PhD Offer (M/F): ecotoxicology of PFAS in a reef environment

Job Description

Thesis Subject

-Ecotoxicology of PFAS in a reef environment in a coastal damselfish in Okinawa: an approach combining transcriptomics, field sampling, and bioassays.

Forty percent of the world's population lives within 100 kilometers of the oceans, causing unprecedented pollution in coastal areas. In tropical and subtropical regions, reef fish—which are essential to reef ecosystems—are therefore subjected to numerous anthropogenic stressors. In particular, per- and polyfluoroalkyl substances (PFAS) constitute a class of persistent pollutants widely detected in coastal environments. In Okinawa, Japan, the activities of US military bases are linked with high levels of PFAS near river mouths. Their chemical stability and bioaccumulation potential raise major concerns regarding their effects on marine organisms, which remain largely unexplored.
Interactions between gene expression and the environment are increasingly studied across a wide range of organisms and show great promise for environmental monitoring. With the rise of sequencing technologies over the past few decades, researchers are increasingly conducting transcriptomic analyses to understand which metabolic and physiological pathways are affected by exposure to pollutants.

Your Work Environment

The main objectives of the thesis will be i) to explore the potential of dose-response modelling approaches to identify signatures of low-doses and chronic PFAS exposure in transcriptomes of the blue damselfish (Chrysiptera cyanea), ii) to establish a link between observed transcriptional effects of exposure to PFAS based on laboratory exposure and on field sampling and iii) to characterize the ecotoxicological effects of PFAS and elucidate their mechanisms of action.
By leveraging several approaches: transcriptomics in the laboratory and the field, environmental/landscape characterization, dose-response modelling, and exploration of adverse outcome pathways, the project aims to link environmental exposure and biological responses across scales. This thesis will provide fundamental insights into the mechanisms of action of PFAS and contribute to the development of tools for assessing ecotoxicological risks and biomonitoring of ecosystems.
The thesis will benefit from the recent works conducted at the IRL EARLY to curate the biological annotation of genes in teleost fish (Herrera et al., 2025, https://doi.org/10.1002/jez.b.23299) and to decipher the constraints affecting a coastal fish, using a landscape transcriptomics approach (Gairin et al., 2026, https://www.biorxiv.org/content/10.64898/2026.01.14.699593v1.full.pdf). It will also rely on methodological developments carried out at the LIEC to interpret transcriptomic data acquired along gradients (R package DRomics, Delignette-Muller et al., 2023, https://doi.org/10.24072/pcjournal.325).
This project is built as a collaboration between Elise Billoir, Associate Professor (HDR), who develops modeling tools for ecotoxicology at LIEC (Interdisciplinary Laboratory for Continental Environments, Metz, France), and Vincent Laudet, Professor of Marine Biology at OIST and Director of IRL EARLY (Eco-Evo-Devo of Coral Reef Fish Life Cycle, International Research Lab CNRS-OIST, Okinawa, Japan), who will supervise the thesis. Sophie Prud'homme, Associate Professor at LIEC, ecotoxicologist specializing in mechanistic analysis of the toxic effects of micropollutants, will also participate in the supervision.
The PhD student will be primary based in LIEC (Metz) and will undertake extended research stays (e.g., 3 to 6 months) in Japan at OIST to conduct field sampling and laboratory experiments. The PhD student will benefit from multidisciplinary supervision and a rich scientific environment, with state-of-the-art infrastructure.
The PhD student (M/F) will develop skills at the intersection of biology (omics approaches), environmental sciences (ecotoxicology, ecological risk assessment, landscape ecology), and data science (biostatistics, modelling, bioinformatics).
The doctoral fellowship receives financial support from the CNRS through the MITI interdisciplinary programs.

Expected skills

Master's degree (or engineering degree) in Life Sciences (e.g. Environmental Toxicology, Biodiversity, Ecology and Evolution, Marine Sciences, Molecular Biology).
Knowledge and technical skills – We are looking for a student with a strong background in biology to explore the molecular basis of organisms' stress responses. Previous experience in reef ecosystem research, ecotoxicology, landscape ecology, bioinformatics, and/or data analysis (using R software)—ideally related to gene expression— would be a plus. Previous experience in diving (e.g. French CAH 1B certification) would be a plus.
Soft skills – We are looking for a well-organized and rigorous person, who is willing to work in the field, in the laboratory, and in the office for data analysis, literature research, and writing.
Finally, strong writing, presentation, and communication skills in English are required to interact with the project's international network.

Constraints and risks

Constraints related to a doctoral fellowship with co-supervision involving international travel to Okinawa (Japan).
Fieldwork.

Compensation and benefits

Compensation

2300 € gross monthly

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

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