Soil nematode community characterized by high-throughput sequencing analysis revealed enhanced soil health in organic vineyards

Vineyards and their associated socio-economic activities are of global importance. However, intensive management and erosion-prone nature make vineyard agroecosystems vulnerable. Conventional viticulture practices, including tillage and agrochemical applications, lead to the loss of soil biodiversity. In the autumn of 2019, we collected composite soil samples from 80 vineyards across the DOCa Rioja region (Northern Spain), categorized based on pest (integrated vs. organic) and soil management (tillage vs. cover cropping). First, we investigated the presence of entomopathogenic nematodes using sucrose centrifugation and species-specific primers/probe qPCR sets, revealing positive effects of organic viticulture on native EPNs, particularly on the abundance and activity of the predominant steinernematid species S. feltiae. However, the impact on EPNs was similar between tilling and cover cropping, despite variations in several abiotic factors. Subsequently, we selected an optimal subset of DNA samples from 57 vineyards out of the total 80 studied to investigate the structure of nematode communities using high-throughput sequencing. To conduct metataxonomic analysis, we employed specific primers and followed the Illumina amplicon protocol. We explored biodiversity measures and identified taxa that exhibited differential abundances, calculating nematode-based indices via the NINJA platform. As observed for EPNs, no significant differences were found between cover cropping and tilling practices but for pest management. Thus, organic viticulture positively enhanced the biodiversity of soil nematodes. Nematode-based indices revealed increased environmental disturbance, a higher occurrence of plant-parasitic nematodes with negative implications for crop health, and a decline in the soil food web structure in vineyards practicing integrated pest management.