Final Report Summary - MICROBIOTAEVOLUTION (A phylogenetic and experimental approach to understand the evolution of microbiota) All organisms have microbes (=microbiota) associated with them, often in high diversities. This diversity is, however, a hurdle in our attempts to understand the evolutionary factors structuring microbiota. Evolutionary models, developed for simple host-symbiont associations can help us to move towards identifying key features of the evolution of host-microbiota interactions. These models predict key roles for the mode of microbiota transmission, host ranges and reciprocal fitness effects. On the other hand, these models do not take interactions among members of the microbiota into account. This ERC project attempted to bring these different levels together, by using an approach including conceptual work, field observations and experiments. The empirical work focused on the microbiota of the crustacean Daphnia (water fleas), a system well suited for studies of host-microbe interactions. Based on material collected from natural populations we were able to show that the composition of microbiota are host-specific, even in cases where different hosts share the same habitat. Detailed analysis allowed us to dissect how body compartment (gut versus skin) differ in their microbiota and how the microbiota change during individual development. The biggest change during host development happens when the host starts feeding, shortly after it was released from the brood chamber of the mother. This indicates at horizontal transmission from the environment as a main source of microbiota acquisition. However, the Daphnia microbiota are distinctively different from the microbiota of the surrounding water. Transmission of microbiota from mother to offspring seems not to play much of a role. Transovarial transmission was never detected, except in case of two intracellular microsporidian parasite species. We showed that experimental removal of microbiota (germ-free, axenic) strongly reduces growth, fecundity and survival of the hosts and even the likelihood of normal larval development. These effects can be rescued with bacteria from the environment, indicating that the bacteria do not need to be highly specific to provide proper function to the host. These effects are to some degree modified by temperature.The big question then arises, how are microbiota communities formed on the host. Host associated microbiota are diverse and different from the environment, although they are mostly (or all) acquired from the environment. We were able to show that the more specific a bacterium is, the more abundant they are on the host, suggesting strong selection on the bacteria picked up from the environment. An important and unexpected consequence of this is that larger and denser host populations harbor richer microbiota. Overall, our work stresses the role of the environment as a repository of microbes forming host specific microbiota communities. This argues again the role of a holobiont (host plus microbes) as an evolving unit. Rather, hosts and microbes do not coevolve directly with each other. However, host evolution is influenced by the environment provided by the bacteria and vice versa.
