Soil physicochemical gradients and management shape vineyard microbial communities

Vineyard soil microbiomes underpin essential ecosystem functions, yet the relative influence of management practices and soil physicochemical gradients remains poorly understood. We investigated bacterial and fungal communities using high-throughput sequencing across 80 commercial vineyards in D.O.Ca. Rioja (Northern Spain), under factorial combinations of pest management (organic vs. integrated pest management) and soil management (tillage vs. no-till, with the latter including spontaneous or sown inter-row vegetation). Overall, bacterial and fungal community composition was only weakly related to broad management categories, whereas soil physicochemical gradients, particularly pH, organic matter, texture, electrical conductivity, and trace elements, were more strongly associated with community structure. Within this strong edaphic context, management modulated selected microbial attributes: organic management was associated with higher bacterial Shannon diversity, while no-till management increased fungal richness. Variation partitioning indicated that measured soil properties accounted for 41.2% and 28.5% of bacterial and fungal community variation, respectively, whereas management categories accounted for 2.4% and 3.6%; these fractions were interpreted as conditional associations rather than independent causal effects. LEfSe analysis identified management-associated bacterial and fungal indicator genera, including taxa containing species with previously reported beneficial or pathogenic roles, although these associations do not demonstrate function or pathogenicity in this study. Co-occurrence networks showed greater connectivity under organic and no-till systems, while FAPROTAX and FUNGuild predicted shifts in microbial functional categories and fungal trophic modes. Overall, our results suggest that reduced-input and soil-conserving practices can modulate selected microbial indicators, but their effects are strongly conditioned by the local soil physicochemical context.