Impact of Organic and Conventional Agricultural Management on Subsurface Soil Microbiota in Mediterranean Vineyards

The impact of long-term organic (ECO) versus conventional (CON) agricultural management on subsurface soil microbiota diversity and soil physicochemical properties remains unclear in Mediterranean vineyards. This study evaluated long-term ECO and CON effects in the Alt Penedès terroir (Spain), focusing on subsurface soil microbial diversity and soil characteristics. ECO increased the fungal-to-bacterial ratio and ammonium-oxidizing bacteria but reduced total subsurface soil bacterial populations and soil organic carbon. While ECO did not enhance annual yield production in the vineyard, fungal abundance, and ammonium-oxidizing archaea, it slightly increased the overall alpha diversity (Shannon and Inverse Simpson indexes) and significantly altered taxa composition in subsurface soil with a more robust and modular community. Crop management, soil texture, training system, and rootstock, but not vine variety, significantly influenced beta diversity in subsurface soil. The Mantel test revealed subsurface soil texture, Ca2+/Mg2+ ratio, and salinity as the main key soil drivers shifting the microbial community (beta diversity), while C/N and topsoil organic matter significantly correlated with bacterial abundance; NH4+ correlated with fungal abundance; and N-Kjeldahl, pH, and Mg2+/K+ correlated with alpha diversity. Integrating soil microbiota and physicochemical monitoring allowed us to confirm the positive effect of long-term agroecological practices on subsurface soil health and to identify the critical factors shaping their microbial communities in Mediterranean vineyards.