NERC RED ALERT CDT studentship for 2024 Entry – Novel methodologies to assess the environmental health of freshwater systems. PhD in Biological Sciences

University of Exeter

Exeter, UK 🇬🇧

About the award


Lead Supervisor

Dr Robert Ellis, Biosciences, University of Exeter,

Additional Supervisors

Dr Eduarda Santos, Biosciences, University of Exeter;

Dr Ceri Lewis, Biosciences, University of Exeter;

Dr Gary Codling, Biosciences, University of Exeter;

Professor Peter Kille, Biosciences, Cardiff University,

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

About the Partnership

Natural Environment Research Council funded RED ALERT Centre for Doctoral Training NERC Centre for Doctoral Training in Real-Time Digital Water-Based Systems (RED-ALERT CDT) will provide training in water-based early warning systems for environmental and public health protection focused around 4 UK and 3 international Living Labs aimed to provide the in-depth knowledge and enable a step-change in managing environmental and public health.

This project is one of a number that are in competition for funding from the NERC Centre for Doctoral Training in Real-Time Digital Water-Based Systems for Environmental Health Protection (RED ALERT CDT).  The NERC RED ALERT CDT consists the University of Bath, Bangor University, Cardiff University and the University of Exeter plus the UK Centre for Ecology and Hydrology.  RED-ALERT CDT’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.

For eligible successful applicants, the studentship comprises:

• A stipend for 3.5 years (£19,237 p.a. for 2024-25) in line with UK Research and Innovation
• Payment of university tuition fee;
• A research budget of £11,000 for conferences, lab, field and research expenses;

Project Background:

Freshwater ecosystems are some of the most threatened on earth, receiving a complex cocktail of natural and man-made chemicals as a result of human activity. These, together with alterations in abiotic parameters (such as temperature, pH and oxygen levels) result in complex exposure scenarios. The complexity of these scenarios poses a major challenge when assessing exposure impacts, and determining safe environmental levels, of novel and existing chemical threats, in the context of individual organisms or ecosystem health. Overcoming this challenge requires the development of highly advanced, innovative, high-throughput approaches for rapid and detailed assessment of chemical exposures. Whilst such advances have been made for many vertebrate models, because of the perception these groups are more important, analogous approaches are currently lacking for many invertebrate groups and for freshwater systems. This creates a significant knowledge gap, which represents a major barrier to the assessment of the health of aquatic organisms and ecosystems.

This project directly addresses this issue, developing and applying highly novel high-throughput methodologies that enable the comprehensive assessment of environmental pollutant impacts on invertebrate systems, with a level of complexity prohibited by existing approaches. As a result, this project will ultimately facilitate the reduction of anthropogenic impacts and the better protection of biodiversity in freshwater environments.

Project Aims and Methods:

The aim of this PhD is to demonstrate and advance the utilisation of a highly novel approach for environmental chemical assessment in freshwater ecosystems. By combining toxicogenomics to determine the effects of environmental chemicals, as well as their mixtures, on freshwater invertebrates, with advanced imaging and data analysis for high-throughput phenotyping (EmbryoPhenomics), this project will develop a rapid and in-depth method to assess the impacts of aquatic stressors on biota.

The projects three main objectives are:

1 – Develop a combination of phenomics (high-throughput imaging, computer vision, deep learning) and transcriptomic (next-generation-sequencing) methodologies to generate an integrated assessment of the impacts of exposure to environmental chemicals and their mixtures on the transcriptome and phenome of aquatic organisms.

2 – Compare the sensitivity and robustness of these methodologies across vertebrates and invertebrates, using Daphnia pulex and Danio rerio as model systems.

3 – Implement the methodology to generate assessments of the impacts of environmental pollutants in the real world environments of the Living Labs (focusing on the Exe/Tamar/Dart lab).

Project partners:

Jonathan Newman, Senior Policy Advisor, Biologically active substances; Environment Agency;;

Oliver Tills, EmbryoPhenomics CIC; embryophenomics@gmail.com;

The project builds on two key collaborative projects that are on-going between the University of Exeter and the Environment Agency, as well as with the EmbryoPhenomics CIC. Moreover, it builds on the extensive collaboration between researchers based at Exeter and Cardiff Universities, and leverages the opportunities afforded by the establishment of the Centre for Environment, Waste and Water, a collaborative centre between the University of Exeter and South West Water. As a result the project supervisory team provide an ideal platform for world-class student training, offering a combination of state-of-the-art facilities and expertise, as well as the ability to undertake fundamental and applied research of direct industrial relevance. Ultimately it will enable the student to address a question of key strategic importance, namely how we can advance chemical testing in freshwater ecosystems.

Training: All supervisors have an extensive track record of successfully supervising students across all levels of higher education. This studentship will therefore provide an ideal environment for the student to develop interdisciplinary skills across ecotoxicology, genomics, bioinformatics, phenomics and advanced data analysis, from leaders in each respective field. In addition to project specific training, PhD students at Exeter will receive general training from the researcher Development Programme within its Employability and Graduate Development unit. All training is carefully tailored to key stages of the PhD life-cycle, providing transferable research skills training, covering over 40 topics, including writing for publication, data collection and management, effective research communication, impact, public engagement, interdisciplinary working and research profile enhancement.

Background reading and references

Tills O, Holmes LA, Quinn E, Everett T, Truebano M, Spicer JI. 2023 Phenomics enables measurement of complex responses of developing animals to global environmental drivers. Science of the Total Environment, 858, 159555.

