Pub Date : 2025-09-01Epub Date: 2025-07-03DOI: 10.1016/j.dsr.2025.104551
Javier Montenegro , Jessica Kolbusz , Yakufu Niyazi , Joan J. Soto-Angel , Aino Hosia , Allen G. Collins , Alan J. Jamieson , Dhugal J. Lindsay
The study of the trachymedusa Botrynema has a long history of research, encompassing over 120 years of exploration in the deep sea. Two distinct morphotypes are recognized within Botrynema: one with a characteristic apical knob and another without it. Both morphotypes are present in the subspecies B. brucei ellinorae, while only specimens with a knob are known for the remainder of B. brucei. Specimens with a knob have been reported across all oceans and latitudes, whereas specimens without a knob are only known from Arctic and Subarctic regions. In this study, we use historical records, molecular tools and phylogenetic analyses to challenge the widely accepted notion of a cosmopolitan distribution for B. brucei as traditionally understood. We propose a range expansion to the subtropical western Atlantic Ocean for B. brucei ellinorae based on molecular data and hypothesize the existence of a mesopelagic soft barrier in the North Atlantic region as a plausible explanation to emerging biogeographical patterns revealed in this study.
{"title":"An unexpected journey – the arctic deep-sea halicreatid trachymedusa Botrynema brucei ellinorae off Florida: a reassessment under an integrative taxonomic approach","authors":"Javier Montenegro , Jessica Kolbusz , Yakufu Niyazi , Joan J. Soto-Angel , Aino Hosia , Allen G. Collins , Alan J. Jamieson , Dhugal J. Lindsay","doi":"10.1016/j.dsr.2025.104551","DOIUrl":"10.1016/j.dsr.2025.104551","url":null,"abstract":"<div><div>The study of the trachymedusa <em>Botrynema</em> has a long history of research, encompassing over 120 years of exploration in the deep sea. Two distinct morphotypes are recognized within <em>Botrynema</em>: one with a characteristic apical knob and another without it. Both morphotypes are present in the subspecies <em>B. brucei ellinorae</em>, while only specimens with a knob are known for the remainder of <em>B. brucei</em>. Specimens with a knob have been reported across all oceans and latitudes, whereas specimens without a knob are only known from Arctic and Subarctic regions. In this study, we use historical records, molecular tools and phylogenetic analyses to challenge the widely accepted notion of a cosmopolitan distribution for <em>B. brucei</em> as traditionally understood. We propose a range expansion to the subtropical western Atlantic Ocean for <em>B. brucei ellinorae</em> based on molecular data and hypothesize the existence of a mesopelagic soft barrier in the North Atlantic region as a plausible explanation to emerging biogeographical patterns revealed in this study.</div></div>","PeriodicalId":51009,"journal":{"name":"Deep-Sea Research Part I-Oceanographic Research Papers","volume":"223 ","pages":"Article 104551"},"PeriodicalIF":2.3,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144579332","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"地球科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-09-01Epub Date: 2025-07-02DOI: 10.1016/j.dsr.2025.104552
Qinyi Zhang , Daidai Wu , Yanting Ling , Xuan Chen , Shengyi Mao , Jie Liu , Guangrong Jin
Seep activity has emerged as a critical area of research for understanding biotic communities and elemental cycling (e.g., carbon, sulfur and iron) in deep extreme environments. While previous studies have predominantly focused on sulfur isotopes in pyrite as a proxy for seep activity, recent advancements highlight the potential of iron isotopes as an additional indicator. However, the detailed mechanism of how sulfur and iron coupled in seep environment is still unclear and thus hamper the further constraint of seep activity by these two key elements. For this reason, the authors analyzed 25 samples from three sediment cores which are collected from seepage sites in the Taixinan Basin (core 973–4) and the Pearl River Mouth Basin (cores GG03 and Z22-3) in the Northern South China Sea. By using SEM-EDS analysis and in-situ sulfur (δ34S) and iron (δ56Fe) isotope measurements, also combining with results from previous studies, the evolution patterns of sulfur and iron in seep environments is explored. The δ34S values of pyrite in core 973–4 range from −18.79 ‰ to 27.26 ‰, indicating a closed-system seep activity. In contrast, pyrite in cores GG03 and Z22-3 exhibit significantly negative δ34S values (−49.75 ‰ to −46.29 ‰ and −53.88 ‰ to −37.11 ‰, respectively), characteristic of more open-system seep activities. Additionally, the δ56Fe values of pyrite are consistently negative across all cores (−1.39 ‰ to −0.31 ‰ in core 973–4, −1.59 ‰ to −0.24 ‰ in core GG03, and −1.10 ‰ to −0.20 ‰ in core Z22-3), suggesting the absence of a heavy iron isotope pool. By integrating these findings with previous results, this study demonstrates that the δ56Fe values of pyrite are influenced by the position of the sulfate-methane transition zone, diverse microbial reduction processes, and varying iron sources. Therefore, this study provides valuable data to decipher how coupled sulfur and iron evolving in seep environments by pyrite, enhancing the further understanding of elemental cycles in extreme settings.
