Sequence-based Analysis of the Vitis vinifera L. cv Cabernet Sauvignon Grape Must Mycobiome in Three South African Vineyards Employing Distinct Agronomic Systems

Abstract

Recent microbiomic research of agricultural habitats has highlighted tremendous microbial biodiversity associated with such ecosystems. Data generated in vineyards have furthermore highlighted significant regional differences in vineyard biodiversity, hinting at the possibility that such differences might be responsible for regional differences in wine style and character, a hypothesis referred to as "microbial terroir." The current study further contributes to this body of work by comparing the mycobiome associated with South African (SA) Cabernet Sauvignon grapes in three neighboring vineyards that employ different agronomic approaches, and comparing the outcome with similar data sets from Californian vineyards. The aim of this study was to fully characterize the mycobiomes associated with the grapes from these vineyards. The data revealed approximately 10 times more fungal diversity than what is typically retrieved from culture-based studies. The Biodynamic vineyard was found to harbor a more diverse fungal community (H = 2.6) than the conventional (H = 2.1) and integrated (H = 1.8) vineyards. The data show that ascomycota are the most abundant phylum in the three vineyards, with Aureobasidium pullulans and its close relative Kabatiella microsticta being the most dominant fungi. This is the first report to reveal a high incidence of K. microsticta in the grape/wine ecosystem. Different common wine yeast species, such as Metschnikowia pulcherrima and Starmerella bacillaris dominated the mycobiome in the three vineyards. The data show that the filamentous fungi are the most abundant community in grape must although they are not regarded as relevant during wine fermentation. Comparison of metagenomic datasets from the three SA vineyards and previously published data from Californian vineyards revealed only 25% of the fungi in the SA dataset was also present in the Californian dataset, with greater variation evident amongst ubiquitous epiphytic fungi.

Keywords: grapevine mycobiome; microbial diversity; microbial terroir; next-generation sequencing; wine yeasts.

FIGURE 1

Rarefaction analysis of community richness estimates based on sequences that passed Phred quality score of 30.

FIGURE 2

Distribution of fungal species recovered across the orders of Ascomycetes, Basidiomycetes, and Zygomycetes.

FIGURE 3

A weighted co-occurrence network of the fungal communities in the grape must prepared from grapes obtained from the biodynamic (BD; green), conventional (CONV; red) and integrated (blue) vineyard.

FIGURE 4

The frequency of occurrence of the abundant fungal taxa as well as major grapevine associated taxa.

FIGURE 5

Relative abundance of yeast species frequently encountered in the wine microbial consortium.

FIGURE 6

A Venn diagram showing yeast species distribution between the amplicon sequencing data and cultivated yeast isolates from the BD, CONV, and IPW vineyard must samples.

FIGURE 7

A Venn diagram representing comparison of yeasts isolated from the BD, CONV and IPW vineyard must samples in SA against the species obtained from amplicon sequencing data derived from the SA and Californian grape must samples.