Composition, diversity and response dynamics of fish skin microbiomes under environmental stress, including antibiotic exposure.

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Microbiomes (the microbes associated with a host) are a fundamental component of human and animal health. Stressors that induce shifts in microbial communities, such as antibiotic exposure, in turn can increase the likelihood of infection, but almost nothing is known in this regard for fish. Antibiotics, that are designed to kill bacteria, enter UK freshwaters via patient and animal use, through manufacturing plants and/or improper disposal and can reach microgram per litre concentrations in some UK surface waters and sewerage treatment plant effluents/wastewaters. Much attention on antibiotics has been focused on their implications for human health through antimicrobial resistance (AMR) but far less attention has been focused on the wider environmental implications of antibiotic impacts to environmental health.This studentship will undertake a combination of field and laboratory based studies to advance understanding on fish skin and gill mucosal microbiomes in natural waters and assess how exposure to antibiotics that are widespread in the environment affect the skin and gill microbiomes and how, in turn, this affects susceptibility to disease infection. The two pathogens for the disease challenges will be the oomycete Saprolegnia parasitica, a fungal-like pathogen that is endemic to freshwater ecosystems and associated with global declines in wild populations of freshwater species, and monogenean parasitic worms that attach to the skins and/or gills, which have widespread fitness consequences across fishes. The project will also investigate the interactions between the viruses contained in the gill and skin microbiomes and the antibiotic effects. The studentship will employ a combination of exciitng and cutting edge sequencing methods inclduing MiSeq and also MinION sequencing (Oxford Nanopore) for profiling microbial (and viral) communities (16S and metagenomes). The fish study species is the roach (Rutilus rutilus) fundamental in lowland ecosystem function.The student will receive training in an exceptional wide range of techniques, including field biology, ecotoxicology, disease biology, molecular biology, evolutionary ecology and genetics, microbiomes, bioinformatics and the analysis of large complex datasets, under expert tuition and in labs that are very well resourced. They will experience different institutional environments including with our stakeholder Cefas, where the student will also get experience also in the business environment