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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

Our new paper in Marine Ecology reports the animal community in the serpentinisation-hosted cold seep on the South Chamorro Seamount, Mariana Forearc. We also found evidence that scientific drilling wiped out a lush community there in 2001 with no signs of recovery 22 years later! OPEN ACCESS: https://doi.org/10.1111/maec.12808<br /> <br /> Abstract:<br /> Deep-sea chemosynthetic ecosystems are ‘oases’ of life powered by reducing geofluids, of which serpentinite-hosted seeps are among the least studied. South Chamorro Seamount, a serpentine mud volcano on the Mariana Arc, has been known to host chemosynthesis-based assemblages since 1996, but no detailed information on the fauna was published. Here, we revisited South Chamorro to characterise its biodiversity. We located two regions of chemosynthetic communities dominated by bathymodioline mussels, vesicomyid clams, and chaetopterid parchment worms: one on the northwestern flank (‘Fryer Site’) and one on the southern summit (‘Summit Site’). We sampled a total of 20 species including 13 molluscs, five annelids, and two crustaceans – all present on the more active Summit Site but only a subset being found at Fryer Site. A mussel bed surrounding the Fryer Site was drilled by the Ocean Drilling Program in 2001 resulting in six holes, the deepest being 266 m (Hole 1200C). Cuttings ~50 cm deep still cover an approximately 60 m radius around Hole 1200C even 22 years later, and there is no sign of recovery. Low geofluid supply in serpentinite-hosted seamounts may not allow decadal recovery of animal colonies, unlike a previous drilling site in an Okinawa Trough vent.<br /> <br /> Chen C*, Watanabe HK, Sawada H, Iwamoto H, Takai K (2024). Serpentinite-hosted chemosynthetic community of South Chamorro Seamount, Mariana Forearc. Marine Ecology, Early View. DOI: 10.1111/maec.12808
We used natural-abundance radiocarbon (Δ14C) and habitat water temperature to reveal carbon sources of deep-sea hydrothermal vent animals! Closer to vent orifice means more carbon (up to 74.8%) from vent fluid CO2 -- unless one uses methane. Just out in Limnology and Oceanography, OPEN ACCESS: https://doi.org/10.1002/lno.12570<br /> <br /> Abstract: <br /> Deep-sea hydrothermal vents host exceptional ecosystems with lush animal communities primarily relying on organic matter (OM) produced by chemoautotrophic microbes. Though energy sources and food webs at vents have been extensively studied, the exact carbon sources of chemosynthetic primary production, such as methane (CH4) and carbon dioxide (CO2) in the vent fluid or bottom water, have not been elucidated quantitatively across spatial scales. Here, we investigate carbon and nitrogen sources of 12 vent animal species at the Iheya North field, Okinawa Trough inhabiting different distances from the central venting area and with various feeding ecologies using natural-abundance radiocarbon (Δ14C) in combination with conventional stable carbon and nitrogen isotope ratios (δ13C and δ15N). Our results show that generally, animals living closer to vent orifices were more depleted in 14C, indicating they assimilate more carbon from vent fluid CO2. Those relying on methanotrophs, however, exhibited low Δ14C values regardless of distance due to the lack of methane in the non-vent-influenced bottom water. Organisms with low Δ14C values also tend to exhibit low δ15N values, implying NH4+ assimilation into biomass in environments with high NH4+ concentrations. Our results demonstrate that 14C can clearly distinguish between chemoautotrophically fixed carbon originating from the vent fluid and detrital OM derived from surface primary production, and also discriminate between CO2- and CH4-based chemoautotrophy. Although vent animals rely on vent fluid energetically, our results highlight that the dependency on vent fluids as carbon source varies greatly depending on habitat, as well as carbon fixation pathways of microbial primary producers.<br /> <br /> Nomaki H*, Chen C, Ogawa NO, Miyairi Y, Ohkouchi N, Makabe A, Kawagucci S, Yokoyama Y, Shimanaga M (2024). Elucidating carbon sources of hydrothermal vent animals using natural 14C abundances and habitat water temperature. Limnology and Oceanography, Early View. DOI: 10.1002/lno.12570
