Environmental DNA Reveals Fish Diversity and Temporal Community Dynamics in Representative Aquatic Germplasm Resources Conservation Areas

Introduction: Environmental DNA (eDNA) metabarcoding provides a non-invasive approach for aquatic biodiversity monitoring, but its application in aquatic germplasm resources conservation areas remains insufficiently evaluated. This study assessed fish diversity, community variation, and conservation applications of eDNA in representative conservation areas in Henan Province, China.

Methods: A total of 54 water samples were collected from two conservation areas along the same river reach during four sampling campaigns from summer 2024 to autumn 2025. Fish eDNA was analyzed using 12S rRNA metabarcoding and a locally curated reference database. Traditional fish surveys and water-quality measurements were conducted in parallel. Hill diversity, Jaccard dissimilarity, PERMANOVA, dbRDA, Mantel tests, and variation partitioning were used to evaluate community patterns and environmental associations.

Results: Processing and analysis of the eDNA samples yielded sequence reads assigned to 44 fish species. For reference-compatible comparison, 33 traditional-survey species were retained; 22 were shared, 22 were detected only by eDNA, and 11 only by traditional surveys, yielding a combined inventory of 55 species. The two conservation areas showed highly similar fish diversity and species composition. Among repeatedly sampled core sites, sampling campaign explained 31.8% of community variation (P < 0.001), whereas reserve identity explained 3.2% (P = 0.188). Environmental variables were associated with community variation, but their independent contribution was limited after accounting for sampling campaign. Qihe crucian carp (Carassius auratus), the focal conservation target of both reserves, was detected by eDNA in each reserve. eDNA also detected the conservation-concern species Onychostoma macrolepis in both reserves, across nine independent sites and two sampling campaigns, with one site confirmed by traditional capture.

Conclusions: eDNA and traditional surveys provided complementary information for fish biodiversity assessment. Temporal variation among sampling campaigns exceeded spatial differences between reserves, while eDNA detected focal and conservation-concern species, supporting its application in long-term biodiversity monitoring and conservation management.