Microbial metagenomics of vineyard soils and wine terroir

Climate change results in increasing water stress due to co-effects of rising evapotranspiration (ET) and decreased precipitation over the past 65 years (Spinoni et al. 2019).

Inorganic phosphonates are known to effectively support the control of grapevine downy mildew in vi- ticulture. Their application helps the plant to induce an earlier and more effective pathogen defense. However, inorganic phosphonates have been banned in organic viticulture due to their classification as plant protection products since October 2013. Despite the ban, phosphonate has been recently detected in organic wines.

Soil is a reservoir of microorganisms playing important roles in biogeochemical cycles and interacting with plants whether in the rhizosphere or in the root endosphere. The composition of the microbial communities thus impacts the plant health. Rhizodeposits (such as sugar, organic and amino acids, secondary metabolites, dead root cells …) are released by the roots and influence the communities of rhizospheric microorganisms, acting as signaling compounds or carbon sources for microbes. The composition of root exudates varies depending on several factors including genotypes. As most of the cultivated grapevines worldwide are grafted plants, the aim of this study was to explore the influence of rootstock and scion genotypes on the microbial communities of the rhizosphere and the root endosphere. The work was conducted in the GreffAdapt plot (55 rootstocks x 5 scions), in which the 275 combinations have been planted into 3 blocks designed according to the soil resistivity. Samples of roots and rhizosphere of 10 scion x rootstock combinations were first collected in May among the blocks 2 and 3. The quantities of bacteria, fungi and archaea have been assessed in the rhizosphere by quantitative PCR, and by cultivable methods for bacteria and fungi. The communities of bacteria, fungi and arbuscular mycorrhizal fungi (AMF) was analyzed by Illumina sequencing of 16S rRNA gene, ITS and 28S rRNA gene, respectively. The level of mycorrhization was also evaluated using black ink coloration of newly formed roots harvested in October. The level of bacteria, fungi and archaea was dependent on rootstock and scion genotypes. A block effect was observed, suggesting that the soil characteristics strongly influenced the microorganisms from the rhizosphere and root endosphere. High-throughput sequencing of the different target genes showed different communities of bacteria, fungi and AMF associated with the scion x rootstock combinations. Finally, all the combinations were naturally mycorrhized. The root mycorrhization intensity was influenced by the rootstock genotype, but not by the scion one. Altogether, these results suggest that both rootstock and scion genotypes influence the rhizosphere and root endophytic microbiomes. It would be interesting to analyze the biochemical composition of the rhizodeposition of these genotypes for a better understanding of the processes involved in the modulation of these microbiomes. Moreover, crossing our data with the plant agronomic characteristics could provide insights into their roles on plant fitness.

All along the red winemaking process, many microorganisms develop in wine, some being beneficial and essential, others being feared spoilers. One of the most feared microbial enemy of wine all around the world is Brettanomyces bruxellensis. Indeed, in red wines, this yeast produces volatile phenols, molecules associated with a flavor described as “horse sweat”, “burnt plastic” or “leather”. To produce significant and detectable concentrations of these undesired molecules, the yeasts should first grow and become numerous enough. Even if the genetic group of the strain present and the cellar temperature may modulate the yeast growth rate¹ and thus the risk of spoilage, the main factor seems to be the wines themselves, some being much more permissive to B. bruxellensis development than others.

Wine is at risk of being labelled as a dangerous health product, based on studies that focus on its alcohol content. However, multiple studies suggest that moderate consumption is healthy. Changing the focus from health impacts to the environmental and socioeconomic impacts that wine companies cause, what can be said?