Non-ribosomal peptides (NRPs) and polyketides (PKs) are among the most profuse families of secondary metabolites (SM) produced by bacteria. These compounds are believed to play an important ecological role in microbe-microbe and microbe-plant interactions in soil and roots microbiomes. Over the years, screening of NRPs and PKs in soil bacteria has resulted in high rates of rediscovery, mainly due to challenges associated with bacterial isolation. The quest to expose compounds in the hidden "unculturable" fraction of the soil microbiome, and to activate existing and novel SM gene clusters in cultivated bacteria, has facilitated a paradigm shift from traditional isolation-based natural product identification platforms to novel 'ecologically inspired' culturing techniques and cutting-edge culture-independent methods. This review provides a comprehensive overview of platforms and applications for studying secondary metabolites in soil and root environments, deliberating the benefits and limitations of the various approaches. Initially, it highlights innovative methodologies to "culture the unculturable" to uncover novel soil bacterial SM. Next, it explores "culture-independent" platforms for the identification of SM-synthesizing gene clusters through next generation sequencing and bioinformatics. It then evaluates innovative approaches for heterologous expression of metabolites from complex soil environments. Finally, it presents a conceptual integrated pipeline for evaluating the potential function and role of root-associated bacterial SM in suppressive soils that inhibit plant pathogens. This pipeline can be modified to address the ecological role of SM in other soil and root ecosystems, which can ultimately enhance our understanding of microbe-microbe and bacterial-plant interactions.

非核糖体肽（NRPs）和聚酮化合物（PKs）是细菌产生的次生代谢物（SM）最丰富的家族。据信这些化合物在土壤和根系微生物群中的微生物-微生物和微生物-植物相互作用中起着重要的生态作用。多年来，对土壤细菌中的NRP和PK进行筛查已导致很高的重新发现率，这主要是由于细菌分离带来的挑战。寻求将化合物暴露在土壤微生物组中隐藏的“不可培养的”部分中，并激活栽培细菌中现有的和新型的SM基因簇，已促使从传统的基于隔离的天然产物鉴定平台向新型的“生态学启发”的模式转变。培养技术和与文化无关的尖端方法。这篇综述为研究土壤和根系环境中的次生代谢产物提供了平台和应用的全面概述，探讨了各种方法的优点和局限性。最初，它着重介绍了“培养不可培养的人”以发现新型土壤细菌SM的创新方法。接下来，它探索了“与文化无关的”平台，用于通过下一代测序和生物信息学鉴定SM合成的基因簇。然后，它评估了复杂土壤环境中代谢物异源表达的创新方法。最后，它提供了一个概念性的集成管道，用于评估与根相关的细菌SM在抑制植物病原体的抑制性土壤中的潜在功能和作用。