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

• Published in: Science (American Association for the Advancement of Science) 2014-04, Vol.344 (6182), p.416-420
• Main Authors: Kashtan, Nadav, Roggensack, Sara E., Rodrigue, Sébastien, Thompson, Jessie W., Biller, Steven J., Coe, Allison, Ding, Huiming, Marttinen, Pekka, Malmstrom, Rex R., Stocker, Roman, Follows, Michael J., Stepanauskas, Ramunas, Chisholm, Sallie W.
• Format: Article
• Language: English
• Subjects: Algae; Alleles; Atlantic Ocean; Bacteria; Biological Evolution; Cellular biology; Ecosystem; Genes, Bacterial; Genetic diversity; Genetic Variation; Genome, Bacterial; Genomes; Genomics; Metagenomics; Molecular Sequence Data; Mutation; Neurons; Phylogeny; Polymorphism, Single Nucleotide; Population genetics; Prochlorococcus - classification; Prochlorococcus - genetics; Prochlorococcus - physiology; Proteins; rev genes; Seasons; Seawater - microbiology; Sequence Analysis, DNA; Single-Cell Analysis
• ISSN: 0036-8075; 1095-9203
• DOI: 10.1126/science.1248575

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.