Host institution: UMR PHIM (Plant Health Institute of Montpellier), France
Duration: 24 months
Start date: Ideally from October 2025 but no later than December 1st, 2025.
Location: based in Montpellier (France), with a field mission in Kenya
Application deadline: open until a suitable candidate is identified
Project Title
Monitoring Rice Diseases and Uncovering the Rice Pathobiome in East Africa through Integrative Sequencing
About the Lab
PHIM (Plant Health Institute of Montpellier) is located in the South of France by the Mediterranean sea and is composed of 16 teams organized in 4 research departments with 140 permanent staff (76 researchers) from several French public research organizations. This institute studies interactions between plants and micro-organisms or insects at various geographic and temporal scales with a focus on plants cultivated in the tropical and Mediterranean areas. PHIM has research programs focused on the microbial and plant molecular mechanisms driving colonization, pathogen genome evolution, the diversity and functioning of the phytobiome as well as monitoring and modeling epidemics. The ultimate goal of this research is to develop new strategies to fight plant diseases (biocontrol, biostimulation, genetic resistance).
Project Summary
This position is funded by IRD (Institut de Recherche pour le Développement), a French public research institution working in partnership with countries in the Global South and in the French overseas territories. Rice is a staple crop in East Africa, yet its production is severely threatened by fungal, bacterial, and viral diseases, many of which are emerging or poorly characterized in the region. Climate change, international trade, and limited diagnostic infrastructure have accelerated the spread of pathogens, threatening food security.
We are seeking a highly motivated postdoctoral researcher to join a project that combines field epidemiology, high-throughput sequencing (Oxford Nanopore Technologies), and ecological and bioinformatic analyses to develop an innovative rice disease surveillance system. The project aims to:
• Identify known and novel rice pathogens using long-read metagenomics,
• Characterize pathogen co-occurrence and potential synergism,
• Investigate rice phage communities as potential biocontrol agents.
This research is part of a broader collaborative effort between the XPLAIN, VICITA, and BLAST teams of UMR PHIM, with strong support from national agricultural systems (NARS) and ongoing field programs in East Africa.
Main Responsibilities
• Optimize nucleic acid extraction methods and implement metagenomic sequencing workflows,
• Participate in field trips abroad (1x ~3 months) and coordinate sample collection and processing,
• Analyze complex microbial and viral communities using state-of-the-art bioinformatic tools,
• Contribute to publications and share results through scientific conferences and collaborative networks.
Candidate Profile
• PhD in microbiology, molecular biology, bioinformatics, plant pathology, or related field with max. 3 years of postdoc experience,
• Proven experience in handling large scale sequencing data such as metagenomic or transcriptomic data analysis,
• Hands-on experience with molecular biology techniques for DNA and RNA processing,
• Willingness to conduct fieldwork abroad,
• Familiarity with host-pathogen interactions and molecular diagnostics is an asset,
• Excellent communication skills and ability to work in a multidisciplinary, multicultural team.
We Offer
• Salary: approximately 2700€/month (gross), with social security and healthcare coverage included.
• Access to cutting-edge sequencing platforms and IRD’s high-performance computing cluster,
• A vibrant research environment with experts in microbial ecology, plant pathology, and molecular diagnostics,
• Opportunities to participate in international collaborations and training sessions in East Africa as a stepping stone to apply for an IRD researcher position.
To apply, please send:
• A one page cover letter outlining your interest and relevant experience,
• Your CV (max 3 pages),
• Contact details for two referees.
Applications should be sent as a single PDF to: sebastien.cunnac@ird.fr
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