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<p>Environmental DNA (eDNA) metabarcoding is widely used for aquatic biodiversity monitoring, but its efficiency across ecosystems and sample types remains to be further evaluated. This study assessed fish diversity using environmental DNA (eDNA) from water and sediment in the river–lake system of China’s Honghu Basin. Our results showed that river water eDNA exhibited the highest species richness (37 species), followed by lake water (17), river sediment (9), and lake sediment (7). Sediment eDNA detected a higher proportion of demersal species than water eDNA in both ecosystems. The&#xa0;river had higher α-diversity and more complex fish communities than lakes. <i>Pseudorasbora parva</i> and <i>Carassius auratus</i> served&#xa0;as key species in the river, whereas <i>Hypophthalmichthys nobilis</i> dominated in the lake. Fish communities in river water were significantly correlated with total phosphorus, whereas those in lake water were primarily associated with turbidity, pH, chlorophyll-a, and dissolved oxygen. These results provide a theoretical basis for optimizing eDNA monitoring and guiding freshwater ecosystem conservation.</p> Graphical abstract <p></p>

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Multi-media eDNA metabarcoding uncovers habitat-specific fish community and monitoring efficiency: implications for ecosystem management in a river–lake system (Honghu lake basin, China)

  • 期刊论文

  • 发表日期：

    2026年5月13日

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  • Ge Li,
  • Borui Zou,
  • Cong Wang,
  • Lu Zhang,
  • Xi Liu,
  • Zhi Wang

摘要

Environmental DNA (eDNA) metabarcoding is widely used for aquatic biodiversity monitoring, but its efficiency across ecosystems and sample types remains to be further evaluated. This study assessed fish diversity using environmental DNA (eDNA) from water and sediment in the river–lake system of China’s Honghu Basin. Our results showed that river water eDNA exhibited the highest species richness (37 species), followed by lake water (17), river sediment (9), and lake sediment (7). Sediment eDNA detected a higher proportion of demersal species than water eDNA in both ecosystems. The river had higher α-diversity and more complex fish communities than lakes. Pseudorasbora parva and Carassius auratus served as key species in the river, whereas Hypophthalmichthys nobilis dominated in the lake. Fish communities in river water were significantly correlated with total phosphorus, whereas those in lake water were primarily associated with turbidity, pH, chlorophyll-a, and dissolved oxygen. These results provide a theoretical basis for optimizing eDNA monitoring and guiding freshwater ecosystem conservation.

Graphical abstract