Single-Cell Genomics Reveals Hundreds of Coexisting Subpopulations in Wild Prochlorococcus

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.Rothschild Foundation (Yad Hanadiv)United States. National Oceanic and Atmospheric Administration (“Climate and Global Change” Postdoctoral Research Fellowships)National Science Foundation (U.S.) (NSF Evolutionary Biology Section and Biological Oceanography Section)National Science Foundation (U.S.) (NSF Center for Microbial Oceanography Research and Education)Geosciences Research Program (United States. Department of Energy)Gordon and Betty Moore Foundation (Marine Microbiology Initiative)United States. Dept. of Energy (DOE contract number DE-AC02-05CH11231