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Migration and horizontal gene transfer divide microbial genomes into multiple niches

Author

Listed:
  • Rene Niehus

    (University of Oxford
    Oxford Centre for Integrative Systems Biology, University of Oxford)

  • Sara Mitri

    (University of Lausanne)

  • Alexander G. Fletcher

    (Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford
    School of Mathematics and Statistics, University of Sheffield)

  • Kevin R. Foster

    (University of Oxford
    Oxford Centre for Integrative Systems Biology, University of Oxford)

Abstract

Horizontal gene transfer is central to microbial evolution, because it enables genetic regions to spread horizontally through diverse communities. However, how gene transfer exerts such a strong effect is not understood. Here we develop an eco-evolutionary model and show how genetic transfer, even when rare, can transform the evolution and ecology of microbes. We recapitulate existing models, which suggest that asexual reproduction will overpower horizontal transfer and greatly limit its effects. We then show that allowing immigration completely changes these predictions. With migration, the rates and impacts of horizontal transfer are greatly increased, and transfer is most frequent for loci under positive natural selection. Our analysis explains how ecologically important loci can sweep through competing strains and species. In this way, microbial genomes can evolve to become ecologically diverse where different genomic regions encode for partially overlapping, but distinct, ecologies. Under these conditions ecological species do not exist, because genes, not species, inhabit niches.

Suggested Citation

  • Rene Niehus & Sara Mitri & Alexander G. Fletcher & Kevin R. Foster, 2015. "Migration and horizontal gene transfer divide microbial genomes into multiple niches," Nature Communications, Nature, vol. 6(1), pages 1-9, December.
    • Handle: RePEc:nat:natcom:v:6:y:2015:i:1:d:10.1038_ncomms9924
    DOI: 10.1038/ncomms9924
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    Cited by:

    1. Klimenko, Alexandra I. & Matushkin, Yury G. & Kolchanov, Nikolay A. & Lashin, Sergey A., 2019. "Spatial heterogeneity promotes antagonistic evolutionary scenarios in microbial community explained by ecological stratification: a simulation study," Ecological Modelling, Elsevier, vol. 399(C), pages 66-76.
    2. Suzanne Humphrey & Alfred Fillol-Salom & Nuria Quiles-Puchalt & Rodrigo Ibarra-Chávez & Andreas F. Haag & John Chen & José R. Penadés, 2021. "Bacterial chromosomal mobility via lateral transduction exceeds that of classical mobile genetic elements," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
    3. Cameron J. Reid & Max L. Cummins & Stefan Börjesson & Michael S. M. Brouwer & Henrik Hasman & Anette M. Hammerum & Louise Roer & Stefanie Hess & Thomas Berendonk & Kristina Nešporová & Marisa Haenni &, 2022. "A role for ColV plasmids in the evolution of pathogenic Escherichia coli ST58," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    4. Pekka Marttinen & William P Hanage, 2017. "Speciation trajectories in recombining bacterial species," PLOS Computational Biology, Public Library of Science, vol. 13(7), pages 1-15, July.
    5. Shiben Zhu & Juken Hong & Teng Wang, 2024. "Horizontal gene transfer is predicted to overcome the diversity limit of competing microbial species," Nature Communications, Nature, vol. 15(1), pages 1-9, December.
    6. Vit Piskovsky & Nuno M. Oliveira, 2023. "Bacterial motility can govern the dynamics of antibiotic resistance evolution," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    7. Akshit Goyal, 2018. "Metabolic adaptations underlying genome flexibility in prokaryotes," PLOS Genetics, Public Library of Science, vol. 14(10), pages 1-15, October.

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