Agricultural Soil Science in a Changing Climate: Soil Health, Carbon Cycling, Nutrient Dynamics and Agroecosystem Resilience

Crop-associated microbiomes are increasingly proposed as tools for stabilising productivity under drought, salinity and nutrient limitation, yet the evidence spans scales from stress-responsive community surveys to single-strain inoculation and field deployment. This critical narrative review integrates literature published from 1 January 2000 to 3 July 2026 to evaluate mechanisms, engineering strategies and translational constraints. Across drought studies, root microbiomes show recurrent stress-driven reassembly, including conserved enrichment patterns in several grasses and crops, but taxonomic shifts alone do not establish adaptive function. Bacterial inoculation, arbuscular mycorrhizal symbiosis and community-selection experiments support causal routes involving root architecture, hormone balance, osmotic adjustment, antioxidant capacity and nutrient acquisition. Salinity mitigation uses overlapping mechanisms but adds ion-homeostasis and microbial halotolerance requirements; the evidence remains weighted towards controlled environments. Nutrient stress provides some of the clearest causal examples of host-directed microbiome recruitment, including genotype-dependent nitrogen-associated communities, flavone-mediated bacterial enrichment, phosphate-starvation–microbiota integration and coumarin-dependent iron acquisition. Synthetic communities, host-mediated microbiome selection and microbiome-aware breeding can convert these mechanisms into interventions, but field performance is constrained by native-community competition, soil heterogeneity, stress definition, genotype × environment × microbiome × management interactions and uncertain persistence. The synthesis supports a context-dependent functional-resilience framework in which function is prioritised over taxonomic identity, persistence is defined by the duration required for activity, and success is judged by yield stability or resource-use efficiency rather than short-term biomass alone. Progress requires causal perturbation, non-sterile validation, multi-site and multi-season testing, realistic combined stresses and explicit ecological safety assessment. The most credible translational pathway is therefore a staged evidence chain linking microbial establishment, in situ functional expression, plant physiological response and agronomic benefit within defined agroecological recommendation domains.