Gallery of Publications – Dr. Chong CHEN

$We developed a novel adhesive for electron microscopy under cryogenic conditions, and as a bonus applied it to study why the shell of the deep-sea margaritid snail Margarites shinkai exhibits a brilliant prismatic purplish luster! Just published in Microscopy and Microanalysis, OPEN ACCESS: https://www.cambridge.org/core/journals/microscopy-and-microanalysis/article/novel-cryogenic-adhesive-retaining-fluidity-at-dryice-temperature-for-lowtemperature-scanning-electron-microscopy/75EA072DFE288395A15ED2D3CB9BA37D Abstract: 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 freeze-stored animal samples. In such cases, sample mounting with a defined orientation is required, but there has been a lack of ideal conductive adhesives that can be used without increasing the sample temperature. Here, we developed a mixture of graphite oxide and 1,3-butanediol as an adhesive, capable of gluing samples at dry-ice temperature and is frozen below that temperature. Dispersion of graphite oxide increased the conductivity and reduced the charge-up contrast. Acquisition of energy-dispersive X-ray spectrum, cross-sectional ion milling, and high-resolution imaging were successfully achieved using the adhesive. We tested and confirmed the usefulness of this new adhesive by applying it to cryo-SEM surface imaging of diatomite, freeze-fractured cross-sectional imaging of chicken liver, and ion milling cross-sectional imaging of a deep-sea snail. The new adhesive is not only useful for food science and field-preserved biological samples but also potentially applicable to wider fields such as archaeological and biological samples preserved under permafrost. Okada S*, Chen C (2022). A novel cryogenic adhesive retaining fluidity at dry-ice temperature for low-temperature scanning electron microscopy. Microscopy and Microanalysis, First View. DOI: 10.1017/S1431927622012296$

In 2019, a paper proposed the hadal amphipod Hirondellea gigas possesses an "aluminium armour" to help tolerate the extreme water pressure. We now show, in a new paper in PLOS ONE led by Satoshi Okada, that this is not true – their signals were mostly artifacts from aluminium stubs etc., while some were actually bromine found to accumulate on certain parts of the animal! OPEN ACCESS: https://dx.plos.org/10.1371/journal.pone.0272032<br />
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Abstract:<br />
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 prevent the dissolution of calcitic exoskeleton below the carbonate compensation depth. However, this has not been investigated under experimental conditions that sufficiently prevent aluminum artefacts, and the possibility of other elements with similar characteristic X-ray energy as aluminum (such as bromine) has not been considered. Here, we show with new electron microscopy data gathered under optimized conditions to minimize aluminum artefacts that H. gigas actually does not have an aluminum shield–instead many parts of its body are enriched in bromine, particularly gastric ossicles and setae. Results from elemental analyses pointed to the use of calcite partially substituted with magnesium by H. gigas in its exoskeleton, in order to suppress dissolution. Our results exemplify the necessity of careful sample preparation and analysis of the signals in energy-dispersive X-ray spectroscopic analysis, and the importance of analyses at different electron energies.<br />
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Okada S*, Chen C, Watanabe HK, Isobe N, Takai K (2022). Unusual bromine enrichment in the gastric mill and setae of the hadal amphipod Hirondellea gigas. PLOS ONE, 17(8): e0272032. DOI: 10.1371/journal.pone.0272032

Introducing deep-sea ‘acoustic coring’, which allows us to visualise animals living inside the sediment in 3D using ultrasound reflections! Our newly developed tool is now published in Scientific Reports, OPEN ACCESS: https://www.nature.com/articles/s41598-022-16356-3<br />
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Abstract:<br />
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 to their sparse distribution and that deep-sea cameras do not visualize animals living below the sediment surface. Here, we newly developed a 3D acoustic “coring” system and applied it to visualize and detect burrowing bivalves in deep-sea sediments. The in situ acoustic observation was conducted at a dense colony of vesicomyid clams in a hydrocarbon seep in Sagami Bay, Japan, focusing on a patch of juvenile clams with a completely infaunal life style. We clearly observed strong backscatters from the top and lower edges of animals in our 3D acoustic data. At least 17 reflectors were identified in the survey area (625 cm2), interpreted to correspond to living clams. The estimated depths of the lower edge of clams ranged between 41 and 98 mm. The acoustic system presented here is effective for detecting and monitoring infauna with calcified exoskeletons. This novel tool will help us better assess and understand the distribution of deep-sea infauna, particularly those groups with hard exoskeletons, as well as biogeochemical cycles.<br />
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Mizuno K*, Nomaki H, Chen C, Seike K (2022). Deep-sea infauna with calcified exoskeletons imaged in situ using a new 3D acoustic coring system (A-core-2000). Scientific Reports, 12: 12101. DOI: 10.1038/s41598-022-16356-3

