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Marine viruses discovered via metagenomics shed light on viral strategies throughout the oceans

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  • Felipe H. Coutinho

    (Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ)
    Centre for Molecular and Biomolecular Informatics (CMBI), Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre
    Theoretical Biology and Bioinformatics, Utrecht University (UU))

  • Cynthia B. Silveira

    (Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ)
    San Diego State University (SDSU))

  • Gustavo B. Gregoracci

    (Universidade Federal de São Paulo (UNIFESP))

  • Cristiane C. Thompson

    (Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ))

  • Robert A. Edwards

    (San Diego State University (SDSU))

  • Corina P. D. Brussaard

    (NIOZ Royal Netherlands Institute for Sea Research, and University of Utrecht
    Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam)

  • Bas E. Dutilh

    (Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ)
    Centre for Molecular and Biomolecular Informatics (CMBI), Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre
    Theoretical Biology and Bioinformatics, Utrecht University (UU))

  • Fabiano L. Thompson

    (Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ)
    Universidade Federal do Rio de Janeiro (UFRJ)/COPPE/SAGE)

Abstract

Marine viruses are key drivers of host diversity, population dynamics and biogeochemical cycling and contribute to the daily flux of billions of tons of organic matter. Despite recent advancements in metagenomics, much of their biodiversity remains uncharacterized. Here we report a data set of 27,346 marine virome contigs that includes 44 complete genomes. These outnumber all currently known phage genomes in marine habitats and include members of previously uncharacterized lineages. We designed a new method for host prediction based on co-occurrence associations that reveals these viruses infect dominant members of the marine microbiome such as Prochlorococcus and Pelagibacter. A negative association between host abundance and the virus-to-host ratio supports the recently proposed Piggyback-the-Winner model of reduced phage lysis at higher host densities. An analysis of the abundance patterns of viruses throughout the oceans revealed how marine viral communities adapt to various seasonal, temperature and photic regimes according to targeted hosts and the diversity of auxiliary metabolic genes.

Suggested Citation

  • Felipe H. Coutinho & Cynthia B. Silveira & Gustavo B. Gregoracci & Cristiane C. Thompson & Robert A. Edwards & Corina P. D. Brussaard & Bas E. Dutilh & Fabiano L. Thompson, 2017. "Marine viruses discovered via metagenomics shed light on viral strategies throughout the oceans," Nature Communications, Nature, vol. 8(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:8:y:2017:i:1:d:10.1038_ncomms15955
    DOI: 10.1038/ncomms15955
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    Cited by:

    1. Gonçalo J. Piedade & Max E. Schön & Cédric Lood & Mikhail V. Fofanov & Ella M. Wesdorp & Tristan E. G. Biggs & Lingyi Wu & Henk Bolhuis & Matthias G. Fischer & Natalya Yutin & Bas E. Dutilh & Corina P, 2024. "Seasonal dynamics and diversity of Antarctic marine viruses reveal a novel viral seascape," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    2. Shicong Du & Xinzhao Tong & Alvin C. K. Lai & Chak K. Chan & Christopher E. Mason & Patrick K. H. Lee, 2023. "Highly host-linked viromes in the built environment possess habitat-dependent diversity and functions for potential virus-host coevolution," Nature Communications, Nature, vol. 14(1), pages 1-15, December.

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