Chong Chen

Japan Agency for Marine-Earth Science Technology | JAMSTEC · X-STAR

Life stages of some animals, including amphibians and insects, are so different that they have historically been seen as different species. ‘Metamorphosis’ broadly encompasses major changes in organism bodies and, importantly, concomitant shifts in trophic strategies. Many marine animals have a biphasic lifestyle, with small pelagic larvae undergoi...

Deep-sea hydrothermal vents were discovered only 40 years ago. We now know that around 600 of these auditorium-sized oases exist in the vast expanse of the ocean, flourishing with unique life that we are nowhere close to fully understanding. This lack of baseline biodiversity assessments creates an ‘out of sight, out of mind’ conservation dilemma f...

The Scaly-foot Snail, Chrysomallon squamiferum, presents a combination of biomineralised features, reminiscent of enigmatic early fossil taxa with complex shells and sclerites such as sachtids, but in a recently-diverged living species which even has iron-infused hard parts. Thus the Scaly-foot Snail is an ideal model to study the genomic mechanism...

Specializing in different dietary niches via morphological adaptation underpins the success of animal radiation when invading a new environment, as seen in examples such as Darwin's finches (De León et al., 2014). Ecomorphological studies of various animal groups, from mammals to arthropods, illustrate adaptations to different food sources, which a...

Neomphaloidean gastropods are endemic to chemosynthesis-based ecosystems ranging from hot vents to organic falls, and their diversity and evolutionary history remain poorly understood. In the southwestern Pacific, deep-sea hydrothermal vents on back-arc basins and volcanic arcs are found in three geographically secluded regions: a western region ar...

Hydrothermal vents are biodiversity hotspots on the deep seafloor powered by chemosynthetic primary production, inhabited by a specially adapted fauna whose composition varies between regions. Sumisu Caldera, located approximately 500 km south of Tokyo, hosts a hot vent with an unusual species composition among the Izu–Ogasawara Arc sites and has b...

A new species of the thorid shrimp genus Lebbeus White, 1847, is described and illustrated on the basis of two specimens collected from the recently discovered Amami Rift hot vent field in the Ryukyu region in southwestern Japan, at a depth of 628 m. Lebbeus parvirostris sp. nov. is morphologically similar to L. microceros (Krøyer, 1841), L. mundus...

Deep-sea hydrothermal vents are biological hotspots driven by microbial chemosynthetic primary production and characterized by a high proportion of endemic, specially adapted species. Vent communities can be unstable depending on the geological setting, as the underlying geofluid supply may change in location and chemical composition over a decadal...

Despite significant advances in phylogenetics over the past decades, the deep relationships within Bivalvia (phylum Mollusca) remain inconclusive. Previous efforts based on morphology or several genes have failed to resolve many key nodes in the phylogeny of Bivalvia. Advances have been made recently using transcriptome data, but the phylogenetic r...

Cold seeps, where geofluids containing methane and other hydrocarbons originating from the subseafloor seeps through the sediment surface, play important roles in the elemental and energy flux between sediment and seawater. These seep sites often harbor communities of endemic animals supported by chemolithoautotrophic bacteria, either through symbi...

The Event‐based Vision Sensor (EVS) is a bio‐inspired sensor that captures detailed motions of objects, aiming to become the ‘eyes’ of machines like self‐driving cars. Compared to conventional frame‐based image sensors, the EVS has an extremely fast motion capture equivalent to 10,000‐fps even with standard optical settings, plus high dynamic range...

Background Discoveries of new species often depend on one or a few specimens, leading to delays as researchers wait for additional context, sometimes for decades. There is currently little professional incentive for a single expert to publish a stand-alone species description. Additionally, while many journals accept taxonomic descriptions, even sp...

Phylogenomics has become a prominent method in systematics, conservation biology, and biomedicine, as it can leverage hundreds to thousands of genes derived from genomic or transcriptomic data to infer evolutionary relationships. However, obtaining high-quality genomes and transcriptomes requires samples preserved with high-quality DNA and RNA and...