Ibbini Z, Spicer JI, Truebano M, Bishop J, Tills O. 2022 HeartCV: a tool for transferable, automated measurement of heart rate and heart rate variability in transparent animals. Journal of Experimental Biology, 225, jeb244729.

Tills O, Spicer JI, Grimmer A, Marini S, Jie VW, Tully E, Rundle SD. 2018. A high-throughput and open-source platform for embryo phenomics. PLoS Biology, 16:e3000074.

Useful Links

For information relating to the research project please contact the lead Supervisor via:

Prospective applicants: For information about the application process please contact the Admissions team via  Each project advertisement has an ‘Apply Now’ button linking to an application portal. Please note that applications received via other routes including a standard programme application route will not be considered for the studentship funding.

Funding Eligibility

NERC RED ALERT CDT studentships are open to UK and Irish nationals who, if successful in their applications, will receive a full studentship including payment of university tuition fees at the home fees rate.

A limited number of full studentships are also available to international students which are defined as EU (excluding Irish nationals), EEA, Swiss and all other non-UK nationals. 

Those not meeting the nationality and residency requirements to be treated as a ‘home’ student may apply for a limited number of full studentships for international students. Although international students are usually charged a higher tuition fee rate than ‘home’ students, those international students offered a NERC RED ALERT CDT full studentship starting in 2024 will only be charged the ‘home’ tuition fee rate (which will be covered by the studentship).

International applicants need to be aware that you will have to cover the cost of your student visa, healthcare surcharge and other costs of moving to the UK to do a PhD. More information on this is available from the universities you are applying to (contact details are provided in the project description that you are interested in.

The conditions for eligibility of home fees status are complex and you will need to seek advice if you have moved to or from the UK (or Republic of Ireland) within the past 3 years or have applied for settled status under the EU Settlement Scheme.

Equality, Diversity and Inclusion

The University of Exeter is committed to promoting and supporting equality, diversity, and inclusion within our working environments and is at the heart of all our activities.  With over 27,000 students and 6,400 staff from 180 different countries we offer a diverse and engaging environment where our diversity is celebrated and valued as a major strength.

We actively encourage applicants with varied experiences and backgrounds and from all sections of the community regardless of age, race, ethnicity, sexual orientation, gender, religion, or disability status.  We are committed to creating an inclusive culture where all members of our community are supported to thrive.
Whilst all applicants will be judged on merit alone, we particularly welcome applications from groups currently underrepresented within our postgraduate research student community.  Reasonable adjustments are available for interviews and workspaces.

Entry requirements

Essential: This project is suitable for a candidate with a strong background in aquatic biology/ecology, who has relevant experience in ecotoxicological approaches and who has some experience with bioinformatics and/or programming (e.g. Python).

Desired: The ideal candidate for this PhD would additionally have experience of aquatic animal physiological research techniques in a research lab environment, and experience of aquatic animal husbandry. They will also have practical experience of molecular techniques/transcriptomics, and some experience researching aquatic animal development (ideally invertebrate).

Applicants should have obtained, or be about to obtain, a First or Upper Second Class UK Honours degree, or the equivalent qualifications gained outside the UK.   Applicants with a Lower Second Class degree will be considered if they also have Master’s degree.  Applicants with a minimum of Upper Second Class degree and significant relevant non-academic experience are encouraged to apply.

All applicants would need to meet our English language requirements by the start of the project

How to apply

Apply now

To apply for this studentship you must apply via the ‘apply now’ button provided above. 

In the application process you will be asked to upload several documents.  Please note our preferred format is PDF, each file named with your surname and the name of the document, eg. “Smith – CV.pdf”, “Smith – Cover Letter.pdf”, “Smith – Transcript.pdf”.

• CV
• Personal Statement
• Transcript(s) giving full details of subjects studied and grades/marks obtained.  This should be an
   interim transcript if you are still studying.
• If you are not a national of a majority English-speaking country you will need to submit evidence
  of your current proficiency in English, please see the entry requirements for details.
• Two references

Reference information

You will be asked to submit two references as part of the application process.  If you are not able to upload your reference documents with your application please ensure you provide details of your referees.  If you provide contact details of referees only, we will not expect receipt of references until after the shortlisting stage. Your referees should not be from the prospective supervisory team.

If you are shortlisted for interview, please ensure that your two academic referees email their references to the, 7 days prior to the interview dates. Please note that we will not be contacting referees to request references, you must arrange for them to be submitted to us by the deadline.

References should be submitted by your referees to us directly in the form of a letter. Referees must email their references to us from their institutional email accounts. We cannot accept references from personal/private email accounts, unless it is a scanned document on institutional headed paper and signed by the referee.

General information

All application documents must be submitted in English. Certified translated copies of academic qualifications must also be provided.

The closing date for applications is 2359 hours GMT Thursday 14 March 2024.

If you have any general enquiries about the application process please email

Please quote reference number 5057 in correspondence.

Project-specific queries should be directed to the lead supervisor.

Data Sharing

During the application process, the University may need to make certain disclosures of your personal data to third parties to be able to administer your application, carry out interviews and select candidates.  These are not limited to, but may include disclosures to:

• the selection panel and/or management board or equivalent of the relevant programme, which is likely to include staff from one or more other HEIs;
• administrative staff at one or more other HEIs participating in the relevant programme.

Such disclosures will always be kept to the minimum amount of personal data required for the specific purpose. Your sensitive personal data (relating to disability and race/ethnicity) will not be disclosed without your explicit consent.


Application deadline:14th March 2024
Value:£19,237 per annum
Duration of award:Not applicable
Contact: Postgraduate Research Admissions





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