Metagenomics Reveals Niche Partitioning Within the Phototrophic Zone of a Microbial Mat

PLoS One. 2018 Sep 11;13(9):e0202792. doi: 10.1371/journal.pone.0202792. eCollection 2018.


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.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Bacteria / classification*
  • Bacteria / genetics
  • Bacteroidetes / classification
  • Bacteroidetes / genetics
  • California
  • Cyanobacteria / classification
  • Cyanobacteria / genetics
  • Evolution, Molecular
  • Gammaproteobacteria / classification
  • Gammaproteobacteria / genetics
  • Metagenomics / methods*
  • Molecular Sequence Annotation
  • Photosynthesis
  • Phylogeny
  • Proteobacteria / classification
  • Proteobacteria / genetics
  • Whole Genome Sequencing / methods*

Grant support

This project is funded by the Department of Energy through the Genome Sciences Program ( under contract SCW1039 to the Lawrence Livermore National Laboratory (LLNL) Biofuels Scientific Focus Area and performed under the auspices of LLNL under Contract DE-AC52-07NA27344. This research used resources of the National Energy Research Scientific Computing Center (NERSC) ( and the DOE Joint Genome Institute (JGI) ( Community Sequencing Program award #701; both DOE Office of Science User Facilities are supported by the Office of Science of the U.S. Department of Energy ( under Contract No. DE-AC02-05CH11231. RCE acknowledges the support of a NASA Postodoctoral Fellowship ( The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.