Thèse Etude de la Modulation de la Virulence de Xylella Fastidiosa et Caractérisation des Mécanismes de Protection des Agents de Biocontrôle par une Approche Multi-Omique H/F - Doctorat.Gouv.Fr

Établissement : Université de Perpignan Via Domitia École doctorale : Energie et Environnement Laboratoire de recherche : Centre de recherches insulaires et observatoire de l'environnement Direction de la thèse : MARIE-VIRGINIE SALVIA ORCID 0000000288061777 Début de la thèse : 2026-10-01 Date limite de candidature : 2026-06-08T23:59:59 La productivité agricole et la sécurité alimentaire sont de plus en plus menacées par l'émergence de pathogènes des plantes, qui causent d'importants dommages économiques, environnementaux et sociaux à l'échelle mondiale. L'un des exemples les plus préoccupants est Xylella fastidiosa, une bactérie phytopathogène de quarantaine qui s'est propagée dans plusieurs régions méditerranéennes d'Europe et représente une menace majeure pour des cultures à forte valeur économique telles que l'olivier, la vigne, l'amandier, les agrumes, ainsi que de nombreuses espèces ornementales et sauvages. X. fastidiosa a été identifiée comme l'agent pathogène de quarantaine présentant le plus fort potentiel d'impact au sein de l'Union européenne.
Les stratégies actuelles de gestion reposent sur des mesures de quarantaine, le contrôle des insectes vecteurs et des traitements chimiques ou biologiques, mais ces approches sont coûteuses, dommageables pour l'environnement et insuffisantes pour enrayer la propagation de la maladie. En l'absence de traitement curatif efficace en conditions de terrain et compte tenu de l'engagement de l'Union européenne à réduire l'usage des pesticides, il existe un besoin urgent d'alternatives durables.
Ce projet vise à identifier les mécanismes impliqués dans la virulence de Xylella fastidiosa et à caractériser les effets protecteurs d'agents de biocontrôle à l'aide d'une approche multi-omique. En combinant la génomique, la transcriptomique et la métabolomique non ciblée, l'étude analysera les modes d'action de composés antimicrobiens (issus de Bacillus et Pseudomonas), ainsi que les déterminants moléculaires de la virulence chez différentes souches de X. fastidiosa. Les résultats attendus devraient contribuer au développement de stratégies de biocontrôle innovantes et respectueuses de l'environnement pour la gestion de ce pathogène émergent. Crop productivity is increasingly threatened by the rising occurrence of pests and diseases, particularly those caused by emerging pathogens. Plant pathogen infections are estimated to generate around one billion dollars in economic losses worldwide each year (Ristaino et al., 2021). Beyond yield reductions and the costs associated with disease management, emerging plant pathogens endanger food security by impairing a region's ability to meet its nutritional needs, disrupting local economies and trade-dependent social structures, and contributing to biodiversity loss in agricultural, forestry, and natural ecosystems.
The outbreaks of the quarantine plant pathogenic bacterium Xylella fastidiosa in Europe illustrate the devastating impact an emerging pathogen can have when it becomes established and spreads in a previously unaffected area. X. fastidiosa has been identified as a major transboundary plant pest posing a severe threat to global food security and the environment (EU Regulation 2019/1702; Sanchez et al., 2019). It ranks as the quarantine pathogen with the highest potential impact in the EU across economic, social, and environmental dimensions, and it was placed first on the EU's priority list of quarantine pests/pathogens according (Sanchez et al., 2019).
This xylem-limited, plant-pathogenic bacterium affects a broad range of hosts, including crops of major economic value, species of cultural or heritage significance, and landscape plants (EFSA 2019a). Among the affected crops are olive, almond, grapevine, prunus species, rosmarinus, and citrus, as well as numerous ornamental, wild, and forest plants. In Europe, X. fastidiosa has been detected in several Mediterranean-climate regions, including Italy, France (Occitanie and Corsica), Spain, and Portugal.
As no practical cure exists for Xylella fastidiosa under field conditions, control measures implemented in the EU have centered on 3 main strategies: (1) exclusion and quarantine, (2) vector management, and (3) direct interventions aimed at curing or reducing disease symptoms in host plants through chemical or biological treatments, the use of naturally resistant or tolerant genotypes, and specific agricultural practices (EFSA 2019a, 2019b). However, tree removal and chemical control of insect vectors carry significant environmental and economic costs for agricultural ecosystems. Moreover, these measures alone have proven insufficient to stop the spread of the pathogen or reduce disease severity, underscoring the urgent need for new approaches to manage X. fastidiosa. In this context, management strategies should prioritize the development of effective and sustainable solutions aligned with the EU Green Deal and the Farm to Fork strategy, which emphasize reducing the use of chemical pesticides. The proposed project will therefore focus on deciphering Xylella fastidiosa virulence modulation and protective mechanisms of biocontrol agents using a multi-omics approach, with the aim of developing new biocontrol treatments to help address the epidemic.
To this end, we will first study the modes of action of antimicrobial compounds (biocontrol products derived from Bacillus and Pseudomonas) on Xylella fastidiosa. We will also seek to identify the molecular mechanisms involved in the virulence of different strains. In order to achieve these goals, a multi-omics approach will be implemented, combining genomics, transcriptomics and untargeted metabolomics. The University of Girona provides the required facilities and regulatory authorization to work on Xylella fastidiosa, along with strong expertise in genomics and transcriptomics. In parallel, the University of Perpignan and CRIOBE will offer complementary facilities and expertise for untargeted metabolomics analyses. The PhD will be divided in 2 main parts in order to investigate:
(1) : the effect of selected antimicrobial compounds (mainly natural and synthetic peptides) with different mechanisms of action against Xylella fastidosa using transcriptomics and untargeted metabolomics approaches (cf PhD work of Robin Cahuzac - PhD supervisor: Cédric Bertrand).
- 3 compounds with different mechanisms of action (p.e. direct lysis of the bacterial membrane, peptides with antibiofilm activity, peptides that interact with bacterial lipopolysaccharides (LPS), peptide-nucleic-acid (PNAs) will be studied,
- the activity will be assessed against the model strain Xylella fastidiosa subsp. fastidiosa (sequence type ST1).
- the findings will be extended to subsp. multiplex (isolated from France/ Spain) and subsp. pauca (isolated from Italy) from European outbreaks.

(2) : the mechanism of virulence/aggressiveness of selected strains of X. fastidiosa
- 3 strains of Xylella fastidiosa with different virulence levels, previously determined by UdG in other projects (e.g. BeXyL from EU) will be used. The transcriptomic and metabolomic profiles of the different strains will be obtained and compared, using the annotated genomes existing in GenBank as reference, to identify the molecular determinants associated with virulence.

Le candidat doit posséder les compétences suivantes :
- Une expertise en biologie, de préférence en microbiologie et en biologie végétale, ainsi que quelques connaissances en biologie moléculaire,
- Une expertise en chimie analytique et quelques connaissances en métabolomique et en transcriptomique,
- De bonnes connaissances en statistiques de base,
- La maîtrise de l'analyse de données à l'aide du logiciel R serait également un atout,
- Un bon sens de l'organisation,
- Un esprit proactif et rigoureux,
- Une bonne aptitude au travail en équipe.