1. Ecology
  2. Microbiology and Infectious Disease
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Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta- genomics

  1. Simon Roux
  2. Alyse K Hawley
  3. Monica Torres Beltran
  4. Melanie Scofield
  5. Patrick Schwientek
  6. Ramunas Stepanauskas
  7. Tanja Woyke
  8. Steven J Hallam
  9. Matthew B Sullivan Is a corresponding author
  1. University of Arizona, United States
  2. University of British Columbia, Canada
  3. U.S Department of Energy Joint Genome Institute, United States
  4. Bigelow Laboratory for Ocean Sciences, United States
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Cite as: eLife 2014;3:e03125 doi: 10.7554/eLife.03125

Abstract

Viruses modulate microbial communities and alter ecosystem functions. However, due to cultivation bottlenecks specific virus-host interaction dynamics remain cryptic. Here we examined 127 single-cell amplified genomes (SAGs) from uncultivated SUP05 bacteria isolated from a marine oxygen minimum zone (OMZ) to identify 69 viral contigs representing five new genera within dsDNA Caudovirales and ssDNA Microviridae. Infection frequencies suggest that ~1/3 of SUP05 bacteria are viral-infected, with higher infection frequency where oxygen-deficiency was most severe. Observed Microviridae clonality suggests recovery of bloom-terminating viruses, while systematic co-infection between dsDNA and ssDNA viruses posits previously unrecognized cooperation modes. Analyses of 186 microbial and viral metagenomes revealed that SUP05 viruses persisted for years, but remained endemic to the OMZ. Finally, identification of virus-encoded dissimilatory sulfite reductase suggests SUP05 viruses reprogram their host's energy metabolism. Together these results demonstrate closely coupled SUP05 virus-host co-evolutionary dynamics with potential to modulate biogeochemical cycling in climate-critical and expanding OMZs.

Article and author information

Author details

  1. Simon Roux

    1. University of Arizona, Tucson, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Alyse K Hawley

    1. University of British Columbia, Vancouver, Canada
    Competing interests
    The authors declare that no competing interests exist.
  3. Monica Torres Beltran

    1. University of British Columbia, Vancouver, Canada
    Competing interests
    The authors declare that no competing interests exist.
  4. Melanie Scofield

    1. University of British Columbia, Vancouver, Canada
    Competing interests
    The authors declare that no competing interests exist.
  5. Patrick Schwientek

    1. U.S Department of Energy Joint Genome Institute, Walnut Creek, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Ramunas Stepanauskas

    1. Bigelow Laboratory for Ocean Sciences, East Boothbay, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Tanja Woyke

    1. U.S Department of Energy Joint Genome Institute, Walnut Creek, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Steven J Hallam

    1. University of British Columbia, Vancouver, Canada
    Competing interests
    The authors declare that no competing interests exist.
  9. Matthew B Sullivan

    1. University of Arizona, Tucson, United States
    For correspondence
    1. mbsulli@email.arizona.edu
    Competing interests
    The authors declare that no competing interests exist.

Reviewing Editor

  1. Nicole Dubilier, Reviewing Editor

Publication history

  1. Received: April 17, 2014
  2. Accepted: August 27, 2014
  3. Accepted Manuscript published: August 29, 2014 (version 1)
  4. Version of Record published: September 16, 2014 (version 2)

Copyright

© 2014, Roux et al

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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