{"title":"Constraining sulfur and iron cycling in seep systems: insights from authigenic pyrite signatures","authors":"Qinyi Zhang , Daidai Wu , Yanting Ling , Xuan Chen , Shengyi Mao , Jie Liu , Guangrong Jin","doi":"10.1016/j.dsr.2025.104552","DOIUrl":"10.1016/j.dsr.2025.104552","url":null,"abstract":"<div><div>Seep activity has emerged as a critical area of research for understanding biotic communities and elemental cycling (e.g., carbon, sulfur and iron) in deep extreme environments. While previous studies have predominantly focused on sulfur isotopes in pyrite as a proxy for seep activity, recent advancements highlight the potential of iron isotopes as an additional indicator. However, the detailed mechanism of how sulfur and iron coupled in seep environment is still unclear and thus hamper the further constraint of seep activity by these two key elements. For this reason, the authors analyzed 25 samples from three sediment cores which are collected from seepage sites in the Taixinan Basin (core 973–4) and the Pearl River Mouth Basin (cores GG03 and Z22-3) in the Northern South China Sea. By using SEM-EDS analysis and in-situ sulfur (δ<sup>34</sup>S) and iron (δ<sup>56</sup>Fe) isotope measurements, also combining with results from previous studies, the evolution patterns of sulfur and iron in seep environments is explored. The δ<sup>34</sup>S values of pyrite in core 973–4 range from −18.79 ‰ to 27.26 ‰, indicating a closed-system seep activity. In contrast, pyrite in cores GG03 and Z22-3 exhibit significantly negative δ<sup>34</sup>S values (−49.75 ‰ to −46.29 ‰ and −53.88 ‰ to −37.11 ‰, respectively), characteristic of more open-system seep activities. Additionally, the δ<sup>56</sup>Fe values of pyrite are consistently negative across all cores (−1.39 ‰ to −0.31 ‰ in core 973–4, −1.59 ‰ to −0.24 ‰ in core GG03, and −1.10 ‰ to −0.20 ‰ in core Z22-3), suggesting the absence of a heavy iron isotope pool. By integrating these findings with previous results, this study demonstrates that the δ<sup>56</sup>Fe values of pyrite are influenced by the position of the sulfate-methane transition zone, diverse microbial reduction processes, and varying iron sources. Therefore, this study provides valuable data to decipher how coupled sulfur and iron evolving in seep environments by pyrite, enhancing the further understanding of elemental cycles in extreme settings.</div></div>","PeriodicalId":51009,"journal":{"name":"Deep-Sea Research Part I-Oceanographic Research Papers","volume":"223 ","pages":"Article 104552"},"PeriodicalIF":2.3,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144556734","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"地球科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-09-01Epub Date: 2025-06-18DOI: 10.1016/j.dsr.2025.104546
Xinlong Li , Anning Mou , Yue Dong , Jing Mo , Xiaomei Liao , Xiao Wang , Zongling Wang , Xuelei Zhang , Qinzeng Xu
Sea cucumbers, widely distributed benthic invertebrates in diverse deep-sea habitats, rely on their gut bacterial communities for essential functions including energy metabolism, biological adaptation, and health. However, the gut bacterial community of deep-sea holothurians in the Indian Ocean remains poorly understood. We used 16S rRNA gene sequencing to characterize bacterial communities in the guts of sea cucumbers and surrounding sediments from two distinct regions of the northern Indian Ocean: the Ninety-East Ridge and the Arabian Sea Basin. This study investigates the composition, diversity, predicted functions, co-occurrence networks, and assembly processes of gut bacterial communities. Alpha diversity of gut bacterial communities did not differ significantly between the two regions. Based on principal coordinate analysis, the bacterial communities of gut formed a distinct cluster from the sediment communities. Actinobacteriota, Proteobacteria, Firmicutes, Chloroflexi, and Bacteroidota were the dominant phyla in both gut and sediment bacterial communities. In the Ninety-East Ridge, the gut microbial network exhibited a higher proportion of positive correlation than the sediment network, suggesting a greater potential for cooperative interactions. Compared to sediment communities, functional predictions indicated that gut communities were enriched in metabolic pathways, including those for amino acid, glycan, vitamin, and lipid metabolism. Stochastic processes were predominant in gut bacterial community assembly, whereas deterministic processes dominated in sediment bacterial communities. This study provides critical insights into the gut microbiota of deep-sea holothurians, advancing our understanding of microbial ecology in extreme marine environments.
