Soil Microbiota and Rhizosphere Dynamics: Ecological Mechanisms Driving Crop Stress Adaptation in Climate‐Smart Agriculture

Abstract

ABSTRACT Climate change‐mediated abiotic stresses limit crop performance, and plant responses are increasingly recognized as emergent properties of the coupling between soil, plants, and microbiomes rather than inherent plant characteristics. This review synthesizes mechanistic evidence from 2020 to 2025 on how rhizosphere microbiota contribute to crop stress adaptation within climate‐smart agriculture. We combined ecological theory with biochemical and physiological investigations to demonstrate how microbial community assembly, functional redundancy, network organization, and cropping‐system legacy interact with soil conditions to shape stress‐mitigating microbial pathways. Microbes employ these pathways, including phytohormone modulation, osmolyte and exopolysaccharide synthesis, volatile‐mediated signaling, and nutrient‐transforming metabolites, to influence plant performance under stress. Instead of considering microbiome interventions as universally transferable solutions, we highlight the constraints on microbial establishment and functioning imposed by soil structure, nutrient stoichiometry, moisture regime, host genotype, and legacy‐conditioned soil ecological contexts. We critically examine existing rhizosphere engineering approaches, including synthetic communities and inoculants, soil amendments, and microbiome‐based plant breeding, and highlight clear evidence of causation, inconsistencies, and unresolved outcomes. Particular emphasis is placed on emerging evidence that prior cropping systems, especially legume‐inclusive rotations, function as ecological conditioning mechanisms that influence microbial recruitment, amendment responsiveness, and intervention persistence. Based on this synthesis, we identify key knowledge gaps and focus on mechanistic research required to enhance the predictability, monitoring, and scalability of microbiome‐based strategies. Overall, we advance the concept of crop resilience as a property of coupled soil‐microbiome systems, and argue that climate‐smart agriculture requires predictable, scalable, and mechanistically grounded microbiome‐based approaches.