Harnessing plant-exuded prebiotics as a next-generation strategy for sustainable agriculture

Global agriculture urgently needs sustainable strategies to boost crop productivity while reducing environmental impact. Harnessing plant-exuded bioactive metabolites, such as polyphenols, flavonoids, and organic acids, as natural prebiotics offers a powerful yet underexploited avenue for modulating rhizosphere microbiomes. These prebiotics complement existing microbial inoculants by leveraging the plant's own chemistry to selectively recruit beneficial microbes, thereby enhancing disease suppression, nutrient acquisition, and soil health more reliably than introduced consortia, which often fail due to ecological instability. However, translating this promise into practice is hampered by the profound complexity of the soil-root-microbe interface. This review establishes a conceptual framework that positions plant prebiotics as actionable tools for precision microbiome engineering. We summarize the biosynthetic pathways and mechanisms through which these specialized metabolites stimulate specific beneficial microbial functions. Building on this synthesis, we introduce the PRE-DDV pipeline (decode-design-validate), a closed-loop strategy integrating multi-omics profiling, synthetic community design, and iterative field validation. To enable commercial-scale field application, we critically examine key translational considerations: Identifying scalable plant sources (including native flora and agro-industrial byproducts), advancing formulation and precision delivery to ensure stability and targeted release, and assessing the economic feasibility, environmental sustainability, and regulatory frameworks governing industrial-scale production. Together, these contributions position prebiotics within a concrete pathway that bridges biological mechanisms and practical scalability, transforming them from a promising concept into a practical cornerstone of sustainable, climate-resilient agriculture.