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

Abstract

Vineyards are home to a wide diversity of microorganisms that interact with plants and with each other. Some microorganisms are grapevine pathogens, such as the oomycete Plasmopara viticola, which causes grapevine downy mildew (DM). Others have positive effects on vine health through protection against pathogens, resistance to abiotic stress and improved nutrition. These beneficial plant-microbe and microbe-microbe interactions, as well as the conservation of microbial diversity, have gained more attention in recent years because they could represent an alternative to the use of fungicides and fertilizer in viticulture and improve vineyard resilience to multiple stresses including those caused by climate change. In this study, we aimed to (i) identify microbial candidates for the biocontrol of DM and (ii) identify microbial biomarkers of high and stable yields over time. We analyzed the microbiota (i) in leaves and topsoil in seven pairs of vineyard plots with contrasting susceptibility to DM according to long-term epidemiological records collected in the Bordeaux region and (ii) in roots and soil in ten pairs of vineyard plots with contrasting yields according to a long-term yield database collected in the Champagne region. We combined differential abundance analyses, Random Forest algorithm, and Threshold Indicator Taxa Analysis (TITAN), and we identified fungal and bacterial taxa that were significantly more abundant in plots with low susceptibility to DM and in plots with high and stable yields. Our results revealed that several species of basidiomycete yeasts were significantly more abundant in the grapevine phyllosphere of plots with low susceptibility to DM, while taxa belonging to arbuscular mycorrhizal fungi were significantly more abundant in plots with high and stable yields. These results suggest that both the aboveground and belowground microbiomes play a role in the performance of grapevine. The relationships between grapevine performance and the abundance of specific microbial taxa should however be analyzed in controlled experiments to demonstrate the role played by microorganisms. I will present results of in vitro confrontation tests between basidiomycete yeasts and P. viticola to show that mining microbiome data can guide the search for microbial taxa beneficial to grapevine.