Combined physiological, transcriptomic, and metabolomic analyses reveal the response mechanisms of Phragmites australis to lead (Pb) stress.

Phragmites australis (P. australis) has potential for wetland phytoremediation through nutrient and heavy metal accumulation; however, the molecular mechanisms underlying its tolerance to lead (Pb) remain poorly understood. This study conducted a pot experiment to investigate physiological, transcriptomic, and metabolomic responses of P. australis to a gradient of Pb concentrations (300, 400, and 500 mg/kg) over three exposure durations (50, 75, and 100 d). The results showed that Pb stress inhibited biomass accumulation in a concentration-dependent manner. The antioxidant system responded dynamically. Peroxidase (POD) activity increased to 1.00-1.29 times that of the control, whereas catalase (CAT) activity and non-enzymatic antioxidants showed temporal and concentration-dependent variations. P. australis preferentially accumulated Pb in roots, with 96-99% of root Pb localized in cell walls, accompanied by significant increases in pectin and lignin contents. Transcriptomic analysis revealed extensive gene expression reprogramming, with differentially expressed genes (DEGs) significantly enriched in pathways related to ribosome function, ABC transporters, and phenylpropanoid and glutathione metabolism. Key functional genes, including those encoding heavy metal ATPases (HMAs) and antioxidant biosynthesis, were specifically upregulated. Metabolomic analysis identified 108 significantly altered metabolites exhibiting concentration-dependent patterns. Under high Pb exposure, pronounced changes were observed in major metabolite categories, including isoprenoids, organic oxygen compounds, and fatty acyls. Integrated multi-omics analysis indicated that Pb detoxification in P. australis primarily relied on root cell wall immobilization and coordinated reprogramming of antioxidant and metabolic pathways. These findings elucidate the mechanisms underlying Pb tolerance in P. australis and provide a scientific basis for assessing its application in the phytoremediation of Pb-contaminated wetlands.