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Dr. Chong CHEN

Dr. Chong CHEN

Deep-sea biologist. Malacologist. Evolutionary biologist. "Mollusc collector", photographer.

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Gallery of Publications

A co-authored paper published in Applied and Environmental Microbiology presents evidences pointing to a symbiotic relationship between Haplosclerida sponges from deep-sea hydrothermal vents in the Okinawa Trough and a sulfur-oxidising bacteria dominant in its microbiome. Furthermore, metagenomic results indicate that the metabolism of the symbiotic bacteria may be supported by viruses in the same environment. <br /> <br /> Abstract: <br /> In deep-sea hydrothermal vent environments, sulfur-oxidizing bacteria belonging to the clade SUP05 are crucial symbionts of invertebrate animals. Marine viruses, as the most abundant biological entities in the ocean, play essential roles in regulating the sulfur metabolism of the SUP05 bacteria. To date, vent sponge-associated SUP05 and their phages have not been well documented. The current study analyzed microbiomes of Haplosclerida sponges from hydrothermal vents in the Okinawa Trough and recovered the dominant SUP05 genome, designated VS-SUP05. Phylogenetic analysis showed that VS-SUP05 was closely related to endosymbiotic SUP05 strains from mussels living in deep-sea hydrothermal vent fields. Homology and metabolic pathway comparisons against free-living and symbiotic SUP05 strains revealed that the VS-SUP05 genome shared many features with the deep-sea mussel symbionts. Supporting a potentially symbiotic lifestyle, the VS-SUP05 genome contained genes involved in the synthesis of essential amino acids and cofactors that are desired by the host. Analysis of sponge-associated viral sequences revealed putative VS-SUP05 phages, all of which were double-stranded viruses belonging to the families Myoviridae, Siphoviridae, Podoviridae, and Microviridae. Among the phage sequences, one contig contained metabolic genes (iscR, iscS, and iscU) involved in iron-sulfur cluster formation. Interestingly, genome sequence comparison revealed horizontal transfer of the iscS gene among phages, VS-SUP05, and other symbiotic SUP05 strains, indicating an interaction between marine phages and SUP05 symbionts. Overall, our findings confirm the presence of SUP05 bacteria and their phages in sponges from deep-sea vents and imply a beneficial interaction that allows adaptation of the host sponge to the hydrothermal vent environment. <br /> <br /> Zhou K, Zhang R, Sun J, Zhang W, Tian R, Chen C, Kawagucci S, Xu Y* (2019). Potential interactions between clade SUP05 sulfur-oxidizing bacteria and phages in hydrothermal vent sponges. Applied and Environmental Microbiology, 85(22): e00992-19. DOI: 10.1128/AEM.00992-19
New lead-authored paper in Biology Letters reveals how deep-sea pectinodontid limpets 'shapeshifts' when growing on different substrates, shown by a three-months long live translocation experiment. These results, combined with morphology+genetic data from nearly 100 limpets, reveal many ‘species’ in two 'genera' to be just ONE variable species. Serradonta is just curvy Bathyacmaea! This also impacts interpretations of the ecology of some extinct species. Read here: https://royalsocietypublishing.org/doi/10.1098/rsbl.2019.0504<br /> <br /> With Hiromi Watanabe-Kayama, Takashi Toyofuku, Ting Xu, Jin Sun, among others. <br /> <br /> Abstract: <br /> Pectinodontid limpets are important members of deep-sea hot vents and cold seeps as can be seen by their conspicuous presence in both extant and extinct systems. They have traditionally been classified into different genera and species based on shell and radula characteristics; the reliability of these characters has been questioned but not tested thoroughly. Here, for the first time in taxa endemic to deep-sea chemosynthetic ecosystems, we combine substrate translocation with molecular data to assess the plasticity and variability of key phenotypic characters. Molecular data revealed that several ‘species’ of extant vent/seep pectinodontids actually represent intergrading morphotypes of a single, highly plastic, evolutionary lineage, with each morphological trait being possibly influenced differently by environmental and genetic factors. Our results challenge previous interpretations of paleoecology at fossil chemosynthetic ecosystems and highlight the importance of modern analogues in understanding fossil systems.<br /> <br /> Chen C*, Watanabe HK, Nagai Y, Toyofuku T, Xu T, Sun J, Qiu J-W, Sasaki T (2019). Complex factors shape phenotypic variation in deep-sea limpets. Biology Letters, 15(10): 20190504. DOI: 10.1098/rsbl. 2019.0504
