Interactions between microbes can both constrain and enhance adaptation, but to date, most studies employ simplified communities and environments. We measured fitness of populations of the soil bacterium Pseudomonas fluorescens that have been evolved in both the presence and absence of a natural potting soil microbial community. Populations from both environments showed similar fitness increases with respect to the ancestor in the absence of the community, suggesting no significant cost of evolving with the community. By contrast, fitness in the presence of the community increased for community-evolved populations, but decreased considerably below the ancestral state for populations evolved in the absence of the community. This suggests some abiotic beneficial mutations are costly in the presence of the community, while others are not, with the former only selected against in the presence of the community. Most mutations underpinning fitness changes were clone specific, supporting the view that there are multiple genetic pathways to adaptation in this complex environment. Such extreme mutational effects have not been observed in comparable in vitro studies that employ much simpler abiotic and biotic environments, and suggest that a caution is need when extrapolating results from simplified in vitro systems to real-world contexts.

This research was experimentally preformed in the lab. On one hand, bacterial fitness was estimated according to the described procedure in the methodology. And in the other hand, whole-genome sequencing data was also following the describe procedure, having all sequences deposited in teh ENA database.