PhD position (M/F) in ecological modeling and risk analysis: distribution of pathogens and antibiotic resistance associated with plastics in coastal socio-ecosystems

Job Description

Thesis Subject

Each year, 14.5 million tonnes of plastic are discharged into the oceans, affecting more than 700 aquatic species, including 65% of wild and commercial fish. By hosting microbial communities on their surfaces, often enriched in opportunistic or potentially pathogenic bacteria, plastics can act as vectors for pathogens and antibiotic-resistant bacteria, promoting their spread and raising growing concerns for public health and food safety. These issues are particularly exacerbated in developing regions, where coastal environments receive substantial inputs of potentially pathogenic and/or resistant bacteria, antibiotics, and plastics from urban, hospital, and agricultural waste. At the same time, intensive aquaculture has expanded rapidly over the past three decades in these regions, particularly in Asia. Vietnam has become the world's fourth-largest producer of fish and the leading producer of crustaceans, and FAO projections indicate that aquaculture production is also increasing in Africa. This growing activity relies heavily on plastic infrastructure (nets, ropes, floats, etc.) and involves the use of hundreds of tonnes of antibiotics each year to prevent and treat bacterial infections, a practice that promotes the emergence and spread of antimicrobial resistance (AMR) in animal and human populations.
This PhD project adopts an interdisciplinary One Health approach to understand the role of aquaculture plastics in the dissemination of pathogens and antibiotic resistance genes in tropical coastal environments. More specifically, the PhD candidate will:
(1) develop an integrated modeling framework aimed at (i) identifying the ecological and anthropogenic drivers structuring the distribution of the plastic-associated pathobiome and resistome, and (ii) predicting their future distributions under different scenarios of plastic pollution and aquaculture intensification. This work will rely on original datasets generated from the PLUME oceanographic campaign (metabarcoding and metagenomics) along the Vietnamese coastline, combined with environmental and anthropogenic data;
(2) in close collaboration with social science researchers involved in the project, analyze aquaculture practices, antibiotic use, and risk perception related to plastics, in order to quantify exposure pathways and identify the social determinants of risk;
(3) integrate biological and socio-environmental data into a quantitative microbial risk assessment framework (QMRA), to estimate risks for human populations and identify potential mitigation strategies.
This project offers an international research environment (France, Vietnam, Indian Ocean) and training at the interface of microbial ecology, modeling, and social sciences. It will lead to several scientific publications and contribute to a better understanding and management of health risks in aquaculture socio-ecosystems.

Your Work Environment

Based in Sète within the UMR MARine Biodiversity, Exploitation and Conservation (MARBEC), the PhD candidate will benefit from a multidisciplinary and international research environment, with supervision provided by Jean-Christophe Auguet and Emmanuelle Roque d'Orbcastel (MARBEC), Gwenn Pulliat (ART-Dev), and Sophie Lecomte (CBMN). The candidate will have access to MARBEC's analytical platforms and research infrastructures, as well as to expertise in ecological modeling developed within the unit. The project relies on strong complementarity between partners specializing in microbial ecology, aquaculture, and modeling (MARBEC), biochemistry (IO), social sciences (ART-Dev), and plastic chemistry (CBMN), ensuring comprehensive interdisciplinary training. The PhD candidate will undertake two extended research stays in Vietnam at the University of Science and Technology of Hanoi (USTH), as well as a field mission in Mauritius, enabling immersion in contrasting aquaculture contexts.
This PhD project is embedded within ongoing collaborative programs (THREATS 2025–2027, CityFish 2024–2028, EXPLOI 2023–2029) and builds on a strong track record of joint publications and partnerships, ensuring a robust scientific framework, project feasibility, and high potential for impactful outputs.

Constraints and risks

Constraints related to a doctoral fellowship with co-supervision involving international travel, which may require adaptation depending on the geopolitical context of the countries visited.
Identified occupational risks:
Risks associated with transportation (frequent use of light vehicles, specialized equipment, boats, etc.) and with physical activity (fieldwork at sea).

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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