Plant–Microbiome Interactions in Agriculture: From Rhizosphere Biology to Crop Health and Productivity

Plant-associated microorganisms contribute to crop performance through nutrient acquisition, competition with pathogens, modification of the chemical environment and regulation of host immunity. Yet community shifts identified by sequencing do not, by themselves, establish disease suppression, and successful antagonism in culture frequently fails to translate into stable protection under field conditions. This critical narrative review examines how rhizosphere, root-endosphere and phyllosphere microbiomes are assembled, how their functions influence disease outcomes, and whether ecological understanding can improve biological control. Peer-reviewed experimental research, pertinent synthesis articles and methodological literature published up to 11 August 2026 were assessed, with emphasis on causal interventions, crop–pathogen specificity, reproducibility and agronomic relevance. Evidence is particularly persuasive where reciprocal soil or microbiome transfer, reduction or reconstitution of communities, metabolite manipulation and host-genetic comparisons converge. Pathogen suppression may emerge from resource competition, niche pre-emption, inhibitory metabolites, interkingdom interactions and induced defence, although their relative importance depends on soil properties, pathogen pressure, crop genotype and temporal succession. Plant exudates and immune signalling can recruit protective microorganisms, but protective taxa and their functions are not necessarily stable across environments. Defined synthetic communities and pathogen-responsive resident assemblages offer experimental precision, whereas their efficacy, persistence and biosafety require stringent validation beyond controlled substrates. Microbial inoculants and organic amendments should therefore be evaluated against appropriate physicochemical controls and integrated management alternatives, rather than inferred to work from taxonomic enrichment alone. The review proposes a causal evidence hierarchy and a context-explicit framework for intervention design, connecting ecological mechanisms to multiseason field outcomes. Future progress will depend on absolute-abundance measurements, manipulative multi-kingdom experiments, representative field trials and transparent reporting of null results. Microbiome-based crop protection is scientifically credible, but dependable biological control remains a property of specified host–pathogen–environment systems rather than of universally beneficial microorganisms.