Identify the biotic and abiotic factors that promote or mitigate the dissemination of antibiotic resistance during the land application of organic waste products

Back to jobs listing

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 is a research unit of the National Research Institute for Agriculture, Food and Environment (INRAE) - Occitanie-Montpellier Centre - located in Narbonne.

Symbolized by the production of bioenergy (e.g., via biomethane and biohydrogen by anaerobic ecosystems), the LBE's research seeks to treat and/or valorize the waste products of human activity, whether they are liquid effluents (agri-food in particular), solid residues (agricultural residues, household waste and sludge from wastewater treatment plants) or specific biomasses such as micro or macroalgae. This valorization is declined by explicitly integrating the constraints of sanitary harmlessness (eg., related to the presence of pharmaceutical residues, detergents, and/or pathogens ...). Its research covers a very broad spectrum of disciplinary skills: microbiology, microbial ecology, biological engineering, process engineering, modeling, automation, life cycle analysis, project engineering, and industrial transfer. It is one of the world's leading laboratories in the field of anaerobic digestion. It benefits from a 4757 m² surface area, including 1882 m² of the experimental hall, and high-performance scientific and analytical equipment, with more than 50 digesters (1 liter to several m3) in operation 24 hours a day and 365 days a year. The LBE relies on excellent research, a plurality of themes, a multidisciplinary approach, but also know-how in terms of technology transfer and innovation.

Job description and scientific context

This position is part of the ATBR-SOL project: « Determinants of the selection or attenuation of AnTiBiotic Resistance after the application of organic waste products on SOiL”, funded by ANSES. Antibiotic resistance is a major concern for public and environmental health. The land application of organic residual products (ORPs), such as composted or digested sludge, and livestock effluents, contributes to the intermittent introduction of antibiotics, antibiotic resistant bacteria (ARB), and antibiotic resistance genes (ARGs) into the environment, thereby promoting the spread of antimicrobial resistance. To address this issue within a “One Health” approach, managing ORPs until their application to the soil is a major lever. The processes used to stabilize ORPs can reduce concentrations of antibiotics, ARBs, and the diversity and abundance of ARGs and associated mobile genetic elements (MGEs). However, this reduction varies greatly depending on the genes considered, the effluent treated, and the process used. Likewise, the evolution of antimicrobial resistance markers after land application depends on soil type and its biodiversity.

Key Objectives

The objectives of ATBR-SOL are to investigate and determine: (i) The role of soil amendment history and its biodiversity (microbial, fungal, and earthworm communities) in the selection or attenuation of antibiotic resistance during amendment; (ii) The role of different components of livestock-effluent-derived digestates (organic matter, antibiotics, and microbiota) in the dissemination of antimicrobial resistance upon land application; (iii) The biotic and abiotic parameters that control the coalescence of microbial communities and resistance genes (evolution and interaction of endogenous soil communities and exogenous communities from digestate or earthworm casts after mixing);
(iv) The dynamics of gene transfer under selective pressures applied to soil communities.

Specific Tasks

Within this project, you will primarily be responsible for objectives (i) to (iii). Using soil microcosm strategies, your tasks will include:

• Setting up and monitoring soil microcosms (sampling for physicochemical analyses, DNA extraction, bioturbation tests);
• Quantifying resistance genes and mobile genetic elements in samples from experimental studies, characterizing microbial abundance and diversity;
• Correlating all data collected throughout the experimental phases (target gene abundances, oxytetracycline concentrations, microbial community structure and diversity);
• Identifying conditions driving antimicrobial resistance prevalence and dissemination, and understanding microbial coalescence between digestate and soil.

Part of the experiments will be conducted in Toulouse at the CRBE (Biodiversity and Environment Research Center), within the "Integrative Ecotoxicology" team, which investigates ecotoxicological and environmental impacts of various contaminants at multiple biological levels (from cells to communities). The rest will be carried out at LBE in Narbonne, in collaboration with the INTHERES unit (Therapeutic Innovation and Resistances).

Training and skills

• Academic Background: PhD in microbiology or microbial ecology.
• Skills: Microbial ecology; bacterial culture; DNA extraction; qPCR; microbial structure and diversity analysis; bioinformatics; statistical analysis; sequencing data analysis (16S rDNA under R using phyloseq/microeco or equivalent); knowledge of soil ecosystems would be appreciated.
• Attributes: Autonomy and initiative; organizational skills and team integration; good English level (mandatory); strong writing skills.

INRAE's life quality

• Cutting-edge research environment: work in a state-of-the-art laboratory equipped with the latest technologies in environmental biotechnology. The equipment is fully shared, so you will have access to all the facilities.
• Mentorship and training: receive guidance from leading experts in the field and access to a comprehensive 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: opportunities for professional development, including workshops, seminars, and networking events.
• Work atmosphere: You will be part of a team that takes their work very seriously. We pride ourselves on fostering a collaborative and supportive atmosphere where researchers and interns work together in a dynamic and friendly environment to drive 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 inexpensive collective restaurants; flexible schedule; access to on-site sports facilities; sunny weather.

How to apply

I send my CV and my motivation letter