Evolving synthetic communities in fluctuating environments

Positive species interactions underlie the functioning of ecosystems. Given their importance, it is crucial to better understand the stability of positive interactions over evolutionary timescales, in both constant and fluctuating environments; e.g. environments interrupted with periods of competition. We addressed this question using a two-species microbial system in which we modulated interactions according to the nutrient provided. We evolved four consortia for 200 generations either in a constant or in a fluctuating environment with daily changes between commensalism and competition. The two species co-existed over 200 generations in the constant commensal environment. In contrast, in the fluctuating environment, co-existence broke down when one of the species went extinct after 120 generations in two out of four cases. To explore why extinction occurred, we sequenced the genome of clones isolated before and after the collapse. In the two consortia in which species coexisted until the end of the experiment, both species fixed one mutation after 92 generations. In the other two consortia, only one of the species fixed a mutation while the other species did not fix any mutations and went extinct. Our results suggest that, in fluctuating environments, initial responses to fluctuating selection can determine the stability of simple communities.