Abstract
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 ∼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 ∼1% 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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Acknowledgements
We are grateful to Virginia Rich and Gene Tyson for helpful discussions regarding the manuscript and Sergei Kosakovsky, Gilean McVean and Thierry Wirth for their help with GARD and LDhat. We also thank Chris Preston, Lynne Christianson and Professor David Karl, and the Hawaii Ocean Time series staff and crew for assistance in sample collection at station ALOHA. We thank the JGI production sequencing staff for whole fosmid and shotgun sequencing. This work was supported by the 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 and the University of California, Lawrence Livermore National Laboratory, under contract no. W-7405-ENG-48, Lawrence Berkeley National Laboratory under contract no. DE-AC03-765F00098 and Los Almos National Laboratory contract no. W-7405-ENG-36.
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Data release The genomic scaffold used in Figure 1 is provided as a supplementary fasta-formated file. All fully sequenced fosmids and the WGS data from 4000-m depth sample are now available in GenBank under the accession numbers: EU016559–EU016674 and ABEF00000000, respectively.
Supplementary Information accompanies the paper on The ISME Journal website (http://www.nature.com/ismej)
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Konstantinidis, K., DeLong, E. Genomic patterns of recombination, clonal divergence and environment in marine microbial populations. ISME J 2, 1052–1065 (2008). https://doi.org/10.1038/ismej.2008.62
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DOI: https://doi.org/10.1038/ismej.2008.62
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