Species interactions promote parallel evolution of global transcriptional regulators in a widespreadStaphylococcusspecies

Experimental studies of microbial evolution have largely focused on monocultures of model organisms, but most microbes live in communities where interactions with other species may impact rates and modes of evolution. Using the cheese rind model microbial community, we determined how species interactions shape the evolution of the widespread food- and animal-associated bacteriumStaphylococcus xylosus. We evolvedS. xylosusfor 450 generations alone or in co-culture with one of three microbes: the yeastDebaryomyces hansenii, the bacteriumBrevibacterium aurantiacum, and the moldPenicillium solitum. We used the frequency of colony morphology mutants (pigment and colony texture phenotypes) and whole-genome sequencing of isolates to quantify phenotypic and genomic evolution after 15 weeks of the evolution. The yeastD. hanseniistrongly promoted diversification ofS. xylosus; by the end of the experiment, all populations co-cultured with the yeast were dominated by pigment and colony morphology mutant phenotypes. Populations ofS. xylosusgrown alone, withBrevibacterium, or withPenicilliumdid not evolve novel phenotypic diversity. Whole-genome sequencing of individual mutant isolates across all four treatments revealed numerous unique mutations in the operons for the SigB, Agr, and WalKR global regulators, but only in theD. hanseniitreatment. Phenotyping and RNA-seq experiments demonstrated that these mutations altered pigment and biofilm production, spreading, stress tolerance, and metabolism ofS. xylosus. Fitness experiments revealed trade-offs of these mutations across biotic environments caused by antagonistic pleiotropy, where beneficial mutations that evolved in the presence of the yeastDebaryomyceshad strong negative fitness effects in other biotic environments.IMPORTANCESubstantial phenotypic and genomic variation exists within microbial species, but the ecological factors that shape this strain diversity are poorly characterized. We demonstrate that the biotic context of a widespreadStaphylococcusspecies can impact the evolution of strain diversity. This work demonstrates the potential for microbes in food production environments to rapidly evolve to novel substrates and biotic environments. Our findings may also help understand how otherStaphylococcusspecies may evolve in multispecies microbiomes.