Thesis In Marine Microbial Ecology M - F H/F Ifremer

Deadline for applications: 04/24/2026

Who are we?

You will be hosted within UMR MARBEC, an internationally recognized research unit dedicated to the study of marine biodiversity, its exploitation, and conservation. The scientific environment is highly interdisciplinary, combining ecology, microbiology, aquaculture, and social sciences.

The project is part of major international programs (ExPLOI, THREATS) focusing on plastic pollution and health risks in aquaculture, involving numerous academic partners across Europe, Africa, and Asia.

You will benefit from state-of-the-art facilities in molecular biology, sequencing, and bioinformatics, as well as an extensive international collaboration network.

You will be supervised by:

- Emmanuelle Roque d'Orbcastel (Ifremer, UMR MARBEC, Sète - France)

- Jean-Christophe Auguet (CNRS, UMR MARBEC - Vietnam)

You will be integrated into a multidisciplinary team combining microbial ecology, aquaculture, and social sciences within UMR MARBEC.

What is the topic of the thesis?

Impact of aquaculture plastics on the spread of virulence and antibiotic resistance genes: risks for aquaculture and human health

This PhD project aims to investigate the role of plastics as vectors of pathogens and antibiotic resistance genes in aquaculture ecosystems, using a comparative approach across different regions of the world and assessing risks for human health.

The study will be conducted in two contrasting regions: Southeast Asia (Vietnam), characterized by intensive aquaculture systems with high antibiotic and plastic pressure; Indian Ocean (Mauritius, Madagascar), with more sustainable practices (low antibiotic use and lower plastic density)

The objective is to understand how aquaculture plastics may contribute to the spread of antibiotic-resistant pathogens and to assess risks related to:

• occupational exposure (aquaculture workers)
• seafood consumption (consumers)

The project is structured around three main axes:

• Characterization of the pathobiome and resistome associated with aquaculture plastics at regional and local scales
• Transfer of model marine pathogens via plastics to animal tissues and their persistence after food processing
• Contribution to human health risk assessment related to microbial contamination and resistance/virulence genes in fish exposed to plastics

What will your mission and activities be ?

1. Environmental and microbiological characterization

• Analysis of resistome and pathobiome associated with aquaculture plastics at regional and local scales
• Use of existing datasets (Plastic Odyssée campaigns, Vectoplastic in Madagascar)
• Acquisition of new field data in Mauritius and Vietnam
• Field sampling (water, sediments, fish, plastics)
• Molecular biology and metagenomic analyses

2. Experimental work

• Design and implementation of controlled experiments on pathogen transfer to edible species
• Monitoring persistence of microorganisms in tissues after different food processing method
  

3. Risk assessment

• Contribution to risk analysis for workers and consumers
• Integration of biological and social data
• Collaboration with another PhD student recruited by CNRS (80 PRIME 2026 program)

4. Interdisciplinary approach

• Participation in surveys with aquaculture stakeholders in the Southwest Indian Ocean
  

5. Scientific dissemination

• Publications (3 scientific articles)
• Presentations at international conferences

Key words :

Plastics, aquaculture, microbiology, antibiotic resistance, pathogens, human health, resistome

How are your activities organized?

The PhD will take place over 3 years and will include:

• Laboratory work (France - Sète / Montpellier)
• Field missions (Vietnam, Mauritius)
• Controlled experiments (Madagascar)
• Data analysis and modeling