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 la...

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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
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cited_by cdi_FETCH-LOGICAL-c347t-b33dd107f29c1fbfc7b85a10e48d8d57bed876e5359964aac1f007f040775faf3
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creator 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.
description 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.
doi_str_mv 10.1126/science.1248575
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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
title Single-Cell Genomics Reveals Hundreds of Coexisting Subpopulations in Wild Prochlorococcus
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