Haibin Zhang, Professor, Director of the Department of Deep-Sea Biology
Email: hzhang@idsse.ac.cn
Research interests:
Deep-sea biology, biodiversity and taxonomy, population genetics, molecular ecology, conservation genetics, phylogenetics
Research funding and awards:
1. National Key Research and Development Program of China (2023YFC2809300, 2017YFC0306604)
2. National Natural Science Foundation of China (41576127)
3. Strategic Priority Research Program of the Chinese Academy of Sciences (XDB06010104, XDA22040502)
4. Major scientific and technological projects of Hainan Province (ZDKJ2019011)
Education and Employment History:
Education
2005, Ph.D., Institute of Oceanology, Chinese Academy of Sciences.
2000, M.S., Ocean University of Qingdao
1995, B.S., Ocean University of Qingdao
Employment History
12/2013-present, Professor, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences.
10/2011-10/2013, Postdoctoral Fellow, Monterey Bay Aquarium Research Institute.
02/2011-09/2011, Postdoctoral Researcher, Louisiana State University.
01/2008-02/2011, Postdoctoral Associate, Cornell University.
03/2005-01/2008, Assistant Professor, Institute of Oceanology, Chinese Academy of Sciences
Publications:
[1] Zhang, H.*, Zhou, Y., and Yang, Z. (2024) Genetic adaptations of marine invertebrates to hydrothermal vent habitats. Trends in Genetics, 40 (12), 1047 - 1059
[2] Pu, Y., Zhou, Y., Liu, J., and Zhang, H.* (2024) A high-quality chromosomal genome assembly of the sea cucumber Chiridota heheva and its hydrothermal adaptation, GigaScience, 13, giad107
[3] Xiao, Y., Zhang, H.* (2024) Three new species and one new record of Deimatidae (Echinodermata, Holothuroidea, Synallactida) discovered in the South China Sea and the Mariana fore-arc area using integrative taxonomic methods. Zookeys. 1195, 309-335.
[4] Zhou, Y., Liu, H., Feng, C., Lu, Z., Liu, J., Huang, Y., Tang, H., Xu, Z., Pu, Y., and Zhang, H.* (2023) Genetic adaptations of sea anemone to hydrothermal environment. Science Advance, 9, eadh0474
[5] Liu, J., Zhou, Y., Pu, Y., and Zhang, H.* (2023) A chromosome-level genome assembly of a deep-sea starfish (Zoroaster cf. ophiactis). Scientific Data, 10, 506.
[6] Li, Y., Chen, Z., Zhang, P., Gao, F., Wang, J., Lin, L., and Zhang, H.* (2023) Characterization of a Novel Superoxide Dismutase from a Deep-sea Sea Cucumber (Psychoropotes verruciaudatus). Antioxidants, 12, 1227.
[7] Nethupul, H., Stöhr, S., and Zhang, H.* (2022). Review of Ophioplinthaca Verrill, 1899 (Echinodermata, Ophiuroidea, Ophiacanthidae), description of new species in Ophioplinthaca and Ophiophthalmus, and new records from the Northwest Pacific and the South China Sea. Zookeys. 1099, 155-202.
[8] Li, Y., Yan, Lei., Kong, X., Chen, J., and Zhang, H.* (2020) Cloning, expression, and characterization of a novel superoxide dismutase from deep-sea sea cucumber, International Journal of Biological Macromolecules, 163, 1875-1883.
[9] Kong, X., Li, Y., and Zhang, H.* (2020) Adaptation evolution and bioactivity of galectin from the deep sea Vesicomyidae clam Archivesica packardana. Fish and Shellfish Immunology, 97, 483–492.
[10] Liang, L., Chen, J., Li, Y., Zhang, H.* (2020) Insights into high-pressure acclimation: comparative transcriptome analysis of sea cucumber Apostichopus japonicus at different hydrostatic pressure exposures. BMC Genomics, 21: 68
Name and position: Shunping He, Adjunct Professor
Email: clad@idsse.ac.cn
Diversity and Formation Mechanisms of Deep-Sea Fish: Conduct large-scale resource surveys, taxonomic studies, and establish scientific databases for hadal fish. Focus on the patterns, processes, and mechanisms of hadal biodiversity.
Multi-Omics and Environmental Adaptation Mechanisms of Deep-Sea Fish: Employ integrative multi-omics approaches to investigate the origins and evolution of hadal organisms, uncovering internal and external factors influencing genetic structures and distribution patterns. Functional genomic analyses aim to identify molecular mechanisms underlying macro-organisms’ adaptations to the hadal environment.
Research funding and awards:
1. The National Natural Science Foundation of China
2. The Strategic Priority Research Program of the Chinese Academy of Sciences
3. The National Key Research and Development Program of China
Education and Employment History:
1993-09 to 1997-12, Ph.D. in Science, National Museum of Natural History, France
1985-09 to 1988-06, Master's Degree, Institute of Hydrobiology, Chinese Academy of Sciences
1979-09 to 1983-06, Bachelor's Degree, Department of Biology, Southwest University
2004-05 to 2004-11, Senior Visiting Scholar, Department of Ecology and Evolution, University of Chicago, USA
1988-07 to Present, Research Assistant to Senior Researcher, Institute of Hydrobiology, Chinese Academy of Sciences
2014-12-31 to 2026-12-31, President, Hubei and Wuhan Zoological Society
2009-12-30 to 2026-12-31, Executive Council Member, Chinese Zoological Society
Publications:
[1] Xupeng Bi, Kun Wang, Liandong Yang, Hailin Pan, Haifeng Jiang, Qiwei Wei, Miaoquan Fang, Hao Yu, Chenglong Zhu, Yiran Cai, Yuming He, Xiaoni Gan, Honghui Zeng, Daqi Yu, Youan Zhu, Huifeng Jiang, Qiang Qiu, Huanming Yang, Yong E. Zhang, Wen Wang, Min Zhu, Shunping He, Guojie Zhang.(2021) Tracing the genetic footprints of vertebrate landing in non-teleost ray-finned fishes, Cell, Volume 184, Issue 5, Pages 1377-1391.
[2] Kun Wang, Jun Wang, Chenglong Zhu, Liandong Yang, Yandong Ren, Jue Ruan, Guangyi Fan, Jiang Hu, Wenjie Xu, Xupeng Bi, Youan Zhu, Yue Song, Huatao Chen, Tiantian Ma, Ruoping Zhao, Haifeng Jiang, Bin Zhang, Chenguang Feng, Yuan Yuan, Xiaoni Gan, Yongxin Li, Honghui Zeng, Qun Liu, Yaolei Zhang, Feng Shao, Shijie Hao, He Zhang, Xun Xu, Xin Liu, Depeng Wang, Min Zhu, Guojie Zhang, Wenming Zhao, Qiang Qiu, Shunping He, Wen Wang.(2021) African lungfish genome sheds light on the vertebrate water-to-land transition, Cell, Volume 184, Issue 5, Pages 1362-1376.
[3] Wang K, Shen Y, Yang Y, Gan X, Liu G, Hu K, Li Y, Gao Z, Zhu L, Yan G et al.(2019) Morphology and genome of a snailfish from the Mariana Trench provide insights into deep-sea adaptation. Nature ecology & evolution, 3(5):823-833.
[4] Baosheng Wu, Chenguang Feng, Chenglong Zhu, Wenjie Xu, Yuan Yuan, Mingliang Hu, Ke Yuan, Yongxin Li, Yandong Ren, Yang Zhou, Haifeng Jiang, Qiang Qiu, Wen Wang, Shunping He, Kun Wang.(2021) The Genomes of Two Billfishes Provide Insights into the Evolution of Endothermy in Teleosts, Molecular Biology and Evolution, Volume 38, Issue 6, Pages 2413–2427.
[5] Chen J, Zeng H, Lv W, Sun N, Wang C, Xu W, Hu M, Gan X, He L, He S, Fang C.(2023)Pseudo-chromosome-length genome assembly for a deep-sea eel Ilyophis brunneus sheds light on the deep-sea adaptation. Sci China Life Sci.66(6):1379-1391. doi: 10.1007/s11427-022-2251-8.
[6] Shen YJ, Dai W, Gao ZM, Yan GY, Gan XN, He SP.(2017) Molecular phylogeny and divergence time estimates using the mitochondrial genome for the hadal snailfish from the Mariana trench. Sci Bull, 62(16):1106-1108.
