Environmental DNA from pumped deep-sea water enables monitoring of deep-sea fish diversity

Monitoring deep-sea biodiversity is challenging because conventional methods, such as net-sampling and visual surveys, require substantial logistical effort. Environmental DNA (eDNA) offers an alternative for detecting marine organisms; however, its application in deep-sea ecosystems is limited by the sampling accessibility. Because the influence of long‑pipeline transportation on eDNA is unknown, we compared two deep-sea water sampling methods: pumped deep-sea water (pumped method) and water collected near the intake using a Niskin bottle (Niskin method). Samples were collected from pumping stations in Sagami and Suruga bays, Japan, and baited camera observations were conducted to verify eDNA-based detections. In Sagami Bay, both sampling methods detected similar numbers of fish species. In Suruga Bay, the Niskin method exhibited higher species diversity and steeper accumulation curves than the pumped method. The habitat depth ranges of identified species corresponded to the water intake depths in both bays, supporting the effectiveness of the pumped method. Fish community composition showed substantial overlap between methods, and baited cameras recorded 11 and 17 fish taxa in Sagami and Suruga bays, respectively, with 7 and 10 taxa matching eDNA detections. These findings indicate that eDNA metabarcoding of pumped deep-sea water is a feasible method for monitoring deep-sea fish biodiversity.