4
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      Freshwater Chlorobia Exhibit Metabolic Specialization among Cosmopolitan and Endemic Populations

      research-article

      Read this article at

      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          The reconstruction of genomes from metagenomes has helped explore the ecology and evolution of environmental microbiota. We applied this approach to 274 metagenomes collected from diverse freshwater habitats that spanned oxic and anoxic zones, sampling seasons, and latitudes.

          ABSTRACT

          Photosynthetic bacteria from the class Chlorobia (formerly phylum Chlorobi) sustain carbon fixation in anoxic water columns. They harvest light at extremely low intensities and use various inorganic electron donors to fix carbon dioxide into biomass. Until now, most information on the functional ecology and local adaptations of Chlorobia members came from isolates and merely 26 sequenced genomes that may not adequately represent natural populations. To address these limitations, we analyzed global metagenomes to profile planktonic Chlorobia cells from the oxyclines of 42 freshwater bodies, spanning subarctic to tropical regions and encompassing all four seasons. We assembled and compiled over 500 genomes, including metagenome-assembled genomes (MAGs), single-amplified genomes (SAGs), and reference genomes from cultures, clustering them into 71 metagenomic operational taxonomic units (mOTUs or “species”). Of the 71 mOTUs, 57 were classified within the genus Chlorobium, and these mOTUs represented up to ∼60% of the microbial communities in the sampled anoxic waters. Several Chlorobium-associated mOTUs were globally distributed, whereas others were endemic to individual lakes. Although most clades encoded the ability to oxidize hydrogen, many lacked genes for the oxidation of specific sulfur and iron substrates. Surprisingly, one globally distributed Scandinavian clade encoded the ability to oxidize hydrogen, sulfur, and iron, suggesting that metabolic versatility facilitated such widespread colonization. Overall, these findings provide new insight into the biogeography of the Chlorobia and the metabolic traits that facilitate niche specialization within lake ecosystems.

          IMPORTANCE The reconstruction of genomes from metagenomes has helped explore the ecology and evolution of environmental microbiota. We applied this approach to 274 metagenomes collected from diverse freshwater habitats that spanned oxic and anoxic zones, sampling seasons, and latitudes. We demonstrate widespread and abundant distributions of planktonic Chlorobia-associated bacteria in hypolimnetic waters of stratified freshwater ecosystems and show they vary in their capacities to use different electron donors. Having photoautotrophic potential, these Chlorobia members could serve as carbon sources that support metalimnetic and hypolimnetic food webs.

          Related collections

          Most cited references75

          • Record: found
          • Abstract: found
          • Article: found
          Is Open Access

          Trimmomatic: a flexible trimmer for Illumina sequence data

          Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.
            Bookmark
            • Record: found
            • Abstract: found
            • Article: not found

            MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.

            We present the latest version of the Molecular Evolutionary Genetics Analysis (Mega) software, which contains many sophisticated methods and tools for phylogenomics and phylomedicine. In this major upgrade, Mega has been optimized for use on 64-bit computing systems for analyzing larger datasets. Researchers can now explore and analyze tens of thousands of sequences in Mega The new version also provides an advanced wizard for building timetrees and includes a new functionality to automatically predict gene duplication events in gene family trees. The 64-bit Mega is made available in two interfaces: graphical and command line. The graphical user interface (GUI) is a native Microsoft Windows application that can also be used on Mac OS X. The command line Mega is available as native applications for Windows, Linux, and Mac OS X. They are intended for use in high-throughput and scripted analysis. Both versions are available from www.megasoftware.net free of charge.
              Bookmark
              • Record: found
              • Abstract: found
              • Article: found
              Is Open Access

              phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

              Background The analysis of microbial communities through DNA sequencing brings many challenges: the integration of different types of data with methods from ecology, genetics, phylogenetics, multivariate statistics, visualization and testing. With the increased breadth of experimental designs now being pursued, project-specific statistical analyses are often needed, and these analyses are often difficult (or impossible) for peer researchers to independently reproduce. The vast majority of the requisite tools for performing these analyses reproducibly are already implemented in R and its extensions (packages), but with limited support for high throughput microbiome census data. Results Here we describe a software project, phyloseq, dedicated to the object-oriented representation and analysis of microbiome census data in R. It supports importing data from a variety of common formats, as well as many analysis techniques. These include calibration, filtering, subsetting, agglomeration, multi-table comparisons, diversity analysis, parallelized Fast UniFrac, ordination methods, and production of publication-quality graphics; all in a manner that is easy to document, share, and modify. We show how to apply functions from other R packages to phyloseq-represented data, illustrating the availability of a large number of open source analysis techniques. We discuss the use of phyloseq with tools for reproducible research, a practice common in other fields but still rare in the analysis of highly parallel microbiome census data. We have made available all of the materials necessary to completely reproduce the analysis and figures included in this article, an example of best practices for reproducible research. Conclusions The phyloseq project for R is a new open-source software package, freely available on the web from both GitHub and Bioconductor.
                Bookmark

                Author and article information

                Contributors
                Role: Editor
                Role: Ad Hoc Peer Reviewer
                Role: Ad Hoc Peer Reviewer
                Journal
                mSystems
                mSystems
                msys
                msys
                mSystems
                mSystems
                American Society for Microbiology (1752 N St., N.W., Washington, DC )
                2379-5077
                11 May 2021
                May-Jun 2021
                : 6
                : 3
                : e01196-20
                Affiliations
                [a ]Department of Ecology and Genetics, Limnology, Uppsala University, Uppsala, Sweden
                [b ]Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
                [c ]Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Uppsala, Sweden
                [d ]Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
                [e ]Department of Civil and Environmental Engineering, University of Wisconsin, Madison, Madison, Wisconsin, USA
                [f ]Department of Bacteriology, University of Wisconsin, Madison, Madison, Wisconsin, USA
                [g ]Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
                [h ]Department of Forest Mycology and Plant Pathology, Science for Life Laboratory, Swedish University of Agricultural Sciences, Uppsala, Uppsala, Sweden
                University of California, Davis
                University of Illinois at Chicago
                Limnological Station, Department of Plant and Microbial Biology, University of Zurich
                Author notes
                Address correspondence to Sarahi L. Garcia, sarahi.garcia@ 123456su.se .
                [*]

                Present address: Jackson M. Tsuji, Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan.

                Sarahi L. Garcia, Maliheh Mehrshad, and Moritz Buck contributed equally to this article. The order of the authors was designated by time commitment in the writing process.

                Citation Garcia SL, Mehrshad M, Buck M, Tsuji JM, Neufeld JD, McMahon KD, Bertilsson S, Greening C, Peura S. 2021. Freshwater Chlorobia exhibit metabolic specialization among cosmopolitan and endemic populations. mSystems 6:e01196-20. https://doi.org/10.1128/mSystems.01196-20.

                Author information
                https://orcid.org/0000-0002-8622-0308
                https://orcid.org/0000-0002-8722-8571
                https://orcid.org/0000-0002-7038-026X
                https://orcid.org/0000-0001-7616-0594
                https://orcid.org/0000-0003-3892-8157
                https://orcid.org/0000-0001-7558-909X
                Article
                mSystems01196-20
                10.1128/mSystems.01196-20
                8125076
                33975970
                93e42c2b-8716-4672-ba0b-338aed34e42a
                Copyright © 2021 Garcia et al.

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

                History
                : 13 November 2020
                : 9 April 2021
                Page count
                supplementary-material: 5, Figures: 6, Tables: 0, Equations: 0, References: 76, Pages: 14, Words: 8832
                Funding
                Funded by: Olsson-Borgh;
                Award Recipient :
                Funded by: Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation), https://doi.org/10.13039/501100004063;
                Award ID: KAW 2013.0091
                Award Recipient : Award Recipient :
                Funded by: National Science Foundation (NSF), https://doi.org/10.13039/100000001;
                Award ID: MCB-0702395
                Award Recipient :
                Funded by: Science for Life Laboratory (SciLifeLab), https://doi.org/10.13039/501100009252;
                Award Recipient : Award Recipient : Award Recipient : Award Recipient :
                Categories
                Research Article
                Custom metadata
                May/June 2021

                chlorobia,freshwater,photosynthetic bacteria,planktonic
                chlorobia, freshwater, photosynthetic bacteria, planktonic

                Comments

                Comment on this article