Our paper in Ecology and Evolution led by Pierre Methou examined reproductive traits of Rimicaris vent shrimps, compiling data from cruises over the last 35 years. We found that diet (i.e. different levels of reliance on symbiosis) impacts reproduction – and surprisingly, a similar rhythm for shrimps from both northern and southern hemispheres, rejecting the usual assumption that such periodicity is linked to surface productivity patterns. The paper is OPEN ACCESS: https://doi.org/10.1002/ece3.9076 <br />
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Abstract<br />
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 case to explore relationships between reproduction, diets, and food supply in these environments. For that, we compared reproductive outputs of three congeneric shrimps differing by their diets. They inhabit vents located under oligotrophic waters of tropical gyres with opposed latitudes, allowing us to also examine the prevalence of phylogenetic vs environmental drivers in their reproductive rhythms. For this, we used both our original data and a compilation of published observations on the presence of ovigerous females covering various seasons over the past 35 years. We report distinct egg production trends between Rimicaris species relying solely on chemosymbiosis—R. exoculata and R. kairei—and one relying on mixotrophy, R. chacei. Besides, our data suggest a reproductive periodicity that does not correspond to seasonal variations in surface production, with substantial proportions of brooding females during the same months of the year, despite those months corresponding to either boreal winter or austral summer depending on the hemisphere. These observations contrast with the long-standing paradigm in deep-sea species for which periodic reproductive patterns have always been attributed to seasonal variations of photosynthetic production sinking from the surface. Our results suggest the presence of an intrinsic basis for biological rhythms in the deep sea, and bring to light the importance of having year-round observations in order to understand the life history of vent animals.<br />
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Methou P*, Chen C, Watanabe HK, Cambon M-A, Pradillon F* (2022). Reproduction in deep-sea vent shrimps is influenced by diet, with rhythms apparently unlinked to surface production. Ecology and Evolution, 12: e9076. DOI: 10.1002/ece3.9076 [Preprint available on bioRxiv, DOI: 10.1101/2021. 09.10.456763]

Meet Provanna exquisita Chen & Watanabe, 2022 – a new provannid snail from the Northwest Eifuku volcano, Mariana Arc just published in ZooKeys! It has a strong latticed sculpture characterised by very prominent raised spiral keels that distinguishes it from all other described Provanna species. The paper is OPEN ACCESS: http://dx.doi.org/10.3897/zookeys.1112.85950<br />
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Abstract:<br />
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 exquisita sp. nov., discovered from the Northwest Eifuku volcano on the Mariana Arc. This new species is distinguished from all other described Provanna species by its exaggerated sculpture characterised by two to three sharply raised, flange-like keels on the teleoconch whorls. The status of P. exquisita sp. nov. is also supported by a molecular phylogeny reconstruction using the mitochondrial cytochrome c oxidase subunit I (COI) gene, which suggested that it is most closely related to a clade of three species described from Okinawa Trough vents including P. clathrata, P. subglabra, and P. fenestrata. Despite being one of the better-explored regions of the world in terms of hydrothermal vent biodiversity, new discoveries like P. exquisita sp. nov. continue to remind us that we are nowhere near fully documenting the species diversity in these unique ecosystems—despite the species being threatened from imminent anthropogenic impacts such as deep-sea mining.<br />
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Chen C*, Watanabe HK (2022). A new provannid snail discovered from Northwest Eifuku Volcano, Mariana Arc. ZooKeys, 1112(5): 123-137. DOI: 10.3897/zookeys.1112.85950

The Scaly-foot Snail (Chrysomallon squamiferum) known for its iron-infused scales is endemic to deep-sea hydrothermal vents and relies on symbionts for energy. In a new paper led by Yi Lan just out in The ISME Journal, we show that it is likely capable of using maternal transmission to pass down the symbionts, in addition to environmental acquisition as previously thought. Furthermore, the snail host buffers the symbionts against differences in the environmental conditions across vent fields, providing them with a stable habitat in their own cells. The paper is OPEN ACCESS: https://www.nature.com/articles/s41396-022-01261-4<br />
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ABSTRACT <br />
The scaly-foot snail (Chrysomallon squamiferum) inhabiting deep-sea hydrothermal vents in the Indian Ocean relies on its sulphur-oxidising gammaproteobacterial endosymbionts for nutrition and energy. In this study, we investigate the specificity, transmission mode, and stability of multiple scaly-foot snail populations dwelling in five vent fields with considerably disparate geological, physical and chemical environmental conditions. Results of population genomics analyses reveal an incongruent phylogeny between the endosymbiont and mitochondrial genomes of the scaly-foot snails in the five vent fields sampled, indicating that the hosts obtain endosymbionts via horizontal transmission in each generation. However, the genetic homogeneity of many symbiont populations implies that vertical transmission cannot be ruled out either. Fluorescence in situ hybridisation of ovarian tissue yields symbiont signals around the oocytes, suggesting that vertical transmission co-occurs with horizontal transmission. Results of in situ environmental measurements and gene expression analyses from in situ fixed samples show that the snail host buffers the differences in environmental conditions to provide the endosymbionts with a stable intracellular micro-environment, where the symbionts serve key metabolic functions and benefit from the host’s cushion. The mixed transmission mode, symbiont specificity at the species level, and stable intracellular environment provided by the host support the evolutionary, ecological, and physiological success of scaly-foot snail holobionts in different vents with unique environmental parameters.<br />
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Lan Y, Sun J, Chen C, Wang H, Xiao Y, Perez M, Yang Y, Kwan YH, Sun Y, Zhou Y, Han X, Miyazaki J, Watsuji T-o, Bissessur D, Qiu J-W, Takai K, Qian P-Y* (2022). Endosymbiont population genomics sheds light on transmission mode, partner specificity, and stability of the scaly-foot snail holobiont. The ISME Journal. DOI: 10.1038/s41396-022-01261-4

