PhD on monitoring the health of coral reefs by combining environmental DNA (eDNA) with epigenetic markers (M/F)

Job Description

Thesis Subject

This PhD project aims to develop an innovative framework for monitoring coral reef health by combining environmental DNA (eDNA) with epigenetic markers in sea cucumbers, with a focus on Stichopus chloronotus in the southwestern Indian Ocean. Coral reef ecosystems deliver key services such as shoreline protection, nutrient cycling, and support for fisheries and biodiversity, but are increasingly threatened by climate change, acidification, coastal development, and pollution, making effective, scalable monitoring tools a priority for management programs like PEPR BRIDGES.
The project builds on recent advances in eDNA methods, where water samples are used to detect species and, under certain conditions, infer organismal abundance using qPCR, ddPCR, and metabarcoding, offering less invasive, standardized, and cost‑effective alternatives to visual surveys. In parallel, the thesis leverages epigenetic approaches, particularly DNA methylation profiling, which have proven powerful for inferring traits such as age, growth, stress exposure, and sex in marine organisms, but have rarely been applied to methylated eDNA (eDNA‑m) in natural environments. By linking eDNA concentration and methylation signatures, the project seeks to derive population‑level indicators (abundance, size structure, sex ratio) from water samples alone, thus expanding the ecological information content of routine monitoring.

Your Work Environment

This funding was secured through a call for proposals under the PEPR BRIDGES programme. The thesis will be supervised by Serge Bernard, who works at the LIRMM in mainland France; the PhD student will be based at Ifremer's Indian Ocean Delegation (a hosting agreement is in place). The thesis will be co-supervised by an interdisciplinary team:
Sylvain Bonhommeau (Chercheur IFREMER, laboratoire DOI Entropie)
Serge Bernard (DR CNRS, laboratoire LIRMM)
Philippe Jourand (IR IRD, Laboratoire Entropie / SantEco)
Patrick Frouin (Mdc Université de la Réunion, laboratoire Entropie)
Mathias Rouan (IR CNRS, Laboratoire SantEco / Entropie)
Dominique Cowart (PhD, Société COOOL)

The post falls within the scope of the Protection of Scientific and Technical Potential (PPST) scheme and therefore, in accordance with the regulations, requires your appointment to be authorised by the relevant authority at the Department for Education and Skills (MESR)

Constraints and risks

Opportunity for fieldwork to collect samples

Compensation and benefits

Compensation

3105€ gross/month (including €2300.00 fixed remuneration and €805/month supplement related to overseas assignment)

Annual leave and RTT

44 jours

Remote Working practice and compensation

Pratique et indemnisation du TT

Transport

Prise en charge à 75% du coût et forfait mobilité durable jusqu’à 300€

About the offer

About the CNRS

The CNRS is a major player in fundamental research on a global scale. The CNRS is the only French organization active in all scientific fields. Its unique position as a multi-specialist allows it to bring together different disciplines to address the most important challenges of the contemporary world, in connection with the actors of change.

CNRS

The research professions