Anthropogenic influence on symbiotic interactions of Australian sea lions (Neophoca cinerea)

Interactions between humans, domestic animals and wildlife populations present an interface for the dissemination of microorganisms. The spread of disease-causing microorganisms can have serious impacts to the health and population dynamics of vulnerable marine wildlife species, particularly those that aggregate in high-density colonies. Therefore, understanding microorganism dissemination at this interface is crucial for the long-term conservation of endangered marine species. Genetic characterization of indicator microorganisms provides a means with which to monitor dissemination of microorganisms of anthropogenic origin. Currently, accurate inferences detailing microorganism transmission routes to wildlife populations at this interface are limited by the low availability of genomic data. I used molecular tools to investigate potential anthropogenic impacts on an endangered endemic marine mammal, the Australian sea lion (Neophoca cinerea), a species whose contemporary disease ecology is largely unstudied. The sea lions’ natural habitat encompasses coastal islands experiencing constant human visitation through to almost completely isolated islands, making the species ideal for the assessment of organism dissemination from anthropogenic sources. Through protozoal and microbial monitoring, I aimed to determine the establishment of terrestrial and human originated organisms in wild versus captive Australian sea lions. Screening for protozoan parasites identified Giardia duodenalis genotypes prominent in human infection in greater frequency in sea lions within close proximity to human settlements compared to more isolated colonies. Cryptosporidium was not detected in sea lion populations. Microbial monitoring indicated similar findings, with the presence of E. coli harbouring integronborne antibiotic resistance mechanisms commonly identified in clinical settings, significantly greater in captive animals. Finally, the application of next-generation sequencing indicated a high level of dissimilarity of microbiota community structure and membership between wild and captive animals. The genetic tools and target indicators described in this thesis can be applied to determine the dissemination of microorganisms from anthropogenic sources in most marine wildlife taxa. Through the identification of target indicators, we can bridge knowledge gaps in microorganism movement, and, as a result, better inform long-term conservation management strategies aimed at reducing anthropogenic impacts to sensitive marine mammal populations.