[7] Wang Y, Shen Y, Feng C, Zhao K, Song Z, Zhang Y, Yang L, He S.(2016) Mitogenomic perspectives on the origin of Tibetan loaches and their adaptation to high altitude. Scientific reports, 6:29690.
[8] Shen Y, Kou Q, Zhong Z, Li X, He L, He S, Gan X.(2017) The first complete mitogenome of the South China deep-sea giant isopod Bathynomus sp. (Crustacea: Isopoda: Cirolanidae) allows insights into the early mitogenomic evolution of isopods. Ecology and evolution, 7(6):1869-1881.
[9] Jiang H, Du K, Gan X, Yang L, He S.(2019) Massive Loss of Olfactory Receptors But Not Trace Amine-Associated Receptors in the World's Deepest-Living Fish (Pseudoliparis swirei). Genes (Basel), 10(11).
[10] Chen J, Yang L, Zhang R, Uebbing S, Zhang C, Jiang H, Lei Y, Lv W, Tian F, Zhao K et al.(2020) Transcriptome-Wide Patterns of the Genetic and Expression Variations in Two Sympatric Schizothoracine Fishes in a Tibetan Plateau Glacier Lake. Genome Biology and Evolution, 12(1):3725-3737.
Name and position: Longfei Wu, Adjunct Professor
Email: wu@idsse.ac.cn
Research interests:
Diversity of Microorganisms and Mechanisms of Their Adaptation to Deep-Sea Environments
Research funding and awards:
1. A*Midex, France 2030, Initiative d’Excellence d’Aix-Marseille Université – A*MIDEX AMX-22-RE-AB-184. Evolution de la multicellularité bactérienne (EvoMulB), 2023/10/10-2027/10/09.
2. CNRS, DBM-2023, CNRS, DBM-2023, Mechanism of infrared restored cell division under high hydrostatic pressure (IR-DIVISION). 2023/01/01-2024/12/31.
National Natural Science Foundation of China, Characterization and mechanism of deep-sea microbial succession and evolution at multiscale. NSFC 92351304. 2024/01-2024/12.
3. National Natural Science Foundation of China, Infrared-driven phototrophic metabolism and mechanism of microorganisms dwelling in deep-sea hydrothermal vent fields. NSFC 42176121. 2022/01-2025/12.
Education and Employment History:
2013-10-- to date, Institute of Deep‑Sea Science and Engineering, Chinese Academy of Sciences
1995-9-- to date, Institute of Mediterranean Microbiology, CNRS France,
1990-10--1995-8, CNRS Lyon France INSA
1988-5--1990-9, University of San Diego USA
Degrees, History of Employment:
1984-9--1988-3，Institut National des Sciences Appliquées de Lyon，Doctor degree
1983-9--1984-6，Université Claude Bernard Lyon 1, Master degree
1978-10--1982-6，Shandong University，Bachelor degree
Publications:
[1] Dai, J., Li, X. G., Zhang TY., Chen H., Zhang, W. J., Li.D, et al.(2024) Illuminating a bacterial adaptation mechanism: Infrared-driven cell division in deep-sea hydrothermal vent environments. The Innovation Geoscience. 2(1): 100050.
[2] Jiao, Z. X., Li, X. G., Zhang, H. H., Xu, J., Bai, S. J., Dai, J., Lin, J., Zhang, W. J., Qi, X. Q., Wu, L. F. (2023). Crassaminicella indica sp. nov., a novel thermophilic anaerobic bacterium isolated from a deep-sea hydrothermal vent. International journal of systematic and evolutionary microbiology, 73(3).
[3] Li, X. G., Dai, J., Zhang, W. J., Jiang, A. J., Li, D. H., Wu, L. F. (2023). Genome analysis of Tepidibacter sp. SWIR-1, an anaerobic endospore-forming bacterium isolated from a deep-sea hydrothermal vent. Marine genomics, 71, 101049.
[4] Dai, J., Li, X. G., Zhang, W. J., Wu, L. F. (2023). Tepidibacter hydrothermalis sp. nov., a novel anaerobic bacterium isolated from a deep-sea hydrothermal vent. International journal of systematic and evolutionary microbiology, 73(11).
[5] W. Zhang, J. Chen, J. Dai, S.Zhu, H. Le Guenno, A. Kosta, H. Pan, X.-X. Qian, C.-L. Santini, N. Menguy, X. Li, Y. Chen, J. Liu, K. Cui, Y. Zhao, G. Liu, E. Durand, W.-J. Zhang, A. Roussel, T. Xiao, L.-F. Wu (2022) Membrane-remodeling protein ESCRT-III homologs incarnate the evolution and morphogenesis of multicellular magnetotactic bacteria. bioRxiv. doi: 10.1101/2022.11.08.515611.
[6] Chen H., Li D., Jiang A., Li X.G., Wu S.J., Chen J.W., Qi X.Q., Dai J., Zhang W.J.*, Liu S.S. and Wu L.-F.* (2022) Metagenomic analysis reveals wide distribution of phototrophic bacteria in hydrothermal vents on the ultraslow-spreading Southwest Indian Ridge. Marine Life Sci. Tech. 4: 255–267
[7] Qian, X. X., Santini, C. L., Kosta, A., Menguy, N., Le Guenno, H., Zhang, W., Li, J., Chen, Y. R., Liu, J., Alberto, F., Espinosa, L., Xiao, T., & Wu, L. F. (2020). Juxtaposed membranes underpin cellular adhesion and display unilateral cell division of multicellular magnetotactic prokaryotes. Environmental microbiology, 22(4), 1481–1494.
Name and position: Lisheng He, Professor
Email: he-lisheng@idsse.ac.cn
Research interests:
Using omics and molecular biological methods, we study the adaptation mechanisms of organisms in extreme environments. The main research fields include the symbiotic microorganisms and their interactions with hosts; the evolution and unique regulation of metabolic pathways in deep-sea organisms; the development of genetic resources; and research and development of deep-sea exploration devices.
Research funding:
1. The National Natural Science Foundation of China, Diversity, community structure and potential functions of gut symbiotic microorganisms of polychaete benthic animals in cold seeps and hydrothermal fluids areas, The Person In Charge;
2. The National Key R&D Program of China, Exploring the adaptive and evolutionary mechanisms of the typical deep-sea snailfish, The Person In Charge of Sub-projects;
3. The Hainan Provincial Natural Science Foundation of China, The research and application of in situ sampling and gene detection equipment for deep sea organisms, The Person In Charge;
4. The Major scientific and technological projects of Hainan Province, Exploring active substances from intestinal microflora of deep sea organisms, The Person In Charge of Sub-projects;
5. The Major scientific and technological projects of Hainan Province, Genome sequencing, assembly and preliminary analysis of hagfish, The Person In Charge of Sub-projects;
6. The National Key R&D Program of China, System integration, load bearing equipment development and sea trial, The Person In Charge of Project;
7. The Key Research and Development Projects of Hainan Province, Comparative study on gut symbiotic microorganisms of benthic amphipods from hadal trench, The Person In Charge;
8. The National Natural Science Foundation of China, Comparative of cement proteins between cyprid and the adult barnacle in Megabalanus Rosa, The Person In Charge;
9. The "Strategic Priority Research Program" of the Chinese Academy of Sciences, Environmental adaptation mechanisms of large invertebrates in the deep sea, The Person In Charge of Project;
10. The Institute and local government cooperation projects of Sanya City, Activity research of antimicrobial peptides from deep-sea hydrothermal shrimp, The Person In Charge of Project.
Awards:
2021, Be awarded the title of “National March 8th Red-Banner Pacesetter” by National Women's Federation;
2016, Won the Second Prize of the National Natural Science Award (as the fourth completer);
2022, Honored as the "Most Beautiful Scientist" in Hainan Province;
2019, Honored in the "South China Sea Series" Talent Cultivation Plan of Hainan Province as "South China Sea Expert";
2019, Honored as "Leading Talent" in Hainan Province.
