Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus

Nadav Kashtan*, Sara E. Roggensack, Sébastien Rodrigue, Jessie W. Thompson, Steven J. Biller, Allison Coe, Huiming Ding, Pekka Marttinen, Rex R. Malmstrom, Roman Stocker, Michael J. Follows, Ramunas Stepanauskas, Sallie W. Chisholm

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

360 Scopus citations

Abstract

Extensive genomic diversity within coexisting members of a microbial species has been revealed through selected cultured isolates and metagenomic assemblies. Yet, the cell-by-cell genomic composition of wild uncultured populations of co-occurring cells is largely unknown. In this work, we applied large-scale single-cell genomics to study populations of the globally abundant marine cyanobacterium Prochlorococcus. We show that they are composed of hundreds of subpopulations with distinct "genomic backbones," each backbone consisting of a different set of core gene alleles linked to a small distinctive set of flexible genes. These subpopulations are estimated to have diverged at least a few million years ago, suggesting ancient, stable niche partitioning. Such a large set of coexisting subpopulations may be a general feature of free-living bacterial species with huge populations in highly mixed habitats.

Original languageAmerican English
Pages (from-to)416-420
Number of pages5
JournalScience
Volume344
Issue number6182
DOIs
StatePublished - 2014
Externally publishedYes

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