Neogastropoda is a large order of predominantly marine gastropod molluscs, typically predatory or parasitic on other animals. It includes over 16,000 species representing a large post-Cretaceous radiation, but the internal phylogenetic relationships of contained taxa are far from resolved, with inconsistent results from nuclear genes, mitogenomes,...

Chemosynthetic ecosystems off Aotearoa/New Zealand comprise both hydrothermal vents on the Kermadec Arc and methane seeps on the Hikurangi Margin which host rich communities of specialized fauna including 4 alvinocaridid shrimp species. The systematic positions of these New Zealand alvinocaridid shrimps have not been studied using genetic tools and...

Caudofoveata is a class of worm-like molluscs (aplacophorans) that typically have an infaunal lifestyle, burrowing in soft bottoms in a wide range of marine habitats from shallow to deep waters. Here, we describe a very large new species of caudofoveate from South China Sea methane seeps growing up to 154 mm in length: Chaetoderma shenloong sp. nov...

Mao et al. (2024) recently published an article comparing the mitochondrial genome and transcriptome of the deep-sea hydrothermal vent barnacle Vulcanolepas fijiensis and the relatively shallower barnacle Scalpellum stearnsi (contradictory to the title, no new species was described). This paper concluded that the mitogenomes and key genes found in...

Monoplacophoran molluscs have been dubbed ‘living fossils’ due to their absence in the fossil record for about 375 million years, until Neopilina galatheae Lemche, 1957 was trawled off Costa Rica in 1952. Since then, over 35 species of living monoplacophorans have been discovered. Nevertheless, in situ observations of these rare deep-sea animals re...

Deep-sea chemosynthetic ecosystems are ‘oases’ of life powered by reducing geofluids, of which serpentinite-hosted seeps are among the least studied. South Chamorro Seamount, a serpentine mud volcano on the Mariana Arc, has been known to host chemosynthesis-based assemblages since 1996, but no detailed information on the fauna was published. Here,...

Deep‐sea hydrothermal vents host exceptional ecosystems with lush animal communities primarily relying on organic matter (OM) produced by chemoautotrophic microbes. Though energy sources and food webs at vents have been extensively studied, the exact carbon sources of chemosynthetic primary production, such as methane (CH4) and carbon dioxide (CO2)...

Deep-sea hydrothermal vents host chemosynthesis-based ecosystems inhabited chiefly by specially adapted animals that do not live anywhere else, and depth has been shown to be a major driver of species composition at vents around Japan. Though the Ryukyu region in southern Japan is home to many hot vents, only two – Minami-Ensei Knoll and Yoron Hole...

Oliver and Chen (2024) introduced the genus name Tartarothyas for a species of hadal bivalve (Thyasiroidea: Thyasiridae) from the Japan Trench. It has now come to our attention that Tartarothyas was already introduced for a genus of water mites (Acari: Hydrachnidia: Hydryphantidae) by Viets in 1934 with the type species T. micrommata Viets, 1934. T...

The hadal bivalves from the Japan Trench originally described as Maorithyas hadalis and Parathyasira kaireiae are reassigned to the genera Tartarothyas n. gen. and Spinaxinus, respectively. The shell, anatomy, and fine structure of the ctenidia are described, and based on these the new genus Tartarothyas is introduced. Both species have modified ct...

Chemosymbiosis is a highly successful strategy that evolved in several animal groups, best known for dominating chemosynthetic ecosystems such as deep-sea hot vents and hydrocarbon seeps but also found in other systems such as reducing sediments in shallow water. The symbiont population structure can be determined by the host genetic inheritance, g...

The sighting of giant bivalves and tubeworms at the Rose Garden vent field on the Galápagos Rift in 1977 marked the discovery of hydrothermal vents, a turning point for modern biology. The following decade saw a flurry of taxonomic descriptions of vent endemic species from the first vents. With the finding of high-temperature "black smokers" on the...

A new species of alvinocaridid shrimp is reported, from the Northwest Eifuku hydrothermal vent field at 1619–1667 m depth on the Mariana Arc. A comprehensive phylogenetic reconstruction of Alvinocarididae based on the mitochondrial cytochrome c oxidase subunit I (COI) gene including this new species reveals the paraphyly of the genus Rimicaris Will...