海参是广泛分布于不同深海栖息地的底栖无脊椎动物，它们依靠肠道细菌群落来实现能量代谢、生物适应和健康等基本功能。然而，人们对印度洋深海全息鱼的肠道细菌群落知之甚少。我们使用16S rRNA基因测序来表征来自北印度洋两个不同区域的海参内脏和周围沉积物中的细菌群落：九十东脊和阿拉伯海盆地。本研究探讨了肠道细菌群落的组成、多样性、预测功能、共生网络和组装过程。两个地区肠道细菌群落的α多样性无显著差异。基于主坐标分析，肠道细菌群落与沉积物群落形成了明显的集群。放线菌门、变形菌门、厚壁菌门、绿菌门和拟杆菌门是肠道和沉积物细菌群落的优势门。在90 east Ridge，肠道微生物网络表现出比沉积物网络更高的正相关比例，表明更大的合作相互作用潜力。与沉积物群落相比，功能预测表明肠道群落在代谢途径中丰富，包括氨基酸、聚糖、维生素和脂质代谢途径。随机过程在肠道细菌群落组装中占主导地位，而确定性过程在沉积物细菌群落中占主导地位。这项研究为深海全息鱼的肠道微生物群提供了重要的见解，促进了我们对极端海洋环境下微生物生态的理解。
{"title":"Bacterial community characterization and relationship in the gut of deep-sea holothurians and sediment from the Northern Indian Ocean","authors":"Xinlong Li , Anning Mou , Yue Dong , Jing Mo , Xiaomei Liao , Xiao Wang , Zongling Wang , Xuelei Zhang , Qinzeng Xu","doi":"10.1016/j.dsr.2025.104546","DOIUrl":"10.1016/j.dsr.2025.104546","url":null,"abstract":"<div><div>Sea cucumbers, widely distributed benthic invertebrates in diverse deep-sea habitats, rely on their gut bacterial communities for essential functions including energy metabolism, biological adaptation, and health. However, the gut bacterial community of deep-sea holothurians in the Indian Ocean remains poorly understood. We used 16S rRNA gene sequencing to characterize bacterial communities in the guts of sea cucumbers and surrounding sediments from two distinct regions of the northern Indian Ocean: the Ninety-East Ridge and the Arabian Sea Basin. This study investigates the composition, diversity, predicted functions, co-occurrence networks, and assembly processes of gut bacterial communities. Alpha diversity of gut bacterial communities did not differ significantly between the two regions. Based on principal coordinate analysis, the bacterial communities of gut formed a distinct cluster from the sediment communities. Actinobacteriota, Proteobacteria, Firmicutes, Chloroflexi, and Bacteroidota were the dominant phyla in both gut and sediment bacterial communities. In the Ninety-East Ridge, the gut microbial network exhibited a higher proportion of positive correlation than the sediment network, suggesting a greater potential for cooperative interactions. Compared to sediment communities, functional predictions indicated that gut communities were enriched in metabolic pathways, including those for amino acid, glycan, vitamin, and lipid metabolism. Stochastic processes were predominant in gut bacterial community assembly, whereas deterministic processes dominated in sediment bacterial communities. This study provides critical insights into the gut microbiota of deep-sea holothurians, advancing our understanding of microbial ecology in extreme marine environments.</div></div>","PeriodicalId":51009,"journal":{"name":"Deep-Sea Research Part I-Oceanographic Research Papers","volume":"223 ","pages":"Article 104546"},"PeriodicalIF":2.3,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144321085","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"地球科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-09-01Epub Date: 2025-06-15DOI: 10.1016/j.dsr.2025.104544
Jason Cleland , Anna Gebruk , J. Murray Roberts , Dmitry Aleynik , Beverly McClenaghan , Rod Mather , Bridget Buxton , Steve W. Ross
The biology of shipwrecks and hard substrata in the deep sea remains poorly explored. These complex habitats alter biodiversity on the deep seafloor and facilitate connecting populations over large distances. We analysed biological and environmental data collected at the RMS Titanic wreck site (3800 m) and a seamount ridge (2900 m) during the 2022 Titanic Expedition (15 June–25 July). The ridge is part of Seamount U, approximately 40 km southeast of the Titanic, and was explored for the first time on July 23, 2022. We analysed megafaunal occurrence across 920 images of the wreck site and 169 images of the ridge site, from digital video. The most common megafauna overall were Ophiuroidea, Munidopsis sp., Cushion-Encrusting Porifera, Geodia spp., and cold-water corals including Keratoisididae and Pennatuloidea. We describe the patterns in community composition across five benthic habitats, likely controlled by substrate type, local hydrodynamics, and food availability. The ridge yielded a higher number of observed megafauna and higher Shannon diversity (n = 73; H = 2.89) than the wreck (n = 21; H = 1.39). The communities associated with the ridge showed high dissimilarity to those at the wreck. We also explored the temporal variability of biofouling organisms on the Titanic using video from 1986 to 2022. We observed a net increase in Chrysogorgia sp. and Lepidisis sp. coral colonies over time with estimated average linear growth rates of up to 10 mm/yr and linear rusticle extensions of up to 14 mm/yr, raising questions about the wreck's ecological succession as it deteriorates.
