Comparative Analysis of Grapevine Epiphytic Microbiomes among Different Varieties, Tissues, and Developmental Stages in the Same Terroir

There is limited knowledge about the relationships of epiphytic microbiomes associated with the phyllosphere of different Vitis vinifera cultivars in the same vineyard and terroir. To address this research gap, we investigated the microbiome compositionof 36 grapevine genotypes grown in the same vineyard in different plant sections during the growing season. Using high-throughput NGS-based metagenomic analysis targeting the ITS2 and the V4 regions of the 16S ribosomal gene of fungal and bacterial communities, respectively, weassessed the impact of grapevine genotypes on microbial assemblages in various parts of the phyllosphere. The results indicated that different phyllosphere tissues display high microbial diversity regardless of the cultivars’ identity and use. The selected three phyllosphere parts representing three distinct phenological stages, namely bark and bud, berry set, and fruit harvest, had almost a similar number of fungal OTUs, while a difference was recorded for the bacterial species. The fruit harvest stage hosted the highest number of bacterial OTUs, whereas the bark and bud stage contained the lower. Bacterial dominant phyla were Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes, and the genera were Gluconacetobacter, Erwinia, Gluconobacter, Zymobacter, Buchnera, Pseudomonas, Pantoea, Hymenobacter, Pedobacter, Frigoribacterium, Sphingomonas, and Massilia. For fungi,the dominant phyla were Ascomycota and Basidiomycota, and the genera were Aureobasidium, Cladosporium, Alternaria, Aspergillus, Davidiella, Phoma, Epicoccum, Rhodosporidium, Glomerella, Botryosphaeria, Metschnikowia, Issatchenkia, and Lewia. Both the genotype of the cultivar and the phenological stage appeared to considerably impact the shape of microbial diversity and structure within the same terroir. Taken together, these results indicate that microbiome analysis could be proved to be an important molecular fingerprint of cultivars and provide an efficient management tool for the traceability of wine and grape end products. Moreover, the unique identity of cultivars’ microbial signatures highlights the need for further development of precision management to support viticulture sustainability in the face of climate change.