The rhizosphere microbiota, often referred to as the plant's "second genome" plays a critical role in modulating root system architecture (RSA). Despite this, existing methods to analyze root phenotypes in the context of root-microbe interactions remain limited, and the precise mechanisms affecting RSA by microbes are still not fully understood. This review comprehensively evaluates current root phenotyping techniques relevant to plant-microbe interactions, discusses their limitations, and explores future directions for integrating advanced technologies to elucidate microbial roles in altering RSA. Here, we summarized that microbial metabolite, primarily through auxin signaling pathways, drive root development changes. By harnessing advanced phenotyping tools, we aim to uncover more detailed mechanisms by which microbes modify RSA, providing valuable insights into strategies for optimizing nutrient uptake, bolstering food security, and enhancing resilience against climate-induced environmental stresses.
Keywords: Beneficial rhizosphere microbes; Carbon trade-off; Plant-soil feedback; Primary and secondary metabolites; Root system architecture (RSA).
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