Education and Employment History:
Education
Sep, 2003—Sep, 2007, Ph.D in Biochemistry, The Hong Kong University of Science and Technology, Supervisor: Robert Qi
Sep, 2000 —Sep, 2003 Master in Clinical Medicine, Peking University Health Science Center
Sep, 1995—Sep, 2000 Bachelor in Clinical Medicine, Peking UniversityHealth Science Center
Employment
Aug, 2013— Present, Institute of Deep-Sea Science and Engineering, Chinese academy of sciences, Professor
Sep, 2010—Aug, 2013, The Hong Kong University of Science and Technology, Biochemistry, Postdoctor
Sep, 2007—Sep, 2010, The Hong Kong University of Science and Technology, Biology, Postdoctor
Publications:
[1] Shi M.K., Li Q., Wang Y. and He L.S.* (2024) The somatic genome of Eptatretus okinoseanus reveals the adaptation to deep-sea oligotrophic environment. BMC Genomics, 27;25(1):807.doi: 10.1186/s12864-024-10727-y
[2] Wei T.S., Liao Y.W., Wang Y., Li J.Y., He L.S.* (2023) Comparably characterizing the gut microbial communities of amphipods from littoral to hadal zones. J. Mar. Sci. Eng., 11(11), 2197.
[3] Li Q., Shi M.K, Zhu F.C., Lian C.A. and He L.S.* (2023) Genomic evidence for the first symbiotic Deferribacterota, a novel gut symbiont from the deep-sea hydrothermal vent shrimp Rimicaris kairei., Front. Microbiol.14:1179935.
[4] Chen J, Zeng H-H, Lv W-Q, Sun N, Wang C, Xu W-J, Hu M-L, Gan X-N, He L-S*, He S-P*, Fang C-C*. (2023) Pseudo-chromosome–length genome assembly for a deep-sea eel Ilyophis brunneus sheds light on the deep-sea adaptation. Science China Life Sciences. 66: 1379–1391.
[5] Guo L.L., Wang S.L., Zhu F.C, Xue F., He L.S.*(2021) Characteristics of two crustins from Alvinocaris longirostris in Hydrothermal Vents. Marine Drugs, 19(11), 600; https://doi.org/10.3390/md19110600
[6] Yan G.Y., Lian C.A., Lan Y., Qian P.Y., He L.S.* (2021) Insights into the vision of the hadal snailfish Pseudoliparis swirei through proteomic analysis of the eye. Proteomics, 2021, 21(19): 2100118.
[7] Lian C.A., Yan G.Y., Huang J.M., Danchin A., Wang Y., He L.S.*(2020) Genomic characterization of a novel gut symbiont from the hadal snailfish. Frontiers in Microbiology, 10:2978.
[8] Li J.Y., Song Z.L., Yan G.Y., He L.S.*(2019) The complete mitochondrial genome of the largest amphipod, Alicella gigantea: Insight into its phylogenetic relationships and deep sea adaptive characters. International Journal of Biological Macromolecules. 141:570-577.
[9] Cheng X.Y., Wang Y., Li J.Y., Yan G.Y., He L.S.*(2019) Comparative analysis of the gut microbial communities between two dominant amphipods from the Challenger Deep, Mariana Trench. Deep Sea Research Part I: Oceanographic Research Papers. 151:103081.
[10] Wang S.L., Li Y.L., Han Z., Chen X., Chen Q.J., Wang Y., He L.S.* (2018) Molecular Characterization of a Novel N-Acetylneuraminate Lyase from a Deep-Sea Symbiotic Mycoplasma. Marine Drugs. 16(80):1-13.
Name and position: Hongmei Jing, Professor
Email: hmjing@idsse.ac.cn
Research interests:
Marine Microbiology, Molecular Ecology. Focusing on habitats such as the deep-sea trenches, cold seeps, and hydrothermal vents, aiming to uncover ecological characteristics of abyssal microorganisms, including community succession, geographical patterns, and metabolic functions.
Research funding and awards:
1. The National Key R&D Program of China (2022YFC2805505)
2. The Innovational Fund for Scientific and Technological Personnel of Hainan Province (KJRC2023C37)
3. The Hainan Province Science and Technology Special Fund (ZDKJ2021036)
Education and Employment History:
Apr. 2002 - Mar. 2006, The University of Hong Kong, Doctor,
Mar. 2013 – Present, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Research,
Mar. 2012 - Feb. 2013, National University of Singapore, Senior Visiting Scholar,
Oct. 2008 - Feb. 2012, The Hong Kong University of Science and Technology, Visiting Scholar,
Nov. 2006 - Oct. 2008, Université du Québec à Montréal, Postdoctor
Publications:
[1] Li, Y., Wang, T., Jing, H.*, & Xiao, Y. (2024). Evolutionary ecology of denitrifying methanotrophic NC10 bacteria in the deep-sea biosphere.Molecular Ecology, 33(12), e17372.
[2] Zhang, Y., Jing, H.*. (2024). Deterministic process controlling the prokaryotic community assembly across seamounts along in the Yap and Mariana trenches. Ecological Indicators, 158,111538.
[3] Jiang, Q., Jing, H.*, Li, X., Wan, Y., Chou, I-M., Hou, L., Dong, H., Niu, Y., & Gao, D. (2023).Active pathways of anaerobic methane oxidization in deep-sea cold seeps of the South China Sea. Microbiology Spectrum,11(6),e0250523.
[4] Zhang, Y., Liu, H., Huang, N., Peng, X., & Jing, H*. (2023). Geographical distribution and driving force of micro-eukaryotes in the seamount sediments along the island arc of the Yap and Mariana trenches. Microbiology Spectrum, 11(6), e02069-23.
[5] Zhang, Y., Huang, N., & Jing, H*. (2022). Biogeography and Population Divergence of Microeukaryotes Associated with Fluids and Chimneys in the Hydrothermal Vents of the Southwest Indian Ocean. Microbiology Spectrum, 10(5), e02632-21.
[6] Jiang, Q., Jing, H.*, Jiang, Q., & Zhang, Y. (2022). Insights into carbon-fixation pathways through metagonomics in the sediments of deep-sea cold seeps.Marine Pollution Bulletin, 176,113458.
[7] Jing, H.*, Xiao, X., Zhang, Y., Li, Z., Jian, H., Luo, Y., & Han, Z. (2022). Composition and Ecological Roles of the Core Microbiome along the Abyssal-Hadal Transition Zone Sediments of the Mariana Trench. Microbiology Spectrum, 10(3),e0198821.
[8] Zhao, J., Jing, H.*, Wang, Z., Wang, L., Jian, H., Zhang, R., Xiao, X., Chen, F., Jiao, N., & Zhang, Y.(2022). Novel Viral Communities Potentially Assisting in Carbon, Nitrogen, and Sulfur Metabolism in the Upper Slope Sediments of Mariana Trench.mSystems, 7(1),e0135821.
[9] Jing, H.*, Wang, R., Jiang, Q., Zhang, Y., & Peng, X. (2020).Anaerobic methane oxidation coupled to denitrification is an important potential methane sink in deep-sea cold seeps. The Science of The Total Environment, 748,142459.
[10] Jing, H.*, Zhu, W., Liu, H., Zheng, L., & Zhang, Y. (2018).Particle-attached and free-living archaeal communities in the benthic boundary layer of the Mariana Trench. Frontiers in Microbiology,9,2821.
Name and position: Weijia Zhang, Professor
Email: wzhang@idsse.ac.cn
Research interests:
High hydrostatic pressure exerts severe effects on multiple cellular processes, including cell division, motility and energy metabolism. Yet, microbes survive and grow in the deep-sea environment where the pressure reaches over 110 MPa and actively participate in the cycling of numerous elements in the deep biosphere. My research focuses on the deep-sea microbial adaptation mechanism of high hydrostatic pressure. On-going works include: 1. Investigating the molecular mechanism of high hydrostatic pressure (HHP) regulated gene expression and bacterial HHP adaptation; 2. Studies of metabolic activity of microorganisms at hadal environments through combination of multi-omics and HHP simulating incubations.
Research funding and awards:
1. Title: Characterization and mechanism of deep-sea microbial succession and evolution at multiscale. NSFC 92351304. 2024/01-2024/12. 3,200,000 CNY. Agency: National Natural Science Foundation of China. Lead-PI.
2. Title: Research on Active Substance Resources of Deep-Sea Abyssal Microorganisms. ZDKJ2021028. 2021/12–2024/12. 10,000,000 CNY. Agency: Department of Science and Technology of Hainan Province.Lead-PI.