Deep-sea chemosynthetic ecosystems harbour high biomass centred around animals with chemoautotrophic symbionts. Despite being intensively studied over the last 4 decades, microscopic animals associated with and/or parasitic on dominating holobionts remain understudied. Here, we combine bulk tissue isotope analysis for carbon and nitrogen and compou...

Since their discovery in 1977, animals specialized to life in active deep-sea hydrothermal vents have been the focus of many studies. Inactive spires in the vent periphery, however, have received little attention. Recent shifts of deep-sea mining interests from active vents to inactive sulphide deposits have led to an urgent need to characterize th...

Biological clocks are a ubiquitous feature of all life, enabling the use of natural environmental cycles to track time. Although studies on circadian rhythms have contributed greatly to the knowledge of chronobiology, biological rhythms in dark biospheres such as the deep sea remain poorly understood. Despite a lack of day-night cycles, the deep se...

Neomphalida is an order of gastropod molluscs with highly diverse morphology and a global distribution across various chemosynthesis-based ecosystems from organic falls to hot vents. The phylogenetic relationships of taxa within this order remain contentious, due to the rarity of material leading to a low taxonomic coverage and few genetic markers...

Plant remains from land, particularly sunken wood, represent significant input of organic matter into the generally oligotrophic deep sea, leading to the formation of macrofaunal assemblages around them. Following the onset of decomposition by wood-boring bivalves, microbes and fungi the wood eventually becomes an anoxic and reducing environment at...

Most animal species have a singular developmental pathway and adult ecology, but developmental plasticity is well-known in some such as honeybees where castes display profoundly different morphology and ecology. An intriguing case is the Atlantic deep-sea hydrothermal vent shrimp pair Rimicaris hybisae and R. chacei that share dominant COI haplotyp...

Most animal species have a singular developmental pathway and adult ecology, but developmental plasticity is well-known in some such as honeybees where castes display profoundly different morphology and ecology. An intriguing case is the Atlantic deep-sea hydrothermal vent shrimp pair Rimicaris hybisae and R. chacei that share dominant COI haplotyp...

The sighting of giant bivalves and tubeworms at the Rose Garden vent field on the Galápagos Rift in 1977 marked the discovery of hydrothermal vents, a turning point for modern biology. The following decade saw a flurry of taxonomic descriptions of vent endemic species from the first vents. With the finding of high-temperature ‘black smokers’ on the...

Aim Deep‐sea hydrothermal vent habitats support a low‐diversity fauna in which most species are unique to the ecosystem. To inform conservation planning around this vulnerable marine ecosystem, we examine species distributions over a wide area to assess the underlying beta‐diversity components and to examine biogeographic patterns. We assess the co...

Patellogastropoda, or the true limpets, is a major group of gastropods widely distributed in marine habitats from the intertidal to deep sea. Though important for understanding their evolutionary radiation, the phylogenetic relationships among the patellogastropod families have always been challenging to reconstruct, with contradictory results like...

Information on genetic divergence and migration patterns of vent- and seep-endemic macrobenthos can help delimit biogeographical provinces and provide scientific guidelines for deep-sea conservation under the growing threats of anthropogenic disturbances. Nevertheless, related studies are still scarce, impeding the informed conservation of these ho...

Monoplacophoran molluscs have been dubbed "living fossils" due to their absence in the fossil record for about 375 million years, until Neopilina galatheae Lemche, 1957 was trawled off Costa Rica in 1952. Since then, over 35 species of living monoplacophorans have been discovered. Nevertheless, in situ observations of these rare deep-sea animals re...

Lepidonotopodinae is a subfamily of Polynoidae endemic to deep-sea chemosynthetic ecosystems around the world. Nevertheless, their species composition and phylogeny have only been systematically studied in hydrothermal vents of the Eastern and Western Pacific. Here, we morphologically and genetically examined worms in Lepidonotopodinae from vents a...

Deep-sea chemosynthetic communities, including hydrothermal vents and cold seeps, harbour hundreds of endemic species currently threatened by deep-sea mining and hydrocarbon extraction. The South China Sea (SCS), a semi-enclosed marginal sea with two well-investigated active seeps (Haima in the west and Site F in the east), provides an opportunity...

