The Vineyard Yeast Microbiome, a Mixed Model Microbial Map

Abstract

Vineyards harbour a wide variety of microorganisms that play a pivotal role in pre- and post-harvest grape quality and will contribute significantly to the final aromatic properties of wine. The aim of the current study was to investigate the spatial distribution of microbial communities within and between individual vineyard management units. For the first time in such a study, we applied the Theory of Sampling (TOS) to sample gapes from adjacent and well established commercial vineyards within the same terroir unit and from several sampling points within each individual vineyard. Cultivation-based and molecular data sets were generated to capture the spatial heterogeneity in microbial populations within and between vineyards and analysed with novel mixed-model networks, which combine sample correlations and microbial community distribution probabilities. The data demonstrate that farming systems have a significant impact on fungal diversity but more importantly that there is significant species heterogeneity between samples in the same vineyard. Cultivation-based methods confirmed that while the same oxidative yeast species dominated in all vineyards, the least treated vineyard displayed significantly higher species richness, including many yeasts with biocontrol potential. The cultivatable yeast population was not fully representative of the more complex populations seen with molecular methods, and only the molecular data allowed discrimination amongst farming practices with multivariate and network analysis methods. Importantly, yeast species distribution is subject to significant intra-vineyard spatial fluctuations and the frequently reported heterogeneity of tank samples of grapes harvested from single vineyards at the same stage of ripeness might therefore, at least in part, be due to the differing microbiota in different sections of the vineyard.

Resilience of the Natural Phyllosphere Microbiota of the Grapevine to Chemical and Biological Pesticides

“…In particular, the relative abundances of indigenous bacteria (Haemophilus, Swaminathania, Paracoccus, Roseomonas, Kineosporia, and Porphyromonas) and fungi (Epicoccum, Teratosphaeria, Exophiala, Claviceps, and Chalastospora) was negatively correlated with downy mildew severity, suggesting that some strains of these genera could have a role as biocontrol agents. Indigenous microbes also play a key role in fruit quality, yield, and the flavors produced during alcoholic fermentation (71)(72)(73). Thus, beneficial communities could be seen as potential plant probiotic agents (74), which could defend the host, promote its growth, and improve fruit quality.…”

Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate

“…Setati et al (52) have demonstrated that intravineyard variation can be greater than intervineyard variation within a single vintage, presumably due to microclimate influences on grape-surface microbiota. By collecting must samples, we have avoided errors arising from such intravineyard variation and sampling biases (i.e., potential spatial variation due to vine position, exposure, microclimate, and stochastic effects), and show that individual vineyard blocks have highly similar must fungal community structures, distinguishing them from neighboring vineyards.…”

Arbuscular mycorrhiza symbiosis in viticulture: a review

“…In comparison, interest for the « microbial terroir » of vines (Gilbert et al 2014) is recent and remains less investigated. Valero et al (2007) and Setati et al (2012) were among the first to study the yeast microbiome in vineyards. More recently, on the basis of the analysis of the wine-grape surface microbiome, Bokulich et al (2014) proposed the existence of a non-random microbial terroir as a determining factor of regional variation among vines.…”