Introduction of antibiotics into agricultural fields poses serious health risks to humans. This study investigated the uptake of antibiotics, their effects on metabolic pathways, and chloroplast structure changes of Allium tuberosum exposed to norfloxacin (NFL), oxytetracycline (OTC), and tetracycline (TC). Among all the antibiotic treatments, the highest accumulation of antibiotics in roots (4.15 mg/kg) and leaves (0.29 mg/kg) was TC, while in bulbs it was NFL (5.94 mg/kg). OTC was with the lowest accumulation in roots: 0.19 mg/kg, bulbs: 0.18 mg/kg, and leaves: 0.11 mg/kg. The number of mitochondira and the number of plastoglobulli increased. The chloroplast structure was disturbed under the stress of NFL, OTC, and TC. Disturbance in the chloroplast ultrastructure leads to altered chlorophyll fluorescence variables. Simultaneously, metabolomic profiling of leaves demonstrated that NFL stress regulated more of metabolic pathways than OTC and TC. Differences in metabolic pathways among the antibiotic treatments showed that each antibiotic has different impact even under the same experimental conditions. TC and NFL have more toxic effects than OTC antibiotic. Metabolic variations induced by antibiotics stress highlighted pools of metabolites that affect the metabolic activities, chlorophyll fluorescence, ultrastructural adjustments, and stimulate defensive impact in A. tubersoum. These findings provide an insight of metabolic destabilization as well as metabolic changes in defensive mechanism and stress response of A. tuberosum to different antibiotics.
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