3. Title: Characterization of TMAO reduction of deep-sea bacteria and the mechanism of regulation in response to high hydrostatic pressure. NSFC91751108. 2018/01–2020/12. 800,000 CNY. Agency: National Natural Science Foundation of China. Lead-PI.
4. Title: Characterization of pressure-regulated TMAO reductase in marine bacteria Vibrio fluvialis QY29. 2018YD01. 2018.11-2020.10. 100,000 CNY. Agency: Bureau of Industry and Information Technology of Sanya. Lead-PI.
5. Title: High-hydrostatic pressure adaptation mechanism of flagellar motility in obligately piezophiles Moritella yayanosii DB21MT-5. NSFC41506147. 2016/01–2018/12. 210,000 CNY. Agency: National Natural Science Foundation of China. Lead-PI.
Title: High hydrostatic pressure adaptation mechanism of deep-sea bacterium. SIDSSE-QN-201408. 2014/10-2016/09. 90,000 CNY. Agency: Sanya Institute of Deep-sea Science and Engineering. Lead-PI.
Education and Employment History:
Education
2006.09 – 2012.01,Ph.D., majored in Microbiology, College of Biological Sciences, China Agricultural University, Supervisor: Prof. Ying LI
2007.11 – 2010.11, Joint Ph.D. program, funded by China Scholarship Council, Laboratoire de Chimie Bactérienne (LCB), Centre National de la Recherche Scientifique (CNRS), France Co-supervisors: Prof. Long-Fei WU (LCB, CNRS)
2002.09 – 2006.06, Bachelor of Science, College of Biological Sciences, China Agricultural University
Employment
2024.01 to present, Researcher, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences
2014.10 2023.12, Associate Researcher, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences
2012.01 – 2014.10, Post-doctoral Fellow, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College
Publications:
[1] Cui X. H., Wei Y. C., Li X. G., Qi X. Q., Wu L. F., Zhang W. J.* (2024). N-terminus GTPase domain of the cytoskeleton protein FtsZ plays a critical role in its adaptation to high hydrostatic pressure. Front Microbiol. Aug 16;15:1441398.
[2] Li, A. Q., Qi, X. Q., Zhang, C., Huang, X. G., Wen, D. Y., Li, X. G., Zhang, W. J.* (2024). Thalassotalea psychrophila sp. nov., Thalassotalea nanhaiensis sp. nov. and Thalassotalea fonticola sp. nov., three psychrophilic bacteria isolated from deep-sea sediment. International journal of systematic and evolutionary microbiology, 74(5).
[3] Li, A. Q., Zhang, W. J.*, Li, X. G., Bao, X. C., Qi, X. Q., Wu, L. F., Bartlett, D. H. (2023). Piezophilic Phenotype Is Growth Condition Dependent and Correlated with the Regulation of Two Sets of ATPase in Deep-Sea Piezophilic Bacterium Photobacterium profundum SS9. Microorganisms, 11(3), 637.
[4] Bao, X. C., Tang, H. Z., Li, X. G., Li, A. Q., Qi, X. Q., Li, D. H., Liu, S. S., Wu, L. F., Zhang, W. J.* (2023). Bioluminescence Contributes to the Adaptation of Deep-Sea Bacterium Photobacterium phosphoreum ANT-2200 to High Hydrostatic Pressure. Microorganisms, 11(6), 1362.
[5] Liu, B., Liu, K., Qi, X., Zhang, W. J.*, Li, B. (2023). Classification of deep-sea cold seep bacteria by transformer combined with Raman spectroscopy. Scientific reports, 13(1), 3240.
[6] Liu, N., Jiang, T., Cui, W. P., Qi, X. Q., Li, X. G., Lu, Y., Wu, L. F., Zhang, W. J.* (2023). The TorRS two component system regulates expression of TMAO reductase in response to high hydrostatic pressure in Vibrio fluvialis. Frontiers in microbiology, 14, 1291578.
[7] Chen, H., Li, D. H., Jiang, A. J., Li, X. G., Wu, S. J., Chen, J. W., Qu, M. J., Qi, X. Q., Dai, J., Zhao, R., Zhang, W. J.*, Liu, S. S., Wu, L. F. (2022). Metagenomic analysis reveals wide distribution of phototrophic bacteria in hydrothermal vents on the ultraslow-spreading Southwest Indian Ridge. Marine life science & technology, 4(2), 255–267.
[8] Zhang, W. J.*, Zhang, C., Zhou, S., Li, X. G., Mangenot, S., Fouteau, S., Guerin, T., Qi, X. Q., Yang, J., Bartlett, D. H., Wu, L. F. (2021). Comparative genomic analysis of obligately piezophilic Moritella yayanosii DB21MT-5 reveals bacterial adaptation to the Challenger Deep, Mariana Trench. Microbial genomics, 7(7), 000591.
[9] Li X. G., Zhang W. J.*, Xiao X., Jian H., Jiang T., Tang H. Z., Qi X. Q. and Wu L. F. (2018) Pressure-regulated gene expression and enzymatic activity of the two periplasmic nitrate reductases in the deep-sea bacterium Shewanella piezotolerans WP3. Frontiers in Microbiology. Frontiers in Microbiology. doi: 10.3389/fmicb.2018.03173
[10] Yin Q. J., Zhang W. J.*, Qi X. Q., Zhang S. D., Jiang T., Li X. G., Chen Y., Santini C. L., Zhou H., Chou I. M. and Wu L. F. (2018) High Hydrostatic Pressure Inducible Trimethylamine N-Oxide Reductase Improves the Pressure Tolerance of Piezosensitive Bacteria Vibrio fluvialis. Frontiers in Microbiology. 8:2646. doi: 10.3389/fmicb.2017.02646
Name and position: Zhaoming Gao, Associate Professor
Email: gaozm@idsse.ac.cn
Research interests:
1. Microbiomes in deep oceans and hadal trenches.
Employing meta-omic approaches to illustrate the diversity, novelty and ecological functions of microbial communities in the deep oceans and hadal trenches, and to reveal their connections with environmental factors. Focusing on key microbial players involving carbon, nitrogen and sulfur cycling.
2. Chemosynthetic holobionts. Researching on symbionts associated with sponges, siboglinid tubeworms and bivalves in the deep oceans. Focusing the adaptive and evolutionary mechanisms of chemosynthetic symbionts in deep extreme environments.
Research funding and awards:
1. Study on the metabolic modes and symbiotic mechanisms modes and symbiotic mechanisms of the cold seeping community of the sponge Myxilla methanophila based on high-throughput sequencing, Principal Investigator, National Task, National Natural Science Foundation of China (2020), 2015-01~2017-12.
2. Chinese Academy of Sciences Youth Academy of Sciences Youth Innovation Promotion Project, Principal Investigator, Chinese Academy of Sciences Program Academy of Sciences Program, 2017-01~2020-12.
3. Study on microbiome and symbiosis of chemosynthesis ecosystem of cold spring in South China Sea, National Task, 2018-08~2021-12
4. Microbiome study on chemosynthetic ecosystem of cold spring in South China Sea, Local task, 2019-12--2022-12
5. Symbiotic evolution and ecological role analysis of symbiotic functional bodies of new tubular worms from Cold spring Sclerolinum, National Task, 2021-01--2024-12
6. Environmental adaptation and symbiotic evolution mechanisms of dominant microbial groups in typical submarine fluid systems, National Task, 2022-12~2026-12
7. Deep sea in situ virology study, National Task, 2022-12~2026-05
Education and Employment History:
01/2015-Present, Associate professor in Microbial Ecology and Bioinformatics Deep Sea Science Department, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences (CAS), Sanya, Hainan, PR China
03/2014-12/2014, Assistant professor in Microbial Ecology and Bioinformatics,Deep Sea Science Department, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences (CAS), Sanya, Hainan, PR China
05/2012-06/2014, Postdoc/Visiting scholar in Microbial Ecology and Bioinformatics,Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
11/2011-10/2014, Postdoc in Marine Microbiology, Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration (SOA), Xiamen, Fujian, PR China
09/2006-06/2011, Ph.D. in Microbiology, Marine Biotechnology Research Center, The State Key Lab of Microbial Technology, Shandong University, Jinan, Shandong, PR China
03/2007-03/2011, Joint-Ph.D program, Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration (SOA), Xiamen, Fujian, PR China
09/2002-06/2006, B.S. in Biotechnology, College of Life Science, Shandong University, Jinan, Shandong, PR China
Publications:
[1] Gao, Z.-M., Zhou, G.-W., Huang, H., and Wang, Y. (2017) The cyanobacteria-dominated sponge Dactylospongia elegans in the South China Sea: prokaryotic community and metagenomic insights. Front Microbiol8: 1387.
