Core microbiome and mycobiome of vineyard soils from Northern Italy

Despite their importance as a reservoir of biodiversity, the factors shaping soil microbial communities are still poorly understood. In particular, the extent by which cultivation impacts the structure of bacterial and fungal communities in soil is not completely known. Using 16S rRNA gene and ITS sequencing, we characterized the soil microbiota of vineyards and of neighbouring permanent grassland soils in the Italian province of Trentino. We found that the soil bacterial communities have a core of conserved taxa that account for more than 60% of each sample, and this core is only modestly affected by cultivation. Differently, the fungal microbiota from the different locations had a much smaller set of conserved taxa. In addition, the fungal communities of vineyards were significantly altered by the presence of grapevine-associated fungi. Cultivation had a site-specific effect on the diversity of the soil microbiota, that in several cases was significantly different from what found in corresponding permanent grassland. We also found that in most locations there was a negative correlation between fungal and bacterial diversity, suggesting that these two component of the soil microbiota compete for resources. Our results highlight the different response of bacterial and fungal communities to environmental factors.

尽管土壤微生物群落作为生物多样性储备库具有重要意义，但目前学界对塑造其群落结构的驱动因素仍知之甚少。目前尚未完全明确农业耕作对土壤细菌与真菌群落结构的影响程度。本研究采用16S rRNA基因（16S rRNA gene）与ITS测序（ITS sequencing）技术，对意大利特伦托省（Trentino）的葡萄园及周边永久草地土壤的微生物组进行了表征分析。研究发现，土壤细菌群落存在一个保守类群核心，其在各样本中的占比均超过60%，且该核心类群仅受耕作活动的轻度影响。与之相反，不同采样点的真菌微生物组所拥有的保守类群规模则要小得多。此外，葡萄园土壤真菌群落会因葡萄藤相关真菌的存在而发生显著改变。耕作活动对土壤微生物组多样性的影响具有位点特异性，在多数采样点中，该多样性与对应永久草地土壤的微生物组多样性存在显著差异。本研究同时发现，多数采样点的真菌与细菌多样性之间存在负相关关系，这表明土壤微生物组的这两个组分存在资源竞争。本研究结果凸显了细菌与真菌群落对环境因子的响应差异。