From soil to sequences: mechanisms and tools unravelling plant-rhizomicrobiome interactions.

The rhizosphere of a plant represents a dynamic interface where interactions with diverse microbial communities drive nutrient cycling, stress tolerance, and crop performance. As agricultural systems increasingly face challenges such as soil degradation, extreme climate variability, and resource limitations, understanding rhizomicrobiome functions and developing sustainable strategies to enhance them has become central to sustainable crop production. This review summarizes current knowledge of plant–rhizomicrobiome interactions, emphasizing the biological mechanisms and signaling pathways that regulate nutrient acquisition, abiotic and biotic stress responses, and rhizosphere microbial communities. It integrates evidence from symbiotic signaling, immune regulation, and microbial communication to demonstrate how coordinated plant–microbe interactions produce emergent effects on plant health and soil function. The review also examines how advances in molecular and omics-based technologies have transformed rhizomicrobiome research by enabling culture-independent, high-resolution analysis of microbial diversity, activity, and function within complex soil environments. Genomics, transcriptomics, proteomics, metabolomics, and related functional approaches have collectively shifted the field from descriptive community profiling toward mechanistic understanding. By synthesizing insights from biological mechanisms and molecular tools that have revealed plant–microbe interactions in the rhizosphere, this review offers an integrated framework for interpreting rhizomicrobiome function and linking molecular discoveries to improved production outcomes in agricultural systems. Collectively, these advances establish the rhizomicrobiome as a tractable biogeochemical system for exploring and enhancing soil health and crop resilience in sustainable agriculture.