Associations among root-derived metabolites, the rhizosphere microbiome, nitrogen cycling, and metabolic characteristics of Codonopsis pilosula under biofertilizer–nitrogen coupling

Nitrogen-saving management is essential for improving productivity and understanding metabolic characteristics in cultivated Codonopsis pilosula , yet the stage-dependent coordination of root exudation, rhizosphere microbiome assembly, soil nitrogen cycling, and plant metabolism under biofertilizer-nitrogen coupling remains unclear. Here, C. pilosula was examined at vining, flowering, fruiting, and harvest stages under 10 treatments, including an unfertilized drip-irrigation control and nine combinations of a composite growth-promoting bacterial inoculant with three nitrogen rates. Compared with the unfertilized and uninoculated drip-irrigation control, the intermediate combined treatment showed 16.4%, 26.1%, 36.5%, 51.2%, and 234.7% higher harvest dry weight, fresh weight, root length, root diameter, and soluble protein content, respectively. The intermediate treatment combining an inoculant concentration of OD600 = 0.6 with 120 mg N pot −1 used 33.3% less nitrogen than the corresponding higher-N treatment receiving 180 mg N pot −1 , while showing 17.2% and 36.5% higher dry and fresh weight, respectively. Across treatments, total nitrogen and nitrate nitrogen increased from vining to flowering, and nitrogenase, nitrate reductase, and nitrite reductase activities were enhanced during flowering-fruiting. Rhizosphere bacterial communities showed significant stage-dependent assembly (Adonis R² = 0.112, P = 0.001), and growth stage explained 45.54%, 13.34%, 25.12%, and 37.15% of variation in soil nitrogen cycling, rhizosphere microbiome, root exudates, and plant putative metabolites, respectively. Stage-specific root exudates were associated with nitrogen-cycling bacterial taxa, including Verrucomicrobiota , Gemmatimonadota , Devosia , and Actinobacteriota across vining, flowering, fruiting, and harvest stages. These exudate-associated microbial patterns coincided with nitrogen transformation dynamics and shifts in plant metabolism from early defense to flowering-fruiting anabolism and harvest-stage secondary metabolism. These findings highlight associations between root exudate patterns, stage-specific nitrogen-cycling bacterial communities, and nitrogen-saving cultivation strategies for cultivated medicinal industrial crops.