We discovered a brand new deep-sea hydrothermal vent field in Japan, on the Amami Rift where Okinawa Trough and Ryukyu Arc meet! We found 29 animal species, including 19 vent specialists. Out now in Journal of the Marine Biological Association of the United Kingdom: https://doi.org/10.1017/S0025315424000304<br /> <br /> Abstract:<br /> Deep-sea hydrothermal vents host chemosynthesis-based ecosystems inhabited chiefly by specially adapted animals that do not live anywhere else, and depth has been shown to be a major driver of species composition at vents around Japan. Though the Ryukyu region in southern Japan is home to many hot vents, only two – Minami-Ensei Knoll and Yoron Hole – have been found shallower than 1000 m. Here, we report the discovery of a new vent field on the Amami Rift northwest off Amami Ōshima at 630 m deep. A total of 29 macrofaunal species were recorded from Amami Rift, including 19 vent specialists. Comparison of species composition across the three shallow Ryukyu vents revealed only three shared species, highlighting that all three display distinct community structure. Amami Rift exhibits distinct zonation patterns and is generally more similar to Minami-Ensei than Yoron Hole, but the presence of key taxa such as the sulphide worm Paralvinella and the mussel ‘Bathymodiolus’ platifrons as well as the absence of the symbiotic squat lobster Shinkaia and the limpet Lepetodrilus exemplify its difference with Minami-Ensei. Furthermore, the non-vent specific predators seen in these two sites were completely different. Overall, the Amami Rift vent field can be considered a shallow vent with a unique set of fauna, warranting future research on the mechanisms shaping disparate macrofaunal diversity between nearby shallow vents such as Amami Rift and Minami-Ensei. The unusual geological setting of Amami Rift at the converging point of Okinawa Trough and Ryukyu Arc may influence fluid chemistry to drive such differences.<br /> <br /> Chen C*, Hookabe N, Komatsu H (2024). Macrofaunal community of a new hot vent field on the Amami Rift. Journal of the Marine Biological Association of the United Kingdom, 104: e39. DOI: 10.1017/S0025315424000304<br /> <br /> PDF: https://www.researchgate.net/publication/379573502_Faunal_community_of_a_new_hot_vent_field_on_the_Amami_Rift
We revised the generic placement of two hadal thyasirid bivalves from cold seeps in the Japan Trench, including naming a new genus for Tartarothyas hadalis (new combination) -- the deepest known bivalve with chemosynthetic symbiosis at over 7400 m depth. This paper is OPEN ACCESS and freely available here: https://doi.org/10.61733/jconch/1405<br /> <br /> Abstract:<br /> The hadal bivalves from the Japan Trench originally described as Maorithyas hadalis and Parathyasira kaireiae are reassigned to the genera Tartarothyas n. gen. and Spinaxinus, respectively. The shell, anatomy, and fine structure of the ctenidia are described, and based on these the new genus Tartarothyas is introduced. Both species have modified ctenidia to host chemosymbiotic bacteria; those of Tartarothyas n. gen. is partly tubular in structure, whereas those of Spinaxinus is of fleshy lamellae.<br /> <br /> Oliver PG*, Chen C (2024). Revision of the generic placement of two hadal bivalves (Bivalvia: Thyasiridae) from the Japan Trench with the introduction of a new genus, Tartarothyas. Journal of Conchology, 45(1): 35-50. DOI: 10.61733/jconch/1405
We updated the list of animals inhabiting Galápagos Rift hydrothermal vents based on new findings from our 2023 Schmidt Ocean Institute Galápagos expedition (+literature review) -- adding 15 new records to make a total of 92 species! We also discovered a new vent field which we named "Tortugas". The paper is OPEN ACCESS in Marine Biodiversity: https://doi.org/10.1007/s12526-024-01408-w<br /> <br /> Abstract: <br /> The sighting of giant bivalves and tubeworms at the Rose Garden vent field on the Galápagos Rift in 1977 marked the discovery of hydrothermal vents, a turning point for modern biology. The following decade saw a flurry of taxonomic descriptions of vent endemic species from the first vents. With the finding of high-temperature “black smokers” on the East Pacific Rise, exploration