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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

We need a service to support taxonomy! We propose a new model to accelerate species descriptions, where an external service supports the acquisition of descriptive data -- pioneered by the Senckenberg Ocean Species Alliance project's Discovery Unit: https://sosa.senckenberg.de/en/who-are-we<br /> The paper is OPEN ACCESS in BioEssays: https://doi.org/10.1002/bies.202300070<br /> <br /> Abstract: <br /> Increasing complexity and specialisation of modern sciences has led to increasingly collaborative publications, as well as the involvement of commercial services. Modern integrative taxonomy likewise depends on many lines of evidence and is increasingly complex, but the trend of collaboration lags and various attempts at ‘turbo taxonomy’ have been unsatisfactory. We are developing a taxonomic service in the Senckenberg Ocean Species Alliance to provide fundamental data for new species descriptions. This will also function as a hub to connect a global network of taxonomists, assembling an alliance of scientists working on potential new species to tackle both the extinction and inclusion crises we face today. The current rate of new species descriptions is simply too slow; the discipline is often dismissed as old fashioned, and there is a crisis level need for taxonomic descriptions to come to grips with the scale of Anthropocene biodiversity loss. Here, we envision how the process of describing and naming species would benefit from a service supporting the acquisition of descriptive data.<br /> <br /> Sigwart JD*# / Chen C#, Tilic E, Vences M, Riehl T (2023). Why is there no service to support taxonomy? BioEssays, 45(9): 2300070. DOI: 10.1002/bies.202300070
Our new paper in Zoological Studies names Paralepetopsis polita, a new deep-sea limpet from a methane seep! Despite having a characteristically neolepetopsid-type radula, molecular phylogeny surprisingly nested it within Lepetidae instead -- hinting at a paraphyletic Neolepetopsidae. This paper is OPEN ACCESS: https://doi.org/10.6620/ZS.2023.62-26<br /> <br /> Abstract: <br /> Neolepetopsidae is a little-studied true limpet family only known from deep-sea chemosynthetic ecosystems, containing just over a dozen species in three genera: Neolepetopsis, Paralepetopsis, and Eulepetopsis. Although considered monophyletic by a recent phylogenetic analysis, a lack of Paralepetopsis sequence linked to morphology casts some uncertainty. Here, we discovered a new species of Paralepetopsis from the Haima methane seep in the South China Sea, described as Paralepetopsis polita sp. nov. The new species is distinct from all other described Paralepetopsis by its smooth and semi-transparent shell, combined with a radula exhibiting pluricuspid teeth with two cusps. We tested its relationship with other neolepetopsids using a molecular phylogeny reconstructed from the mitochondrial COI gene, revealing a surprising position nested within Lepetidae, a family with a very different radula morphology. The clade containing lepetids and our new species was recovered sister to other neolepetopsids with sequence data available. This hints at a paraphyletic Neolepetopsidae, and suggests the neolepetopsid-type radula might not be exclusive to one monophyletic group of limpets. <br /> <br /> Chen C*, Zhong Z, Qiu J-W, Sun J (2023). A new Paralepetopsis limpet from a South China Sea seep hints at a paraphyletic Neolepetopsidae. Zoological Studies, 62: 26. DOI: 10.6620/ZS.2023.62-26
New paper in Marine Biology reveals population structures and life-history / reproductive biology of four alvinocaridid shrimps endemic to deep-sea hot vents and cold seeps around Japan! Read the paper here: https://www.researchgate.net/publication/370685419_Life-history_traits_of_alvinocaridid_shrimps_inhabiting_chemosynthetic_ecosystems_around_Japan<br /> <br /> Abstract: <br /> Alvinocaridid shrimps are endemic and globally widespread in chemosynthetic ecosystems such as hydrothermal vents and hydrocarbon seeps. Though the biology of Atlantic alvinocaridid species have received considerable attention, little is known about their Pacific relatives. Here we described population structures and reproductive biology of three Pacific alvinocaridid species—Shinkaicaris leurokolos, Opaepele loihi, Alvinocaris longirostris—with notes on a fourth species—A. dissimilis—from several