Quantitative analysis of soil microbial genes as possible bioindicators of vineyard conditions in the Franciacorta and Lugana areas

Soil health is a key component of sustainable agriculture, yet reliable bioindicators for vineyard soils are limited. This study assessed a set of microbial functional genes as potential indicators of soil health and vineyard condition in two major wine regions of Northern Italy, Franciacorta and Lugana. Soils from 88 vineyards were analyzed through quantitative PCR targeting bacterial and fungal abundance (16S, 18S), nitrogen cycling (nifH, amoA AOA/AOB, nirK, nosZ), cellulose degradation (gh48), arbuscular mycorrhizal fungi (AMG1), and secondary plant growth-promoting metabolite production (NRPS, non-ribosomal peptide synthesis). By integrating molecular, physico-chemical, sensory (visual soil assessment), and biological data, the research explored how soil properties, management practices, and environmental factors influence soil microbiota and vineyard conditions. Results revealed that microbial gene abundances were responsive to the soil physico-chemical parameters. Distinct microbial terroirs emerged between the two wine regions: Lugana soils showed higher abundances of nifH, AMG1, and NRPS, whereas Franciacorta soils had higher levels of AOA and fungi. Vineyard management was a key driver of soil microbiomes: vineyards using cattle manure and digestate fertilization had higher nifH and AMG1 abundances compared to those using compost; vineyards with seeded cover crops exhibited improved fungal abundance and VSA scores; while tilled fields displayed reduced fungi and nirK. Vineyards implementing under-row mowing had higher arbuscular mycorrhizal fungi abundance but lower VSA scores compared to under-row tillage. Long-term organic management and vineyard age positively influenced several gene abundances, indicating a gradual enhancement of soil biological functionality. Problematic vineyards affected by diseases, compaction, or poor drainage exhibited a general decline in microbial and arthropod indicators, indicating compromised soil functioning. Among traditional indicators, VSA correlated positively with fungi and total dsDNA, confirming their link with soil structure. Overall, the results demonstrate that microbial functional genes are responsive bioindicators of vineyard conditions and soil health. Their integration with traditional soil assessments could provide an innovative tool for soil monitoring and support the development of regenerative, knowledge-based viticulture.