Microbiology and Biotechnology Research: An Overview Vol. 10

Agricultural microbiome research has progressed from descriptive inventories of root- and soil-associated taxa towards deliberate manipulation of microbial functions. This transition is strategically important because climate-resilient production and greenhouse-gas mitigation are often treated as separate objectives even though both depend on coupled plant, microbial and biogeochemical processes in the rhizosphere. This critical narrative review evaluates how plant-soil microbiomes can be engineered to improve crop performance under climatic stress while reducing emission-intensive nitrogen and carbon losses. Literature published from 1 January 2000 to 4 July 2026 was prioritised, with earlier evidence considered only when mechanistically indispensable. Evidence was appraised according to experimental control, ecological realism, causal manipulation, persistence, directness of agronomic and gas-flux outcomes, and transferability across soils and genotypes. The strongest causal evidence for microbiome function comes from reductionist synthetic-community and root-exudate studies, whereas the strongest field-relevant evidence is concentrated in host-genotype effects, biological nitrification inhibition, selected nitrous-oxide-reducing rhizobia, and long-term management effects on resident microbiomes. Drought and salinity studies support a role for beneficial bacteria and arbuscular mycorrhizal fungi, but treatment responses remain heterogeneous and mechanistic gene-expression claims are less consistent than broad plant-performance responses. For low-emission agriculture, biological nitrification inhibition and microbial nitrous oxide sinks have unusually clear process targets, although their performance is strongly soil- and crop-dependent. Microbial carbon-use efficiency, necromass formation and methane cycling provide plausible additional targets, but direct field evidence that microbiome engineering produces durable soil-carbon gains or reliably suppresses rice methane remains comparatively limited. Translation therefore requires a shift from taxonomic signatures to function-first design, multi-environment validation, direct greenhouse-gas measurements, persistence testing, and simultaneous assessment of yield stability and environmental trade-offs.