Just published in the Journal of Molluscan Studies of The Malacological Society of London, our new paper describes two new deep-sea abyssochrysoidean snails endemic to hot vents and gives insights on their ecology. Provanna beebei is from vents in the Caribbean Sea nearly 5000 m deep, and Provanna cooki is from the Southern Ocean including Antarctic waters at over 2000 m deep. Read here: http://bit.ly/Provanna<br /> <br /> Abstract: <br /> The recent discovery and exploration of deep-sea hydrothermal vent fields in the Mid-Cayman Spreading Centre, Caribbean Sea (Beebe Vent Field, 4956–4972 m depth) and the East Scotia Ridge, Southern Ocean (E2 and E9 vent fields, 2394–2641 m depth) have yielded extensive collections of two new provannid species, Provanna beebei n. sp. and P. cooki n. sp. Morphological and molecular taxonomy (530 bp of the mitochondrial cytochrome c oxidase subunit I gene) confirm P. beebei n. sp. and P. cooki n. sp. as distinct species; these species are formally described, and details are provided of their distribution, habitat and species associations. Bayesian and maximum likelihood analyses support the placement of P. beebei n. sp. and P. cooki n. sp within the genus Provanna and show that these two new deep-sea species form a well-supported clade with the abyssal West Pacific P. cingulata. Provanna beebei n. sp. and P. cooki n. sp. represent the first records of Provanna from hydrothermal vents in the Caribbean Sea and Southern Ocean, respectively, and extend the known geographic range of the genus. For the first time, intraspecific phenotypic variation in size and sculpture has been reported for Provanna. At the East Scotia Ridge, shell-size frequency distributions and median shell size of P. cooki n. sp. varied significantly between the E2 and E9 vent fields, as well as between diffuse flow and high-temperature venting habitats within each field. The variation in shell sculpture in relation to habitat was also observed in P. cooki n. sp. <br /> <br /> Linse K / Nye V, Copley JT, Chen C (2019). On the systematics and ecology of two new species of Provanna (Gastropoda: Provannidae) from deep-sea hydrothermal vents in the Caribbean Sea and Southern Ocean. Journal of Molluscan Studies, eyz024, https://doi.org/10.1093/mollus/eyz024
A new paper published in Marine Biodiversity describes Bruceiella indurata Chen & Linse from deep-sea hot vents in Antarctica over 2000 m in depth! The shell is usually heavily corroded as is the norm for this vent-endemic genus. Both radular characters and molecular data were distinctive from other described congeners. Read for free: https://rdcu.be/bTS4u<br /> <br /> Abstract: <br /> Hydrothermal vents at the East Scotia Ridge (ESR) were the first vents to be visually confirmed and surveyed in the Southern Ocean. A trochoid snail was recovered from low diffuse flow venting sites of both E2 and E9 segments of the ESR. Taxonomic and systematic investigations revealed it to be a species hitherto unknown to science in the skeneid genus Bruceiella, which is apparently endemic to the chemosynthetic ecosystems. The new species is characterised by a large size for the genus (up to 5 mm shell width), a very broad central tooth with moderately raised horizontal basal ridge, inner marginal teeth with one single prominent protrusion on the shaft, and is described herein as Bruceiella indurata sp. nov. Described members of the genus are known from the Indian and Pacific oceans, drawing interest to the biogeographic origins of the present new species. Closest relative of the present species is Bruceiella wareni Okutani, Hashimoto & Sasaki, 2004 from Kairei vent field, Central Indian Ridge, further indicating the close relationship between East Scotia Ridge and Indian Ocean vent fauna as has been previously suggested. <br /> <br /> Chen C*, Linse K (2019). A new trochoidean gastropod (Vetigastropoda: Skeneidae) discovered from deep-sea hydrothermal vents in the Southern Ocean. Marine Biodiversity, Early Online. DOI: 10.1007/s12526-019-01005-2
In an exciting new paper published in PNAS today, we revealed how the now-endangered Scaly-foot Snail (a.k.a. Sea Pangolin) produces iron sulfide nanoparticles in its scales — by actively secreting sulfur into the scales which then reacts with iron ions diffusing in from the surrounding hot vent fluid. As the sulfur likely originate from the snail's sulfur-oxidising endosymbiotic bacteria (which the snail relies on for energy), these results indicate a strong link between the evolution of the snail's unique scales with its symbiosis. Paper: https://www.pnas.org/content/early/2019/09/23/1908533116<br /> Press release: http://www.jamstec.go.jp/e/about/press_release/20190910/<br /> <br /> Significance: <br /> Highly adapted to deep-sea hot vents, the scaly-foot gastropod Chrysomallon squamiferum is unique among living and extinct animals in possessing an imbricating scale-armor reinforced by iron sulfide nanoparticles. Mechanisms behind its biogenic sulfide synthesis are expected to revolutionize industrial production of metal chalcogenide nanoparticles, but how the gastropod manages such processes remains entirely unknown. Here, using state-of-art microscopy and elemental analyses, we show that the living animal mediates biomineralization of iron sulfide nanoparticles via a channel-like columnar organic matrix that transports sulfur, which then reacts with iron ions diffusing in from the surrounding vent fluid. This allows the snail to make iron sulfide nanoparticles in a dynamic low-temperature environment, opening the potential to significantly reduce the industrial production costs of such particles. <br /> <br /> Okada S*, Chen C, Watsuji T-o, Nishizawa M, Suzuki Y, Sano Y, Bissessur D, Deguchi S, Takai K (2019). The making of natural iron sulfide nanoparticles in a hot vent snail. Proceedings of the National Academy of Sciences, USA. DOI: 10.1073/pnas.1908533116
