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PMID: 25171894 Published · epublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

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

eLife ·Vol. 3 ·2014-08-29 ·Pages e03125

Roux S, Hawley AK, Torres Beltran M, Scofield M, Schwientek P, Stepanauskas R, Woyke T, Hallam SJ, Sullivan MB

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.

Keywords
SUP05 bacteriophages ecology infectious disease microbiology oxygen minimum zone single cell genomics viral dark matter viruses
MeSH Terms
British Columbia Caudovirales/genetics,metabolism,physiology DNA, Single-Stranded/genetics Ecology Ecosystem Evolution, Molecular Gammaproteobacteria/classification,genetics,virology Genome, Bacterial/genetics Genome, Viral/genetics Genomics Host-Pathogen Interactions Metagenome/genetics Microviridae/genetics,metabolism,physiology Oxygen/metabolism Phylogeny Seawater/chemistry,microbiology,virology Sulfur/metabolism
Chemicals
DNA, Single-Stranded Sulfur Oxygen
Authors & Affiliations
9 authors, click to expand affiliations / ORCID
Roux Simon
Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, United States.
Hawley Alyse K
Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada.
Torres Beltran Monica
Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada.
Scofield Melanie
Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada.
Schwientek Patrick
U.S Department of Energy Joint Genome Institute, Walnut Creek, United States.
Stepanauskas Ramunas
Bigelow Laboratory for Ocean Sciences, East Boothbay, United States.
Woyke Tanja
U.S Department of Energy Joint Genome Institute, Walnut Creek, United States.
Hallam Steven J
Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada.
Sullivan Matthew B
Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, United States.
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Article Info
Journal
eLife
Abbr.
Elife
ISSN
2050-084X
DOI
10.7554/eLife.03125
Published
2014-08-29
Epub
2014-00-29
Pages
e03125
Language
English
Region
England
NLM ID
101579614
PMCID
PMC4164917
Subset
IM
Corrections
CommentIn
PMID: 25310237
External Links
PubMed source DOI: 10.7554/eLife.03125 PMC Full Text View journal details
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