About the Project
Lead Supervisor:
Dr Aimee Murray, European Centre for Environment and Human Health, University of Exeter Medical School
Additional Supervisors:
Professor Jason Snape, AstraZeneca
Dr William Gaze, European Centre for Environment and Human Health, University of Exeter Medical School
Professor Barbara Kasprzyk-Hordern, University of Bath
Professor Ed Feil, University of Bath
Location: Environment and Sustainability Institute, University of Exeter, Penryn Campus, Penryn, Cornwall, TR10 9FE, UK
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 www.gw4fresh.co.uk
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:
A growing body of research indicates low concentrations of antibiotics, such as those found in freshwater environments, select for antimicrobial resistance (AMR). A recent Nature study found non-antibiotic drugs (NADs) have antimicrobial effects, and so they may be an emerging risk contributing to the evolution and dissemination of AMR in aquatic systems where they are present as micropollutants. The selective pressure for AMR NADs pose alongside antibiotics in freshwater environments has not been previously studied. The selective NADs identified in the Nature study will be used in an established experimental microcosm system, where freshwater bacterial communities will be exposed to environmentally relevant NAD concentrations.
Objective 1: Identify NAD resistance mechanisms A combination of metagenomics and culture based methods will identify impacts on community diversity and identify genes which confer cross-resistance to NADs and antibiotics. Knock out mutants of resistant colonies and cloning of functional genes will identify novel resistance determinants. Objective 2: Determine minimal selective concentrations of NADs in isolation and in mixtures
Genes identified in Objective 1 will be used as real-time qPCR targets to accurately determine minimal selective concentrations (MSCs) of NADs - the lowest concentration which selects for AMR. Effects of multiple selective pressures will be investigated by testing for additive and other interactive effects of NADs and antibiotics. Objective 3: Explore selection by NADs in different freshwater contexts To explore potential spatio-temporal factors within freshwater systems, the experimental system will be developed to test different nutrient levels, temperatures and aquatic microbial communities. Chemical quantification of NADs will be performed alongside these experiments with support from Bath collaborators to understand fate and levels of biodegradation by resistant bacterial populations.
These results will inform water quality policy on release of NADs into freshwater ecosystems in relation to AMR evolution. The student will benefit from a multi-disciplinary team of supervisors to gain skills in molecular biology, microbiology, bioinformatics, analytical chemistry, ecotoxicity and environmental risk assessment. The student will be based in state-of-the-art microbiology labs at the Environment & Sustainability Institute, which includes a qPCR machine with 384-well plate capacity. Exeter has an in-house Sequencing Service and the student will have access to a high performance computing cluster to facilitate rapid metagenome analyses. The student will also access mass spectrometry instrumentation for identification and quantification of NADs at Bath.Through collaboration with the AstraZeneca stake holder supervisor and existing contacts within Defra, the waste water industry and the Environment Agency, the student will engage with policy makers and industrial stakeholders.
Eligibility:
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 http://www.gw4fresh.co.uk/how-to-apply/doctoral-students/
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 http://www.gw4fresh.co.uk/how-to-apply/doctoral-students/ also sending a copy of your CV and a covering letter to the CDT by 9:00 on 17th December 2018.
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