Microbial diversification in experimentally evolved communities

Microbial communities are incredibly diverse. Molecular techniques using ‘omics’ approaches have uncovered a vast number of microbial ‘species’ in communities from natural environments. Yet, the eco-evolutionary processes originating this microbial diversity remain understudied. Here, we experimentally determined the role that commensal interactions play in the formation of new bacterial ‘species’ in communities. We studied a commensal interaction between two bacterial species in which Acinetobacter cross-feeds resources to Pseudomonas. We evolved in parallel four experimental replicates of species growing in isolation or together in consortia for 200 generations. After 60 generations, Pseudomonas diversified into two morphotypes that coexisted until the end of the experiment. Morphotypes differed from the ancestor and each other in one point mutation. One of the morphotypes had mutations in the fleQ gene encoding the master regulator of flagella and biofilm formation. We experimentally confirmed that the fleQ mutants were unable to swim and form biofilms but had a higher yield compared to the ancestor. Interestingly, the coexistence of mutants was only observed in the presence of Acinetobacter and not in isolation. We hypothesize that Acinetobacter modulates the coexistence of newly formed lineagesthrough a yield-foraging tradeoff. While motile cells pay the metabolic burden of motility, they can swim toward the nutrients leaked from Acinetobacter (i.e., chemotaxis), giving them preferential access to new resources. Given that both chemotaxis and cross-feeding are widespread in microbial communities, the yield-foraging tradeoff has the potential to be a general mechanism contributing to the formation of new bacterial ‘species’ in microbial communities.