$The Scaly-foot Snail (Chrysomallon squamiferum) is a species well-known for having imbricating hard scales on its foot, but the composition of the scales has remained unclear, with the hypothesis being it is entirely proteinaceous. In a paper published in Journal of The Royal Society Interface, we combined various analytical methods to analyse the scale, revealing that it uses β-chitin nanofibers as the building framework. The paper is OPEN ACCESS: https://doi.org/10.1098/rsif.2022.0120 Abstract Organisms use various forms and orientations of chitin nanofibers to make structures with a wide-range of functions, from insect wings to mussel shells. Lophotrochozoan animals such as snails and annelid worms possess an ancient ‘biomineralization toolkit’, enabling them to flexibly and rapidly evolve unique hard parts. The Scaly-foot Snail is a gastropod endemic to deep-sea hydrothermal vents, unique in producing dermal sclerites used as sites of sulfur detoxification. Once considered to be strictly proteinaceous, recent data pointed to the presence of chitin in these sclerites, but direct evidence is still lacking. Here, we show that β-chitin fibres (~5% of native weight) is indeed the building framework, through a combination of solid-state NMR, wide-angle X-ray diffraction, and electron microscopy. The fibres are uniaxially oriented, likely forming a structural basis for column-like channels into which the scaly-foot snail is known to actively secrete sulfur waste – expanding the known function of chitinous hard parts in animals. Our results add to the existing evidence that animals are capable of modifying and co-opting chitin synthesis pathways flexibly and rapidly, in order to serve novel functions during their evolution. Isobe N, Chen C, Daicho K, Saito T, Bissessur D, Takai K, Okada S* (In press). Uniaxial orientation of β-chitin nanofibres used as an organic framework in the scales of a hot vent snail. Journal of the Royal Society Interface. DOI: 10.1098/rsif.2022.0120$

A new co-authored paper led by Naoto Jimi is now out in Zootaxa! Meet Branchinotogluma nikkoensis Jimi, Chen & Fujiwara, 2022 and Branchinotogluma sagamiensis Jimi, Chen & Fujiwara, 2022 -- two new scale-worm species from Japan collected from Nikko Seamount vent in the northern Mariana Arc and the Off Hatsushima seep in Sagami Bay! Link to paper: https://doi.org/10.11646/zootaxa.5138.1.2<br />
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Abstract: <br />
The widely distributed polychaete family Polynoidae Kinberg, 1856 is found across all oceans and from shallow to deep waters, including deep-sea hydrothermal vents and hydrocarbon seeps. Taxa inhabiting chemosynthesis-based ecosystems are often endemic to those specific habitats commonly targeted by deep-sea mining, and understanding their species diversity is essential for shaping conservation plans. Here, we report two previously undescribed scale-worms in the genus Branchinotogluma Pettibone, 1985 from the Off Hatsushima hydrocarbon seep of Sagami Bay and the Nikko Seamount hydrothermal vent on the Izu-Ogasawara Arc, and describe them as B. nikkoensis sp. nov. and B. sagamiensis sp. nov. Branchinotogluma nikkoensis sp. nov. is distinguished from the known species by the following characters: i) ventral segmental lamellae near ventral bases of neuropodia present on segments 13–17, ii) dorsal tentacular cirri being longer than ventral tentacular cirri, iii) absence of dorsal tubercles. Branchinotogluma sagamiensis sp. nov. can be differentiated from other congeners by i) 20 segments, ii) dorsal tentacular cirri being longer than ventral tentacular cirri, iii) ventral segmental lamellae near ventral bases of neuropodia present on segments 13–18, and iv) thin median antennae. The two new species are distinct in both morphology and four gene sequences from the only two species previously known from Japan including Branchinotogluma japonicus (Miura & Hashimoto, 1991) and B. elytropapillata Zhang, Chen & Qiu, 2018, originally described from Kaikata Seamount vent on the Izu-Ogasawara Arc and Okinawa Trough, respectively. <br />
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Jimi N*, Chen C, Y Fujiwara (2022). Two new species of Branchinotogluma (Polynoidae: Annelida) from chemosynthesis-based ecosystems in Japan. Zootaxa, 5138(1): 17-30. DOI: 10.11646/zootaxa.5138.1.2

Just published in Diversity & Distributions, a new paper co-led by Yadong Zhou and myself identified 3 biogeographic regions of Indian Ocean hot vents supported by species composition, population genetics, and β-diversity clustering. As this region is targeted for deep-sea mining by four countries, this result has significant conservation implications for these unique habitats. The paper is OPEN ACCESS: https://doi.org/10.1111/ddi.13535<br />
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Abstract <br />
The pattern of biodiversity and biogeography is crucial to informing management and conservation strategy. But a lack of study across multiple ridge systems, especially for the Carlsberg Ridge, has hampered the conception of the overall picture for the Indian Ocean vents, a top target for deep-sea exploration of massive sulphides. Here, we aim to characterize fauna from three new vent fields on the Carlsberg Ridge (CR) for the first time, in combination with data from vents on the Central Indian Ridge (CIR), and Southwest Indian Ridge (SWIR), to answer 1) what is the biogeographic pattern for vent fauna within the Indian Ocean and 2) how does this pattern guide the future environmental management on the Indian Ocean ridges. Samples, still images and videos were collected from vent fields by either submersible or TV-guided grab. A comprehensive dataset of 11 fields on Indian Ocean ridges were obtained based on taxa identification and compilation. Genetic connectivity was analysed for six species using COI sequences. A framework for identifying biogeographic regions based on beta diversity measurement βsim was employed to reveal species turnover along the Indian Ocean ridges. Faunal assemblages at three new vents on the CR hosted a total of 34 species. Significant genetic differentiation was detected between southern SWIR and CIR (plus Tiancheng) for three species, and between CIR (plus Tiancheng) and CR for four species. Species turnover along the ridges supported the separation of Indian Ocean vents into three discrete biogeographic units, boundaries between which largely corresponded to genetic breaks for shared species with lower dispersal capabilities. The results clearly show that the conservation of Indian Ocean vents must target three provinces, simultaneously.<br />
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Zhou Y# / Chen C#, Zhang D, Wang Y, Watanabe HK, Sun J, Bissessur D, Zhang R, Han Y, Sun D, Xu P, Lu B, Zhai H, Han X, Tao C, Qiu Z, Sun Y, Liu Z, Qiu J-W, Wang C* (2022). Delineating biogeographic regions in Indian Ocean deep-sea vents and implications for conservation. Diversity and Distributions, Early View. DOI: 10.1111/ddi.13535

