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Antibiotic exposure impacts on fish health in natural freshwaters. NERC FRESH CDT studentship, PhD in Biosciences

  • Full or part time
  • Application Deadline
    Monday, December 17, 2018
  • Competition Funded PhD Project (European/UK Students Only)
    Competition Funded PhD Project (European/UK Students Only)

Project Description

Lead Supervisor
Professor Charles Tyler

Additional Supervisors
Dr David Bass, Centre for Enviroment Fisheries and Aquaculture Sciences (CEFAS)
Professor Joanne Cable, Cardiff University
Dr Ben Temperton, University of Exter
Dr Jackie Lighten, University of Exeter

Location: Streatham Campus, University of Exeter, Exeter, Devon.

The NERC Centre for Doctoral Training in Freshwater Biosciences and Sustainability (GW4 FRESH CDT) will provide 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 23 other studentship projects available across the GW4 FRESH CDT Partnership. Up to 12 studentships will be awarded to the best applicants.

Project Details
Microbiomes (the microbes associated with a host) are a fundamental component of human and animal health. Stressors that induce shifts in microbial communities including antibiotic exposure, have been associated with increased disease and infection in humans, but almost nothing is known in this regard for fish.

Antibiotics that target bacteria can reach microgram per litre concentrations in some UK surface waters (Monteiro and Boxall 2010) and some are now on the European Chemicals Watch list because of concern for human health through antimicrobial resistance (AMR). Bacteria can evolve resistance to natural phages (viruses) also, but doing so often involves a phenotypic trade-off such as increased susceptibility to antibiotics (Chan et al. 2018). Thus, the spread of AMR may be mitigated by host-virus interactions in natural communities. Understanding interactions between antibiotic and phage resistance in microbiome shifts and disease susceptibility is important for modelling the spread of AMR in both natural fish populations and aquaculture; as well as identifying and directing putative treatments through phage therapy.

This studentship will focus on achieving the following objectives:

Objective 1. Characterise skin and gill microbiomes (16S, metagenomes) in wild roach, a species fundamental in lowland ecosystem freshwater function, both at different life stages and at different times of the year at selected river sites with little or no known pollution inputs.

Objective 2. Through laboratory-based studies establish whether chronic exposure to environmentally realistic concentrations of selected antibiotics (clarithromycin and erythromycin) separately and in combination, re-shapes the microbiome compared to non-exposed communities, by selecting taxa that are more amenable to resistance, and investigate the dynamics of this process.

Objective 3. Establish whether the shifts in the microbiome assemblages on the skin and gills induced by the antibiotic exposures impacts fish health and alters susceptibility to infection challenges with two key fish pathogens Saprolegnia parasitica and/or Gyrodactylus vimbi (via assessing infection rates and subsequent disease progression).

Objective 4. Investigate whether presence of natural phage communities reverses/limits any effects in the bacterial microbiome (and susceptibility to infection) driven by the antibiotics exposure because of the need to maintain resistance to natural phage communities.

The successful applicant will receive training in an exceptional wide range of techniques under expert tuition, including with the stakeholder Cefas. The student will be integrated into large research teams at Exeter, Cardiff and Cefas with international profiles working extensively with government bodies, regulators and major industries and this will bring further benefits in terms of additional support, and expertise for the student’s professional development.

GW4 FRESH CDT welcomes applications from both UK and EU applicants. For further information regarding the eligibility criteria please see the Student Eligibilty section in the following web page

How to apply:
Applications open on Monday 8th October and close at 9:00 on 17th December 2018

You will need to complete an application to the GW4 FRESH CDT for an “offer of funding”.

Please complete the application form at also sending a copy of your CV and a covering letter to the CDT by 9:00 on 17th December 2018.

After the closing deadline all applications and CVs will be forwarded to the lead Supervisor of the project(s) you have selected. They will interview you at a mutually convenient date in January 2019 (tbc) and submit their preferred candidate to FRESH CDT.

Shortlisted candidates will be invited to a panel interview in Cardiff in the week commencing 25th February 2019. Further details will be included in the shortlisting letter

For further details regarding the application process please see the following web page

Funding Notes

This project is a 3.5 year studentship consisting of full UK/EU tuition fees, as well as a Doctoral Stipend matching UK Research Council National Minimum.

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