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.

葡萄园及其相关社会经济活动具有全球重要性。然而，集约化管理与土壤易侵蚀的特性使得葡萄园农业生态系统较为脆弱。传统葡萄栽培模式（包括耕作与农用化学品施用）会导致土壤生物多样性丧失。2019年秋季，我们从西班牙北部里奥哈法定产区（DOCa Rioja）的80座葡萄园采集了混合土壤样本，样本按虫害管理模式（综合防治 vs 有机种植）与土壤管理方式（耕作 vs 覆盖种植）进行分类。首先，我们通过蔗糖离心法与物种特异性引物/探针qPCR组合检测了昆虫病原线虫（entomopathogenic nematodes, EPNs）的存在情况，结果显示有机葡萄栽培对本土EPNs具有正向作用，尤其对优势斯氏线虫科物种斯氏线虫（S. feltiae）的丰度与活性提升显著。不过，尽管多项非生物因子存在差异，但耕作与覆盖种植两种土壤管理方式对EPNs的影响并无显著不同。随后，我们从全部80个研究样本中筛选出57座葡萄园的DNA样本作为最优子集，采用高通量测序技术探究线虫群落结构。为开展宏分类组学分析，我们使用了特异性引物，并遵循Illumina扩增子测序流程进行实验。我们分析了多项生物多样性指标，筛选出丰度存在显著差异的分类单元，并通过NINJA平台计算基于线虫的群落指数。与EPNs的检测结果一致，除虫害管理模式外，覆盖种植与耕作两种土壤管理方式间未出现显著差异。由此可见，有机葡萄栽培可有效提升土壤线虫的生物多样性。基于线虫的群落指数分析显示，采用综合虫害管理模式的葡萄园面临的环境干扰程度更高，植物寄生线虫的检出率也随之上升，这对作物健康存在不利影响，同时其土壤食物网结构也出现退化。