The Japanese research vessel Hakuho Maru has been in service since 1989 and has taken scientists on research cruises from waters around Japan all the way to the polar oceans. Between 2019 and 2020, she went on a round-the-world expedition to celebrate her 30th Anniversary. I joined a group of taxonomists to identify the benthic animals collected around Antarctica during these cruises, the result of which were published in the journal Polar Science! The paper is OPEN ACCESS: https://doi.org/10.1016/j.polar.2022.100846<br />
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Abstract <br />
The Southern Ocean is widely recognized for its unique benthic ecosystems, but benthic sampling has been largely restricted to shallower continental zones and much remains to be learned about biodiversity in the bathyal and abyssal zones. In this study, we collected and investigated the deep-sea benthic habitat using geological dredges, a multiple corer, and a bait trap on-board the R/V Hakuho Maru in bathyal to abyssal depths between the latitude of 39°38.16′S–66°36.03′S and the longitude of 62°19.55′W–67°37.95′E in the Southern Ocean and the surrounding subantarctic region, focusing on West Antarctica. We carried out 20 geological dredges, 14 multiple corers, and a bait trap survey. Here, we present the taxonomic and distributional description of 180 species of Annelida, Mollusca, Ostracoda, Decapoda, and Echinodermata identified from our samples, including species-level identifications where possible and detailed occurrence information. Although West Antarctica is the most highly investigated area for benthic biodiversity around Antarctica, our collection includes the annelid Flabelligena hakuhoae Jimi et al. 2020 which was new to science at the time of collection, and other potentially undescribed species of Annelida, Ostracoda, Asteroidea, and Holothuroidea. Several specimens collected updated the distribution ranges of their species.<br />
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Ogawa A*, Jimi N, Hiruta SF, Chen C, Kobayashi I, Pratama GA, Tanaka H, Okanishi M, Komatsu H, Ikehara M (2022). Taxonomy and distribution of deep benthos collected in and around the Southern Ocean during the 30th Anniversary Expeditions of R/V Hakuho Maru: Annelida, Mollusca, Ostracoda, Decapoda, and Echinodermata. Polar Science. DOI: 10.1016/j.polar.2022.100846

Hydrothermal vent shrimps in the genus Rimicaris are among the most charismatic deep-sea animals, often occurring on towering black smokers in dense aggregates of thousands of individuals. Although this dominance is only possible because of symbiosis, no study on the symbiosis of Indian Ocean Rimicaris species has been conducted. In a paper just out in Applied and Environmental Microbiology, we characterise the symbiosis of the Indian Ocean vent shrimp Rimicaris kairei for the first time by combining molecular, microscopic, and elemental analyses. The paper is OPEN ACCESS: https://journals.asm.org/doi/10.1128/aem.00185-22<br />
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Abstract<br />
Hydrothermal vent ecosystems are home to a wide array of symbioses between animals and chemosynthetic microbes, among which shrimps in the genus Rimicaris is one of the most iconic. So far, studies of Rimicaris symbioses have been restricted to Atlantic species, including Rimicaris exoculata, which is totally reliant on the symbionts for nutrition, and the mixotrophic species Rimicaris chacei. Here, we expand this by investigating and characterizing the symbiosis of the Indian Ocean species Rimicaris kairei using specimens from two vent fields, Kairei and Edmond. We also aimed to evaluate the differences in mineralogy and microbial communities between two cephalothorax color morphs, black and brown, through a combination of 16S metabarcoding, scanning electron microscopy, fluorescent in situ hybridization, energy-dispersive X-ray spectroscopy, and synchrotron near-edge X-ray absorption structure analyses. Overall, our results highlight that R. kairei exhibits similar symbiont lineages to those of its Atlantic congeners, although with a few differences, such as the lack of Zetaproteobacteria. We found distinct mineralization processes behind the two color morphs that were linked to differences in the vent fluid composition, but the symbiotic community composition was surprisingly similar. In R. exoculata, such mineralogical differences have been shown to stem from disparity in the microbial communities, but our results indicate that in R. kairei this is instead due to the shift of dominant metabolisms by the same symbiotic partners. We suggest that a combination of local environmental factors and biogeographic barriers likely contribute to the differences between Atlantic and Indian Ocean Rimicaris symbioses.<br />
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Methou P*, Hikosaka M, Chen C, Watanabe HK, Miyamoto N, Makita H, Jenkins RG (2022). Symbiont community composition in Rimicaris kairei shrimps from Indian Ocean vents with notes on mineralogy. Applied and Environmental Microbiology. DOI: 10.1128/aem.00185-22

