Reimagining Soil Microbiome Engineering for Climate-Resilient Ecosystem Functioning

Environmental change is intensifying abiotic stresses such as heat, salinity, drought, and nutrient imbalance, threatening agricultural sustainability and destabilizing soil ecosystems, whose resilience is essential for maintaining carbon dynamics, nutrient cycling, and plant stress responses. Engineering the soil’s microbiome might be a solution to these problems. However, current microbiome-engineering approaches are often reductionist, relying on individual microbial strains or short-term interventions that do not adequately account for soil heterogeneity, resident microbial communities, plant genotype, and environmental variability. In this review, we reframe soil microbiome engineering as a dynamic and adaptive process in which interventions are designed according to the functional limitations of specific soil-plant systems. We propose a Soil-Plant-Microbiome Resilience Framework that integrates soil physicochemical properties, microbial community dynamics, plant physiological responses, management practices, and environmental stressors through feedback-regulated interactions. We further translate this framework into a practical engineering pathway based on site diagnosis, selection of microbial or habitat-based interventions, field deployment, monitoring, and adaptive management. Particular, attention is given to the context-dependent performance of bacterial and fungal inoculants and to property-based selection of biochar rather than its use as a generic amendment. By linking ecological mechanisms with site-specific management, this framework provides a basis for developing more reliable, field-relevant, and resilient soil microbiome interventions under environmental change.