Data_Sheet_1_Unraveling the Complexity of Soil Microbiomes in a Large-Scale Study Subjected to Different Agricultural Management in Styria.PDF

Healthy soil microbiomes are crucial for achieving high productivity in combination with crop quality, but our understanding of microbial diversity is still limited. In a large-scale study including 116 composite samples from vineyards, orchards and other crops from all over Styria (south-east Austria), agricultural management as well as distinct soil parameters were identified as drivers of the indigenous microbial communities in agricultural soils. The analysis of the soil microbiota based on microbial profiling of prokaryotic 16S rRNA gene fragments and fungal ITS regions revealed high bacterial and fungal diversity within Styrian agricultural soils; 206,596 prokaryotic and 53,710 fungal OTUs. Vineyards revealed a significantly higher diversity and distinct composition of soil fungi over orchards and other agricultural soils, whereas the prokaryotic diversity was unaffected. Soil pH was identified as one of the most important edaphic modulators of microbial community structure in both, vineyard and orchard soils. In general, the acid-base balance, disorders in the soil sorption complex, content and quality of organic substance as well as individual nutrients were identified as important drivers of the microbial community structure of Styrian vineyard and orchard soils. However, responses to distinct parameters differed in orchards and vineyards, and prokaryotic and fungal community responded differently to the same abiotic factor. In comparison to orchards, the microbiome of vineyard soils maintained a higher stability when herbicides were applied. Orchard soils exhibited drastic shifts within community composition; herbicides seem to have a substantial impact on the bacterial order Chthoniobacterales as well as potential plant growth promoters and antagonists of phytopathogens (Flavobacterium, Monographella), with a decreased abundance in herbicide-treated soils. Moreover, soils of herbicide-treated orchards revealed a significantly higher presence of potential apple pathogenic fungi (Nectria, Thelonectria). These findings provide the basis to adapt soil management practices in the future in order to maintain a healthy microbiome in agricultural soils.

健康的土壤微生物组（soil microbiome）对于实现作物高产与品质提升的双重目标至关重要，但当前学界对微生物多样性的认知仍较为有限。本研究为大规模田野调查，共采集奥地利东南部施蒂利亚州全境葡萄园、果园及其他耕地的116份混合土壤样本，研究发现农业管理措施与特定土壤参数是调控农田土壤土著微生物群落的核心驱动因素。基于原核生物16S rRNA基因片段与真菌内部转录间隔区（Internal Transcribed Spacer，ITS）的微生物组谱分析，本研究揭示了施蒂利亚州农田土壤中极高的细菌与真菌多样性，共鉴定出206596个原核生物操作分类单元（Operational Taxonomic Unit，OTU）及53710个真菌OTU。相较于果园与其他耕地，葡萄园土壤的真菌多样性显著更高，群落组成也更为独特，但原核生物多样性未受此影响。土壤pH被证实为调控葡萄园与果园土壤微生物群落结构的关键土壤因子之一。总体而言，土壤酸碱平衡、土壤吸附复合体失衡、有机质含量与品质以及单一养分含量，均为影响施蒂利亚州葡萄园与果园土壤微生物群落结构的重要驱动因素。不过，果园与葡萄园对特定土壤参数的响应存在显著差异，且原核生物与真菌群落对同一非生物因子的响应模式亦不相同。与果园土壤相比，施用除草剂后葡萄园土壤微生物组的稳定性更高。果园土壤的微生物群落组成发生剧烈变化；除草剂似乎对细菌土杆菌目（Chthoniobacterales）、潜在植物生长促生菌及植物病原菌拮抗菌（黄杆菌属Flavobacterium、单格孢属Monographella）产生显著影响，经除草剂处理的果园土壤中这些类群的丰度显著降低。此外，经除草剂处理的果园土壤中，潜在苹果致病真菌（丛赤壳属Nectria、暗壳囊孢属Thelonectria）的丰度显著更高。本研究结果为未来优化农田土壤管理措施、维持健康的农田土壤微生物组提供了坚实的理论依据。