Global agriculture faces a challenge to grow more food while causing less harm to the environment. One popular idea is to use probiotic microbes to boost crop growth, but this strategy often fails in the field due to ecological instability.

In a study published in Journal of Integrative Plant Biology, researchers from the Xishuangbanna Tropical Botanical Garden (XTBG) of the Chinese Academy of Sciences have unveiled a comprehensive roadmap for using plant-exuded prebiotics as an eco-friendly alternative to conventional fertilizers and pesticides.

These plant-exuded prebiotics include compounds such as polyphenols, flavonoids, and organic acids. The researchers demonstrated that these substances can selectively attract beneficial soil microbes that help suppress plant diseases, improve nutrient uptake, and restore soil health. Compared to directly adding probiotics, this prebiotic strategy is more stable and reliable under field conditions.

The researchers introduced a simple, three-step PRE-DDV (Decode–Design–Validate) closed-loop strategy involving analyzing plant and soil microbiomes, designing synthetic microbial communities, and testing them in the field. They defined a plant-exuded prebiotic as a small, non-living molecule (such as malate, citrate, or coumarins) that only beneficial root microbes can use. Not all root exudates are suitable; pathogens shouldn't be able to break them down faster or more effectively than beneficial microbes.

"The pipeline integrates multi-omics profiling, synthetic community design, and iterative field validation, transforming prebiotics from a promising concept into a practical cornerstone of climate-resilient agriculture," said LIANG Gang of XTBG.

The researchers also reviewed how plants produce these prebiotic compounds and how they activate specific microbial functions. To make this technology commercially viable, the researchers identified several challenges, including developing affordable plant-based materials (e.g., native plants or agricultural waste), improving delivery methods, and evaluating costs, environmental impact, and regulations.

By integrating molecular pathways, microbe-plant interactions, and field applications, the study establishes plant-exuded prebiotics as a fundamental tool for sustainable, microbiome-guided agriculture.

"This approach can reduce our dependence on chemical inputs, make crops more resilient, and help secure a sustainable future for global food production," said LIANG Gang.