Abstract
Plants harbor in their external surfaces and internal tissues a highly diverse and finely structured microbial assembly, the microbiota. Each plant compartment usually represents a unique ecological niche hosting a distinct microbial community and niche differentiation, which may mirror distinct functions of a specialized microbiota, has been mainly investigated for bacteria. Far less is known for the fungal components of the plant-associated microbiota. Here, we applied a metabarcoding approach to describe the fungal assemblages in different organs of Vaccinium myrtillus plants (Ericaceae) collected in a subalpine meadow in North-West Italy, and identified specific taxa enriched in internal tissues of roots, stems, leaves and flowers. We also traced the distribution of some important fungi commonly associated with plants of the family Ericaceae, namely the ericoid mycorrhizal (ErM) fungi and the dark septate endophytes (DSE), both playing important roles in plant growth and health. Operational taxonomic units attributed to established ErM fungal species in the genus Hyaloscypha and to DSE species in the Phialocephala-Acephala applanata complex (PAC) were found in all the plant organs. Mycorrhizal fungi are thought to be strictly associated with the plant roots, and this first observation of ErM fungi in the above-ground organs of the host plant may be explained by the evolutionary closeness of ErM fungi in the genus Hyaloscypha with non mycorrhizal fungal endophytes. This is also witnessed by the closer similarities of the ErM fungal genomes with the genomes of plant endophytes than with those of other mycorrhizal fungi, such as arbuscular or ectomycorrhizal fungi.