Experimental evolution of symbiotic microbes without their partners can imply the presence of cooperative or antagonistic adaptations

Microbes adapt to the presence of other species, but the fitness consequences of specific interactions are difficult to study in their natural context. We experimentally evolved symbiotic microbes in an artificial environment without access to the partners with whom they interact in nature. As organisms will tend to lose adaptations that they do not need due to drift or pleiotropic tradeoffs, we expect normally symbiotic microbes evolved in isolation to lose adaptations to help or harm their natural partners. The direction and magnitude of such changes can suggest whether the microbes had historically been selected to help or harm one another. We apply this method to the symbiosis between the social amoeba Dictyostelium discoideum and three intracellular bacterial endosymbionts, Paraburkholderia agricolaris, P. hayleyella, and P. bonniea. A minority of strains of Paraburkholderia and D. discoideum evolved differences in their effects on one anothers fitnesses, implying the existence of adaptations to one another that were lost when no longer relevant. Our results suggest that the degree to which D. discoideum and Paraburkholderia have adapted to help or harm one another can differ substantially between strains within each species, with some strains appearing to have a historically adversarial relationship, some strains a more benign relationship, and many strains no clear adaptations to one another at all. Our results underscore the complexity of microbial interactions in nature and suggest experimental evolution under relaxed selection is a potentially useful approach for studying adaptation in microbes.