potential yield, in $ ha-1 yr-1 units. This value can then be traded, or payments made against one another, at spatio-temporal scales relevant for farmer and national policy objectives. Implementation of this framework into current P fertility management strategies would allow for the integration and interaction of different stakeholder interests in ES delivery on-farm and in the wider landscape. Further progress in biophysical modeling of soil P dynamics is needed to inform its adoption across diverse landscapes.}, }
@article {pmid30171270, year = {2018}, author = {Szafranek-Nakonieczna, A and Wolińska, A and Zielenkiewicz, U and Kowalczyk, A and Stępniewska, Z and Błaszczyk, M}, title = {Activity and Identification of Methanotrophic Bacteria in Arable and No-Tillage Soils from Lublin Region (Poland).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1248-3}, pmid = {30171270}, issn = {1432-184X}, support = {DEC-2013/09/D/NZ9/02482//Narodowe Centrum Nauki/ ; }, abstract = {Methanotrophic bacteria are able to use methane (CH4) as a sole carbon and energy source. Photochemical oxidation of methane takes place in the stratosphere, whereas in the troposphere, this process is carried out by methanotrophic bacteria. On the one hand, it is known that the efficiency of biological CH4 oxidation is dependent on the mode of land use but, on the other hand, the knowledge of this impact on methanotrophic activity (MTA) is still limited. Thus, the aim of the study was to determine the CH4 oxidation ability of methanotrophic bacteria inhabiting selected arable and no-tillage soils from the Lublin region (Albic Luvisol, Brunic Arenosol, Haplic Chernozem, Calcaric Cambisol) and to identify bacteria involved in this process. MTA was determined based on incubation of soils in air with addition of methane at the concentrations of 0.002, 0.5, 1, 5, and 10%. The experiment was conducted in a temperature range of 10-30 °C. Methanotrophs in soils were identified by next-generation sequencing (NGS). MTA was confirmed in all investigated soils (in the entire range of the tested methane concentrations and temperatures, except for the arable Albic Luvisol). Importantly, the MTA values in the no-tillage soil were nearly two-fold higher than in the cultivated soils. Statistical analysis indicated a significant influence of land use, type of soil, temperature, and especially methane concentration (p < 0.05) on MTA. Metagenomic analysis confirmed the presence of methanotrophs from the genus Methylocystis (Alphaproteobacteria) in the studied soils (except for the arable Albic Luvisol). Our results also proved the ability of methanotrophic bacteria to oxidize methane although they constituted only up to 0.1% of the total bacterial community.}, }
@article {pmid30168107, year = {2018}, author = {Xu, G and Abdullah Al, M and Sikder, MNA and Warren, A and Xu, H}, title = {Identifying indicator redundancy of biofilm-dwelling protozoa for bioassessment in marine ecosystems.}, journal = {Environmental science and pollution research international}, volume = {25}, number = {30}, pages = {30441-30450}, doi = {10.1007/s11356-018-3063-2}, pmid = {30168107}, issn = {1614-7499}, abstract = {A multivariate peeling method of data analysis was applied to determine indicator redundancy and for identifying indicator units (IUs) among biofilm-dwelling ciliate communities used for bioassessment of marine water quality. Samples were taken monthly over a 1-year period at four stations in coastal waters of the Yellow Sea: one heavily polluted, one moderately polluted, one intermittently polluted, and one unpolluted. Four IUs (IU1-4) were identified consisting of 22, 13, 14, and 17 species, respectively, out of a total of 144 species. The IUs showed significant correlation with temporal and spatial variations in environmental variables. The redundancy levels of IUs were interchangeable in time and space. However, IU1 and IU2 generally dominated the communities in moderately and intermittently polluted areas during cool (e.g., early spring, late autumn, and winter) and warm (late spring and early autumn) seasons; IU3 dominated in warm seasons (e.g., late spring to autumn) in the heavily polluted area; and IU4 mainly dominated the samples in the unpolluted and moderately polluted areas during the late summer and early autumn. Furthermore, different trophic-functional groupings were represented within the four IUs and these were generally associated with water quality status. These findings suggest that there is high indicator redundancy in marine biofilm-dwelling ciliate communities subjected to different levels of water quality.}, }
@article {pmid30166150, year = {2018}, author = {Houngbédji, M and Johansen, P and Padonou, SW and Akissoé, N and Arneborg, N and Nielsen, DS and Hounhouigan, DJ and Jespersen, L}, title = {Occurrence of lactic acid bacteria and yeasts at species and strain level during spontaneous fermentation of mawè, a cereal dough produced in West Africa.}, journal = {Food microbiology}, volume = {76}, number = {}, pages = {267-278}, doi = {10.1016/j.fm.2018.06.005}, pmid = {30166150}, issn = {1095-9998}, abstract = {Mawè is a West African spontaneous fermented cereal-based dough. Different types of mawè exist varying in type of cereal and/or production condition, with fermentations lasting 24-48 h. With the aim of obtaining a comprehensive understanding of the microbial ecology of mawè processing, a microbiological characterisation was performed for four mawè types, produced at eight sites in Benin. At the onset of the fermentations lactic acid bacteria (LAB) and yeast counts were on average 7.5 ± 1.03 and 4.8 ± 0.79 Log10 cfu/g, which increased to 9.2 ± 0.38 and 7.4 ± 0.42 Log10 cfu/g, respectively, at the end of the fermentations. LAB (n = 321) and yeasts (n = 298), isolated during the fermentations, were identified. The predominant LAB and yeast species were Lactobacillus fermentum and Pichia kudriavzevii, respectively, followed by Kluyveromyces marxianus, all present throughout the mawè fermentations. Further, microbial successions took place with Weissella confusa occurring mostly at the onset, while Pediococcus acidilactici and Saccharomyces cerevisiae were mainly associated with the end of the fermentations. Species diversity was influenced both by type of cereal and production condition. The dominating strain clusters of L. fermentum and P. kudriavzevii were ubiquitous and strain diversities were influenced by type of cereal and production site.}, }
@article {pmid30158906, year = {2018}, author = {Mackelprang, R and Grube, AM and Lamendella, R and Jesus, EDC and Copeland, A and Liang, C and Jackson, RD and Rice, CW and Kapucija, S and Parsa, B and Tringe, SG and Tiedje, JM and Jansson, JK}, title = {Microbial Community Structure and Functional Potential in Cultivated and Native Tallgrass Prairie Soils of the Midwestern United States.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1775}, doi = {10.3389/fmicb.2018.01775}, pmid = {30158906}, issn = {1664-302X}, abstract = {The North American prairie covered about 3.6 million-km2 of the continent prior to European contact. Only 1-2% of the original prairie remains, but the soils that developed under these prairies are some of the most productive and fertile in the world, containing over 35% of the soil carbon in the continental United States. Cultivation may alter microbial diversity and composition, influencing the metabolism of carbon, nitrogen, and other elements. Here, we explored the structure and functional potential of the soil microbiome in paired cultivated-corn (at the time of sampling) and never-cultivated native prairie soils across a three-states transect (Wisconsin, Iowa, and Kansas) using metagenomic and 16S rRNA gene sequencing and lipid analysis. At the Wisconsin site, we also sampled adjacent restored prairie and switchgrass plots. We found that agricultural practices drove differences in community composition and diversity across the transect. Microbial biomass in prairie samples was twice that of cultivated soils, but alpha diversity was higher with cultivation. Metagenome analyses revealed denitrification and starch degradation genes were abundant across all soils, as were core genes involved in response to osmotic stress, resource transport, and environmental sensing. Together, these data indicate that cultivation shifted the microbiome in consistent ways across different regions of the prairie, but also suggest that many functions are resilient to changes caused by land management practices - perhaps reflecting adaptations to conditions common to tallgrass prairie soils in the region (e.g., soil type, parent material, development under grasses, temperature and rainfall patterns, and annual freeze-thaw cycles). These findings are important for understanding the long-term consequences of land management practices to prairie soil microbial communities and their genetic potential to carry out key functions.}, }
@article {pmid30155556, year = {2018}, author = {Ma, ZS}, title = {Sketching the Human Microbiome Biogeography with DAR (Diversity-Area Relationship) Profiles.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1245-6}, pmid = {30155556}, issn = {1432-184X}, abstract = {SAR (species area relationship) is a classic ecological theory that has been extensively investigated and applied in the studies of global biogeography and biodiversity conservation in macro-ecology. It has also found important applications in microbial ecology in recent years thanks to the breakthroughs in metagenomic sequencing technology. Nevertheless, SAR has a serious limitation for practical applications-ignoring the species abundance and treating all species as equally abundant. This study aims to explore the biogeography discoveries of human microbiome over 18 sites of 5 major microbiome habitats, establish the baseline DAR (diversity-area scaling relationship) parameters, and perform comparisons with the classic SAR. The extension from SAR to DAR by adopting the Hill numbers as diversity measures not only overcomes the previously mentioned flaw of SAR but also allows for obtaining a series of important findings on the human microbiome biodiversity and biogeography. Specifically, two types of DAR models were built, the traditional power law (PL) and power law with exponential cutoff (PLEC), using comprehensive datasets from the HMP (human microbiome project). Furthermore, the biogeography &quot;maps&quot; for 18 human microbiome sites using their DAR profiles for assessing and predicting the diversity scaling across individuals, PDO profiles (pair-wise diversity overlap) for measuring diversity overlap (similarity), and MAD profile (for predicting the maximal accrual diversity in a population) were sketched out. The baseline biogeography maps for the healthy human microbiome diversity can offer guidelines for conserving human microbiome diversity and investigating the health implications of the human microbiome diversity and heterogeneity.}, }
@article {pmid30154827, year = {2018}, author = {Cairns, J and Jokela, R and Hultman, J and Tamminen, M and Virta, M and Hiltunen, T}, title = {Construction and Characterization of Synthetic Bacterial Community for Experimental Ecology and Evolution.}, journal = {Frontiers in genetics}, volume = {9}, number = {}, pages = {312}, doi = {10.3389/fgene.2018.00312}, pmid = {30154827}, issn = {1664-8021}, abstract = {Experimental microbial ecology and evolution have yielded foundational insights into ecological and evolutionary processes using simple microcosm setups and phenotypic assays with one- or two-species model systems. The fields are now increasingly incorporating more complex systems and exploration of the molecular basis of observations. For this purpose, simplified, manageable and well-defined multispecies model systems are required that can be easily investigated using culturing and high-throughput sequencing approaches, bridging the gap between simpler and more complex synthetic or natural systems. Here we address this need by constructing a completely synthetic 33 bacterial strain community that can be cultured in simple laboratory conditions. We provide whole-genome data for all the strains as well as metadata about genomic features and phenotypic traits that allow resolving individual strains by amplicon sequencing and facilitate a variety of envisioned mechanistic studies. We further show that a large proportion of the strains exhibit coexistence in co-culture over serial transfer for 48 days in the absence of any experimental manipulation to maintain diversity. The constructed bacterial community can be a valuable resource in future experimental work.}, }
@article {pmid30154761, year = {2018}, author = {Plominsky, AM and Henríquez-Castillo, C and Delherbe, N and Podell, S and Ramirez-Flandes, S and Ugalde, JA and Santibañez, JF and van den Engh, G and Hanselmann, K and Ulloa, O and De la Iglesia, R and Allen, EE and Trefault, N}, title = {Distinctive Archaeal Composition of an Artisanal Crystallizer Pond and Functional Insights Into Salt-Saturated Hypersaline Environment Adaptation.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1800}, doi = {10.3389/fmicb.2018.01800}, pmid = {30154761}, issn = {1664-302X}, abstract = {Hypersaline environments represent some of the most challenging settings for life on Earth. Extremely halophilic microorganisms have been selected to colonize and thrive in these extreme environments by virtue of a broad spectrum of adaptations to counter high salinity and osmotic stress. Although there is substantial data on microbial taxonomic diversity in these challenging ecosystems and their primary osmoadaptation mechanisms, less is known about how hypersaline environments shape the genomes of microbial inhabitants at the functional level. In this study, we analyzed the microbial communities in five ponds along the discontinuous salinity gradient from brackish to salt-saturated environments and sequenced the metagenome of the salt (halite) precipitation pond in the artisanal Cáhuil Solar Saltern system. We combined field measurements with spectrophotometric pigment analysis and flow cytometry to characterize the microbial ecology of the pond ecosystems, including primary producers and applied metagenomic sequencing for analysis of archaeal and bacterial taxonomic diversity of the salt crystallizer harvest pond. Comparative metagenomic analysis of the Cáhuil salt crystallizer pond against microbial communities from other salt-saturated aquatic environments revealed a dominance of the archaeal genus Halorubrum and showed an unexpectedly low abundance of Haloquadratum in the Cáhuil system. Functional comparison of 26 hypersaline microbial metagenomes revealed a high proportion of sequences associated with nucleotide excision repair, helicases, replication and restriction-methylation systems in all of them. Moreover, we found distinctive functional signatures between the microbial communities from salt-saturated (>30% [w/v] total salinity) compared to sub-saturated hypersaline environments mainly due to a higher representation of sequences related to replication, recombination and DNA repair in the former. The current study expands our understanding of the diversity and distribution of halophilic microbial populations inhabiting salt-saturated habitats and the functional attributes that sustain them.}, }
@article {pmid30153641, year = {2018}, author = {Xie, H and Wang, H and Ji, F and Liang, Y and Song, M and Zhang, J}, title = {Tetrabromobisphenol A alters soil microbial community via selective antibacterial activity.}, journal = {Ecotoxicology and environmental safety}, volume = {164}, number = {}, pages = {597-603}, doi = {10.1016/j.ecoenv.2018.08.053}, pmid = {30153641}, issn = {1090-2414}, mesh = {Anti-Bacterial Agents/*toxicity ; Bacteria/*drug effects ; Biodiversity ; Environment ; Environmental Pollution ; Flame Retardants/*toxicity ; Polybrominated Biphenyls/*toxicity ; *Soil Microbiology ; Soil Pollutants/*toxicity ; }, abstract = {Tetrabromobisphenol A (TBBPA) is the most widely used brominated flame retardant. Most studies regarding TBBPA have concentrated on its occurrence, distribution, toxicity and degradation in the environment. However, little is known about its ecological effects on soil microbial communities. In this study, we investigated the effect of TBBPA on soil microbial community. Overall, the data suggested that the growth and composition of soil microorganisms were correlated to the TBBPA concentration and exposure time. Phospholipid-derived fatty acid analysis (PLFAs) showed that significant microbial growth inhibitions were 46.1% and 46.9% in 40 mg/kg TBBPA-treated soils after 45-day incubation under aerobic and anaerobic conditions, respectively. Results of PLFAs and llumina sequencing indicated that TBBPA mainly inhibited Gram-positive bacteria, but not Gram-negative bacteria. The selective antibacterial activity of TBBPA toward Gram-positive bacteria was further confirmed in pure bacteria cultures. These data suggested that, in addition to their effect on microbial growth and composition, TBBPA may affect the microbial ecology. Additional research should be carried out to identify the ecological risk of TBBPA in soil.}, }
@article {pmid30153548, year = {2018}, author = {Vandekerckhove, TGL and De Mulder, C and Boon, N and Vlaeminck, SE}, title = {Temperature impact on sludge yield, settleability and kinetics of three heterotrophic conversions corroborates the prospect of thermophilic biological nitrogen removal.}, journal = {Bioresource technology}, volume = {269}, number = {}, pages = {104-112}, doi = {10.1016/j.biortech.2018.08.012}, pmid = {30153548}, issn = {1873-2976}, mesh = {*Bioreactors ; *Denitrification ; Kinetics ; Nitrogen ; *Sewage ; Temperature ; Waste Disposal, Fluid ; }, abstract = {In specific municipal and industrial cases, thermophilic wastewater treatment (>45 °C) might bring cost advantages over commonly applied mesophilic processes (10-35 °C). To develop such a novel process, one needs sound parameters on kinetics, sludge yield and sludge settleability of three heterotrophic conversions: aerobic carbon removal, denitritation and denitrification. These features were evaluated in acetate-fed sequencing batch reactors (30, 40, 50 and 60 °C). Higher temperatures were accompanied by lower sludge production and maximum specific removal rates, resulting mainly from lower maximum growth rates. Thermophilic denitritation was demonstrated for the first time, with lower sludge production (18-26%), higher nitrogen removal rates (24-92%) and lower carbon requirement (40%) compared to denitrification. Acceptable settling of thermophilic aerobic (60 °C) and anoxic biomass (50 and 60 °C) was obtained. Overall, this parameter set may catalyze the establishment of thermophilic nitrogen removal, once nitritation and nitratation are characterized. Furthermore, waters with low COD/N ratio might benefit from thermophilic nitritation/denitritation.}, }
