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.affiliation: Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, United States.
authors.forename: Simon
authors.initials: S
authors.lastname: Roux
authors.affiliation: Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada.
authors.forename: Alyse K
authors.initials: AK
authors.lastname: Hawley
authors.affiliation: Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada.
authors.forename: Monica
authors.initials: M
authors.lastname: Torres Beltran
authors.affiliation: Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada.
authors.forename: Melanie
authors.initials: M
authors.lastname: Scofield
authors.affiliation: U.S Department of Energy Joint Genome Institute, Walnut Creek, United States.
authors.forename: Patrick
authors.initials: P
authors.lastname: Schwientek
authors.affiliation: Bigelow Laboratory for Ocean Sciences, East Boothbay, United States.
authors.forename: Ramunas
authors.initials: R
authors.lastname: Stepanauskas
authors.affiliation: U.S Department of Energy Joint Genome Institute, Walnut Creek, United States.
authors.forename: Tanja
authors.initials: T
authors.lastname: Woyke
authors.affiliation: Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada.
authors.forename: Steven J
authors.initials: SJ
authors.lastname: Hallam
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, United States.
authors.forename: Matthew B
authors.initials: MB
authors.lastname: Sullivan
mesh_terms: D001955:British Columbia; D017899:Caudovirales / Q000235:genetics* / Q000378:metabolism / Q000502:physiology; D004277:DNA, Single-Stranded / Q000235:genetics; D004463:Ecology; D017753:Ecosystem; D019143:Evolution, Molecular; D020563:Gammaproteobacteria / Q000145:classification / Q000235:genetics* / Q000821:virology; D016680:Genome, Bacterial / Q000235:genetics; D016679:Genome, Viral / Q000235:genetics; D023281:Genomics; D054884:Host-Pathogen Interactions; D054892:Metagenome / Q000235:genetics*; D017914:Microviridae / Q000235:genetics* / Q000378:metabolism / Q000502:physiology; D010100:Oxygen / Q000378:metabolism; D010802:Phylogeny; D012623:Seawater / Q000737:chemistry / Q000382:microbiology / Q000821:virology; D013455:Sulfur / Q000378:metabolism
chemical_list: D004277:DNA, Single-Stranded; D013455:Sulfur; D010100:Oxygen
keywords: SUP05; bacteriophages; ecology; infectious disease; microbiology; oxygen minimum zone; single cell genomics; viral dark matter; viruses