title: Genome Reconstruction from Metagenomic Data Sets Reveals Novel Microbes in the Brackish Waters of the Caspian Sea.
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.
authors.affiliation: Extremophiles Laboratory, Department of Microbiology, Faculty of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran.
authors.forename: Maliheh
authors.initials: M
authors.lastname: Mehrshad
authors.affiliation: Extremophiles Laboratory, Department of Microbiology, Faculty of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran amoozegar@ut.ac.ir.
authors.forename: Mohammad Ali
authors.initials: MA
authors.lastname: Amoozegar
authors.affiliation: Evolutionary Genomics Group, Universidad Miguel Hernández, San Juan de Alicante, Spain.
authors.forename: Rohit
authors.initials: R
authors.lastname: Ghai
authors.affiliation: Microorganisms Bank, Iranian Biological Resource Centre (IBRC), ACECR, Tehran, Iran.|Department of Molecular and Cellular Biology, Faculty of Basic Sciences and Advanced Technologies in Biology, University of Science and Culture, Tehran, Iran.
authors.forename: Seyed Abolhassan
authors.initials: SA
authors.lastname: Shahzadeh Fazeli
authors.affiliation: Evolutionary Genomics Group, Universidad Miguel Hernández, San Juan de Alicante, Spain.
authors.forename: Francisco
authors.initials: F
authors.lastname: Rodriguez-Valera
mesh_terms: D001105:Archaea / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D058448:Biota; D005618:Fresh Water / Q000382:microbiology*; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D056186:Metagenomics; D008969:Molecular Sequence Data; D010802:Phylogeny; D000068357:Saline Waters; D017422:Sequence Analysis, DNA