Our short paper in the journal Mitochondrial DNA Part B led by Jin Sun presents the mitogenome of the deep-sea limpet Bathyacmaea nipponica. The paper is Open Access and free to read here: https://www.tandfonline.com/doi/full/10.1080/23802359.2019.1668732<br /> <br /> Abstract: <br /> The deep-sea limpet Bathyacmaea nipponica is endemic to hydrothermal vents and hydrocarbon seeps in the Western Pacific. We report the complete mitochondrial genome of B. nipponica, which is 16,792 bp in length containing 13 protein-coding genes (PCGs), 22 tRNA genes, and two rRNA genes. Phylogenetic analysis using 13 PCGs shows that B. nipponica is within Patellogastropoda and is sister to a clade comprising Cellana and Nacella, among the taxa included. <br /> <br /> Sun J, Liu Y, Xu T, Zhang Y, Chen C, Qiu J-W, Qian P-Y* (2019). The mitochondrial genome of the deep-sea limpet Bathyacmaea nipponica (Patellogastropoda: Pectinodontidae). Mitochondrial DNA Part B: Resources, 4(2): 3175-3176. DOI: 10.1080/23802359.2019.1668732
Lead-authored paper published in Royal Society Open Science describes four new species of provannid snails from hot vents and cold seeps around Japan! Open access: https://royalsocietypublishing.org/doi/10.1098/rsos.190393<br /> <br /> Abstract<br /> Recently, the species richness of provannid gastropods inhabiting chemosynthetic ecosystems in the northwestern Pacific has been reassessed, revealing a much higher diversity than previously realized. Here, we describe four further new species, two in the genus Desbruyeresia and two in the genus Provanna. Their generic placement was confirmed by both shell and radula morphology, as well as phylogenetic reconstruction using the mitochondrial cytochrome c oxidase subunit I gene. Desbruyeresia armata n. sp. from vent fields in the Izu-Ogasawara Arc is characterized by a stout shell with numerous tubercles or short spines and marginal teeth coarsely serrated into only four denticles. Desbruyeresia costata n. sp. from Okinawa Trough vents is distinguished from other congeners by an elongate shell with strong axial ribs and obsolete spiral ribs. These represent the first Desbruyeresia species from Japanese waters. Provanna fenestrata n. sp. discovered from two vent fields in the Okinawa Trough is instantly recognizable from its uniquely regular rectangular lattice sculpture; Provanna stephanos n. sp. is a surprising new discovery from the supposedly well-explored ‘Off Hatsushima’ hydrocarbon seep site in Sagami Bay, and is highly distinctive with two characteristic rows of strongly spinous spiral ribs. The discovery of these new species in relatively well-explored chemosynthetic ecosystems in Japan indicates that the biodiversity of such systems remains poorly documented.<br /> <br /> Chen C*, Watanabe HK, Sasaki T (2019). Four new deep-sea provannid snails (Gastropoda: Abyssochrysoidea) discovered from hydrocarbon seep and hydrothermal vents in Japan. Royal Society Open Science, 6(7): 190393. DOI: 10.1098/rsos.190393
A co-authored paper published in Global Ecology and Biogeography presents the first global‐scale trait database for deep‐sea hydrothermal‐vent fauna – sFDvent (sDiv‐funded trait database for the Functional Diversity of vents). This database will be a valuable resource for studying and assessing how hydrothermal vent ecosystems function, as well as their resilience in the face of upcoming deep-sea mining. The database is to be updated every five years. OPEN ACCESS: https://onlinelibrary.wiley.com/doi/full/10.1111/geb.12975<br /> <br /> Abstract<br /> Traits are increasingly being used to quantify global biodiversity patterns, with trait databases growing in size and number, across diverse taxa. Despite growing interest in a trait‐based approach to the biodiversity of the deep sea, where the impacts of human activities (including seabed mining) accelerate, there is no single repository for species traits for deep‐sea chemosynthesis‐based ecosystems, including hydrothermal vents. Using an international, collaborative approach, we have compiled the first global‐scale trait database for deep‐sea hydrothermal‐vent fauna – sFDvent (sDiv‐funded trait database for the Functional Diversity of vents). We formed a funded working group to select traits appropriate to: (a) capture the performance of vent species and their influence on ecosystem processes, and (b) compare trait‐based diversity in different ecosystems. Forty contributors, representing expertise across most known hydrothermal‐vent systems and taxa, scored species traits using online collaborative tools and shared workspaces. Here, we characterise the sFDvent database, describe our approach, and evaluate its scope. Finally, we compare the sFDvent database to similar databases from shallow‐marine and terrestrial ecosystems to highlight how the sFDvent database can inform cross‐ecosystem comparisons. We also make the sFDvent database publicly available online by assigning a persistent, unique doi.<br /> <br /> Main types of variable contained: Six hundred and forty‐six vent species names, associated location information (33 regions), and scores for 13 traits (in categories: community structure, generalist/specialist, geographic distribution, habitat use, life history, mobility, species associations, symbiont, and trophic structure). Contributor IDs, certainty scores, and references are also provided.<br /> <br /> Spatial location and grain: Global coverage (grain size: ocean basin), spanning eight ocean basins, including vents on 12 mid‐ocean ridges and 6 back‐arc spreading centres.<br /> <br /> Chapman ASA*, Beaulieu SE, Colaço A, Gebruk AV, Hilario A, Kihara TC, Ramirez-Llodra E, Sarrazin J, Tunnicliffe V, Amon DJ, Baker M, Boschen-Rose RE, Chen C, Cooper IJ, Copley JT, Corbari L, Cordes EE, Cuvelier D, Duperron S, Du Preez C, Gollner S, Horton T, Hourdez S, Krylova EM, Linse K, LokaBharathi PA, Marsh L, Matabos M, Mills SW, Mullineaux LS, Rapp HT, Reid WDK, Rybakova (Goroslavskaya) E, Thomas TRA, Southgate SJ, Stöhr S, Turner PJ, Watanabe HK, Yasuhara M, Bates AE (In press). sFDvent: a global functional trait database for deep-sea hydrothermal vent fauna. Global Ecology and Biogeography. DOI: 10.1111/geb.12975
