Abstract
Background: Fungi living inside seeds, leaves and roots of plants affect many aspects of plant health. Understanding the role of plant genotype, presence of fungal inoculum in the environment, abiotic environmental factors, and interaction of those factors in shaping the plant-associated fungal microbiome is of great relevance for modern agriculture. This knowledge can have direct implications in plant disease management, plant breeding, and development of microorganism-based biocontrol agents. These are important tools also in the context of increasing sustainability and adaption of crop production to a changing climate. In order to disentangle the effects of host genotype, environmental factors, and fungi present in seed stock, air and soil on endophytic fungal communities over one generation, we conducted a large-scale pot experiment with closely related cultivars of wheat over one growth-season. We studied fungi present inside the plants (endophytic fungi), in soil and air with metabarcoding, and monitored abiotic factors during the experimental period.Results: Abiotic environmental factors, wheat genotype, and wheat tissue type were all found to influence fungal communities significantly. While the effect of wheat genotype was limited, there was evidence for host genetic control of fungal communities in leaves and roots but not in seeds. The degree of relatedness between wheat cultivars and resistance levels to the leaf disease STB was not reflected in the microbiome. The effect of host genetic control on the fungal community did not differ between abiotic environments. For the phyllosphere, abiotic environmental factors largely explained differences in fungal community abundance, diversity, and presence of pathogens between the locations, whereas location-dependent differences affected the rhizosphere communities to an only small extent. We found indications that airborne fungi are the primary source of inoculum for above-ground fungal communities of wheat, since a large proportion of leaf-associated fungi were also present in the air but not in soil and seed stocks.Conclusions: Our study demonstrates how the factors genotype, environment, and presence of fungi in the environment shape the endophytic fungal community in wheat over one growing season.
Bacterial endophyte communities in Pinus flexilis are structured by host age, tissue type, and environmental factors