shifted away from Galápagos. A faunal list of Galápagos vents with 65 species was published in 1991, then updated to 74 species in 2006. Since then, few expeditions returned to the Galápagos Rift. Here, we revisited several Galápagos vents including recently confirmed high-temperature sites and inactive sulfide mounds. From our collecting efforts and observations, as well as revisions from the literature, we update the faunal list to 92 species including 15 new records, restricted to obvious vent associates. Accurate regional faunal lists are important for understanding the biogeography of vent fauna, and our list will also be valuable for setting management strategies.<br /> <br /> Chen C*, Jamieson JW, Tunnicliffe V (2024). Hydrothermal vent fauna of the Galápagos Rift: updated species list with new records. Marine Biodiversity, 54: 16. DOI: 10.1007/s12526-024-01408-w [Preprint available on bioRxiv, DOI: 10.1101/2023.11.28.568903]
In a Zootaxa paper, we revised the hot vent shrimp genus Rimicaris, synonymising a number of genera with it in order to rectify the long-standing issue of its paraphyly. We also described a new species -- Rimicaris cambonae, named after Marie-Anne Cambon from IFREMER in France! Link: https://mapress.com/zt/article/view/zootaxa.5406.4.1<br /> <br /> Abstract: <br /> A new species of alvinocaridid shrimp is reported, from the Northwest Eifuku hydrothermal vent field at 1619–1667 m depth on the Mariana Arc. A comprehensive phylogenetic reconstruction of Alvinocarididae based on the mitochondrial cytochrome c oxidase subunit I (COI) gene including this new species reveals the paraphyly of the genus Rimicaris Williams & Rona, 1986 with four other genera—Alvinocaridinides, Manuscaris, Opaepele, and Shinkaicaris—nested within it. We re-examine material of these four problematic genera, and synonymise them under Rimicaris whose diagnosis has been amended, in order to maintain a monophyletic Rimicaris. Our new species, Rimicaris cambonae sp. nov. is genetically close to Rimicaris loihi (Williams & Dobbs, 1995) comb. nov. (previously Opaepele loihi) with which it co-occurs, but can be morphologically distinguished by the less elevated dorsal surface of the rostrum, this being devoid of a median carina, a stronger pterygostomial tooth on the carapace, and a blunt rather than acuminate proximolateral process on the antennular stylocerite. Species previously assigned to the above listed, synonymized genera are also discussed, with new material examined for three key species: R. loihi, R. acuminata, and R. leurokolos. Further, Alvinocaridinides formosa Komai & Chan, 2010 and Manuscaris liui Wang & Sha, 2016 are synonymized under Rimicaris leurokolos (Kikuchi & Hashimoto, 2000) comb. nov. and R. acuminata (Komai & Tsuchida, 2015) comb. nov., respectively. Revised diagnoses are presented for R. loihi, R. acuminata, and R. leurokolos. After the present revision revision, Rimicaris now consists of 15 species.<br /> <br /> Methou P*, Chen C, Komai T (2024). Revision of the alvinocaridid shrimp genus Rimicaris Williams & Rona, 1986 (Decapoda: Caridea) with description of a new species from the Mariana Arc hydrothermal vents. Zootaxa, 5406(4): 501-518. DOI: 10.11646/zootaxa.5406.4.1 PDF: https://www.researchgate.net/publication/378040507_Revision_of_the_alvinocaridid_shrimp_genus_Rimicaris_Williams_Rona_1986_Decapoda_Caridea_with_description_of_a_new_species_from_the_Mariana_Arc_hydrothermal_vents
We used amino acid nitrogen isotopes to clearly show that two cold seep copepods gain nutrition from their host animals, in the first application of this technique to parasite-host pairs in deep-sea chemosynthetic ecosystems. Out now in Marine Ecology Progress Series: https://doi.org/10.3354/meps14503<br /> <br /> Abstract: <br /> Deep-sea chemosynthetic ecosystems harbour high biomass centred around animals with chemoautotrophic symbionts. Despite being intensively studied over the last 4 decades, microscopic animals associated with and/or parasitic on dominating holobionts remain understudied. Here, we combine bulk tissue isotope analysis for carbon and nitrogen and compound-specific isotope analysis of amino acids (CSIA-AA) for nitrogen to elucidate the relationship between 2 copepod-host pairs from the Off Hatsushima hydrothermal