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

THESIS OFFER :
Bioaccumulation of chemical contaminants and impacts on the marine biofilm diversity
in the Mediterranean coastal environment
o RESEARCH FIELD(S)
Biology – Marine microbial ecology and ecotoxicology
o JOB DESCRIPTION
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.
o QUALIFICATIONS/SKILLS/EDUCATION & RESEARCH REQUIREMENTS
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.
o APPLICATION DEADLINE
7th of May 2024
o STARTING DATE
The position is available for 3 years ideally starting in October 2024
o JOB LOCATION
MAPIEM laboratory, Université Toulon, La Garde (83)
o REQUESTED DOCUMENTS OF APPLICATION
Letter of motivation, CV and 2 reference letters.
o CONTACTS TO APPLY
Principal supervisor : J.-F. Briand / briand@univ-tln.fr
Co-supervisor : M. Bouchoucha / Marc.Bouchoucha@ifremer.fr
Co-supervisor : E. Catao / elisa.catao@univ-tln.fr