chemosynthetic ecosystems around Japan and compared their size frequency distributions and reproductive outputs. We showed that population demographics differ among these species, including a significantly larger proportion of juveniles in O. loihi and spatial variation of sex ratio in S. leurokolos, but all shared sex ratios biased toward females. The three shrimp species were characterized by relatively small sizes at onset of maturity, although this varied among sites for A. longirostris. Overall, size-specific fecundities and egg volumes of A. longirostris, O. loihi and S. leurokolos were in a similar range to Atlantic alvinocaridids. In addition, we performed egg incubation experiments of O. loihi under different temperature conditions to characterize thermal physiology during its brooding period. This confirmed a strong influence of temperature on both brooding duration and hatching rate, with a thermal preference that differs from previously published data for A. longirostris and S. leurokolos. Finally, our results indicated that these alvinocaridid species from the northwestern Pacific likely differ in reproductive timing, either through distinct brooding durations and/or distinct brooding periodicity, although further investigations are required to confirm these patterns.<br /> <br /> Methou P*, Nye V, Copley JT, Watanabe HK, Nagai Y, Chen C (2023). Life-history traits of alvinocaridid shrimps inhabiting chemosynthetic ecosystems around Japan. Marine Biology, 170: 75. https://doi.org/10.1007/s00227-023-04221-4
We designed, constructed, and successfully tested the world's first functional DEEP-SEA FREEZER! Now out in Frontiers in Marine Science: https://doi.org/10.3389/fmars.2023.1179818<br /> <br /> Abstract: <br /> Recovery of samples from the deep ocean in pristine condition is difficult due to large environmental differences between the deep and surface waters through which the samples necessarily must be transported. Here, we propose a concept for deep-sea sample recovery: a deep-sea freezer using thermoelectric cooling capable of generating ice in the deep and recover them frozen on-board ships. As a proof of concept, we present the DSF-α, a prototype Deep-Sea Freezer based on Peltier device rated at 2000 m. In situ assessments of the DSF-α on remotely operated vehicles showed its capacity to reach freezing (-13.0°C) temperatures in the deep, as well as recovering seawater frozen on deck. Although the DSF-α is limited in that achieving sufficient freezing for useful sample recovery is time consuming, the deep-sea freezer opens a whole frontier of new possibilities for preserving various types of deep-sea samples and has the potential to be adapted according to various needs of the deep-sea research community. With the first literal ‘marine snow’ in the deep, we offer a glimpse to a future where the recovery of reliable bathyal samples is no longer laborious.<br /> <br /> Kawagucci S#* / Matsui Y#, Nomaki H, Chen C (2023). Deep-sea freezer. Frontiers in Marine Science, 10: 1179818. DOI: 10.3389/fmars.2023.1179818
Seven new vent gastropod species and one new genus are now published in Zootaxa! These are from southwestern Pacific deep-sea hot vents and were studied by the German malacologist Lothar A. Beck since the 1990s but were never published. Beck passed away in 2020 -- we then took the baton. This paper is Open Access: https://doi.org/10.11646/zootaxa.5270.3.2<br /> <br /> Abstract <br /> Deep-sea hydrothermal vents host many endemic species adapted to these chemosynthesis-based ecosystems. The exploration of vent fields including those in the tropical Pacific is currently accelerating, due to the development of deep-sea mining for valuable minerals. Molecular evidence has shown that many vent endemic gastropod lineages include sibling species pairs in adjacent oceanic basins. While the fauna of the Manus Basin is relatively well described, many lineages in adjacent regions in North Fiji or Lau Basins are recognised as separate species, but unnamed. Valuable material from this fauna was studied by Lothar A. Beck in the 1990s, who fully drafted descriptions for these species, but did not publish them. Beck’s manuscript names, prior to the present study, represented real species but nomina nuda without taxonomic validity. Here we present the descriptions of seven new species and one new genus, extracted from Beck’s unpublished manuscript that was rediscovered after his death in 2020. The publication of these descriptions makes them taxonomically available and respects the scientific contributions of Beck. Providing valid descriptions of these species is critically important now to enable the recognition of species that may require conservation in the face of future environmental destruction.