Soil microbiota plays a key role in suppressing soil-borne plant pathogens improving the natural soil suppressiveness. Microbiome disturbance triggers specific perturbation to change and shape the soil microbial communities’ network for increasing suppression against phytopathogens and related diseases. Very important goals have been reached in manipulation of soil microbiota through agronomical practices based on soil pre-fumigation, organic amendment, crop rotation and intercropping. Nevertheless, to limit inconsistencies, drawbacks and failures related to soil microbiota disturbance, a detailed understanding of the microbiome shifts during its manipulation is needed under the light of the microbiome-assisted strategies. Next-generation sequencing often offers a better overview of the soil microbial communities during microbiomes manipulation, but sometime it does not provide information related to the highest taxonomic resolution of the soil microbial communities. This review work reports and discusses the most reliable findings in relation to a comprehensive understanding of soil microbiota and how its manipulation can improve suppression against soil-borne diseases in organic farming systems. Role and functionality of the soil microbiota in suppressing soil-borne pathogens affecting crops have been basically described in the first section of the paper. Characterization of the soil microbiomes network by high-throughput sequencing has been introduced in the second section. Some relevant findings by which soil microbiota manipulation can address the design of novel sustainable cropping systems to sustain crops’ health without use (or reduced use) of synthetic fungicides and fumigants have been extensively presented and discussed in the third and fourth sections, respectively, under the light of the new microbiome-assisted strategies. Critical comparisons on the next-generation sequencing have been provided in the fifth section. Concluding remarks have been drawn in the last section.

中文翻译：

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微生物组辅助策略下土壤微生物群的操纵及其在有机耕作系统中抑制土壤传播的植物病原体的作用

土壤微生物群在抑制土壤传播的植物病原体，提高自然土壤抑制能力方面起着关键作用。微生物组扰动触发特定的扰动，以改变和塑造土壤微生物群落的网络，从而进一步抑制植物病原体和相关疾病。通过基于土壤熏蒸，有机改良，轮作和间作的农艺实践，在控制土壤微生物群方面已经实现了非常重要的目标。然而，为了限制与土壤微生物群扰动有关的不一致，缺点和失败，需要根据微生物群辅助策略来详细了解其在操纵过程中微生物群的变化。下一代测序通常可以更好地概述微生物群操纵过程中的土壤微生物群落，但有时它不提供与土壤微生物群落的最高生物分类分辨率有关的信息。这项审查工作报告并讨论了与对土壤微生物群的全面理解有关的最可靠的发现，以及对微生物群的操纵如何能够改善对有机农业系统中土壤传播疾病的抑制作用。本文第一部分已基本描述了土壤微生物群在抑制影响农作物的土壤传播病原体中的作用和功能。第二部分介绍了通过高通量测序对土壤微生物群落网络进行表征的方法。第三部分和第四部分分别广泛介绍和讨论了一些相关发现，土壤微生物群处理可以解决不使用（或减少使用）合成杀真菌剂和熏蒸剂来维持作物健康的新型可持续作物种植系统的设计。新的微生物组辅助策略。第五部分提供了有关下一代测序的关键比较。最后一节已作总结。