Cultivar-Dependent Variations in the Microbiome of Grapevine Leaves

The grapevine (Vitis vinifera) is a major fruit crop of economic importance worldwide. Commercial grapevine cultivars are susceptible to infection by pathogenic microorganisms that cause diseases both in leaves and fruits, and it is known that the leaf microbiome plays an important role in plant health and fitness. In this study, shotgun metagenomic sequencing was used to characterize the microbial communities associated with grapevine leaves in three commercial varieties, Cabernet Sauvignon, Garnacha, and Marselan, grown in the same biogeographical unit. Metagenomic data revealed a differential enrichment of the microbial communities living inside grapevine leaves or on the leaf surface in the three varieties. The most abundant fungal taxa associated with grapevine leaves belong to the phylum Ascomycota, which included relevant pathogenic fungi for grapevines, such as Botrytis cinerea, Sclerotinia sclerotium, and Alternaria alternata, as well as several fungal species potentially pathogenic for grapevines (e.g., members of the Colletotrichum, Aspergillus, and Penicillium genera). Basidiomycota constituted a minor fraction of the fungal microbial communities. Grapevine leaves also harbored a diversity of bacterial taxa. At the phylum level, bacterial communities in all three varieties were primarily composed of Pseudomonadata, Bacillota, Bacteroidota, and a lower proportion of Actinomycetota. Differences in the fungal and bacterial community structures were observed between varieties, although they were more important in fungi. In particular, S. sclerotiorum and B. cinerea were found to preferentially colonize leaves in the Marselan and Garnacha varieties, respectively. These findings further support that the host genotype can shape its own microbiome in grapevines. A better understanding of the leaf microbiome in grapevines will provide the basis for the development of tailored strategies to prevent diseases in vineyards while helping to increase sustainability in grapevine production.