Exogenous nootkatone impairs nitrogen nutrition by promoting ammonium over nitrate uptake in Arabidopsis thaliana

• Nootkatone impairs growth and photosynthesis in Arabidopsis thaliana • Metabolomic profiles show that nootkatone affects nitrogen-related pathways • Nootkatone promotes the uptake of ammonium over nitrate • Nootkatone toxicity is related to ammonium accumulation Nootkatone, a natural sesquiterpenoid, has recently emerged as a candidate allelochemical for sustainable weed management. However, its phytotoxic effects and underlying mechanisms in plants remain poorly understood. In this study, we present a comprehensive characterization of nootkatone-induced toxicity in Arabidopsis thaliana , integrating physiological, metabolomic, and nutritional analyses. Exposure to increasing concentrations of nootkatone resulted in dose-dependent reductions in biomass and photosynthetic efficiency, accompanied by visible morphological damage. GC–MS-based metabolomic profiling revealed significant reprogramming of primary metabolism, particularly affecting amino acid biosynthesis and nitrogen-related pathways. Network analysis identified glutamic acid as an important metabolic hub, linking nitrogen assimilation to stress-related responses. Nutritional profiling and stable isotope analysis demonstrated that nootkatone disrupts nitrogen homeostasis by promoting ammonium uptake over nitrate assimilation. This shift was confirmed by 15 N-labeled experiments, which showed reduced nitrate uptake and compensatory ammonium absorption. The altered nitrogen source preference was associated with increased accumulation of ammonium, free amino acids, and nitrogen-rich intermediates, consistent with typical symptoms of ammonium toxicity. These findings suggest a potential mechanism underlying nootkatone-induced phytotoxicity and underscore its promise as a bioactive compound for sustainable and environmentally friendly weed management strategies.