Rotala rotundifolia is an amphibious aquatic plant that can live in submerged and emergent forms. It is superior in nitrogen and phosphorus removal and has been used as a traditional medicine in China for over a hundred years. In this study, the bioactive constituents from different tissues of submerged and emergent R. rotundifolia at different growth periods were investigated. The response surface method was used to optimize the flavonoids extraction condition. The amount of flavonoids and triterpenoids from different tissues of R. rotundifolia were much higher than tannins and alkaloids. The highest total flavonoids amount from the leaves of submerged R. rotundifolia was 270.92 ± 13.34 mg/g at day 30 (phyllomorphosis finished), 1.8 times that of the emergent form (150.45 ± 15.11 mg/g). The highest triterpenoids content from the submerged and emergent forms was 242.20 ± 11.51 and 163.09 ± 14.87 mg/g at days 90 and 150 (flowering stage), respectively. The optimal flavonoid extraction conditions were: extraction time 50 min, ultrasonic power 333 W, ethanol concentration 79.3%, and a solid–liquid ratio of 1:60. The LC-MS/MS analysis showed that the extracts from submerged and emergent R. rotundifolia contained 26 and 22 flavonoids, respectively. This study provides phytochemical evidence for the further utilization of R. rotundifolia.
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