Abstract
Interactions between microbes can both constrain and enhance their adaptation to the environment. However, most studies to date have employed simplified microbial communities and environmental conditions. We determined how the presence of a commercial potting compost microbial community affected adaptation of the soil bacterium Pseudomonas fluorescens SBW25 in potting compost. Pseudomonas fluorescens clones isolated from populations evolved in both the presence and absence of the community showed similar fitness increases when measured in the absence of the community. This suggests the presence of the community did not constrain adaptation. By contrast, fitness measured in the presence of the community increased for community-evolved populations, but decreased below the ancestral state for populations evolved in the absence of the community. This suggests some, but not all, mutations that were beneficial with respect to the abiotic environment were costly in the presence of the community, with the former selected against in the presence of the community. Whole-genome sequencing supports this interpretation: most mutations underpinning fitness changes were clone-specific, suggesting multiple genetic pathways to adaptation. Such extreme mutational effects have not been observed in comparable in vitro studies, suggesting that caution is needed when extrapolating results from simplified in vitro systems to natural contexts.
Highlights
Competition experiments between all bacterial clones and a lacZ-marked SBW25 ancestor were carried out as in previous studies [20,21] to estimate the fitness of evolved bacteria in both the presence and absence of the soil microbial community
We measured the fitness of each bacterial clone in both selective environments, and found that there was a significant interaction between the selection environment and the environment in which fitness was measured (F1,58 = 82.32, p < 0.001)
The novelty of the abiotic environments and the high densities of other organisms will invariably impose very strong selection on the focal organism, potentially leading to findings that may not be observed under more natural conditions
Summary
Biología Aplicada del Segura (CEBAS-CSIC), Murcia, Spain. Biology, ETH-Zurich, Zurich, Switzerland. Competition experiments between all bacterial clones and a lacZ-marked SBW25 ancestor were carried out as in previous studies [20,21] to estimate the fitness of evolved bacteria in both the presence and absence of the soil microbial community. Relative fitness analysis for each individual bacterial clone was performed with a linear mixed effects model fitted with REML, where the selective environment ( presence and absence of the community) was fitted as a main factor, and nested replicates (n = 3) as a random effect. This was carried out in JMP software.
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