Endophytic fungal microbiome of wheat

genotype, presence of fungi in the environment, and abiotic factors in shaping the plant microbiome is of significance for modern agriculture, with implications in disease management, breeding, and development of biocontrol agents. We conducted a large-scale pot experiment with related wheat cultivars over one growth-season, to disentangle the effects of host genotype, environment, and fungi present in seed stock, air and soil on endophytic fungal communities in roots, leaves and seeds. We studied communities with metabarcoding and monitored abiotic factors during the experimental period. Host genotype, tissue and abiotic factors influenced fungal communities significantly. The effect of host genetic control was limited to leaves and roots and location-independent; relatedness between cultivars was not reflected in the microbiome. For the phyllosphere, abiotic factors largely explained differences in abundance, diversity, and presence of pathogens between the locations, while the rhizosphere communities were less affected by abiotic factors. We found indications that airborne fungi are the primary inoculum source for above-ground fungal communities. Our study demonstrates that host genotype, environment, and presence of fungi in the environment shape the endophytic fungal community in wheat over one growing season.