<br /> Symmetriapelta Beck, gen. nov. is described as new genus. Bathyacmaea nadinae Beck, sp. nov., Pyropelta ovalis Beck, sp. nov., Pseudorimula leisei Beck, sp. nov., Lepetodrilus fijiensis Beck, sp. nov., Shinkailepas conspira Beck, sp. nov., Symmetromphalus mcleani Beck, sp. nov. and Symmetriapelta wareni Beck, sp. nov. are introduced as new species. <br /> <br /> Chen C*, Sigwart JD (2023). The lost vent gastropod species of Lothar A. Beck. Zootaxa, 5270(3): 401-436. DOI: 10.11646/zootaxa.5270.3.2
A new paper in Ecology and Evolution presents our "favourite burrows" from the RV SONNE "AleutBio" expedition in Autumn 2022! We found enigmatic linear series of holes in the Bering Sea, and propose that they are constructed by large amphipods. Read more about our Amphipod Hypothesis in the OPEN ACCESS paper here: https://doi.org/10.1002/ece3.9867<br /> <br /> Abstract: <br /> Trails, burrows, and other “life traces” in sediment provide important evidence for understanding ecology—both of the maker and of other users—and behavioral information often lacking in inaccessible ecosystems, such as the deep sea or those that are already extinct. Here, we report novel sublinear rows of openings in the abyssal plains of the North Pacific, and the first plausible hypothesis for a maker of these constructions. Enigmatic serial burrows have now been recorded in the Pacific and Atlantic deep sea. Based on image and specimen evidence, we propose that these Bering Sea excavations represent amphipod burrows, while the maker of the previously known Mid-Atlantic Ridge constructions remains undetermined. We propose that maerid amphipods could create the Pacific burrows by eating–digging horizontally below the surface along a nutrient-rich layer in the sediment, making the serial openings above them as they go, for conveniently removing excavated sediment as the excavation progresses. These striking structures contribute to local biodiversity, and their maker could be considered a deep-sea ecosystem engineer.<br /> <br /> Brandt A# / Chen C#, Tandberg AHS, Miguez-Salas O, Sigwart JD* (2023). Complex sublinear burrows in the deep sea may be amphipod nests. Ecology and Evolution, 13(3): e9867. DOI: 10.1002/ece3.9867
By applying "ancient DNA" techniques, we successfully sequenced empty shells from an enigmatic vesicomyid clam, Archivesica nanshaensis, collected from a 3000m-deep cold seep. This clam has never been collected alive, and the shells were carbon-dated to 1500 years old. Read for free here: https://doi.org/10.24272/j.issn.2095-8137.2022.404<br /> <br /> Abstract: <br /> Ancient DNA (aDNA) from mollusc shells is considered a potential archive of historical biodiversity and evolution. However, such information is currently lacking for mollusc shells from the deep ocean, especially those from acidic chemosynthetic environments theoretically unsuitable for long-term DNA preservation. Here, we report on the recovery of mitochondrial and nuclear gene markers by Illumina sequencing of aDNA from three shells of Archivesica nanshaensis – a hydrocarbon-seep vesicomyid clam previously known only from a pair of empty shells collected at a depth of 2 626 m in the South China Sea. Carbon-14 analysis showed that the shells collected here from a depth of 3 003 m were about 1 500 years old. Sequence analysis indicated that A. nanshaensis was distinct from other vesicomyids with available molecular evidence and was sister to A. marissinica with a K2P distance of 3.4% in the mitochondrial cytochrome c oxidase I (COI) gene. Fossil-calibrated molecular dating indicated that A. nanshaensis and A. marissinica diverged approximately 8.5 million years ago (Ma) (4.8–13.1 Ma, 95% highest posterior density (HPD)) in the middle Miocene. This study demonstrates the potential of high-throughput sequencing of DNA from ancient shells to unravel the evolution and historical diversification of deep-sea molluscs, especially for those species described based solely on empty shells.<br /> <br /> Li Y-X, Zhang Y, Ip JC-H, Liu J, Chen C, Little CTS, Yokoyama Y, Yasuhara M, Qiu J-W* (2023). Phylogenetic context of a deep-sea clam (Bivalvia: Vesicomyidae) revealed by DNA from 1500-year-old shells. Zoological Research, 44(2): 353-356. DOI: 10.24272/j.issn.2095-8137.2022.404
