Evolution of diversity explains the impact of pre-adaptation of a focal species on the structure of a natural microbial community


Rapid within-species evolution can alter community structure, yet the mechanisms underpinning this effect remain unknown. Populations that rapidly evolve large amounts of phenotypic diversity are likely to interact with more species and have the largest impact on community structure. However, the evolution of phenotypic diversity is, in turn, influenced by the presence of other species. Here, we investigate how microbial community structure changes as a consequence of rapidly evolved within-species diversity using Pseudomonas fluorescens as a focal species. Evolved P. fluorescens populations showed substantial phenotypic diversification in resource-use (and correlated genomic change) irrespective of whether they were pre-adapted in isolation or in a community context. Manipulating diversity revealed that more diverse P. fluorescens populations had the greatest impact on community structure, by suppressing some bacterial taxa, but facilitating others. These findings suggest that conditions that promote the evolution of high within-population diversity should result in a larger impact on community structure.

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Fig. 1: Overview of experimental design.
Fig. 2: Differences in resource use between clones.
Fig. 3: Phenotypic variation in resource use after pre-adaptation reflects associated genomic changes.
Fig. 4: Effect of diversity on community composition.
Fig. 5: Effect of pre-adaptation on community structure at different levels of diversity.
Fig. 6: Effect of diversity on the abundance of common bacterial ASVs.
Fig. 7: Density of the focal species at the end of the experiment.

Data availability

All data and R code used in the analysis will be made available on GitHub and archived on Zenodo.


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This work was funded by a NERC grant awarded to AB, SP, and RG.

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AB, DP, AV, and EH conceived the study and designed the experiments. AV, DP, and EH conducted the experiments and DP analysed the data. SP and RG provided new perspectives. DP, EH, and AB wrote the first draft of the manuscript, with all authors contributing to the final version

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Correspondence to Daniel Padfield or Elze Hesse.

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Padfield, D., Vujakovic, A., Paterson, S. et al. Evolution of diversity explains the impact of pre-adaptation of a focal species on the structure of a natural microbial community. ISME J (2020). https://doi.org/10.1038/s41396-020-00755-3

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