Cultivar-dependent variations in the microbiome of grapevine leaves and potential of the antifungal protein AFP from Aspergillus giganteus against Botrytis cinerea

Grapevine (Vitis vinifera) is a major fruit crop of economic importance worldwide. Commercial grapevine cultivars are susceptible to infection by a large number of pathogenic microorganisms that cause diseases both in leaves and fruits. In particular, grey mold caused by the fungal pathogen Botrytis cinerea represents one of the most important problems for grapevine worldwide. In this study, shotgun metagenomic sequencing was used to characterize the microbiome associated to grapevine leaves in three commercial varieties, Cabernet, Garnacha and Marselan, grown in the same vineyard. The most abundant fungal taxa associated to grapevine leaves belongs to the phylum Ascomycota, which includes a number of relevant pathogenic fungi for grapevine, whereas Basidiomycota represented a minor fraction of the fungal microbial communities. Differences in the microbial community structure between varieties were observed, supporting the hypothesis that the host genotype can shape its own microbiome. Sclerotinia sclerotiorum and B. cinerea were found to preferentially colonize leaves in the Marselan and Garnacha varieties, respectively. Our metagenomic data also revealed that B. cinerea colonizing Garnacha leaves belongs to the transposa-type subpopulation. We also show that the antifungal protein (AFP) from the soil fungus Aspergillus giganteus is effective for inhibition of B. cinerea growth. Thus, application of AFP protects grapevine leaves and grapes from B. cinerea infection. The information gained in this study on the leaf microbiome in grapevine will be useful for the development of tailored strategies to improve disease resistance in vineyards while helping to increase sustainability of grapevine production.