Just out in Frontiers in Marine Science, our paper reveals striking biological heterogeneity among three abyssal plain stations in the Bering Sea using ultra-high-resolution image transects! The paper is Open Access: https://www.frontiersin.org/articles/10.3389/fmars.2022.1037482/full<br /> <br /> Abstract:<br /> The abyssal plains are vast areas without large scale relief that occupy much of the ocean floor. Although long considered relatively featureless, they are now known to display substantial biological heterogeneity across different spatial scales. Ecological research in these regions benefits increasingly from non-destructive visual sampling of epifaunal organisms with imaging technology. We analysed images from ultra-high-definition towed camera transects at depths of around 3500 m across three stations (100–130 km apart) in the Bering Sea, to ask whether the density and distribution of visible epifauna indicated any substantial heterogeneity. We identified 71 different megafaunal taxa, of which 24 occurred at only one station. Measurements of the two most abundant faunal elements, the holothurian Elpidia minutissima and two xenophyophores morphotypes (the more common identifiable as Syringammina limosa), indicated significant differences in local densities and patchy aggregations that were strikingly dissimilar among stations. One station was dominated by xenophyophores, one was relatively depauperate in both target taxa as well as other identified megafauna, and the third station was dominated by Elpidia. This is an unexpected level of variation within comparable transects in a well-mixed oceanic basin, reinforcing the emerging view that abyssal habitats encompass biological heterogeneity at similar spatial scales to terrestrial continental realms.<br /> <br /> Sigwart JD, Brandt A, Di Franco D, Escobar E, Gerken S, Gooday AJ, Grimes CJ, Głuchowska K, Hoffman S, Jażdżewska AM, Kamyab E, Kelch A, Knauber H, Kohlenbach K, Miguez-Salas O, Moreau C, Ogawa A, Poliseno A, Santín Muriel A, Tandberg AHS, Theising F, Walter T, Wölfl A-C, Chen C* (2023). Heterogeneity on the abyssal plains: A case study in the Bering Sea. Frontiers in Marine Science, 9: 1037482. DOI: 10.3389/fmars.2022.1037482
During the 2022 "AleutBio" expedition to Aleutian Trench on-board R/V SONNE, we sighted the iconic swimming "Dreamer Holothurian" Enypniastes eximia from over 5000 m deep -- a northern range extension for the species. This finding was just published in Marine Biodiversity, the paper is OPEN ACCESS: https://doi.org/10.1007/s12526-022-01314-z<br /> <br /> The monotypic Enypniastes eximia is distributed worldwide, mainly in warm water regions. Here, we report the northernmost seabed sighting of this species to the Aleutian Trench off Alaska in the northeast Pacific. This represents a significant northern range extension especially for the Pacific. During the recent “AleutBio” expedition on board RV SONNE (cruise SO293 July–September 2022), we deployed the ship’s “Ocean Floor Observation System” towed-camera system that captures full-HD video. We recorded sightings of two Enypniastes separated by 2.1 km on a single dive, between 5272 and 5320 m depth. This is in the deeper part of its known range; the deepest record is at 6900 m in the Java Trench. An early specimen from the Southern Ocean hinted its range extends to higher latitudes, recently substantiated by an adult sighting off East Antarctica. Here, we confirm the same for the northern hemisphere to show that it truly has a global distribution. <br /> <br /> Sigwart JD, Ogawa A, Chen C* (2023). “Dreamer holothurians” in the north. Marine Biodiversity, 53: 8. DOI: 10.1007/s12526-022-01314-z
