Soil microbiomes drive key functions in agroecosystems, determining soil fertility, crop productivity and stress tolerance. The microbiome is intricately linked with soil structure, such as aggregation and pore connectivity, because this structure regulates the flow of water, oxygen and nutrients through the system. In this Review, we summarize the key functions of soil microbiomes in agroecosystems, highlight the dependence of these functions on the structural integrity of the soil, and discuss how agricultural practices influence the link between soil structure and microbiome functioning. System-level agricultural management practices can induce structural alterations to the soil, thereby changing the microbial processes occurring at the microscale. These changes have large-scale consequences, such as soil erosion, reduced soil fertility and increased greenhouse gas emissions. Sustainable approaches such as integrated soil fertility management and integrated pest management seek to improve soil structure and enhance microbial biodiversity, but we lack a mechanistic understanding of how multifaceted decisions at the farm level shape these context-dependent small-scale processes in the long term. Future research needs to bridge the microscale and field scale to inform agricultural management decisions for building climate-smart, resource-efficient and stress-resilient agroecosystems, and to harness the soil microbiome as a nature-based solution for sustainable agriculture.

土壤微生物组驱动着农业生态系统的关键功能，决定着土壤肥力、作物生产力和胁迫耐受性。微生物组与土壤结构有着错综复杂的联系，例如聚集和孔隙连通性，因为这种结构调节着系统中水、氧气和养分的流动。在这篇综述中，我们总结了土壤微生物组在农业生态系统中的关键功能，强调了这些功能对土壤结构完整性的依赖性，并讨论了农业实践如何影响土壤结构和微生物组功能之间的联系。系统级农业管理实践可以引起土壤结构改变，从而改变微观尺度上发生的微生物过程。这些变化会产生大规模的后果，例如土壤侵蚀，土壤肥力下降，温室气体排放增加。土壤肥力综合管理和病虫害综合管理等可持续方法旨在改善土壤结构并增强微生物生物多样性，但我们缺乏对农场层面的多方面决策如何长期影响这些依赖于环境的小规模过程的机制理解。未来的研究需要弥​​合微观尺度和田间尺度，为建设气候智能型、资源高效型和抗压型农业生态系统的农业管理决策提供信息，并利用土壤微生物组作为可持续农业的基于自然的解决方案。土壤肥力综合管理和病虫害综合管理等可持续方法旨在改善土壤结构并增强微生物生物多样性，但我们缺乏对农场层面的多方面决策如何长期影响这些依赖于环境的小规模过程的机制理解。未来的研究需要弥​​合微观尺度和田间尺度，为建设气候智能型、资源高效型和抗压型农业生态系统的农业管理决策提供信息，并利用土壤微生物组作为可持续农业的基于自然的解决方案。土壤肥力综合管理和病虫害综合管理等可持续方法旨在改善土壤结构并增强微生物生物多样性，但我们缺乏对农场层面的多方面决策如何长期影响这些依赖于环境的小规模过程的机制理解。未来的研究需要弥​​合微观尺度和田间尺度，为建设气候智能型、资源高效型和抗压型农业生态系统的农业管理决策提供信息，并利用土壤微生物组作为可持续农业的基于自然的解决方案。