Neighbor predation linked to natural competence fosters the transfer of large genomic regions in Vibrio cholerae

  1. Noémie Matthey
  2. Sandrine Stutzmann
  3. Candice Stoudmann
  4. Nicolas Guex
  5. Christian Iseli
  6. Melanie Blokesch  Is a corresponding author
  1. Ecole Polytechnique Fédérale de Lausanne, Switzerland
  2. Swiss Institute of Bioinformatics, Switzerland

Abstract

Natural competence for transformation is a primary mode of horizontal gene transfer. Competent bacteria are able to absorb free DNA from their surroundings and exchange this DNA against pieces of their own genome when sufficiently homologous. However, the prevalence of non-degraded DNA with sufficient coding capacity is not well understood. In this context, we previously showed that naturally competent Vibrio cholerae use their type VI secretion system (T6SS) to actively acquire DNA from non-kin neighbors. Here, we explored the conditions of the DNA released through T6SS-mediated killing versus passive cell lysis and the extent of the transfers that occur due to these conditions. We show that competent V. cholerae acquire DNA fragments with a length exceeding 150 kbp in a T6SS-dependent manner. Collectively, our data support the notion that the environmental lifestyle of V. cholerae fosters the exchange of genetic material with sufficient coding capacity to significantly accelerate bacterial evolution.

Data availability

Sequencing reads have been deposited in NCBI's Sequence Read Archive (SRA) under SRA accession numbers SRR6934824 to SRR6935183. The Bioproject accession number is PRJNA447902.

The following previously published data sets were used

Article and author information

Author details

  1. Noémie Matthey

    Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6056-2756
  2. Sandrine Stutzmann

    Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  3. Candice Stoudmann

    Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  4. Nicolas Guex

    Vital-IT, Swiss Institute of Bioinformatics, Lausanne, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  5. Christian Iseli

    Vital-IT, Swiss Institute of Bioinformatics, Lausanne, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2296-2863
  6. Melanie Blokesch

    Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
    For correspondence
    melanie.blokesch@epfl.ch
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7024-1489

Funding

Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (31003A_162551)

  • Melanie Blokesch

Seventh Framework Programme (309064-VIR4ENV)

  • Melanie Blokesch

H2020 European Research Council (724630-CholeraIndex)

  • Melanie Blokesch

Howard Hughes Medical Institute (55008726)

  • Melanie Blokesch

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Tâm Mignot, CNRS-Aix Marseille University, France

Publication history

  1. Received: May 5, 2019
  2. Accepted: September 3, 2019
  3. Accepted Manuscript published: September 3, 2019 (version 1)
  4. Version of Record published: October 8, 2019 (version 2)

Copyright

© 2019, Matthey et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Noémie Matthey
  2. Sandrine Stutzmann
  3. Candice Stoudmann
  4. Nicolas Guex
  5. Christian Iseli
  6. Melanie Blokesch
(2019)
Neighbor predation linked to natural competence fosters the transfer of large genomic regions in Vibrio cholerae
eLife 8:e48212.
https://doi.org/10.7554/eLife.48212

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