[2] Gao, Z.-M., Wang, Y., Tian, R.-M., Wong, Y.H., Batang, Z.B., Al-Suwailem, A.M. et al. (2014) Symbiotic adaptation drives genome streamlining of the cyanobacterial sponge symbiont “Candidatus Synechococcus spongiarum”. MBio5: 00079-00014.
[3] Gao, Z.-M., Xu, T., Chen, H.-G., Lu, R., Tao, J., Wang, H.-B. et al. (2023) Early genome erosion and internal phage-symbiont-host interaction in the endosymbionts of a cold-seep tubeworm. iScience.
[4] Gao, Z.-M., Wang, Y., Tian, R.-M., Lee, O.O., Wong, Y.H., Batang, Z.B. et al. (2015) Pyrosequencing revealed shifts of prokaryotic communities between healthy and disease-like tissues of the Red Sea sponge Crella cyathophora. PeerJ3: e890.
[5] Gao, Z.M., Huang, J.M., Cui, G.J., Li, W.L., Li, J., Wei, Z.F. et al. (2019) In situ meta‐omic insights into the community compositions and ecological roles of hadal microbes in the Mariana Trench. Environmental microbiology21: 4092-4108.
[6] Lu, R., Gao, Z.-M., Li, W.-L., Wei, Z.-F., Wei, T.-S., Huang, J.-M. et al. (2021) Asgard archaea in the Haima cold seep: Spatial distribution and genomic insights. Deep Sea Research Part I: Oceanographic Research Papers170: 103489.
[7] Wang, Y., Gong, L., Gao, Z., Wang, Y., Zhao, F., Fu, L., and Li, X. (2023) Host-specific bacterial communities associated with six cold-seep sponge species in the South China Sea. Frontiers in Marine Science.
[8] Wei, T.-S., Gao, Z.-M., Gong, L., Li, Q.-M., Zhou, Y.-L., Chen, H.-G. et al. (2023) Genome-centric view of the microbiome in a new deep-sea glass sponge species Bathydorus sp. Frontiers in Microbiology14: 1078171.
Name and position: Zhuang Han, Associate Professor
Email: zhuanghan@idsse.ac.cn
Research interests:
My research focuses on deep-sea microbial natural products, particularly exploring secondary metabolites from extreme environments such as abyssal zones, cold seeps, and hydrothermal vents. I am interested in discovering novel bioactive compounds with applications in medicine and biotechnology, including anti-tumor, antibacterial, and antiviral agents. Additionally, I investigate biosynthetic pathways, mechanisms of action, and employ innovative approaches like genome mining and heterologous expression to activate silent gene clusters, aiming to unlock the potential of unexplored microbial genetic and chemical diversity.
Research funding and awards:
1. The National Key Research & Development Program of China (2022YFC2805505)
2. Major Scientific and Technological Projects of Hainan Province (ZDKJ2021036)
3. Major Scientific and Technological Projects of Hainan Province (ZDKJ2019011)
4. The National Key Research & Development Program of China (2018YFC0309800)
Education and Employment History:
2017.12 – Present, Associate Researcher, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences
2019.09 - 2020.11, Visiting Scholar, Boston University
2013.06 - 2017.12, Assistant Researcher, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences
2013.12 - 2014.12, Visiting Scholar, Hong Kong University of Science and Technology
2009.09 - 2013.06, PhD Student in Marine Chemistry, University of Chinese Academy of Sciences
(2010.02 - 2013.02, Joint PhD Training Program in Marine Biology, Hong Kong University of Science and Technology)
Publications:
[1] Zhu, BY., Cen, ZY., Chen, YQ., Shang, K., Zhai, JA., Han, MG., Wang, JW., Chen, ZY., Wei, TS., Han, Z*. (2024）α-Pyrone mediates quorum sensing through the conservon system in Nocardiopsis sp.. Microbiological Research. 285, 127767.
[2] Bai, SJ., Shang, K., Zeng, SQ., Huang, ZM., Han, Z*. (2024) Genome analysis of Salinimicrobium sp. 3283s, a deep-sea bacterium isolated from the sediments of South China Sea, China, Marine Genomics. Volume 76,2024,101125, ISSN 1874-7787
[3] Yang, LJ., Han, Z., Gu, YC., Shao, CL., Wang, CY*. (2024) New Sulfurated Butyrolactones from the Fungus Penicillium janthinellum. Chem. Biodiversity. e202401966.
[4] Wang, JW., Shang, K., Wu, SY., Zhu, BY., Han, MG., Zhao, Y., Chen, YQ., Xie, J., Huang, B., Han, Z*. Complete genome sequence of piezotolerant Stutzerimonas kunmingensis 7850S isolated from the sediment of the Mariana Trench. (2022) Marine Genomics. 66:100996.
[5] Zhang, XY., Wu, KY., Han, Z., Chen, ZH., Liu, ZY., Sun, ZW., Shao, LY., Zhao, ZL*., Zhou, L*. (2022) Microbial diversity and biogeochemical cycling potential in deep-sea sediments associated with seamount, trench, and cold seep ecosystems. Frontiers in Microbiology. 13:1029564.
[6] Chi-Ho Ip, J., Xu, T., Sun, J., Li, RS., Chen, C., Lan, Y., Han, Z., Zhang, HB., Wei, JG., Wang, HB., Tao, J., Cai, ZW., Qian, PY., Qiu, JW. Host–Endosymbiont Genome Integration in a Deep-Sea Chemosymbiotic Clam. (2021) Molecular Biology and Evolution. 38 (2), 502-518.
[7] Sun, YN., Sun, J., Yang, Y., Lan, Y., Chi-Ho Ip, J., Wong, WC., Kwan, YH., Zhang, YJ., Han, Z., Qiu, JW., Qian, PY.*. Genomic Signatures Supporting the Symbiosis and Formation of Chitinous Tube in the Deep-Sea Tubeworm Paraescarpia echinospica. (2021)Molecular Biology and Evolution. 38 (10), 4116-4134.
[8] Kong, WN., Zhao, C., Gao, XW., Wang, LP., Tian, QQ., Liu, Y., Xue, SW., Han, Z., Chen, FL., Wang, SW. Characterization and Transcriptome Analysis of a Long-Chain n-Alkane-Degrading Strain Acinetobacter pittii SW-1. (2021) International Journal of Environmental Research and Public Health. 18(12):6365.
[9] Han, Z., Li, XY., Liu, LL., Lu, L., Qian, PY. (2017). Thielavins w–z7, new antifouling thielavins from the marine-derived fungus thielavia sp. ust030930-004. Marine Drugs, 15(5), 128.
[10] Han, Z., Sun, J., Zhang, Y., He, F., Xu, Y., Matsumura, K., He, LS., Qiu, JW., Qi, SH., Qian, PY. (2013). iTRAQ-Based Proteomic Profiling of the Barnacle Balanus amphitrite in Response to the Antifouling Compound Meleagrin. Journal of Proteome Research. 12(5), 2090.
Name and position: Helu Liu, Associate Professor
Email: @idsse.ac.cn
Research interests:
Education and Employment History:
Education
09/2011 – 06/2014, PhD, Shantou University, Shantou, Guangdong, China
09/2008 – 06/2011, MA, Shantou University, Shantou, Guangdong, China
09/2004 – 06/2008, BA, Hubei University, Wuhan, Hubei , China
Employment
07/2014– present, Institute of Deep-sea Science and Engineering, CAS, Sanya, Hainan, China
02/2018 –05/2021, Columbia University Medical Center, New York, USA, Postdoctoral Research
Publications:
[1] YangZhou, Helu Liu, Chenguang Feng, Zaiqing Lu, Jun Liu, Yanan Huang, Huanhuan Tang, Zehui Xu, Yujin Pu, and Haibin Zhang.(2023). Genetic adaptations of sea anemone to hydrothermal environment. Science Advances. 9(42):eadh0474.