{"title":"Megafauna of the RMS Titanic shipwreck and a nearby seamount ridge in the deep sea of the western North Atlantic","authors":"Jason Cleland , Anna Gebruk , J. Murray Roberts , Dmitry Aleynik , Beverly McClenaghan , Rod Mather , Bridget Buxton , Steve W. Ross","doi":"10.1016/j.dsr.2025.104544","DOIUrl":"10.1016/j.dsr.2025.104544","url":null,"abstract":"<div><div>The biology of shipwrecks and hard substrata in the deep sea remains poorly explored. These complex habitats alter biodiversity on the deep seafloor and facilitate connecting populations over large distances. We analysed biological and environmental data collected at the RMS <em>Titanic</em> wreck site (3800 m) and a seamount ridge (2900 m) during the 2022 <em>Titanic</em> Expedition (15 June–25 July). The ridge is part of Seamount U, approximately 40 km southeast of the <em>Titanic,</em> and was explored for the first time on July 23, 2022. We analysed megafaunal occurrence across 920 images of the wreck site and 169 images of the ridge site, from digital video. The most common megafauna overall were Ophiuroidea, <em>Munidopsis</em> sp., Cushion-Encrusting Porifera, <em>Geodia</em> spp., and cold-water corals including Keratoisididae and Pennatuloidea. We describe the patterns in community composition across five benthic habitats, likely controlled by substrate type, local hydrodynamics, and food availability. The ridge yielded a higher number of observed megafauna and higher Shannon diversity (n = 73; H = 2.89) than the wreck (n = 21; H = 1.39). The communities associated with the ridge showed high dissimilarity to those at the wreck. We also explored the temporal variability of biofouling organisms on the <em>Titanic</em> using video from 1986 to 2022. We observed a net increase in <em>Chrysogorgia</em> sp. and <em>Lepidisis</em> sp. coral colonies over time with estimated average linear growth rates of up to 10 mm/yr and linear rusticle extensions of up to 14 mm/yr, raising questions about the wreck's ecological succession as it deteriorates.</div></div>","PeriodicalId":51009,"journal":{"name":"Deep-Sea Research Part I-Oceanographic Research Papers","volume":"223 ","pages":"Article 104544"},"PeriodicalIF":2.3,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144480960","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"地球科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-09-01Epub Date: 2025-06-11DOI: 10.1016/j.dsr.2025.104545
Xuanguang Liang , Mingmin Du , Yuxin Qin , Wenlong Cai , Junrou Huang , Genmei Lin , Jianguo Lu
Deep-sea cold seeps that discharge fluids rich in methane, hydrogen sulfide, and heavy metals present extreme conditions under which only a few organisms, such as deep-sea mussels, can survive. Deep-sea mussels exploit chemosynthetic energy via symbiotic microorganisms. This study compared environmental sensing and stress responses in different tissues of Gigantidas haimaensis from the Haima cold seep through transcriptome and microbiome sequencing, biochemistry index measurements and metal content assessments to decipher its adaptive mechanisms. Transcriptomic analysis revealed distinct expression patterns among three tissues, with more genes expressed in the gill. Compared to the mantle and adductor muscle, the gill had 2519 and 4508 differentially expressed genes (DEGs), respectively, while 1453 DEGs were identified between the mantle and the adductor muscle. Up-regulated DEGs in the gill were associated with symbiont acquisition, pathogen recognition, pathogen removal, symbiotic substance exchange, and oxidative stress response. Meanwhile, the gill microbiota was dominated by methanotrophic Methylomonaceae (>85 % relative abundance). Of the 13 metals analyzed, Zn, Fe, and Cu exhibited the highest concentrations. Genes associated with distinct metal-binding pathways were expressed in different tissues. The gill also showed heightened antioxidant capacity and metal accumulation, underscoring its role in the stress response. The up-regulated genes in the adductor muscle were related to muscle contraction, while in the mantle, the up-regulated protease inhibitors were linked to humoral immunity. This study demonstrates the gill's crucial functions in symbiont and pathogen regulation as well as metal stress response, thus extending our understanding of the adaptive mechanism of G. haimaensis inhabiting cold seeps.
