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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 described and named four new species of scale worms inhabiting Indian Ocean deep-sea hydrothermal vents in a Zoological Journal of the Linnean Society paper led by Yuru Han and Yadong Zhou! Phylogeography revealed at least three separate historical invasions to Indian Ocean vents. Link to paper: https://doi.org/10.1093/zoolinnean/zlad140<br /> <br /> Abstract: <br /> Lepidonotopodinae is a subfamily of Polynoidae endemic to deep-sea chemosynthetic ecosystems around the world. Nevertheless, their species composition and phylogeny have only been systematically studied in hydrothermal vents of the Eastern and Western Pacific. Here, we morphologically and genetically examined worms in Lepidonotopodinae from vents across three Indian Ocean ridges, revealing two new Branchinotogluma species (B. jiaolongae sp. nov. and B. kaireiensis sp. nov.) and two new Levensteiniella species (L. pettiboneae sp. nov. and L. longqiensis sp. nov.). Primary morphological characters distinguishing them from other congeners include the number and arrangement of both pharyngeal papillae and ventral papillae. The reconstructed molecular phylogeny of Lepidonotopodinae supports a monophyletic Levensteiniella, with the two new Indian Ocean species recovered as sisters. As revealed in previous studies, a paraphyletic Branchinotogluma was also found, with the three Indian Ocean species separated into distinct clades with sister-relationships to species from the Mid-Atlantic, Alarcon Rise, and Manus Basin, respectively. This indicates three separate historical invasions to Indian Ocean vents. Our findings increase the number of Indian Ocean Lepidonotopodinae worms to seven, now the most diverse annelid group there, and help to elucidate the biodiversity, distribution, and biogeography of this subfamily in the Indian Ocean.<br /> <br /> Han Y, Zhou Y*, Chen C, Wang Y (2023). Diversity and biogeography of scale worms in the subfamily Lepidonotopodinae from Indian Ocean hydrothermal vents with descriptions of four new species. Zoological Journal of the Linnean Society, Advanced Access. DOI: 10.1093/zoolinnean/zlad140
In a new study led by Xing HE and Ting Xu, we carried out biogeographic analyses of Indo-W Pacific deep-sea chemosynthetic ecosystems using a much improved community composition dataset for Haima seep, South China Sea and also seeps off India and Pakistan -- revealing their close biogeographic ties. Now out in The Innovation Geoscience, OPEN ACCESS: https://www.the-innovation.org/article/doi/10.59717/j.xinn-geo.2023.100019<br /> <br /> Abstract: <br /> Deep-sea chemosynthetic communities, including hydrothermal vents and cold seeps, harbour hundreds of endemic species currently threatened by deep-sea mining and hydrocarbon extraction. The South China Sea (SCS), a semi-enclosed marginal sea with two well-investigated active seeps (Haima in the west and Site F in the east), provides an opportunity to understand the biogeography of chemosynthetic ecosystems. Here, we conducted extensive field surveys using Remotely Operated Vehicles (ROVs) and collected specimens for morphological observations, molecular barcoding, phylogenetic analysis, and stable isotope analysis. Cluster analyses were applied to reveal the community structure of vents and seeps in the Western Pacific and Northern Indian Ocean. A total of 65 species covering seven phyla and 14 classes have been identified from Haima, doubling the number of species reported previously. Among them, 35 species are currently known only from Haima. Stable isotope analysis shows a typical chemosynthesis-based biological community. Community structure analysis at the genus level clustered Haima with Site F, though the species compositions and dominance of two seeps are fairly distinct. Between the two active seeps in the SCS, the higher species richness and endemism at Haima are potentially due to multiple factors, including the unique environmental factors there and the geographic isolation in the northwestern corner of the SCS. Moreover, a similarity in community compositions at the genus level between seeps in the SCS and North Indian Ocean was revealed, potentially mediated by the Early Pliocene opening of the Indonesian islands and the strong westward Indonesia Throughflow. Given the ongoing gas hydrate exploration activities in the SCS, our results will contribute to establishing a global network of marine protected areas for chemosynthetic-based ecosystems. The rich and endemic biodiversity at Haima calls for policymakers to formulate regulations to conserve the unique biodiversity there. <br /> <br /> He X# / Xu T#, Chen C, Liu X, Li Y-X, Zhong Z, Gu X, Lin Y-T, Lan Y, Yan G, Sun Y, Qiu J-W*, Qian P-Y*, Sun J* (2023). Same (sea) bed different dreams: Biological community structure of the Haima seep reveals distinct biogeographic affinities. The Innovation Geoscience, 1(2): 100019. DOI: 10.59717/j.xinn-geo.2023.100019
