Vineyard decline is affiliated to soil microbiome dysbiosis in diversity and functionality

Vineyard decline is characterized by a decrease of plant growth and berry yield that can lead to vine death. Some of these declines are not explainable by pathogen infection or unbalance of soil nutrients. A previous analysis in four vineyards showed a disruption in the taxonomy and functionality of the soil microbiome in symptomatic (S) declining areas compared to healthy asymptomatic (AS) ones. As soil is a microbial reservoir in which grapevine uptakes its associated microbiome through roots compartment, its diversity is considered as interesting biological indicator of plant health. The objective of this work was to pursue the analysis in one of the previously studied vineyards by exploring the bacterial and fungal microbiome of the root endosphere, rhizosphere, and bulk soils of vines grown in the S and AS zones. Declining vines had poor berry quality and lower petiole mineral content than those in AS zones. Profiles of the deeper soil horizons could not explain this observed decline, but the bulk soil from zone S showed a dysregulation of enzyme and microbial activities. Bacterial richness and fungal diversity were lower in symptomatic soils and roots, respectively, highlighting the root functionality of acting as a selective barrier for microbes. However, higher microbial activities, as well as enrichment of potentially beneficial bacterial and fungal pathogens were found in the S soils. These results could not explain the observed decline but revealed stressed vines with active microbial profiles in the belowground compartments, highlighting the interest of exploring the functional microbiota of plants under stressed conditions.