{"title":"Functional and microbial insights into the gill symbiosis and metal tolerance of the cold seep mussel Gigantidas haimaensis","authors":"Xuanguang Liang , Mingmin Du , Yuxin Qin , Wenlong Cai , Junrou Huang , Genmei Lin , Jianguo Lu","doi":"10.1016/j.dsr.2025.104545","DOIUrl":"10.1016/j.dsr.2025.104545","url":null,"abstract":"<div><div>Deep-sea cold seeps that discharge fluids rich in methane, hydrogen sulfide, and heavy metals present extreme conditions under which only a few organisms, such as deep-sea mussels, can survive. Deep-sea mussels exploit chemosynthetic energy via symbiotic microorganisms. This study compared environmental sensing and stress responses in different tissues of <em>Gigantidas haimaensis</em> from the Haima cold seep through transcriptome and microbiome sequencing, biochemistry index measurements and metal content assessments to decipher its adaptive mechanisms. Transcriptomic analysis revealed distinct expression patterns among three tissues, with more genes expressed in the gill. Compared to the mantle and adductor muscle, the gill had 2519 and 4508 differentially expressed genes (DEGs), respectively, while 1453 DEGs were identified between the mantle and the adductor muscle. Up-regulated DEGs in the gill were associated with symbiont acquisition, pathogen recognition, pathogen removal, symbiotic substance exchange, and oxidative stress response. Meanwhile, the gill microbiota was dominated by methanotrophic Methylomonaceae (>85 % relative abundance). Of the 13 metals analyzed, Zn, Fe, and Cu exhibited the highest concentrations. Genes associated with distinct metal-binding pathways were expressed in different tissues. The gill also showed heightened antioxidant capacity and metal accumulation, underscoring its role in the stress response. The up-regulated genes in the adductor muscle were related to muscle contraction, while in the mantle, the up-regulated protease inhibitors were linked to humoral immunity. This study demonstrates the gill's crucial functions in symbiont and pathogen regulation as well as metal stress response, thus extending our understanding of the adaptive mechanism of <em>G. haimaensis</em> inhabiting cold seeps.</div></div>","PeriodicalId":51009,"journal":{"name":"Deep-Sea Research Part I-Oceanographic Research Papers","volume":"223 ","pages":"Article 104545"},"PeriodicalIF":2.3,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144279541","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"地球科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-09-01Epub Date: 2025-05-27DOI: 10.1016/j.dsr.2025.104517
Jiushuang Zhang, Yong Wang
Application of deep learning technology for deep-sea ecological studies is still in its infancy stage especially in the field of automatic taxonomic identification and statistics. In this study, we created a novel dataset containing annotated videos for the rare species of hadal snailfish inhabiting in depth below 6000 meters, and conducted control experiments by combining models of different specifications and adding different attention mechanisms. We successfully generated a set of benchmark test data from a quantitative perspective. In addition, based on out of set data with completely different data distributions from the training and validation sets, the generalization ability of the model trained on the new dataset in real-world scenarios was qualitatively analyzed. Other researchers can continue to expand and supplement the dataset based on our benchmarks, or directly apply our results to actual deep-sea videos collected, and accurately identify and capture deep-sea snailfish in the videos. With this deep learning video processing technology, distribution pattern and biodiversity of the deep-sea organisms will be accomplished efficiently.
{"title":"A video dataset for hadal snailfish along with the benchmark","authors":"Jiushuang Zhang, Yong Wang","doi":"10.1016/j.dsr.2025.104517","DOIUrl":"10.1016/j.dsr.2025.104517","url":null,"abstract":"<div><div>Application of deep learning technology for deep-sea ecological studies is still in its infancy stage especially in the field of automatic taxonomic identification and statistics. In this study, we created a novel dataset containing annotated videos for the rare species of hadal snailfish inhabiting in depth below 6000 meters, and conducted control experiments by combining models of different specifications and adding different attention mechanisms. We successfully generated a set of benchmark test data from a quantitative perspective. In addition, based on out of set data with completely different data distributions from the training and validation sets, the generalization ability of the model trained on the new dataset in real-world scenarios was qualitatively analyzed. Other researchers can continue to expand and supplement the dataset based on our benchmarks, or directly apply our results to actual deep-sea videos collected, and accurately identify and capture deep-sea snailfish in the videos. With this deep learning video processing technology, distribution pattern and biodiversity of the deep-sea organisms will be accomplished efficiently.</div></div>","PeriodicalId":51009,"journal":{"name":"Deep-Sea Research Part I-Oceanographic Research Papers","volume":"223 ","pages":"Article 104517"},"PeriodicalIF":2.3,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144271459","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"地球科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-09-01Epub Date: 2025-07-04DOI: 10.1016/j.dsr.2025.104554
Matthew P. Quinan , William M. Berelson , Jaclyn E.P. Cetiner , Nick E. Rollins , Frank J. Pavia , Sijia Dong , Janice L. Jones , Mark A. Brzezinski , Jess F. Adkins
The cycling of silicon (Si) in marine sediments can have major impacts on global ocean nutrient dynamics and productivity. Si cycling in the sediment of the Cocos Ridge and overlying waters of the eastern equatorial Pacific was investigated using unique in situ and traditional ex situ pore water collection techniques as well as solid phase analysis, core incubation, and sediment trap collection. Si remineralization and burial fluxes show little variation between the four sites investigated, regardless of a ∼1600 m difference in water depth among stations. Dissolved Si concentrations in pore water from sediment depths >10 cm collected in situ were significantly and consistently higher than those collected ex situ implying a previously unrecognized sampling artifact associated with sediment core recovery and processing. The loss of dissolved Si in the ex situ pore waters is also associated with the fractionation of Si isotopes. In situ pore water δ30Si is lighter than ex situ pore water δ30Si at three of the four stations, though only significantly lighter at one. The preferential loss of light Si in ex situ pore waters is attributed to authigenic clay formation during core collection and transport from the cold, high pressure benthos to the ocean's surface. However, consistency between in situ and ex situ pore water Si gradients within 10 cm of the sediment water interface indicates remineralization fluxes previously determined using sediment core-derived pore waters remain accurate.