seep in Sagami Bay, Japan: the vesicomyid clam Phreagena okutanii and Hyphalion sagamiense living on its mantle, and the tubeworm Lamellibrachia columna and Dirivultus kaiko found on its plume. Bulk tissue isotope analyses found overall large variations in δ13C and δ15N values across both associations, and did not allow conclusions on the trophic relationship between each pair. In contrast, CSIA-AA for Phreagena-Hyphalion clearly showed trophic positions (TPGlu/Phe) increasing from gill (symbiont) to adductor muscle (host tissue) to H. sagamiense. In the case of Lamellibrachia-Dirivultus, a similar increase in TPGlu/Phe was found from the plume to D. kaiko. These results show that both H. sagamiense and D. kaiko are nutritionally dependent on their respective hosts and therefore should be considered parasites despite being from copepod families that are typically not recognised as parasitic. Our CSIA-AA results represent the first use of this technique to document host-parasite relationships in chemosynthetic ecosystems. Understanding the role of parasites is of great importance in reconstructing energy flow in ecosystems, and our results underscore the promising nature of CSIA-AA in revealing their otherwise hidden relationships. <br /> <br /> Ishikawa NF*, Chen C, Hashimoto R, Ogawa NO, Uyeno D, Nomaki H (2024). Amino acid nitrogen isotopic compositions show seep copepods gain nutrition from host animals. Marine Ecology Progress Series, 727: 81-90. DOI: 10.3354/meps14503<br /> PDF: https://www.researchgate.net/publication/376659302_Amino_acid_nitrogen_isotopic_compositions_show_seep_copepods_gain_nutrition_from_host_animals
We discovered two new deep-sea snails from inactive vent chimneys on the East Pacific Rise -- described as Melanodrymia laurelin and M. telperion, named after the Two Trees of Valinor in J.R.R. Tolkien's legendarium! Link to the paper: https://www.tandfonline.com/eprint/NK6DIQX9QHTYRUAYHMAM/full?target=10.1080/14772000.2023.2294014<br /> <br /> Abstract:<br /> Since their discovery in 1977, animals specialized to life in active deep-sea hydrothermal vents have been the focus of many studies. Inactive spires in the vent periphery, however, have received little attention. Recent shifts of deep-sea mining interests from active vents to inactive sulphide deposits have led to an urgent need to characterize the inactive vent fauna. Here, we report two new species of the vent-endemic genus Melanodrymia that are apparently specific to surfaces of inactive sulphides on the East Pacific Rise. Melanodrymia laurelin sp. nov. and M. telperion sp. nov. are easily distinguished from other congeners by shell shape and sculpture; their standings as distinct species are supported by molecular analyses using the mitochondrial cytochrome c oxidase subunit I (COI) gene. They were collected together with numerous specimens of M. galeronae, another species originally described some distance away from active vents. Phylogenetic reconstruction indicates Melanodrymia species living in active vents likely evolved from ancestors specializing in inactive spires, and in turn from sunken wood. Our findings add to the growing evidence that inactive sulphides host unique species, bolstering the need to better understand these systems before any anthropogenic exploitation takes place.<br /> <br /> Chen C*, Y Li, Sun J, Beaulieu SE, Mullineaux LS (2024). Two new melanodrymiid snails from the East Pacific Rise indicate the potential role of inactive vents as evolutionary stepping-stones. Systematics and Biodiversity, 22(1): 2294014. PDF: https://www.researchgate.net/publication/377577317_Two_new_melanodrymiid_snails_from_the_East_Pacific_Rise_indicate_the_potential_role_of_inactive_vents_as_evolutionary_stepping-stones
