Josephine Bay Paul Center in Comparative Molecular Biology and Evolution
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The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution explores the evolution and interaction of genomes of diverse organisms that play significant roles in environmental biology and human health. This dynamic research program integrates the powerful tools of genome science, molecular phylogenetics, and molecular ecology to advance our understanding of how living organisms are related to each other, to provide the tools to quantify and assess biodiversity, and to identify genes and underlying mechanisms of biomedical importance. Projects span all evolutionary time scales, ranging from deep phylogenetic divergence of ancient eukaryotic and prokaryotic lineages, to ecological analyses of how members of diverse communities contribute and respond to environmental change.
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Browsing Josephine Bay Paul Center in Comparative Molecular Biology and Evolution by Subject "Microbial diversity"
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ArticleBacterial biogeography across the Amazon river-ocean continuum(Frontiers Media, 2017-05-23) Doherty, Mary ; Yager, Patricia L. ; Moran, Mary Ann ; Coles, Victoria J. ; Fortunato, Caroline S. ; Krusche, Alex V. ; Medeiros, Patricia M. ; Payet, Jérôme P. ; Richey, Jeffrey E. ; Satinsky, Brandon ; Sawakuchi, Henrique O. ; Ward, Nicholas D. ; Crump, Byron C.Spatial and temporal patterns in microbial biodiversity across the Amazon river-ocean continuum were investigated along ∼675 km of the lower Amazon River mainstem, in the Tapajós River tributary, and in the plume and coastal ocean during low and high river discharge using amplicon sequencing of 16S rRNA genes in whole water and size-fractionated samples (0.2–2.0 μm and >2.0 μm). River communities varied among tributaries, but mainstem communities were spatially homogeneous and tracked seasonal changes in river discharge and co-varying factors. Co-occurrence network analysis identified strongly interconnected river assemblages during high (May) and low (December) discharge periods, and weakly interconnected transitional assemblages in September, suggesting that this system supports two seasonal microbial communities linked to river discharge. In contrast, plume communities showed little seasonal differences and instead varied spatially tracking salinity. However, salinity explained only a small fraction of community variability, and plume communities in blooms of diatom-diazotroph assemblages were strikingly different than those in other high salinity plume samples. This suggests that while salinity physically structures plumes through buoyancy and mixing, the composition of plume-specific communities is controlled by other factors including nutrients, phytoplankton community composition, and dissolved organic matter chemistry. Co-occurrence networks identified interconnected assemblages associated with the highly productive low salinity near-shore region, diatom-diazotroph blooms, and the plume edge region, and weakly interconnected assemblages in high salinity regions. This suggests that the plume supports a transitional community influenced by immigration of ocean bacteria from the plume edge, and by species sorting as these communities adapt to local environmental conditions. Few studies have explored patterns of microbial diversity in tropical rivers and coastal oceans. Comparison of Amazon continuum microbial communities to those from temperate and arctic systems suggest that river discharge and salinity are master variables structuring a range of environmental conditions that control bacterial communities across the river-ocean continuum.
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ArticleOligotyping : differentiating between closely related microbial taxa using 16S rRNA gene data(John Wiley & Sons, 2013-10-23) Eren, A. Murat ; Maignien, Lois ; Sul, Woo Jun ; Murphy, Leslie G. ; Grim, Sharon L. ; Morrison, Hilary G. ; Sogin, Mitchell L.Bacteria comprise the most diverse domain of life on Earth, where they occupy nearly every possible ecological niche and play key roles in biological and chemical processes. Studying the composition and ecology of bacterial ecosystems and understanding their function are of prime importance. High-throughput sequencing technologies enable nearly comprehensive descriptions of bacterial diversity through 16S ribosomal RNA gene amplicons. Analyses of these communities generally rely upon taxonomic assignments through reference data bases or clustering approaches using de facto sequence similarity thresholds to identify operational taxonomic units. However, these methods often fail to resolve ecologically meaningful differences between closely related organisms in complex microbial data sets. In this paper, we describe oligotyping, a novel supervised computational method that allows researchers to investigate the diversity of closely related but distinct bacterial organisms in final operational taxonomic units identified in environmental data sets through 16S ribosomal RNA gene data by the canonical approaches. Our analysis of two data sets from two different environments demonstrates the capacity of oligotyping at discriminating distinct microbial populations of ecological importance. Oligotyping can resolve the distribution of closely related organisms across environments and unveil previously overlooked ecological patterns for microbial communities. The URL http://oligotyping.org offers an open-source software pipeline for oligotyping.
