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Thesis In Marine Microbial Ecology M - F H/F
Ifremer
Sète, France
Posted on Apr 3, 2026
Les missions du poste
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, funded by AFD-FFEM and implemented by the COI and IRD; THREATS, funded by ExposUM) 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
Le profil recherché
Who are you?
- Master's degree (MSc, Bac +5) or engineering degree (or equivalent) in ecology, microbiology, or marine sciences
You have the following skills, knowledge and experience:
- Microbial and/or environmental ecology
- Molecular biology techniques
- Data analysis (R required)
- Bioinformatics (appreciated)
- Laboratory and/or field experience
- Good level of scientific English
You have the following qualities:
- Scientific rigor
- Autonomy and initiative
- Analytical and synthesis skills
- Interest in interdisciplinary and international work
- Teamwork and strong interpersonal skills
Bienvenue chez Ifremer
Join Ifremer, an ally of planetary well-being, to gain a better understanding of and better protection for the ocean.
From the abyss to the surface, from the coast to the open SEA, Ifremer is the French research institute that is wholly dedicated to the Ocean. Its teams carry out research, innovate and produce expert reports to protect the ocean, exploit its resources in a responsible manner and shares marine data.
Ifremer contributes its scientific expertise to throw light on public policies and develops solutions drawn from the ocean to meet the challenges of the ecological transition. Ifremer is the operator of France's oceanographic fleet with its shipbuilding subsidiary Genavir, and imagines, designs and deploys leading edge technological means to solve the ocean's mysteries.
Join our teams, made up of 1500 scientists and research support staff, present all along the coastal areas of France and French overseas territories.
www.ifremer.fr
Infos complémentaires
What are your benefits?
- We have a teleworking agreement and our staff have 12 comp time days (after 6 months' seniority) and supra statutory leave.
- We allocate a significant budget to developing skills, through individual or collective training actions.
- We have a CSR policy inspired by the purposes of the institute (sustainable mobility allowance, etc.)
How to apply?
Your application file must include in a pdf file:
- a curriculum vitae
- a covering letter
- a reference letter
- an academic transcript (Bachelor + Master 1 and first semester Master 2)
The deadline for applications is April 24th, 2026. Nevertheless, we strongly urge you to let us know as soon as possible of your intention to apply, by contacting the subject supervisor:
- Emmanuelle Roque
- Jean-Christophe Auguet
Doctoral students' contracts will start as of October 5th, 2026, subject to the submission of administrative documents authorizing Ifremer to recruit the doctoral student (certificate of completion of the Master 2 or engineering degree + visa for foreign doctoral students outside the EU).
What are the next steps?
- Review of your application
- Interview before a doctoral school committee, with representatives from the doctoral school and Ifremer
- Approval of your application by the doctoral school council
La carte
87 Avenue Jean Monnet
34200 Sète
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Publiée le 03/04/2026 - Réf : 3935046/28224224 2026-1851/1