Agricultural land use shapes the soil mycobiome at microgeographic scales

Agricultural land use alters soil fungal communities and ecological functioning, yet the contribution of local factors to changes in fungal diversity remains poorly understood. This study investigated the diversity, community composition and abundance of topsoil fungal communities from two different types of land use at local and very small spatial scales in Switzerland. ITS2 metabarcoding in annual croplands and adjacent perennial grass verges revealed a total of 4565 fungal amplicon sequence variants (ASVs). The number of ASVs at three study sites was similar between croplands and grass verges and 27 % of all taxa were shared between sites. Of the 629 genera detected, Cladosporium (Ascomycota) was most prevalent in both croplands (11.6 % of reads) and grass verges (13.3 % of reads). Out of 16 differentially abundant genera, 11 were significantly more abundant in croplands and 5 in grass verges. There were significant differences in the mycobiome composition between study sites but also between types of land use at paired sampling points (distance: 1 m). Mycobiome dissimilarity increased with geographical distance between sampling points at the local scale, and mycobiomes were strongly associated with soil pH at all sites. Characterizing the processes associated with soil microbial communities from different types of land use can be an important contribution in ensuring belowground ecological functioning, health and resilience, all of which are declining due to anthropogenic disturbances. • Annual croplands and perennial grass verges harbor high fungal alpha diversity. • Land use drives mycobiome dissimilarity between adjacent habitats. • Mycobiome dissimilarity increases with geographical distance. • Highly abundant fungal genera differ across very small spatial scales.