title: Single-cell genomics-based analysis of virus-host interactions in marine surface bacterioplankton.
abstract: Viral infections dynamically alter the composition and metabolic potential of marine microbial communities and the evolutionary trajectories of host populations with resulting feedback on biogeochemical cycles. It is quite possible that all microbial populations in the ocean are impacted by viral infections. Our knowledge of virus-host relationships, however, has been limited to a minute fraction of cultivated host groups. Here, we utilized single-cell sequencing to obtain genomic blueprints of viruses inside or attached to individual bacterial and archaeal cells captured in their native environment, circumventing the need for host and virus cultivation. A combination of comparative genomics, metagenomic fragment recruitment, sequence anomalies and irregularities in sequence coverage depth and genome recovery were utilized to detect viruses and to decipher modes of virus-host interactions. Members of all three tailed phage families were identified in 20 out of 58 phylogenetically and geographically diverse single amplified genomes (SAGs) of marine bacteria and archaea. At least four phage-host interactions had the characteristics of late lytic infections, all of which were found in metabolically active cells. One virus had genetic potential for lysogeny. Our findings include first known viruses of Thaumarchaeota, Marinimicrobia, Verrucomicrobia and Gammaproteobacteria clusters SAR86 and SAR92. Viruses were also found in SAGs of Alphaproteobacteria and Bacteroidetes. A high fragment recruitment of viral metagenomic reads confirmed that most of the SAG-associated viruses are abundant in the ocean. Our study demonstrates that single-cell genomics, in conjunction with sequence-based computational tools, enable in situ, cultivation-independent insights into host-virus interactions in complex microbial communities.
authors.affiliation: Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA.
authors.forename: Jessica M
authors.initials: JM
authors.lastname: Labonté
authors.affiliation: Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA.
authors.forename: Brandon K
authors.initials: BK
authors.lastname: Swan
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA.
authors.forename: Bonnie
authors.initials: B
authors.lastname: Poulos
authors.affiliation: School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
authors.forename: Haiwei
authors.initials: H
authors.lastname: Luo
authors.affiliation: National Biodefense Analysis and Countermeasures Center, Frederick, MD, USA.
authors.forename: Sergey
authors.initials: S
authors.lastname: Koren
authors.affiliation: Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada.
authors.forename: Steven J
authors.initials: SJ
authors.lastname: Hallam
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA.
authors.forename: Matthew B
authors.initials: MB
authors.lastname: Sullivan
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, CA, USA.
authors.forename: Tanja
authors.initials: T
authors.lastname: Woyke
authors.affiliation: Department of Plant and Soil Sciences, University of Delaware, Newark, DE, USA.
authors.forename: K Eric
authors.initials: KE
authors.lastname: Wommack
authors.affiliation: Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA.
authors.forename: Ramunas
authors.initials: R
authors.lastname: Stepanauskas
mesh_terms: D001105:Archaea / Q000821:virology; D001435:Bacteriophages / Q000235:genetics*; D041963:Bacteroidetes / Q000821:virology; D004279:DNA, Viral / Q000235:genetics; D020563:Gammaproteobacteria / Q000821:virology*; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D023281:Genomics; D019015:Geologic Sediments / Q000382:microbiology*; D056186:Metagenomics; D010802:Phylogeny; D010933:Plankton / Q000821:virology*; D059010:Single-Cell Analysis; D061327:Verrucomicrobia / Q000821:virology
chemical_list: D004279:DNA, Viral
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