The intra-host composition of horizontally transmitted microbial symbionts can vary across host populations due to interactive effects of host genetics, environmental, and geographic factors. While adaptation to local habitat conditions can drive geographic subdivision of symbiont strains, it is unknown how differences in ecological characteristics...

Understanding how animals evolve to become parasites is key to unravelling how biodiversity is generated as a whole, as parasites could account for half of all species richness. Two significant impediments to this are that parasites fossilize poorly and that they retain few clear shared morphological features with non-parasitic relatives. Barnacles...

Deep-sea polynoid scale worms endemic to hydrothermal vents have evolved an adaptive strategy to the chronic hypoxic environment, but its underlying molecular mechanisms remain elusive. Here, we assembled a chromosome-scale genome of a vent-endemic scale worm Branchipolynoe longqiensis (first annotated genome in the subclass Errantia) and annotated...

Most animal species have a singular developmental pathway and adult ecology, but developmental plasticity is well-known in some like honeybees where castes display profoundly different morphology and ecology. An intriguing case is the Atlantic deep-sea hydrothermal vent shrimp Rimicaris hybisae/chacei that share dominant COI haplotypes but develops...

Lakes of molten sulfur are features sometimes found in seafloor hydrothermal vent systems. Daikoku of the northern Mariana Arc is notable for being home to one of such features inside its summit caldera, the “Sulfur Cauldron” discovered in 2006. A number of oceanographic research cruises since then have revealed significant volcanic activities on D...

Chemosynthetic ecosystems powered by microbial primary production are rare ‘hot spots’ of biological activity in the deep-sea characterized by dense aggregations of specially adapted animal species. Among settings where such systems have been found, serpentinite-hosted seep systems supported by alkaline geofluid are particularly understudied with j...

Increasing complexity and specialisation of modern sciences has led to increasingly collaborative publications, as well as the involvement of commercial services. Modern integrative taxonomy likewise depends on many lines of evidence and is increasingly complex, but the trend of collaboration lags and various attempts at ‘turbo taxonomy’ have been...

Neolepetopsidae is a little-studied true limpet family only known from deep-sea chemosynthetic ecosystems, containing just over a dozen species in three genera: Neolepetopsis, Paralepetopsis, and Eulepetopsis. Although considered monophyletic by a recent phylogenetic analysis, a lack of Paralepetopsis sequence linked to morphology casts some uncert...

Alvinocaridid shrimps are endemic and globally widespread in chemosynthetic ecosystems such as hydrothermal vents and hydrocarbon seeps. Though the biology of Atlantic alvinocaridid species have received considerable attention, little is known about their Pacific relatives. Here we described population structures and reproductive biology of three P...

Recovery of samples from the deep ocean in pristine condition is difficult due to large environmental differences between the deep and surface waters through which the samples necessarily must be transported. Here, we propose a concept for deep-sea sample recovery: a deep-sea freezer using thermoelectric cooling capable of generating ice in the dee...

Deep-sea hydrothermal vents host many endemic species adapted to these chemosynthesis-based ecosystems. The exploration of vent fields including those in the tropical Pacific is currently accelerating, due to the development of deep-sea mining for valuable minerals. Molecular evidence has shown that many vent endemic gastropod lineages include sibl...

1 | INTRODUC TI ON Animals make burrows and nests for shelter, hibernation, reproduction , food storage, and other reasons. Some organisms build complex and (relatively) colossal structures, such as termite nests and beaver dams, which reveal their engineering capabilities and intricate social lives. These are not only important for the makers: sec...

Ancient DNA (aDNA) from mollusc shells is considered a potential archive of historical biodiversity and evolution. However, such information is currently lacking for mollusc shells from the deep ocean, especially those from acidic chemosynthetic environments theoretically unsuitable for long-term DNA preservation. Here, we report on the recovery of...

The abyssal plains are vast areas without large scale relief that occupy much of the ocean floor. Although long considered relatively featureless, they are now known to display substantial biological heterogeneity across different spatial scales. Ecological research in these regions benefits increasingly from non-destructive visual sampling of epif...

