Microbial diversification is maintained in an experimentally evolved synthetic community

Abstract

Microbial communities are incredibly diverse. Yet, the eco-evolutionary processes originating and maintaining this diversity remain understudied. Here, we investigate the patterns of diversification for Pseudomonas putida evolving in isolation and with Acinetobacter johnsonii leaking resources used by P. putida. We experimentally evolved four experimental replicates in monoculture and co-culture for 200 generations. We observed that P. putida diversified into two distinct morphotypes that differed from their ancestor by single-point mutations. One of the most prominent mutations hit the fleQ gene encoding the master regulator of flagella and biofilm formation. We experimentally confirmed that fleQ mutants were unable to swim and formed less biofilm than their ancestor, but they also produced higher yields. Interestingly, the fleQ genotype and other mutations swept to fixation in monocultures but not in co-cultures. In co-cultures, the two lineages stably coexisted for approximately 150 generations. We hypothesized that A. johnsonii modulates the coexistence of the two lineages through frequency-dependent selection. However, invasion experiments with two genotypes in monoculture and co-culture did not support this hypothesis. Instead, we found that, at the population level, the two morphotypes coexisted at similar relative abundances in the presence of A. johnsonii whereas, in its absence, one of the morphotypes was overrepresented in the population. Overall, our study suggests that interspecies interactions play an important role in shaping patterns of diversification in microbial communities.