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

      Remarkably coherent population structure for a dominant Antarctic Chlorobium species

      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

          Background

          In Antarctica, summer sunlight enables phototrophic microorganisms to drive primary production, thereby “feeding” ecosystems to enable their persistence through the long, dark winter months. In Ace Lake, a stratified marine-derived system in the Vestfold Hills of East Antarctica, a Chlorobium species of green sulphur bacteria (GSB) is the dominant phototroph, although its seasonal abundance changes more than 100-fold. Here, we analysed 413 Gb of Antarctic metagenome data including 59 Chlorobium metagenome-assembled genomes (MAGs) from Ace Lake and nearby stratified marine basins to determine how genome variation and population structure across a 7-year period impacted ecosystem function.

          Results

          A single species, Candidatus Chlorobium antarcticum (most similar to Chlorobium phaeovibrioides DSM265) prevails in all three aquatic systems and harbours very little genomic variation (≥ 99% average nucleotide identity). A notable feature of variation that did exist related to the genomic capacity to biosynthesize cobalamin. The abundance of phylotypes with this capacity changed seasonally ~ 2-fold, consistent with the population balancing the value of a bolstered photosynthetic capacity in summer against an energetic cost in winter. The very high GSB concentration (> 10 8 cells ml −1 in Ace Lake) and seasonal cycle of cell lysis likely make Ca. Chlorobium antarcticum a major provider of cobalamin to the food web. Analysis of Ca. Chlorobium antarcticum viruses revealed the species to be infected by generalist (rather than specialist) viruses with a broad host range (e.g., infecting Gammaproteobacteria) that were present in diverse Antarctic lakes. The marked seasonal decrease in Ca. Chlorobium antarcticum abundance may restrict specialist viruses from establishing effective lifecycles, whereas generalist viruses may augment their proliferation using other hosts.

          Conclusion

          The factors shaping Antarctic microbial communities are gradually being defined. In addition to the cold, the annual variation in sunlight hours dictates which phototrophic species can grow and the extent to which they contribute to ecosystem processes. The Chlorobium population studied was inferred to provide cobalamin, in addition to carbon, nitrogen, hydrogen, and sulphur cycling, as critical ecosystem services. The specific Antarctic environmental factors and major ecosystem benefits afforded by this GSB likely explain why such a coherent population structure has developed in this Chlorobium species.

          Supplementary Information

          The online version contains supplementary material available at 10.1186/s40168-021-01173-z.

          Related collections

          Most cited references122

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

          Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

          In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. The DESeq2 package is available at http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0550-8) contains supplementary material, which is available to authorized users.
            Bookmark
            • Record: found
            • Abstract: found
            • Article: found
            Is Open Access

            The Sequence Alignment/Map format and SAMtools

            Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: http://samtools.sourceforge.net Contact: rd@sanger.ac.uk
              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

              The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.
                Bookmark

                Author and article information

                Contributors
                r.cavicchioli@unsw.edu.au
                Journal
                Microbiome
                Microbiome
                Microbiome
                BioMed Central (London )
                2049-2618
                26 November 2021
                26 November 2021
                2021
                : 9
                Affiliations
                [1 ]GRID grid.1005.4, ISNI 0000 0004 4902 0432, School of Biotechnology and Biomolecular Sciences, , UNSW Sydney, ; Sydney, New South Wales 2052 Australia
                [2 ]GRID grid.1004.5, ISNI 0000 0001 2158 5405, Present address: Department of Molecular Sciences, , Macquarie University, ; Sydney, New South Wales 2109 Australia
                [3 ]Present address: Pegarah, Australia
                [4 ]GRID grid.1009.8, ISNI 0000 0004 1936 826X, Present address: Institute for Marine and Antarctic Studies, , University of Tasmania, ; 20 Castray Esplanade, Battery Point, Tasmania Australia
                [5 ]GRID grid.451309.a, ISNI 0000 0004 0449 479X, Department of Energy Joint Genome Institute, ; Berkeley, CA USA
                [6 ]GRID grid.508097.3, Present address: Mammoth Biosciences, Inc., ; 1000 Marina Blvd. Suite 600, Brisbane, CA USA
                Article
                1173
                10.1186/s40168-021-01173-z
                8620254
                34823595
                37377202-3592-4b4f-9732-b5aba3569860
                © The Author(s) 2021

                Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

                Funding
                Funded by: Australian Research Council
                Award ID: DP150100244
                Award Recipient :
                Funded by: Australian Antarctic Science program
                Award ID: 4031
                Award Recipient :
                Funded by: Office of Science of the US Department of Energy
                Award ID: AC02-05CH11231
                Categories
                Research
                Custom metadata
                © The Author(s) 2021

                antarctic microbiology,green sulphur bacteria,chlorobi,vitamin b12,metagenome-assembled genomes,phylotype,ecotype,population structure,host-virus interactions,generalist virus,meromictic lake,microbial food web

                Comments

                Comment on this article