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Hidden diversity of soil giant viruses

Author

Listed:
  • Frederik Schulz

    (Joint Genome Institute)

  • Lauren Alteio

    (University of Massachusetts)

  • Danielle Goudeau

    (Joint Genome Institute)

  • Elizabeth M. Ryan

    (Joint Genome Institute)

  • Feiqiao B. Yu

    (Stanford University)

  • Rex R. Malmstrom

    (Joint Genome Institute)

  • Jeffrey Blanchard

    (University of Massachusetts)

  • Tanja Woyke

    (Joint Genome Institute)

Abstract

Known giant virus diversity is currently skewed towards viruses isolated from aquatic environments and cultivated in the laboratory. Here, we employ cultivation-independent metagenomics and mini-metagenomics on soils from the Harvard Forest, leading to the discovery of 16 novel giant viruses, chiefly recovered by mini-metagenomics. The candidate viruses greatly expand phylogenetic diversity of known giant viruses and either represented novel lineages or are affiliated with klosneuviruses, Cafeteria roenbergensis virus or tupanviruses. One assembled genome with a size of 2.4 Mb represents the largest currently known viral genome in the Mimiviridae, and others encode up to 80% orphan genes. In addition, we find more than 240 major capsid proteins encoded on unbinned metagenome fragments, further indicating that giant viruses are underexplored in soil ecosystems. The fact that most of these novel viruses evaded detection in bulk metagenomes suggests that mini-metagenomics could be a valuable approach to unearth viral giants.

Suggested Citation

  • Frederik Schulz & Lauren Alteio & Danielle Goudeau & Elizabeth M. Ryan & Feiqiao B. Yu & Rex R. Malmstrom & Jeffrey Blanchard & Tanja Woyke, 2018. "Hidden diversity of soil giant viruses," Nature Communications, Nature, vol. 9(1), pages 1-9, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-07335-2
    DOI: 10.1038/s41467-018-07335-2
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    Cited by:

    1. Sofia Rigou & Sébastien Santini & Chantal Abergel & Jean-Michel Claverie & Matthieu Legendre, 2022. "Past and present giant viruses diversity explored through permafrost metagenomics," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    2. Alexandra Bessenay & Hugo Bisio & Lucid Belmudes & Yohann Couté & Lionel Bertaux & Jean-Michel Claverie & Chantal Abergel & Sandra Jeudy & Matthieu Legendre, 2024. "Complex transcriptional regulations of a hyperparasitic quadripartite system in giant viruses infecting protists," Nature Communications, Nature, vol. 15(1), pages 1-15, December.

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