@article {pmid30152425, year = {2018}, author = {Samanta, A and Patra, A and Mandal, S and Roy, S and Das, K and Kar, S and Nandi, DK}, title = {Hypoxia: A cause of acute renal failure and alteration of gastrointestinal microbial ecology.}, journal = {Saudi journal of kidney diseases and transplantation : an official publication of the Saudi Center for Organ Transplantation, Saudi Arabia}, volume = {29}, number = {4}, pages = {879-888}, doi = {10.4103/1319-2442.239653}, pmid = {30152425}, issn = {1319-2442}, abstract = {Oxygen is very important to the existence of life. Oxygen deficiency, defined as hypoxia, elicits adaptive responses in cells and tissues. Lower oxygen concentration can cause the alteration of renal function, affects the maintenance of a balance of the body fluids, electrolytes, pH, and blood pressure homeostasis. Impaired fluid regulation could, in addition, contribute to the precipitation of pulmonary edema and exacerbate hypoxemia which may accelerate the progression of chronic kidney disease. In this context, the present study attempted to evaluate the association of renal injury and oxidative stress at different atmospheric pressures (1829, 3657, and 5486 m). Limited fecal analysis of experimental animals was also done to evaluate the impact of hypobaric hypoxia on the composition of dominant gastrointestinal microbiota. The study was performed on 24 male Wister strain rats and divided into four groups (C, HA-I, HA-II, and HA-III), and exposure was carried out for seven days period. In hypoxic exposure rats, plasma urea, creatinine, electrolytes and malonaldehyde level elevated and catalase and superoxide dismutase level diminished significantly compared to the controls. Increase in blood uremia profile, toxicity markers, and lipid peroxidation marker enzymes indicated that hypoxia causes renal failure. Histological structures of the kidney of group HA-II and HA-III animals showed severe disorganization of glomerulus and dilation of renal tubules. These results indicate nephrotoxicity or acute renal failure can occur at hypobaric hypoxia and it also affected the gut microbial population. This alteration was observed significantly above 3000 m.}, }
@article {pmid30152327, year = {2018}, author = {Bittleston, LS and Wolock, CJ and Yahya, BE and Chan, XY and Chan, KG and Pierce, NE and Pringle, A}, title = {Convergence between the microcosms of Southeast Asian and North American pitcher plants.}, journal = {eLife}, volume = {7}, number = {}, pages = {}, doi = {10.7554/eLife.36741}, pmid = {30152327}, issn = {2050-084X}, support = {NSF Graduate Fellowship and Doctoral Dissertation Improvement Grant DEB-1400982//National Science Foundation/International ; Foundational Questions In Evolutionary Biology//John Templeton Foundation/International ; Putnam Expedition Grant//Harvard University Museum of Comparative Zoology/International ; High Impact Research Grant, UM-MOHE HIR Grant UM.C/625/1/HIR/MOHE/CHAN/14/1//Universiti Malaya/International ; SES-0750480//National Science Foundation/International ; High Impact Research Grant, H-50001-A000027//Universiti Malaya/International ; High Impact Research Grant, A-000001-50001//Universiti Malaya/International ; Foundational Questions In Evolutionary Biology//Templeton Foundation/International ; Putnam Grant//Harvard University Museum of Comparative Zoology Putnam Expedition Grant/International ; UM-MOHE HIR Grant UM.C/625/1/HIR/MOHE/CHAN/14/1//University of Malaya High Impact Research Grant/International ; H-50001-A000027//University of Malaya High Impact Research Grant/International ; A-000001-50001//University of Malaya High Impact Research Grant/International ; }, abstract = {The 'pitchers' of carnivorous pitcher plants are exquisite examples of convergent evolution. An open question is whether the living communities housed in pitchers also converge in structure or function. Using samples from more than 330 field-collected pitchers of eight species of Southeast Asian Nepenthes and six species of North American Sarracenia, we demonstrate that the pitcher microcosms, or miniature ecosystems with complex communities, are strikingly similar. Compared to communities from surrounding habitats, pitcher communities house fewer species. While communities associated with the two genera contain different microbial organisms and arthropods, the species are predominantly from the same phylogenetic clades. Microbiomes from both genera are enriched in degradation pathways and have high abundances of key degradation enzymes. Moreover, in a manipulative field experiment, Nepenthes pitchers placed in a North American bog assembled Sarracenia-like communities. An understanding of the convergent interactions in pitcher microcosms facilitates identification of selective pressures shaping the communities.}, }
@article {pmid30152021, year = {2018}, author = {Peyyala, R and Emecen-Huja, P and Ebersole, JL}, title = {Environmental lead effects on gene expression in oral epithelial cells.}, journal = {Journal of periodontal research}, volume = {53}, number = {6}, pages = {961-971}, doi = {10.1111/jre.12594}, pmid = {30152021}, issn = {1600-0765}, support = {GM103538//National Institute of General Medical Sciences/ ; //Center for Oral Health Research in the University of Kentucky College of Dentistry/ ; }, abstract = {BACKGROUND AND OBJECTIVE: Host responses in periodontitis span a range of local and emigrating cell types and biomolecules. Accumulating evidence regarding the expression of this disease across the population suggests some component of genetic variation that controls onset and severity of disease, in concert with the qualitative and quantitative parameters of the oral microbiome at sites of disease. However, there remains little information regarding the capacity of accruing environmental stressors or modifiers over a lifespan at both the host genetic and microbial ecology levels to understand fully the population variation in disease. This study evaluated the impact of environmental lead exposure on the responses of oral epithelial cells to challenge with a model pathogenic oral biofilm.<br><br>METHODS AND RESULTS: Using NanoString technology to quantify gene expression profiles of an array of 511 host response-associated genes in the epithelial cells, we identified an interesting primary panel of basal responses of the cells with numerous genes not previously considered as major response markers for epithelial cells, eg, interleukin (IL)-32, CTNNB1, CD59, MIF, CD44 and CD99. Even high levels of environment lead had little effect on these constitutive responses. Challenge of the cells with the biofilms (Streptococcus gordonii/Fusobacterium nucleatum/Porphyromonas gingivalis) resulted in significant increases in an array of host immune-related genes (134 of 511). The greatest magnitude in differential expression was observed with many genes not previously described as major response genes in epithelial cells, including IL-32, CD44, NFKBIA, CTSC, TNFAIP3, IL-1A, IL-1B, IL-8 and CCL20. The effects of environmental lead on responses to the biofilms were mixed, although levels of IL-8, CCL20 and CD70 were significantly decreased at lead concentrations of 1 and/or 5 μmol/L.<br><br>CONCLUSION: The results provided new information on a portfolio of genes expressed by oral epithelial cells, targeted substantial increases in an array of immune-related genes post-biofilm challenge, and a focused impact of environmental lead on these induced responses.}, }
@article {pmid30151669, year = {2018}, author = {Szubert-Kruszyńska, A and Stańczak, J and Cieniuch, S and Podsiadły, E and Postawa, T and Michalik, J}, title = {Bartonella and Rickettsia Infections in Haematophagous Spinturnix myoti Mites (Acari: Mesostigmata) and their Bat Host, Myotis myotis (Yangochiroptera: Vespertilionidae), from Poland.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1246-5}, pmid = {30151669}, issn = {1432-184X}, support = {N N303819640//Ministerstwo Nauki i Szkolnictwa Wyższego/ ; }, abstract = {Hematophagous Spinturnix myoti mites and their host, the greater mouse-eared bat (Myotis myotis), were tested for the presence of Bartonella spp., Rickettsia spp., and Anaplasma phagocytophilum. In total, Bartonella spp. DNA was amplified in 28% of 134 mite pools and in 25% of 59 bats tested by PCR targeting a fragment of citrate synthase gltA gen. Adult mites were at least threefold more frequently infected compared to immature stages. The overall infection prevalence among mite pools from cave-dwelling bats was higher than for those collected from attic shelters. Three distinct genotypes were detected. The most prevalent genotype in mites and bats matched closely with Candidatus Bartonella hemsundetiensis identified in bats from Finland and was relatively distant from bat-borne Bartonella strains described in the UK and France. Importantly, most sequences were close to those reported in forest workers from Poland. The presence of identical genotype among S. myoti samples and M. myotis bats suggests that bartonellae can be shared between mites and their bat hosts. In this case, wing mites could serve as vectors, whereas their hosts as reservoirs. One blood sample was positive by PCR for the msp2 gene of A. phagocytophilum. Two mite pools yielded Rickettsia spp. DNA. Both sequences were distinct from any known species but can be classified as spotted fever group Rickettsia spp. Our findings expanded our knowledge on the role of spinturnicid mites in the ecology and epidemiology of bacterial infections associated with vespertilionid bats, especially regarding the genus Bartonella.}, }
@article {pmid30150233, year = {2018}, author = {Perault, AI and Cotter, PA}, title = {Three distinct contact-dependent growth inhibition systems mediate interbacterial competition by the cystic fibrosis pathogen Burkholderia dolosa.}, journal = {Journal of bacteriology}, volume = {}, number = {}, pages = {}, doi = {10.1128/JB.00428-18}, pmid = {30150233}, issn = {1098-5530}, support = {R01 GM121110/GM/NIGMS NIH HHS/United States ; R21 AI112764/AI/NIAID NIH HHS/United States ; }, abstract = {The respiratory tracts of individuals afflicted with cystic fibrosis (CF) harbor complex polymicrobial communities. By an unknown mechanism, species of the Gram-negative Burkholderia cepacia complex, such as Burkholderia dolosa, can displace other bacteria in the CF lung, causing cepacia syndrome, which has a poor prognosis. The genome of B. dolosa strain AU0158 (BdAU0158) contains three loci that are predicted to encode Contact-Dependent growth Inhibition (CDI) systems. CDI systems function by translocating the toxic C-terminus of a large exoprotein directly into target cells, resulting in growth inhibition or death unless the target cells produce a cognate immunity protein. We demonstrate here that each of the three bcpAIOB loci in BdAU0158 encodes a distinct CDI system that mediates interbacterial competition in an allele-specific manner. While only two of the three bcpAIOB loci are expressed under the in vitro conditions tested, the third conferred immunity under these conditions due to the presence of an internal promoter driving expression of the bcpI gene. One BdAU0158 bcpAIOB allele is highly similar to bcpAIOB in Burkholderia thailandensis strain E264 (BtE264), and we showed that their BcpI proteins are functionally interchangeable, but Contact-Dependent Signaling (CDS) phenotypes were not observed in BdAU0158. Our findings suggest that the CDI systems of BdAU0158 may provide this pathogen an ecological advantage during polymicrobial infections of the CF respiratory tract.IMPORTANCE Human-associated polymicrobial communities can promote health and disease, and interbacterial interactions influence the microbial ecology of such communities. Polymicrobial infections of the cystic fibrosis respiratory tract impair lung function and lead to death of individuals suffering from this disorder; therefore, a greater understanding of these microbial communities is necessary for improving treatment strategies. Bacteria utilize contact-dependent growth inhibition systems to kill neighboring competitors and maintain their niche within multicellular communities. Several cystic fibrosis pathogens have the potential to gain an ecological advantage during infection via contact-dependent growth inhibition systems, including Burkholderia dolosa Our research is significant as it has identified three functional contact-dependent growth inhibition systems in B. dolosa that may provide this pathogen a competitive advantage during polymicrobial infections.}, }
@article {pmid30149801, year = {2018}, author = {Bascuñán, P and Niño-Garcia, JP and Galeano-Castañeda, Y and Serre, D and Correa, MM}, title = {Factors shaping the gut bacterial community assembly in two main Colombian malaria vectors.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {148}, doi = {10.1186/s40168-018-0528-y}, pmid = {30149801}, issn = {2049-2618}, support = {project code No. 2015-8423//Departamento Administrativo de Ciencia, Tecnología e Innovación - Colciencias and Universidad de Antioquia/ ; Code No. ES84160123//Estrategia para la Sostenibilidad de Grupos de Investigación, Universidad de Antioquia 2016-2017/ ; grant No. 656-2014 &quot;Es tiempo de volver&quot;//PB is a postdoctoral fellow of Colciencias/ ; }, abstract = {BACKGROUND: The understanding of the roles of gut bacteria in the fitness and vectorial capacity of mosquitoes that transmit malaria, is improving; however, the factors shaping the composition and structure of such bacterial communities remain elusive. In this study, a high-throughput 16S rRNA gene sequencing was conducted to understand the effect of developmental stage, feeding status, species, and geography on the composition of the gut bacterial microbiota of two main Colombian malaria vectors, Anopheles nuneztovari and Anopheles darlingi.<br><br>RESULTS: The results revealed that mosquito developmental stage, followed by geographical location, are more important determinants of the gut bacterial composition than mosquito species or adult feeding status. Further, they showed that mosquito gut is a major filter for environmental bacteria colonization.<br><br>CONCLUSIONS: The sampling design and analytical approach of this study allowed to untangle the influence of factors that are simultaneously shaping the microbiota composition of two Latin-American malaria vectors, essential aspect for the design of vector biocontrol strategies.}, }
@article {pmid30146914, year = {2018}, author = {Papathanasiou, P and Erdmann, S and Leon-Sobrino, C and Sharma, K and Urlaub, H and Garrett, RA and Peng, X}, title = {Stable maintenance of the rudivirus SIRV3 in a carrier state in Sulfolobus islandicus despite activation of the CRISPR-Cas immune response by a second virus SMV1.}, journal = {RNA biology}, volume = {}, number = {}, pages = {1-9}, doi = {10.1080/15476286.2018.1511674}, pmid = {30146914}, issn = {1555-8584}, abstract = {Carrier state viral infection constitutes an equilibrium state in which a limited fraction of a cellular population is infected while the remaining cells are transiently resistant to infection. This type of infection has been characterized for several bacteriophages but not, to date, for archaeal viruses. Here we demonstrate that the rudivirus SIRV3 can produce a host-dependent carrier state infection in the model crenarchaeon Sulfolobus. SIRV3 only infected a fraction of a Sulfolobus islandicus REY15A culture over several days during which host growth was unimpaired and no chromosomal DNA degradation was observed. CRISPR spacer acquisition from SIRV3 DNA was induced by coinfecting with the monocaudavirus SMV1 and it was coincident with increased transcript levels from subtype I-A adaptation and interference cas genes. However, this response did not significantly affect the carrier state infection of SIRV3 and both viruses were maintained in the culture over 12 days during which SIRV3 anti-CRISPR genes were shown to be expressed. Transcriptome and proteome analyses demonstrated that most SIRV3 genes were expressed at varying levels over time whereas SMV1 gene expression was generally low. The study yields insights into the basis for the stable infection of SIRV3 and the resistance to the different host CRISPR-Cas interference mechanisms. It also provides a rationale for the commonly observed coinfection of archaeal cells by different viruses in natural environments.}, }
@article {pmid30145477, year = {2018}, author = {Daghio, M and Vaiopoulou, E and Aulenta, F and Sherry, A and Head, I and Franzetti, A and Rabaey, K}, title = {Anode potential selection for sulfide removal in contaminated marine sediments.}, journal = {Journal of hazardous materials}, volume = {360}, number = {}, pages = {498-503}, doi = {10.1016/j.jhazmat.2018.08.016}, pmid = {30145477}, issn = {1873-3336}, abstract = {Sulfate reducing microorganisms are typically involved in hydrocarbon biodegradation in the sea sediment, with their metabolism resulting in the by-production of toxic sulfide. In this context, it is of utmost importance identifying the optimal value for anodic potential which ensures efficient toxic sulfide removal. Along this line, in this study the (bio)electrochemical removal of sulfide was tested at anodic potentials of -205 mV, +195 mV and +300 mV (vs Ag/AgCl), also in the presence of a pure culture of the sulfur-oxidizing bacterium Desulfobulbus propionicus. Current production, sulfide concentration and sulfate concentration were monitored over time. At the end of the experiment sulfur deposition on the electrodes and the microbial communities were characterized by SEM-EDS and by next generation sequencing of the 16S rRNA gene respectively. Results confirmed that current production was linked to sulfide removal and D. propionicus promoted back oxidation of deposited sulfur to sulfate. The highest electron recovery was observed at +195 mV vs Ag/AgCl, and the lowest sulfur deposition was obtained at -205 mV vs Ag/AgCl anode polarization.}, }
@article {pmid30145102, year = {2018}, author = {Chen, L and Xu, W and Lee, A and He, J and Huang, B and Zheng, W and Su, T and Lai, S and Long, Y and Chu, H and Chen, Y and Wang, L and Wang, K and Si, J and Chen, S}, title = {The impact of Helicobacter pylori infection, eradication therapy and probiotic supplementation on gut microenvironment homeostasis: An open-label, randomized clinical trial.}, journal = {EBioMedicine}, volume = {35}, number = {}, pages = {87-96}, doi = {10.1016/j.ebiom.2018.08.028}, pmid = {30145102}, issn = {2352-3964}, support = {KL2 TR002241/TR/NCATS NIH HHS/United States ; }, abstract = {BACKGROUND: Helicobacter pylori (H. pylori) infection is associated with remodeling of gastric microbiota. However, comprehensive analyses of the impact of H. pylori infection, eradication therapy and probiotic supplementation on gut microbiota are still lacking. We aimed to provide evidence for clinical decision making.<br><br>METHODS: Seventy H. pylori-positive and 35 H. pylori-negative patients (group C) were enrolled. H. pylori-positive patients were randomly assigned to group A (14-day bismuth-containing quadruple therapy) and group B (quadruple therapy supplemented with Clostridium butyricum). Stool samples of group A and B were collected on day 0, 14 and 56 while stool samples of group C were collected on day 0. Gut microbiota was investigated by 16S rRNA sequencing.<br><br>FINDINGS: The Sobs index (richness estimator) was significantly higher in H. pylori-positive samples than H. pylori-negative samples (p < .05). Several metabolic pathways were more abundant in H. pylori-positive communities while some disease-associated pathways had higher potential in H. pylori-negative community through KEGG pathway analysis. Abundances of most butyrate-producing bacteria significantly decreased, while several detrimental bacteria increased after eradication therapy. Probiotic supplementation was associated with improved gastrointestinal symptoms as well as increased Bacteroidetes:Firmicutes ratio.<br><br>INTERPRETATION: While H. pylori infection may not be necessarily detrimental in all patients, eradication of H. pylori was associated with widespread changes in gut microbial ecology and structure. Probiotic supplementation could relieve more gastrointestinal symptoms by inducing alterations in gut microbiota and host immune responses. As such, the decision to eradicate H. pylori should be based on comprehensive analysis of individual patients.}, }
