The ecology of amphibian-associated bacterial communities

Multicellular organisms are habitat for a diverse bacterial community (microbiome) that can often be associated with host health and well-being. To better understand that relationship I explored several ecological aspects of the host-associated microbiomes using pre- and post-metamorphic amphibians. First, I investigated the relative roles of local selection (due to host species identity) and regional effects (due to water body identity) on the community structure of the gut microbiome of tadpoles. I found that each water body represents a relatively distinct species pool of bacteria available for community assembly, making the water body more important in shaping the microbiome of tadpoles than their species identity. I then showed that the gut microbiome of tadpoles is not homogeneous throughout its gut length as there are changes in composition, abundance, richness, and diversity from the anterior to the posterior parts of the gut. Moreover, the gut microbiome of the anterior portion is unstable, i.e., it is highly influenced by exposition to external bacteria, while the microbiome of the posterior gut has higher stability. The posterior part harbors the functional microbiome that helps tadpoles with digestion. In fact, I found that most of the essential amino acids in the tadpole tissue are derived from bacteria. I then manipulated their gut microbiome and diet and found that the composition of the microbiome can have profound impacts on the performance and fitness of the tadpole, as distinct microbiomes affect growth, development, and mortality of the host. Finally, as tadpoles metamorphose and leave the water, their microbiome is reshaped due to changes in conditions related to both the environment and the host. I tested and showed that closely related species of adult amphibians have a tendency to harbor similar skin microbiome, but the same signal was not found for their gut microbiome. In summary, I found that the gut of tadpoles harbor several distinct but connected microbiomes that vary in composition, diversity, and stability and that can profoundly affect the fitness of the host. Its composition is ultimately determined by the environmental bacteria tadpoles were exposed to. For adult amphibians, closely related species have more similar skin but not gut microbiome.Ecology, Evolution and Behavio