A new publication in Nature Ecology & Evolution with Julia among others highlights how IUCN Red List can help save deep-sea animals from the threat of deep-sea mining! This is exemplified by the Scaly-foot Snail or Sea Pangolin (Chrysomallon squamiferum) which has just been formally listed as Endangered. Read for free: https://rdcu.be/bLimC<br /> <br /> "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 for deep-sea biodiversity, which is threatened by surging interest in seafloor sulfide mining. We argue that the International Union for the Conservation of Nature (IUCN) Red List of Threatened Species — with formal goals to draw attention to threatened biodiversity and provide objective information to guide conservation actions and international policy — is the ideal tool to make deep-sea species more visible."<br /> <br /> Sigwart JD, Chen C*, Thomas E, Allcock AL, Böhm M, Seddon M. (2019). Red Listing can protect deep-sea biodiversity. Nature Ecology & Evolution, DOI: 10.1038/s41559-019-0930-2
In a co-authored paper with Katrin Linse and Nicolai Roterman just published in Frontiers in Marine Science, we describe a new lepetodrilid limpet Lepetodrilus concentricus from Antarctic deep-sea hydrothermal vents, and show that it exhibits great morphological variation in shell form depending on the substrate. The paper is Open Access: https://www.frontiersin.org/articles/10.3389/fmars.2019.00381/<br /> <br /> Abstract: <br /> The recently discovered hydrothermal vent ecosystems in the Southern Ocean host a suite of vent-endemic species, including lepetodrilid limpets dominating in abundance. Limpets were collected from chimneys, basalts and megafauna of the East Scotia Ridge segments E2 and E9 and the Kemp Caldera at the southern end of the South Sandwich Island arc. The limpets varied in size and shell morphology between vent fields and displayed a high degree of phenotypic plasticity. Size frequency analyses between vent fields suggests continuous reproduction in the limpet and irregular colonisation events. Phylogenetic reconstructions and comparisons of mitochondrial COI gene sequences revealed a level of genetic similarity between individuals from the three vent fields consistent with them belonging to a single molecular operational taxonomic unit. Here we describe Lepetodrilus concentricus n. sp., and evaluate its genetic distinctness and pylogenetic position with congeners based on the same gene. Results indicate that L. concentricus n. sp. is a sister species to L. atlanticus from Atlantic vents, with the two species estimated to have diverged within the last ∼5 million years. <br /> <br /> Linse K, Roterman CN, Chen C (2019). A new vent limpet in the genus Lepetodrilus (Gastropoda: Lepetodrilidae) from Southern Ocean hydrothermal vent fields showing high phenotypic plasticity. Frontiers in Marine Science, 6: 381. DOI: 10.3389/fmars.2019.00381
A new co-authored publication in the journal Check List led by the polychaete expert Naoto Jimi presents a range extension of the hydrothermal vent polychaete worm Archinome jasoni to deep-sea vents in Okinawa Trough, Japan using morphological and molecular data. This is its first record from the northwestern Pacific, adding to previous records from the Indian Ocean, Atlantic Ocean, and the southwestern Pacific. It appears to basically have a global distribution! The paper is OPEN ACCESS and available for free here: https://checklist.pensoft.net/article/34067/<br /> <br /> Abstract: <br /> The hydrothermal vent-endemic polychaete Archinome jasoni Borda et al., 2013 is known from the Atlantic, Indian, and Southwest Pacific oceans. In this study, we report A. jasoni from Okinawa Trough, Japan, which represents the first record of this species and the genus from the Northwest Pacific. We determined 16S and 28S rRNA gene sequences from 1 of the 7 specimens collected. We compared our Northwest Pacific specimens to specimens from the Southwest Pacific, Atlantic, and Indian oceans, and our specimen was genetically most closely related to individuals from the Southwest Pacific. <br /> <br /> Jimi N*, Chen C, Kajihara H (2019). New records of the hydrothermal-vent-endemic polychaete Archinome jasoni (Annelida: Amphinomidae) from the northwestern Pacific. Check List, 15(3): 523-526. DOI: 10.15560/15.3.523
