Mining belowground and aboveground microbiome data to identify microbial biomarkers of grapevine health and yield

Vineyards host a wide diversity of microorganisms that interact both with plants and among themselves. Some are pathogens, such as the oomycete Plasmopara viticola, which causes grapevine downy mildew (DM). Others contribute positively to vine health by protecting against pathogens, enhancing resistance to abiotic stress, and improving nutrient uptake. In recent years, beneficial plant-microbe and microbe-microbe interactions, as well as the conservation of microbial diversity, have attracted increasing attention as potential alternatives to fungicide and fertilizer use in viticulture, and as a means to improve vineyard resilience to multiple stresses, including those related to climate change. In this study, we aimed to (i) identify microbial candidates for the biocontrol of DM and (ii) identify microbial biomarkers associated with high and stable yields over time. We analyzed the microbiota in (i) leaves and topsoil from seven pairs of vineyard plots with contrasting susceptibility to DM, based on long-term epidemiological records from the Bordeaux region, and (ii) roots and soil from ten pairs of vineyard plots with contrasting yields, based on long-term yield data from the Champagne region. Using differential abundance analyses, the Random Forest algorithm, and Threshold Indicator Taxa Analysis (TITAN), we identified fungal and bacterial taxa that were significantly more abundant in plots with low DM susceptibility and in those with high and stable yields. Our results revealed that several basidiomycete yeast species were significantly more abundant in the grapevine phyllosphere of plots with low DM susceptibility, while taxa affiliated with arbuscular mycorrhizal fungi were significantly enriched in plots with high and stable yields. These findings highlight specific microbial taxa, living both above- and belowground, that act as biomarkers of grapevine health and yield. However, causal relationships between specific microbial taxa and vine performance remain to be demonstrated. To this end, I will present results from in vitro confrontation assays between basidiomycete yeast consortia and P. viticola, illustrating how mining microbiome data can guide the identification of microbial taxa beneficial to grapevine.