[2] HeluLiu, Huijun Li, Zhihua Jiang, Shibo Jin, Rui Song, Ying Yang, Jun Li, Jingshu Huang, Xiaoqing Zhang, Xuesong Dong, Munemasa Mori, Marvin J Fritzler, Lin He, Wellington Cardoso, Jining Lu. (2023). A local translation program regulates centriole amplification in the airway epithelium. Scientific Reports,13(1):7090.
[3] Huang, Yanan, Helu Liu, Yang Zhou, Zaiqing Lu, Yujin Pu, and Haibin Zhang.(2023). Cloning and functional characterization of the oxidative squalene cyclase gene in the deep-sea holothurian Chiridota sp. Gene, p.147971.
[4] Carlos F.H. Serra, Helu Liu, Jun Qian, Munemasa Mori, Jining Lu, and Wellington V. Cardoso. (2022). Prominin 1 and Notch regulate ciliary length and dynamics in multiciliated cells of the airway epithelium. iScience, 25(8): 104751.
[5] Jessica E Shui, Wei Wang, Helu Liu, Anna Stepanova, Grace Liao, Jun Qian, Xingbin Ai, Vadim Ten, Jining Lu, Wellington V Cardoso. (2021). Prematurity alters the progenitor cell program of the upper respiratory tract of neonates. Scientific reports, 11(1): 10799.
Name and position: Jun Liu, Associate Professor
Email: liujun@idsse.ac.cn
Research interests:
My research interests lie in evolution and adaptation of deep-sea animals and the deep-sea benthic biodiversity. I am particularly engaged in studying phylogeny and adaptation of deep-sea echinoderms by combining multi-source data, such as genomics, transcriptomics, and proteomics, etc. Additionally, I am also interested in exploring the benthic biodiversity distribution patterns and drivers in the deep sea, by using environmental DNA metabarcoding method and video/image data analysis. The goal is to contribute to a better understanding of the biodiversity and evolution in the deep-sea ecosystems.
Research funding and awards:
1. National Natural Science Foundation of China(42106121)
2. Strategic Priority Research Program of the Chinese Academy of Sciences (XDA22050303)
3. Major scientific and technological projects of Hainan Province (ZDKJ2019011)
Education and Employment History:
Ph.D., Ocean University of China, 2007-2012
B.Sc., Ocean University of China, 2003-2007
Associate Research Fellow, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences (CAS), 2021-present
Assistant Research Fellow, Institute of Deep-Sea Science and Engineering, CAS, 2014-2021
Postdoctoral Research Fellow, Institute of Zoology, CAS, 2012–2014
Publications:
[1] Liu, J., Zhou, Y., Pu, Y., and Zhang, H. (2023) A chromosome-level genome assembly of a deep-sea starfish (Zoroaster cf. ophiactis). Sci Data 10, 506.
[2] Liu, J., Du, L., Sun, Z., and Zhang, H. (2022) Comparison of structure and diversity of benthic communities in the Okinawa Trough and Mariana Trench by environmental DNA metabarcoding. Deep Sea Res I: Oceanogr Res Pap 185, 103806.
[3] Liu, J., and Zhang, H. (2021) Combining multiple markers in environmental DNA metabarcoding to assess deep-sea benthic biodiversity. Front Mar Sci 8, 684955.
[4] Liu, J., Cui, D., Wang, H., Chen, J., Liu, H., and Zhang, H. (2020) Extensive cryptic diversity of giant clams (Cardiidae: Tridacninae) revealed by DNA-sequence-based species delimitation approaches with new data from Hainan Island, South China Sea. J Molluscan Stud 86, 56-63.
[5] Liu, J., Liu, H., and Zhang, H. (2018) Phylogeny and evolutionary radiation of the marine mussels (Bivalvia: Mytilidae) based on mitochondrial and nuclear genes. Mol Phylogen Evol 126, 233-240.
[6] Liu, J., Wang, C., Fu, D., Hu, X., Xie, X., Liu, P., Zhang, Q., and Li, M.-H. (2015) Phylogeography of Nanorana parkeri (Anura: Ranidae) and multiple refugia on the Tibetan Plateau revealed by mitochondrial and nuclear DNA. Sci Rep 5, 9857.
[7] Liu, J., Shikano, T., Leinonen, T., Cano, J.M., Li, M.-H., and Merilä, J. (2014) Identification of major and minor QTL for ecologically important morphological traits in three-spined sticklebacks (Gasterosteus aculeatus). G3: Genes Genom Genet 4, 595-604.
[8] Liu, J., Li, Q., Kong, L., and Zheng, X. (2011) Cryptic diversity in the pen shell Atrina pectinata (Bivalvia: Pinnidae): high divergence and hybridization revealed by molecular and morphological data. Mol Ecol 20, 4332-4345.
Name and position: Xuegong Li, Associate Professor
Email: xuegongli@idsse.ac.cn
Research interests:
Develop and design simulators for extreme environments to study the diversity of culturable microorganisms and their high-pressure adaptation mechanisms in extreme ocean environments like hadal trench and hydrothermal vents.
1) How does light stimulate the growth of bacteria from deep-sea hydrothermal vent?
2) How do microorganisms adapt to high-pressure environments in Hadal?
Research funding and awards:
1. National Natural Science Foundation of China (NSFC42376123)；
2. National Key R&D Program of China (2023YFC2812804, 2022YFC2805404).
Education and Employment History:
Education
2022-05--2023-04, French National Centre for Scientific Research (CNRS)，Mediterranean Institute of Microbiology, Visiting scholars
2010-09--2014-06, Ocean University of China Doctor degree
2006-09--2009-06, Guangdong Ocean University Master degree
2002-09--2006-06, Huazhong Agricultural University Bachelor degree
Employment
2014-09--to date, Institute of Deep-sea Science and Engineering, Chinese Academy of Science
Publications:
[1] Dai, J.,Li, X. G.,Zhang TY.,Chen H.,Zhang, W. J.,Li.D, et al.(2024) Illuminating a bacterial adaptation mechanism: Infrared-driven cell division in deep-sea hydrothermal vent environments. The Innovation Geoscience. 2(1): 100050.
[2] Jiao, Z. X., Li, X. G., Zhang, H. H., Xu, J., Bai, S. J., Dai, J., Lin, J., Zhang, W. J., Qi, X. Q., Wu, L. F. (2023). Crassaminicella indica sp. nov., a novel thermophilic anaerobic bacterium isolated from a deep-sea hydrothermal vent. International journal of systematic and evolutionary microbiology, 73(3).
[3] Li, X. G., Dai, J., Zhang, W. J., Jiang, A. J., Li, D. H., Wu, L. F. (2023). Genome analysis of Tepidibacter sp. SWIR-1, an anaerobic endospore-forming bacterium isolated from a deep-sea hydrothermal vent. Marine genomics, 71, 101049.
[4] Dai, J., Li, X. G., Zhang, W. J., Wu, L. F. (2023). Tepidibacter hydrothermalis sp. nov., a novel anaerobic bacterium isolated from a deep-sea hydrothermal vent. International journal of systematic and evolutionary microbiology, 73(11).
[5] Li X. G., Tang H. Z., Zhang W. J., Qi X. Q., Qu Z. G., Xu J., Wu, L. F. (2021). Thermococcus aciditolerans sp. nov., a piezotolerant, hyperthermophilic archaeon isolated from a deep-sea hydrothermal vent chimney in the Southwest Indian Ridge. International journal of systematic and evolutionary microbiology, 71(8).
[6] Li X. G., Lin J., Bai S. J., Dai J., Jiao Z. X., Tang H. Z., Qi X. Q., Zhang W. J., Liu M., Xu J. S., Wu, L. F. (2021). Crassaminicella thermophila sp. nov., a moderately thermophilic bacterium isolated from a deep-sea hydrothermal vent chimney and emended description of the genus Crassaminicella. International journal of systematic and evolutionary microbiology, 71(11).
[7] Li X. G., Zhang W. J., Qi X. Q., Wu, L. F. (2019).Genome analysis of Crassaminicella sp. SY095, an anaerobic mesophilic marine bacterium isolated from a deep-sea hydrothermal vent on the Southwest Indian Ridge. Marine genomics, 52, 100733.