{"title":"Biogenic Si cycling along the Cocos Ridge: differences between in situ and ex situ extracted pore waters imply rapid rates of dissolved Si uptake upon core recovery","authors":"Matthew P. Quinan , William M. Berelson , Jaclyn E.P. Cetiner , Nick E. Rollins , Frank J. Pavia , Sijia Dong , Janice L. Jones , Mark A. Brzezinski , Jess F. Adkins","doi":"10.1016/j.dsr.2025.104554","DOIUrl":"10.1016/j.dsr.2025.104554","url":null,"abstract":"<div><div>The cycling of silicon (Si) in marine sediments can have major impacts on global ocean nutrient dynamics and productivity. Si cycling in the sediment of the Cocos Ridge and overlying waters of the eastern equatorial Pacific was investigated using unique <em>in situ</em> and traditional <em>ex situ</em> pore water collection techniques as well as solid phase analysis, core incubation, and sediment trap collection. Si remineralization and burial fluxes show little variation between the four sites investigated, regardless of a ∼1600 m difference in water depth among stations. Dissolved Si concentrations in pore water from sediment depths >10 cm collected <em>in situ</em> were significantly and consistently higher than those collected <em>ex situ</em> implying a previously unrecognized sampling artifact associated with sediment core recovery and processing. The loss of dissolved Si in the <em>ex situ</em> pore waters is also associated with the fractionation of Si isotopes. <em>In situ</em> pore water δ<sup>30</sup>Si is lighter than <em>ex situ</em> pore water δ<sup>30</sup>Si at three of the four stations, though only significantly lighter at one. The preferential loss of light Si in <em>ex situ</em> pore waters is attributed to authigenic clay formation during core collection and transport from the cold, high pressure benthos to the ocean's surface. However, consistency between <em>in situ</em> and <em>ex situ</em> pore water Si gradients within 10 cm of the sediment water interface indicates remineralization fluxes previously determined using sediment core-derived pore waters remain accurate.</div></div>","PeriodicalId":51009,"journal":{"name":"Deep-Sea Research Part I-Oceanographic Research Papers","volume":"223 ","pages":"Article 104554"},"PeriodicalIF":2.3,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144589074","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"地球科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-09-01Epub Date: 2025-06-16DOI: 10.1016/j.dsr.2025.104543
Rengaiyan Periasamy , Baban Ingole
The family Victorgorgiidae Moore et al., 2017 comprises deep-sea gorgonian corals typically characterized by purple colonies and distinctive josephinae clubs in their polyp tentacles. Despite this, the family exhibits low species diversity and the ones from the deep Indian Ocean remain poorly unknown, remarking the need for more research to better understand their ecological role and evolutionary history. A new species, Victorgorgia indica sp. nov., was discovered on a seamount along the Central Indian Ridge (CIR) at depths of 1917–2053 m, representing the first record of Victorgorgiidae in the Indian Ocean. Among the nine known species of Victorgorgia López-González and Briand, 2002), V. indica sp. nov. is morphologically most similar to V. flabellata Li et al., 2020 and V. iocasica Li et al., 2020, particularly in the arrangement of the calyx, which is mainly isolated in three sides of the branches. However, this arrangement can vary in different parts of a colony and may be influenced by local habitat conditions. V. indica sp. nov. differs from these species by having tuberculate rods, a thorn club in the tentacle rachis, and curved rodlets with tall tubercules along their edges in the pinnules. Phylogenetic analysis at the family level using the MutS-like protein (MutS) gene supports Victorgorgiidae as a monophyletic group. The evolutionary relationships of the new CIR species suggest a close affinity with its Pacific Ocean congeners, including V. flabellata, V. iocasica and V. eminens Moore et al., 2017. This points to the CIR seamount system potentially acting as a link for gene flow between the Indian and Pacific Oceans. Analyses of the reproductions of these species showed that V. indica sp. nov. is a brooder, with planula larvae developing within clumped autozooids—the only mature polyps—and settling on dead deep-sea coral. Here we presented also the complete mitochondrial genome of V. indica sp. nov., which is 18,715 base pairs in size, and includes 14 protein-coding genes (PCGs), two ribosomal RNA genes (rrnS and rrnL), and one transfer RNA gene. The gene order of the mitogenome is identical to that of other sequenced Victorgorgiidae species.
