From diversity to function: microbiome-mediated plant growth promotion, secondary metabolism, and antimicrobial resistance in

Introduction: This study presents the first metagenomic analysis of the root and rhizosphere microbiomes of Methods: High-throughput Illumina sequencing and bioinformatics analysis were used to profile the microbial communities. Functional annotation was performed to identify plant growth-promoting traits using PLABASE, to predict pathways for the biosynthesis of novel bioactive compounds using antiSMASH, and to identify antimicrobial resistance genes using ResFinder. Results: The analysis revealed highly diverse microbial communities in both habitats, predominantly composed of Pseudomonadota, Bacillota, and Actinomycetota, with minor but consistent contributions from archaea and eukaryotes. Functional annotation identified extensive PGPTs, including genes associated with phosphate solubilization, nitrogen fixation, siderophore-mediated iron acquisition, and stress tolerance. The rhizosphere microbiome exhibited greater metabolic versatility and stress tolerance, characterized by a higher copy number of heavy metal efflux pumps, whereas the root microbiome was enriched in genes involved in plant hormone regulation and plant-microbe interactions. A diverse array of non-ribosomal peptide synthase, polyketide synthase, and lasso peptide pathways were predicted, underscoring the potential to produce novel bioactive compounds. These distinct functional profiles demonstrates that the protected root endomicrobiome specializes in plant signalling and nutrient assimilation, while the rhizosphere microbiome, facing higher competition, specializes in nutrient acquisition and stress resilience. Conclusion: These findings provide novel insights into the ecological specialization and biotechnological potential of the