In a remarkable advancement for marine biology, researchers have confirmed the discovery of 38 new species in the deep waters surrounding Japan, shedding new light on the country's rich deep-sea biodiversity. This breakthrough stems from a landmark expedition conducted in June 2025 by the Japan Agency for Marine-Earth Science and Technology (JAMSTEC), in collaboration with the Nippon Foundation-Nekton Ocean Census and leading Japanese universities such as Nagoya University and Hokkaido University. The findings, published in peer-reviewed journals, highlight previously unexplored ecosystems in the Nankai Trough and Shichiyo Seamount Chain, areas teeming with life at depths exceeding 4,600 meters.
These discoveries underscore Japan's pivotal role in global deep-sea research, where academic institutions play a crucial part in training the next generation of marine scientists and driving innovation in submersible technology. The expedition not only expanded known biodiversity by fivefold in key sites but also revealed unique symbiotic relationships, such as polychaete worms dwelling within glass sponges dubbed a 'glass castle.' As Japanese universities continue to lead in this field, the results promise significant implications for conservation amid rising threats like deep-sea mining.
The Groundbreaking Expedition: JAMSTEC's Shinkai 6500 in Action
The expedition aboard the research vessel RV Yokosuka marked the first deep-sea collaboration between JAMSTEC and the Ocean Census initiative. Over 20 days, the team deployed the iconic Shinkai 6500 manned submersible—one of the world's deepest-diving vehicles, capable of reaching 6,500 meters—for 11 biological dives. This technology, developed by JAMSTEC since 1990 with over 1,800 dives to its credit, allowed scientists to collect more than 528 specimens through high-definition imaging, suction sampling, and grabs.
Key partners included faculty from Nagoya University's Sugashima Marine Biological Laboratory and Hokkaido University's Graduate School of Science, Department of Natural History Sciences. Their expertise in taxonomy and ecology was instrumental, bridging JAMSTEC's engineering prowess with academic analysis. A post-expedition Species Discovery Workshop at JAMSTEC headquarters in Yokosuka convened taxonomists worldwide, accelerating identifications.
Exploring the Nankai Trough and Shichiyo Seamount Chain
The Nankai Trough, located 500-600 km southwest of Tokyo off Kochi Prefecture, features methane seeps fueling chemosynthetic ecosystems at depths from 600 to 4,600 meters. Sites like Daini Tenryu Knoll, Ryuyo Canyon, Oomine Ridge, Yukie Ridge, and Off Cape Muroto revealed a fivefold biodiversity surge—from 14 to 80 macro- and megafaunal species. Depth segregation was evident, with vesicomyid clams specializing at 1,000-meter intervals and high endemism (most species site-specific).
The Shichiyo Seamount Chain, 500-700 km southeast of Tokyo near Izu and Ogasawara Islands, comprises submerged volcanic peaks hosting sponge gardens and coral habitats. Here, five new squat lobster species from the genus Munidopsis were among highlights. These regions, within Japan's Exclusive Economic Zone, represent understudied hotspots vulnerable to resource extraction.
A Parade of New Species: From Crabs to Ribbon Worms
The 38 confirmed species span diverse phyla, including arthropods (crabs, squat lobsters, shrimp, amphipods), annelids (polychaetes, lugworms), echinoderms (sea stars, brittlestars, sea cucumbers), molluscs (snails, clams), nemerteans (ribbon worms), cnidarians (zooanthids, anemones), and more. An additional 28 candidates await formal description.
- Squat lobsters (Munidopsis spp.): Five new species, key seamount dwellers.
- Polychaete worms: Including glisten-worms and undescribed forms like Ampharetidae indet.
- Vesicomyid clams: New taxa like Archivesica sp. Muroto, highlighting seep specialization.
- Bryozoans and octocorals: Expanding known deep-sea reef builders.
These finds, detailed in studies like the Ecosphere paper on Nankai seeps, boost Japan's marine inventory and reveal evolutionary adaptations to extreme pressures and chemistry.
Photo by Chinh Le Duc on Unsplash
Life in the 'Glass Castle': Symbiotic Marvels
One standout discovery is two new polychaete worms—Dalhousiella yabukii and Leocratides watanabeae—living symbiotically inside a novel hexactinellid glass sponge at Getsuyo Seamount, ~5,000 meters deep. Dubbed a 'glass castle' for its silica lattice, the sponge hosts these worms in a rare commensal relationship, evolved convergently across Hesionidae annelids.
Led by Naoto Jimi from Nagoya University, this was published in the Zoological Journal of the Linnean Society. In situ observations via Shinkai 6500 confirmed the association, advancing understanding of deep-sea symbioses. For details, explore the full study.
Academic Contributions from Nagoya and Hokkaido Universities
Japanese higher education shines through Nagoya and Hokkaido Universities' involvement. At Nagoya's Sugashima Marine Biological Laboratory, Lecturer Naoto Jimi co-authored key papers, leveraging the lab's expertise in polychaete taxonomy and deep-sea ecology. Hokkaido's Shoki Shiraki contributed to seep biodiversity analysis from the Graduate School of Science.
These institutions offer robust marine biology programs, training PhD students in submersible operations and molecular systematics. Collaborations with JAMSTEC provide hands-on fieldwork, fostering faculty positions in deep-sea research. Such partnerships exemplify how universities drive Japan's marine science leadership.
Scientific Publications and Methodological Rigor
Rapid publication underscores the rigor: Chong Chen (JAMSTEC) led the Nankai Trough survey in Ecosphere, documenting 80 species with nMDS analysis revealing distinct communities. Jimi's symbiosis paper used morphological and genetic data. Open-access data via Ocean Census platforms ensures global academic access. Read the Nankai findings here.
Methods combined video transects, sampling, and lab taxonomy, setting baselines for monitoring amid climate and human pressures.
Biodiversity Implications and Conservation Urgency
The discoveries reveal Japan's deep sea as a biodiversity frontier, with seeps and seamounts hosting endemic assemblages. Threats include seabed mining for methane hydrates in Nankai and minerals elsewhere in the EEZ. JAMSTEC's Hiromi Watanabe notes surveys aid impact assessments. Conservation calls for protected areas, informed by university-led research.
Technological and Educational Frontiers
Shinkai 6500's legacy enables precise sampling, training university pilots and observers. Programs at Nagoya and Hokkaido integrate such tech into curricula, preparing students for research jobs. JAMSTEC-university ties fund PhDs, postdocs in marine genomics and ecology.
Future Outlook: Sustaining Japan's Deep-Sea Legacy
Upcoming expeditions target more EEZ sites, with universities expanding AI taxonomy and eDNA tools. This breakthrough inspires STEM enrollment, positioning Japan as a hub for deep-sea careers. As biodiversity data grows, so does the case for policy protecting these hidden realms.
Explore JAMSTEC's ongoing work via their expedition announcement and recent NHK coverage here.