MULTI-OMICS-GUIDED PLANT–BENEFICIAL MICROBE INTERACTIONS FOR SUSTAINABLE CROP PROTECTION, DISEASE SUPPRESSION, AND ABIOTIC STRESS RESILIENCE

Abstract

Global agricultural productivity is increasingly threatened by climate change, environmental degradation, and shrinking arable land, with abiotic stressors such as drought, salinity, thermal extremes, and heavy metal toxicity reducing potential crop yields by up to 70%. Plants mitigate these challenges through intimate associations with endophytic bacteria, forming a functional holobiont in which bacterial endophytes colonize internal plant tissues and act as key regulators of nutrient acquisition, systemic signaling, and stress adaptation. This review provides a comprehensive synthesis of multi-omics approaches spanning genomics, metagenomics, transcriptomics including dual RNA-sequencing, proteomics, metabolomics, and spatially resolved single-cell platforms that have transformed our understanding of plant–endophytic bacterial interactions. We dissect the molecular mechanisms underlying endophyte-mediated growth promotion and abiotic stress mitigation, including nitrogen fixation, phosphate and potassium solubilization, siderophore production, phytohormone modulation, ACC deaminase activity, osmotic adjustment, ROS scavenging, and biological priming. Special emphasis is placed on spatially resolved and single-cell omics technologies, such as scRNA-seq, MERFISH, STARmap, MALDI-MSI, and LAESI-MSI, which overcome the limitations of bulk tissue averaging by resolving cellular heterogeneity and localized host–microbe interactions within the endosphere. Through case studies on drought, salinity, temperature extremes, and heavy metal stress, we illustrate how integrated multi-omics pipelines reveal mechanistic insights into crop stress mitigation. We further discuss bioinformatic integration frameworks, including MOFA2, DIABLO, WGCNA, and genome-scale metabolic modeling, alongside translational challenges in developing synthetic communities and commercial bioinoculants. This review highlights how multi-omics-driven dissection of plant–endophyte interactions can accelerate the development of climate-smart agricultural strategies for sustainable crop production.