A co-first authored paper has been published in Marine Biology! Read here: https://rdcu.be/bmGJr <br /> By using images over a five years period from a cabled deep-sea observatory placed in colony of Phreagena spp. vesicomyid clams in Sagami Bay, Japan, we show that their density showed an overall decline across the time period from natural disturbances (and a ROV visit), and earthquake-induced disturbances wiped out the population in the end. This implies vesicomyid clams, a dominant taxa in many deep-sea chemosynthetic ecosystems, are unlikely to survive potential impacts of deep-sea mining. <br /> <br /> Abstract: <br /> Cabled seafloor platforms can overcome many constraints of stand-alone systems and archived long-term seafloor monitoring, and their advantages include unlimited power, real time communication, a synchronized clock, and virtually unlimited data storage. Using monthly images from a fixed camera on a cabled deep-sea observatory in the Off Hatsushima seep site in Sagami Bay, Japan, fluctuations in clam density (Phreagena soyoae and P. okutanii) were observed over five years, March 1994–July 1999. Eight disturbances were seen, including five phytodetritus deposition events associated with seasonal blooms, two earthquake-associated turbid flows, and one caused by a maintenance visit by a remotely operated vehicle. Overall, these observations indicate that the vesicomyids experienced an ongoing decline throughout the observation series, and strong disturbance events such as earthquakes appeared to be too severe for the clams to survive. As such, vesicomyid clams are unlikely to survive the forseeable impacts of deep-sea mining. These results show that long-term observations of deep-sea chemosynthetic communities are useful for understanding their resilience and for making an environmental impact assessment.<br /> <br /> Nakajima R#*, Chen C#, Iwase R, Yamamoto H, Fujikura K (2019). Clams after storms: the impact of multiple disturbances on seep vesicomyid clams revealed by long-term monitoring. Marine Biology, 166: 35. DOI: 10.1007/s00227-019-3484-6
A co-authored paper on gut microbiota of the giant deep-sea trench isopod Hirondellea gigas (Birstein & Vinogradov, 1955) from Mariana Trench and Japan Trench has been published in Applied and Environmental Microbiology: https://aem.asm.org/content/85/1/e02032-18<br /> <br /> Abstract: <br /> Hadal environments sustain diverse microorganisms. A few studies have investigated hadal microbial communities consisting of free-living or particle-associated bacteria and archaea. However, animal-associated microbial communities in hadal environments remain largely unexplored, and comparative analyses of animal gut microbiota between two isolated hadal environments have never been done so far. In the present study, 228 Gb of gut metagenomes of the giant amphipod Hirondellea gigas from two hadal trenches, the Mariana Trench and Japan Trench, were sequenced and analyzed. Taxonomic analysis identified 49 microbial genera commonly shared by the gut microbiota of the two H. gigas populations. However, the results of statistical analysis, in congruency with the alpha and beta diversity analyses, revealed significant differences in gut microbial composition across the two trenches. Abundance variation of Psychromonas, Propionibacterium, and Pseudoalteromonas species was observed. Microbial cooccurrence was demonstrated for microbes that were overrepresented in the Mariana trench. Comparison of functional potential showed that the percentage of carbohydrate metabolic genes among the total microbial genes was significantly higher in the guts of H. gigas specimens from the Mariana Trench. Integrating carbon input information and geological characters of the two hadal trenches, we propose that the differences in the community structure might be due to several selective factors, such as environmental variations and microbial interactions. <br /> <br /> Zhang W, Watanabe HK, Ding W, Lan Y. Tian R-M, Sun J, Chen C, Cai L, Li Y, Oguri K, Toyofuku T, Kitazato H, Drazen JC, Bartlett D, Qian P-Y (2018). Gut microbial divergence between two populations of the hadal amphipod Hirondellea gigas. Applied and Environmental Microbiology, 85(1): e02032-18. DOI: 10.1128/AEM.02032-18
Our new paper published in Zootaxa yesterday introduces a new chiton (polyplacophoran mollusc), Hanleyella henrici Sigwart & Chen, 2018, from deep-sea hydrothermal vents in Okinawa Trough! https://www.mapress.com/j/zt/article/view/zootaxa.4531.3.7<br /> <br /> Abstract: <br /> Recent expeditions exploring deep-sea hydrothermal vent ecosystems in the Okinawa Trough, East China Sea resulted in the collection of a hitherto undescribed species of polyplacophoran mollusc found living at three different vent fields at depths of 950–1178 m. This new chiton is a member of the small lepidopleuran family Protochitonidae and is morphologically similar to Hanleyella japonica Saito, 1997. The two species differ in small morphological differences of the valve shape and elevation, are divergent in the standard molecular barcoding mitochondrial gene cytochrome oxidase I (COI), and furthermore the known distribution range of H. japonica is considerably more northern and also shallower. The new species is described herein as Hanleyella henrici n. sp. Additional in situ observations taken in the course of collecting material for this study indicates that chitons are more abundant in the vicinity of hydrothermal vents than was previously appreciated, and perhaps more speciose.<br /> <br /> As always, please let me know if you would like to have a PDF copy of the paper. <br /> <br /> Sigwart JD, Chen C (2018). A new deep water chiton (Mollusca: Polyplacophora) from hydrothermal vent ecosystems in the Okinawa Trough, Japan. Zootaxa, 4531(3): 430-436. DOI: 10.11646/zootaxa.4531.3.7
