PhD Fellowship in Evolutionary Genomics of the plant-microbiome interaction

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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

The PhD will contribute to the HoloE2Plant project - Exploring the Holobiont concept through Plant Experimental Evolution - coordinated by Claudia Bartoli at the INRAE of Toulouse (France). The position is funded by the ERC (European Research Council). At first, the PhD will contribute to the selection of microbial strains by using whole-genome sequenced microbes and their metabolic capabilities previously characterized. The PhD will thus integrate this genomic and metabolic information to select Synthetic Microbial Communities (SynComs) with the lowest number of species that optimize the interactions with the plant and minimize interaction within the SynCom. The selected SynComs will be tested on fast-cycling Brassica rapa plants for their ability to reduce disease caused by the fungal pathogen Rhizoctonia solani. These SynComs will also be tested for their biostimulation activities on Arabidopsis thaliana, and their potential synergistic effect when grew with Pseudomonas siliginis strains well characterized in the team. In a second step, three SynComs conferring an intermediate level of resistance will be used to carry out a novel evolutionary experiment by combining the host (B. rapa), the SynCom and the pathogen. The impact of SynComs diversity and genomic complexity on disease modulation will be tested during the project. The PhD will be working with a technician in molecular biology and microbiology. We are looking for applicants with a strong academic background who have completed a five-year master degree (3+2) (or equivalent according to NARIC) in Ecology and Evolution. The candidate should demonstrate to have solid skills in bioinformatics, statistics and programming at least in R, Python or Perl is mandatory for this position. Skills in molecular biology such as DNA extraction and RT-PCR are welcome but not mandatory. The candidate will also participate with the support of a technician to plant phenotyping, however, skills in plant pathology are not mandatory. A good English level, the ability for the scientific writing and communication are required. Applicants need to demonstrate their ability to work in a team.

Training and skills

Solid skills in bioinformatics, statistics and programming

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.

How to apply

I send my CV and my motivation letter