A Bacterial Metapopulation Adapts Locally to Phage Predation Despite Global Dispersal

Victor Kunin; Shaomei He; Falk Warnecke; S. Brook Peterson; Hector Garcia Martin; Matthew Haynes; Natalia Ivanova; Linda Blackall; Mya Breitbart; Forest Rohwer; Katherine McMahon; Philip Hugenholtz

doi:10.1101/gr.6835308

A Bacterial Metapopulation Adapts Locally to Phage Predation Despite Global Dispersal

Victor Kunin, Shaomei He, Falk Warnecke, S. Brook Peterson, Hector Garcia Martin, Matthew Haynes, Natalia Ivanova, Linda Blackall, Mya Breitbart, Forest Rohwer, Katherine McMahon, Philip Hugenholtz

College of Marine Science

Research output: Contribution to journal › Article › peer-review

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.

Original language	American English
Journal	Genome Research
Volume	18
DOIs	https://doi.org/10.1101/gr.6835308
State	Published - Jan 1 2008

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Life Sciences

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A Bacterial Metapopulation Adapts Locally to Phage Predation DespFinal published version, 450 KBLicense: CC BY

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title = "A Bacterial Metapopulation Adapts Locally to Phage Predation Despite Global Dispersal",

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. ",

author = "Victor Kunin and Shaomei He and Falk Warnecke and Peterson, {S. Brook} and Martin, {Hector Garcia} and Matthew Haynes and Natalia Ivanova and Linda Blackall and Mya Breitbart and Forest Rohwer and Katherine McMahon and Philip Hugenholtz",

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doi = "10.1101/gr.6835308",

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T1 - A Bacterial Metapopulation Adapts Locally to Phage Predation Despite Global Dispersal

AU - Kunin, Victor

AU - He, Shaomei

AU - Warnecke, Falk

AU - Peterson, S. Brook

AU - Martin, Hector Garcia

AU - Haynes, Matthew

AU - Ivanova, Natalia

AU - Blackall, Linda

AU - Breitbart, Mya

AU - Rohwer, Forest

AU - McMahon, Katherine

AU - Hugenholtz, Philip

PY - 2008/1/1

Y1 - 2008/1/1

N2 - 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.

AB - 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.

UR - https://digitalcommons.usf.edu/msc_facpub/775

U2 - 10.1101/gr.6835308

DO - 10.1101/gr.6835308

M3 - Article

C2 - 18077539

VL - 18

JO - Genome Research

JF - Genome Research

ER -

A Bacterial Metapopulation Adapts Locally to Phage Predation Despite Global Dispersal

Abstract

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