victororggiidae Moore等人，2017包括深海柳珊瑚，其典型特征是紫色的群落和在其水螅触须上独特的josephinae棒。尽管如此，这个家族的物种多样性很低，来自印度洋深处的物种仍然鲜为人知，这表明需要更多的研究来更好地了解它们的生态作用和进化历史。一新种victororggia indica sp. nov.在印度洋中部山脊（CIR）深处1917-2053米的海底山上被发现，这是在印度洋首次记录到victororgorgiidae。在已知的9个victorgorggia （López-González and Briand, 2002）种中，V. indica sp. nov.在形态上与V. flabellata Li et al.， 2020和V. iocasica Li et al.， 2020最相似，特别是花萼的排列方式，花萼主要分离在枝的三面。然而，这种安排在一个群体的不同部分可能会有所不同，并可能受到当地栖息地条件的影响。与这些种的不同之处在于在触手轴上有有结核的茎，刺棒和弯曲的小茎，在小叶尖的边缘有高的结节。利用MutS样蛋白（MutS -like protein, MutS）基因在家族水平上进行系统发育分析，支持vicorgorgiidae为单系类群。新的CIR物种的进化关系表明其与太平洋同系物（包括V. flabellata， V. iocasica和V. eminens Moore等，2017）有密切的亲缘关系。这表明CIR海底山系统可能作为印度洋和太平洋之间基因流动的纽带。对这些物种繁殖的分析表明，印度浮藻是一种孵卵动物，浮藻幼虫在成团的自生动物（唯一成熟的珊瑚虫）中发育，并定居在死的深海珊瑚上。本文还报道了印度血吸虫线粒体基因组全长18715个碱基对，包括14个蛋白质编码基因（PCGs）、2个核糖体RNA基因（rrnS和rrnL）和1个转移RNA基因。有丝分裂基因组的基因顺序与其他有丝分裂科物种相同。
{"title":"Evolutionary affinity of a novel deep-sea coral from the Central Indian Ridge seamount, and its links to Pacific Ocean species","authors":"Rengaiyan Periasamy , Baban Ingole","doi":"10.1016/j.dsr.2025.104543","DOIUrl":"10.1016/j.dsr.2025.104543","url":null,"abstract":"<div><div>The family Victorgorgiidae Moore et al., 2017 comprises deep-sea gorgonian corals typically characterized by purple colonies and distinctive josephinae clubs in their polyp tentacles. Despite this, the family exhibits low species diversity and the ones from the deep Indian Ocean remain poorly unknown, remarking the need for more research to better understand their ecological role and evolutionary history. A new species, <em>Victorgorgia indica</em> sp. nov., was discovered on a seamount along the Central Indian Ridge (CIR) at depths of 1917–2053 m, representing the first record of Victorgorgiidae in the Indian Ocean. Among the nine known species of <em>Victorgorgia</em> López-González and Briand, 2002), <em>V. indica</em> sp. nov. is morphologically most similar to <em>V. flabellata</em> Li et al., 2020 and <em>V. iocasica</em> Li et al., 2020, particularly in the arrangement of the calyx, which is mainly isolated in three sides of the branches. However, this arrangement can vary in different parts of a colony and may be influenced by local habitat conditions. <em>V. indica</em> sp. nov. differs from these species by having tuberculate rods, a thorn club in the tentacle rachis, and curved rodlets with tall tubercules along their edges in the pinnules. Phylogenetic analysis at the family level using the MutS-like protein (MutS) gene supports Victorgorgiidae as a monophyletic group. The evolutionary relationships of the new CIR species suggest a close affinity with its Pacific Ocean congeners, including <em>V. flabellat</em><em>a</em>, <em>V. iocasica</em> and <em>V. eminens</em> Moore et al., 2017. This points to the CIR seamount system potentially acting as a link for gene flow between the Indian and Pacific Oceans. Analyses of the reproductions of these species showed that <em>V. indica</em> sp. nov. is a brooder, with planula larvae developing within clumped autozooids—the only mature polyps—and settling on dead deep-sea coral. Here we presented also the complete mitochondrial genome of <em>V. indica</em> sp. nov., which is 18,715 base pairs in size, and includes 14 protein-coding genes (PCGs), two ribosomal RNA genes (rrnS and rrnL), and one transfer RNA gene. The gene order of the mitogenome is identical to that of other sequenced Victorgorgiidae species.</div></div>","PeriodicalId":51009,"journal":{"name":"Deep-Sea Research Part I-Oceanographic Research Papers","volume":"223 ","pages":"Article 104543"},"PeriodicalIF":2.3,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144502790","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"地球科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-08-01Epub Date: 2025-05-15DOI: 10.1016/j.dsr.2025.104519
Zhou Le , Dongxiao Wang , Tingting Zu , M.V. Subrahmanyam , Ke Huang , Guangli Zhang
The Bay of Bengal (BOB), a marginal sea of the northern Indian Ocean, experiences significant monsoon influences. Satellite observations show considerable inter-annual variability in the seasonal oceanic gyre and the summertime offshore jet extending from the Western Boundary Currents (WBC). While the Indian Ocean Dipole (IOD) mode is well-known, the recently identified Indian Ocean Tripole (IOT) mode has also attracted attention. However, the impact of the IOT mode on BOB circulation remains underexplored. This study examines the effects of the boreal autumn-matured IOD and the summer-matured IOT on BOB circulation using analyses of merged satellite data and outputs from a 1.5-layer reduced-gravity numerical model. Results indicate that both the IOD and IOT modes can influence BOB ocean circulation by generating local wind anomalies over the BOB. Unlike the IOD mode, the IOT mode induce less equatorial wind anomalies that can remotely affect the northern BOB circulation. Further analyses indicate that upper seawater warming during boreal spring leads to land-sea breezes over the western BOB, driving the western boundary offshore jet to higher latitudes. Unexpectedly, under scenario of northward offshore jet shift, the gyre response in the northern BOB and near the western boundary is more strongly attributed to wind anomalies associated with the IOT mode than the IOD mode. This study enhances our understanding of land-sea-atmosphere interactions in the marginal sea of monsoon region.