In deep-sea hot vents of Okinawa, we found some Shinkaia crosnieri – a squat lobster known for ‘farming’ symbiotic bacteria on its ‘chest’ for nutrition – with swollen carapace. Opening up these squat lobsters revealed a parasitic isopod of the superfamily Bopyroidea that has never been seen at vents before! And it’s a new species, now described as Pleurocryptella shinkai after the Japanese submersibles DSV Shinkai 2000 and DSV Shinkai 6500. Paper available here: https://doi.org/10.2108/zs210117<br />
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Abstract: <br />
Deep-sea hydrothermal vents are ‘extreme’ environments harboring diverse animal communities, powered by chemosynthesis. Though vent-endemic macrofauna have been a center of interest since their discovery in 1977, macroparasites have received little attention. Here, we report a bopyrid epicaridean isopod infesting the symbiotic munidopsid squat lobster Shinkaia crosnieri Baba and Williams, 1998 from three vent fields of Okinawa Trough, and describe it as Pleurocryptella shinkai sp. nov. Although morphologically close to the congeners Pleurocryptella formosa Bonnier, 1900, Pleurocryptella wolffi Bourdon, 1972, and Pleurocryptella altalis Williams, Boyko, and Marin, 2020, both females (via body proportion and characters of barbula, antennae, pleopods, and pleomeres) and males (via features of the head, pleomeres, and uropods) of the new species exhibit distinctive characters. Phylogenetic reconstruction based on the 18S rRNA gene (850 bp) was insufficiently resolved to clarify the relationship of different epicaridean lineages or the exact position of P. shinkai sp. nov., but it recovered P. shinkai sp. nov. in a distant position from the type genus of Pseudioninae, indicating non-monophyly of this subfamily. Crustaceans are successful in vents but this is only the second vent epicaridean reported, after Thermaloniscus cotylophorus Bourdon, 1983 from the East Pacific Rise described from a single cryptoniscus larva. As such, this is the first report of a vent bopyrid isopod and the first vent epicaridean with a known host. Some epicaridean lineages have adapted to tolerating the conditions of hydrothermal vents, and future research will likely uncover more epicarideans and other interesting parasites from these extreme habitats. <br />
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Kato N# / Chen C#*, Watanabe HK, Yamamoto M, Shimomura M (2022). The first deep-sea bopyrid isopod from hydrothermal vents: Pleurocryptella shinkai sp. nov. (Isopoda: Bopyridae) parasitizing Shinkaia crosnieri. Zoological Science, 39(3). DOI: 10.2108/zs210117

I joined a group of researchers, led by Diva Amon, to highlight scientific gaps that we need to fill to make evidence-based decisions about the deep sea. We've made incredible progress in building our knowledge about life in the deep ocean, but our study published in Marine Policy shows how far we still have to go to make evidence-based decisions to protect the deep sea from seabed mining’s impacts. This comes at a crucial time, as the International Seabed Authority could finalize regulations that would allow deep-sea mining to begin as soon as July 2023. Our new paper can help policymakers make evidence-based decisions to protect the ocean's depths. The paper is OPEN ACCESS: https://doi.org/10.1016/j.marpol.2022.105006<br />
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Abstract: <br />
A comprehensive understanding of the deep-sea environment and mining’s likely impacts is necessary to assess whether and under what conditions deep-seabed mining operations comply with the International Seabed Authority’s obligations to prevent ‘serious harm’ and ensure the ‘effective protection of the marine environment from harmful effects’ in accordance with the United Nations Convention on the Law of the Sea. A synthesis of the peer-reviewed literature and consultations with deep-seabed mining stakeholders revealed that, despite an increase in deep-sea research, there are few categories of publicly available scientific knowledge comprehensive enough to enable evidence-based decision-making regarding environmental management, including whether to proceed with mining in regions where exploration contracts have been granted by the International Seabed Authority. Further information on deep-sea environmental baselines and mining impacts is critical for this emerging industry. Closing the scientific gaps related to deep-seabed mining is a monumental task that is essential to fulfilling the overarching obligation to prevent serious harm and ensure effective protection, and will require clear direction, substantial resources, and robust coordination and collaboration. Based on the information gathered, we propose a potential high-level road map of activities that could stimulate a much-needed discussion on the steps that should be taken to close key scientific gaps before any exploitation is considered. These steps include the definition of environmental goals and objectives, the establishment of an international research agenda to generate new deep-sea environmental, biological, and ecological information, and the synthesis of data that already exist.<br />
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Amon DJ*, Gollner S, Morato T, Smith CR, Chen C, Christiansen S, Currie B, Drazen JC, Fukushima T, Gianni M, Gjerde K, Gooday AJ, Grillo GG, Haeckel M, Joyini T, Ju S-J, Levin L, Metaxas A, Mianowicz K, Molodstova T, Narberhaus I, Orcutt B, Swaddling A, Tuhumwire J, Palacio PU, Walker M, Weaver P, Xu X-W, Mulalap CY, Edwards PET, Pickens C (2022). Assessment of scientific gaps related to the effective environmental management of deep-seabed mining. Marine Policy, Available Online: 105006. DOI: 10.1016/j.marpol.2022.105006

