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.
Department of Civil and Environmental Engineering, Massachusetts Institute of Technology (MIT), 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
Nadav
N
Kashtan
Sara E
SE
Roggensack
Sébastien
S
Rodrigue
Jessie W
JW
Thompson
Steven J
SJ
Biller
Allison
A
Coe
Huiming
H
Ding
Pekka
P
Marttinen
Rex R
RR
Malmstrom
Roman
R
Stocker
Michael J
MJ
Follows
Ramunas
R
Stepanauskas
Sallie W
SW
Chisholm
D001267:Atlantic Ocean; D005075:Biological Evolution; D017753:Ecosystem; D005798:Genes, Bacterial; D014644:Genetic Variation; D016680:Genome, Bacterial; D056186:Metagenomics; D008969:Molecular Sequence Data; D009154:Mutation; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D048929:Prochlorococcus / Q000145:classification / Q000235:genetics* / Q000502:physiology*; D012621:Seasons; D012623:Seawater / Q000382:microbiology*; D017422:Sequence Analysis, DNA; D059010:Single-Cell Analysis