The monotypic Enypniastes eximia is distributed worldwide, mainly in warm water regions. Here, we report the northernmost seabed sighting of this species to the Aleutian Trench off Alaska in the northeast Pacific. This represents a significant northern range extension especially for the Pacific. During the recent “AleutBio” expedition on board RV S...

The Event-based Vision Sensor (EVS) is a bio-inspired sensor that captures detailed motions of objects, developed with the applicability to become the eyes of machines and especially self-driving cars. Compared to conventional frame-based image sensors as employed in video cameras, EVS has an extremely fast motion capture equivalent to 10,000-fps e...

The distribution of species among spatially isolated habitat patches supports regional biodiversity and stability, so understanding the underlying processes and structure is a key target of conservation. Although multivariate statistics can infer the connectivity processes driving species distribution, such as dispersal and habitat suitability, the...

World leaders and representatives of 196 contracting states are joining the 15th Conference of the Parties (COP15) to the Convention on Biological Diversity (CBD) in Montréal to discuss strategies to stem global biodiversity loss. Worldwide, one million species are currently threatened with extinction from increasing anthropogenic impacts. Recently...

Gastropoda is the most speciose class in Mollusca, the second largest animal phylum. The internal relationships of major gastropod groups remain largely unsettled, partly due to the insufficient data from key deep-water endemic lineages such as the subclass Neomphaliones. Neomphaliones currently includes two orders: Cocculinida, best known from sun...

Deep-sea hydrothermal vents host lush chemosynthetic communities, dominated by endemic fauna that cannot live in other ecosystems. Despite over 500 active vents found worldwide, the Arctic has remained a little-studied piece of vent biogeography. Though located as early as 2001, the faunal communities of the Aurora Vent Field on the ultra-slow spre...

Chitin is a key component of hard parts in many organisms, but the biosynthesis of the two distinctive chitin allomorphs, α- and β-chitin, is not well understood. The accurate determination of chitin allomorphs in natural biomaterials is vital. Many chitin-secreting living organisms, however, produce poorly crystalline chitin. This leads to spectru...

Scanning electron microscopy operated at cryogenic temperature (cryo-SEM) is a powerful tool for investigating surface and cross-sectional nanostructures of water-containing samples. Typically, cryo-SEM samples are frozen just before observation in specific metal carriers. However, pre-frozen samples are also of interest, such as frozen food and fr...

The intra-host composition of horizontally transmitted microbial symbionts can vary across host populations due to interactive effects of host genetic, environmental and geographic factors. While adaptation to local habitat conditions can drive geographic subdivision of symbiont strains in autotrophic symbioses, little is known about the processes...

The hadal amphipod Hirondellea gigas is an emblematic animal of the Pacific trenches, and has a number of special adaptations to thrive in this ‘extreme’ environment, which includes the deepest part of the Earth’s ocean. One such adaptation that has been suggested is the presence of an ‘aluminum gel shield’ on the surface of its body in order to pr...

The deep ocean is Earth’s largest habitable space inhabited by diverse benthic organisms. Infauna play crucial roles in shaping sedimentary structures, relocating organic matter, porewater chemistry, and hence biogeochemical cycles. However, the visualization and quantification of infauna in situ inside deep-sea sediment has been challenging, due t...

The distribution of species among spatially isolated habitat patches supports regional biodiversity and stability, so understanding the underlying processes and structure is a key target of conservation. Although multivariate statistics can infer the connectivity processes driving species distribution, such as dispersal and habitat suitability, the...

Variations in offspring production according to feeding strategies or food supply have been recognized in many animals from various ecosystems. Despite an unusual trophic structure based on non-photosynthetic primary production, these relationships remain largely under-studied in chemosynthetic ecosystems. Here, we use Rimicaris shrimps as a study...

Gastropods in the family Provannidae are characteristic members of deep-sea chemosynthesis-based communities. Recently, surveys of hydrothermal vents and hydrocarbon seeps in the western Pacific have revealed a high diversity of provannids, with new discoveries continuing to be made. Here, we report and describe a further new species, Provanna exqu...