Metagenomics reveals niche partitioning within the phototrophic zone of a microbial mat

Lee, Jackson Z.; Everroad, R. Craig; Karaoz, Ulas; Detweiler, Angela M.; Pett-Ridge, Jennifer; Weber, Peter K.; Prufert-Bebout, Leslie; Bebout, Brad M.

doi:10.1371/journal.pone.0202792

Title: Metagenomics reveals niche partitioning within the phototrophic zone of a microbial mat

Journal Article · Tue Sep 11 00:00:00 EDT 2018 · PLoS ONE

DOI:https://doi.org/10.1371/journal.pone.0202792· OSTI ID:1477376

^[1]; Everroad, R. Craig ^[2]; Karaoz, Ulas ^[3];

^[1]; Pett-Ridge, Jennifer ^[4]; Weber, Peter K. ^[4]; Prufert-Bebout, Leslie ^[2]; Bebout, Brad M. ^[2]

NASA Ames Research Center (ARC), Moffett Field, Mountain View, CA (United States). Exobiology Branch; Bay Area Environmental Research Institute, Petaluma, CA (United States)
NASA Ames Research Center (ARC), Moffett Field, Mountain View, CA (United States). Exobiology Branch
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Earth and Environmental Sciences
Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Physical and Life Sciences Directorate

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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC); USDOE National Nuclear Security Administration (NNSA)

Grant/Contract Number:: AC02-05CH11231; AC52-07NA27344

OSTI ID:: 1477376

Alternate ID(s):: OSTI ID: 1513102

Report Number(s):: LLNL-JRNL-731625; ark:/13030/qt87s3w18d

Journal Information:: PLoS ONE, Vol. 13, Issue 9; ISSN 1932-6203

Publisher:: Public Library of ScienceCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 1 work

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