We studied the population genomics of the symbiont allying with the vent mussel Bathymodiolus septemdierum, finding overall structuring by geographic location but a single strain dominanting regardless -- a contrasting pattern from co-occurring snail symbioses. Out now in mSystems, OPEN ACCESS: https://doi.org/10.1128/msystems.00284-23<br /> <br /> Abstract: <br /> The intra-host composition of horizontally transmitted microbial symbionts can vary across host populations due to interactive effects of host genetics, environmental, and geographic factors. While adaptation to local habitat conditions can drive geographic subdivision of symbiont strains, it is unknown how differences in ecological characteristics among host-symbiont associations influence the genomic structure of symbiont populations. To address this question, we sequenced metagenomes of different populations of the deep-sea mussel Bathymodiolus septemdierum, which are common at Western Pacific deep-sea hydrothermal vents and show characteristic patterns of niche partitioning with sympatric gastropod symbioses. Bathymodiolus septemdierum lives in close symbiotic relationship with sulfur-oxidizing chemosynthetic bacteria but supplements its symbiotrophic diet through filter-feeding, enabling it to occupy ecological niches with little exposure to geochemical reductants. Our analyses indicate that symbiont populations associated with B. septemdierum show structuring by geographic location, but that the dominant symbiont strain is uncorrelated with vent site. These patterns are in contrast to co-occurring Alviniconcha and Ifremeria gastropod symbioses that exhibit greater symbiont nutritional dependence and occupy habitats with higher spatial variability in environmental conditions. Our results suggest that relative habitat homogeneity combined with sufficient symbiont dispersal and genomic mixing might promote persistence of similar symbiont strains across geographic locations, while mixotrophy might decrease selective pressures on the host to affiliate with locally adapted symbiont strains. Overall, these data contribute to our understanding of the potential mechanisms influencing symbiont population structure across a spectrum of marine microbial symbioses that occupy contrasting ecological niches.<br /> <br /> Breusing C*, Xiao Y, Russell SL, Corbett-Detig RB, Li S, Sun J, Chen C, Lan Y, Qian P-Y, Beinart RA* (2023). Ecological differences among hydrothermal vent symbioses may drive contrasting patterns of symbiont population differentiation. mSystems, Ahead of Print. DOI: 10.1128/msystems.00284-23 [Preprint available on bioRxiv, DOI: 10.1101/2022.08.30.505939]
Our new paper in Genome Biology and Evolution presents a chromosome-scale genome of the vent-endemic scale worm Branchipolynoe longqiensis! This is the first annotated genome of the annelid subclass Errantia. The paper is OPEN ACCESS: https://doi.org/10.1093/gbe/evad125<br /> <br /> Abstract: <br /> Deep-sea polynoid scale worms endemic to hydrothermal vents have evolved an adaptive strategy to the chronically hypoxic environment, but its underlying molecular mechanisms remain elusive. Here, we assembled a chromosome-scale genome of the vent-endemic scale worm Branchipolynoe longqiensis (the first annotated genome in the subclass Errantia) and annotated two shallow-water polynoid genomes, aiming to elucidate the adaptive mechanisms. We present a genome-wide molecular phylogeny of Annelida which calls for extensive taxonomy revision by including more genomes from key lineages. The B. longqiensis genome with a genome size of 1.86 Gb and 18 pseudochromosomes is larger than the genomes of two shallow-water polynoids, possibly due to the expansion of various transposable elements (TEs) and transposons. We revealed two interchromosomal rearrangements in B. longqiensis when compared with the two shallow-water polynoid genomes. The intron elongation and interchromosomal rearrangement can influence a number of biological processes, such as vesicle transport, microtubules, and transcription factors. Furthermore, the expansion of cytoskeleton-related gene families may favor the cell structure maintenance of B. longqiensis in the deep ocean. The expansion of synaptic vesicle exocytosis genes has possibly contributed to the unique complex structure of the nerve system in B. longqiensis. Finally, we uncovered an expansion of single-domain hemoglobin and a unique formation of tetra-domain hemoglobin via tandem duplications, which may be related to the adaptation to a hypoxic environment.<br /> <br /> He X, Wang H, Xu T, Zhang Y, Chen C, Qiu J-W, Zhou Y*, Sun J* (2023). Genomic analysis of a scale worm provides insights into its adaptation to deep-sea hydrothermal vents. Genome Biology and Evolution, 15(7): evad125. DOI: 10.1093/gbe/evad125
