Variations in environmental DNA deteAQBOT 103954ction of aquatic plants across water body types: A case study of the Tokachi River

Abstract

The conservation of aquatic plants in freshwater ecosystems is essential for supporting aquatic animal communities. However, conducting field surveys of aquatic plants in riverine environments remains challenging, posing as a barrier to understanding their habitats. In this study, vegetation surveys and environmental DNA (eDNA) metabarcoding were conducted in the main channel, connected ponds, and isolated ponds of the Tokachi River—one of the major rivers in Japan. The aim of this study was to (i) compare species detection between eDNA metabarcoding and field survey results using multiple markers, (ii) determine whether eDNA detection of aquatic plants varies across water body types, and (iii) identify whether detection differences are associated with taxonomic groups or life forms of aquatic plants. A total of 34 species were recorded through field surveys, and 29 species were detected through eDNA analysis. At the species level, 24 species (approximately 80 %) could only be detected using one marker. Isolated ponds yielded the highest number of species in field and eDNA surveys. The families Potamogetonaceae and Poaceae were most frequently detected by eDNA (five species each); notably, both families were also well represented in vegetation surveys across many sites. Overall, submerged plants were detected more frequently by eDNA than emergent plants across all water body type. Additionally, eDNA was able to detect rare species. These findings suggest that eDNA surveys are a valuable tool for detecting submerged and rare aquatic plant species in large river systems, particularly where field-based identification is limited.