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Quantifying the local adaptive landscape of a nascent bacterial community

Author

Listed:
  • Joao A. Ascensao

    (University of California, Berkeley)

  • Kelly M. Wetmore

    (Lawrence Berkeley National Laboratory)

  • Benjamin H. Good

    (Stanford University)

  • Adam P. Arkin

    (University of California, Berkeley
    Lawrence Berkeley National Laboratory)

  • Oskar Hallatschek

    (University of California, Berkeley
    University of California, Berkeley
    Leipzig University)

Abstract

The fitness effects of all possible mutations available to an organism largely shape the dynamics of evolutionary adaptation. Yet, whether and how this adaptive landscape changes over evolutionary times, especially upon ecological diversification and changes in community composition, remains poorly understood. We sought to fill this gap by analyzing a stable community of two closely related ecotypes (“L” and “S”) shortly after they emerged within the E. coli Long-Term Evolution Experiment (LTEE). We engineered genome-wide barcoded transposon libraries to measure the invasion fitness effects of all possible gene knockouts in the coexisting strains as well as their ancestor, for many different, ecologically relevant conditions. We find consistent statistical patterns of fitness effect variation across both genetic background and community composition, despite the idiosyncratic behavior of individual knockouts. Additionally, fitness effects are correlated with evolutionary outcomes for a number of conditions, possibly revealing shifting patterns of adaptation. Together, our results reveal how ecological and epistatic effects combine to shape the adaptive landscape in a nascent ecological community.

Suggested Citation

  • Joao A. Ascensao & Kelly M. Wetmore & Benjamin H. Good & Adam P. Arkin & Oskar Hallatschek, 2023. "Quantifying the local adaptive landscape of a nascent bacterial community," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-022-35677-5
    DOI: 10.1038/s41467-022-35677-5
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    Cited by:

    1. Daniel P. G. H. Wong & Benjamin H. Good, 2024. "Quantifying the adaptive landscape of commensal gut bacteria using high-resolution lineage tracking," Nature Communications, Nature, vol. 15(1), pages 1-14, December.

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