Over the last decade or so, we have been organising and participating in many research cruises to investigate deep-sea hydrothermal vents of the northwest Pacific. Now in a paper published in Ecology and Evolution, we use species distribution data updated as a result of these cruises to carry out network analyses, identifying the key sites for conservation. This includes data for 117 species from 36 hydrothermal vent fields! The paper is OPEN ACCESS and can be read here: https://doi.org/10.1002/ece3.9612<br /> <br /> Abstract<br /> The distribution of species among spatially isolated habitat patches supports regional biodiversity and stability, so understanding the underlying processes and structure is a key target of conservation. Although multivariate statistics can infer the connectivity processes driving species distribution, such as dispersal and habitat suitability, they rarely explore the structure. Methods from graph theory, applied to distribution data, give insights into both connectivity pathways and processes by intuitively formatting the data as a network of habitat patches. We apply these methods to empirical data from the hydrothermal vent habitats of the Northwest Pacific. Hydrothermal vents are “oases” of biological productivity and endemicity on the seafloor that are imminently threatened by anthropogenic disturbances with unknown consequences to biodiversity. Here, we describe the structure of species assemblage networks at hydrothermal vents, how local and regional parameters affect their structure, and the implications for conservation. Two complementary networks were formed from an extensive species assemblage dataset: a similarity network of vent site nodes linked by weighted edges based on their pairwise assemblage similarity and a bipartite network of species nodes linked to vent site nodes at which they are present. Using these networks, we assessed the role of individual vent sites in maintaining network connectivity and identified biogeographic sub-regions. The three sub-regions and two outlying sites are separated by their spatial arrangement and local environmental filters. Both networks detected vent sites that play a disproportionately important role in regional pathways, while the bipartite network also identified key vent sites maintaining the distinct species assemblages of their sub-regions. These regional connectivity pathways provide insights into historical colonization routes, while sub-regional connectivity pathways are of value when selecting sites for conservation and/or estimating the multivent impacts from proposed deep-sea mining.<br /> <br /> Brunner O*, Chen C, Giguère T, Kawagucci S, Watanabe HK, Tunnicliffe V, Mitarai S (2022). Hydrothermal vent species assemblage networks identify regional connectivity patterns in the Northwest Pacific. Ecology and Evolution, 12(12): e9612. [Preprint available on bioRxiv, DOI: 10.1101/2022.07.20.500901]
Just published in Ecology, our paper reveals stark anatomical shifts linked with distinct diets in closely related deep-sea snails, using 3D reconstructions from synchrotron-CT data. We suggest that organ volumetrics can be useful in predicting diets of rare animals known from only preserved specimens. OPEN ACCESS: https://doi.org/10.1002/ecy.3847<br /> <br /> Summary:<br /> Specializing in different dietary niches via morphological adaptation underpins the success of animal radiation when invading a new environment, as seen in examples such as Darwin's finches (De León et al., 2014). Ecomorphological studies of various animal groups, from mammals to arthropods, illustrate adaptations to different food sources, which are often coupled with shifts in internal anatomy, particularly the digestive system (Duque-Correa et al., 2021; Griffen & Mosblack, 2011). A widely accepted pattern in terrestrial systems is that herbivorous mammals require longer and more voluminous gastrointestinal tracts in order to digest plant matter, whereas carnivorous mammals have smaller intestines since meat is much more digestible (Duque-Correa et al., 2021). Such research has mostly focused on animals in land-based ecosystems powered by photosynthesis, but these ecosystems only account for a fraction of the broad diversity of ecosystems on Earth. “Extreme” deep-sea ecosystems, such as hydrothermal vents, hydrocarbon seeps, and organic falls, are powered by microbial chemosynthesis (Childress & Girguis, 2011) and host numerous endemic fauna with special adaptations (Sogin et al., 2020), offering an opportunity to explore how the anatomy of animals evolved to specialize in unusual diets. Our results demonstrated that adapting to each peculiar deep-sea food source is linked to specific anatomical shifts, expanding the applicability of ecomorphology to a range of unusual diets. The deep sea remains little known and unexplored, despite its many habitats, including hydrothermal vents, which are being targeted for deep-sea mining, threatening endemic species (Thomas et al., 2022). Understanding the trophic