@article {pmid30143799, year = {2018}, author = {Hall, EK and Bernhardt, ES and Bier, RL and Bradford, MA and Boot, CM and Cotner, JB and Del Giorgio, PA and Evans, SE and Graham, EB and Jones, SE and Lennon, JT and Locey, KJ and Nemergut, D and Osborne, BB and Rocca, JD and Schimel, JP and Waldrop, MP and Wallenstein, MD}, title = {Understanding how microbiomes influence the systems they inhabit.}, journal = {Nature microbiology}, volume = {3}, number = {9}, pages = {977-982}, doi = {10.1038/s41564-018-0201-z}, pmid = {30143799}, issn = {2058-5276}, abstract = {Translating the ever-increasing wealth of information on microbiomes (environment, host or built environment) to advance our understanding of system-level processes is proving to be an exceptional research challenge. One reason for this challenge is that relationships between characteristics of microbiomes and the system-level processes that they influence are often evaluated in the absence of a robust conceptual framework and reported without elucidating the underlying causal mechanisms. The reliance on correlative approaches limits the potential to expand the inference of a single relationship to additional systems and advance the field. We propose that research focused on how microbiomes influence the systems they inhabit should work within a common framework and target known microbial processes that contribute to the system-level processes of interest. Here, we identify three distinct categories of microbiome characteristics (microbial processes, microbial community properties and microbial membership) and propose a framework to empirically link each of these categories to each other and the broader system-level processes that they affect. We posit that it is particularly important to distinguish microbial community properties that can be predicted using constituent taxa (community-aggregated traits) from those properties that cannot currently be predicted using constituent taxa (emergent properties). Existing methods in microbial ecology can be applied to more explicitly elucidate properties within each of these three categories of microbial characteristics and connect them with each other. We view this proposed framework, gleaned from a breadth of research on environmental microbiomes and ecosystem processes, as a promising pathway with the potential to advance discovery and understanding across a broad range of microbiome science.}, }
@article {pmid30143666, year = {2018}, author = {Benicio, LM and Simionato, AS and Novello, CR and Guimarães, JR and Felicidade, I and de Oliveira, AG and de Mello, JCP and Mantovani, MS and Chryssafidis, AL and Andrade, G and de Syllos Colus, IM and de Oliveira, MT}, title = {RNAm expression profile of cancer marker genes in HepG2 cells treated with different concentrations of a new indolin-3-one from Pseudomonas aeruginosa.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {12781}, doi = {10.1038/s41598-018-30893-w}, pmid = {30143666}, issn = {2045-2322}, abstract = {The present study tested the effects of a newly identified indolin-3-one compound (compound 1), produced by Pseudomonas aeruginosa, on HepG2 cells. The MTT assays demonstrated decreased metabolic activities in HepG2 cells treated with compound 1, with dose- and time-dependent intensifying effect, starting at a concentration of 40 µM. The IC50 after 24, 48, 72, and 96 h treatments were 41.35, 52.7, 92.79 and 66.65 μM of compound 1, respectively. Below 80 µM, no significative damage on erythrocytes membranes was observed by the hemolytic assays. The RT-qPCR revealed that the compound modulated key genes involved in carcinogenesis process, indicating possible indolin-3-one mechanisms of action. The data showed that gene expression alterations promoted by compound 1, in concentrations up to 60 μM after 48 h, led to a decrease in cellular progression and there was no direct cellular damage. In addition, non-cytotoxic concentrations of compound 1 halved the concentration of the chemotherapeutic doxorubicin, maintaining similar therapeutic effect against HepG2 cells. The novelty of the molecule and the biological activities observed in the present study emphasize the potential of the compound 1 in cancer therapy research.}, }
@article {pmid30142153, year = {2018}, author = {Pace, NR}, title = {The small things can matter.}, journal = {PLoS biology}, volume = {16}, number = {8}, pages = {e3000009}, doi = {10.1371/journal.pbio.3000009}, pmid = {30142153}, issn = {1545-7885}, abstract = {In the context of biology as a whole and of our own personal lives, seemingly small things can prove surprisingly influential. Here, I consider the powerful impact of small organisms-the inhabitants of the microbial world-and the small events that shaped my own development as a scientist. I reflect on the early days of the fields of molecular biology and microbial ecology and my own role in the origin story of what we now call &quot;metagenomics&quot;.}, }
@article {pmid30141128, year = {2018}, author = {Li, H and Mishra, M and Ding, S and Miyamoto, MM}, title = {Diversity and Dynamics of &quot;Candidatus Endobugula&quot; and Other Symbiotic Bacteria in Chinese Populations of the Bryozoan, Bugula neritina.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1233-x}, pmid = {30141128}, issn = {1432-184X}, support = {201205024-2//Public Welfare Project of the State Oceanic Administration/ ; 2013FY110700//National Basic Research Foundation of China/ ; }, abstract = {Bugula neritina is a common invasive cosmopolitan bryozoan that harbors (like many sessile marine invertebrates) a symbiotic bacterial (SB) community. Among the SB of B. neritina, &quot;Candidatus Endobugula sertula&quot; continues to receive the greatest attention, because it is the source of bryostatins. The bryostatins are potent bioactive polyketides, which have been investigated for their therapeutic potential to treat various cancers, Alzheimer's disease, and AIDS. In this study, we compare the metagenomics sequences for the 16S ribosomal RNA gene of the SB communities from different geographic and life cycle samples of Chinese B. neritina. Using a variety of approaches for estimating alpha/beta diversity and taxonomic abundance, we find that the SB communities vary geographically with invertebrate and fish mariculture and with latitude and environmental temperature. During the B. neritina life cycle, we find that the diversity and taxonomic abundances of the SB communities change with the onset of host metamorphosis, filter feeding, colony formation, reproduction, and increased bryostatin production. &quot;Ca. Endobugula sertula&quot; is confirmed as the symbiont of the Chinese &quot;Ca. Endobugula&quot;/B. neritina symbiosis. Our study extends our knowledge about B. neritina symbiosis from the New to the Old World and offers new insights into the environmental and life cycle factors that can influence its SB communities, &quot;Ca. Endobugula,&quot; and bryostatins more globally.}, }
@article {pmid30141127, year = {2018}, author = {Choi, Y and Banerjee, A and McNish, S and Couch, KS and Torralba, MG and Lucas, S and Tovchigrechko, A and Madupu, R and Yooseph, S and Nelson, KE and Shanmugam, VK and Chan, AP}, title = {Co-occurrence of Anaerobes in Human Chronic Wounds.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1231-z}, pmid = {30141127}, issn = {1432-184X}, support = {R01NR013888//National Institute of Nursing Research/ ; UL1 TR000075//National Center for Advancing Translational Sciences/ ; }, abstract = {Chronic wounds are wounds that have failed to heal after 3 months of appropriate wound care. Previous reports have identified a diverse collection of bacteria in chronic wounds, and it has been postulated that bacterial profile may contribute to delayed healing. The purpose of this study was to perform a microbiome assessment of the Wound Healing and Etiology (WE-HEAL) Study cohort, including underlying comorbidities less commonly studied in the context of chronic wounds, such as autoimmune diseases, and investigate possible relationships of the wound microbiota with clinical healing trends. We examined chronic wound specimens from 60 patients collected through the WE-HEAL Study using 16S ribosomal RNA gene sequencing. A group of co-occurring obligate anaerobes was identified from taxonomic analysis guided by Dirichlet multinomial mixtures (DMM) modeling. The group includes members of the Gram-positive anaerobic cocci (GPAC) of the Clostridia class (i.e., Anaerococcus, Finegoldia, and Peptoniphilus) and additional strict anaerobes (i.e., Porphyromonas and Prevotella). We showed that the co-occurring group of obligate anaerobes not only co-exists with commonly identified wound species (such as Staphylococcus aureus, Staphylococcus epidermidis, Pseudomonas, Corynebacterium, and Streptococcus), but importantly, they could also predominate the wound microbiota. Furthermore, examination of clinical comorbidities of the WE-HEAL specimens showed that specific obligate and facultative anaerobes were significantly reduced in wounds presented with autoimmune disease. With respect to future healing trends, no association with the wound microbiome community or the abundance of individual wound species could be established. In conclusion, we identified a co-occurring obligate anaerobic community type that predominated some human chronic wounds and underrepresentation of anaerobes in wounds associated with autoimmune diseases. Possible elucidation of host environments or key factors that influence anaerobe colonization warrants further investigation in a larger cohort.}, }
@article {pmid30138752, year = {2018}, author = {Zeineldin, M and Barakat, R and Elolimy, A and Salem, AZM and Elghandour, MMY and Monroy, JC}, title = {Synergetic action between the rumen microbiota and bovine health.}, journal = {Microbial pathogenesis}, volume = {124}, number = {}, pages = {106-115}, doi = {10.1016/j.micpath.2018.08.038}, pmid = {30138752}, issn = {1096-1208}, abstract = {Host-rumen-microbe interactions are essential components of many physiological processes, and therefore can affect ruminant health. Classical knowledge of rumen microbiology is based on culture-dependent methodologies, which only account for 10-20% of the rumen bacterial communities. While, the advancement in DNA sequencing and bioinformatics platforms provide novel approaches to investigate the composition and dynamics of the rumen microbiota. Recent studies demonstrated that the ruminal ecosystem is highly diverse and harbors numerous microbial communities. The composition of these microbial communities are affected by various environmental factors such as nutrition and different management strategies. Disturbance in the microbial ecology of the rumen is associated with the development of various diseases. Despite the flow of recent rumen-based studies, rumen microbiota is still not fully characterized. This review provides an overview of recent efforts to characterize rumen microbiota and its potential role in rumen health and disease. Moreover, the recent effects of dietary interventions and probiotics on rumen microbiota are discussed.}, }
@article {pmid30137564, year = {2018}, author = {Lekeux, G and Laurent, C and Joris, M and Jadoul, A and Jiang, D and Bosman, B and Carnol, M and Motte, P and Xiao, Z and Galleni, M and Hanikenne, M}, title = {di-Cysteine motifs in the C-terminus of plant HMA4 proteins confer nanomolar affinity for zinc and are essential for HMA4 function in vivo.}, journal = {Journal of experimental botany}, volume = {69}, number = {22}, pages = {5547-5560}, doi = {10.1093/jxb/ery311}, pmid = {30137564}, issn = {1460-2431}, abstract = {The PIB ATPase heavy metal ATPase 4 (HMA4) has a central role in the zinc homeostasis network of Arabidopsis thaliana. This membrane protein loads metal from the pericycle cells into the xylem in roots, thereby allowing root to shoot metal translocation. Moreover, HMA4 is key for zinc hyperaccumulation as well as zinc and cadmium hypertolerance in the pseudometallophyte Arabidopsis halleri. The plant-specific cytosolic C-terminal extension of HMA4 is rich in putative metal-binding residues and has substantially diverged between A. thaliana and A. halleri. To clarify the function of the domain in both species, protein variants with truncated C-terminal extension, as well as with mutated di-Cys motifs and/or a His-stretch, were functionally characterized. We show that di-Cys motifs, but not the His-stretch, contribute to high affinity zinc binding and function in planta. We suggest that the HMA4 C-terminal extension is at least partly responsible for protein targeting to the plasma membrane. Finally, we reveal that the C-terminal extensions of both A. thaliana and A. halleri HMA4 proteins share similar function, despite marginally different zinc-binding capacity.}, }
@article {pmid30137345, year = {2018}, author = {Luk, AW and Beckmann, S and Manefield, M}, title = {Dependency of DNA extraction efficiency on cell concentration confounds molecular quantification of microorganisms in groundwater.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {10}, pages = {}, doi = {10.1093/femsec/fiy146}, pmid = {30137345}, issn = {1574-6941}, abstract = {Quantification of microbes in water systems is essential to industrial practices ranging from drinking water and wastewater treatment to groundwater remediation. While quantification using DNA-based molecular methods is precise, the accuracy is dependent on DNA extraction efficiencies. We show that the DNA yield is strongly impacted by the cell concentration in groundwater samples (r = -0.92, P < 0.0001). This has major implications for industrial applications using quantitative polymerase chain reaction (qPCR) to determine cell concentrations in water, including bioremediation. We propose a simple normalization method using a DNA recovery ratio, calculated with the total cell count and DNA yield. Application of this method to enumeration of bacteria and archaea in groundwater samples targeting phylogenetic markers (16S rRNA) demonstrated an increased goodness of fit after normalization (7.04 vs 0.94 difference in Akaike's information criteria). Furthermore, normalization was applied to qPCR quantification of functional genes and combined with DNA sequencing of archaeal and bacterial 16S rRNA genes to monitor changes in abundance of methanogenic archaea and sulphate-reducing bacteria in groundwater. The integration of qPCR and DNA sequencing with appropriate normalization enables high-throughput quantification of microbial groups using increasingly affordable and accessible techniques. This research has implications for microbial ecology and engineering research as well as industrial practice.}, }
@article {pmid30137328, year = {2018}, author = {Geesink, P and Tyc, O and Küsel, K and Taubert, M and van de Velde, C and Kumar, S and Garbeva, P}, title = {Growth promotion and inhibition induced by interactions of groundwater bacteria.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {11}, pages = {}, doi = {10.1093/femsec/fiy164}, pmid = {30137328}, issn = {1574-6941}, abstract = {Microorganisms can produce a plethora of secondary metabolites, some acting as signaling compounds and others as suppressing agents. As yet, the potential of groundwater microbes to produce antimicrobial compounds to increase their competitiveness against other bacteria has not been examined. In this study, we developed an AlamarBlue® based high-throughput screening method that allowed for a fast and highly standardized evaluation of both growth-inhibiting and -promoting metabolites. With this technique, 149 screened bacterial isolates were grown in monocultures and in 1402 co-cultures. Co-cultivation did not increase the frequency of growth inhibition against the two tested model organisms (Staphylococcus aureus 533R4 and Escherichia coli WA321) compared to monocultures. Mainly co-cultivation of Proteobacteria induced growth inhibition of both model organisms. Only slightly increased growth promotion of S. aureus 533R4 was observed. Growth-promoting effects on E. coli WA321 were observed by supernatants from co-cultures between Bacteroidetes and Firmicutes. With the standardized screening for both growth-inhibiting and -promoting effects, this method will enable further studies to elaborate and better understand complex inter-specific interactions and networks in aquatic communities as well as in other environments.}, }
@article {pmid30135980, year = {2018}, author = {Vikström, K and Wikner, J}, title = {Importance of Bacterial Maintenance Respiration in a Subarctic Estuary: a Proof of Concept from the Field.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1244-7}, pmid = {30135980}, issn = {1432-184X}, abstract = {Bacterial respiration contributes to atmospheric carbon dioxide accumulation and development of hypoxia and is a critical, often overlooked, component of ecosystem function. This study investigates the concept that maintenance respiration is a significant proportion of bacterial respiration at natural nutrient levels in the field, advancing our understanding of bacterial living conditions and energy strategies. Two river-sea transects of respiration and specific growth rates were analyzed representing low- and high-productivity conditions (by in situ bacterial biomass production) in a subarctic estuary, using an established ecophysiological linear model (the Pirt model) estimating maintenance respiration. The Pirt model was applicable to field conditions during high, but not low, bacterial biomass production. However, a quadratic model provided a better fit to observed data, accounting for the maintained respiration at low μ. A first estimate of maintenance respiration was 0.58 fmol O2 day-1 cell-1 by the quadratic model. Twenty percent to nearly all of the bacterial respiration was due to maintenance respiration over the observed range of μ (0.21-0.002 day-1). In the less productive condition, bacterial specific respiration was high and without dependence on μ, suggesting enhanced bacterial energy expenditure during starvation. Annual maintenance respiration accounted for 58% of the total bacterioplankton respiration based on μ from monitoring data. Phosphorus availability occasionally, but inconsistently, explained some of the remaining variation in bacterial specific respiration. Bacterial maintenance respiration can constitute a large share of pelagic respiration and merit further study to understand bacterial energetics and oxygen dynamics in the aquatic environment.}, }
