PhD: Ecological Impacts of Aquatic Contaminants using Next Generation Gene Sequencing via FindAPhD

About the Project

Project Overview:

State-of-the-Art Gene Sequencing technologies will be applied to scrutinise and understand the complex interplay between aquatic pollutants and exposed ecosystems, elucidating the drivers behind ecological impacts of chemical hazards. The multidisciplinary project will develop methods based on cutting-edge Nanopore Sequencing technology, implemented with novel technologies for field-based analysis.

Project Description:

Ecosystem change and biodiversity loss caused by the release of human-made pollutants into natural water systems is one of the greatest challenges facing current and future generations. For example, the release of nutrients from sewerage overflows and eutrophication of fertilisers combined with warming waters from climate change directly influence the frequency, severity and longevity of toxic phytoplankton blooms. Exposure of ecosystems to chemical contaminants causes widespread ecosystem disruption and biodiversity loss. We cannot manage and mitigate what we cannot measure. Therefore, this project will explore the use of state-of-the-art technology for gene sequencing to discover the impacts to, and drivers of ecosystem health in response to pollution. The student will receive training and full access to cutting edge Nanopore sequencing technologies and associated methods with the opportunity to adopt these techniques to analyse the structure and function of threatened aquatic ecosystems in a range of environments, from estuarine to coastal to deep sea. In the first instance the student will be able to apply existing, proven sequencing workflows to measure the biodiversity of different groups, from microorganisms to macro-fauna, and investigate responses of key species to contamination by analysing gene regulation. With experience, they will have the opportunity to develop their own tailored workflows towards applications of interest. They will also receive full access to a range of fieldable technologies and concepts, with the opportunity to exploit these towards field analysis systems, including the use of eDNA autosamplers.

This project will be located in Southampton.

Training:

The IGNITE programme provides comprehensive personal and professional development training alongside extensive opportunities for students to expand their multi-disciplinary outlook through interactions with a wide network of academic, research and industrial/policy partners.

This project will be based heavily on the use of next generation sequencing technologies, specifically the Nanopore MinION sequencing system from Oxford Nanopore Technologies. The student will learn how to collect environmental samples, including the use of eDNA autosamplers, how to extract high quality DNA, prepare DNA sequencing ‘libraries’ and how to undertake Nanopore sequencing workflows. The student will receive training in sequence data analysis to interpret biodiversity and gene expression profiles. The student will also learn about the use of in situ aquatic sensors including microfluidic Lab on a Chip technologies for the analysis of environmental DNA.

Entry Requirements:

A UK bachelor’s degree with upper second-class honours or higher in a relevant subject. See international equivalent qualifications on the University’s website: https://www.southampton.ac.uk/international/entry-qualification-equivalencies. English language: IELTS 6.5 overall, with a minimum of 6.0 in all components. We accept other English language tests: https://www.southampton.ac.uk/studentadmin/admissions/admissions-policies/language.page

How to apply:

All applications to the IGNITE Doctoral Landscape Award should be submitted by 11:59pm on Thursday 8th January 2026. Please be aware that this project is full-time only. Please use the following link to apply:

Full time

We advise you to contact the lead supervisor of a project to discuss the project and check your suitability before submitting an application. You are strongly advised to apply for one project so that you can tailor your application to the project but you can apply for a maximum of two projects. Both UK and international students are eligible to apply for an IGNITE award. However, NERC stipulates that a maximum of 30% of IGNITE studentships (usually 5 studentships per year) can be provided to international applicants so competition for these studentships is very high. We welcome applications from applicants from a diverse range of backgrounds but recognise systemic barriers to entry into postgraduate research for certain groups. To support this, IGNITE has an opt-in guaranteed interview scheme for qualifying UK applicants who self-identify as racially minoritised (i.e., come from a Black, Asian or minority ethnic background). Please contact nerc-dla@soton.ac.uk once you have submitted a complete application to opt into this scheme.

IGNITE DLA Webinar

Watch the IGNITE Doctoral Landscape Award webinar here. Find out more about the IGNITE DLA programme, the application process and what happens if you are shortlisted for interview.

Funding Notes

The IGNITE Doctoral Landscape Award funds PhD researchers for 3.5 years, full- or part-time. An IGNITE DLA studentship includes a tax-free stipend at the UKRI standard rate (£20,780 for the academic year 2025/26). Funding covers Home tuition fees; the difference between Home and International tuition fees will be waived by the University. The IGNITE DLA provides a Research Training Support Grant of £2200 per year (£7700 across the 3.5 years) to be used on small project costs, conference attendance and individual training needs.

References

Doorenspleet, K., Jansen, L., Oosterbroek, S., Kamermans, P., Bos, O., Wurz, E., Murk, A. and Nijland, R., 2025. The Long and the Short of It: Nanopore‐Based eDNA Metabarcoding of Marine Vertebrates Works; Sensitivity and Species‐Level Assignment Depend on Amplicon Lengths. Molecular Ecology Resources, 25(4), p.e14079. Gygax, D., Ramirez, S., Chibesa, M., Simpamba, T., Riffel, M., Riffel, T., Srivathsan, A., Nijland, R. and Urban, L., 2025. Evaluation of nanopore sequencing for increasing accessibility of eDNA studies in biodiverse countries. bioRxiv, pp.2025-04. Al Malik, M.D., Ambariyanto, A., Hartati, R., Nursalim, N., Kholilah, N., Kurniasih, E.M., Anggoro, A.W., Prasetia, R., Syamsyuni, Y., Muh, F. and Cahyani, N.K.D., 2025. eDNA uncovers hidden fish diversity in the coral reef ecosystems of Karimunjawa National Park, Indonesia. Regional Studies in Marine Science, 81, p.103945.