Letter | Published:

Viral tagging reveals discrete populations in Synechococcus viral genome sequence space

Nature volume 513, pages 242245 (11 September 2014) | Download Citation

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Abstract

Microbes and their viruses drive myriad processes across ecosystems ranging from oceans and soils to bioreactors and humans1,2,3,4. Despite this importance, microbial diversity is only now being mapped at scales relevant to nature5, 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 107 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.

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Change history

  • 10 September 2014

    Minor changes were made to Extended Data Fig. 2.

Accessions

Primary accessions

GenBank/EMBL/DDBJ

Data deposits

Data for viral genomes have been deposited in GenBank under accession numbers JN371768 and KF156338-40; metagenomic data have been deposited in CAMERA under accession numbers CAM_P_0001068 and CAM_P_0000915; raw data including gp23 sequences and informatic pipelines, assemblies and data for figures are available at http://datadryad.org/resource/doi:10.5061/dryad.gr3ks.

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Acknowledgements

Funding was provided by the US Department of Energy (DOE) Joint Genome Institute (JGI) Community Sequencing Program, Biosphere 2, BIO5, US National Science Foundation (NSF) OCE0940390, and Gordon and Betty Moore Foundation grants to M.B.S., as well as NSF OCE1233760 and Burroughs Wellcome Fund grants to J.S.W. We thank J. Fuhrman for suggesting stable-isotope-labelled host DNA; A. Z. Worden and the CANON Initiative for the cruise opportunity; Worden laboratory members; the captain and crew of the R/V Western Flyer for operational/sampling support; J. B. Waterbury, S. W. Chisholm and A. Wichels for strains; the Tucson Marine Phage laboratory; Institute of Groundwater Ecology of Helmholtz Munich; and N. Pace, M. Young, S. W. Chisholm and S. Yilmaz for technical/analytical support and manuscript comments. We acknowledge the University of Arizona Genetics Core for viral-tagging metagenomic sequencing; iCyt and the Arizona Cancer Center and Arizona Research Laboratories (ARL) Division of Biotechnology Cytometry Core Facility for cytometry support; the University Information Technology Services Research Computing Group and the ARL Biotechnology Computing for high-performance computing clusters (HPCC) access and support. Community metagenomic sequencing was provided by the DOE JGI Community Sequencing Program under the Office of Science of the US DOE contract no. DE-AC02-05CH11231.

Author information

Author notes

    • Li Deng

    Present address: Helmholtz Zentrum München-German Research Center for Environmental Health, Institute of Groundwater Ecology, Neuherberg 85764, Germany.

    • Li Deng
    •  & J. Cesar Ignacio-Espinoza

    These authors contributed equally to this work.

Affiliations

  1. Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85719, USA

    • Li Deng
    • , Ann C. Gregory
    • , Bonnie T. Poulos
    •  & Matthew B. Sullivan
  2. Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85719, USA

    • J. Cesar Ignacio-Espinoza
    •  & Matthew B. Sullivan
  3. School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA

    • Joshua S. Weitz
  4. School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA

    • Joshua S. Weitz
  5. Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences & Institute for Molecular Bioscience, The University of Queensland, St Lucia QLB 4072, Australia

    • Philip Hugenholtz

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Contributions

L.D., P.H. and M.B.S. designed the experiments. L.D. collected samples. L.D., A.C.G. and B.T.P. performed the experiments. L.D., J.C.I.-E., J.S.W., P.H. and M.B.S. analysed data, interpreted results and wrote the paper.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Matthew B. Sullivan.

Extended data

Supplementary information

PDF files

  1. 1.

    Supplementary Table 1

    Morphological taxonomic assignation of published viral isolates on Synechococcus WH7803.

Excel files

  1. 1.

    Supplementary Data 1

    Annotation of open reading frames (ORFs) on 26 CGs (worksheet1) and all small contigs larger than 1.5 Kb (worksheet2).

  2. 2.

    Supplementary Data 2

    This file contains source data for Table 1 (in the main paper), Extended Data Figure 3 and Extended Data Figure 7.

About this article

Publication history

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DOI

https://doi.org/10.1038/nature13459

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