Cropping systems have fertilized soils for decades with undetermined consequences for the productivity and functioning of terrestrial ecosystems. One of the critical unknowns is the role of soil biodiversity in controlling crop production after decades of fertilization. This knowledge gap limits our capacity to assess how changes in soil biodiversity could alter crop production and soil health in changing environments. Here, we used multitrophic ecological networks to investigate the importance of soil biodiversity, in particular, the biodiversity of key-stone taxa in controlling soil functioning and wheat production in a 35-year field fertilization experiment. We found strong and positive associations between soil functional genes, crop production and the biodiversity of key-stone phylotypes; soils supporting a larger number of key-stone nematode, bacteria and fungi phylotypes yielded the highest wheat production. These key-stone phylotypes were also positively associated with plant growth (phototrophic bacteria, nitrogen fixers) and multiple functional genes related to nutrient cycling. The retrieved information on the genomes clustered with key-stone bacterial phylotypes indicated that the key-stone taxa had higher gene copies of oxidoreductases (participating most biogeochemical cycles of ecosystems and linking to microbial energetics) and 71 essential functional genes associated with carbon, nitrogen, phosphorus, and sulfur cycling. Altogether, our work highlights the fundamental role of the biodiversity of key-stone phylotypes in maintaining soil functioning and crop production after several decades of fertilization, and provides a list of key-stone phylotypes linking to crop production and soil nutrient cycling, which could give science-based guidance for sustainable food production.

几十年来，耕作系统一直为土壤施肥，对陆地生态系统的生产力和功能产生了不确定的影响。关键的未知数之一是土壤生物多样性在经过数十年的施肥后在控制作物生产中的作用。这种知识差距限制了我们评估土壤生物多样性的变化如何在不断变化的环境中改变作物生产和土壤健康的能力。在这里，我们使用多营养生态网络来研究土壤生物多样性的重要性，特别是在 35 年的田间施肥实验中，关键类群的生物多样性在控制土壤功能和小麦生产方面的重要性。我们发现土壤功能基因、作物产量和关键系统发育型的生物多样性之间存在强烈的正相关；支持大量关键线虫的土壤，细菌和真菌系统型的小麦产量最高。这些关键的系统发育型也与植物生长（光养细菌、固氮剂）和与养分循环相关的多种功能基因呈正相关。检索到的与关键细菌系统发育型聚类的基因组信息表明，关键类群具有较高的氧化还原酶基因拷贝（参与生态系统的大多数生物地球化学循环并与微生物能量学相关）和 71 个与碳、氮、磷、硫循环。总而言之，我们的工作强调了关键石种系的生物多样性在经过数十年的施肥后在维持土壤功能和作物生产中的基本作用，