Molybdenum regulates phosphorus cycling species diversity and improves soil phosphorus availability through key flavonoids in the soybean (Glycine max)

• Mo application reduced soil Al-P and organic P content, while increased soil available P content. • Mo altered the metabolites and microbial composition of soybean rhizosphere soil. • Mo application significantly increased the content of chrysin and phlorizin in the soil. • Chrysin and phlorizin increased soil P cycling genes and microbial abundance. • Chrysin and phlorizin increased soil available P content. Applying molybdenum (Mo) fertilizer can improve soil phosphorus (P) bioavailability, reduce the need for P fertilizers in agriculture, and enhance crop growth. However, the precise mechanisms behind these benefits are not yet fully understood. For the first time, we demonstrate the impact of Mo application on the transformation of P forms, metabolites, and microorganisms in the soybean rhizosphere. We carried out a series of pot experiments under controlled conditions, applying varying levels of Mo and collecting samples from the soybean rhizosphere across different treatments to analyze P forms, metabolic profiles, and microbial communities comprehensively. Mo application enhanced soybean P uptake and growth by promoted the conversion of aluminum-bound P (Al-P) and organic P to available P. The underlying mechanism involves the regulatory effect of Mo on the abundance of metabolites in the soil, thereby reshaping the structure of the rhizosphere microbial community. Two key Mo-mediated flavonoids, chrysin (Cs) and phlorizin (Pz), significantly promoted soybean growth and P absorption. Subsequently, Soil metagenomics and phosphate-solubilizing bacteria (PSB) addition experiments confirmed that these flavonoids increased P cycling genes (e.g., gcd and phoD ) and microorganisms, facilitating stable P transformation into labile P, and aiding PSB ( Bacillus subtilis ) in further enhancing soil P availability. In summary, we have demonstrated for the first time that trace metals regulate the abundance of soil P cycling microorganisms by influencing crop-secreted flavonoids. This ultimately improves soil P bioavailability, providing a new insight for sustainable agricultural development.