dynamics in these systems and the role each species plays is crucial to successful conservation, yet numerous species have never been observed in their natural habitat. The accurate reconstruction of organ volumetrics using noninvasive methods, such as μ-CT scans, can be a useful tool in predicting the diet of deep-sea animals even when only preserved specimens are available, similarly to how ecomorphology has been used to reconstruct habitat preferences in fossil mammals (DeGusta & Vrba, 2005). This would clearly require the future accumulation of 3D anatomical data from a wide range of deep-sea species with various unique diets, which will undoubtedly reveal many anatomical surprises.<br /> <br /> Chen C*, Watanabe HK, Gena K, Johnson SB (2022). Anatomical shifts linked with unusual diets in deep-sea snails. Ecology, Early View: e3847. DOI: 10.1002/ecy.3847
The gastropod subclass Neomphaliones (comprising the two orders Neomphalida and Cocculinida) typically inhabit deep-waters and are thus often poorly sampled in phylogenetic analyses. In a paper just published in Frontiers in Ecology and Evolution, we report nine new mitogenomes from Neomphaliones and recover some clade-specific gene orders! The paper is OPEN ACCESS: https://doi.org/10.3389/fevo.2022.973485<br /> <br /> Abstract: <br /> Gastropoda is the most speciose class in Mollusca, the second largest animal phylum. The internal relationships of major gastropod groups remain largely unsettled, partly due to the insufficient data from key deep-water endemic lineages such as the subclass Neomphaliones. Neomphaliones currently includes two orders: Cocculinida, best known from sunken wood habitats, and Neomphalida, best known from hydrothermal vents and often referred to as the “hot vent clade.” Phylogenetic controversy has also been observed in this subclass across different studies, requesting additional investigations. Here, we assembled nine new mitogenomes from two Cocculinida and seven Neomphalida species and analyzed them with published gastropod mitogenomes, with a particular focus on Neomphaliones. The phylogenetic reconstruction of Gastropoda based on 13 mitochondrial protein-coding genes resulted in a topology largely congruent with previous reconstructions based on morphological characters. Furthermore, we recovered characteristic mitochondrial gene order arrangements of Cocculinida and Neomphalida compared to the hypothetical ancestral gastropod gene order, at a level similar to other subclass-level clades. Divergence time estimation showed that Cocculinida and Neomphalida diverged approximately 322.68 million years ago. In addition to characteristic gene order arrangements for the clade, Cocculinida mitogenomes also exhibit some minor rearrangements even among congeners. Within Neomphalida, our tree adds support to monophyletic Peltospiridae and Neomphalidae, with unique gene arrangement recovered for each family. Our results offer new insights into the rearrangement of mitogenomes in Gastropoda, providing another clue to the evolutionary history of gastropods.<br /> <br /> Zhong Z, Lan Y, Chen C, Zhou Y, Linse K, Li R, Sun J* (2022). New mitogenomes in deep-water endemic Cocculinida and Neomphalida shed light on lineage-specific gene orders in major gastropod clades. Frontiers in Ecology and Evolution, 10: 973485. DOI: 10.3389/fevo.2022.973485
The Aurora Vent Field located >3800 m deep in the Central Arctic Ocean is the world's northernmost deep-sea hydrothermal vent at 82°53.82'N. In this paper we describe a new cocculinid limpet, Cocculina aurora, from this unusual locality! This is the only vent-endemic cocculinid known to date (they typically occur on sunken wood). As Aurora is under permanent Arctic sea ice cover, sampling there was extremely difficult and took multiple attempts using ice breakers. OPEN ACCESS in Royal Society Open Science: https://doi.org/10.1098/rsos.220885<br /> <br /> Abstract: <br /> Deep-sea hydrothermal vents host lush chemosynthetic communities, dominated by endemic fauna that cannot live in other ecosystems. Despite over 500 active vents found worldwide, the Arctic has remained a little-studied piece of vent biogeography. Though located as early as 2001, the faunal communities of the Aurora Vent Field on the ultra-slow spreading Gakkel Ridge remained unsampled until recently, owing to difficulties with sampling on complex topography below permanent ice. Here, we report an unusual