[8] Li X. G., Zhang W. J., X X., Jian H. H., Jiang T., Tang H. Z., Qi X. Q., Wu, L. F. (2018).Pressure-Regulated Gene Expression and Enzymatic Activity of the Two Periplasmic Nitrate Reductases in the Deep-Sea Bacterium Shewanella piezotolerans WP3. Frontiers in Microbiology, 9, 3173
Name and position: Shijie Bai, Associate Professor
Email: baishijie@idsse.ac.cn
Research interests:
My research interests are microorganisms in different environments, including bacteria, archaea, viruses and microeukaryotes. My current research interests focus on deep-sea geological microbiology, including the relationship between deep-sea minerals and microbes, microbial-mediated mechanisms of heavy metal cycling in the deep sea, and geochronology and microbes. At the same time, we also carry out some work on the gut microbiology of marine mammals. We use a range of analytical techniques, including microbiology, geology, geochemistry and bioinformatics.
Research funding and awards:
1. The National Natural Science Foundation of China, The regulative mechanisms of bacterial community structure influenced by viruses in Qiongdong upwelling, The Person In Charge;
2. The Natural Science Foundation of Hainan Province, Effects of Marine viruses on upwelling bacterial community structure, The Person In Charge;
3. The Natural Science Foundation of Sanya City, Study on the viral diversity of reservoir in Sanya city, The Person In Charge;
4. National Key Research and Development Project, Application of ROV biogeochemical exploration technology, The Person In Charge;
5. National Key Research and Development Project, Development of in situ microbial enrichment and experimental system, The Person In Charge;
6. The Natural Science Foundation of Hainan Province, Mechanisms of volcanic ash input on deep-sea ecosystem evolution and deep-sea iron cycling, The Person In Charge;
7. The Natural Science Foundation of Hainan Province, Characteristics of spatial and temporal distribution of viruses in Sanya Bay sediments and environmental constraints, The Person In Charge;
8. Special Project for Deep Sea Technology Industry Promotion of Deep Sea Technology Innovation Center of Hainan Province, Deep-sea Sediment Pore Water Pressure Retention Sampler, The Person In Charge
Education and Employment History:
Jan, 2021 — Now, Institute of Deep-Sea Science and Engineering, Chinese academy of sciences, Associate Professor
Jan, 2014 — Dec, 2020, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Assistant Professor
Nov, 2017 — Dec, 2018, The Ohio State University, Department of Microbiology, USA, Visiting scientist, Supervisor: Matthew B. Sullivan
Sep, 2012 — Dec, 2013, Institute of hydrobiology, Chinese Academy of Sciences, Postdoctor, Supervisor: Dongru Qiu
Sep, 2008 — July, 2012, Xiamen University, School of Life Science, Microbiology, Supervisor: Tianling Zhen
Oct, 2009 — Nov, 2011, The University of Oklahoma, Department of Microbiology and Plant Biology, USA, Joint PhD student, Supervisor: Jizhong Zhou
Sep, 2005 — June, 2008 Guangdong Ocean University, College of Fisheries, Aquaculture, Supervisor: Dequan Qiu
Sep, 2001 — June, 2005 Central South University of Forestry and Technology, College of life sciences and technology, Biotechnology
Publications:
[1] Shijie, Bai., Peijun, Zhang., Xiaoxue, Qi., Jun, Liu., Dongjiao, Liu., Guangmou, Wang., Lei, Pang., Songhai, Li. (2024) Similarities and differences in gastrointestinal microbiomes between wild and human-cared spotted dolphins (Stenella attenuata) in natural waters. Water. Biology and Security. 3, 100288.
[2] Bai, S., Shang, K., Zeng, S., Huang, Z., Han, Z. (2024) Genome analysis of Salinimicrobium sp. 3283s, a deep-sea bacterium isolated from the sediments of South China Sea, China. Mar Genomics. 76, 101125.
[3] Bai, S., Huang, Z., Li, X.G. (2024) Genome analysis of Rossellomorea sp. y25, a deep sea bacterium isolated from the sediments of South China Sea. Mar Genomics. 75, 101110.
[4] Liang, Y., Wang, Z., Gao, N., Qi, X., Zeng, J., Cui, K., Lu, W., Bai S*. (2024) Variations and Interseasonal Changes in the Gut Microbial Communities of Seven Wild Fish Species in a Natural Lake with Limited Water Exchange during the Closed Fishing Season. Microorganisms. 12, 800.
[5] Bai, S., Zhang, J., Qi, X., Zeng, J., Wu, S., Peng, X. (2023) Changes of In Situ Prokaryotic and Eukaryotic Communities in the Upper Sanya River to the Sea over a Nine-Hour Period. Microorganisms. 11, 536.
[6] Bai, S., Zhang, P., Zhang, X., Yang, Z., Li, S. (2022) Gut Microbial Characterization of Melon-Headed Whales (Peponocephala electra) Stranded in China. Microorganisms. 10, 572.
[7] Bai, S., Zhang, P., Zhang, C., Du, J., Du, X., Zhu, C., Liu, J., Xie, P., Li, S. (2021) Comparative Study of the Gut Microbiota Among Four Different Marine Mammals in an Aquarium. Front Microbiol. 12, 769012.
[8] Bai, Shijie, Xu, Hengchao, Peng, Xiaotong. (2021) Microbial Communities of the Hydrothermal Scaly-Foot Snails From Kairei and Longqi Vent Fields. Front Mar Sci. 8, 764000.
[9] Li, J., Yang, J., Sun, M., Su, L., Bai, S*. (2020). Distribution and succession of microbial communities along the dispersal pathway of hydrothermal plumes on the southwest indian ridge. Front Mar Sci. 7, 581381.
[10] Li, L.,l Bai, S.,l Li, J., Wang, S., Peng, X. (2020) Volcanic ash inputs enhance the deep-sea seabed metal-biogeochemical cycle: a case study in the yap trench, western pacific ocean. Marine Geology. 430, 106340. (Co-first author)
Name and position: Hao Liu, Associate Researcher
Email: liuh@idsse.ac.cn
Research interests:
Marine Microbial Ecology, Marine Microbiology, Marine Ecology. Focusing on the succession of microbial communities and C and N biogeochemical cycles in deep-sea abyssal environments, as well as their ecological effects to the environments
Research funding and awards:
1. The National Key R&D Program of China (2023YFC2812804)
2. The National Natural Science Foundation of China (41606165)
3. The Hainan Provincial Natural Science Foundation of China (424MS115)
Education and Employment History:
Sep. 2011 - Dec. 2015, Sun Yat-sen University, Doctor,
Sep. 2005 - Jun. 2009, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Master,
Sep. 2000 - Jun. 2005, University of Science and Technology of China, Bachelor.
Nov. 2023 – Present, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Research Associate,
Jun. 2019 - Nov. 2023, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Research Assistant,
Jan. 2016 - Dec. 2019, Sun Yat-sen University,Research Assistant,
Aug. 2009 - Mar. 2011, The Hong Kong University of Science and Technology, Assistant Researcher.
Publications:
[1] Liu, H., Jing, H. (2024). The vertical metabolic activity and community structure of prokaryotes along different water depths in the Kermadec and Diamantina trenches. Microorganisms,12(4),708.
[2] Liu, H., Jing, H., & Wang, F. (2023). Archaea predominate in the ammonia oxidation process in the sediments of the Yap and Mariana Trenches. Frontiers in Microbiology, 14,1268790.
[3] Liu, H., Wang, F., Liu, H., & Jing, H. (2022). Metabolic activity and community structure of prokaryotes associated with particles in the twilight zone of the South China Sea. Frontiers in Microbiology,13,1056860.
[4] Zhang, Y., Song, X., Harrison, P.J., Liu, S., Yu, Z., Kan, J., Qian, P., Liu, H.*, & Yin, K. (2018). Regeneration and utilization of nutrients during collapse of a Mesodinium rubrum red tide and its influence on phytoplankton species composition. SCIENCE CHINA Earth Sciences, 61, 1384-1396
[5] Huang, J.#, Liu, H.#, & Yin, K.(2018). Effects of meteorological factors on the temporal distribution of red tides in Tolo Harbour, Hong Kong. Marine Pollution Bulletin, 126, 419-427.
