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      Diversity of the microbial community and cultivable protease-producing bacteria in the sediments of the Bohai Sea, Yellow Sea and South China Sea

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          Abstract

          The nitrogen (N) cycle is closely related to the stability of marine ecosystems. Microbial communities have been directly linked to marine N-cycling processes. However, systematic research on the bacterial community composition and diversity involved in N cycles in different seas is lacking. In this study, microbial diversity in the Bohai Sea (BHS), Yellow Sea (YS) and South China Sea (SCS) was surveyed by targeting the hypervariable V4 regions of the 16S rRNA gene using next-generation sequencing (NGS) technology. A total of 2,505,721 clean reads and 15,307 operational taxonomic units (OTUs) were obtained from 86 sediment samples from the three studied China seas. LEfSe analysis demonstrated that the SCS had more abundant microbial taxa than the BHS and YS. Diversity indices demonstrated that Proteobacteria and Planctomycetes were the dominant phyla in all three China seas. Canonical correspondence analysis (CCA) indicated that pH ( P = 0.034) was the principal determining factors, while the organic matter content, depth and temperature had a minor correlated with the variations in sedimentary microbial community distribution. Cluster and functional analyses of microbial communities showed that chemoheterotrophic and aerobic chemoheterotrophic microorganisms widely exist in these three seas. Further research found that the cultivable protease-producing bacteria were mainly affiliated with the phyla Proteobacteria, Firmicutes and Bacteroidetes. It was very clear that Pseudoalteromonadaceae possessed the highest relative abundance in the three sea areas. The predominant protease-producing genera were Pseudoalteromonas and Bacillus. These results shed light on the differences in bacterial community composition, especially protease-producing bacteria, in these three China seas.

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          Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor.

          Ecogenomic investigation of a methanogenic bioreactor degrading terephthalate (TA) allowed elucidation of complex synergistic networks of uncultivated microorganisms, including those from candidate phyla with no cultivated representatives. Our previous metagenomic investigation proposed that Pelotomaculum and methanogens may interact with uncultivated organisms to degrade TA; however, many members of the community remained unaddressed because of past technological limitations. In further pursuit, this study employed state-of-the-art omics tools to generate draft genomes and transcriptomes for uncultivated organisms spanning 15 phyla and reports the first genomic insight into candidate phyla Atribacteria, Hydrogenedentes and Marinimicrobia in methanogenic environments. Metabolic reconstruction revealed that these organisms perform fermentative, syntrophic and acetogenic catabolism facilitated by energy conservation revolving around H2 metabolism. Several of these organisms could degrade TA catabolism by-products (acetate, butyrate and H2) and syntrophically support Pelotomaculum. Other taxa could scavenge anabolic products (protein and lipids) presumably derived from detrital biomass produced by the TA-degrading community. The protein scavengers expressed complementary metabolic pathways indicating syntrophic and fermentative step-wise protein degradation through amino acids, branched-chain fatty acids and propionate. Thus, the uncultivated organisms may interact to form an intricate syntrophy-supported food web with Pelotomaculum and methanogens to metabolize catabolic by-products and detritus, whereby facilitating holistic TA mineralization to CO2 and CH4.
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            Correlating microbial community profiles with geochemical data in highly stratified sediments from the Arctic Mid-Ocean Ridge.

            Microbial communities and their associated metabolic activity in marine sediments have a profound impact on global biogeochemical cycles. Their composition and structure are attributed to geochemical and physical factors, but finding direct correlations has remained a challenge. Here we show a significant statistical relationship between variation in geochemical composition and prokaryotic community structure within deep-sea sediments. We obtained comprehensive geochemical data from two gravity cores near the hydrothermal vent field Loki's Castle at the Arctic Mid-Ocean Ridge, in the Norwegian-Greenland Sea. Geochemical properties in the rift valley sediments exhibited strong centimeter-scale stratigraphic variability. Microbial populations were profiled by pyrosequencing from 15 sediment horizons (59,364 16S rRNA gene tags), quantitatively assessed by qPCR, and phylogenetically analyzed. Although the same taxa were generally present in all samples, their relative abundances varied substantially among horizons and fluctuated between Bacteria- and Archaea-dominated communities. By independently summarizing covariance structures of the relative abundance data and geochemical data, using principal components analysis, we found a significant correlation between changes in geochemical composition and changes in community structure. Differences in organic carbon and mineralogy shaped the relative abundance of microbial taxa. We used correlations to build hypotheses about energy metabolisms, particularly of the Deep Sea Archaeal Group, specific Deltaproteobacteria, and sediment lineages of potentially anaerobic Marine Group I Archaea. We demonstrate that total prokaryotic community structure can be directly correlated to geochemistry within these sediments, thus enhancing our understanding of biogeochemical cycling and our ability to predict metabolisms of uncultured microbes in deep-sea sediments.
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              Impacts of infection with different toxigenic Clostridium difficile strains on faecal microbiota in children

