Characteristic rhizosphere metabolites of low-cadmium-accumulating rice drive microbially induced soil cadmium speciation transformation

Introduction Cadmium (Cd) contamination in paddy soils threatens global rice safety. However, the mechanisms by which interactions between rhizosphere metabolites and microorganisms regulate Cd bioavailability in the rhizosphere microecosystem of low-Cd-accumulating rice (LAR) remain unclear. Methods To elucidate the mechanisms by which metabolite-microbe interactions in the rhizosphere microenvironment of LAR regulate Cd bioavailability, a microplot experiment was performed to classify fifteen rice cultivars into LAR ( n = 4) and high-Cd-accumulating rice (HAR, n = 3) groups. Results Rhizosphere omics analyses revealed that LAR tends to form a highly specialized metabolite profile and microbial community at the cost of overall diversity, thereby promoting Cd immobilization. Multiomics integrated analysis demonstrated that characteristic LAR metabolites (Compared with HAR, the rhizosphere metabolites significantly enriched in LAR) serve as carbon sources to enrich Cd-immobilizing bacteria ( Desulfopila aestuarii and Paludibacter sp.) while inhibiting Cd-mobilizing bacteria ( Sulfuriferula sp. AH1, Nocardioides deserti , and Nocardioides glacieisoli ) through antimicrobial activity. These interactions establish a microecological mechanism that suppresses Cd mobilization and enhances immobilization. Moreover, LAR metabolites increase the abundance of microbial genes encoding enzymes for sinapic acid and biotin biosynthesis-including caffeoyl-CoA O-methyltransferase (EC: 2.1.1.104) and 6-carboxyhexanoate–CoA ligase (EC: 6.2.1.14)-and promote the enrichment of related functional microorganisms such as Candidatus Sulfobium mesophilum and Deltaproteobacteria bacterium, thereby further regulating Cd speciation. Validation experiments revealed that a consortium of 23 characteristic LAR metabolites (e.g., sinapic acid, biotin, isosteviol, hydroxyisocaproic acid, 2-hydroxyhexanoic acid, lumichrome, and hypoxanthine) reduced exchangeable Cd by 10-21% and increased Fe-Mn oxide-bound Cd by 28-56% in both natural and sterilized soils. Conclusion These findings reveal that characteristic LAR metabolites directly promote Cd immobilization and drive directional microbial assembly and functional optimization, thereby providing novel insights that can facilitate the establishment of a rhizosphere ecological barrier that can increase resistance to Cd stress in rice.