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Major bacterial lineages are essentially devoid of CRISPR-Cas viral defence systems

Author

Listed:
  • David Burstein

    (University of California, Berkeley)

  • Christine L. Sun

    (University of California, Berkeley
    Stanford University School of Medicine)

  • Christopher T. Brown

    (University of California, Berkeley)

  • Itai Sharon

    (University of California, Berkeley)

  • Karthik Anantharaman

    (University of California, Berkeley)

  • Alexander J. Probst

    (University of California, Berkeley)

  • Brian C. Thomas

    (University of California, Berkeley)

  • Jillian F. Banfield

    (University of California, Berkeley
    Policy and Management, University of California)

Abstract

Current understanding of microorganism–virus interactions, which shape the evolution and functioning of Earth’s ecosystems, is based primarily on cultivated organisms. Here we investigate thousands of viral and microbial genomes recovered using a cultivation-independent approach to study the frequency, variety and taxonomic distribution of viral defence mechanisms. CRISPR-Cas systems that confer microorganisms with immunity to viruses are present in only 10% of 1,724 sampled microorganisms, compared with previous reports of 40% occurrence in bacteria and 81% in archaea. We attribute this large difference to the lack of CRISPR-Cas systems across major bacterial lineages that have no cultivated representatives. We correlate absence of CRISPR-Cas with lack of nucleotide biosynthesis capacity and a symbiotic lifestyle. Restriction systems are well represented in these lineages and might provide both non-specific viral defence and access to nucleotides.

Suggested Citation

  • David Burstein & Christine L. Sun & Christopher T. Brown & Itai Sharon & Karthik Anantharaman & Alexander J. Probst & Brian C. Thomas & Jillian F. Banfield, 2016. "Major bacterial lineages are essentially devoid of CRISPR-Cas viral defence systems," Nature Communications, Nature, vol. 7(1), pages 1-8, April.
    • Handle: RePEc:nat:natcom:v:7:y:2016:i:1:d:10.1038_ncomms10613
    DOI: 10.1038/ncomms10613
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    Cited by:

    1. 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.
    2. Patrick A. Jonge & Koen Wortelboer & Torsten P. M. Scheithauer & Bert-Jan H. Born & Aeilko H. Zwinderman & Franklin L. Nobrega & Bas E. Dutilh & Max Nieuwdorp & Hilde Herrema, 2022. "Gut virome profiling identifies a widespread bacteriophage family associated with metabolic syndrome," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    3. Alexa M. Nicolas & Ella T. Sieradzki & Jennifer Pett-Ridge & Jillian F. Banfield & Michiko E. Taga & Mary K. Firestone & Steven J. Blazewicz, 2023. "A subset of viruses thrives following microbial resuscitation during rewetting of a seasonally dry California grassland soil," Nature Communications, Nature, vol. 14(1), pages 1-16, December.

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