Abstract
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.
Acknowledgements
We thank Shizuoka Prefecture and Akazawa Onsen Village (previous owner, DHC Corporation) for providing pumped deep-sea water; Messrs. Michiyasu Nomura (DHC Corporation), Yusuke Sano, and Hideo Kawai (Shizuoka Prefectural Deep-Sea Water Pumping Facility) for their technical assistance with sample collection; and Dr. Rachel Atanacio (FishBase) for providing the FishBase dataset. We also thank Dr. Katsuhisa Yamada (DHC Corporation), Mr. Takahiro Amano (Shizuoka Prefectural Government Office), and Ms. Keiko Maeda (Shizuoka Prefectural deep-sea water pumping facility) for their logistic support when utilising pumped water. We also thank Mr. Tetsuji Maki (JAMSTEC), the captain and crew of R/V Kaimei, the operation team of KM-ROV, and CTD operation team from Marine Work Japan for the KM20-09 cruise. We also thank Messrs. Hisashi Hasegawa and Kazutaka Hasegawa for operating Chokane Maru. We are grateful to the two anonymous reviewers for their careful and constructive comments, which helped improve this manuscript.
Funding
This study was funded by the Japan Agency for Marine-Earth Science and Technology.
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Yoshida, T., Kawato, M., Tsuchida, S. et al. Environmental DNA from pumped deep-sea water enables monitoring of deep-sea fish diversity.
Sci Rep (2026). https://doi.org/10.1038/s41598-026-56998-1
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DOI: https://doi.org/10.1038/s41598-026-56998-1
Keywords
- eDNA
- Biodiversity
- Deep-sea water
- Fish metabarcoding
- Continuous monitoring
Source: Ecology - nature.com