@article {pmid30131799, year = {2018}, author = {Seugendo, M and Janssen, I and Lang, V and Hasibuan, I and Bohne, W and Cooper, P and Daniel, R and Gunka, K and Kusumawati, RL and Mshana, SE and von Müller, L and Okamo, B and Ortlepp, JR and Overmann, J and Riedel, T and Rupnik, M and Zimmermann, O and Groß, U}, title = {Prevalence and Strain Characterization of Clostridioides (Clostridium) difficile in Representative Regions of Germany, Ghana, Tanzania and Indonesia - A Comparative Multi-Center Cross-Sectional Study.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1843}, doi = {10.3389/fmicb.2018.01843}, pmid = {30131799}, issn = {1664-302X}, abstract = {Clostridioides (Clostridium) difficile infections (CDI) are considered worldwide as emerging health threat. Uptake of C. difficile spores may result in asymptomatic carrier status or lead to CDI that could range from mild diarrhea, eventually developing into pseudomembranous colitis up to a toxic megacolon that often results in high mortality. Most epidemiological studies to date have been performed in middle- and high income countries. Beside others, the use of antibiotics and the composition of the microbiome have been identified as major risk factors for the development of CDI. We therefore postulate that prevalence rates of CDI and the distribution of C. difficile strains differ between geographical regions depending on the regional use of antibiotics and food habits. A total of 593 healthy control individuals and 608 patients suffering from diarrhea in communities in Germany, Ghana, Tanzania and Indonesia were selected for a comparative multi-center cross-sectional study. The study populations were screened for the presence of C. difficile in stool samples. Cultured C. difficile strains (n = 84) were further subtyped and characterized using PCR-ribotyping, determination of toxin production, and antibiotic susceptibility testing. Prevalence rates of C. difficile varied widely between the countries. Whereas high prevalence rates were observed in symptomatic patients living in Germany and Indonesia (24.0 and 14.7%), patients from Ghana and Tanzania showed low detection rates (4.5 and 6.4%). Differences were also obvious for ribotype distribution and toxin repertoires. Toxin A+/B+ ribotypes 001/072 and 078 predominated in Germany, whereas most strains isolated from Indonesian patients belonged to toxin A+/B+ ribotype SLO160 and toxin A-/B+ ribotype 017. With 42.9-73.3%, non-toxigenic strains were most abundant in Africa, but were also found in Indonesia at a rate of 18.2%. All isolates were susceptible to vancomycin and metronidazole. Mirroring the antibiotic use, however, moxifloxacin resistance was absent in African C. difficile isolates but present in Indonesian (24.2%) and German ones (65.5%). This study showed that CDI is a global health threat with geographically different prevalence rates which might reflect distinct use of antibiotics. Significant differences for distributions of ribotypes, toxin production, and antibiotic susceptibilities were observed.}, }
@article {pmid30130114, year = {2018}, author = {Eshrati, M and Amadei, F and Van de Wiele, T and Veschgini, M and Kaufmann, S and Tanaka, M}, title = {Biopolymer-Based Minimal Formulations Boost Viability and Metabolic Functionality of Probiotics Lactobacillus rhamnosus GG through Gastrointestinal Passage.}, journal = {Langmuir : the ACS journal of surfaces and colloids}, volume = {34}, number = {37}, pages = {11167-11175}, doi = {10.1021/acs.langmuir.8b01915}, pmid = {30130114}, issn = {1520-5827}, abstract = {The delivery of probiotic microorganisms as food additives via oral administration is a straightforward strategy to improve the intestinal microbiota. To protect probiotics from the harsh environments in the stomach and small intestine, it is necessary to formulate them in biocompatible carriers, which finally release them in the ileum and colon without losing their viability and functions. Despite major progresses in various polymer-based formulations, many of them are highly heterogeneous and too large in size and hence often &quot;felt&quot; by the tongue. In this study, we established a new formulation for probiotics Lactobacillus rhamnosus GG (LGG) and systematically correlated the physicochemical properties of formulations with the functions of probiotics after the delivery to different gastrointestinal compartments. By reducing the stirring speed by 1 order of magnitude during the emulsification of polyalginate in the presence of xanthan gum, we fabricated microparticles with a size well below the limit of human oral sensory systems. To improve the chemical stability, we deposited chitosan and polyalginate layers on particle surfaces and found that the deposition of a 20 nm-thick layer is already sufficient to perfectly sustain the viability of all LGG. Compared to free LGG, the colony-forming units of LGG in these formulations were by factors of 107 larger in stomach fluid and 104 larger in small intestine fluid. The metabolic functionality of LGG in polymer formulations was assessed by measuring the amount of lactate produced by LGG in a human gastrointestinal simulator, showing 5 orders of magnitude larger values compared to free LGG. The obtained results have demonstrated that the minimal formulation of LGG established here boosts not only the viability but also the metabolic functionality of probiotics throughout oral uptake, passage through the gastrointestinal tract, and delivery to the ileum and colon.}, }
@article {pmid30128178, year = {2018}, author = {Wallace, J and Laforest-Lapointe, I and Kembel, SW}, title = {Variation in the leaf and root microbiome of sugar maple (Acer saccharum) at an elevational range limit.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e5293}, doi = {10.7717/peerj.5293}, pmid = {30128178}, issn = {2167-8359}, abstract = {Background: Bacteria, archaea, viruses and fungi live in various plant compartments including leaves and roots. These plant-associated microbial communities have many effects on host fitness and function. Global climate change is impacting plant species distributions, a phenomenon that will affect plant-microbe interactions both directly and indirectly. In order to predict plant responses to global climate change, it will be crucial to improve our understanding of plant-microbe interactions within and at the edge of plant species natural ranges. While microbes affect their hosts, in turn the plant's attributes and the surrounding environment drive the structure and assembly of the microbial communities themselves. However, the patterns and dynamics of these interactions and their causes are poorly understood.<br><br>Methods: In this study, we quantified the microbial communities of the leaves and roots of seedlings of the deciduous tree species sugar maple (Acer saccharum Marshall) within its natural range and at the species' elevational range limit at Mont-Mégantic, Quebec. Using high-throughput DNA sequencing, we quantified the bacterial and fungal community structure in four plant compartments: the epiphytes and endophytes of leaves and roots. We also quantified endophytic fungal communities in roots.<br><br>Results: The bacterial and fungal communities of A. saccharum seedlings differ across elevational range limits for all four plant compartments. Distinct microbial communities colonize each compartment, although the microbial communities inside a plant's structure (endophytes) were found to be a subset of the communities found outside the plant's structure (epiphytes). Plant-associated bacterial communities were dominated by the phyla Proteobacteria, Acidobacteria, Actinobacteria and Bacteroidetes while the main fungal taxa present were Ascomycota.<br><br>Discussion: We demonstrate that microbial communities associated with sugar maple seedlings at the edge of the species' elevational range differ from those within the natural range. Variation in microbial communities differed among plant components, suggesting the importance of each compartment's exposure to changes in biotic and abiotic conditions in determining variability in community structure. These findings provide a greater understanding of the ecological processes driving the structure and diversity of plant-associated microbial communities within and at the edge of a plant species range, and suggest the potential for biotic interactions between plants and their associated microbiota to influence the dynamics of plant range edge boundaries and responses to global change.}, }
@article {pmid30127345, year = {2018}, author = {Gilbert, JA and Stephens, B}, title = {Microbiology of the built environment.}, journal = {Nature reviews. Microbiology}, volume = {16}, number = {11}, pages = {661-670}, doi = {10.1038/s41579-018-0065-5}, pmid = {30127345}, issn = {1740-1534}, abstract = {The built environment comprises all structures built by humans, including our homes, workplaces, schools and vehicles. As in any ecosystem on Earth, microorganisms have been found in every part of the built environment that has been studied. They exist in the air, on surfaces and on building materials, usually dispersed by humans, animals and outdoor sources. Those microbial communities and their metabolites have been implied to cause (or exacerbate) and prevent (or mitigate) human disease. In this Review, we outline the history of the field of microbiology of the built environment and discuss recent insights that have been gained into microbial ecology, adaptation and evolution of this ecosystem. Finally, we consider the implications of this research, specifically, how it is changing the types of materials we use in buildings and how our built environments affect human health.}, }
@article {pmid30126070, year = {2018}, author = {De Paepe, K and Verspreet, J and Verbeke, K and Raes, J and Courtin, CM and Van de Wiele, T}, title = {Introducing insoluble wheat bran as a gut microbiota niche in an in vitro dynamic gut model stimulates propionate and butyrate production and induces colon region specific shifts in the luminal and mucosal microbial community.}, journal = {Environmental microbiology}, volume = {20}, number = {9}, pages = {3406-3426}, doi = {10.1111/1462-2920.14381}, pmid = {30126070}, issn = {1462-2920}, support = {IWT130028//Fonds Wetenschappelijk Onderzoek/ ; }, abstract = {The spatial organization of gut microorganisms is important with respect to their functional role in the gut ecosystem. Regional differences in the longitudinal and lateral direction are, however, not frequently studied, given the difficulty to sample these human gut regions in vivo. Particularly the insoluble food particle-associated microbiota is poorly studied. Therefore, the long-term effects of insoluble wheat bran supplementation on the composition and functionality of the gut microbial community derived from six individuals were explored in the Dietary Particle-Mucosal-Simulator of the Human Intestinal Microbial Ecosystem in vitro model. Wheat bran stimulated propionate and butyrate production and induced shifts in the luminal and mucosal microbial community composition. The insoluble wheat bran residue and the mucus layer were identified as crucial platforms in sustaining diversity by selectively enriching species, which are not thriving in the luminal environment, including Lactobacillus, Bifidobacterium and Dialister species, Roseburia faecis, Prevotella copri and Bacteroides ovatus. Despite the evident habitat preference, some parallels could be drawn between the enrichment of taxa on bran platforms and their stimulation in the luminal and mucosal communities. Removing wheat bran during the wash-out period reversed the functional effects and gave rise to a blooming of some taxa that are considered opportunistic pathogens.}, }
@article {pmid30124400, year = {2018}, author = {Jung, MY and Islam, MA and Gwak, JH and Kim, JG and Rhee, SK}, title = {Nitrosarchaeum koreense gen. nov., sp. nov., an aerobic and mesophilic, ammonia-oxidizing archaeon member of the phylum Thaumarchaeota isolated from agricultural soil.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {68}, number = {10}, pages = {3084-3095}, doi = {10.1099/ijsem.0.002926}, pmid = {30124400}, issn = {1466-5034}, mesh = {Agriculture ; Ammonia/*metabolism ; Archaea/*classification/genetics/isolation &amp; purification ; Base Composition ; Genes, Archaeal ; Glyceryl Ethers/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Sequence Analysis, DNA ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {A mesophilic, chemolithoautotrophic, neutrophilic and aerobic ammonia-oxidizing archaeon, designated strain MY1T, was isolated from agricultural soil. Microscopic observation revealed short, rod-shaped cells with a diameter of 0.3-0.5 µm and length of 0.6-1.0 µm. The isolate had no flagella and pili, and possessed no genes associated with archaeal flagella synthesis. The major membrane lipids consisted mainly of the glycerol dibiphytanyl glycerol tetraether (GDGT) lipids GDGT-0 to GDGT-4 and crenarchaeol. The major intact polar lipids (IPLs) were determined as hexose plus phosphohexose IPL and dihexose IPL. Strain MY1T obtains energy by aerobically oxidizing ammonia and carbon by fixing CO2. An optimal growth was observed at 25 °C, at pH 7 and with 0.2-0.4 % (w/v) salinity that corresponds with its terrestrial habitat. The addition of α-keto acids was necessary to stimulate growth. The strain tolerated ammonium and nitrite concentrations up to 10 and 5 mM, respectively. The MY1T genome has a DNA G+C content of 32.7 mol%. Phylogenetic analysis based on the 16S rRNA gene showed that strain MY1T belongs to the family Nitrosopumilaceaeof the phylum Thaumarchaeota, sharing the highest 16S rRNA gene sequence similarity (96.6-97.1 %) with marine isolates of the genus Nitrosopumilus. The average nucleotide identity was 78 % between strain MY1T and Nitrosopumilus maritimus SCM1T, indicating distant relatedness. Based on the phenotypic, phylogenetic and genomic analyses, it was concluded that strain MY1T belongs to the novel genus Nitrosarchaeum, under which the name Nitrosarchaeum koreense sp. nov. is proposed as the type species. The type strain is MY1T (=JCM 31640T=KCTC 4249T).}, }
@article {pmid30123820, year = {2018}, author = {Williamson, IA and Arnold, JW and Samsa, LA and Gaynor, L and DiSalvo, M and Cocchiaro, JL and Carroll, I and Azcarate-Peril, MA and Rawls, JF and Allbritton, NL and Magness, ST}, title = {A High-Throughput Organoid Microinjection Platform to Study Gastrointestinal Microbiota and Luminal Physiology.}, journal = {Cellular and molecular gastroenterology and hepatology}, volume = {6}, number = {3}, pages = {301-319}, doi = {10.1016/j.jcmgh.2018.05.004}, pmid = {30123820}, issn = {2352-345X}, support = {UL1 TR001111/TR/NCATS NIH HHS/United States ; R01 DK091427/DK/NIDDK NIH HHS/United States ; P30 DK034987/DK/NIDDK NIH HHS/United States ; R01 DK081426/DK/NIDDK NIH HHS/United States ; R01 DK109559/DK/NIDDK NIH HHS/United States ; UL1 TR001117/TR/NCATS NIH HHS/United States ; }, abstract = {Background &amp; Aims: The human gut microbiota is becoming increasingly recognized as a key factor in homeostasis and disease. The lack of physiologically relevant in vitro models to investigate host-microbe interactions is considered a substantial bottleneck for microbiota research. Organoids represent an attractive model system because they are derived from primary tissues and embody key properties of the native gut lumen; however, access to the organoid lumen for experimental perturbation is challenging. Here, we report the development and validation of a high-throughput organoid microinjection system for cargo delivery to the organoid lumen and high-content sampling.<br><br>Methods: A microinjection platform was engineered using off-the-shelf and 3-dimensional printed components. Microinjection needles were modified for vertical trajectories and reproducible injection volumes. Computer vision (CVis) and microfabricated CellRaft Arrays (Cell Microsystems, Research Triangle Park, NC) were used to increase throughput and enable high-content sampling of mock bacterial communities. Modeling preformed using the COMSOL Multiphysics platform predicted a hypoxic luminal environment that was functionally validated by transplantation of fecal-derived microbial communities and monocultures of a nonsporulating anaerobe.<br><br>Results: CVis identified and logged locations of organoids suitable for injection. Reproducible loads of 0.2 nL could be microinjected into the organoid lumen at approximately 90 organoids/h. CVis analyzed and confirmed retention of injected cargos in approximately 500 organoids over 18 hours and showed the requirement to normalize for organoid growth for accurate assessment of barrier function. CVis analyzed growth dynamics of a mock community of green fluorescent protein- or Discosoma sp. red fluorescent protein-expressing bacteria, which grew within the organoid lumen even in the presence of antibiotics to control media contamination. Complex microbiota communities from fecal samples survived and grew in the colonoid lumen without appreciable changes in complexity.<br><br>Conclusions: High-throughput microinjection into organoids represents a next-generation in vitro approach to investigate gastrointestinal luminal physiology and the gastrointestinal microbiota.}, }
@article {pmid30121434, year = {2018}, author = {Props, R and Rubbens, P and Besmer, M and Buysschaert, B and Sigrist, J and Weilenmann, H and Waegeman, W and Boon, N and Hammes, F}, title = {Detection of microbial disturbances in a drinking water microbial community through continuous acquisition and advanced analysis of flow cytometry data.}, journal = {Water research}, volume = {145}, number = {}, pages = {73-82}, doi = {10.1016/j.watres.2018.08.013}, pmid = {30121434}, issn = {1879-2448}, abstract = {Detecting disturbances in microbial communities is an important aspect of managing natural and engineered microbial communities. Here, we implemented a custom-built continuous staining device in combination with real-time flow cytometry (RT-FCM) data acquisition, which, combined with advanced FCM fingerprinting methods, presents a powerful new approach to track and quantify disturbances in aquatic microbial communities. Through this new approach we were able to resolve various natural community and single-species microbial contaminations in a flow-through drinking water reactor. Next to conventional FCM metrics, we applied metrics from a recently developed fingerprinting technique in order to gain additional insight into the microbial dynamics during these contamination events. Importantly, we found that multiple community FCM metrics based on different statistical approaches were required to fully characterize all contaminations. Furthermore we found that for accurate cell concentration measurements and accurate inference from the FCM metrics (coefficient of variation ≤ 5%), at least 1000 cells should be measured, which makes the achievable temporal resolution a function of the prevalent bacterial concentration in the system-of-interest. The integrated RT-FCM acquisition and analysis approach presented herein provides a considerable improvement in the temporal resolution by which microbial disturbances can be observed and simultaneously provides a multi-faceted toolset to characterize such disturbances.}, }
