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

Roux, Simon; Hawley, Alyse K.; Torres Beltran, Monica; Scofield, Melanie; Schwientek, Patrick; Stepanauskas, Ramunas; Woyke, Tanja; Hallam, Steven J.; Sullivan, Matthew B.

doi:10.7554/eLife.03125

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

Journal Article · Fri Aug 29 00:00:00 EDT 2014 · eLife

DOI:https://doi.org/10.7554/eLife.03125· OSTI ID:1197677

Roux, Simon ^[1]; Hawley, Alyse K. ^[2]; Torres Beltran, Monica ^[2]; Scofield, Melanie ^[2]; Schwientek, Patrick ^[3]; Stepanauskas, Ramunas ^[4]; Woyke, Tanja ^[3]; Hallam, Steven J. ^[5]; Sullivan, Matthew B. ^[1]

Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, United States
Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
U.S Department of Energy Joint Genome Institute, Walnut Creek, United States
Bigelow Laboratory for Ocean Sciences, East Boothbay, United States
Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada, Graduate Program in Bioinformatics, University of British Columbia, Vancouver, Canada

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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC02-05CH1123; AC02-05CH11231

OSTI ID:: 1197677

Alternate ID(s):: OSTI ID: 1197678; OSTI ID: 1628813

Journal Information:: eLife, Journal Name: eLife Vol. 3; ISSN 2050-084X

Publisher:: eLife Sciences Publications, Ltd.Copyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 132 works

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