CD : Manipulation de l'immunité et de la nutrition de l'arbre par des effecteurs produits par des champignons endophytes et mycorrhiziens associés aux racines

école doctorale

équipe

ECOGENOMIQUE DES INTERACTIONS

contexte

Forests and tree plantations provide ecosystem services (timber and wood energy, carbon sequestration, water purification and biodiversity reservoirs), but are threatened by climate change, which is increasing tree mortality and reducing the success of forest plantations. Tree root microbiota are considered to be an extension of tree genomes, and have the particularity of exhibiting a high degree of plasticity, being highly dynamic and having a greater capacity to adapt to environmental variations and disturbances than the host tree1. Poplar and its associated microbes are one of the most extensively studied perennial plant systems2,3, as poplar is one of the few tree species capable of interacting with the full range of mutualistic fungi: endomycorrhizal fungi, ectomycorrhizal fungi (ECM) and endophytes. Moreover, endophytes and ECM fungi make up the bulk of the Populus root mycobiome in many natural ecosystems4. Dominant in boreal and temperate forests, where it is necessary for mineral nutrition and tree growth5,6, ectomycorrhizal symbiosis is well characterized. In comparison, and despite their diversity and potential contribution to tree growth and productivity7, the ways in which endophytic fungi interact with their host and their physiological importance are largely unknown8. The stability of the root microbiota is dictated by environmental conditions, microbe-microbe interactions and the control of the host immune system9. As root-associated micro-organisms, endophytic fungi and ECM are confronted with plant immune responses10 and must mitigate these in order to colonize the root system effectively, without over-colonising11,12. For example, control by ECM fungi of the jasmonic acid signaling pathway via JAZ (JA-mediated signaling pathway repressor) targeted by the fungal effector is a prerequisite for successful in planta growth11. At present, we do not have a detailed understanding of how plant immune responses and their manipulation by micro-organisms contribute to the balance between the ECM and endophytic fungi. We do not know if and how fungus-fungus interactions modify host physiology. These gaps in knowledge are particularly striking for long-lived perennial plants and are made more complex by the diversity of their mycobiome. The main questions we want to address with this PhD thesis are: What are the fungal effectors (proteins, small RNAs, metabolites) allowing endophytic and ECM colonization of roots? Are there common host hubs that plant-interacting fungi must control to colonize roots? How do fungi-fungi interactions modify fungal and host responses observed in binary interactions? Do these fungi compete or act in synergy? The objectives are to: 1) describe the set of fungal effectors, small RNA and metabolites from endophytic and ectomycorrhizal fungi required for root colonisation and mycobiota interaction; 2) characterize tree immune responses during root colonization by endophytic and ECM fungi. We hypothesize that 1) endophytic and ECM fungi use common toolkits (effectors such as small-secreted proteins, small RNAs) to interact with the plant immune system; 2) fungal effectors (SSPs) from different fungal guilds target the same plant immune system pathway hubs; 3) fungi interact with each other through effector proteins and metabolites and 4) poplar root cells trigger a common genetic toolkit supporting root colonization and symbiotic functions.

spécialité

Biologie et écologie des forêts et des agrosystèmes

laboratoire

IAM - Interactions Arbres Microrganismes