Journal
ISME JOURNAL
Volume 2, Issue 10, Pages 1052-1065Publisher
NATURE PUBLISHING GROUP
DOI: 10.1038/ismej.2008.62
Keywords
metagenomics; marine; population; recombination; speciation
Categories
Funding
- Gordon and Betty Moore Foundation
- Department of Energy Microbial Genome Sequencing program
- US Department of Energy's Office of Science
- Biological and Environmental Research Program
- University of California
- Lawrence Livermore National Laboratory [W-7405-ENG-48]
- Lawrence Berkeley National Laboratory [DE-AC03-765F00098]
- Los Almos National Laboratory [W-7405-ENG-36]
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Microorganisms represent the largest reservoir of biodiversity on Earth, both in numbers and total genetic diversity, but it remains unclear whether this biodiversity is organized in discrete units that correspond to ecologically coherent species. To further explore this question, we examined patterns of genomic diversity in sympatric microbial populations. Analyses of a total of similar to 200 Mb of microbial community genomic DNA sequence recovered from 4000 m depth in the Pacific Ocean revealed discrete sequence-defined populations of Bacteria and Archaea, with intrapopulation genomic sequence divergence ranging from similar to 1% to similar to 6%. The populations appeared to be maintained, at least in part, by intrapopulation genetic exchange (homologous recombination), although the frequency of recombination was estimated to be about three times lower than that observed previously in thermoacidophilic archaeal biofilm populations. Furthermore, the genotypes of a given population were clearly distinguishable from their closest co-occurring relatives based on their relative abundance in situ. The genetic distinctiveness and the matching sympatric abundances imply that these genotypes share similar ecophysiological properties, and therefore may represent fundamental units of microbial diversity in the deep sea. Comparisons to surface-dwelling relatives of the Sargasso Sea revealed that distinct sequence-based clusters were not always detectable, presumably due to environmental variations, further underscoring the important relationship between environmental contexts and genetic mechanisms, which together shape and sustain microbial population structure.
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