Single-cell genomics-based analysis of virus–host interactions in marine surface bacterioplankton

Labonté, Jessica M.; Swan, Brandon K.; Poulos, Bonnie; Luo, Haiwei; Koren, Sergey; Hallam, Steven J.; Sullivan, Matthew B.; Woyke, Tanja; Eric Wommack, K.; Stepanauskas, Ramunas

doi:10.1038/ismej.2015.48

Title: Single-cell genomics-based analysis of virus–host interactions in marine surface bacterioplankton

Journal Article · Tue Apr 07 00:00:00 EDT 2015 · The ISME Journal

DOI:https://doi.org/10.1038/ismej.2015.48· OSTI ID:1347108

Labonté, Jessica M. ^[1]; Swan, Brandon K. ^[1]; Poulos, Bonnie ^[2]; Luo, Haiwei ^[3]; Koren, Sergey ^[4]; Hallam, Steven J. ^[5]; Sullivan, Matthew B. ^[2]; Woyke, Tanja ^[6]; Eric Wommack, K. ^[7]; Stepanauskas, Ramunas ^[1]

Bigelow Lab. for Ocean Sciences, East Boothbay, ME (United States)
Univ. of Arizona, Tucson, AZ (United States). Dept. of Ecology and Evoloutionary Biology
Chinese Univ. of Hong Kong (China). School of Life Sciences
National Biodefense Analysis and Countermeasure Center, Frederick, MD (United States)
Univ. of British Columbia, Vancouver, BC (Canada). Dept. of Microbiology and Immunology
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Univ. of Delaware, Newark, DE (United States). Dept. of Plant and Soil Sciences

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. Furthermore, 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. This 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.

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Research Organization:: USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1347108

Journal Information:: The ISME Journal, Vol. 9, Issue 11; ISSN 1751-7362

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 144 works

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