Structure of core fungal endobiome in Ulmus minor: patterns within the tree and across genotypes differing in tolerance to Dutch elm disease

Plants harbour a diverse fungal community with complex symbiotic interactions and significant roles in host physiology. However, the cues that steer the composition and structure of this community are poorly understood. Trees are useful models for assessing these factors because their large size and long lifespan give these ecosystems time and space to evolve and mature. Investigation of well-characterised pathosystems such as Dutch elm disease (DED) can reveal links between endomycobiome and pathogens. We examined the endophytic mycobiome across the aerial part of a landmark elm tree to identify structural patterns within plant hosts, highlighting not only commonalities but also the effect of local infections in some branches of the crown. We used a common garden trial of trees with varying levels of genotypic susceptibility to DED to identify associations between susceptibility and endomycobiome. Three families of yeasts were linked to higher DED tolerance: Buckleyzymaceae, Herpotrichiellaceae and Tremellaceae. Surveying a natural population with a gradient of vitality, we found some taxa enriched in declining trees. By combining all surveys and adding a further study in a distant natural population, we found evidence of a U. minor core mycobiome, pervasive within the tree and ubiquitous across locations, genotypes and health status.