Microbiology and Biotechnology Research: An Overview Vol. 11

Climate change exposes crops to recurrent drought, heat, salinity and interacting biotic stresses while simultaneously altering the soil microbial communities on which plant nutrition and stress adaptation partly depend. Plant–soil microbiome engineering has therefore moved from descriptive community profiling towards interventions that seek to steer microbial functions, yet the evidential chain from association to reliable field performance remains incomplete. This critical narrative review evaluates how multi-omics, host-mediated microbiome selection, microbial inoculation and synthetic microbial communities (SynComs) can be integrated into a mechanistically grounded strategy for climate-resilient agriculture. Literature published from 2012 to 5 July 2026 was evaluated, with earlier foundational work included where necessary. The strongest evidence shows that plant genotype, root metabolites, nutrient status, immune signalling and environmental stress jointly structure root-associated microbiota, and that drought and temperature perturbations can reproducibly reorganise bacterial communities. Multi-omics can connect these compositional shifts to transcriptional and metabolic activity, but relative-abundance bias, compositionality, protocol dependence and weak temporal resolution constrain causal inference. SynComs address part of this problem by enabling controlled perturbation, strain drop-out and reconstitution experiments; studies in Arabidopsis and crop systems demonstrate priority effects, keystone-like interactions, interkingdom control and context-dependent protection against drought or salinity. Translation remains limited by colonisation failure, resident-community resistance, genotype-by-environment interactions, formulation, ecological safety and the scarcity of multi-site field validation. The review argues that microbiome engineering should be treated as an iterative design–build–test–learn process in which multi-omics discovers candidate functions, culture collections and modelling define testable communities, mechanistic experiments establish causality, and staged field trials determine durability. Climate resilience is most likely to emerge from context-aware, functionally redundant and monitorable plant–microbe systems rather than universal microbial products.