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PreprintSalt marsh sediment diversity : a test of the variability of the rare biosphere among environmental replicates( 2011-12-17) Bowen, Jennifer L. ; Morrison, Hilary G. ; Hobbie, John E. ; Sogin, Mitchell L.Much of the phylogenetic diversity in microbial systems arises from rare taxa that comprise the long tail of taxon rank distribution curves. This vast diversity presents a challenge to testing hypotheses about the effects of perturbations on microbial community composition because within site variability of the rare taxa may be sufficiently large that it would require a prohibitive degree of sequencing to discern differences among samples. In this study we used pyrosequencing of 16S rRNA tags to examine the diversity and local scale variability of salt marsh sediment bacteria. Our goal was to determine whether pyrosequencing could produce similar patterns in community composition among replicate environmental samples from the same location. We hypothesized that repeated sampling from the same location would produce different snapshots of the rare community due to incomplete sequencing of the taxonomically rich rare biosphere. The concern was that variation resulting from incomplete sequencing could mask subtle community shifts caused by environmental perturbations. Our data indicate that salt marsh sediments contain a remarkably diverse array of bacterial taxa and, in contrast to our hypothesis, repeated sampling from within the same site produces reliably similar patterns in bacterial community composition, even among rare organisms. These results demonstrate that deep sequencing of 16s tags is well suited to distinguish site-specific similarities and differences among rare taxa and is a valuable tool for hypothesis testing in microbial ecology.
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ArticleVAMPS : a website for visualization and analysis of microbial population structures(BioMed Central, 2014-02-05) Huse, Susan M. ; Mark Welch, David B. ; Voorhis, Andy ; Shipunova, Anna ; Morrison, Hilary G. ; Eren, A. Murat ; Sogin, Mitchell L.The advent of next-generation DNA sequencing platforms has revolutionized molecular microbial ecology by making the detailed analysis of complex communities over time and space a tractable research pursuit for small research groups. However, the ability to generate 105–108 reads with relative ease brings with it many downstream complications. Beyond the computational resources and skills needed to process and analyze data, it is difficult to compare datasets in an intuitive and interactive manner that leads to hypothesis generation and testing. We developed the free web service VAMPS (Visualization and Analysis of Microbial Population Structures, http://vamps.mbl.edu webcite) to address these challenges and to facilitate research by individuals or collaborating groups working on projects with large-scale sequencing data. Users can upload marker gene sequences and associated metadata; reads are quality filtered and assigned to both taxonomic structures and to taxonomy-independent clusters. A simple point-and-click interface allows users to select for analysis any combination of their own or their collaborators’ private data and data from public projects, filter these by their choice of taxonomic and/or abundance criteria, and then explore these data using a wide range of analytic methods and visualizations. Each result is extensively hyperlinked to other analysis and visualization options, promoting data exploration and leading to a greater understanding of data relationships. VAMPS allows researchers using marker gene sequence data to analyze the diversity of microbial communities and the relationships between communities, to explore these analyses in an intuitive visual context, and to download data, results, and images for publication. VAMPS obviates the need for individual research groups to make the considerable investment in computational infrastructure and bioinformatic support otherwise necessary to process, analyze, and interpret massive amounts of next-generation sequence data. Any web-capable device can be used to upload, process, explore, and extract data and results from VAMPS. VAMPS encourages researchers to share sequence and metadata, and fosters collaboration between researchers of disparate biomes who recognize common patterns in shared data.