Viral tagging reveals discrete populations in Synechococcus viral genome sequence space

Li Deng, J. Cesar Ignacio-Espinoza, Ann C. Gregory, Bonnie T. Poulos, Joshua S. Weitz, Philip Hugenholtz, Matthew Sullivan

Research output: Contribution to journalArticle

79 Citations (Scopus)

Abstract

Microbes and their viruses drive myriad processes across ecosystems ranging from oceans and soils to bioreactors and humans. Despite this importance, microbial diversity is only now being mapped at scales relevant to nature, while the viral diversity associated with any particular host remains little researched. Here we quantify host-associated viral diversity using viral-tagged metagenomics, which links viruses to specific host cells for high-throughput screening and sequencing. In a single experiment, we screened 10 Pacific Ocean viruses against a single strain of Synechococcus and found that naturally occurring cyanophage genome sequence space is statistically clustered into discrete populations. These population-based, host-linked viral ecological data suggest that, for this single host and seawater sample alone, there are at least 26 double-stranded DNA viral populations with estimated relative abundances ranging from 0.06 to 18.2%. These populations include previously cultivated cyanophage and new viral types missed by decades of isolate-based studies. Nucleotide identities of homologous genes mostly varied by less than 1% within populations, even in hypervariable genome regions, and by 42-71% between populations, which provides benchmarks for viral metagenomics and genome-based viral species definitions. Together these findings showcase a new approach to viral ecology that quantitatively links objectively defined environmental viral populations, and their genomes, to their hosts.

Original languageEnglish (US)
Pages (from-to)242-245
Number of pages4
JournalNature
Volume513
Issue number7517
DOIs
StatePublished - Sep 11 2014

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Synechococcus
Viral Genome
Population
Metagenomics
Genome
Viruses
Pacific Ocean
Benchmarking
Seawater
Bioreactors
Ecology
Oceans and Seas
Ecosystem
Soil
Nucleotides
DNA

ASJC Scopus subject areas

  • General

Cite this

Deng, L., Ignacio-Espinoza, J. C., Gregory, A. C., Poulos, B. T., Weitz, J. S., Hugenholtz, P., & Sullivan, M. (2014). Viral tagging reveals discrete populations in Synechococcus viral genome sequence space. Nature, 513(7517), 242-245. https://doi.org/10.1038/nature13459

Viral tagging reveals discrete populations in Synechococcus viral genome sequence space. / Deng, Li; Ignacio-Espinoza, J. Cesar; Gregory, Ann C.; Poulos, Bonnie T.; Weitz, Joshua S.; Hugenholtz, Philip; Sullivan, Matthew.

In: Nature, Vol. 513, No. 7517, 11.09.2014, p. 242-245.

Research output: Contribution to journalArticle

Deng, L, Ignacio-Espinoza, JC, Gregory, AC, Poulos, BT, Weitz, JS, Hugenholtz, P & Sullivan, M 2014, 'Viral tagging reveals discrete populations in Synechococcus viral genome sequence space', Nature, vol. 513, no. 7517, pp. 242-245. https://doi.org/10.1038/nature13459
Deng L, Ignacio-Espinoza JC, Gregory AC, Poulos BT, Weitz JS, Hugenholtz P et al. Viral tagging reveals discrete populations in Synechococcus viral genome sequence space. Nature. 2014 Sep 11;513(7517):242-245. https://doi.org/10.1038/nature13459
Deng, Li ; Ignacio-Espinoza, J. Cesar ; Gregory, Ann C. ; Poulos, Bonnie T. ; Weitz, Joshua S. ; Hugenholtz, Philip ; Sullivan, Matthew. / Viral tagging reveals discrete populations in Synechococcus viral genome sequence space. In: Nature. 2014 ; Vol. 513, No. 7517. pp. 242-245.
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