Abstract
Organisms and their resident microbial communities form a complex and mostly stable ecosystem. It is known that the specific composition and abundance of certain bacterial species affect host health and Darwinian fitness, but the processes that lead to these microbial patterns are unknown.
We investigate this by deconstructing the simple microbiome of the freshwater polyp Hydra. We contrast the performance of its two main bacterial associates, Curvibacter and Duganella, on germ free hosts with two in vitro environments over time. We show that interactions within the microbiome but also host modulation lead to the observed species frequencies and abundances. More specifically we find that rare microbiome members are essential for achieving the observed community composition, which ultimately sets the maximum carrying capacity. Bacterial fitness strongly depends on the environment: while Duganella performs better than Curvibacter in a non-host habitat, Curvibacter benefits through the host association.
This is of particular interest because Curvibacter and its host show a history of co-evolution, as inferred from phylogenies, whereas the colonization with Duganella seems to be a recent event. Our findings oppose the assumption that bacteria always benefit through the association with the host and poses questions regarding the long-term maintenance of such relationships.
