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. 2019 Jan 8:9:3203.
doi: 10.3389/fmicb.2018.03203. eCollection 2018.

Bark and Grape Microbiome of Vitis vinifera: Influence of Geographic Patterns and Agronomic Management on Bacterial Diversity

Nicola Vitulo  1 , Wilson José Fernandes Lemos Jr  1 , Matteo Calgaro  1 , Marco Confalone  1 , Giovanna E Felis  1 , Giacomo Zapparoli  1 , Tiziana Nardi  2
Affiliations

Bark and Grape Microbiome of Vitis vinifera: Influence of Geographic Patterns and Agronomic Management on Bacterial Diversity

Nicola Vitulo et al. Front Microbiol. .

Abstract

In recent years, the concept of "microbial terroir" has been introduced in the frame of the more renowned notion of "vitivinicultural terroir,' since several studies demonstrated that wine characteristics are related to regional microbial community compositions. Most of the existing research focused on grape berries microbiota, since it can directly impact wine quality. In this work we studied, for the first time through next-generation sequencing, the epiphytic bacterial community of vine bark and its relationships with grape microbiota. The study was carried out in two Italian wine appellations (situated in different regions) to explore the impact of biogeography, and the influence of two agronomical practices (biodynamic and conventional) was evaluated as well. Overall, our results show that grapevine bark harbors a rich epiphytic microbiota and displays a higher microbial biodiversity than grape berry. Moreover, this study suggests that geographic and anthropogenic factors impact both bark and grape bacteriomes, but to a different extent. The evidence of a "microbial terroir" seems to be even more marked in bark than in berries, possibly due to its permanence over time and to its physical proximity with soil. The importance of vine trunk bark, as potential source of inoculum for grapes and as interesting bacterial diversity habitat, is evidenced. This opens new fields of investigation, not only for researchers that aim at describing this little-known habitat within the vineyard, but also for stakeholders from the wine industry that want to understand the roles of microorganisms on the entire winemaking process, from vineyard to cellar.

Keywords: 16S rRNA; Vitis vinifera; bark microbiota; grape microbiota; next-generation sequencing; terroir; wine.

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Figures

FIGURE 1
FIGURE 1
Experimental design and phylum-level abundance of bacterial epiphytes in bark and grape samples (A). Venn diagram of shared bacterial ASVs between bark and grape (B).
FIGURE 2
FIGURE 2
Alpha diversity calculated on the whole dataset, measured as Shannon and Simpson diversity indexes.
FIGURE 3
FIGURE 3
Beta diversity calculated on the whole dataset: PCoA using UniFrac distance.
FIGURE 4
FIGURE 4
Factor analysis on bark dataset (PCoA based on UniFrac distances). Sample variable ordination by: Region (A), Region and Management (B), and Region and Season (C).
FIGURE 5
FIGURE 5
Factor analysis on grape dataset (PCoA based on UniFrac distances). Sample variable ordination by: Region (A) and Management (B).
FIGURE 6
FIGURE 6
Heat map of discriminant features identified by the sPLS-DA analysis on bark dataset.
FIGURE 7
FIGURE 7
Heat map of discriminant features identified by the sPLS-DA analysis on grape dataset.
See this image and copyright information in PMC

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