Our paper analysing the gut microbiome of the chemosymbiotic hot vent snail Alviniconcha marisinidica, led by Yang Yi, is now out in Animal Microbiome! We used genomic and transcriptomic methods to characterise the gut microbiota and investigated how these microbes may contribute to metabolism of the Alviniconcha symbiotic system as a whole. The paper is OPEN ACCESS and available for free: https://doi.org/10.1186/s42523-021-00150-z<br />
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Abstract: <br />
Marine animals often exhibit complex symbiotic relationship with gut microbes to attain better use of the available resources. Many animals endemic to deep-sea chemosynthetic ecosystems host chemoautotrophic bacteria endocellularly, and they are thought to rely entirely on these symbionts for energy and nutrition. Numerous investigations have been conducted on the interdependence between these animal hosts and their chemoautotrophic symbionts. The provannid snail Alviniconcha marisindica from the Indian Ocean hydrothermal vent fields hosts a Campylobacterial endosymbiont in its gill. Unlike many other chemosymbiotic animals, the gut of A. marisindica is reduced but remains functional; yet the contribution of gut microbiomes and their interactions with the host remain poorly characterised. Metagenomic and metatranscriptomic analyses showed that the gut microbiome of A. marisindica plays key nutritional and metabolic roles. The composition and relative abundance of gut microbiota of A. marisindica were different from those of snails that do not depend on endosymbiosis. The relative abundance of microbial taxa was similar amongst three individuals of A. marisindica with significant inter-taxa correlations. These correlations suggest the potential for interactions between taxa that may influence community assembly and stability. Functional profiles of the gut microbiome revealed thousands of additional genes that assist in the use of vent-supplied inorganic compounds (autotrophic energy source), digest host-ingested organics (carbon source), and recycle the metabolic waste of the host. In addition, members of five taxonomic classes have the potential to form slime capsules to protect themselves from the host immune system, thereby contributing to homeostasis. Gut microbial ecology and its interplay with the host thus contribute to the nutritional and metabolic demands of A. marisindica. The findings advance the understanding of how deep-sea chemosymbiotic animals use available resources through contributions from gut microbiota. Gut microbiota may be critical in the survival of invertebrate hosts with autotrophic endosymbionts in extreme environments. <br />
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Yang Y, Sun J, Chen C, Zhou Y, Van Dover CL, Wang C, Qiu J-W, Qian P-Y* (2022). Metagenomic and metatranscriptomic analyses reveal minor-yet-crucial roles of gut microbiome in deep-sea hydrothermal vent snail. Animal Microbiome, 4: 3. DOI: 10.1186/s42523-021-00150-z

New co-authored paper led by Elin Thomas out today in Conservation Biology! We applied the IUCN Red List to assess the extinction risks of molluscs endemic to hydrothermal vent ecosystems threatened by deep-sea mining, showing that robust and rapid assessments can be done even for data-limited species. The global recognition of the Red List is crucial in communicating the urgency of conserving vent endemic species. The same method used can be applied to other insular marine ecosystems. The paper is Open Access and can be accessed freely: https://conbio.onlinelibrary.wiley.com/doi/10.1111/cobi.13854<br />
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Abstract: <br />
Hydrothermal vents are rare deep-sea oases that house faunal assemblages with a similar density of life as coral reefs. Only approximately 600 of these hotspots are known worldwide, most only one-third of a football field in size. With advancing development of the deep-sea mining industry, there is an urgent need to protect these unique, insular ecosystems and their specialist endemic faunas. We applied the IUCN (International Union for the Conservation of Nature) Red List criteria to assess the extinction risk of vent-endemic molluscs with varying exposure to potential deep-sea mining. We assessed 31 species from three key areas under different regulatory frameworks in the Indian, West Pacific, and Southern Oceans. Three vent mollusc species were also examined as case studies of different threat contexts (protected or not from potential mining) to explore the interaction of local regulatory frameworks and IUCN Red List category assignment. We found that these assessments were robust even when there was some uncertainty in the total range of individual species, allowing assessment of species that have only recently been named and described. For vent-endemic species, regulatory changes to area-based management can have a greater impact on IUCN Red List assessment outcomes than incorporating additional data about species distributions. Our approach revealed the most useful IUCN Red List criteria for vent-endemic species: criteria B and D2. This approach, combining regulatory framework and distribution, has the potential to rapidly gauge assessment outcomes for species in insular systems worldwide.<br />
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Thomas EA*, Böhm M, Pollock C, Chen C, Seddon M, Sigwart JD (2021). Assessing the extinction risk of insular, under-studied marine species. Conservation Biology. DOI: 10.1111/cobi.13854

Our new paper on deep-sea true limpets in the enigmatic family Neolepetopsidae is now published in Zoological Journal of Linnean Society! In addition to describing three new species, we present the first molecular phylogeny that includes all genera in the family. This supported monophyly of the genera, and shed light on a potential ‘stepping-stone’ evolutionary pathway from organic falls to hot vents in the family. The paper is available here: https://academic.oup.com/zoolinnean/advance-article-abstract/doi/10.1093/zoolinnean/zlab081/6408716<br />
Please let me know if you would like a PDF copy. <br />
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Abstract<br />
Neolepetopsidae is a family of true limpets restricted to deep-sea chemosynthesis-based ecosystems. It is a small and little-studied family with about a dozen species in three genera, namely Eulepetopsis, Neolepetopsis and Paralepetopsis, and all named species were from the Pacific or Atlantic Oceans. Here, we describe three new species from Indian Ocean vents, namely Eulepetopsis crystallina sp. nov. found across three ridges, Neolepetopsis ardua sp. nov. from the Southwest Indian Ridge and Neolepetopsis prismatica sp. nov. from the Carlsberg Ridge. Given that Neolepetopsis appears to specialize on inactive sulfide deposits, the apparent wider distribution of E. crystallina is probably attributable to bias in sampling effort at inactive chimneys. The molecular phylogeny of Patellogastropoda, reconstructed using the COI gene, supported the monophyly of Neolepetopsidae. These are the first molecular data available for Neolepetopsis, confirming that the three genera are genetically distinct. Eulepetopsis appears to be adapted to active vents, and its derived position compared with Paralepetopsis indicates a possible ‘stepping-stone’ evolutionary pathway from seeps and organic falls to vents. Our results provide new insights into this enigmatic family and highlight the importance of surveying the vent periphery, especially given that inactive vents are being eyed as a replacement for active ones in deep-sea mining.<br />
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Chen C*, Zhou Y*, Watanabe HK, Zhang R, Wang C (2021). Neolepetopsid true limpets (Gastropoda: Patellogastropoda) from Indian Ocean hot vents shed light on relationships among genera. Zoological Journal of the Linnean Society, zlab081. DOI: 10.1093/zoolinnean/zlab081

