Fungal Assemblages in Northern Elms—Impacts of Host Identity and Health, Growth Environment, and Presence of Dutch Elm Disease

Dutch elm disease (DED), caused by the pathogenic ascomycete Ophiostoma novo-ulmi, has devastated natural elm (Ulmus spp.) populations in Europe and North America. Elm species vary in their susceptibility to this vascular disease, which may partly reflect differences in their associated mycobiomes. To investigate the diversity and composition of fungal endophyte communities in relation to host genotype, health status, and environment, we analyzed twig-associated fungi in symptomatic and asymptomatic individuals of highly susceptible U. glabra, less susceptible U. laevis, and hybrid elms growing in Estonia and Russia. Fungal communities were analyzed using PacBio long-read amplicon sequencing of the ITS1-5.8S-ITS2 gene region. Tree species exhibited distinct fungal community profiles. Ophiostoma novo-ulmi was detected exclusively in symptomatic trees and was dominant in U. glabra; it was absent in symptomatic hybrid elms. In contrast, the canker-associated pathogen Sphaeropsis ulmicola occurred in both symptomatic and asymptomatic trees, was dominant in symptomatic U. laevis, and common in symptomatic and healthy U. glabra, though less prevalent in symptomatic hybrid elms. Remarkably, S. ulmicola was associated with the highest level of damage in U. laevis while being present also in hybrid elms. While O. novo-ulmi's presence did not affect overall fungal richness, S. ulmicola was linked to higher fungal diversity. Additionally, fungal species richness was significantly greater in urban compared to rural environments. This was the first comparable analysis of fungal diversity and composition on three different Ulmus species shoots.