Metabolomics combined with physiology and transcriptomics reveals key metabolic pathway responses in ginseng roots to nitrogen and potassium deficiency

• Synergistic N-K deficiency severely inhibits ginseng growth (biomass), photosynthesis (chlorophyll, Rubisco), and ginsenoside biosynthesis. • Integrated omics reveals disrupted C-N allocation: N/K deficiency inhibits key N assimilation enzymes (GS, NR) and ABC transporter function, repressing secondary metabolism (esp. terpenoids). • Transcriptional reprogramming under stress: N-K interaction synergistically regulates nitrate transporters ( NRT2.1 ), terpenoid biosynthetic genes ( HMGR1 , DXS2 ), and efflux transporters ( PDR1 ). • Resource competition-metabolic trade-off: Short-term defense activation (e.g., upregulated NRT , HMGR , PDR5 ) leads to long-term energy depletion, oxidative damage, and ginsenoside reduction. • First molecular elucidation: Provides the mechanism for N-K co-regulation of ginsenoside biosynthesis, guiding optimized nutrient management in medicinal plants. Nitrogen (N) and potassium (K) are essential macronutrients for plant growth and development; however, the molecular mechanisms underlying their synergistic regulation of secondary metabolism in medicinal plants remain elusive. Herein, we employed an integrated physiological, metabolomic, and transcriptomic approach to systematically examine the metabolic response network in ginseng roots under N and K deficiency stress. Four treatment approaches were employed: N and K sufficiency (N1K1), N deficiency (N0K1), K deficiency (N1K0), and dual N–K deficiency (N0K0). N and/or K deficiencies significantly reduced root biomass accumulation and photosynthetic efficiency, inhibited ginsenoside biosynthesis, and induced oxidative stress responses. Metabolomic analysis revealed that N and K deficiency stress disrupted C–N resource allocation by inhibiting key N assimilation enzymes (glutamine synthetase and nitrate reductase) and ABC transporter function, thereby repressing secondary metabolic pathways, particularly terpenoid backbone biosynthesis. Transcriptomic analysis further revealed that N–K interaction synergistically regulated the expression levels of nitrate transporter genes, terpenoid biosynthetic genes, and efflux transporters. This reprogramming activated short-term defense mechanisms but ultimately resulted in energy depletion and oxidative damage under prolonged stress. This study offers the first molecular insight into how N and K synergistically regulate ginsenoside biosynthesis, mediated by resource competition and metabolic trade-offs, laying a theoretical foundation for optimizing mineral nutrient management in medicinal plants to simultaneously enhance growth and secondary metabolite production.