The Landmark JAMSTEC-Ocean Census Expedition: A Dive into Japan's Deep-Sea Frontiers

In June 2025, a groundbreaking collaboration between Japan's Agency for Marine-Earth Science and Technology (JAMSTEC), the Nippon Foundation-Nekton Ocean Census, and international partners set sail aboard the research vessel RV Yokosuka. Equipped with the state-of-the-art human-occupied vehicle (HOV) Shinkai 6500, capable of descending to 6,500 meters, the 20-day mission targeted under-explored deep-sea ecosystems within Japan's Exclusive Economic Zone (EEZ). This expedition not only advanced our understanding of marine biodiversity but also highlighted JAMSTEC's pivotal role in global oceanography research.

The primary focus areas were the geologically dynamic Nankai Trough and the volcanic Shichiyo Seamount Chain. Over 528 specimens were collected through meticulous dives, employing high-definition cameras, suction samplers, and manipulator arms. These efforts culminated in a post-expedition Species Discovery Workshop in October 2025 at JAMSTEC's Yokosuka headquarters, where taxonomists confirmed remarkable findings.

Decoding the Nankai Trough: Geology Meets Extraordinary Biodiversity

The Nankai Trough, stretching along Japan's southeastern coast where the Philippine Sea Plate subducts beneath the Eurasian Plate, is a hotspot of tectonic activity. This subduction zone fuels mud volcanoes, carbonate crusts, and active cold methane seeps—chemosynthetic ecosystems where life thrives on methane-oxidizing bacteria rather than sunlight. Depths range from 600 to 4,600 meters across five key sites: Daini Tenryu Knoll, Ryuyo Canyon, Yukie Ridge, Oomine Ridge, and Off Cape Muroto.

Prior surveys had documented only 14-35 seep-associated species here, but the 2025 dives revealed 80 macro- and megafaunal species—a five-fold biodiversity surge. This includes 33 molluscs (like vesicomyid clams such as Archivesica kawamurai and Abyssogena kaikoi), 23 annelids (polychaetes and tubeworms like Lamellibrachia columna), 11 arthropods (squat lobsters Munidopsis sp., amphipods), five nemerteans, four echinoderms, three cnidarians, and one bryozoan. At least 22 species harbor endosymbiotic bacteria, underscoring the unique chemosynthetic food web.

Site-specific richness varied: Oomine Ridge boasted 30 species, while Daini Tenryu had 15. High endemism prevailed, with most species unique to single sites, reflecting depth segregation and temporal stability in some areas (e.g., persistent tubeworm bouquets since the 1990s).

The Ecosphere Paper: A Comprehensive Baseline for Nankai Trough Seeps

Published in November 2025 in the open-access journal Ecosphere, the flagship paper "Biological surveys reveal unexpectedly high faunal diversity at Nankai Trough methane seeps" by lead author Dr. Chong Chen (JAMSTEC X-STAR) and colleagues provides the definitive account. Co-authors from JAMSTEC, Hokkaido University, Nagoya University, and Ocean Census detail methods like in situ HD imaging and sieved sampling (100 μm and 0.5 mm meshes).

Key visuals include comparative photos showing community persistence over decades and representative in situ images of clam beds, tubeworm bouquets, and worm aggregations around bacterial mats. The study used Sørensen similarity indices and nMDS ordination to map community overlaps, revealing intermediate-depth similarities. Undescribed taxa like Archivesica sp. Muroto (vesicomyid clam), Lepetelloidea indet. 1-2 (limpets), and pleated-tube ampharetids signal >10 potential new species.

This work establishes a biodiversity baseline critical amid Japan's methane hydrate extraction plans (e.g., JOGMEC tests nearby). It urges site-specific conservation, noting risks to endemic, depth-zoned communities from mining disturbances.Read the full Ecosphere paper

Shichiyo Seamount Chain: Volcanic Peaks Teeming with Life

Southeast of Tokyo, the Shichiyo Seamount Chain—submerged volcanoes along the Izu-Ogasawara Arc—yielded five new squat lobster species (Munidopsis genus), two symbiotic polychaetes (Dalhousiella yabukii, Leocratides watanabeae) dwelling in glass sponges dubbed "glass castles," plus octocorals, nemerteans, amphipods, gastropods, and kinorhynchs. Previously rare species now have national records, revealing dense sponge fields and coral gardens.

Dr. Naoto Jimi (Nagoya University) led research on these sponge symbionts, published in The Zoological Journal of the Linnean Society, tracing their evolutionary history.

Photo by Artyom Korshunov on Unsplash

Technological Marvel: Shinkai 6500 and JAMSTEC's Legacy

Since 1990, Shinkai 6500 has logged over 1,800 dives, equipped with HD cameras, sonar, CTD sensors, and sampling tools. JAMSTEC, Japan's premier marine research agency, drives this via institutes like X-STAR and collaborates with universities such as Hokkaido and Nagoya. Their Young Research Fellow program offers early-career PhDs cutting-edge opportunities in oceanography.Explore marine research positions

The expedition's data joins the Ocean Census Biodiversity Data Platform, promoting open science.Ocean Census press release

Broader Implications: Conservation Amid Deep-Sea Mining Threats

With 38 confirmed and 28 potential new species, the expedition underscores that 80-90% of ocean species remain undescribed. Nankai's seeps contribute to carbon sequestration via methane consumption, but hydrate mining poses risks. High endemism demands protected areas, aligning with UN Ocean Decade goals.

• Five-fold biodiversity boost signals underestimation in active margins.
• Depth zonation (e.g., clams every ~1000m) informs biogeography.
• Range extensions link seeps to vents, expanding habitat knowledge.

Stakeholders like Nippon Foundation emphasize safeguarding these frontiers.Career advice for ocean scientists

University Collaborations Fueling Japan's Marine Science Boom

JAMSTEC partners with Hokkaido University (Shoki Shiraki) and Nagoya University (Naoto Jimi, Sugashima Marine Lab), training next-gen researchers. Kochi University hosts JAMSTEC's Kochi Core Center. These ties offer students fieldwork on Shinkai dives, fostering expertise in chemosynthesis and tectonics.Japanese academic opportunities

Programs like JAMSTEC Young Research Fellows attract global talent, bridging higher ed and national research.

Future Horizons: Ongoing Analysis and Global Missions

Multiple papers are in review; data fuels IUCN assessments. Ocean Census plans more expeditions, positioning Japan as a leader. For aspiring researchers, JAMSTEC-university links promise PhD/postdoc roles in deep-sea biology.Postdoc opportunities

This expedition exemplifies how collaborative research unveils ocean secrets, informing policy and inspiring careers.

Photo by Jonathan Gong on Unsplash

Opportunities in Marine Research: Join Japan's Deep-Sea Revolution

From JAMSTEC fellowships to university labs at Hokkaido and Nagoya, Japan's marine sector thrives. Explore faculty positions, research assistant roles, or professor jobs in oceanography. Browse research jobs | University positions | Rate professors | Career advice | Higher ed jobs. Stay engaged with Japan's cutting-edge science.