Complexity and Dynamics of the Winemaking Bacterial Communities in Berries, Musts, and Wines from Apulian Grape Cultivars through Time and Space

Abstract

Currently, there is very little information available regarding the microbiome associated with the wine production chain. Here, we used an amplicon sequencing approach based on high-throughput sequencing (HTS) to obtain a comprehensive assessment of the bacterial community associated with the production of three Apulian red wines, from grape to final product. The relationships among grape variety, the microbial community, and fermentation was investigated. Moreover, the winery microbiota was evaluated compared to the autochthonous species in vineyards that persist until the end of the winemaking process. The analysis highlighted the remarkable dynamics within the microbial communities during fermentation. A common microbial core shared among the examined wine varieties was observed, and the unique taxonomic signature of each wine appellation was revealed. New species belonging to the genus Halomonas were also reported. This study demonstrates the potential of this metagenomic approach, supported by optimized protocols, for identifying the biodiversity of the wine supply chain. The developed experimental pipeline offers new prospects for other research fields in which a comprehensive view of microbial community complexity and dynamics is desirable.

Grape cultivar features differentiate the grape rhizosphere of microbiota

“…consistent with the theory mentioned above, most of these genera come from the soil, and therefore, we can infer that the Cab microflora in that case was significantly richer in Amnibacterium, Methylobacterium, Hymenobacter, Sphingomonas and Thermomonas [35] . However, in our study,…”

Contribution of the Microbiome as a Tool for Estimating Wine’s Fermentation Output and Authentication

“…Primitivo Apulian red wines' production process, highlighting the alterations in the bacterial population during vinification [14]. Although a common microbiome core was identified among the three wine varieties, comprised by the genera Candidatus liberibacter, Gilliamella, Gluconobacter, Halomonas, Halospirulina, Komagataeibacter, Pseudomonas, and Shewanella, each wine was discriminated by a unique taxonomic signature.…”

“…High-throughput sequencing techniques have allowed the discrimination of the microbial diversity as dynamically formed from the initiation of fermentation until wine production, identifying also the non-culturable microorganisms, as well as the limited represented species [12][13][14][15][16] (Figure 2). During the process of fermentation, the microbial community is reshaped and become dominated by the fermentative organisms.…”

“…The development of high-throughput sequencing technologies has allowed the evaluation of the microbial consortium comprising grapes' microbiome in terms of revealing the concept of the microbial terroir [12][13][14][15][16]. The contribution of originassociated factors of grape varieties, including climate and microclimate, region site, as well as grape cultivar, in the microbial community formation and the final metabolic profiles, has been recently investigated [12,[17][18][19][20].…”

“…These labels were established by the European Union (EU) to guarantee the authentication of the local products produced in distinct geographic origin, applying traditional specialties. Metagenomic studies have been recently applied to identify the microbial communities that influence the original sensorial characteristics of PDO wines [14,16].…”