European Journal of Sustainable Agroecosystems

Background: The rhizosphere, the narrow zone of soil influenced by root activity, harbours a taxonomically and functionally diverse microbiota that mediates nutrient cycling, phytohormone signalling, stress tolerance, and disease suppression. As global agriculture confronts the dual pressures of food security and environmental sustainability, functional characterization of rhizosphere microbiota has emerged as a central strategy for reducing dependence on synthetic agrochemicals.
Objective This review synthesizes peer-reviewed literature published mainly between 2015 and 2026 to critically evaluate the functional roles, drivers, and management levers of rhizosphere microbiota in sustainable cropping systems, and to identify unresolved research gaps.
Method A structured search of PubMed, Scopus, Web of Science, Google Scholar, and institutional/government repositories (including FAO reports) was conducted using combinations of terms such as “rhizosphere microbiome,” “plant growth-promoting rhizobacteria,” “synthetic microbial community,” “disease-suppressive soil,” and “sustainable agriculture.”
Result The reviewed literature converges on several functional axes of rhizosphere microbiota: biological nitrogen fixation and phosphate solubilization, phytohormone-mediated growth promotion, induced systemic resistance and biocontrol, and drought/abiotic-stress buffering through root-exudate-mediated recruitment. Multi-omics approaches (metagenomics, metatranscriptomics, metabolomics) and rationally designed synthetic microbial communities (SynComs) are increasingly used to move beyond taxonomic description toward functional and mechanistic understanding. Agricultural management practices—tillage intensity, crop rotation, cover cropping, and organic amendments—consistently reshape microbiome-mediated disease suppressiveness, although effect sizes vary substantially across soils, climates, and cropping systems.
Persistent gaps include limited field validation of laboratory-derived inoculants, inconsistent methodological standards across studies, insufficient understanding of the plant genetic loci governing microbiome assembly, and a scarcity of longitudinal, multi-site data linking microbiome function to yield outcomes under real-world management.
Conclusion Functional characterization of rhizosphere microbiota offers substantial promise for advancing sustainable cropping systems, but translating mechanistic insight into reliable field-scale interventions requires standardized methodologies, long-term multi-omics datasets, and closer integration between microbiome science and agronomic practice.