{"title":"Attribution of upper gyre's variability in the western Bay of Bengal boundary through Indian Ocean climate modes","authors":"Zhou Le , Dongxiao Wang , Tingting Zu , M.V. Subrahmanyam , Ke Huang , Guangli Zhang","doi":"10.1016/j.dsr.2025.104519","DOIUrl":"10.1016/j.dsr.2025.104519","url":null,"abstract":"<div><div>The Bay of Bengal (BOB), a marginal sea of the northern Indian Ocean, experiences significant monsoon influences. Satellite observations show considerable inter-annual variability in the seasonal oceanic gyre and the summertime offshore jet extending from the Western Boundary Currents (WBC). While the Indian Ocean Dipole (IOD) mode is well-known, the recently identified Indian Ocean Tripole (IOT) mode has also attracted attention. However, the impact of the IOT mode on BOB circulation remains underexplored. This study examines the effects of the boreal autumn-matured IOD and the summer-matured IOT on BOB circulation using analyses of merged satellite data and outputs from a 1.5-layer reduced-gravity numerical model. Results indicate that both the IOD and IOT modes can influence BOB ocean circulation by generating local wind anomalies over the BOB. Unlike the IOD mode, the IOT mode induce less equatorial wind anomalies that can remotely affect the northern BOB circulation. Further analyses indicate that upper seawater warming during boreal spring leads to land-sea breezes over the western BOB, driving the western boundary offshore jet to higher latitudes. Unexpectedly, under scenario of northward offshore jet shift, the gyre response in the northern BOB and near the western boundary is more strongly attributed to wind anomalies associated with the IOT mode than the IOD mode. This study enhances our understanding of land-sea-atmosphere interactions in the marginal sea of monsoon region.</div></div>","PeriodicalId":51009,"journal":{"name":"Deep-Sea Research Part I-Oceanographic Research Papers","volume":"222 ","pages":"Article 104519"},"PeriodicalIF":2.3,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144131165","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"地球科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-08-01Epub Date: 2025-05-26DOI: 10.1016/j.dsr.2025.104533
V.P. Singh , N.G. Rudraswami
Annually, Earth accumulates ∼40,000 tons of cosmic dust, with ∼4000–6000 tons reaching the surface as micrometeorites (MMs). This study analyzes ∼3 tons of wet sediments and ∼5000 MMs from the Central Indian Ocean Basin, using a machine learning algorithm based on terrestrial sedimentation rate (TSR) and MM abundance to identify optimal collection regions. Deep-sea sediments (TSR <0.01 cm/kyr) contain ∼50 MM/kg of dry sediments, yet remain largely unexplored. Moderately deep-sea sediments (0.01 < TSR <0.1 cm/kyr), like those in this study, average ∼15 MM/kg, while shallow-sea sediments yield far fewer. Modelling indicates that ocean regions between 45° N and 45° S latitude are ideal for MM collection. The eastern Pacific Ocean (10-40° N and 10-30° S) and the Central Indian Ocean (0-45° S) are particularly suitable. Apart from deep-sea collection, ancient rocks deposited in calm environments with low TSR (e.g. shale, claystone, mudstone, chert, and limestone) are promising for collecting fossil MMs. Overall, this research enhances micrometeorite collection strategies, enabling more accurate flux estimation and providing a foundation for researchers to effectively target specific ocean areas and ancient rock formations, thereby facilitating investigations into extraterrestrial activities and their impacts on Earth's processes.
{"title":"Spatial variation of micrometeorite abundance in global ocean","authors":"V.P. Singh , N.G. Rudraswami","doi":"10.1016/j.dsr.2025.104533","DOIUrl":"10.1016/j.dsr.2025.104533","url":null,"abstract":"<div><div>Annually, Earth accumulates ∼40,000 tons of cosmic dust, with ∼4000–6000 tons reaching the surface as micrometeorites (MMs). This study analyzes ∼3 tons of wet sediments and ∼5000 MMs from the Central Indian Ocean Basin, using a machine learning algorithm based on terrestrial sedimentation rate (TSR) and MM abundance to identify optimal collection regions. Deep-sea sediments (TSR <0.01 cm/kyr) contain ∼50 MM/kg of dry sediments, yet remain largely unexplored. Moderately deep-sea sediments (0.01 < TSR <0.1 cm/kyr), like those in this study, average ∼15 MM/kg, while shallow-sea sediments yield far fewer. Modelling indicates that ocean regions between 45° N and 45° S latitude are ideal for MM collection. The eastern Pacific Ocean (10-40° N and 10-30° S) and the Central Indian Ocean (0-45° S) are particularly suitable. Apart from deep-sea collection, ancient rocks deposited in calm environments with low TSR (e.g. shale, claystone, mudstone, chert, and limestone) are promising for collecting fossil MMs. Overall, this research enhances micrometeorite collection strategies, enabling more accurate flux estimation and providing a foundation for researchers to effectively target specific ocean areas and ancient rock formations, thereby facilitating investigations into extraterrestrial activities and their impacts on Earth's processes.</div></div>","PeriodicalId":51009,"journal":{"name":"Deep-Sea Research Part I-Oceanographic Research Papers","volume":"222 ","pages":"Article 104533"},"PeriodicalIF":2.3,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144167724","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"地球科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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