We discovered an abyssal wood-fall community at 5505 m depth in the NW Pacific! Total of 27 associated species found, including the ultra-rare sea stars Crinitostella and Xyloplax, plus many likely undescribed snails. Out now in Marine Biology Research: https://www.tandfonline.com/eprint/ZQEPTKHYXXFXM64CKXYF/full?target=10.1080/17451000.2023.2291579<br /> <br /> Abstract: <br /> Plant remains from land, particularly sunken wood, represent significant input of organic matter into the generally oligotrophic deep sea, leading to the formation of macrofaunal assemblages around them. Following the onset of decomposition by wood-boring bivalves, microbes and fungi the wood eventually becomes an anoxic and reducing environment attracting chemosynthetic fauna. Wood falls have primarily been studied by either opportunistic sampling by trawls or artificial deployments, while in situ observations of natural systems remain scarce. Here, we report a natural late-stage wood-fall community at 5505 m depth in the Northwestern Pacific abyssal plain by a manned submersible. Our observations revealed details in faunal distribution that cannot be obtained by trawled material, including the presence of associated xenophyophores. We identified a total of 26 animal species and one xenophyophore from the wood fall including both wood-associated and chemosymbiotic taxa, although cocculiniform limpets were conspicuously missing. Living xylophagaid bivalves were also not observed, but the wood was heavily burrowed and they were clearly once present. This rare finding improves our understanding of deep abyssal wood falls at the senescence stage, and highlights the importance of direct seafloor observations.<br /> <br /> Chen C*, Isobe N, Nomaki H (2024). A deep abyssal natural wood fall in the northwestern Pacific and its associated fauna. Marine Biology Research, Online First. DOI: 10.1080/17451000.2023.2291579
We reconstructed the most complete phylogeny so far for the enigmatic gastropod order Neomphalida using mitogenomes! Our tree implies multiple habitat shifts, including from hot vents to sunken wood; and we also found a unique gene order for each of the three families. Just out in Frontiers in Marine Science (OPEN ACCESS): https://doi.org/10.3389/fmars.2023.1341869<br /> <br /> Abstract: <br /> Neomphalida is an order of gastropod molluscs with highly diverse morphology and a global distribution across various chemosynthesis-based ecosystems from organic falls to hot vents. The phylogenetic relationships of taxa within this order remain contentious, due to the rarity of material leading to a low taxonomic coverage and few genetic markers used. Neomphalida includes three families—Melanodrymiidae, Neomphalidae, and Peltospiridae—and molecular sequences are especially lacking in Melanodrymiidae. Here, we assembled a total of 11 mitogenomes covering these three families and 14 genus-level groups to reconstruct the most complete phylogeny of Neomphalida to date. Our current result recovered the monophyly of three families with maximum support and a likely interfamilial relationship of (Melanodrymiidae + Neomphalidae) + Peltospiridae. These indicate the possibility of habitat shifting from non-chemosynthetic deep sea to hot vent and then to sunken wood, accompanied by elevated mitogenome rearrangements and amino acid substitution rates in Melanodrymiidae. By mapping species distribution on the phylogeny, our findings suggest a Pacific origin of Neomphalida and multiple historical dispersal events of Peltospiridae to the Indian Ocean and at least once to the Atlantic.<br /> <br /> Zhang L, Gu X, Chen C, HE X, Qi Y, Sun J* (2024). Mitogenome-based phylogeny of the gastropod order Neomphalida points to multiple habitat shifts and a Pacific origin. Frontiers in Marine Science, 10: 1341869. DOI: 10.3389/fmars.2023.1341869
Our new paper in Evolution reveals anatomical shifts (using 3D reconstruction!) and development of symbiosis in Rimicaris vent shrimps along their ontogeny. The genetically indistinguishable but morphologically distinct R. hybisae (entirely relying on symbiosis) and R. chacei (mixotrophic) diverge anatomically before reaching adulthood, possibly driven by the level of symbiosis reached during a 'critical period'. The paper is OPEN ACCESS and available here: https://doi.org/10.1093/evolut/qpad217<br /> <br /> Abstract: <br /> Most animal species have a singular developmental pathway and adult ecology, but developmental plasticity is well-known in some such as honeybees where castes display profoundly different morphology and ecology. An intriguing case is the Atlantic deep-sea hydrothermal vent shrimp pair Rimicaris hybisae and R. chacei that share dominant COI haplotypes and could represent very recently diverging lineages or even morphs of the same species. Rimicaris hybisae