@article {pmid30121040, year = {2019}, author = {Petersen, NB and Madsen, T and Glaring, MA and Dobbs, FC and Jørgensen, NOG}, title = {Ballast water treatment and bacteria: Analysis of bacterial activity and diversity after treatment of simulated ballast water by electrochlorination and UV exposure.}, journal = {The Science of the total environment}, volume = {648}, number = {}, pages = {408-421}, doi = {10.1016/j.scitotenv.2018.08.080}, pmid = {30121040}, issn = {1879-1026}, mesh = {Bacteria/*drug effects/*radiation effects ; Electrochemical Techniques ; *Halogenation ; *Photolysis ; Ultraviolet Rays ; Waste Disposal, Fluid/*methods ; Waste Water/*analysis ; }, abstract = {Effects of ballast water (BW) treatment by ultra-violet (UV) light and electrochlorination (EC) on survival, activity and diversity of marine bacterioplankton and release of organic matter from cell damage were examined at discharge in a large-scale BW test facility (250 m3 tanks) at Hundested harbour, Denmark. The tests were performed in accordance with the requirements for type approval testing by International Maritime Organization (IMO) and US Coast Guard. After treatment, the water was held in the tanks for one day (EC) before discharge, or 6 days (UV, including also a final UV re-treatment) before discharge. In the discharged and treated water, numbers of viable bacteria and bacterial growth rate had decreased significantly relative to the untreated water, but the total number of bacteria only was reduced in the EC-treated water. After additional storage for up to 10 days in small-scale laboratory incubations, significant regrowth of bacteria was observed after either treatment. Sequencing of 16S rRNA gene amplicons demonstrated that α-Proteobacteria initially were dominant, but γ-Proteobacteria dominated after regrowth. Bacteria used to document BW treatment efficiency (E. coli, Vibrio spp., enterococci) survived both treatments; neither treatment reduced the risk of pathogen dispersal. Concentrations of amino acids in the water were used as indicators of treatment-induced cell damage and demonstrated higher concentrations at discharge, but only after the EC treatments. Our results indicate that activity of bacteria, rather than their abundances, should be used when examining effects by ballast water treatment on microorganisms and that none of the examined treatment technologies could eliminate pathogenic bacteria.}, }
@article {pmid30117593, year = {2018}, author = {Ngo, TTN and Senior, AM and Culina, A and Santos, ESA and Vlak, JM and Zwart, MP}, title = {Quantitative analysis of the dose-response of white spot syndrome virus in shrimp.}, journal = {Journal of fish diseases}, volume = {41}, number = {11}, pages = {1733-1744}, doi = {10.1111/jfd.12877}, pmid = {30117593}, issn = {1365-2761}, abstract = {White spot syndrome virus (WSSV) is an important cause of mortality and economic losses in shrimp farming. Although WSSV-induced mortality is virus dose dependent and WSSV infection does not necessarily lead to mortality, the relationships between virus-particle dose, infection and mortality have not been analysed quantitatively. Here, we explored WSSV dose-response by a combination of experiments, modelling and meta-analysis. We performed dose-response experiments in Penaeus vannamei postlarvae, recorded host mortality and detected WSSV infection. When we fitted infection models to these data, two models-differing in whether they incorporated heterogeneous host susceptibility to the virus or not-were supported for two independent experiments. To determine the generality of these results, we reanalysed published data sets and then performed a meta-analysis. We found that WSSV dose-response kinetics is indeed variable over experiments. We could not clearly identify which specific infection model has the most support by meta-analysis, but we argue that these results also are most concordant with a model incorporating varying levels of heterogeneous host susceptibility to WSSV. We have identified suitable models for analysing WSSV dose-response, which can elucidate the most basic virus-host interactions and help to avoid underestimating WSSV infection at low virus doses.}, }
@article {pmid30115327, year = {2018}, author = {Zimudzi, J and van der Waals, JE and Coutinho, TA and Cowan, DA and Valverde, A}, title = {Temporal shifts of fungal communities in the rhizosphere and on tubers in potato fields.}, journal = {Fungal biology}, volume = {122}, number = {9}, pages = {928-934}, doi = {10.1016/j.funbio.2018.05.008}, pmid = {30115327}, issn = {1878-6146}, abstract = {Soil fungal communities perform important ecological roles determining, at least in part, agricultural productivity. This study aimed at examining the fungal community dynamics in the potato rhizosphere across different development stages in two consecutive growing seasons (winter and summer). Microbial fingerprinting of rhizosphere soil samples collected at pre-planting, tuber initiation, flowering and at senescence was performed using ARISA in conjunction with Next Generation Sequencing (Illumina MiSeq). The epiphytic fungal communities on tubers at harvest were also investigated. Alpha-diversity was stable over time within and across the two seasons. In contrast, rhizospheric fungal community structure and composition were different between the two seasons and in the different plant growth stages within a given season, indicating the significance of the rhizosphere in shaping microbial communities. The phylum Ascomycota was dominant in the potato fungal rhizosphere, with Operational Taxonomic Units (OTUs) belonging to the genus Peyronellaea being the most abundant in all samples. Important fungal pathogens of potato, together with potential biological control agents and saprophytic species, were identified as indicator OTUs at different plant growth stages. These findings indicate that potato rhizosphere fungal communities are functionally diverse, which may contribute to soil health.}, }
@article {pmid30115122, year = {2018}, author = {Pérez-Jaramillo, JE and Carrión, VJ and de Hollander, M and Raaijmakers, JM}, title = {The wild side of plant microbiomes.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {143}, doi = {10.1186/s40168-018-0519-z}, pmid = {30115122}, issn = {2049-2618}, support = {568-2012-15517825//Departamento Administrativo de Ciencia, Tecnología e Innovación/ ; Back to the Roots//Stichting voor de Technische Wetenschappen/ ; Back to the Roots//Stichting voor de Technische Wetenschappen/ ; }, }
@article {pmid30110640, year = {2018}, author = {Kearney, SM and Gibbons, SM and Erdman, SE and Alm, EJ}, title = {Orthogonal Dietary Niche Enables Reversible Engraftment of a Gut Bacterial Commensal.}, journal = {Cell reports}, volume = {24}, number = {7}, pages = {1842-1851}, doi = {10.1016/j.celrep.2018.07.032}, pmid = {30110640}, issn = {2211-1247}, abstract = {Interest in manipulating the gut microbiota to treat disease has led to a need for understanding how organisms can establish themselves when introduced into a host with an intact microbial community. Here, we employ the concept of orthogonal niche engineering: a resource typically absent from the diet, seaweed, creates a customized niche for an introduced organism. In the short term, co-introduction of this resource at 1% in the diet along with an organism with exclusive access to this resource, Bacteroides plebeius DSM 17135, enables it to colonize at a median abundance of 1% and frequently up to 10 or more percent, both on pulsed and constant seaweed diets. In a two-month follow-up after the initial treatment period, B. plebeius stops responding to seaweed in mice initially on the constant seaweed diet, suggesting treatment regime will affect controllability. These results offer potential for diet-based intervention to introduce and control target organisms.}, }
@article {pmid30108568, year = {2018}, author = {van Kruistum, H and Bodelier, PLE and Ho, A and Meima-Franke, M and Veraart, AJ}, title = {Resistance and Recovery of Methane-Oxidizing Communities Depends on Stress Regime and History; A Microcosm Study.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1714}, doi = {10.3389/fmicb.2018.01714}, pmid = {30108568}, issn = {1664-302X}, abstract = {Although soil microbes are responsible for important ecosystem functions, and soils are under increasing environmental pressure, little is known about their resistance and resilience to multiple stressors. Here, we test resistance and recovery of soil methane-oxidizing communities to two different, repeated, perturbations: soil drying, ammonium addition and their combination. In replicated soil microcosms we measured methane oxidation before and after perturbations, while monitoring microbial abundance and community composition using quantitative PCR assays for the bacterial 16S rRNA and pmoA gene, and sequencing of the bacterial 16S rRNA gene. Although microbial community composition changed after soil drying, methane oxidation rates recovered, even after four desiccation events. Moreover, microcosms subjected to soil drying recovered significantly better from ammonium addition compared to microcosms not subjected to soil drying. Our results show the flexibility of microbial communities, even if abundances of dominant populations drop, ecosystem functions can recover. In addition, a history of stress may induce changes in community composition and functioning, which may in turn affect its future tolerance to different stressors.}, }
@article {pmid30106224, year = {2018}, author = {Otwell, AE and López García de Lomana, A and Gibbons, SM and Orellana, MV and Baliga, NS}, title = {Systems biology approaches towards predictive microbial ecology.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14378}, pmid = {30106224}, issn = {1462-2920}, support = {//Washington Research Foundation/ ; //Office of Science/ ; //U.S. Department of Energy/ ; //Lawrence Berkeley National Laboratory/ ; //National Science Foundation/ ; }, abstract = {Through complex interspecies interactions, microbial processes drive nutrient cycling and biogeochemistry. However, we still struggle to predict specifically which organisms, communities and biotic and abiotic processes are determining ecosystem function and how environmental changes will alter their roles and stability. While the tools to create such a predictive microbial ecology capability exist, cross-disciplinary integration of high-resolution field measurements, detailed laboratory studies and computation is essential. In this perspective, we emphasize the importance of pursuing a multiscale, systems approach to iteratively link ecological processes measured in the field to testable hypotheses that drive high-throughput laboratory experimentation. Mechanistic understanding of microbial processes gained in controlled lab systems will lead to the development of theory that can be tested back in the field. Using N2 O production as an example, we review the current status of field and laboratory research and layout a plausible path to the kind of integration that is needed to enable prediction of how N-cycling microbial communities will respond to environmental changes. We advocate for the development of realistic and predictive gene regulatory network models for environmental responses that extend from single-cell resolution to ecosystems, which is essential to understand how microbial communities involved in N2 O production and consumption will respond to future environmental conditions.}, }
@article {pmid30105506, year = {2018}, author = {Hotaling, S and Quackenbush, CR and Bennett-Ponsford, J and New, DD and Arias-Rodriguez, L and Tobler, M and Kelley, JL}, title = {Bacterial Diversity in Replicated Hydrogen Sulfide-Rich Streams.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1237-6}, pmid = {30105506}, issn = {1432-184X}, support = {IOS-1557860//National Science Foundation/ ; IOS-1557795//National Science Foundation/ ; W911NF-15-1-0175//United States Army Research Office/ ; }, abstract = {Extreme environments typically require costly adaptations for survival, an attribute that often translates to an elevated influence of habitat conditions on biotic communities. Microbes, primarily bacteria, are successful colonizers of extreme environments worldwide, yet in many instances, the interplay between harsh conditions, dispersal, and microbial biogeography remains unclear. This lack of clarity is particularly true for habitats where extreme temperature is not the overarching stressor, highlighting a need for studies that focus on the role other primary stressors (e.g., toxicants) play in shaping biogeographic patterns. In this study, we leveraged a naturally paired stream system in southern Mexico to explore how elevated hydrogen sulfide (H2S) influences microbial diversity. We sequenced a portion of the 16S rRNA gene using bacterial primers for water sampled from three geographically proximate pairings of streams with high (> 20 μM) or low (~ 0 μM) H2S concentrations. After exploring bacterial diversity within and among sites, we compared our results to a previous study of macroinvertebrates and fish for the same sites. By spanning multiple organismal groups, we were able to illuminate how H2S may differentially affect biodiversity. The presence of elevated H2S had no effect on overall bacterial diversity (p = 0.21), a large effect on community composition (25.8% of variation explained, p < 0.0001), and variable influence depending upon the group-whether fish, macroinvertebrates, or bacteria-being considered. For bacterial diversity, we recovered nine abundant operational taxonomic units (OTUs) that comprised a core H2S-rich stream microbiome in the region. Many H2S-associated OTUs were members of the Epsilonproteobacteria and Gammaproteobacteria, which both have been implicated in endosymbiotic relationships between sulfur-oxidizing bacteria and eukaryotes, suggesting the potential for symbioses that remain to be discovered in these habitats.}, }
@article {pmid30105505, year = {2018}, author = {Castelli, M and Serra, V and Senra, MVX and Basuri, CK and Soares, CAG and Fokin, SI and Modeo, L and Petroni, G}, title = {The Hidden World of Rickettsiales Symbionts: &quot;Candidatus Spectririckettsia obscura,&quot; a Novel Bacterium Found in Brazilian and Indian Paramecium caudatum.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1243-8}, pmid = {30105505}, issn = {1432-184X}, support = {247658//FP7 People: Marie-Curie Actions/ ; PRA_2016_58//Università di Pisa/ ; }, abstract = {Symbioses between bacteria and eukaryotes are widespread and may have significant impact on the evolutionary history of symbiotic partners. The order Rickettsiales is a lineage of intracellular Alphaproteobacteria characterized by an obligate association with a wide range of eukaryotic hosts, including several unicellular organisms, such as ciliates and amoebas. In this work, we characterized the Rickettsiales symbionts associated with two different genotypes of the freshwater ciliate Paramecium caudatum originated from freshwater environments in distant geographical areas. Phylogenetic analyses based on 16S rRNA gene showed that the two symbionts are closely related to each other (99.4% identity), belong to the family Rickettsiaceae, but are far-related with respect to previously characterized Rickettsiales. Consequently, they were assigned to a new species of a novel genus, namely &quot;Candidatus Spectririckettsia obscura.&quot; Screening on a database of short reads from 16S rRNA gene amplicon-based profiling studies confirmed that bacterial sequences related to the new symbiont are preferentially retrieved from freshwater environments, apparently with extremely scarce occurrence (< 0.1% positive samples). The present work provides new information on the still under-explored biodiversity of Rickettsiales, in particular those associated to ciliate host cells.}, }
@article {pmid30105504, year = {2018}, author = {Albright, MBN and Timalsina, B and Martiny, JBH and Dunbar, J}, title = {Comparative Genomics of Nitrogen Cycling Pathways in Bacteria and Archaea.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1239-4}, pmid = {30105504}, issn = {1432-184X}, support = {F260LANL2018//U.S. Department of Energy, Office of Science, Biological and Environmental Research Division/ ; Graduate Student Research (SCGSR) Fellowship//U.S. Department of Energy, Office of Science/ ; }, abstract = {Despite the explosion of metagenomic sequencing data, using -omics data to predict environmental biogeochemistry remains a challenge. One or a few genes (referred to as marker genes) in a metabolic pathway of interest in meta-omic data are typically used to represent the prevalence of a biogeochemical reaction. This approach often fails to demonstrate a consistent relationship between gene abundance and an ecosystem process rate. One reason this may occur is if a marker gene is not a good representative of a complete pathway. Here, we map the presence of 11 nitrogen (N)-cycling pathways in over 6000 complete bacterial and archaeal genomes using the Integrated Microbial Genomes database. Incomplete N-cycling pathways occurred in 39% of surveyed archaeal and bacterial species revealing a weakness in current marker-gene analyses. Furthermore, we found that most organisms have limited ability to utilize inorganic N in multiple oxidation states. This suggests that inter-organism exchange of inorganic N compounds is common, highlighting the importance of both community composition and spatial structure in determining the extent of recycling versus loss in an ecosystem.}, }
@article {pmid30105011, year = {2018}, author = {Doster, E and Rovira, P and Noyes, NR and Burgess, BA and Yang, X and Weinroth, MD and Lakin, SM and Dean, CJ and Linke, L and Magnuson, R and Jones, KI and Boucher, C and Ruiz, J and Belk, KE and Morley, PS}, title = {Investigating Effects of Tulathromycin Metaphylaxis on the Fecal Resistome and Microbiome of Commercial Feedlot Cattle Early in the Feeding Period.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1715}, doi = {10.3389/fmicb.2018.01715}, pmid = {30105011}, issn = {1664-302X}, abstract = {The objective was to examine effects of treating commercial beef feedlot cattle with therapeutic doses of tulathromycin, a macrolide antimicrobial drug, on changes in the fecal resistome and microbiome using shotgun metagenomic sequencing. Two pens of cattle were used, with all cattle in one pen receiving metaphylaxis treatment (800 mg subcutaneous tulathromycin) at arrival to the feedlot, and all cattle in the other pen remaining unexposed to parenteral antibiotics throughout the study period. Fecal samples were collected from 15 selected cattle in each group just prior to treatment (Day 1), and again 11 days later (Day 11). Shotgun sequencing was performed on isolated metagenomic DNA, and reads were aligned to a resistance and a taxonomic database to identify alignments to antimicrobial resistance (AMR) gene accessions and microbiome content. Overall, we identified AMR genes accessions encompassing 9 classes of AMR drugs and encoding 24 unique AMR mechanisms. Statistical analysis was used to identify differences in the resistome and microbiome between the untreated and treated groups at both timepoints, as well as over time. Based on composition and ordination analyses, the resistome and microbiome were not significantly different between the two groups on Day 1 or on Day 11. However, both the resistome and microbiome changed significantly between these two sampling dates. These results indicate that the transition into the feedlot-and associated changes in diet, geography, conspecific exposure, and environment-may exert a greater influence over the fecal resistome and microbiome of feedlot cattle than common metaphylactic antimicrobial drug treatment.}, }
