Crop plants carry an enormous diversity of microbiota that provide massive benefits to hosts. Protists, as the main microbial consumers and a pivotal driver of biogeochemical cycling processes, remain largely understudied in the plant microbiome. Here, we characterized the diversity and composition of protists in sorghum leaf phyllosphere, and rhizosphere and bulk soils, collected from an 8‐year field experiment with multiple fertilization regimes. Phyllosphere was an important habitat for protists, dominated by Rhizaria, Alveolata and Amoebozoa. Rhizosphere and bulk soils had a significantly higher diversity of protists than the phyllosphere, and the protistan community structure significantly differed among the three plant–soil compartments. Fertilization significantly altered specific functional groups of protistan consumers and parasites. Variation partitioning models revealed that soil properties, bacteria and fungi predicted a significant proportion of the variation in the protistan communities. Changes in protists may in turn significantly alter the compositions of bacterial and fungal communities from the top‐down control in food webs. Altogether, we provide novel evidence that fertilization significantly affects the functional groups of protistan consumers and parasites in crop‐associated microbiomes, which have implications for the potential changes in their ecological functions under intensive agricultural managements.

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施肥改变了作物相关微生物组中的原生生物消费者和寄生虫

作物植物携带着巨大多样性的微生物群，可为寄主带来巨大利益。原生生物作为主要的微生物消费者和生物地球化学循环过程的关键驱动因素，在植物微生物组中仍未得到充分研究。在这里，我们表征了高粱叶叶际、根际和大块土壤中原生生物的多样性和组成，这些生物是从具有多种施肥方式的 8 年田间试验中收集的。叶缘是原生生物的重要栖息地，以根瘤菌、肺泡纲和变形虫为主。根际和大块土壤的原生生物多样性显着高于叶际，并且三个植物 - 土壤区室之间的原生生物群落结构存在显着差异。施肥显着改变了原生生物消费者和寄生虫的特定功能组。变异划分模型显示，土壤特性、细菌和真菌预测了原生生物群落变异的很大一部分。原生生物的变化可能反过来显着改变食物网中自上而下控制的细菌和真菌群落的组成。总而言之，我们提供了新的证据，表明施肥显着影响了作物相关微生物组中原生生物消费者和寄生虫的功能群，这对集约化农业管理下其生态功能的潜在变化具有影响。原生生物的变化可能反过来显着改变食物网中自上而下控制的细菌和真菌群落的组成。总而言之，我们提供了新的证据，表明施肥显着影响了作物相关微生物组中原生生物消费者和寄生虫的功能群，这对集约化农业管理下其生态功能的潜在变化具有影响。原生生物的变化可能反过来显着改变食物网中自上而下控制的细菌和真菌群落的组成。总而言之，我们提供了新的证据，表明施肥显着影响了作物相关微生物组中原生生物消费者和寄生虫的功能群，这对集约化农业管理下其生态功能的潜在变化具有影响。