A new co-authored article has been published in the Open Access journal eLife! Read for free: https://elifesciences.org/articles/41319<br /> <br /> Here, we present our thoughts that our ability to come up with a conservation framework for managing and developing deep-sea resources exploitation is constrained by the fact that we don't even know what lives there -- and hence it is not (yet) feasible to model how ecosystems will be affected by such activities. We make a case that a taxon-focused approach with high-throughput taxonomy (like describing 1000 species in 5 years) is achievable, and needs to, be done for regions with foreseeable industrial activity. <br /> <br /> Thanks goes to Adrian, Helena, and Thomas for including me in this work! It was a real pleasure : D <br /> <br /> Abstract: <br /> Ensuring that the wealth of resources contained in our oceans are managed and developed in a sustainable manner is a priority for the emerging 'blue economy'. However, modern ecosystem-based management approaches do not translate well to regions where we know almost nothing about the individual species found in the ecosystem. Here, we propose a new taxon-focused approach to deep-sea conservation that includes regulatory oversight to set targets for the delivery of taxonomic data. For example, a five-year plan to deliver taxonomic and genomic knowledge on a thousand species in regions of the ocean earmarked for industrial activity is an achievable target. High-throughput, integrative taxonomy can, therefore, provide the data that is needed to monitor various ecosystem services (such as the natural history, connectivity, value and function of species) and to help break the regulatory deadlock of high-seas conservation. <br /> <br /> Glover AG, Wiklund H, Chen C, Dahlgren TG (2018). Managing a sustainable deep-sea ‘blue economy’ requires knowledge of what actually lives there. eLife, 7: e41319. DOI: 10.7554/eLife.41319
Co-authored paper with Yukiko Nagai, Takashi Toyofuku, and others published in the journal Biogeosciences reveals how foraminifera "weave" their tests ('shells') with fine threads of cytoplasm, using high-res microscopy and time-lapse imaging. This has implications on how geochemical signatures in foraminifera tests are shaped, and thus contribute to interpreting such signatures from fossils and using them as biogeochemical proxies. This paper is Open Access: https://www.biogeosciences.net/15/6773/2018/bg-15-6773-2018.html<br /> <br /> Abstract: <br /> Elemental and/or isotopic signatures of calcareous tests of foraminifera are commonly used to reconstruct paleoenvironmental conditions. A major problem, often referred to as the "vital effect", is that such geochemical signatures stored in inorganic calcium carbonates differ greatly under the same environmental conditions, as well as between taxa, species, individuals, etc. This effect was previously explained by relative contributions between passive vs. active ion transport patterns, but their details are still under investigation. In this study, the functional role of pseudopodial structures during chamber formation is elucidated by detailed observation of Ammonia beccarii (Linnaeus, 1758) using a time-lapse optical imaging system and high-resolution electron microscopy. We document triple organic layers sandwiching carbonate precipitation sites for the first time. The three major organic layers (outer organic layer, primary organic sheet, and inner organic layer) are formed by an initial framework of pseudopodia overlaid with further layer-like pseudopodia. The primary organic sheet seems to facilitate early calcium carbonate nucleation, then entrapped by double precipitation sites. We further show that calcification starts when outer or inner organic layers still exhibit tiny gaps (holes within the framework) that may serve as pathways for passive ion exchange (e.g. Mg2+) between seawater and the confined precipitation space. Nevertheless, the majority of wall thickening occurs when the precipitation site is completely isolated from seawater, which implies active ion exchange. This may explain the differences in Mg∕Ca ratios in early and later stages of calcification observed in previous studies. Our study provides insight into resolving a key "missing piece" in understanding foraminiferal calcification through culture experiments and in-depth observations of living animals. Our findings contribute to interpreting and understanding biogeochemical proxies by showing that the "vital effect", specifically elemental and isotopic ratios along chamber walls, is directly linked to spatio-temporal organization of the "biomineralization sandwich" controlled by the three major organic layers.<br /> <br /> Nagai Y, Uematsu K, Chen C, Wani R, Tyszka J, Toyofuku T (2018). Weaving of biomineralization framework in rotaliid foraminifera: Implications for paleoceanographic proxies. Biogeosciences, 15: 6773-6789. DOI: 10.5194/10.5194/bg-15-6773-2018
