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Title: Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics

Abstract

Viruses modulate microbial communities and alter ecosystem functions. However, due to cultivation bottlenecks, specific virus–host interaction dynamics remain cryptic. In this study, we examined 127 single-cell amplified genomes (SAGs) from uncultivated SUP05 bacteria isolated from a model 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 is 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 the potential to modulate biogeochemical cycling in climate-critical and expanding OMZs.

Authors:
 [1];  [2];  [2];  [2];  [3];  [4];  [3];  [5];  [1]
  1. Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, United States
  2. Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
  3. U.S Department of Energy Joint Genome Institute, Walnut Creek, United States
  4. Bigelow Laboratory for Ocean Sciences, East Boothbay, United States
  5. Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada, Graduate Program in Bioinformatics, University of British Columbia, Vancouver, Canada
Publication Date:
Sponsoring Org.:
USDOE
OSTI Identifier:
1197677
Alternate Identifier(s):
OSTI ID: 1197678
Grant/Contract Number:  
AC02-05CH1123
Resource Type:
Published Article
Journal Name:
eLife
Additional Journal Information:
Journal Name: eLife Journal Volume: 3; Journal ID: ISSN 2050-084X
Publisher:
eLife Sciences Publications, Ltd.
Country of Publication:
United States
Language:
English

Citation Formats

Roux, Simon, Hawley, Alyse K., Torres Beltran, Monica, Scofield, Melanie, Schwientek, Patrick, Stepanauskas, Ramunas, Woyke, Tanja, Hallam, Steven J., and Sullivan, Matthew B. Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics. United States: N. p., 2014. Web. doi:10.7554/eLife.03125.
Roux, Simon, Hawley, Alyse K., Torres Beltran, Monica, Scofield, Melanie, Schwientek, Patrick, Stepanauskas, Ramunas, Woyke, Tanja, Hallam, Steven J., & Sullivan, Matthew B. Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics. United States. doi:10.7554/eLife.03125.
Roux, Simon, Hawley, Alyse K., Torres Beltran, Monica, Scofield, Melanie, Schwientek, Patrick, Stepanauskas, Ramunas, Woyke, Tanja, Hallam, Steven J., and Sullivan, Matthew B. Fri . "Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics". United States. doi:10.7554/eLife.03125.
@article{osti_1197677,
title = {Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics},
author = {Roux, Simon and Hawley, Alyse K. and Torres Beltran, Monica and Scofield, Melanie and Schwientek, Patrick and Stepanauskas, Ramunas and Woyke, Tanja and Hallam, Steven J. and Sullivan, Matthew B.},
abstractNote = {Viruses modulate microbial communities and alter ecosystem functions. However, due to cultivation bottlenecks, specific virus–host interaction dynamics remain cryptic. In this study, we examined 127 single-cell amplified genomes (SAGs) from uncultivated SUP05 bacteria isolated from a model 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 is 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 the potential to modulate biogeochemical cycling in climate-critical and expanding OMZs.},
doi = {10.7554/eLife.03125},
journal = {eLife},
number = ,
volume = 3,
place = {United States},
year = {2014},
month = {8}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.7554/eLife.03125

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Cited by: 52 works
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