Establishing the links between skin microbiome, pollution and disease susceptibility in a native UK amphibian species

Emerging infectious diseases pose a significant threat to wildlife health. Understanding the factors that predict individual susceptibility to infection is vital for developing practical strategies for wildlife conservation and disease control.

Bacterial communities living in association with hosts, known as the microbiome, can be key to protecting individuals from infection by pathogens. In the UK, populations of common frog (Rana temporaria) differ markedly in their response to the pathogen ranavirus. Whilst some populations have exhibited catastrophic outbreaks of the disease ranavirosis, others appear relatively stable, and these patterns appear to be linked to variation in their skin microbiome. However, almost nothing is known about what determines variation in amphibian host microbiome structure. Colonisation of host-protective bacteria is strongly influenced by the environment, and one possibility is that the presence of environmental contaminants such as antimicrobial pollutants can negatively affect these colonisation dynamics, with important consequences for host health.

This project will use a combination of field surveys, controlled experiments and molecular tools to investigate the links between the amphibian skin microbiome, ranavirus infection, and antimicrobial pollutants in populations of the UK common frog. The overall aim of the project is to test the hypothesis that antimicrobial pollutants alter the susceptibility of amphibian hosts to disease by modifying structure of their skin microbiome.

The student will
- Perform an extensive survey of wild common frogs in a network of sites in the south west of England to estimate spatial (co)variation in skin microbiome structure, using both 16S amplicon sequencing and shotgun metagenomics.
- Use qPCR to quantify ranavirus infection loads in the environment, and how these infection loads change seasonally
- Generate chemical profiles of pondwater from each site to quantify spatial (co)variation in levels of antimicrobial compounds
- Use inhibition assays to test the ability of the common frog mucosome to inactivate ranavirus virions in vitro
- Use controlled experiments on frogs reared in common garden conditions to test the effect of exposure to pond water containing varying levels of pollutants on skin microbiome structure
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