@article {pmid30103819, year = {2018}, author = {Lourenço, KS and Suleiman, AKA and Pijl, A and van Veen, JA and Cantarella, H and Kuramae, EE}, title = {Resilience of the resident soil microbiome to organic and inorganic amendment disturbances and to temporary bacterial invasion.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {142}, doi = {10.1186/s40168-018-0525-1}, pmid = {30103819}, issn = {2049-2618}, support = {729.004.003//NWO/ ; 2013/50365-5//FAPESP/ ; 2014/24141-5, 2013/12716-0//FAPESP/ ; }, abstract = {BACKGROUND: Vinasse, a by-product of sugarcane ethanol production, is recycled by sugarcane plantations as a fertilizer due to its rich nutrient content. However, the impacts of the chemical and microbial composition of vinasse on soil microbiome dynamics are unknown. Here, we evaluate the recovery of the native soil microbiome after multiple disturbances caused by the application of organic vinasse residue, inorganic nitrogen, or a combination of both during the sugarcane crop-growing season (389 days). Additionally, we evaluated the resistance of the resident soil microbial community to the vinasse microbiome.<br><br>RESULTS: Vinasse applied alone or 30 days prior to N resulted in similar changes in the soil microbial community. Furthermore, the impact of the application of vinasse together with N fertilizer on the soil microbial community differed from that of N fertilizer alone. Organic vinasse is a source of microbes, nutrients, and organic matter, and the combination of these factors drove the changes in the resident soil microbial community. However, these changes were restricted to a short period of time due to the capacity of the soil community to recover. The invasive bacteria present in the vinasse microbiome were unable to survive in the soil conditions and disappeared after 31 days, with the exception of the Acetobacteraceae (native in the soil) and Lactobacillaceae families.<br><br>CONCLUSION: Our analysis showed that the resident soil microbial community was not resistant to vinasse and inorganic N application but was highly resilient.}, }
@article {pmid30101801, year = {2018}, author = {Muys, M and Coppens, J and Boon, N and Vlaeminck, SE}, title = {Photosynthetic oxygenation for urine nitrification.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {78}, number = {1-2}, pages = {183-194}, doi = {10.2166/wst.2018.200}, pmid = {30101801}, issn = {0273-1223}, abstract = {Human urine accounts for only a fraction of the sewage volume, but it contains the majority of valuable nutrient load in wastewater. In this study, synthetic urine was nitrified in a closed photo-bioreactor through photosynthetic oxygenation by means of a consortium of microalgae and nitrifying bacteria. In situ production of oxygen by photosynthetic organisms has the potential to reduce the energy costs linked to conventional aeration. This energy-efficient strategy results in stable urine for further nutrient recovery, while part of the nutrients are biologically recovered in the form of valuable biomass. In this study, urine was nitrified for the first time without conventional aeration at a maximum photosynthetic oxygenation rate of 160 mg O2 gVSS-1 d-1 (VSS: volatile suspended solids). A maximum volumetric nitrification rate of 67 mg N L-1 d-1 was achieved on 12% diluted synthetic urine. Chemical oxygen demand (COD) removal efficiencies were situated between 44% and 83% at a removal rate of 24 mg COD gVSS-1 d-1. After 180 days, microscopic observations revealed that Scenedesmus sp. was the dominant microalga. Overall, photosynthetic oxygenation for urine nitrification is promising as a highly electricity efficient approach for further nutrient recovery.}, }
@article {pmid30098679, year = {2018}, author = {Kroon, SJ and Ravel, J and Huston, WM}, title = {Cervicovaginal microbiota, women's health, and reproductive outcomes.}, journal = {Fertility and sterility}, volume = {110}, number = {3}, pages = {327-336}, doi = {10.1016/j.fertnstert.2018.06.036}, pmid = {30098679}, issn = {1556-5653}, abstract = {The human microbiome project has shown a remarkable diversity of microbial ecology within the human body. The vaginal microbiota is unique in that in many women it is most often dominated by Lactobacillus species. However, in some women it lacks Lactobacillus spp. and is comprised of a wide array of strict and facultative anaerobes, a state that broadly correlates with increased risk for infection, disease, and poor reproductive and obstetric outcomes. Interestingly, the level of protection against infection can also vary by species and strains of Lactobacillus, and some species although dominant are not always optimal. This factors into the risk of contracting sexually transmitted infections and possibly influences the occurrence of resultant adverse reproductive outcomes such as tubal factor infertility. The composition and function of the vaginal microbiota appear to play an important role in pregnancy and fertility treatment outcomes and future research in this field will shed further translational mechanistic understanding onto the interplay of the vaginal microbiota with women's health and reproduction.}, }
@article {pmid30097682, year = {2018}, author = {Green, TJ and Siboni, N and King, WL and Labbate, M and Seymour, JR and Raftos, D}, title = {Simulated Marine Heat Wave Alters Abundance and Structure of Vibrio Populations Associated with the Pacific Oyster Resulting in a Mass Mortality Event.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1242-9}, pmid = {30097682}, issn = {1432-184X}, support = {9201300681//Macquarie University/ ; FT130100218//Australian Research Council/ ; LP160101785//Australian Research Council/ ; }, abstract = {Marine heat waves are predicted to become more frequent and intense due to anthropogenically induced climate change, which will impact global production of seafood. Links between rising seawater temperature and disease have been documented for many aquaculture species, including the Pacific oyster Crassostrea gigas. The oyster harbours a diverse microbial community that may act as a source of opportunistic pathogens during temperature stress. We rapidly raised the seawater temperature from 20 °C to 25 °C resulting in an oyster mortality rate of 77.4%. Under the same temperature conditions and with the addition of antibiotics, the mortality rate was only 4.3%, strongly indicating a role for bacteria in temperature-induced mortality. 16S rRNA amplicon sequencing revealed a change in the oyster microbiome when the temperature was increased to 25 °C, with a notable increase in the proportion of Vibrio sequences. This pattern was confirmed by qPCR, which revealed heat stress increased the abundance of Vibrio harveyi and Vibrio fortis by 324-fold and 10-fold, respectively. Our findings indicate that heat stress-induced mortality of C. gigas coincides with an increase in the abundance of putative bacterial pathogens in the oyster microbiome and highlights the negative consequences of marine heat waves on food production from aquaculture.}, }
@article {pmid30097447, year = {2018}, author = {Burns, AS and Padilla, CC and Pratte, ZA and Gilde, K and Regensburger, M and Hall, E and Dove, ADM and Stewart, FJ}, title = {Broad Phylogenetic Diversity Associated with Nitrogen Loss through Sulfur Oxidation in a Large Public Marine Aquarium.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {20}, pages = {}, doi = {10.1128/AEM.01250-18}, pmid = {30097447}, issn = {1098-5336}, abstract = {Denitrification by sulfur-oxidizing bacteria is an effective nitrate removal strategy in engineered aquatic systems. However, the community taxonomic and metabolic diversity of sulfur-driven denitrification (SDN) systems, as well as the relationship between nitrate removal and SDN community structure, remains underexplored. This is particularly true for SDN reactors applied to marine aquaria, despite the increasing use of this technology to supplement filtration. We applied 16S rRNA gene, metagenomic, and metatranscriptomic analyses to explore the microbial basis of SDN reactors operating on Georgia Aquarium's Ocean Voyager, the largest indoor closed-system seawater exhibit in the United States. The exhibit's two SDN systems vary in water retention time and nitrate removal efficiency. The systems also support significantly different microbial communities. These communities contain canonical SDN bacteria, including a strain related to Thiobacillus thioparus that dominates the system with the higher water retention time and nitrate removal but is effectively absent from the other system. Both systems contain a wide diversity of other microbes whose metagenome-assembled genomes contain genes of SDN metabolism. These include hundreds of strains of the epsilonproteobacterium Sulfurimonas, as well as gammaproteobacterial sulfur oxidizers of the Thiotrichales and Chromatiales, and a relative of Sedimenticolathiotaurini with complete denitrification potential. The SDN genes are transcribed and the taxonomic richness of the transcript pool varies markedly among the enzymatic steps, with some steps dominated by transcripts from noncanonical SDN taxa. These results indicate complex and variable SDN communities that may involve chemical dependencies among taxa as well as the potential for altering community structure to optimize nitrate removal.IMPORTANCE Engineered aquatic systems such as aquaria and aquaculture facilities have large societal value. Ensuring the health of animals in these systems requires understanding how microorganisms contribute to chemical cycling and waste removal. Focusing on the largest seawater aquarium in the United States, we explore the microbial communities in specialized reactors designed to remove excess nitrogen through the metabolic activity of sulfur-consuming microbes. We show that the diversity of microbes in these reactors is both high and highly variable, with distinct community types associated with significant differences in nitrogen removal rate. We also show that the genes encoding the metabolic steps of nitrogen removal are distributed broadly throughout community members, suggesting that the chemical transformations in this system are likely a result of microbes relying on other microbes. These results provide a framework for future studies exploring the contributions of different community members, both in waste removal and in structuring microbial biodiversity.}, }
@article {pmid30094615, year = {2018}, author = {Ren, F and Kovalchuk, A and Mukrimin, M and Liu, M and Zeng, Z and Ghimire, RP and Kivimäenpää, M and Holopainen, JK and Sun, H and Asiegbu, FO}, title = {Tissue Microbiome of Norway Spruce Affected by Heterobasidion-Induced Wood Decay.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1240-y}, pmid = {30094615}, issn = {1432-184X}, support = {276862//Academy of Finland/ ; 278424//Academy of Finland/ ; 165010015//Jiangsu Specially-Appointed Professor, China/ ; }, abstract = {Plants live in close association with microbial symbionts, which may affect the host fitness, productivity, and tolerance against biotic and abiotic stressors. The composition of plant microbial communities is influenced by many biotic and abiotic factors, but little is known about the effect of plant pathogens on the structure of these communities. In this study, we investigated the structure of bacterial communities associated with different tissues of asymptomatic and symptomatic (Heterobasidion-rotten) Norway spruce (Picea abies (L.) Karst.) trees. Our results demonstrated that each of the investigated anatomic tissues (root, bark, down stem, upper stem, and needles) harbored a unique bacterial assemblage. However, the health status of the host trees had little effect on the structure of bacterial communities, as the only significant differences among asymptomatic and symptomatic trees were found in the composition of the bacterial communities of needles. Proteobacteria was predominant in all anatomic regions with the highest abundance in needles (86.7%), whereas Actinobacteria showed an opposite trend, being more abundant in the woody tissues than in needles. Additionally, we performed profiling of terpenoid compounds present in spruce xylem and phloem. Total concentrations of monoterpenes and sesquiterpenes were considerably higher in asymptomatic trees. However, we found no significant correlations between terpenoid profiles of spruce trees and the composition of their bacterial communities. Our results provide an insight into the diversity of bacteria associated with Norway spruce tree tissues. At the same time, the health status and terpenoid content of host trees had a limited effect on the composition of bacterial communities in our survey.}, }
@article {pmid30093611, year = {2018}, author = {Liang, J and Zhou, Z and Huo, C and Shi, Z and Cole, JR and Huang, L and Konstantinidis, KT and Li, X and Liu, B and Luo, Z and Penton, CR and Schuur, EAG and Tiedje, JM and Wang, YP and Wu, L and Xia, J and Zhou, J and Luo, Y}, title = {More replenishment than priming loss of soil organic carbon with additional carbon input.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {3175}, doi = {10.1038/s41467-018-05667-7}, pmid = {30093611}, issn = {2041-1723}, support = {DE SC00114085//U.S. Department of Energy (DOE)/International ; DE SC0004601//U.S. Department of Energy (DOE)/International ; DE SC0010715//U.S. Department of Energy (DOE)/International ; OIA-1301789//National Science Foundation (NSF)/International ; }, abstract = {Increases in carbon (C) inputs to soil can replenish soil organic C (SOC) through various mechanisms. However, recent studies have suggested that the increased C input can also stimulate the decomposition of old SOC via priming. Whether the loss of old SOC by priming can override C replenishment has not been rigorously examined. Here we show, through data-model synthesis, that the magnitude of replenishment is greater than that of priming, resulting in a net increase in SOC by a mean of 32% of the added new C. The magnitude of the net increase in SOC is positively correlated with the nitrogen-to-C ratio of the added substrates. Additionally, model evaluation indicates that a two-pool interactive model is a parsimonious model to represent the SOC decomposition with priming and replenishment. Our findings suggest that increasing C input to soils likely promote SOC accumulation despite the enhanced decomposition of old C via priming.}, }
@article {pmid30092404, year = {2018}, author = {Lian, Y and Yan, C and Xu, H and Yang, J and Yu, Y and Zhou, J and Shi, Y and Ren, J and Ji, G and Wang, K}, title = {A Novel lncRNA, LINC00460, Affects Cell Proliferation and Apoptosis by Regulating KLF2 and CUL4A Expression in Colorectal Cancer.}, journal = {Molecular therapy. Nucleic acids}, volume = {12}, number = {}, pages = {684-697}, doi = {10.1016/j.omtn.2018.06.012}, pmid = {30092404}, issn = {2162-2531}, abstract = {Emerging evidence has proven that long noncoding RNAs (lncRNAs) play important roles in human colorectal cancer (CRC) biology, although few lncRNAs have been characterized in CRC. Therefore, the functional significance of lncRNAs in the malignant progression of CRC still needs to be further explored. In this study, through analyzing TCGA RNA sequencing data and other publicly available microarray data, we found a novel lncRNA, LINC00460, whose expression was significantly upregulated in CRC tissues compared to adjacent normal tissues. Consistently, real-time qPCR results also verified that LINC00460 was overexpressed in CRC tissues and cells. Furthermore, high LINC00460 expression levels in CRC specimens were correlated with larger tumor size, advanced tumor stage, lymph node metastasis and shorter overall survival. In vitro and in vivo assays of LINC00460 alterations revealed a complex integrated phenotype affecting cell growth and apoptosis. Mechanistically, LINC00460 repressed Krüppel-like factor 2 (KLF2) transcription by binding to enhancer of zeste homolog 2 (EZH2). LINC00460 also functioned as a molecular sponge for miR-149-5p, antagonizing its ability to repress cullin 4A (CUL4A) protein translation. Taken together, our findings support a model in which the LINC00460/EZH2/KLF2 and LINC00460/miR-149-5p/CUL4A crosstalk serve as critical effectors in CRC tumorigenesis and progression, suggesting new therapeutic directions in CRC.}, }
@article {pmid30088464, year = {2018}, author = {Gil-Pulido, B and Tarpey, E and Finnegan, W and Zhan, X and Dobson, AD and O'Leary, N}, title = {Dominance of the genus Polaromonas in the microbial ecology of an Intermittently Aerated Sequencing Batch Reactor (IASBR) treating dairy processing wastewater under varying aeration rates.}, journal = {The Journal of dairy research}, volume = {85}, number = {3}, pages = {388-390}, doi = {10.1017/S0022029918000572}, pmid = {30088464}, issn = {1469-7629}, mesh = {Comamonadaceae/classification/isolation &amp; purification/*physiology ; DNA, Bacterial/analysis ; *Dairy Products ; Food-Processing Industry/*methods ; Oxygen/*administration &amp; dosage ; Sewage/microbiology ; Waste Water/*microbiology ; Water Purification/*instrumentation/methods ; }, abstract = {In this Research Communication we investigate potential correlations between key bacterial groups and nutrient removal efficiency in an Intermittently Aerated Sequencing Batch Reactor (IASBR) treating synthetic dairy processing wastewater. Reactor aeration rates of 0·6 and 0·4 litre per minute (LPM) were applied to an 8 l laboratory scale system and the relative impacts on IASBR microbial community structure and orthophosphate (PO4-P) and ammonium (NH4-N) removal efficiencies compared. Aeration at 0·6 LPM over several sludge retention times (SRTs) resulted in approximately 92% removal efficiencies for both PO4-P and NH4-N. Biomass samples subjected to next-generation sequencing (NGS), 16S rRNA profiling revealed a concomitant enrichment of Polaromonas under 0·6 LPM conditions, up to ~50% relative abundance within the reactor biomass. The subsequent shift in reactor aeration to 0·4 LPM, over a period of 3 SRTs, resulted in markedly reduced nutrient removal efficiencies for PO4-P (50%) and NH4-N (45%). An 85·7% reduction in the genus level relative abundance of Polaromonas was observed under 0·4 LPM aeration conditions over the same period.}, }
@article {pmid30088023, year = {2018}, author = {Polano, C and Martini, M and Savian, F and Moruzzi, S and Ermacora, P and Firrao, G}, title = {Genome Sequence and Antifungal Activity of Two Niche-Sharing Pseudomonas protegens Related Strains Isolated from Hydroponics.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1238-5}, pmid = {30088023}, issn = {1432-184X}, support = {2370 - STAYFRESH//Ager - Agroalimentare e Ricerca/ ; }, abstract = {This work reports the comparison of the genome sequence and the ability to inhibit fungal growth of two Pseudomonas protegens related strains that were isolated from the same hydroponic culture of lamb's lettuce. The two strains were very similar in their core genome but one strain, Pf4, contained three gene clusters for the production of secondary metabolites, i.e., pyoluteorin (plt), pyrrolnitrin (prn), and rhizoxin (rzx), that were missing in the other strain, Pf11. The difference between the two strains was not due to simple insertion events, but to a relatively complex differentiation focused on the accessory genomes. In dual culture assays, both strains inhibited nearly all tested fungal strains, yet Pf4 exerted a significantly stronger fungal growth inhibition than Pf11. In addition to the differences in the secondary metabolite production associated genes abundance, the genome of Pf4 was more stable, smaller in size and with a lower number of transposons. The preservation of a dynamic equilibrium within natural populations of different strains comprised in the same species but differing in their secondary metabolite repertoire and in their genome stability may be functional to the adaptation to environmental changes.}, }
