Taxonomic Guilds, Action Mechanisms, and Agronomic Deployment of Maize Rhizosphere Microbiota for Yield Enhancement: Unraveling G×M×E Interactions and Translational Barriers via Multi Omics

Maize (Zea mays L.) productivity is increasingly constrained by edaphic stressors—including soil salinization, drought, and acidification—posing mounting threats to global food security. Plant growth-promoting microorganisms (PGPM) offer a sustainable alternative to synthetic fertilizers, yet despite their pronounced performance under controlled laboratory settings, their beneficial effects often prove inconsistent in open-field environments, largely due to spatial heterogeneity and genotype-specific responses. Herein, we present a comprehensive synthesis of the core microbial guilds that have been robustly associated with maize yield enhancement. The mechanisms underlying these effects are examined across several dimensions, including biological nitrogen fixation, phosphate and potassium solubilization, phytohormone production, ethylene regulation, stress tolerance, and rhizosphere colonization. Genomic, transcriptomic, metagenomic, and metabolomic data are integrated to construct an interaction network between maize and rhizosphere microbes. We identify the genotype-by-microbiome-by-environment (G×M×E) interplay as the principal bottleneck hampering field-scale translational success. To address this issue, three priorities are proposed: (i) designing synthetic microbial consortia, (ii) using multi-omics to examine mechanisms, and (iii) developing tools for site-specific deployment. In conclusion, these sections provide a framework for developing more reliable microbial inoculants for maize.