              Increasing evidence suggests that altered intestinal microbial composition and function result in an increased risk of Clostridium difficile-associated diarrhoea (CDAD); however, the specific changes of intestinal microbiota in children suffering from CDAD and their associations with C. difficile strain toxigenicity are poorly understood. High-throughput pyrosequencing showed that reduced faecal bacterial diversity and dramatic shifts of microbial composition were found in children with CDAD. The Firmicutes/Bacteroidetes ratio was increased significantly in patients with CDAD, which indicated that dysbiosis of faecal microbiota was closely associated with CDAD. C. difficile infection resulted in an increase in lactate-producing phylotypes, with a corresponding decrease in butyrate-producing bacteria. The decrease in butyrate and lactate buildup impaired intestinal colonisation resistance, which increased the susceptibility to C. difficile colonisation. Strains of C. difficile which were positive for both toxin A and toxin B reduced faecal bacterial diversity to a greater degree than strains that were only toxin B-positive, and were associated with unusually abundant Enterococcus, which implies that the C. difficile toxins have different impacts on the faecal microbiota of children. Greater understanding of the relationships between disruption of the normal faecal microbiota and colonisation with C. difficile that produces different toxins might lead to improved treatment.
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                Author and article information

                Contributors
                Role: Data curationRole: Formal analysisRole: Writing – original draft
                Role: Formal analysisRole: Software
                Role: InvestigationRole: MethodologyRole: ResourcesRole: Writing – original draft
                Role: Software
                Role: Funding acquisitionRole: Resources
                Role: ConceptualizationRole: Writing – original draft
                Role: MethodologyRole: Resources
                Role: ConceptualizationRole: Formal analysisRole: Funding acquisitionRole: MethodologyRole: Project administrationRole: SupervisionRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: Formal analysisRole: MethodologyRole: SoftwareRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                11 April 2019
                2019
                : 14
                : 4
                : e0215328
                Affiliations
                [1 ] School of Life Science, Central South University, Changsha, China
                [2 ] Sanway Gene Technology Inc., Changsha, China
                [3 ] Shandong Province Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, China
                Universite Paris-Sud, FRANCE
                Author notes

                Competing Interests: The authors have the following interests: Ming Chen, Xinwu Guo and Jun Wang are employee of Sanway Gene Technology. There are no patents, products in development or marketed products to declare. This does not alter our adherence to all the PLOS ONE policies on sharing data and materials.

                Author information
                http://orcid.org/0000-0002-2997-8446
                Article
                PONE-D-19-01058
                10.1371/journal.pone.0215328
                6459509
                30973915
                78ffec04-773f-4bb1-a903-b5b25e0da7f2
                © 2019 Zhang et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 12 January 2019
                : 30 March 2019
                Page count
                Figures: 7, Tables: 3, Pages: 18
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/501100001809, National Natural Science Foundation of China;
                Award ID: 31370104, 31300005, 41349901
                Award Recipient :
                Funded by: Hunan Provincial Natural Science Foundation of China
                Award ID: 2018JJ2497
                Award Recipient :
                Funded by: Opening Foundation of the Chinese National Engineering Research Center for Control and Treatment of Heavy Metal Pollution
                Award ID: No. 2015CNERC-CTHMP-07
                Award Recipient :
                Funded by: Hunan Provincial Innovation Foundation for Postgraduates
                Award ID: CX2017B074
                Award Recipient :
                Funded by: Fundamental Research Funds for the Central Universities of Central South University
                Award ID: 2018zzts119, 2018zzts392, 2017zzts076, 2017zzts351
                Award Recipient :
                The work was supported by the National Natural Science Foundation of China (31370104, 31300005), the Hunan Provincial Natural Science Foundation of China (2018JJ2497), the Opening Foundation of the Chinese National Engineering Research Center for Control and Treatment of Heavy Metal Pollution (No. 2015CNERC-CTHMP-07), the Hunan Provincial Innovation Foundation for Postgraduates (CX2017B074) and the Fundamental Research Funds for the Central Universities of Central South University (2018zzts119, 2018zzts392, 2017zzts076, 2017zzts351). The sediments of the BHS and YS were collected during the Bohai and Yellow Sea oceanological comprehensive scientific investigation organized by the National Nature Science Foundation of China (41349901). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Authors Ming Chen, Xinwu Guo and Jun Wang are employed by Sanway Gene Technology Inc.. Sanway Gene Technology Inc. provided support in the form of salaries for authors MC, XG and JW, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Earth Sciences
                Geology
                Petrology
                Sediment
                Earth Sciences
                Geology
                Sedimentary Geology
                Sediment
                Biology and Life Sciences
                Organisms
                Bacteria
                Marine Bacteria
                Biology and Life Sciences
                Organisms
                Bacteria
                Ecology and Environmental Sciences
                Aquatic Environments
                Marine Environments
                Earth Sciences
                Marine and Aquatic Sciences
                Aquatic Environments
                Marine Environments
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                Community Ecology
                Community Structure
                Ecology and Environmental Sciences
                Ecology
                Community Ecology
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                Biology and Life Sciences
                Ecology
                Biodiversity
                Ecology and Environmental Sciences
                Ecology
                Biodiversity
                Biology and Life Sciences
                Marine Biology
                Earth Sciences
                Marine and Aquatic Sciences
                Marine Biology
                Biology and Life Sciences
                Ecology
                Marine Ecology
                Ecology and Environmental Sciences
                Ecology
                Marine Ecology
                Biology and Life Sciences
                Marine Biology
                Marine Ecology
                Earth Sciences
                Marine and Aquatic Sciences
                Marine Biology
                Marine Ecology
                Custom metadata
                All relevant data are within the manuscript and its Supporting Information files. The raw sequences generated in the present study were deposited in the Genome Sequence Archive in the BIG Data Center (BIG Data Center Members 2017), Beijing Institute of Genomics (BIG), Chinese Academy of Sciences, under accession number CRA000634. This information is publicly accessible at http://bigd.big.ac.cn/gsa.

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