Host development and pathogen presence interact to shape the skin-associated microbes on endangered Colorado boreal toads (Anaxyrus boreas)

Background/Question/Methods

Exploration into host-associated microbes has allowed for new ecological perspectives into health and disease. Investigations of diverse host-pathogen systems are needed to advance our understanding of how a host’s microbes can mediate pathogen establishment, colonization, and proliferation.  Amphibian skin-associated microbiota interact with the fungal pathogen, Batrachochytrium dendrobatidis (Bd), but little is known about how the microbiota vary through host development, which can further inform their role in immune function. In this study, we surveyed the skin microbiota of Colorado’s endangered boreal toads (Anaxyrus boreas). We compared individuals across many of Colorado’s remaining populations, both Bdpositive (n = 6 sites) and negative (n = 11 sites), with the aims: (1) to investigate the microbial community structure and explain variation among individual microbiomes, (2) to characterize shifts in community structure that occur across amphibian developmental life-stages, and (3) to identify bacterial taxa that correlate with pathogen presence and infection intensity.  We explored the variation of individual skin samples using high-throughput 16S and 18S rRNA gene sequencing (Illumina MiSeq) to examine both bacteria and micro-eukaryotics, respectively.

Results/Conclusions

We characterized skin microbial communities of 181 toads, from 17 sites, across four life-stages (tadpoles, metamorphs, subadults, and adults). We found life-stage to be the best predictor of individual microbial community, with both site and Bd presence as significant secondary predictors of community structure. Bacteria on tadpoles were dominated by members of the phyla Proteobacteria that became gradually replaced by Actinobacteria through development. Other phyla, including Bacteroidetes, Acidobacteria and Verrucomicrobia, remained relatively constant through development.  Micro-eukaryotes on tadpoles were dominated by the class Alveolata and Stramenopiles. Fungi replaced these groups after metamorphosis and were the most abundant micro-eukaryotes on metamorphs, subadults, and adult life-stages. Increased proportions of skin-associated fungi in post metamorphic developmental stages correspond with a reduction of known antifungal (anti-Bd) bacteria. This suggests that host bacteria may regulate fungal communities on the host. Examination of the natural variation in cutaneous microbial communities can provide new insight into the role of microbial communities in host health, resistance to disease, and may also allow better understanding of the factors that underlie skin microbiome community assembly.