We are on the cover of Biology Letters! Read our paper for FREE and find out how the ultra-rare and super-weird parasitic barnacle Rhizolepas evolved from its free-living ancestors: https://doi.org/10.1098/rsbl.2022.0550<br /> <br /> Abstract:<br /> Understanding how animals evolve to become parasites is key to unravelling how biodiversity is generated as a whole, as parasites could account for half of all species richness. Two significant impediments to this are that parasites fossilize poorly and that they retain few clear shared morphological features with non-parasitic relatives. Barnacles include some of the most astonishingly adapted parasites with the adult body reduced to just a network of tubes plus an external reproductive body, but how they originated from the sessile, filter-feeding form is still a mystery. Here, we present compelling molecular evidence that the exceedingly rare scale-worm parasite barnacle Rhizolepas is positioned within a clade comprising species currently assigned to Octolasmis, a genus exclusively commensal with at least six different phyla of animals. Our results imply that species in this genus-level clade represent an array of species at various transitional stages from free-living to parasitic in terms of plate reduction and host-parasite intimacy. Diverging only about 19.15 million years ago, the route to parasitism in Rhizolepas was associated with rapid modifications in anatomy, a pattern that was likely true for many other parasitic lineages.<br /> <br /> Hiromi Watanabe-Kayama, Uyeno D, Yamamori L, Naoto Jimi, Chen C* (2023). From commensalism to parasitism within a genus-level clade of barnacles. Biology Letters, 19: 20220550. DOI: 10.1098/rsbl.2022.0550
Our new paper in the journal Island Arc reports a huge undersea lake of molten sulfur on Daikoku Seamount vent field, Mariana Arc! We attempted to sample it using a method inspired by cheese fondue....?! Check it out for free: https://onlinelibrary.wiley.com/share/author/A9AWFMXEGRNZQ93F9UKU?target=10.1111/iar.12489<br /> Make sure to look at the acknowledgements!!<br /> <br /> Abstract:<br /> Lakes of molten sulfur are features sometimes found in seafloor hydrothermal vent systems. Daikoku of the northern Mariana Arc is notable for being home to one of such features inside its summit caldera, the “Sulfur Cauldron” discovered in 2006. A number of oceanographic research cruises since then have revealed significant volcanic activities on Daikoku Seamount, including an eruption event in 2014 leading to the formation of a new basin-like crater. How this event impacted the sulfur lake on Daikoku Seamount remained unclear. Here, we revisited Daikoku Seamount with a remotely operated vehicle to show that the new crater is currently home to a much larger molten sulfur lake than the Sulfur Cauldron, which we name the “Rengoku” sulfur lake. Our samples provided new insights on the structure of submarine sulfur lakes, and contribute to the time-series observation of volcanic and hydrothermal activities on Daikoku Seamount.<br /> <br /> Sawada H*# / Chen C#, Iwamoto H, Takai K (2023). A trip into molten sulfur. Island Arc, 32(1): e12489. DOI: 10.1111/iar.12489
We found a new cold seep animal community on Asùt Tesoru (Blg Blue) serpentinite seamount on the Mariana Forearc! With only small-sized and infaunal species, this chemosynthetic system has been overlooked for decades. The paper is OPEN ACCESS in Marine Ecology: https://doi.org/10.1111/maec.12759<br /> <br /> Abstract: <br /> Chemosynthetic ecosystems powered by microbial primary production are rare ‘hot spots’ of biological activity in the deep-sea characterized by dense aggregations of specially adapted animal species. Among settings where such systems have been found, serpentinite-hosted seep systems supported by alkaline geofluid are particularly understudied with just a few known sites worldwide. Mariana Forearc hosts the world's only series of active serpentinite mud volcanoes, but seep communities have only been reported from South Chamorro Seamount where large bathymodioline mussels dominate. Here, we report the discovery of a serpentinite-hosted seep on the conical summit of Asùt Tesoru Seamount, Mariana Forearc. Named the ‘Big Blue Seep’, this field features white, likely carbonate crusts inhabited by animals, under which fluid seepage could be seen. We confirm 16 animal species, including typical seep-associated fauna such as Desbruyeresia gastropods and Acharax awning-clams. This is surprising as previous research expeditions did not notice any sign of chemosynthesis-based ecosystems on this seamount, although the community is indeed difficult to spot due to the lack of large-bodied epifauna such as mussels. The Big Blue Seep is adjacent to three drill holes made by the International Ocean Discovery Program expedition 366 (Holes U1496A-C), which may have impact on seepage. Our findings represent the second chemosynthesis-based ecosystem associated with serpentinite mud volcanism, suggestive of further such communities on other Mariana Forearc mud volcanoes.<br /> <br /> Chen C*, Watanabe HK, Sawada H, Iwamoto H, Takai K (2023). Unexpected discovery of a serpentinite-hosted chemosynthetic ecosystem on Asùt Tesoru Seamount, Mariana Forearc. Marine Ecology, Early View: e12759. DOI: 10.1111/maec.12759
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]
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