Adaptive reprogramming of carbon–nitrogen metabolism in Klebsiella aerogenes under nitrate-rich conditions

Introduction: B23, a newly isolated marine strain, exhibits efficient nitrate assimilation and denitrification with minimal intermediate accumulation. Methods: This study examined its physiological and metabolomic responses to nitrogen‑deficient (DM1) and nitrate‑rich (DM2) conditions using nitrogen balance analysis and metabolomic profiling. Results: Nitrogen balance analysis showed that 83.28% of supplied nitrate in DM2 was incorporated into biomass, with 16.16% released as gaseous nitrogen. Metabolomic profiling revealed upregulation of TCA cycle intermediates (e.g., α‑ketoglutaric acid, succinic acid) and amino acids (e.g., lysine, arginine) under DM2, indicating enhanced carbon flux toward nitrogen assimilation. Downregulation of isocitric acid and acetyl‑CoA suggested rerouting of carbon skeletons to support active nitrogen utilization. KEGG pathway analysis highlighted lysine degradation, glyoxylate metabolism, and taurine pathways in facilitating this metabolic shift. Discussion: B23 efficiently couples energy production with nitrogen assimilation, offering potential for sustainable nitrate removal in aquaculture and wastewater treatment. Further proteomic studies may clarify the molecular basis of its versatile nitrogen metabolism.