@article {pmid30087659, year = {2018}, author = {Trivedi, CB and Lau, GE and Grasby, SE and Templeton, AS and Spear, JR}, title = {Low-Temperature Sulfidic-Ice Microbial Communities, Borup Fiord Pass, Canadian High Arctic.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1622}, doi = {10.3389/fmicb.2018.01622}, pmid = {30087659}, issn = {1664-302X}, abstract = {A sulfur-dominated supraglacial spring system found at Borup Fiord Pass (BFP), Ellesmere Island, Nunavut, Canada, is a unique sulfur-on-ice system expressed along the toe of a glacier. BFP has an intermittent flowing, subsurface-derived, glacial spring that creates a large white-yellow icing (aufeis) that extends down-valley. Over field campaigns in 2014, 2016, and 2017, numerous samples were collected and analyzed for both microbial community composition and aqueous geochemistry. Samples were collected from multiple site types: spring discharge fluid, aufeis (spring-derived ice), melt pools with sedimented cryoconite material, and mineral precipitate scrapings, to probe how microbial communities differed between site types in a dynamic freeze/thaw sulfur-rich system. Dissolved sulfate varied between 0.07 and 11.6 mM and was correlated with chloride concentrations, where the fluids were saltiest among spring fluids. The highest sulfate samples exhibited high dissolved sulfide values between 0.22 and 2.25 mM. 16S rRNA gene sequencing from melt pool and aufeis samples from the 2014 campaign were highly abundant in operational taxonomic units (OTUs) closely related to sulfur-oxidizing microorganisms (SOM; Sulfurimonas, Sulfurovum, and Sulfuricurvum). Subsequent sampling 2 weeks later had fewer SOMs and showed an increased abundance of the genus Flavobacterium. Desulfocapsa, an organism that specializes in the disproportionation of inorganic sulfur compounds was also found. Samples from 2016 and 2017 revealed that microorganisms present were highly similar in community composition to 2014 samples, primarily echoed by the continued presence of Flavobacterium sp. Results suggest that while there may be acute events where sulfur cycling organisms dominate, a basal community structure appears to dominate over time and site type. These results further enhance our knowledge of low-temperature sulfur systems on Earth, and help to guide the search for potential life on extraterrestrial worlds, such as Europa, where similar low-temperature sulfur-rich conditions may exist.}, }
@article {pmid30087358, year = {2018}, author = {Chaib De Mares, M and Jiménez, DJ and Palladino, G and Gutleben, J and Lebrun, LA and Muller, EEL and Wilmes, P and Sipkema, D and van Elsas, JD}, title = {Expressed protein profile of a Tectomicrobium and other microbial symbionts in the marine sponge Aplysina aerophoba as evidenced by metaproteomics.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {11795}, doi = {10.1038/s41598-018-30134-0}, pmid = {30087358}, issn = {2045-2322}, support = {607786//EC | Seventh Framework Programme (European Union Seventh Framework Programme)/ ; 607786//EC | Seventh Framework Programme (European Union Seventh Framework Programme)/ ; 607786//EC | Seventh Framework Programme (European Union Seventh Framework Programme)/ ; 607786//EC | Seventh Framework Programme (European Union Seventh Framework Programme)/ ; }, abstract = {Aplysina aerophoba is an emerging model marine sponge, with a well-characterized microbial community in terms of diversity and structure. However, little is known about the expressed functional capabilities of its associated microbes. Here, we present the first metaproteomics-based study of the microbiome of A. aerophoba. We found that transport and degradation of halogenated and chloroaromatic compounds are common active processes in the sponge microbiomes. Our data further reveal that the highest number of proteins were affiliated to a sponge-associated Tectomicrobium, presumably from the family Entotheonellaceae, as well as to the well-known symbiont &quot;Candidatus Synechococcus spongiarium&quot;, suggesting a high metabolic activity of these two microorganisms in situ. Evidence for nitric oxide (NO) conversion to nitrous oxide was consistently observed for Tectomicrobia across replicates, by production of the NorQ protein. Moreover, we found a potential energy-yielding pathway through CO oxidation by putative Chloroflexi bacteria. Finally, we observed expression of enzymes that may be involved in the transformation of chitin, glycoproteins, glycolipids and glucans into smaller molecules, consistent with glycosyl hydrolases predicted from analyses of the genomes of Poribacteria sponge symbionts. Thus, this study provides crucial links between expressed proteins and specific members of the A. aerophoba microbiome.}, }
@article {pmid30086814, year = {2018}, author = {Yurchenko, V and Lukeš, J}, title = {Parasites and their (endo)symbiotic microbes.}, journal = {Parasitology}, volume = {145}, number = {10}, pages = {1261-1264}, doi = {10.1017/S0031182018001257}, pmid = {30086814}, issn = {1469-8161}, abstract = {Thanks to modern molecular biology methods, our understanding of the impact of (endo)symbiotic bacteria on parasitic protists and helminths is growing fast. In this issue, 9 papers have been brought together that describe various facets of the relationships between these microorganisms, reveal their range and high frequency, as well as their capacity to create novel biological complexity. Comparative analyses of these host-endosymbiont interactions indicate that there may be no discrete types of relationships but rather a continuum ranging from a dispensable endosymbiont minimally integrated within the host cell to organelles, such as mitochondria and plastids that evolved into an indispensable, deeply integrated components of the cell. We hope that this series of studies on parasites and (endo)symbiotic bacteria will increase awareness about these relationships and their representation in microbial ecology models.}, }
@article {pmid30084932, year = {2018}, author = {Cantos-Parra, E and Ramió-Pujol, S and Colprim, J and Puig, S and Bañeras, L}, title = {Specific detection of &quot;Clostridium autoethanogenum&quot;, Clostridium ljungdahlii and Clostridium carboxidivorans in complex bioreactor samples.}, journal = {FEMS microbiology letters}, volume = {365}, number = {18}, pages = {}, doi = {10.1093/femsle/fny191}, pmid = {30084932}, issn = {1574-6968}, abstract = {The high genetic similarity between some carboxydotrophic bacteria does not allow for the use of common sequencing techniques targeting the 16S rRNA gene for species identification. 16S rRNA sequencing fails to discriminate among Clostridium ljungdahlii and 'Clostridium autoethanogenum', despite this two species exhibit significant differences in CO2 assimilation and alcohol production. In this work we designed PCR primers targeting for the DNA gyrase subunit A (gyrA) and a putative formate/nitrite transporter (fnt) to specifically detect the presence of 'C. autoethanogenum', C. ljungdahlii or Clostridium carboxidivorans. We could confirm the simultaneous presence of C. ljungdahlii and 'C. autoethanogenum' in different bioreactors, and a preference of the latter for high CO2 content.}, }
@article {pmid30083828, year = {2018}, author = {Bai, M and Sen, B and Wang, Q and Xie, Y and He, Y and Wang, G}, title = {Molecular Detection and Spatiotemporal Characterization of Labyrinthulomycete Protist Diversity in the Coastal Waters Along the Pearl River Delta.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1235-8}, pmid = {30083828}, issn = {1432-184X}, support = {31670044//National Natural Science Foundation of China/ ; 91751115//National Natural Science Foundation of China/ ; 2017YFC1404500//National Key R&amp;D program of China/ ; }, abstract = {The heterotrophic labyrinthulomycete protists have long been known to play an important role in the nutrient cycling of coastal seawater. Yet, their spatiotemporal abundance and diversity in polluted coastal waters remain poorly discussed, due in part to the paucity of a rapid detection method. To this end, we developed a qPCR detection method based on a newly designed primer pair targeting their 18S rRNA gene. Using this method, we studied the population dynamics of labyrinthulomycete protists in nutrient-rich (Shenzhen Bay) and low-nutrient (Daya) coastal habitats along the Pearl River Delta. We found a significantly (P < 0.05) higher abundance of Labyrinthulomycetes in the Shenzhen bay (average 3455 gene copies mL-1) than that in Daya Bay (average 378 gene copies mL-1). Their abundance gradient positively correlated (P < 0.05) with the levels of inorganic nitrogen and phosphates. Further characterization of the molecular diversity of these protists in Shenzhen Bay using different primer sets revealed the presence of several genera besides a large number of unclassified OTUs. Regardless of the primer biases, our results show significant (P < 0.05) spatiotemporal changes in the molecular abundance and diversity of these heterotrophic protists. Overall, this study provides a rapid molecular detection tool for Labyrinthulomycetes and expands our current understanding of their dynamics controlled by physicochemical gradients in coastal waters.}, }
@article {pmid30083827, year = {2018}, author = {Weinisch, L and Kirchner, I and Grimm, M and Kühner, S and Pierik, AJ and Rosselló-Móra, R and Filker, S}, title = {Correction to: Glycine Betaine and Ectoine Are the Major Compatible Solutes Used by Four Different Halophilic Heterotrophic Ciliates.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1241-x}, pmid = {30083827}, issn = {1432-184X}, abstract = {The original version of this article unfortunately contained mistakes in the author affiliation, the references given in two tables and in a figure legend.}, }
@article {pmid30083145, year = {2018}, author = {Costa, OYA and Raaijmakers, JM and Kuramae, EE}, title = {Microbial Extracellular Polymeric Substances: Ecological Function and Impact on Soil Aggregation.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1636}, doi = {10.3389/fmicb.2018.01636}, pmid = {30083145}, issn = {1664-302X}, abstract = {A wide range of microorganisms produce extracellular polymeric substances (EPS), highly hydrated polymers that are mainly composed of polysaccharides, proteins, and DNA. EPS are fundamental for microbial life and provide an ideal environment for chemical reactions, nutrient entrapment, and protection against environmental stresses such as salinity and drought. Microbial EPS can enhance the aggregation of soil particles and benefit plants by maintaining the moisture of the environment and trapping nutrients. In addition, EPS have unique characteristics, such as biocompatibility, gelling, and thickening capabilities, with industrial applications. However, despite decades of research on the industrial potential of EPS, only a few polymers are widely used in different areas, especially in agriculture. This review provides an overview of current knowledge on the ecological functions of microbial EPSs and their application in agricultural soils to improve soil particle aggregation, an important factor for soil structure, health, and fertility.}, }
@article {pmid30083144, year = {2018}, author = {Kroeger, ME and Delmont, TO and Eren, AM and Meyer, KM and Guo, J and Khan, K and Rodrigues, JLM and Bohannan, BJM and Tringe, SG and Borges, CD and Tiedje, JM and Tsai, SM and Nüsslein, K}, title = {New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1635}, doi = {10.3389/fmicb.2018.01635}, pmid = {30083144}, issn = {1664-302X}, support = {P30 DK042086/DK/NIDDK NIH HHS/United States ; }, abstract = {Deforestation in the Brazilian Amazon occurs at an alarming rate, which has broad effects on global greenhouse gas emissions, carbon storage, and biogeochemical cycles. In this study, soil metagenomes and metagenome-assembled genomes (MAGs) were analyzed for alterations to microbial community composition, functional groups, and putative physiology as it related to land-use change and tropical soil. A total of 28 MAGs were assembled encompassing 10 phyla, including both dominant and rare biosphere lineages. Amazon Acidobacteria subdivision 3, Melainabacteria, Microgenomates, and Parcubacteria were found exclusively in pasture soil samples, while Candidatus Rokubacteria was predominant in the adjacent rainforest soil. These shifts in relative abundance between land-use types were supported by the different putative physiologies and life strategies employed by the taxa. This research provides unique biological insights into candidate phyla in tropical soil and how deforestation may impact the carbon cycle and affect climate change.}, }
@article {pmid30081136, year = {2018}, author = {Losasso, C and Di Cesare, A and Mastrorilli, E and Patuzzi, I and Cibin, V and Eckert, EM and Fontaneto, D and Vanzo, A and Ricci, A and Corno, G}, title = {Assessing antimicrobial resistance gene load in vegan, vegetarian and omnivore human gut microbiota.}, journal = {International journal of antimicrobial agents}, volume = {52}, number = {5}, pages = {702-705}, doi = {10.1016/j.ijantimicag.2018.07.023}, pmid = {30081136}, issn = {1872-7913}, abstract = {Massive antimicrobial use in animal farming is considered as the greatest contributor to the presence of antimicrobial-resistant bacteria (ARB) in food of animal origin. Nevertheless, sewage from treated animals may impact on vegetables grown on fertilised fields, but it is largely unknown whether and to what extent ARB are transferred to vegetables and the human gut. It could be hypothesised that food of animal and vegetal origin have a different role in ARB transfer to the human gut and that different diets could be characterised by different antimicrobial resistance gene (ARG) loads. This study included three groups comprising vegans (n = 26), vegetarians (n = 32) and omnivores (n = 43). Metadata regarding food consumption and anthropometric parameters were collected. Gut microbial communities were investigated by 16S rDNA analysis. Four ARGs (sul2, tetA, blaTEM and strB) were quantified by qPCR. The results showed a lower total load of investigated ARGs in vegan diet (pairwise comparison adjusted results: omnivorous-vegan, P = 0.0119; omnivorous-vegetarian, P = 0.7416; and vegan-vegetarian, P = 0.0119). No significant differences in abundance of each gene separately were found between the three groups. Neither the amount of animal protein nor the occurrence of ARGs was significant in explaining differences in the gut microbial community of individuals, and a large proportion of the differences between community composition (PERMANOVA, 46.87%) was not explained by the analysed variables. The results support the role of omnivorous and vegetarian diets in accumulating ARGs, suggesting a possible role for animal-derived food consumption.}, }
@article {pmid30078567, year = {2018}, author = {Cordero, RJB and Robert, V and Cardinali, G and Arinze, ES and Thon, SM and Casadevall, A}, title = {Impact of Yeast Pigmentation on Heat Capture and Latitudinal Distribution.}, journal = {Current biology : CB}, volume = {28}, number = {16}, pages = {2657-2664.e3}, doi = {10.1016/j.cub.2018.06.034}, pmid = {30078567}, issn = {1879-0445}, support = {R01 AI052733/AI/NIAID NIH HHS/United States ; }, abstract = {Pigmentation is a fundamental characteristic of living organisms that is used to absorb radiation energy and to regulate temperature. Since darker pigments absorb more radiation than lighter ones, they stream more heat, which can provide an adaptive advantage at higher latitudes and a disadvantage near the Tropics, because of the risk of overheating. This intuitive process of color-mediated thermoregulation, also known as the theory of thermal melanism (TTM), has been only tested in ectothermic animal models [1-8]. Here, we report an association between yeast pigmentation and their latitude of isolation, with dark-pigmented isolates being more frequent away from the Tropics. To measure the impact of microbial pigmentation in energy capture from radiation, we generated 20 pigmented variants of Cryptococcus neoformans and Candida spp. Infrared thermography revealed that dark-pigmented yeasts heated up faster and reached higher temperatures (up to 2-fold) than lighter ones following irradiation. Melanin-pigmented C. neoformans exhibited a growth advantage relative to non-melanized yeasts when incubated under the light at 4°C but increased thermal susceptibility at 25°C ambient temperatures. Our results extend the TTM to microbiology and suggest pigmentation as an ancient adaptation mechanism for gaining thermal energy from radiation. The contribution of microbial pigmentation in heat absorption is relevant to microbial ecology and for estimating global temperatures. The color variations available in yeasts provide new opportunities in chromatology to quantify radiative heat transfer and validate biophysical models of heat flow [9] that are not possible with plants or animals.}, }
@article {pmid30077912, year = {2018}, author = {Seuntjens, D and Carvajal-Arroyo, JM and Ruopp, M and Bunse, P and De Mulder, CP and Lochmatter, S and Agrawal, S and Boon, N and Lackner, S and Vlaeminck, SE}, title = {High-resolution mapping and modeling of anammox recovery from recurrent oxygen exposure.}, journal = {Water research}, volume = {144}, number = {}, pages = {522-531}, doi = {10.1016/j.watres.2018.07.024}, pmid = {30077912}, issn = {1879-2448}, abstract = {Oxygen inhibits anammox, a bioconversion executed by anoxic ammonium oxidizing bacteria (AnAOB). Nonetheless, oxygen is mostly found in the proximity of AnAOB in nitrogen removal applications, being a substrate for nitritation. The experiments performed to date were mostly limited to batch activity tests where AnAOB activity is estimated during oxygen exposure. However, little attention has been paid to the recovery and reversibility of activity following aerobic conditions, of direct relevance for bioreactor operation. In this work, anoxic and autotrophic reactor cultivation at 20 °C yielded an enriched microbial community in AnAOB, consisting for 75% of a member of the genus Brocadia. High-resolution kinetic data were obtained with online ammonium measurements and further processed with a newly developed Python data pipeline. The experimentally obtained AnAOB response showed complete inhibition until micro-aerobic conditions were reached again (<0.02 mg O2 L-1). After oxygen inhibition, AnAOB recovered gradually, with recovery times of 5-37 h to reach a steady-state activity, dependent on the perceived inhibition. The recovery immediately after inhibition was lowest when exposed to higher oxygen concentrations (range: 0.5-8 mg O2 L-1) with long contact times (range: 9-24 h). The experimental data did not fit well with a conventional 'instant recovery' Monod-type inhibition model. Yet, the fit greatly improved by incorporating a dynamic growth rate formula accurately describing gradual activity recovery. With the upgraded model, long-term kinetic simulations for partial nitritation/anammox (PN/A) with intermittent aeration showed a decrease in growth rate compared to the instant recovery mode. These results indicate that recovery of AnAOB after oxygen exposure was previously overlooked. It is recommended to account for this effect in the intensification of partial nitritation/anammox.}, }