A co-authored paper reviewing the cold seep systems in the South China Sea has been published online in Journal of Asian Earth Sciences: https://doi.org/10.1016/j.jseaes.2018.09.021 <br /> This review comprehensively covers various relevant diciplines, and I was responsible for the macroecology section. <br /> <br /> Abstract: <br /> Three decades after the discovery of cold seep systems, various sites of hydrocarbon seepage have been found in the South China Sea (SCS). Over the past decade, these sites have become model systems for understanding the variability of hydrocarbon seepage and associated biogeochemical processes. In this review, we describe the cold seep systems of the SCS with an emphasis on seafloor manifestations, fluid sources, biogeochemical processes, and macroecology. Seafloor features associated with seeps include mud volcanoes, pockmarks, and carbonate deposits. A common characteristic of cold seeps is the occurrence of authigenic (i.e., in situ precipitated) carbonate minerals. These carbonates commonly exhibit low δ13C and high δ18O values, suggesting the incorporation of methane-derived carbon and oxygen derived from gas hydrate water. Biogeochemical processes such as sulfate-driven anaerobic oxidation of methane (SD-AOM), the key process at seeps, have been studied in detail with the aim of establishing geochemical proxies to trace these processes into the geological past. We also detail the features characterizing seep ecosystems. Understanding the impact of decomposing methane hydrate on the marine carbon budget remains challenging and requires additional seafloor observations as well as models predicting how gas hydrate responds to changing conditions such as temperature increase, sea level rise, and episodic mass wasting. <br /> <br /> Feng D, Qiu J-W, Hu Y, Peckmann J, Guan H, Tong H, Chen C, Chen J, Gong S, Li N, Chen D (2018). Cold seep systems in the South China Sea: An overview. Journal of Asian Earth Sciences. DOI: 10.1016/j.jseaes.2018.09.021
The first paper on the physiology of Indian Ocean vent animals has been published in The Biological Bulletin! Link: https://www.journals.uchicago.edu/doi/abs/10.1086/699326<br /> <br /> We used closed-chamber respirometry to investigate whether the scaly-foot snail (Chrysomallon squamiferum)'s strategy of having an internal symbiont-housing organ increased its routine metabolism. By comparing the oxygen consumption of both Chrysomallon and Alviniconcha marisindica at different temperatures, we show that housing symbionts in an internal organ does not fundamentally increase the oxygen requirement. The Scaly-foot, however, was able to maintain a steady metabolic demand across experiment temperatures, while Alviniconcha showed stress responses at low temperature. Vent habitats have steep temperature gradients between the superheated vent fluid and the cold surrounding seawater, and such physiological constraints likely play important roles in defining niches in these environments. <br /> <br /> Abstract: <br /> Physiological traits are the foundation of an organism’s success in a dynamic environment, yet basic measurements are unavailable for many taxa and even ecosystems. We measured routine metabolism in two hydrothermal vent gastropods, Alviniconcha marisindica (n = 40) and the scaly-foot gastropod Chrysomallon squamiferum (n = 18), from Kairei and Edmond vent fields on the Central Indian Ridge (23–25°S, about 3000 meter depth). No previous studies have measured metabolism in any Indian Ocean vent animals. After recovering healthy animals to the surface, we performed shipboard closed-chamber respirometry experiments to compare oxygen uptake at different temperatures (10, 16, and 25 °C) at surface pressure (1 atm). The physiology of these species is driven by the demands of their chemoautotrophic symbionts. Chrysomallon has very enlarged respiratory and circulatory systems, and endosymbionts are housed in its trophosome-like internal esophageal gland. By contrast, Alviniconcha has chemoautotrophic bacteria within the gill and less extensive associated anatomical adaptations. Thus, we predicted that routine oxygen consumption of Chrysomallon might be higher than that of Alviniconcha. However, oxygen consumption of Chrysomallon was not higher than that of Alviniconcha, and, further, Chrysomallon maintained a steady metabolic demand in two widely separated experimental temperatures, while Alviniconcha did not. We interpret that these findings indicate that (1) the “trophosome” does not fundamentally increase oxygen requirement compared to other gastropod holobionts, and (2) cold temperatures (10 °C) induce a stress response in Alviniconcha, resulting in aberrantly high uptake. While these two large gastropod species co-occur, differences in oxygen consumption may reflect the separate niches they occupy in the vent ecosystem.<br /> <br /> Sigwart JD, Chen C (2018). Comparative oxygen consumption of gastropod holobionts from deep-sea hydrothermal vents in the Indian Ocean. The Biological Bulletin, 235(2). DOI: 10.1086/699326