Our new paper in Molecular Biology and Evolution led by Ting Xu unravels demographic history and population connectivity of the deep-sea limpet Bathyacmaea nipponica across hot vents and cold seeps, using a genome-wide set of genetic markers consisting of nearly 10000 single nucleotide polymorphisms (SNPs) and supplemented by physical ocean modeling! The paper is *open access* and available for free here: https://doi.org/10.1093/molbev/msab278<br />
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Abstract: <br />
Hydrothermal vents and hydrocarbon seeps in the deep ocean are rare oases fueled by chemosynthesis. Biological communities inhabiting these ecosystems are often distributed in widely separated habitats, raising intriguing questions on how these organisms achieve connectivity and whether habitat types facilitate intraspecific divergence. The deep-sea patellogastropod limpet Bathyacmaea nipponica that colonizes both vents and seeps across ∼2,400 km in the Northwest Pacific is a feasible model to answer these questions. We analyzed 123 individuals from four vents and three seeps using a comprehensive method incorporating population genomics and physical ocean modeling. Genome survey sequencing and genotyping-by-sequencing resulted in 9,838 single-nucleotide polymorphisms for population genomic analyses. Genetic divergence and demographic analyses revealed four habitat-linked (i.e., three seep and one vent) genetic groups, with the vent genetic group established via the opportunistic invasion of a few limpet larvae from a nearby seep genetic group. TreeMix analysis uncovered three historical seep-to-vent migration events. ADMIXTURE and divMigrate analyses elucidated weak contemporary gene flow from a seep genetic group to the vent genetic group. Physical ocean modeling underlined the potential roles of seafloor topography and ocean currents in shaping the genetic connectivity, contemporary migration, and local hybridization of these deep-sea limpets. Our study highlighted the power of integrating genomic and oceanographic approaches in deciphering the demography and diversification of deep-sea organisms. Given the increasing anthropogenic activities (e.g., mining and gas hydrate extraction) affecting the deep ocean, our results have implications for the conservation of deep-sea biodiversity and establishment of marine protected areas.<br />
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Xu T, Wang Y, Sun J, Chen C, Watanabe HK, Chen J, Qian P-Y*, Qiu J-W* (2021). Hidden historical habitat-linked population divergence and contemporary gene flow in a deep-sea patellogastropod limpet. Molecular Biology and Evolution, Advance Article msab278. DOI: 10.1093/molbev/msab278

Ever wondered what the deep sea sounds like? Our new paper in Limnology and Oceanography presents results from analysing soundscapes from four deep-sea habitats including a hydrothermal vent and the abyssal plain, recorded using pressure-resistant hydrophones! OPEN ACCESS: https://aslopubs.onlinelibrary.wiley.com/doi/full/10.1002/lno.11911<br />
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All audio data used are freely available on Depositar: https://data.depositar.io/en/dataset/deep-sea-soundscapes-of-japan<br />
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Abstract: <br />
Underwater soundscapes, though invisible, are crucial in shaping the biodiversity of marine ecosystems by acting as habitat-specific settlement cues for larvae. The deep sea has received little attention in soundscape research, but it is being targeted for mineral extraction to feed the ever-growing needs of our society. Anthropogenic impacts on soundscapes influence the resilience of key shallow-water habitats, and the same likely applies to the deep. Japan is a forerunner in deep-sea mining, but virtually no deep soundscape baselines exist for Japanese waters. Here, we report baseline soundscapes from four deep-sea locations in Japan, including the Suiyo Seamount hydrothermal vent, the abyssal plain around the Minamitorishima Island home to manganese nodule fields and muds rich in rare-earth elements, twilight depths off Sanriku, as well as a typical bathyal system in Suruga Bay. Long-duration audio recordings were visualized and factorized by an unsupervised machine learning model, revealing differing characteristics among the habitats. Two locations near the coast are highly influenced by shipping noise. The Suiyo vent is characterized by low-frequency sounds from venting, and the abyssal Minamitorishima is quiet with a flat spectral shape. Noise from observation platforms is likely sufficient to alter soundscape characteristics, especially in offshore locations, suggesting offshore mining-targeted areas are susceptible to impacts from anthropogenic noise. We argue that the monitoring of soundscapes is an indispensable component for assessing potential mining impacts on deep-sea ecosystems. Our results establish reference points for future soundscape monitoring and assessment in Japanese waters as well as similar ecosystems globally.<br />
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Chen C# / Lin T-H#*, Watanabe HK, Akamatsu T, Kawagucci S (2021). Baseline soundscapes of deep-sea habitats reveal heterogeneity among ecosystems and sensitivity to anthropogenic impacts. Limnology and Oceanography, Early View: 1-14. DOI: 10.1002/lno.11911