@article {pmid30077104, year = {2018}, author = {Zhou, L and Xu, X and Xia, S}, title = {Effects of sulfate on simultaneous nitrate and selenate removal in a hydrogen-based membrane biofilm reactor for groundwater treatment: Performance and biofilm microbial ecology.}, journal = {Chemosphere}, volume = {211}, number = {}, pages = {254-260}, doi = {10.1016/j.chemosphere.2018.07.092}, pmid = {30077104}, issn = {1879-1298}, mesh = {Biofilms/*drug effects ; Bioreactors/*microbiology ; Groundwater/*chemistry ; Hydrogen/*chemistry ; Nitrates/*chemistry ; Selenic Acid/*chemistry ; Sulfates/*chemistry ; }, abstract = {Effects of sulfate on simultaneous nitrate and selenate removal in a hydrogen-based membrane biofilm reactor (MBfR) for groundwater treatment was identified with performance and biofilm microbial ecology. In whole operation, MBfR had almost 100% removal of nitration even with 50 mg mL-1 sulfate. Moreover, selenate degradation increased from 95% to approximate 100% with sulfate addition, indicating that sulfate had no obvious effects on nitrate degradation, and even partly promoted selenate removal. Short-term sulfate effect experiment further showed that Gibbs free energy of reduction (majority) and abiotic sulfide oxidation (especially between sulfate and selenate) contributed to degradable performance with sulfate. Microbial ecology showed that high percentage of Hydrogenophaga (≥75%) was one of the contributors for the stable and efficient nitrate degradation. Chemoheterotrophy (ratio>0.3) and dark hydrogen oxidation (ratio>0.3) were the majority of functional profile for biofilm in MBfR, and sulfate led to profiles of sulfate respiration and respiration of sulfur compounds in biofilm. Additionally, no special bacteria for selenate degradation was identified in biofilm microbial ecology, and selenate degradation was relied on Hydrogenophaga (75% of ecology percentage with sulfate addition) and Desulfovibrionaceae (4% of ecology percentage with sulfate addition). But with overloading sulfate, Desulfovibrionaceae was prior to sulfate degradation for energy supply and thus inhibited selenate removal.}, }
@article {pmid30076592, year = {2018}, author = {Nottingham, AT and Fierer, N and Turner, BL and Whitaker, J and Ostle, NJ and McNamara, NP and Bardgett, RD and Leff, JW and Salinas, N and Silman, MR and Kruuk, LEB and Meir, P}, title = {Microbes follow Humboldt: temperature drives plant and soil microbial diversity patterns from the Amazon to the Andes.}, journal = {Ecology}, volume = {99}, number = {11}, pages = {2455-2466}, doi = {10.1002/ecy.2482}, pmid = {30076592}, issn = {0012-9658}, support = {NE/G018278/1//UK Natural Environment Research Council (NERC)/ ; NE/N006852/1//UK Natural Environment Research Council (NERC)/ ; DP170104091//Australian Research Council (ARC)/ ; FT1110100453//Australian Research Council (ARC)/ ; FP7-2012-329360//European Union Marie-Curie Fellowship/ ; }, abstract = {More than 200 years ago, Alexander von Humboldt reported that tropical plant species richness decreased with increasing elevation and decreasing temperature. Surprisingly, coordinated patterns in plant, bacterial, and fungal diversity on tropical mountains have not yet been observed, despite the central role of soil microorganisms in terrestrial biogeochemistry and ecology. We studied an Andean transect traversing 3.5 km in elevation to test whether the species diversity and composition of tropical forest plants, soil bacteria, and fungi follow similar biogeographical patterns with shared environmental drivers. We found coordinated changes with elevation in all three groups: species richness declined as elevation increased, and the compositional dissimilarity among communities increased with increased separation in elevation, although changes in plant diversity were larger than in bacteria and fungi. Temperature was the dominant driver of these diversity gradients, with weak influences of edaphic properties, including soil pH. The gradients in microbial diversity were strongly correlated with the activities of enzymes involved in organic matter cycling, and were accompanied by a transition in microbial traits towards slower-growing, oligotrophic taxa at higher elevations. We provide the first evidence of coordinated temperature-driven patterns in the diversity and distribution of three major biotic groups in tropical ecosystems: soil bacteria, fungi, and plants. These findings suggest that interrelated and fundamental patterns of plant and microbial communities with shared environmental drivers occur across landscape scales. These patterns are revealed where soil pH is relatively constant, and have implications for tropical forest communities under future climate change.}, }
@article {pmid30070653, year = {2018}, author = {Winkelmann, T and Smalla, K and Amelung, W and Baab, G and Grunewaldt-Stöcker, G and Kanfra, X and Meyhöfer, R and Reim, S and Schmitz, M and Vetterlein, D and Wrede, A and Zühlke, S and Grunewaldt, J and Weiß, S and Schloter, M}, title = {Apple Replant Disease: Causes and Mitigation Strategies.}, journal = {Current issues in molecular biology}, volume = {30}, number = {}, pages = {89-106}, doi = {10.21775/cimb.030.089}, pmid = {30070653}, issn = {1467-3045}, abstract = {After replanting apple (Malus domestica Borkh.) on the same site severe growth suppressions, and a decline in yield and fruit quality are observed in all apple producing areas worldwide. The causes of this complex phenomenon, called apple replant disease (ARD), are only poorly understood up to now which is in part due to inconsistencies in terms and methodologies. Therefore we suggest the following definition for ARD: ARD describes a harmfully disturbed physiological and morphological reaction of apple plants to soils that faced alterations in their (micro-) biome due to the previous apple cultures. The underlying interactions likely have multiple causes that extend beyond common analytical tools in microbial ecology. They are influenced by soil properties, faunal vectors, and trophic cascades, with genotype-specific effects on plant secondary metabolism, particularly phytoalexin biosynthesis. Yet, emerging tools allow to unravel the soil and rhizosphere (micro-) biome, to characterize alterations of habitat quality, and to decipher the plant reactions. Thereby, deep insights into the reactions taking place at the root rhizosphere interface will be gained. Counteractions are suggested, taking into account that culture management should emphasize on improving soil microbial and faunal diversity as well as habitat quality rather than focus on soil disinfection.}, }
@article {pmid30069710, year = {2018}, author = {McFrederick, QS and Rehan, SM}, title = {Wild Bee Pollen Usage and Microbial Communities Co-vary Across Landscapes.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1232-y}, pmid = {30069710}, issn = {1432-184X}, support = {CA-R-ENT-5109-H//National Institute of Food and Agriculture/ ; NC1173//National Institute of Food and Agriculture/ ; 1638728//Directorate for Biological Sciences/ ; 1456296//Directorate for Biological Sciences/ ; 9659-15//National Geographic Society/ ; }, abstract = {Bees forage for pollen and nectar at flowers but simultaneously acquire pathogenic, commensal, and likely beneficial microbes from these same flowers. Characterizing pollen usage of wild bees is therefore crucial to their conservation yet remains a challenging task. To understand pollen usage across landscapes and how this affects microbial communities found in the pollen provisions collected from flowers, we studied the generalist small carpenter bee Ceratina australensis. We collected C. australensis nests from three different climatic zones across eastern and southern Australia. To characterize the plant, fungal, and bacterial composition of these pollen provisions, we used a metabarcoding and next-generation sequencing approach. We found that the species richness of plant types, fungi, and bacteria was highest in a subtropical zone compared to a temperate or a grassland zone. The composition of these communities also differentiated by zone, particularly in pollen composition and fungal communities. Moreover, pollen composition strongly correlated with fungal community composition, suggesting that variation in pollen usage across landscapes results in variation in microbial communities. While how these pollen usage and microbial community patterns affect bee health merits additional work, these data further our understanding of how flowering plant community composition affects not only the pollen usage of a generalist bee but also its associated microbial communities.}, }
@article {pmid30065892, year = {2018}, author = {Schlemper, TR and Dimitrov, MR and Silva Gutierrez, FAO and van Veen, JA and Silveira, APD and Kuramae, EE}, title = {Effect of Burkholderia tropica and Herbaspirillum frisingense strains on sorghum growth is plant genotype dependent.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e5346}, doi = {10.7717/peerj.5346}, pmid = {30065892}, issn = {2167-8359}, abstract = {Sorghum is a multipurpose crop that is cultivated worldwide. Plant growth-promoting bacteria (PGPB) have important roles in enhancing sorghum biomass and nutrient uptake and suppressing plant pathogens. The aim of this research was to test the effects of the endophytic bacterial species Kosakonia radicincitans strain IAC/BECa 99, Enterobacter asburiae strain IAC/BECa 128, Pseudomonas fluorescens strain IAC/BECa 141, Burkholderia tropica strain IAC/BECa 135 and Herbaspirillum frisingense strain IAC/BECa 152 on the growth and root architecture of four sorghum cultivars (SRN-39, Shanqui-Red, BRS330, BRS509), with different uses and strigolactone profiles. We hypothesized that the different bacterial species would trigger different growth plant responses in different sorghum cultivars. Burkholderia tropica and H. frisingense significantly increased the plant biomass of cultivars SRN-39 and BRS330. Moreover, cultivar BRS330 inoculated with either strain displayed isolates significant decrease in average root diameter. This study shows that Burkholderia tropica strain IAC/BECa 135 and H. frisingense strain IAC/BECa 152 are promising PGPB strains for use as inocula for sustainable sorghum cultivation.}, }
@article {pmid30065353, year = {2018}, author = {Rahlff, J and Ribas-Ribas, M and Brown, SM and Mustaffa, NIH and Renz, J and Peck, MA and Bird, K and Cunliffe, M and Melkonian, K and Zappa, CJ}, title = {Blue pigmentation of neustonic copepods benefits exploitation of a prey-rich niche at the air-sea boundary.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {11510}, doi = {10.1038/s41598-018-29869-7}, pmid = {30065353}, issn = {2045-2322}, support = {GA336408//EC | European Research Council (ERC)/ ; GA336408//EC | European Research Council (ERC)/ ; GA336408//EC | European Research Council (ERC)/ ; }, abstract = {The sea-surface microlayer (SML) at the air-sea interface is a distinct, under-studied habitat compared to the subsurface and copepods, important components of ocean food webs, have developed key adaptations to exploit this niche. By using automated SML sampling, high-throughput sequencing and unmanned aerial vehicles, we report on the distribution and abundance of pontellid copepods in relation to the unique biophysicochemical signature of the SML. We found copepods in the SML even during high exposure to sun-derived ultraviolet radiation and their abundance was significantly correlated to increased algal biomass. We additionally investigated the significance of the pontellids' blue pigmentation and found that the reflectance peak of the blue pigment matched the water-leaving spectral radiance of the ocean surface. This feature could reduce high visibility at the air-sea boundary and potentially provide camouflage of copepods from their predators.}, }
@article {pmid30063956, year = {2018}, author = {Thompson, HF and Lesaulnier, C and Pelikan, C and Gutierrez, T}, title = {Visualisation of the obligate hydrocarbonoclastic bacteria Polycyclovorans algicola and Algiphilus aromaticivorans in co-cultures with micro-algae by CARD-FISH.}, journal = {Journal of microbiological methods}, volume = {152}, number = {}, pages = {73-79}, doi = {10.1016/j.mimet.2018.07.016}, pmid = {30063956}, issn = {1872-8359}, abstract = {Some studies have described the isolation and 16S rRNA gene sequence-based identification of hydrocarbon-degrading bacteria living associated with marine eukaryotic phytoplankton, and thus far the direct visual observation of these bacteria on micro-algal cell surfaces ('phycosphere') has not yet been reported. Here, we developed two new 16S rRNA-targeted oligonucleotide probes, PCY223 and ALGAR209, to respectively detect and enumerate the obligate hydrocarbonoclastic bacteria Polycyclovorans algicola and Algiphilus aromaticivorans by Catalyzed Reporter Deposition Fluorescence in situ Hybridization (CARD-FISH). To enhance the hybridization specificity with the ALGAR209 probe, a competitor probe was developed. These probes were tested and optimized using pure cultures, and then used in enrichment experiments with laboratory cultures of micro-algae exposed to phenanthrene, and with coastal water enriched with crude oil. Microscopic analysis revealed these bacteria are found in culture with the micro-algal cells, some of which were found attached to algal cells, and whose abundance increased after phenanthrene or crude oil enrichment. These new probes are a valuable tool for identifying and studying the ecology of P. algicola and A. aromaticivorans in laboratory and field samples of micro-algae, as well as opening new fields of research that could harness their ability to enhance the bioremediation of contaminated sites.}, }
@article {pmid30061909, year = {2018}, author = {Sobhy, IS and Baets, D and Goelen, T and Herrera-Malaver, B and Bosmans, L and Van den Ende, W and Verstrepen, KJ and Wäckers, F and Jacquemyn, H and Lievens, B}, title = {Sweet Scents: Nectar Specialist Yeasts Enhance Nectar Attraction of a Generalist Aphid Parasitoid Without Affecting Survival.}, journal = {Frontiers in plant science}, volume = {9}, number = {}, pages = {1009}, doi = {10.3389/fpls.2018.01009}, pmid = {30061909}, issn = {1664-462X}, abstract = {Floral nectar is commonly inhabited by microorganisms, mostly yeasts and bacteria, which can have a strong impact on nectar chemistry and scent. Yet, little is known about the effects of nectar microbes on the behavior and survival of insects belonging to the third trophic level such as parasitoids. Here, we used five nectar-inhabiting yeast species to test the hypothesis that yeast species that almost solely occur in nectar, and therefore substantially rely on floral visitors for dispersal, produce volatile compounds that enhance insect attraction without compromising insect life history parameters, such as survival. Experiments were performed using two nectar specialist yeasts (Metschnikowia gruessii and M. reukaufii) and three generalist species (Aureobasidium pullulans, Hanseniaspora uvarum, and Sporobolomyces roseus). Saccharomyces cerevisiae was included as a reference yeast. We compared olfactory responses of the generalist aphid parasitoid Aphidius ervi (Haliday) (Hymenoptera: Braconidae) when exposed to these microorganisms inoculated in synthetic nectar. Nectar-inhabiting yeasts had a significant impact on nectar chemistry and produced distinct volatile blends, some of which were attractive, while others were neutral or repellent. Among the different yeast species tested, the nectar specialists M. gruessii and M. reukaufii were the only species that produced a highly attractive nectar to parasitoid females, which simultaneously had no adverse effects on longevity and survival of adults. By contrast, parasitoids that fed on nectars fermented with the reference strain, A. pullulans, H. uvarum or S. roseus showed shortest longevity and lowest survival. Additionally, nectars fermented by A. pullulans or S. roseus were consumed significantly less, suggesting a lack of important nutrients or undesirable changes in the nectar chemical profiles. Altogether our results indicate that nectar-inhabiting yeasts play an important, but so far largely overlooked, role in plant-insect interactions by modulating the chemical composition of nectar, and may have important ecological consequences for plant pollination and biological control of herbivorous insects.}, }
@article {pmid30061657, year = {2018}, author = {Butler, S and O'Dwyer, JP}, title = {Stability criteria for complex microbial communities.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {2970}, doi = {10.1038/s41467-018-05308-z}, pmid = {30061657}, issn = {2041-1723}, abstract = {Competition and mutualism are inevitable processes in microbial ecology, and a central question is which and how many taxa will persist in the face of these interactions. Ecological theory has demonstrated that when direct, pairwise interactions among a group of species are too numerous, or too strong, then the coexistence of these species will be unstable to any slight perturbation. Here, we refine and to some extent overturn that understanding, by considering explicitly the resources that microbes consume and produce. In contrast to more complex organisms, microbial cells consume primarily abiotic resources, and mutualistic interactions are often mediated through the mechanism of crossfeeding. We show that if microbes consume, but do not produce resources, then any positive equilibrium will always be stable to small perturbations. We go on to show that in the presence of crossfeeding, stability is no longer guaranteed. However, positive equilibria remain stable whenever mutualistic interactions are either sufficiently weak, or when all pairs of taxa reciprocate each other's assistance.}, }
@article {pmid30061355, year = {2018}, author = {van der Aart, LT and Spijksma, GK and Harms, A and Vollmer, W and Hankemeier, T and van Wezel, GP}, title = {High-Resolution Analysis of the Peptidoglycan Composition in Streptomyces coelicolor.}, journal = {Journal of bacteriology}, volume = {200}, number = {20}, pages = {}, doi = {10.1128/JB.00290-18}, pmid = {30061355}, issn = {1098-5530}, abstract = {The bacterial cell wall maintains cell shape and protects against bursting by turgor. A major constituent of the cell wall is peptidoglycan (PG), which is continuously modified to enable cell growth and differentiation through the concerted activity of biosynthetic and hydrolytic enzymes. Streptomycetes are Gram-positive bacteria with a complex multicellular life style alternating between mycelial growth and the formation of reproductive spores. This involves cell wall remodeling at apical sites of the hyphae during cell elongation and autolytic degradation of the vegetative mycelium during the onset of development and antibiotic production. Here, we show that there are distinct differences in the cross-linking and maturation of the PGs between exponentially growing vegetative hyphae and the aerial hyphae that undergo sporulation. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis identified over 80 different muropeptides, revealing that major PG hydrolysis takes place over the course of mycelial growth. Half of the dimers lacked one of the disaccharide units in transition-phase cells, most likely due to autolytic activity. The deacetylation of MurNAc to MurN was particularly pronounced in spores and strongly reduced in sporulation mutants with a deletion of bldD or whiG, suggesting that MurN is developmentally regulated. Altogether, our work highlights the dynamic and growth phase-dependent changes in the composition of the PG in StreptomycesIMPORTANCE Streptomycetes are bacteria with a complex lifestyle and are