Development and application of molecular methods to enhance understanding of the amphibian-emerging infectious disease pathobiome

275 pagesDevelopment and application of practical conservation measures to combat emerging infectious diseases are challenged by incomplete understanding of the complicated interactions between host, host-associated microbiota, pathogen, and environment that dictate disease outcome. In this dissertation, I shed light on several different aspects the amphibian- emerging infectious disease system using both novel and adapted molecular tools. I found that noninvasive surveillance of host populations using environmental DNA is useful and can potentially facilitate monitoring of large areas. However, host biology and specific context of sample collection play critical roles in environmental DNA detection, such that alone the environmental DNA tools are not a panacea for monitoring. Furthermore, the assumed relationships between environmental pathogen loads and host burdens were not closely related, indicating the need for more understanding of environmental factors and alternative hosts in the landscape that may be affecting environmental disease detection. Finally, I used a gene expression study of an amphibian vaccination trial to understand host, pathogen, and microbiome interactions at different stages of vaccination and infection. I discovered that eastern hellbender salamanders (Cryptobranchus alleganiensis alleganiensis) successfully mount an acquired immune response to Batrachochytrium dendrobatidis following oral vaccination, but the response is ineffective at controlling disease. Further examination of the innate immune system revealed that the hellbender skin microbiome is unlikely to explain the observed tolerance to infections. Pathogen gene expression changes later in infections may represent a mechanism for pathogen-induced community changes in the microbiome. Collectively, these findings build on recent advances in our understanding of the effect of emerging infectious diseases on amphibians, yet the discoveries that emerge from our enhanced ability to observe these pathogens in the environment reveal limitations to many core assumptions made about these systems which were based on other vertebrate models.2023-06-0