cocculinid limpet abundant on inactive chimneys in Aurora (3883–3884 m depth), describing it as Cocculina aurora n. sp. using an integrative approach combining traditional dissection, electron microscopy, molecular phylogeny, and three-dimensional anatomical reconstruction. Gross anatomy of the new species was typical for Cocculina, but it has a unique radula with broad, multi-cuspid rachidian where the outermost lateral is reduced compared to typical cocculinids. A phylogenetic reconstruction using the mitochondrial COI gene also confirmed its placement in Cocculina. Only the second cocculinid found at vents following the description of the Antarctic Cocculina enigmadonta, this is currently the sole cocculinid restricted to vents. Our discovery adds to the evidence that Arctic vents host animal communities closely associated with wood falls and distinct from other parts of the world.<br /> <br /> Chen C*, Hilário A, Rodrigues CF, Ramirez-Llodra E (2022). Integrative taxonomy of a new cocculinid limpet dominating the Aurora vent field in the central Arctic ocean. Royal Society Open Science, 9(10): 220885. DOI: 10.1098/rsos.220885
We developed a novel method for identifying the two chitin allotypes (α and β) by using ethylenediamine (EDA) as a complexing agent! This works even for near-amorphous natural samples, which have been difficult to discern with existing methods. This method will pave the way to building an overarching understanding of chitin biosynthesis and its evolutionary history. Led by Noriyuki Isobe, just out in Biomacromolecules. OPEN ACCESS: https://doi.org/10.1021/acs.biomac.2c00714<br /> <br /> Abstract: <br /> Chitin is a key component of hard parts in many organisms, but the biosynthesis of the two distinctive chitin allomorphs, α- and β-chitin, is not well understood. The accurate determination of chitin allomorphs in natural biomaterials is vital. Many chitin-secreting living organisms, however, produce poorly crystalline chitin. This leads to spectrums with only broad lines and imprecise peak positions under conventional analytical methods such as X-ray diffraction (XRD), Fourier-transform infrared spectroscopy, and solid-state nuclear magnetic resonance spectroscopy, resulting in inconclusive identification of chitin allomorphs. Here, we developed a novel method for discerning chitin allomorphs based on their different complexation capacity and guest selectivity, using ethylenediamine (EDA) as a complexing agent. From the peak shift observed in XRD profiles of the chitin/EDA complex, the chitin allomorphs can be clearly discerned. By testing this method on a series of samples with different chitin allomorphs and crystallinity, we show that the sensitivity is sufficiently high to detect the chitin allomorphs even in near-amorphous, very poorly crystalline samples. This is a powerful tool for determining the chitin allomorphs in phylogenetically important chitin-producing organisms and will pave the way for clarifying the evolution and mechanism of chitin biosynthesis.<br /> <br /> Isobe N*, Kaku Y, Okada S, Kawada S, Tanaka K, Fujiwara Y, Nakajima R, Bissessur D, Chen C (2022). Identification of chitin allomorphs in poorly crystalline samples based on the complexation with ethylenediamine. Biomacromolecules, Articles ASAP. DOI: 10.1021/acs.biomac.2c00714 [Preprint available on ChemRxiv, DOI: 10.26434/chemrxiv- 2022-5mj8x-v2]
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<br /> <br /> Abstract:<br /> 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.<br /> <br /> 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 /> <br /> 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 /> <br /> 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 /> <br /> 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 /> <br /> 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 /> <br /> 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 /> <br /> 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 /> <br /> 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 /> <br /> 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 /> <br /> 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 /> <br /> 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<br /> <br /> Abstract<br /> 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.<br /> <br /> 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
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