The integration of omics technologies—genomics, transcriptomics, proteomics, metabolomics, and metagenomics—has revolutionized our understanding of plant–microbe interactions, offering profound insights for sustainable crop improvement. These multidimensional approaches unravel the complex molecular dialogues between plants and associated microorganisms, including beneficial rhizobacteria, mycorrhizal fungi, and endophytes, which collectively influence plant health, stress tolerance, and productivity. Omics-based analyses facilitate the identification of microbial taxa and plant genes involved in nutrient acquisition, disease resistance, and abiotic stress mitigation, thereby enabling the development of bioinoculants, bio stimulants, and genetically enhanced crops. Functional genomics and meta transcriptomics uncover gene expression patterns in both plants and microbes during interaction phases, while proteomics and metabolomics elucidate the active proteins and metabolites that mediate symbiosis or antagonism. This holistic understanding supports precision agriculture by guiding microbiome engineering and breeding strategies aimed at enhancing crop yield and resilience in the face of climate variability, resource limitations, and pathogen pressures.
Salvadi et al. (Tue,) studied this question.