A bacterial metapopulation adapts locally to phage predation despite global dispersal
- Victor Kunin1,
- Shaomei He2,
- Falk Warnecke1,
- S. Brook Peterson3,
- Hector Garcia Martin1,
- Matthew Haynes4,
- Natalia Ivanova5,
- Linda L. Blackall6,
- Mya Breitbart7,
- Forest Rohwer4,
- Katherine D. McMahon2, and
- Philip Hugenholtz1,8
- 1 Microbial Ecology Program, Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA;
- 2 Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA;
- 3 Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin 53706 USA;
- 4 Department of Biology, San Diego State University, San Diego, California 92182, USA;
- 5 Genome Biology Program, Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA;
- 6 Advanced Wastewater Management Centre, University of Queensland, St Lucia 4072, Queensland, Australia;
- 7 University of South Florida, St. Petersburg, Florida 33701 USA
Abstract
Using a combination of bacterial and phage-targeted metagenomics, we analyzed two geographically remote sludge bioreactors enriched in a single bacterial species Candidatus Accumulibacter phosphatis (CAP). We inferred unrestricted global movement of this species and identified aquatic ecosystems as the primary environmental reservoirs facilitating dispersal. Highly related and geographically remote CAP strains differed principally in genomic regions encoding phage defense mechanisms. We found that CAP populations were high density, clonal, and nonrecombining, providing natural targets for “kill-the-winner” phage predation. Community expression analysis demonstrated that phages were consistently active in the bioreactor community. Genomic signatures linking CAP to past phage exposures were observed mostly between local phage and host. We conclude that CAP strains disperse globally but must adapt to phage predation pressure locally.
Footnotes
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↵8 Corresponding author.
↵8 E-mail phugenholtz{at}lbl.gov; fax (925) 296-5720.
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[Supplemental material is available online at www.genome.org.]
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Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.6835308
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- Received June 22, 2007.
- Accepted October 14, 2007.
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Freely available online through the Genome Research Open Access option.
- Copyright © 2008, Cold Spring Harbor Laboratory Press
