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

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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

(2018) Long-Read-Based Genome Sequences of Pandemic and Environmental Vibrio cholerae Strains
NCBI Bioproject, PRJNA447902.

https://www.ncbi.nlm.nih.gov/bioproject/PRJNA447902

Article and author information

Author details

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.

"This ORCID iD identifies the author of this article:" 0000-0002-6056-2756
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.
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.
Nicolas Guex

Vital-IT, Swiss Institute of Bioinformatics, Lausanne, Switzerland

Competing interests
The authors declare that no competing interests exist.
Christian Iseli

Vital-IT, Swiss Institute of Bioinformatics, Lausanne, Switzerland

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-2296-2863
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.

"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.

Copyright

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.