Pathogenic bacteria and antimicrobial resistance in a mountain-river-lake continuum: assessment[...]

Remuneration: between 2300 and 2900 € (gross salary) depending on experience

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

Framework:

The One-health concept is based on the principle that protecting human health depends on animal and environment health protection. Rivers and lakes are impacted by human activities, which induced microbiological contaminations. Consequently, microbial communities inhabiting such ecosystems can act as reservoirs and vectors for fecal bacteria, pathogens, or carriers of antibiotic resistance genes (ARG). These communities can impact human health if waters are used. Monitoring this risk is important, especially in the region of Lake Geneva where 100s thousands of people are using these water ecosystems (bathing, drinking, fishing…).

Work context:

This recruitment will enable to fulfill a temporary mission of a research engineer (post-doc) mobilizing knowledge in molecular biology and environmental microbiology. Applications of engineer (master degree) with good experience will be considered. The person will work with scientists of the UMR Carrtel INRAE (F. Rimet, N. Tromas, E. Lyautet and 3 other post-doc and an engineer) on very similar topic (freshwater microbiology, metagenomics, biomonitoring, functional ecology).

Mission:

Several shotgun Illumina NovaSeq runs (at least 3 runs) have been already sequenced and bioinformatic analyses have been already carried out (various pipelines were used SqeezeMeta, MetaNGS…). From these analyses, the engaged postdoc (or engineer) will have to detect and semi-quantify pathogenic bacteria and ARG. She/He will have to link these findings to environmental factors (wastewater treatment plants, agriculture) and risks for populations (drinking water, bathing…).

Training and skills

Recommended education

• oPhD (preferred) in microbial ecology
• oEventually engineer (master degree) with a good experience

Required skills

• ountargeted metagenomics applied to environmental/complex samples,
• ogood skills in bash, python, R,
• ogood knowledge in bioinformatics and biostatistics
• oability for communication: writing papers, oral presentations

Desired skills

• oLeadership and critical thinking skills
• oAbility to work in a team

Benefits

• up to 30 days of annual leave + 15 days "Reduction of Working Time" (for a full time);
• 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.

How to apply

Send by email a cover letter and a CV including your publications list and contacts of your supervisors.

Application deadline: before 1st July 2026