NERC RED-ALERT CDT PhD project: An e-DNA probe to enable microbial source apportionment from environmental samples

This project is one of a number of projects that are in competition for funding from the Centre for Doctoral Training in Real-Time Digital Water-Based Systems for Environmental Health Protection (RED-ALERT CDT).

The RED-ALERT CDT is a new doctoral training centre designed to improve the health of the UK’s rivers and lakes. RED-ALERT’s vision is to train and empower a new generation of leaders to transform how we manage aquatic environmental health via Real-Time Digital Water-Based Systems.

Doctoral training within RED-ALERT will focus on challenge-led multidisciplinary research and problem-solving skills. Leveraging nationally leading research facilities, international networks and whole system “Living Labs” to provide the in-depth knowledge and breadth of understanding, it will enable a step-change in managing environmental health.

Studentships are available for entry in September 2024.

Supervisory Team:

Lead supervisor: Dr Tom Arnot, Department of Chemical Engineering, University of Bath (email: cestca@bath.ac.uk).

• Co-supervisors: Prof Ed Feil, University of Bath; Prof Pedro Estrela (University of Bath); Dr Andrew Singer (UK-CEH).

The Project:

The overarching aim of this exciting multidisciplinary project is to provide a method for the rapid source attribution of contaminating, and potentially pathogenic, bacteria in waterways. These contaminants can enter river water systems via point source discharges or more diffuse run-off pollution sources. There are two strands to the project, first to identify and validate novel target sequences that are indicative of specific host species, including humans, cattle, pigs, sheep, and chickens. Second, to provide proof of principle that sensor technology based on these probes can provide rapid profiling reflective of bacterial provenance. This technology would facilitate both more precise advice about bathing water quality from a public health perspective, and more robust evidence as to the microbial pollution source, thus informing effective water management strategies.

The two parallel strands will involve the following:

• Use existing DNA tags to develop an electrochemical sensor for environmental DNA (eDNA) detection for quantification of microbial contaminants in water. We will use off-chip amplification techniques as well as evaluating on-chip amplification from a cost perspective.
• Bioinformatic analysis of existing large genome datasets (for Klebsiella spp. and E.coli) to enhance specific source host identification. We will use publicly available data and the thousands of closed genomes generated by the Feil group; these will be informative for identifying specific plasmids and other mobile genetic elements that are associated with different hosts.
• Bringing these two aspects together and trial the approach by sampling in river catchments.

The project will be done in collaboration with the UK Centre for Ecology and Hydrology, and Wessex Water, subject to a final agreement.

Project keywords: Environmental DNA, microbial contaminants, bioinformatics, electrochemical sensors.

Candidate Requirements:

This PhD project is ideally suited for candidates from diverse academic backgrounds such as Environmental Engineering, Chemical Engineering, Chemistry, Biology, Microbiology, Ecology, Natural Science, and other related disciplines. Applicants should hold, or expect to receive, a First Class or good Upper Second Class UK Honours degree (or the equivalent) in a related discipline. A master’s level qualification would also be advantageous but is not essential.

Non-UK applicants must meet our English language entry requirement.

Enquiries and Applications:

Applicants are encouraged to contact Dr Tom Arnot on email address cestca@bath.ac.uk before applying to find out more about the project and to discuss their suitability for the role.

Formal applications should be made via the University of Bath’s online application form for a PhD in Chemical Engineering.

IMPORTANT:

1. In the ‘Funding your studies’ section of the application form, please select ‘CDT’ from the first drop-down menu and enter “NERC RED-ALERT” in the space below.
2. In the ‘Your PhD project’ section, please quote the project title and lead supervisor’s name in the appropriate fields.

Failure to complete these steps will cause a delay in processing your application and may cause you to miss the deadline.

More information about applying for a PhD at Bath may be found on our website.

Equality, Diversity and Inclusion:

We value a diverse research environment and aim to be an inclusive university, where difference is celebrated and respected. We welcome and encourage applications from under-represented groups.

If you have circumstances that you feel we should be aware of that have affected your educational attainment, then please feel free to tell us about it in your application form. The best way to do this is a short paragraph at the end of your personal statement.