PhD Offer at the University of Toulouse (France) and the University of the Balearic Islands (Spain)
Topic: Plant core microbiota as biomarker of Xylella fastidiosa infection status
General Information
Workplace: Toulouse area (24 months) and Balearic Islands (12 months)
Contract Period: 36 months
Indicative start date: September/ October 2027
Proportion of work: Full Time
Remuneration: 2450-2550 € / month including Mobility allowance. 29.400-30.600 € / year. If eligible (fellow with 1 or more dependent child), Family allowance: additional 100 € / month.
Requirements: Master’s degree (or equivalent) in Microbiology, Microbial Ecology, Plant Biology, Ecology, Environmental Sciences, Agronomy or a related field.
Context and Rationale
Around 38% of global land is dedicated to agriculture, and while intensive farming has supported population growth, it has also driven significant biodiversity losses, particularly in soil microbial communities. This decline may compromise key ecosystem functions such as nutrient cycling, plant health, and crop productivity. Despite its importance, there are currently no robust, standardized indicators to assess soil biological health across agricultural systems.
The core microbiota—a subset of microbial taxa consistently associated with plants across environments—may provide a promising basis for such indicators due to its stability and potential functional role. This PhD project aims to investigate whether core plant-associated microbiota can serve as a reliable marker of soil health in Mediterranean agroecosystems, using as a working model the pathogen Xylella fastidiosa, a priority quarantine organism that must be controlled in Europe, with a focus on almond trees as host plants, but that could be extended to other cultivated crops across Occitania and the Balearic Islands..
Objectives
The project will combine field studies across Occitania and the Balearic Islands with metagenomic and ecological approaches to (i) identify core microbiota under contrasting infection status, (ii) link their composition and function to soil health indicators such as nutrient cycling, soil organic matter dynamics, and disease suppression, and (iii) explore their potential for microbiome-informed disease management.
Designed as an interdisciplinary and collaborative project, it integrates expertise in microbiology, agronomy, plant pathology, microbial ecology and bioinformatics. Additionally, the project will benefit from partnerships with agricultural stakeholders to support the translation of results into practical tools for sustainable soil management in Mediterranean agriculture.
Required Skills and Competences
The ideal candidate will have a background in microbial ecology, microbiology, plant–microbe interactions, environmental sciences or a related field, with demonstrated interest or experience in microbiome research and quantitative data analysis. Previous experience in molecular biology, metagenomics, bioinformatics, microbial cultivation, or field sampling will be considered an advantage. Given the interdisciplinary nature of the project, the candidate should be motivated to develop complementary skills in both experimental and computational approaches and to work across different disciplines.
The candidate should be highly organized, rigorous, responsible, and able to work independently while contributing effectively to a collaborative research environment. Good planning and attention to detail will be particularly important for field sampling, experimental work, data management, and the integration of results from different sites. Flexibility and adaptability will also be essential, as the PhD will be carried out between France and Spain and will involve working within two research institutions and interacting with different scientific teams. A good working knowledge of English is essential for scientific communication, scientific writing, presentations and participation in international conferences. The candidate should be comfortable working in multilingual and multicultural environments.
Expected Results
At the local scale, the project will generate site-specific insights into soil–plant–microbiome interactions in agricultural sites, affected by Xylella infection. At the regional scale, it will enable comparisons across contrasting Mediterranean agroecosystems, improving the robustness of identified microbial indicators. At the Mediterranean scale, the integration of datasets will support the development of transferable microbiome-based indicators of soil health applicable across similar climatic regions and with similar epidemiological conditions.
Application: More information can be found at: https://terra-med.euroregio.eu/wp-content/uploads/2026/10/UT4_PhD-offer.pdf
The application deadline is 31 December 2026.