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Antibiotic exposure impacts on fish health in natural freshwaters. PhD in Biosciences (NERC FRESH)

  • Full or part time
  • Application Deadline
    Monday, December 16, 2019
  • Competition Funded PhD Project (European/UK Students Only)
    Competition Funded PhD Project (European/UK Students Only)

Project Description

Lead supervisor
Professor Charles Tyler, Department of Biosciences, College of Life and Environmental Sciences, University of Exeter

Additional supervisors
Professor Joanne Cable, School of Biosciences, Cardiff University
Dr Ben Temperton, Department of Biosciences, College of Life and Environmental Sciences, University of Exeter
Dr Jackie Lighten, Department of Biosciences, College of Life and Environmental Sciences, University of Exeter
Dr David Bass, CEFAS (Centre for Environment, Fisheries & Aquaculture Sciences)

The NERC Centre for Doctoral Training in Freshwater Biosciences and Sustainability (GW4 FRESH CDT) provides a world-class doctoral research and training environment, for the next generation of interdisciplinary freshwater scientists equipped to tackle future global water challenges. GW4 FRESH harnesses freshwater scientists from four of the UK’s most research-intensive universities (Bath, Bristol, Cardiff and Exeter) plus world-class research organisations the Centre for Ecology and Hydrology (CEH) and British Geological Survey (BGS).

For an overview of the GW4 FRESH CDT please see website

Note, the research projects listed are in competition with other studentship projects available across the GW4 FRESH CDT Partnership. Up to 14 studentships will be awarded to the best applicants.

Project Description
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. 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 fish study species is the roach (Rutilus rutilus) fundamental in lowland ecosystem function and the services they provide (coarse angling nationally, for which roach is one of the most important, has a GVA of £800 million; EA, 2009)

This studentship will focus on achieving the following objectives:

Objective 1. Characterise skin and gill microbiomes (16S, metagenomes; via MiSeq and MinION sequencing) for profiling microbial (and viral) communities in wild roach at different locations along selected river reaches and with differing pollution loads (effluent levels from sewage treatment works) and assess for animal variation and ’location signatures’. Investigate possible associations between skin and gill micro-organisms assemblages and disease and parasite loads.
Objective 2. Undertake in situ translocations of roach (caged studies) between clean and polluted sites to study shifts in the skin and gill microbiome and whether this relates to change in disease organism burdens.
Objective 3. Establish impacts on the skin and gill microbiomes in roach of exposure to the antibiotics, clarithromycin and erythromycin separately and in combination, for concentrations including those relevant to natural UK freshwaters in laboratory controlled exposures. Conduct sequential analyses on the skin and gill over a period up to 3 months to study the microbiome based changes over time.
Objective 4. Establish the susceptibility of antibiotic treated roach with altered skin and gill microbiomes to infection challenges with Saprolegnia parasitica and/or Gyrodactylus vimbi to assess infection rates and subsequent disease progression.

The student will receive training in an exceptional wide range of techniques, including ecotoxicology, disease biology, molecular biology, evolutionary ecology and genetics, microbiomes, bioinformatics and the analysis of large complex datasets, under expert tuition and they will experience different institutional environments, including with the stakeholder Cefas. The studentship provides an opportunity to strengthen links between Exeter, Cardiff and Cefas for advancing research in freshwater environmental protection.

Project specific enquiries should be directed to the lead supervisor, Professor Charles Tyler:

Funding Notes

3.5 year studentship consisting of full UK/EU tuition fees, as well as a Doctoral Stipend matching UK Research Council National Minimum (£15,009 for 2019/20)

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