In February 2021 we visited the deep seabed in Sagami Bay, Japan with a remotely operated vehicle, and here's a paper reporting some interesting (mollusc-related) finds from the cruise. Among other things, we report the first evidence for living naticid snails feeding on seep vesicomyid clams, previously only seen in fossils. Read for free here: https://rdcu.be/cpeeE<br />
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Abstract: <br />
Sagami Bay is among the most surveyed areas in Japan and the northwestern Pacific for marine biodiversity, partly owing to collecting efforts by the Showa Emperor, Hirohito. It was also here that the first chemosynthesis-based community was found in Japan, in the Off Hatsushima hydrocarbon seep site dominated by large vesicomyid clams. Nevertheless, new discoveries continue to be made in the deep. Here, we report observations of rare bathyal gastropods from unusual habitats. From the Off Hatsushima seep, the calliostomatid snail Otukaia kiheiziebisu was found living on tubeworm, the second record of the family from seeps. The cocculinid limpet Cocculina tenuitesta, previously only known from Suruga Bay, was found on a piece of branch-like plant debris inside the actively seeping clam field. This supports the step-wise evolutionary scenario from organic falls to hot vents recently suggested for this family. The predatory naticid snail Cryptonatica affinis represents the second record for the family at seeps, and we also show the first evidence for naticids feeding on chemosymbiotic clams—a phenomenon formerly only known from fossil seeps. We also found live individuals of Provanna stephanos, hitherto known from just two empty shells. Outside the seep area, the lepetid true limpet Sagamilepeta sagamiensis was found living on plastic debris, highlighting the function of plastic in the deep sea as settlement substrates among the muddy expanse. Our observations here have ecological and evolutionary implications, underscoring how much remains to be learned from the deep sea, even in well-studied areas like Sagami Bay.<br />
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Chen C*, Nomaki H (2021). Noteworthy observations and records of rare bathyal gastropods from unusual habitats in Sagami Bay, Japan. Marine Biodiversity, 51: 66. DOI: 10.1007/s12526-021-01212-w

Our new paper in Journal of Natural History presents Lirapex felix, a new species of peltospirid hydrothermal vent snail from the Indian Ocean! Only known from two specimens taken on a single chimney structure in the Longqi vent field despite considerable sampling efforts, it appears to be a rare species. The specific epithet 'felix' means 'lucky, happy, or blessed' in Latin, named in reference to the fortunate finding of a second specimen that allowed for a comprehensive description. <br />
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Abstract: <br />
The biodiversity of deep-sea hydrothermal vents in the Indian Ocean remains poorly characterised compared with that of their Pacific and Atlantic counterparts. Although the Longqi hydrothermal vent field is the most extensively explored vent site on the ultra-slow-spreading Southwest Indian Ridge, it is still a source of new discoveries. Here, we report and formally describe a new peltospirid snail from Longqi – Lirapex felix sp. nov. Known from only two specimens, it differs from other named Lirapex species by a depressed spire and the lack of coil loosening on the body whorl. Examinations of the external anatomy and radular characteristics agree with its placement in Lirapex, which is also supported by a molecular phylogeny reconstructed using the barcoding fragment of the mitochondrial cytochrome c oxidase I (COI) gene. This is the fifth peltospirid snail known to inhabit the Longqi field, three of which (including Lirapex felix sp. nov.) have been found nowhere else. There is growing evidence that the Longqi field represents a biogeographically unique site among Indian Ocean vents. The discovery of Lirapex felix sp. nov. adds to the unique biodiversity of Longqi field, with implications for conservation in the light of potential deep-sea mining.<br />
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Chen C*, Han Y, Copley JT, Zhou Y* (2021). A new peltospirid snail (Gastropoda: Neomphalida) adds to the unique biodiversity of Longqi vent field, Southwest Indian Ridge. Journal of Natural History, 55 (13-14): 851-866. DOI: 10.1080/00222933.2021.1923851

Co-authored paper just published in Marine Pollution Bulletin reveals the main source of coral erosion in Hong Kong is grazing by sea urchins, through a two years deployment experiment of coral blocks followed 3D reconstruction and quantification. Read for free here: https://authors.elsevier.com/a/1d8VY,ash%7ER7k<br />
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Abstract: <br />
Erosion of coral substrate plays a crucial role in reef calcium carbonate budget, but little is known about erosion in subtropical corals. In a 2-year study of coral substrate erosion, we deployed Porites skeletal blocks at nine sites across subtropical Hong Kong waters. External erosion varied from 0.05 to 3.07 kg m−2 yr−1 and accounted for 23.4–99.2% of the total erosion. More than half of the study sites had substantial external erosion (> 1 kg m−2 yr−1), and the values were positively correlated with density of the sea urchin Diadema setosum. Excluding urchins from access to the skeletal blocks using cages reduced external erosion by more than 90%. Overall, our study revealed that external erosion caused by urchin grazing contributed predominantly to the total coral skeletal loss in Hong Kong waters. Control of sea urchin population is needed to reduce coral erosion in places with high urchin density. <br />
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Yeung YH# / Xie JY#, Zhao Y, Yu HY, Chen C, Lu WW, Qiu J-W* (2021). Rapid external erosion of coral substrate in subtropical Hong Kong waters. Marine Pollution Bulletin, 169: 112495. DOI: 10.1016/j.marpolbul.2021.112495