Junior research scientist in microbiology of in planta bacterial aggressiveness

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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 conduct your research at the Research Institute on Horticulture and Seeds (IRHS, joint research unit INRAE/Institut Agro/University of Angers), dedicated to research on the quality and health of plants and seeds. You will join the ResPom (focused on apple tree resistance to pests) which includes pathologists, geneticists and ecophysiologists (7 INRAE scientists from the SPE, BAP and AES divisions, and 5 lecturer-researchers), and more widely the “BONUS-MALUS” operational group comprising 7 other teams/platforms from the IRHS and the Horticultural Experimental Unit, united around the quality and health of the apple tree and bringing together expertise in (epi)genetics, microbiology, molecular biology, high-throughput phenotyping, bioinformatics, and orchard management. You will have access to all necessary local facilities, including BSL2 laboratories and BSL2/3 greenhouses, phenotyping and genomics platforms, and high-performance computing servers.
Control strategies for plant bacterial diseases are limited, and their cost/efficiency ratio is often unfavourable. Mobilising host defences/resistance mechanisms through various approaches (plant resistance inducers, genetics) represents a promising strategy. However, our research on the Erwinia amylovora (Ea)/apple tree (fire blight) model has shown that such approaches do not consistently reduce bacterial aggressiveness under certain growing conditions, which likely promote plant susceptibility (or hosting) factors. In addition, Ea exhibits inter-strain variability in aggressiveness despite its near-clonal genetic background. Your primary objective will be to identify the bacterial determinants responsible for the varying aggressiveness of Ea and to understand how they are regulated during interactions with the host plant across various environments.
To achieve this, you will :
-leverage existing knowledge on the pathosystem to formulate and address relevant research questions.
- contribute to consolidating the central position of the team, and more broadly the unit, in the field of apple tree immunity.
- fulfill the core missions expected of a Research Scientist (production, promotion and dissemination of knowledge, development of collaborations, supervision and training through research, search for external funding).
Although key Ea pathogenicity factors and apple tree colonisation stages have been identified, the bacterial determinants of aggressiveness and their regulation in planta remain poorly understood. You will lead their identification and characterisation using a diverse collection of bacterial strains, contrasting host growing conditions *and, in the longer term, the host's genetic diversity.
You will initially focus on a single host genotype, with particular attention to infection stages that may constitute a ‘bottleneck’ for the bacterium during its progression in the plant. To initiate your project, you will build on the team’s experimental results and designs, which reveal the variable capacity of Ea to colonise tissues. To identify determinants of aggressiveness and their regulatory mechanisms, you will use reverse genetics and transcriptomics approaches together with your expertise in bacterial genetics and plant pathology. You will also investigate the epigenetic regulation of bacterial phenotypic plasticity by developing partnerships with the INRAE centre in Toulouse. In close collaboration with the team’s plant specialists, you will develop a project to identify plant susceptibility factors that promote bacterial aggressiveness. In collaboration with modellers, this research, addressing the scientific area of nutritional aggressiveness, will contribute to defining the bacterial biological networks of the infection. In the longer term, and in collaboration with the team’s geneticists, you will extend your work to generate broader insights by assessing the impact of aggressiveness traits across a range of apple tree phenotypes with varying fire blight susceptibility.

Experiments involving phytosanitary products in containment level 2/3 greenhouses are to be expected.

Training and skills

Competition open to candidates with a PhD (or equivalent).
Recommended training: PhD in microbiology, specialisation in plant pathology
Decider level CertiPhyto (Individual certification of phytopharmaceutical products) will be required, but may be obtained after recruitment.
Desired knowledge: bacterial physiology and genetics, plant pathogenic bacteria-plant interactions, basic knowledge in plant immunity (further developed through contact with team members), bioinformatics and statistical data analyses.
Experience appreciated: design and use of a mutant library, acquisition, analysis and potential integration of omics data. Experience in recreating metabolic networks and in bacterial epigenetics would be useful.
Desired skills: ability to analyse datasets; ability to design and monitor experiments in greenhouses and in vitro; taste for collaborative work and supervising students; ability to communicate and participate in working groups; ability to summarise. Proven skills in scientific writing are necessary.
Candidates should have excellent writen and oral communication skills in English, and long-term international experience would also be desirable. Successful candidates who have not yet acquired this experience abroad will be expected to complete an international mobility period 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-SPE-2
3. I apply GO