is symbiont-reliant with a hypertrophied head chamber (in the Mid-Cayman Spreading Centre), while R. chacei is mixotrophic with a narrow head chamber (on the Mid-Atlantic Ridge). Here, we use X-ray micro-computed tomography and fluorescence in situ hybridization to show that key anatomical shifts in both occur during the juvenile–subadult transition, when R. hybisae has fully established symbiosis but not R. chacei. On the Mid-Atlantic Ridge, the diet of R. chacei has been hypothetically linked to competition with the obligatorily symbiotic congener R. exoculata, and we find anatomical evidence that R. exoculata is indeed better adapted for symbiosis. We speculate the possibility that the distinct development trajectories in R. hybisae and R. chacei may be determined by symbiont colonization at a “critical period” before subadulthood, though further genetic studies are warranted to test this hypothesis along with the true relationship between R. hybisae and R. chacei.<br /> <br /> Methou P*, Guéganton M, Copley JT, Watanabe HK, Pradillon F, Cambon-Bonavita M-A, Chen C (2023). Distinct development trajectories and symbiosis modes in vent shrimps. Evolution, qpad217. DOI: 10.1093/evolut/qpad217 [Preprint available on bioRxiv, DOI: 10.1101/2023.07.02.547428]
Our network analyses using 295 species records across 11 Western Pacific hydrothermal vent systems reveal two distinct vent biogeographic regions separated by the equator! We also find high endemism within each vent system, and identify systems especially in need of conservation. These represent important information for future marine spatial planning. Out now in Diversity and Distributions, OPEN ACCESS: https://doi.org/10.1111/ddi.13794<br /> <br /> Abstract<br /> <br /> Aim: Deep-sea hydrothermal vent habitats support a low-diversity fauna in which most species are unique to the ecosystem. To inform conservation planning around this vulnerable marine ecosystem, we examine species distributions over a wide area to assess the underlying beta-diversity components and to examine biogeographic patterns. We assess the concept of a highly connected fauna that would repopulate areas of local extinction from distal locations.<br /> <br /> Location: Western Pacific Ocean from Japan to New Zealand.<br /> <br /> Methods: We assemble a database of 295 confirmed species records for 11 western Pacific vent systems. The SET beta-diversity framework supports query of the distribution of pairwise pattern components in comparisons among vent systems. We build a network based in graph theory to examine connectivity among vent systems based on shared species similarity. A bipartite network revealed the relative role of each species in linkages among vent system nodes. We assess the importance of sampling bias and distance between systems.<br /> <br /> Results: Overall, two-thirds of the taxa are restricted to a single basin or arc. The Mariana Trough system has the highest corrected weighted endemism for vent-specific species, followed by that of the Okinawa Trough. Species replacement is the dominant feature of beta-diversity. Eleven vent systems form seven network modules with stronger connectivity in the Southwest than Northwest Pacific. The Manus Basin vent system emerges as a network ‘hub’ reflecting its central geographic near the equator.<br /> <br /> Main Conclusion: Two western Pacific biogeographic provinces arise, north and south of the equator that few species transcend. Local and regional conservation plans should consider the low network connectivity and high system endemism in management of hydrothermal vent ecosystems in the event of seabed mining. Species recruitment is unlikely to transcend vent system boundaries. We identify Okinawa Trough, Mariana Trough, Manus Basin, Feni-Tabar Arc and Kermadec Arc for development of conservation plans that initiate or expand protection.<br /> <br /> Tunnicliffe V*, Chen C, Giguère T, Rowden AA, Watanabe HK, Brunner O (2023). Hydrothermal vent fauna of the western Pacific Ocean: Distribution patterns and biogeographic networks. Diversity and Distributions, Early View. DOI: 10.1111/ddi.13794
