Lichen-inhabiting fungi represent a large and diversified but still unknown ecological group. They can live on host thalli symptomatically, showing characteristic phenotypes and different degrees of specificity (lichenicolous fungi), or asymptomatically (endolichenic fungi), detectable only through culture and molecular techniques. Here we aim at studying the whole diversity of lichen-associated fungi using a metabarcoding analysis of the internal-transcribed-spacer regions, as parts of the fungal standard barcode, comparing the results obtained by sequencing separately both the ITS1 and the ITS2 segments In this way we also avoid the analysis of group I intron occurring in some ITS1 fragments and achieve with the ITS2 a higher resolution on species composition. We analyzed thalli with and without symptoms of fungal infection collected from Alpine lichen communities on the Koralpe Massif (Austria). The first ITS1 amplicon sequencing highlighted a great taxonomic diversity. The majority of detected OTUs epresents fungi of the two main classes Dothideomycetes and Eurotiomycetes. Shared endolichenic fungal composition in the thalli varies in different lichen species and does not correlate with the symptomatic fungal infections. Metabarcoding allows the exploration of lichens as ecological
niches, revealing the organization of complex symbiotic communities and potentially the presence of coherent patterns.
