Fish community assessment using eDNA and conventional methods across river systems, sections, microhabitats, and seasons: Toward improved monitoring strategies in Korea

Biodiversity in freshwater ecosystems has declined drastically, with vertebrate populations decreasing by 69% over the past several decades. This decline calls for efficient biodiversity monitoring approaches. Conventional fish monitoring methods, such as cast and kick nets, however, remain widely used but are often labour-intensive and limited in their ability to detect rare or elusive species. Environmental DNA (eDNA) has emerged as a sensitive, cost-effective and non-invasive alternative, although its use for freshwater biodiversity monitoring in Korea remains limited. This study aimed to utilize eDNA metabarcoding to assess fish community structure and species diversity across different river systems, river sections, and microhabitat types during different seasons in Korea. By comparing eDNA results with those from conventional surveys across four freshwater ecosystems (three rivers and one reservoir), we found that eDNA not only detected a higher total number of fish species, but also showed strong agreement with traditional methods in identifying community structure. Significant differences were observed in fish eDNA communities for river system, section (up-, mid-, and downstream), although non-significant for microhabitat type (riffle, run, and pool) and season (March and August). Notably, eDNA demonstrated superior sensitivity in detecting rare and migratory species, including ~89% of nine endangered species and all three invasive species analysed. While 50 species (~85%) were commonly detected by both methods, several species were exclusively identified through eDNA, indicating its effectiveness in capturing cryptic or low-abundance species. Furthermore, significant positive relationships were found in all the species diversity indices between eDNA and conventional methods. The findings support the ecological validity of eDNA-based monitoring and highlight its potential as a complementary or alternative method to conventional surveys.