Abstract: Multicellular life relies on microbial symbionts, and yet the processes that govern the establishment and dynamics of host-associated microbial communities remains elusive. We have recently begun using the embryos and larvae of amphibians to experimentally investigate the ecological processes driving initial microbiome establishment. In one study, we obtained eggs from pairs of spring peepers (Pseudacris crucifer) that were bred under sterile laboratory conditions or with pond water in field enclosures, and we reared a subset of the offspring in pond enclosures for one month. We characterized bacterial community diversity and composition using 16S rRNA amplicon sequencing. We found that the bacterial composition of hatchlings from the same clutch were more similar to one another than to unrelated hatchlings, and that hatchlings from eggs laid in ponds harbored more diverse bacterial communities than those laid in sterile water. Interestingly, the clutch effects we observed in pond-laid embryos persisted into the tadpole stage, supporting that priority effects or strong host selection may outweigh the influences of drift or subsequent dispersal of environmental microbes. In a second experiment, we reared wood frogs (Rana sylvatica) with and without environmental sources of bacteria. We again found that bacterial diversity and community composition were influenced by source environment—most notably, addition of pond water or pond soil increased the relative abundance of Firmicutes in the gut—and this impacted developmental rate. Our findings demonstrate the importance of the regional source pool—which determines the availability of microbes that may disperse to the host—during microbiome establishment, and how this may contribute to interindividual variation in microbial symbiont community composition and structure observed in wild populations.
