Junior research scientist on the impact of the microbiota on tree health

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INRAE presentation

INRAE, the French National Research Institute for Agriculture, Food, and Environment, is a public research organization bringing together 12,000 employees across 272 units in 18 centers across France. As the world’s leading institute specializing in agriculture, food, and the environment, INRAE plays a key role in supporting the necessary transitions to address global challenges.

Faced with population growth, food security challenges, climate change, resource depletion, and biodiversity loss, INRAE is committed to developing scientific solutions and supporting the evolution of agricultural, food, and environmental practices.

INRAE is recruiting researchers by open competition and offering permanent position.

Work environment, missions and activities

You will join the Tree-Microbe Interactions (IAM) Joint Research Unit (UMR) 1136, which has around 90 staff, including 46 permanent employees, divided into three teams (INRAE and University of Lorraine). The research conducted at IAM focuses on the biology and ecology of interactions between microorganisms and forest trees. It aims to improve our understanding of the interactions between trees, fungi (pathogenic, symbiotic and saprotrophic) and rhizosphere bacteria, which contribute to the functioning and sustainability of forest ecosystems. The host team (Ecology of Forest Pathogenic Fungi), composed of three researchers, two engineers, two assistant engineers, and three technicians, conducts research on the biology of forest pathogenic fungal populations.

In this context, you will be responsible for developing an emerging theme within the unit, which will focus on the role of microbiota in the development of tree diseases. Trees host a collection of microorganisms (bacteria, archaea, fungi, oomycetes and viruses), commonly referred to as the microbiota. This microbiota colonises the tree's various ecological niches, such as the phyllosphere, rhizosphere, and endosphere and, together with the host plant, forms the plant holobiont. The regulatory role of tree microbiota in disease development has been demonstrated in certain cases and constitutes an innovative area of research. Recent work by the host team has highlighted the role of microbiota in regulating ash dieback. However, knowledge remains incomplete, particularly regarding the other pathosystems studied by the team. In the short term, your mission will be to study the role of microbiota in the development of one of the forest diseases studied by the team, Diplodia shoot blight of pine. In this pathosystem, the pathogen is present in trees in endophytic form long before symptoms appear. It has been shown that the wood microbiota plays a role in triggering the disease by modifying the composition of key metabolites in the tissues. 
You will be responsible for studies aimed at elucidating the role of endophytic microbiota in the epidemiological cycle of the pathogen. Initially, you will characterise the microbiota of symptomatic and non-symptomatic pine stems under natural conditions and its relationship with the onset of symptoms using metabarcoding and/or metagenomics approaches. In a second phase, you will develop innovative approaches for manipulating the microbiota (synthetic microbial consortia) in greenhouses in order to functionally validate its role. These experimental approaches may incorporate simulations of different climate change scenarios in order to study the interactions between plants, pathogens, microbiota, and climate. Furthermore, the study of the rhizosphere microbiota of trees, in particular ectomycorrhizal fungi and associated bacterial communities, is a topic that has been extensively studied within the unit, which will promote collective dynamics.

You will thus benefit from the appropriate infrastructures and tools available locally and from the expertise in metabarcoding and metagenomics data analysis already present in the unit and, more widely, on the Lorraine site. 
More broadly, you will be involved in national (ECODIV Division, Holoflux Metaprogramme, RisqFor, SymbiPhyt and PhytoMic networks, Francophone Forest Pathology Group, PEPR Forestt) and international scientific networks (cross-border networks, European projects, IUFRO workgroups, Phytobiome Alliance) in the field of plant microbiota and forest health.

Trips over several days with overnight stays in France and Europe are to be expected.

Training and skills

Competition open to candidates with a PhD (or equivalent).
A strong background in community ecology of plant-associated microbes and practical experience in the use of metabarcoding and/or metagenomics techniques and related analyses are highly recommended. Any additional skills you may have in plant pathology and/or fungal biology would be highly appreciated, but are not essential. 
Candidates should have a good command of English, and long-term international experience would also be desirable. Successful candidates who have not yet acquired this experience abroad will be required to do so after their probationary period (1st year).

INRAE's life quality

By joining our teams, you benefit from:

- 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.

For international scientists: please visit your guide to facilitate your arrival and stay at INRAE. 

How to apply

1. I download the applicant guide Guide for applicants 2026 pdf - 1.41 MB
2. I write down the profile number CR26-ECODIV-3
3. I apply GO