Monitoring deep-sea fish biodiversity via a direct deep-water intake from 612 m: Insights into taxonomic composition and temporal dynamics revealed by eDNA metabarcoding

We investigated the taxonomic composition and temporal dynamics of deep-sea fish assemblages off subtropical Kume Island, Japan, using environmental DNA (eDNA) metabarcoding of water samples from a fixed deep-water intake system. Over 26 months (December 2020–February 2023), 60 high-volume samples (20 L each) were collected from an intake mouth located near the seafloor of the continental slope at 612 m depth during six sampling events. MiFish metabarcoding identified 283 deep-sea fish taxa. Comparison with a regional checklist showed high overlap at family and genus levels but limited species-level overlap. The eDNA dataset included bathydemersal taxa alongside pelagic and mesopelagic groups (e.g., Myctophidae, Stomiidae), which were proportionally more prominent than in the regional checklist. Despite relatively stable environmental conditions at 612 m, NMDS and PERMANOVA revealed significant differences in community composition among sampling events. The February 2023 assemblage showed the greatest separation from the other events. The similarity between December 2020 and December 2021 suggests that seasonal processes may contribute to the observed temporal variation, but the present sampling design does not establish a recurring annual cycle. These findings highlight the potential of intake-based eDNA monitoring as a repeatable framework for detecting broad-scale ecological shifts in the deep ocean.