Multi-omics reveals metabolic reprogramming underlying differential modulation of nodulation and root development by nitrate and ammonium in soybean

Introduction: Nitrogen form and concentration are key environmental regulators that mediate symbiotic nitrogen fixation and root development in legumes. Methods: To understand the metabolic and molecular mechanisms underlying the effects of distinct nitrogen sources (nitrate and ammonium) on soybean nodulation and root development, this study evaluated root and nodulation phenotypes, and their corresponding transcriptional and metabolomic responses under different concentrations of NH₄Cl or KNO₃. Results: Results showed that both high concentrations of NH₄Cl and KNO₃ significantly suppressed nodulation and promoted root growth, with nitrate exerting a stronger effect than ammonium. Metabolomic analysis revealed that ammonium treatment enhanced nitrogen assimilation and primary metabolism while suppressing symbiosis-related flavonoids. Nitrate specifically activated chemical defense pathways and inhibited parts of central carbon metabolism. Integrated multi-omics analysis indicated that the nitrogen sources differentially regulated key genes and metabolites involved in nitrogen metabolism, flavonoid/isoflavonoid biosynthesis, and arginine metabolism, leading to distinct metabolic fluxes. Discussion: Our results demonstrate that soybean perceives different nitrogen forms to orchestrate a metabolic trade-off between autonomous growth, defense, and symbiosis, thereby providing new insights into the mechanistic basis of nitrogen-form adaptation in legumes.