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

Abstract

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.

Comparative microbiome analysis reveals the variation in microbial communities between ‘Kyoho’ grape and its bud mutant variety

“…Awad et al [ 26 ] investigated the microbiome in the tissues of bud and bark in 37 different grapevine varieties under the same viticulture environment, revealing that the genotypes of grapevines may also influence microbiome diversity regardless of growth conditions. At the same time, Awad et al [ 27 ] further confirmed this conclusion by exploring microbial diversity in 36 grapevine varieties, indicating the impact of the genotypes and the phenological stages on the microbial communities. These researches unveiled and characterized the microbiome diversity in grapevines, suggesting that it is necessary for researchers to identify more microbial species in more tissues and terroirs.…”

“…‘Kyoho’ is mainly used as table grapes, but recent studies have also shown that the microbes inside table grapes can also significantly affect grape quality and disease resistance [ 41 ]. However, studies on the microbial composition of table grapes are far behind that of wine grapes, and most of them focused on the rhizosphere, with relatively less attention paid to leaves, fruits, and stems [ 26 , 27 , 42 , 43 ]. Therefore, in this study, we investigated the microbiome in leaves, stems and fruits of ‘Kyoho’, a representative of table grapes.…”

Lentil Landrace Seed Origin and Genotype Affects Rhizosphere Microbiome

“…Library preparation and high-throughput sequencing was performed at the Sequencing Facility of the Laboratory of Genetics and Plant Breeding, School of Agriculture, Aristotle University of Thessaloniki, Greece, following a similar approach as in [7] with modifications. Briefly, instead of using a Thermo 16S metagenomics kit, we amplified bacterial (V4) and fungal (ITS2) targets using the Platinum™ II Hot-Start PCR Master Mix (Thermo Fisher, USA) (see Supplementary Table S1 for primers and PCR protocols).…”

“…Nowadays, mounting evidence from research indicates that the plant genome has a central and dynamic role in shaping the composition of the microbiome [5,6]. Awad and coworkers have shown that the phyllosphere microbiome in grapevine cultivars is governed by the cultivar genotype in a collection of grapevine cultivars grown in the same orchard [7], thus, demonstrating that the plant genotype is key player of the above-ground plant microbiome. Lentil, as a member of the Fabaceae family, maintains symbiotic associations with rhizobia species that are responsible for biological nitrogen fixation.…”

Spatiotemporal Dynamics of Assyrtiko Grape Microbiota

“…Recent studies highlight that the microbial terroir of grapevines is influenced by various factors, such as grapevine genotype, geographical location, and agricultural practices [ 22 , 23 ]. When considering grapevine genotype, microbial communities exhibit significant differences among various Vitis vinifera varieties, as evidenced by a study involving 36 different varieties cultivated within the same vineyard [ 24 ]. Furthermore, there is evidence of geographic correlation in the structure of microbial community across vineyards in different countries, including the USA, China, and Spain [ 13 , 23 , 25 ].…”