Tracking horizontal gene transfer of antibiotic resistance and virulence genes across agroecosystems

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INRAE presentation

The French National Research Institute for Agriculture, Food, and Environment (INRAE) is a major player in research and innovation. It is a community of 12,000 people with 272 research, experimental research, and support units located in 18 regional centres throughout France. Internationally, INRAE is among the top research organisations in the agricultural and food sciences, plant and animal sciences, as well as in ecology and environmental science. It is the world’s leading research organisation specialising in agriculture, food and the environment. INRAE’s goal is to be a key player in the transitions necessary to address major global challenges. Faced with a growing world population, climate change, resource scarcity, and declining biodiversity, the Institute has a major role to play in building solutions and supporting the necessary acceleration of agricultural, food and environmental transitions.

Work environment, missions and activities

Introducing the LBE

The Laboratory of Environmental Biotechnology (LBE) is a research unit of the INRAE Occitanie-Montpellier Centre, located in Narbonne.

Symbolized by the production of bioenergy (e.g., biomethane and biohydrogen by anaerobic ecosystems), the LBE's research seeks to treat and/or valorize the waste products resulting from human activities, including liquid effluents (particularly from the agri-food sector), solid residues (agricultural residues, household waste, and sludge from wastewater treatment plants) and specific biomasses such as micro- and macroalgae. This valorization approach explicitly integrates sanitary safety constraints, particularly those related to the presence of pharmaceutical residues, detergents, and/or pathogens.

Its research covers a broad spectrum of disciplinary expertise including microbiology, microbial ecology, biological engineering, process engineering, modeling, automation, life cycle analysis, project engineering, and industrial transfer. The LBE is recognized as one of the world's leading laboratories in the field of anaerobic digestion. 

The laboratory benefits from a total surface of 4,757 m², including 1,882 m² of the experimental facilities, as well as high-performance scientific and analytical equipment. More than 50 digesters ranging from one liter to several cubic meters, operate continuously, 24 hours a day and 365 days a year. The LBE relies on research excellence, thematic diversity, a multidisciplinary approach, and strong expertise in technology transfer and innovation.

Job description and scientific context

Antibiotic resistance is considered one of the major global health challenges of our time. Bacteria can exchange resistance and virulence genes between each other, making infections harder to treat and increasing risks for human, animal, and environmental health.

At the same time, agriculture increasingly reuses organic waste such as manure and digestate as natural fertilizers to support sustainable farming and circular economy practices. But can these materials contribute to the spread of antibiotic resistance and virulence genes in soils and crops?

This PhD project aims to answer this important question by studying how these genes move through agricultural ecosystems, from organic waste to soil and crops.

You will work at the frontier of environmental microbiology, biotechnology, and genomics, using advanced molecular and bioinformatic tools in a highly collaborative and international research environment.

Key Objectives

This PhD project aims to improve our understanding of how antibiotic resistance and virulence traits spread in agricultural environments, with a focus on their movement between microorganisms rather than just their presence.

Specifically, the project will:

• Explore the factors that influence the dissemination of antibiotic resistance and virulence determinants in environments impacted by organic waste reuse. 
• Investigate how agricultural practices and waste treatment processes may shape microbial communities and their associated gene transfer potential. 
• Improve our understanding of the environmental pathways that connect waste, soil, and plant-associated microbiomes.
• Identify key microbial players involved in the maintenance and spread of clinically relevant traits in environmental systems. 
• Generate evidence to support safer and more sustainable organic waste reuse policies in agriculture.

Specific Tasks

During the PhD, the candidate will contribute to both experimental and computational research activities, including:

• Setting up and working with laboratory-scale experimental systems related to organic waste treatment
• Conducting molecular biology experiments to study microbial communities and gene transfer processes 
• Analyzing high-throughput sequencing data using bioinformatic and statistical approaches 
• Working with interdisciplinary datasets linking microbiology, environment, and agricultural systems 
• Designing and contributing to experimental studies under controlled conditions (e.g., soil and plant systems)
• Communicating results through scientific publications and presentations at conferences

Training and skills

Requirements

• Academic Background: Master's degree in Microbiology, Molecular Biology, Biotechnology, or a related field.
• Skills: hands-on experience in some of the following areas is appreciated:
• Molecular biology techniques (DNA extraction, qPCR, sequencing)
• Microbial community analysis (e.g. amplicon sequencing, metagenomics)
• Bacterial genetics
• Bioinformatics and data analysis (R, Linux, or similar)
• Personal qualities: curious and motivated. Organized and rigorous. Comfortable working both independently and as part of a team. Good written and oral communication skills in English. Enjoys mentoring and co-supervising students.
• Language: fluent English is required. French is a plus, but not mandatory.

INRAE's life quality

By joining our teams, you benefit from (depending on the type of contract and its duration):

- up to 30 days of annual leave + 15 days "Reduction of Working Time" (for a full time);
- parenting support: CESU childcare, leisure services;
- skills development systems: training, career advise;
- social support: advice and listening, social assistance and loans;
- holiday and leisure services: holiday vouchers, accommodation at preferential rates;
- sports and cultural activities;
- collective catering.

What We Offer

• Cutting-edge research environment: work in a state-of-the-art laboratory equipped with advanced technologies in environmental biotechnology. All equipment and facilities are fully shared, providing access to a wide range of experimental and analytical platforms.
• Mentorship and training: benefit from close supervision by leading experts in the field and access to a comprehensive scientific and professional training program.
• Collaborative network: engage with a dynamic team of researchers and industry partners, both nationally and internationally.
• Funding and resources: competitive stipend and funding for research-related expenses, including conference travel and publications.
• Career development: access professional development opportunities through workshops, seminars, and networking events.
• Supportive work atmosphere: you will be part of a team that takes its work very seriously. We foster a collaborative and supportive environment where researchers and interns work together in a dynamic and friendly setting to develop innovative solutions for environmental sustainability. 
• Great working conditions: 30 days of holidays per year (+15 if time recovery is affected); support for parenting; access to affordable collective restaurants; flexible working hours; access to on-site sports facilities; sunny weather.
• Salary: 2300 €/month before tax

How to apply

Interested candidates should submit the following documents by June 20, 2026, to laura.alvarez-fraga@inrae.fr and dominique.patureau@inrae.fr:

• A detailed CV, including academic achievements and research experience.
• A cover letter outlining your motivation and suitability for the PhD project.

We look forward to receiving your applications and welcoming you to our team at INRAE-LBE, where your research will contribute to a sustainable future.