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 experimentally evolved four consortia for 200 generations either in a constant or in a fluctuating environment with daily changes between commensalism and competition. To investigate the genetic basis underlying community evolution, we sequenced full genomes of single clones isolated at different time points during the experiment and identified all de novo mutations relative to the ancestral genomes.
Results/Conclusions
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. We showed that extinction was highly deterministic: when we replayed the evolution experiment from an intermediate time-point we repeatably reproduced species extinction. 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. In conclusion, our combination of experimental evolution of synthetic communities and genomics revealed fundamental insights into the genetics of adaptation in an ecological relevant context: we found that in fluctuating environments, the first steps of adaptation determined the fate of the community: early adaptation of one of the community members played a decisive role in determining whether the other species went extinct.