Application of emerging environmental DNA (eDNA) techniques for the determination of important fish species distributions.
Working towards the monitoring and protection of aquatic species.
An opportunity for a fully-funded PhD studentship is currently being offered by the Faculty of Health and Applied Sciences at UWE Bristol.
Closing date for applications is Monday 6th February 2017.
Background to the PhD
This studentship focuses on the development and application of environmental DNA (eDNA) as a technique for investigating elusive and endangered species. Recently developed techniques to capture and analyse free-floating DNA, known as environmental DNA (eDNA), have the potential to provide a rapid and robust method for determining the presence and distribution of aquatic species. A further and increasingly important feature of this emerging technology is that the use of eDNA is both non-invasive and non-damaging to species and ecosystems.
The dramatic decline in recruitment of the European Eel (Anguilla anguilla)over the last 25 years in UK and European waters has led to its classification as ‘Critically Endangered’ on theIUCN Red List andthe introduction of the EU Eel regulation (EC 1100/2007). Assessing eel populations by traditional methods is notoriously difficult as they have a complex life history, are migratory and live cryptically in a range of habitats. All monitoring methods are damaging to the eels or permanently remove individuals from the population. The successful application of eDNA will enable frequent routine sampling which is urgently needed by water companies and regulatory bodies which use and inform current EU Eel Management Plans.
The development of eDNA markers will provide a much needed monitoring tool for assessing and estimating European Eel populations within European waters. The application of this approach would reduce time and labour requirements and would be easily adopted by European water companies and/or environmental regulators. Using this novel method for the monitoring of European Eel populations in UK waters will generate vital data which will further our understanding of environmental parameters to which European Eel populations are particularly sensitized. Data generated would contribute to the development of Eel Management Plans in the UK initially, with the ultimate ambition of impacting across Europe.
This research will initially focus on developing and validating this novel method of detecting eels. We plan to further develop these techniques to assess application for other estuarine and coastal fish groups, such as other migratory species of conservation concern or more elusive commercial species. This part of the project will be in association with Dr Jim Ellis (Centre for Environment, Fisheries and Aquaculture Science, CEFAS). This PhD studentship will also build on existing links with the Sustainable Eel Group, Bristol Water, Bristol Zoological Society and Bristol Aquarium. The nature of this applied research will allow the successful candidate to develop strong links with collaborators.
The aims of this project are to:
- Develop and validate an eDNA technique using water samples for the identification and quantification of target fish species
- Apply this novel technique to evaluate existing species distribution models
- Application ofeDNA techniques for tracking potential changes in species distributions.
The student undertaking this project will receive in-depth training in ecological and genetic survey techniques; DNA extraction, using DNA markers, real time PCR, sequence analysis, and experience of working closely with strategic collaborators.
The nature of this applied research will allow the successful candidate to develop strong links with collaborators. Using eDNA is of great interest to water companies and regulatory bodies yet these techniques are still in their infancy and need to be fully developed. Therefore this PhD studentship will build on existing links with the Sustainable Eel Group, CEFAS – an agency of DEFRA, Bristol Water, Bristol Zoological Society and Bristol Aquarium.
Supervision team and research environment
This PhD studentship will be based at UWE Bristol. The supervisory team will comprise Dr Lyn Newton (Director of Studies), Dr Stephanie Sargeant, Dr Heather Macdonald and dr Mark Steer (all UWE Bristol). The student will have regular meetings with the Director of Studies and input from other members of the team in response to the specific needs of the student and the research. This studentship adds to an existing research project, the student will be joining the research team and benefit from working closely together in the laboratory to develop these novel eDNA techniques.
- Dr Lyn Newton, Head of Department (UWE Bristol), is a marine ecologist researching the effects of contaminants on aquatic organisms, in particular using biomarkers to detect stress; examining sub-lethal responses to pollutants using behavioral assays; examining the long-term changes in plankton communities of the Severn Estuary, Reef fish communities of Cuba.
- Dr Stephanie Sargeant, Senior Lecturer in Environmental Science (UWE Bristol), is a marine microbial ecologist interested in the use of molecular markers to understand and conserve aquatic systems; microbial utilisation of climatically relevant compounds in seawater and their impact on the cycling of carbon in the oceans.
- Dr Heather Macdonald, Senior Lecturer in Molecular Biology (UWE Bristol),is a molecular biologist researching the potential of microalgae as a biofuel; proteomic responses to biotic and abiotic stresses; regulation and effect of plant hormones.
- Dr Mark Steer, Senior Lecturer in Conservation Biology (UWE Bristol), is a practical conservation biologist with an interest in genetic survey techniques and ecological networks.
The PhD student will join the Centre for Research in Biosciences (CRIB) which brings together world class multidisciplinary, collaborative research with focus on the following themes: agri-food, biomedicine, bio-sensing, plant science and environmental science. CRIB addresses both, fundamental and applied aspects of research. Close links with national and international academic partners, health organisations and industry ensure that our research has real social and economic impact.
The PhD student will be a member of the Faculty of Health & Applied Sciences, which provides a programme of training and support for PhD students. This includes access to any relevant UWE modules, or external university modules/courses to meet their specific training needs for 60 Master’s level credits. Additional short courses are available free of charge to all postgraduate research students through the Graduate School Researcher Development Programme which is delivered by the UWE Graduate School.
Why choose this PhD? This studentship:
•Provides in-depth training in ecological and genetic survey techniques; DNA extraction, using DNA markers and bioinformatics.
•Is a great opportunity to work closely with strategic collaborators in a research capacity, helping to guide practical conservation projects to safeguard aquatic ecosystems and influence policy.
•Will generate vital data regarding fish species including European Eel populations in UK waters which will contribute directly to the protection of this critically endangered species.
•To join a strong research centre with excellent facilities including laboratories at UWE Bristol.
The student undertaking this project will receive in-depth training in ecological and genetic survey techniques; DNA extraction, using DNA markers, real time PCR, sequence analysis, and experience of working closely with strategic collaborators.
We are looking for a highly motivated and enthusiastic student capable of working independently with a broad interest in ecology and conservation. They should be willing to learn and develop the interdisciplinary skills required for this project. Although the successful student will receive in-depth training it is desirable that applicants have some experience of molecular work. The successful applicant will be working primarily in an academic environment, supported by a range of experts and should demonstrate a willingness to engage with collaborating organisations, such as local water companies and regulatory bodies to whom this work will be of interest.
Applicants must have a good honours degree (2.1 or equivalent) in Biological or Environmental disciplines. A relevant Masters qualification is desirable, but not essential if the applicant has relevant research experience. If the language of first degree or Master’s degree is not English,a recognisedEnglish language qualificationis required.
For an informal discussion about the studentship, please contact Dr Stephanie Sargeant , 0117 32 87542.