Abstract

The rhizosphere microbiome plays a pivotal role in plant health by contributing to nutrient cycling, growth promotion and protection against pathogens. Traditional culture-based methods have provided only a limited view of this complex ecosystem, as many microorganisms cannot be cultivated under laboratory conditions. Metagenomic has emerged as a powerful tool to overcome these limitations, enabling comprehensive analysis of microbial communities directly from environmental samples. This review synthesizes recent advances in metagenomic approaches applied to rhizosphere microbiomes, with a particular focus on mechanisms of plant disease resistance, including nutrient competition, antibiotic and enzyme production, and the induction of systemic resistance. Practical applications are highlighted across major crops such as rice, maize, tomato, and industrial plants including coffee and pepper, drawing on both international studies and pioneering research conducted in Vietnam.

A distinctive contribution of this review lies in its integration of global findings with local case studies, offering insights into tropical agroecosystems that have been underrepresented in previous reviews. Furthermore, emerging research trends are discussed, including multi‑omics integration, artificial intelligence for big data analysis, and the design of synthetic microbial communities tailored to enhance plant resilience. By bridging fundamental knowledge with applied perspectives, this review underscores the transformative potential of metagenomic in developing sustainable, biologically based strategies for plant disease management.