Our new paper in Molecular Phylogenetics and Evolution uses mitogenome phylogenies and phylogenomics to reveal a single deep-sea colonisation event in Patellogastropoda (the “true limpets”)! Read for free from this link: https://authors.elsevier.com/c/1i9OI3m3nNAEqx<br /> <br /> Abstract:<br /> Patellogastropoda, the true limpets, is a major group of gastropods widely distributed in marine habitats from the intertidal to deep sea. Though important for understanding their evolutionary radiation, the phylogenetic relationships among the patellogastropod families have always been challenging to reconstruct, with contradictory results likely due to insufficient sampling. Here, we obtained mitogenomic and phylogenomic data (transcriptomic or genomic) from six species representing the three predominantly deep-water patellogastropod families: Lepetidae, Neolepetopsidae, and Pectinodontidae. By using various phylogenetic methods, we show that mitogenome phylogeny recovers monophyly of eight families in most of the trees, though the relationships among families remain contentious. Meanwhile, a more robust family-level topology consistent with morphology was achieved by phylogenomics. This also reveals that these mainly deep-water families are monophyletic, suggesting a single colonisation of the deep water around the Jurassic. We also found a lack of significant correlation between genome size and habitat depth, despite some deep-water species exhibiting larger genome sizes. Our phylogenomic tree provides a stable phylogenetic backbone for Patellogastropoda that includes seven of the nine recognized families and paves the way for future evolutionary analyses in this major group of molluscs.<br /> <br /> Qi Y# / Zhong Z#, Liu X, He X, Zhou Y, Zhang L, Chen C, Linse K, Qiu J-W, Sun J* (2023). Phylogenomic analyses reveal a single deep-water colonisation in Patellogastropoda. Molecular Phylogenetics and Evolution, 190: 107968. DOI: 10.1016/j.ympev.2023.107968
Our new paper in Molecular Ecology led by Ting Xu uses genomic methods to look at the population connectivity and demographic history of Shinkaia crosnieri, an emblematic squat lobster living in hot vents and cold seeps of the Western Pacific! The paper is OPEN ACCESS: https://onlinelibrary.wiley.com/doi/full/10.1111/mec.17200<br /> <br /> Abstract:<br /> Information on genetic divergence and migration patterns of vent- and seep-endemic macrobenthos can help delimit biogeographical provinces and provide scientific guidelines for deep-sea conservation under the growing threats of anthropogenic disturbances. Nevertheless, related studies are still scarce, impeding the informed conservation of these hotspots of deep-sea biodiversity. To bridge this knowledge gap, we conducted a population connectivity study on the galatheoid squat lobster Shinkaia crosnieri – a deep-sea foundation species widely distributed in vent and seep ecosystems in the Northwest Pacific. With the application of an interdisciplinary methodology involving population genomics and oceanographic approaches, we unveiled two semi-isolated lineages of S. crosnieri with limited and asymmetrical gene flow potentially shaped by the geographic settings, habitat types, and ocean currents – one comprising vent populations in the Okinawa Trough, with those inhabiting the southern trough area likely serving as the source; the other being the Jiaolong (JR) seep population in the South China Sea. The latter might have recently experienced a pronounced demographic contraction and exhibited genetic introgression from the Okinawa Trough lineage, potentially mediated by the intrusion of the North Pacific Intermediate Water. We then compared the biogeographic patterns between S. crosnieri and two other representative and co-occurring vent- and seep-endemic species using published data. Based on their biogeographical subdivisions and source-sink dynamics, we highlighted the southern Okinawa Trough vents and the JR seep warrant imperative conservation efforts to sustain the deep-sea biodiversity in the Northwest Pacific.<br /> <br /> Xu T, Chai X, Chen C, Watanabe HK, Sun J, Xiao Y, Wang Y, Chen J, Qiu J-W*, Qian P-Y* (2023). Genetic divergence and migration patterns of a galatheoid squat lobster highlight the need for deep-sea conservation. Molecular Ecology, Early View. DOI: 10.1111/mec.17200
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
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