A paper using genome-wide SNPs to elucidate population genetic of the deep-sea mussel Bathymodiolus platifrons that I co-authored is now available for free (Open Access) online! Many thanks for the lead author Ting Xu and the co-authors, including Jin Sun, Hiromi Watanabe-Kayama, Masako Nakamura, among others. Link: https://onlinelibrary.wiley.com/doi/abs/10.1111/eva.12696<br /> <br /> Abstract: <br /> Studying population genetics of deep‐sea animals helps us understand their history of habitat colonization and population divergence. Here, we report a population genetic study of the deep‐sea mussel Bathymodiolus platifrons (Bivalvia: Mytilidae) widely distributed in chemosynthesis‐based ecosystems in the Northwest Pacific. Three mitochondrial genes (i.e., atp6, cox1, and nad4) and 6,398 genomewide single nucleotide polymorphisms (SNPs) were obtained from 110 individuals from four hydrothermal vents and two methane seeps. When using the three mitochondrial genes, nearly no genetic differentiation was detected for B. platifrons in the Northwest Pacific. Nevertheless, when using SNP datasets, all individuals in the South China Sea (SCS) and three individuals in Sagami Bay (SB) together formed one genetic cluster that was distinct from the remaining individuals. Such genetic divergence indicated a genetic barrier to gene flow between the SCS and the open Northwest Pacific, resulting in the co‐occurrence of two cryptic semi‐isolated lineages. When using 125 outlier SNPs identified focusing on individuals in the Okinawa Trough (OT) and SB, a minor genetic subdivision was detected between individuals in the southern OT (S‐OT) and those in the middle OT (M‐OT) and SB. This result indicated that, although under the influence of the Kuroshio Current and the North Pacific Intermediate Water, subtle geographic barriers may exist between the S‐OT and the M‐OT. Introgression analyses based on these outlier SNPs revealed that Hatoma Knoll in the S‐OT represents a possible contact zone for individuals in the OT‐SB region. Furthermore, migration dynamic analyses uncovered stronger gene flow from Dai‐yon Yonaguni Knoll in the S‐OT to the other local populations, compared to the reverse directions. Taken together, the present study offered novel perspectives on the genetic connectivity of B. platifrons mussels, revealing the potential interaction of ocean currents and geographic barriers with adaption and reproductive isolation in shaping their migration patterns and genetic differentiation in the Northwest Pacific. <br /> <br /> Xu T, Sun J, Watanabe HK, Chen C, Nakamura M, Ji R, Feng D, Lv J, Wang S, Bao Z, Qian P-Y, Qiu J-W (2018). Population genetic structure of the deep-sea mussel Bathymodiolus platifrons (Bivalvia: Mytilidae) in the Northwest Pacific. Evolutionary Applications. DOI: 10.1111/eva.12696
A new co-authored proceedings paper on using micro-CT scans to visualise molluscs is now published! It is Open Access and can be read for free here: https://dx.doi.org/10.1007/978-981-13-1002-7_9<br /> <br /> Abstract: <br /> Three-dimensional (3D) reconstruction is an essential approach in morphological studies in biology and paleontology. Seeking an optimized protocol for nondestructive observations, we attempted 3D visualization of various molluscan shells and animals with X-ray micro-computed tomography (micro-CT). Calcified parts of molluscs were easily visualized except for cases with marked differences in thickness heterogeneity. 3D imaging of shell microstructure was difficult. Visualization of soft tissue requires staining to enhance the image contrast. Especially for soft tissues, synchrotron X-ray microtomography is the most advanced method to generate clear 3D images. 3D data facilitates morphological quantification, enabling calculations of length and volume even for very complex forms. X-ray micro-CT is extremely useful in the morphologic examination of mineralized and soft tissues, although microstructural and histological details should be supplemented by other microscopic techniques. <br /> <br /> Sasaki T, Maekawa Y, Takeda Y, Atsushiba M, Chen C, Noshita K, Uesugi K, Hoshino M (2018). 3D visualization of calcified and non-calcified molluscan tissues using computed tomography. In: Endo K, Kogure T, Nagasawa H (eds.) Biomineralization: From Molecular and Nano-structural Analyses to Environmental Science, pp. 83-93. Springer, Singapore. DOI: 10.1007/978-981-13-1002-7_9
A new co-authored paper with Tomomi Ogura and Hiromi Watanabe-Kayama (among others) has been published in the open-access journal PeerJ! We investigated the genetic connectivity and population history of five deep-sea abyssochrysoid snails in the genus Provanna from vents and seeps. Read for free here: https://peerj.com/articles/5673/<br /> <br /> Abstract: <br /> Gastropods of the genus Provanna are abundant and widely distributed in deep-sea chemosynthetic environments with seven extant species described in the northwestern Pacific. We investigated the population history and connectivity of five Provanna species in the northwestern Pacific through population genetic analyses using partial sequences of the cytochrome c oxidase subunit I gene. We found that P. subglabra, the most abundant and genetically diverse species, is genetically segregated by depth. Among the five species, the three comparatively shallower species (P. lucida, P. kuroshimensis, P. glabra) had a more constant demographic history compared to the deeper species (P. subglabra, P. clathrata).<br /> <br /> Ogura T, Watanabe HK, Chen C, Sasaki T, Kojima S, Ishibashi J-i, Fujikura K (2018). Population history of deep-sea vent and seep Provanna snails (Mollusca: Abyssochrysoidea) in the northwestern Pacific. PeerJ. DOI: 10.7717/peerj.5673
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