Laboratoire MAPIEM (UR 4323)

Matériaux Polymères Interfaces Environnement Marin

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THESIS OFFER : Bioaccumulation of chemical contaminants and impacts on the marine biofilm diversity in the Mediterranean coastal environment


Bioaccumulation of chemical contaminants and impacts on the marine biofilm diversity
in the Mediterranean coastal environment


Biology – Marine microbial ecology and ecotoxicology


The proposed thesis supports the BIOFINDIC+ project (Agence de l’eau RMC), which builds on the successful BIOFINDIC initiative, and focuses on marine biofilms, in particular diatoms communities as bioindicators of marine chemical pollution.
Biofilms are intricate microbial communities with diatoms as an important autotrophic component. The BIOFINDIC project validated the potential of biofilms as bioindicators via bioaccumulation of organic and metal contaminants, and demonstrated their potential for water quality assessment. The upcoming BIOFINDIC+ project has three main objectives: 1/ to compare bioaccumulation levels and their effects on diatom communities between 2021 and 2024, 2/ to assess biofilm community responses to pollutants at fine spatial scales, and 3/ to understand microbial response mechanisms.
Biofilm samples will be collected from surfaces immersed during the Suchimed 2024 campaign at 34 sites along the French Mediterranean coast, supported by Ifremer. The project also includes the exposure of surfaces in the Bay of Toulon and the Thau lagoon to study the historical effects of pollution at short spatial scales. In addition, mesocosm experiments will be used to expose biofilms to increasing amounts of contaminants in order to analyze specific responses. Various analyses including environmental scanning electron microscopy,contaminants bioaccumulation (in collaboration), DNA metabarcoding, metagenomics and
biochemical characterizations, will be performed on these biofilms. In addition, for specific sites, an innovative approach will be used to couple « omics » analyses and targeted quantification of resistance genes. Expected outcomes include an understanding of biofilm responses to multi-pollution, and key factors influencing ecological responses to contamination profiles. The project aims to contribute to the understanding of microbial communities’ behavior in a context of changing marine environment exposed to a multitude of anthropogenic impacts, with a potential objective of bioindication.


The desired candidate for this PhD thesis should have a Master’s degree, ideally in marine sciences, marine microbiology or microbial ecology, with multidisciplinary knowledge in environmental microbiology, ecotoxicology, and a basic understanding of chemistry. The candidate should be enthusiastic about going on marine field trips to collect samples. In addition, the candidate should have skills in molecular biology for DNA extraction, PCR, and mesocosm setup. Ideally, the candidate should have basic knowledge and be highly motivated to perform bioinformatic analysis, such as metabarcoding (DADA2, FROGS), and at least basic notions on R and Linux for metagenomic analysis in a remote cluster.


7th of May 2024


The position is available for 3 years ideally starting in October 2024


MAPIEM laboratory, Université Toulon, La Garde (83)


Letter of motivation, CV and 2 reference letters.


Principal supervisor : J.-F. Briand /
Co-supervisor : M. Bouchoucha /
Co-supervisor : E. Catao /