Genome Reconstruction from Metagenomic Data Sets Reveals Novel Microbes in the Brackish Waters of the Caspian Sea

Appl Environ Microbiol. 2016 Jan 4;82(5):1599-1612. doi: 10.1128/AEM.03381-15.

Abstract

We present here the findings from a study of the microbiome of the southern basin of the Caspian Sea, the largest water body on Earth disconnected from any ocean and a brackish inland sea. By high-throughput metagenomics, we were able to reconstruct the genomes of representative microbes. The gross community structure (at the phylum level) was different from the structure of typical marine and freshwater communities in temperate open oceans, with the Caspian Sea having freshwater-like amounts of Actinobacteria and Alphaproteobacteria, while Gammaproteobacteria and Betaproteobacteria were present at intermediate levels. We assembled the genomes of several groups and provide detailed descriptions of partial genomes from Actinobacteria, Thaumarchaea, and Alphaproteobacteria. Most belonged to hitherto unknown groups, although they were related to either marine or freshwater groups. The phylogenetic placement of the Caspian genomes indicates that the organisms have multiple and separate phylogenetic origins and that they are related to organisms with both freshwater and marine lineages. Comparative recruitment from global aquatic metagenomes indicated that most Caspian microbes are endemic. However, some Caspian genomes were recruited significantly from either marine water (a member of the Alphaproteobacteria) or freshwater (a member of the Actinobacteria). Reciprocally, some genomes of other origins, such as the marine thaumarchaeon " Candidatus Nitrosopelagicus" or the actinobacterium "Candidatus Actinomarina," were recruited from the Caspian Sea, indicating some degree of overlap with the microbiota of other water bodies. Some of these microbes seem to have a remarkably widespread geographic and environmental distribution.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Archaea / classification
  • Archaea / genetics
  • Archaea / isolation & purification*
  • Bacteria / classification
  • Bacteria / genetics
  • Bacteria / isolation & purification*
  • Biota*
  • Fresh Water / microbiology*
  • Genome, Archaeal
  • Genome, Bacterial
  • Metagenomics*
  • Molecular Sequence Data
  • Phylogeny
  • Saline Waters*
  • Sequence Analysis, DNA

Grant support

This work was supported by a grant from the Iranian Biological Resource Centre (IBRC) (MI-1391-20) (to M. A. Amoozegar) and project MEDIMAX BFPU2013-48007-P of the Spanish Ministerio de Economia y Competitividad, MaCuMBA project 311975 of the European Commission FP7 (FEDER funds supported this project), and PROMETEO II2014/012 project AQUAMET of the Generalitat Valenciana (to F. Rodriguez-Valera).