ED Sciences et environnements
Anticipating, understanding and analysing complex and emerging pathologies of oaks
by Lisa EICHENLAUB (BIOGECO - BIOdiversité, Gènes & Communautés)
The defense will take place at 9h00 - AIRIAL - Salle des Chênaies, INRAE - UMR BIOGECO 1202, Domaine de l'Hermitage, 69 Route d'Arcachon, CS 80227, 33612 Cestas CEDEX
in front of the jury composed of
- Cécile ROBIN - Directrice de recherche - INRAE - UMR BIOGECO 1202 - Directeur de these
- Marie-Agnès JACQUES - Directrice de recherche - IRHS - INRAE - Rapporteur
- Renaud IOOS - Directeur de recherche - Laboratoire de la santé des végétaux (USC INRAE LSV-mycologie, site de Nancy) - Rapporteur
- Benoit MARCAIS - Directeur de recherche - INRAE - UMR IAM - Examinateur
- Beat RUFFNER - Chargée de recherche - Institut fédéral de recherches sur la forêt, la neige et le paysage WS - Examinateur
European oaks (Quercus robur, pedunculate oak and Q. petraea, sessile oak) are two emblematic forest species with important ecological, economical and cultural roles. These species are essential in many ecosystems and represent respectively 11 and 12% of the volume of standing wood of deciduous trees in France. However, they are subject to biotic and abiotic disturbances, which have increased in frequency and intensity due to global changes. Declines, which are multifactorial syndromes, and diseases caused by exotic or native pathogens, have strongly affected oaks since the beginning of the 20th century. The nature of these declines, as well as the interactions between biotic and abiotic factors causing them, are not fully understood. This thesis proposes to define part of their etiology through a study of the cortical and root pathobiomes. Finally, it stresses the importance of territorial surveillance as a way to prevent the introduction of exotic pathogens, especially the threat represented by quarantine organisms. Acute Oak Decline (AOD) is currently affecting oak populations in the United-Kingdom. Mediated by abiotic factors (temperature and precipitation), AOD would be triggered by insects (mainly Agrilus biguttatus) and a complex of bacterial species. This disease perfectly illustrates the pathobiome paradigm, as the complex host-pathobiome-insect interactions are essential to its development. In order to clarify the prevalence of symptoms associated with AOD in France and the role played by bacteria in the observed declines, a study of the etiology of cortical necroses associated or not with attacks of A. biguttatus on declining oaks has been observed. The first report on the presence of bacteria Brenneria goodwinii, Gibbsiella quercinecans and Rahnella victoriana in necroses has been made on Q. robur and Q. petraea in France. However, these bacteria have been isolated less frequently in the lesions than the fungi Fusarium quercinum, F. falsibabinda, Neonectria sp., N. punicea. Moreover, their pathogenicity was confirmed by the inoculations of young oak plants. This confirms the importance of the pathobiome in the symptoms associated with AOD and suggests a significant role of fungal pathogens, which was previously underestimated. The relationships between soil microbiota and chronic oak decline were analyzed in the Chantilly Forest (Oise, France) and with a comparison approach by pair of declining and non-declining oaks, an analysis of the fungal and oomycetes diversities by metabarcoding was performed. The study revealed that the compositions mainly depend on the types of soil and the health status of the trees according to the compartment sampled (bulk soil, rhizosphere or roots). Finally, to help the diagnosis and the identification of phytosanitary problems on Quercus spp. in France, an interactive tool called NESTOR (phytosaNitary survEillance and diagnoSTics of Oaks in FRance), has been developed. Inventorying the main bioaggressors and abiotic problems on oaks with this tool is intended to encourage passive surveillance of the territory by the general public and professionals and also to support the active surveillance of the territory led by the Forest Health Department of the French Ministry of Agriculture and Food in France. In 2022-2023, intensified surveillance of oak wilt disease, caused by the vascular fungus Bretziella fagacearum, was carried out by collecting samples from symptomatic trees. The isolations and diagnoses conducted during this thesis confirmed that the fungus is still absent from the territory, but that it remains important to stay vigilant about its possible introduction in France.