[6] Yin, K., Liu, H.*, & Harrison, P. J.(2017). Sequential nutrient uptake as a potential mechanism for phytoplankton to maintain high primary productivity and balanced nutrient stoichiometry, Biogeosciences, 14, 2469-2480.
[7] Chong, K.Y.#, Liu, H.#, Yin, K., Harrison, P.J., & Kau, K.K. (2017). A bottom water sampler for determining chemical gradients across the water-sediment interface. Marine Pollution Bulletin, 117, 61-65.
[8] Liu, H., Yuan, X., Xu, J., Harrison, P.J., He, L., & Yin, K. (2015). Effects of viruses on bacterial functions under contrasting nutritional conditions for four species of bacteria isolated from Hong Kong waters. Scientific Reports, 5,14217.
Name and position:Xikun Song, Professor
Email: xksong@idsse.ac.cn
Research interests:
Biodiversity and ecology of natural and artificial hard substrates in hadal trenches and deep seas: rocks, whale falls and macroplastics
Degrees:
2010-2017, PhD, University of Chinese Academy of Sciences/Institute of Oceanology, Chinese Academy of Sciences
2003-2006, Master, Xiamen University
2000-2003, Bachelor, Liaocheng University
History of Employment:
2006-2010, Research assistant, Monitoring Centre of Marine Environment and Fishery Resources, Fujian Province
2017/03–2022/09, Postdoc, Xiamen University
2019/09-12, Visiting scientist, Zoologische Staatssammlung Muenchen, Germany
2018/09-12, Visiting scientist, the Korea Polar Research Institute (KOPRI)
2022/10-present, Associate Researcher, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences
Publications:
[1] Gu, Z., Ruthensteiner, B., Moura, C.J., Liu, L., Zhang, R., Song, X. (2022) Systematic affinities of Zygophylacidae (Cnidaria: Hydrozoa: Macrocolonia) with new description and re-description of fifteen deep-sea species. Zool. J. Linn. Soc., 196: 52-87
[2] Song, X., Lyu, M., Zhang, X., Ruthensteiner, B., Ahn, I., Pastorino, G., Wang, Y., Gu, Y., Ta, K., Sun, J., Liu, X., Han, J., Ke, C., Peng, X (2021) Large plastic debris dumps: new biodiversity hot spots emerging on the deep-sea floor. Environ. Sci. Tech. Let. 8(2), 148–154.
[3] Song, X., Ruthensteiner, B., Lyu, M., Liu, X., Wang, J., Han, J. (2021) Advanced Cambrian hydroid fossils (Cnidaria: Hydrozoa) extend the medusozoan evolutionary history. P. Roy. Soc. B-Biol Sci, 20202939.
[4] Song, X. (2019) Biodiversity of Sertulariidae Lamouroux, 1812 (Cnidaria: Hydrozoa) in Chinese Seas, with records from Chinese National Arctic and Antarctic Research Expeditions. Beijing: Science Press. 1–261. ISBN 978-7-03-061849-8
Name and position: Ming Yang, Research Assistant
Email: zhangyue@idsse.ac.cn
Research interests:
Dr. Yang's research focus on the deep-sea viral diversity and ecological roles, combining metagenomics with microbiological methods. He investigates the unique viral communities inhabiting extreme deep-sea environments, their interactions with microbial hosts, and their influence on ecosystem functions such as nutrient cycling and carbon sequestration. His work delves into the adaptive strategies these viruses use to endure high hydrostatic pressure, low temperatures, and limited nutrients. By uncovering the ecological dynamics of these communities, Dr. Yang aims to advance our understanding of the deep sea as a critical and largely uncharted component of Earth's biosphere.
Research funding and awards:
1. Major Science and Technology Plan Project of Hainan Province (ZDKJ2021028)
2. Natural Science Foundation of Hainan Province (420MS077)
3. Special Research Assistant Project of the Chinese Academy of Sciences and China 4. Postdoctoral Science Foundation (2022M720039)
Education and Employment History:
Sep. 2003 - Jul. 2007, Jiangxi Agriculture University, Bachelor
Sep. 2007 - Jul. 2010, Northeast Normal University, Master
Jul. 2010 - Jul. 2016, BGI-Shenzhen China, Bioinformatics Research Engineer
Jul. 2016 - Jul. 2020, Fulgent Genetics Inc. (China), Director of Bioinformatic Department
Mar. 2021 - Oct. 2021, Vision Medicals Technology Co., Ltd. Bioinformatics Scientist
Oct. 2021 – Present, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Research Assistant
Publications:
[1] Selvarajan, R., Yang, M., Ogola, H.-J.-O., Sibanda, T., Abia, A.-L.-K. Evaluating the Impact of Environmental Factors on Bacterial Populations in Riverine, Estuarine, and Coastal Sediments. Diversity 2024, 16, 749.
[2] Xu, P.-K., Yang, M., He, L.-S., Zhang, H.-X., Gao, Z.-M., Jiang, Y.-L., Wang, Y. (2023) Discovery of Prevalent Ciliophora, Discoba, and Copepoda Protists in Deep Sea Water by In Situ Nucleotide Extraction. Journal of Marine Science and Engineering, 12, 61.
[3] Wang, X.-Q., Wang, W.-S., Tai, S.-S., Li, M., Gao, Q., Hu, Z.-Q., Hu, W.-S., Wu, Z.-C., Zhu, X.-Y., Xie, J.-M., Li, F.-M., Zhang, Z.-F., Zhi, L.-R., Zhang, F., Ma, X.-Q., Yang, M., Xu, J.-B., Li, Y.-H., Li, W.-Z., Zhang, X.-Y., Yang, Y.-Zhao, Z., B.-Y., Fu, X.-Q., Zhao, J.-J., Li, M.-W., Wang, Z.-Y., Yue, X.-D., Fang, W., Yin, Y., Zhang, G.-Y., Xu, J.-L., Zhang, H.-L., Zhang, Z.-C., Li, Z.-K. (2022). Selective and comparative genome architecture of Asian cultivated rice (Oryza sativa L.) attributed to domestication and modern breeding. Journal of Advanced Research, 42, 1-16.
[4] Yang, M., Zhao J.-J., Yuan Y., Chen X.-Y., Yang F., Li X.-Z. (2021) Comparative metagenomic discovery of the dynamic cellulose-degrading process from a synergistic cellulolytic microbiota[J]. Cellulose, 28, 2105~2123.
[5] Yang, M., Yuan Y., Li X.-Z, Yang F, (2020) Differential analysis of diversity in cellulose-decomposing bacterial bommunities from diverse environments. 2020，42, 174-186.
[6] Zarrella, I., Herten, K., Maes, G., E., Tai, S.-S., Yang, M., Seuntjens, E., Ritschard, A., Zach, M., Styfhals, R., Sanges, R., Simakov, O., Ponte, G., (2019) The survey and reference assisted assembly of the Octopus vulgaris genome. Scientific data, 6(1), 13.
[7] Unver, T.-U., Zhangyan, W., Sterck, L., Turktas, M., Lohaus, R., Li, Zhen, Y.-M., He, L.-J., Deng, T., Javier, F.-C., Escalante, Francisco, C., Llorens, F., J.-R., Roig, Parmaksiz, I., Dundar, E., Xie, F.-B., Zhang, Baohong, Ipek, A., Uranbey, S., Erayman, M., Ilhan, E.-O., Badad, H.-G., Lightfoot, D.-A., Kasarla, P., Colantonio, V., Tombuloglu, H., Metin, N., Cetin, O.-Z., Van Montagu, M., Yang, H.-Q., Gao, Q.-G., (2017) Gabriel Dorado and Yves Van de Peer. Genome of wild olive and the evolution of oil biosynthesis. Proceedings of the National Academy of Sciences of the United States of America, 114: E9413-E9422.
Name and position: Yue Zhang, Research Assistant
Email: zhangyue@idsse.ac.cn
Research interests:
Marine Biology; Molecular Ecology
Research funding and awards:
1. The National Key R&D Program of China (2022YFC2805304)
2. The Hainan Provincial Natural Science Foundation of China (424QN341)
Education and Employment History:
Aug. 2021 – Present, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Research Assistant,
Sep. 2016 - Jun. 2021, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Doctor,
Sep. 2013 - Jun. 2016, Ludong University, Master,
Sep. 2011 - Jun. 2013, Dezhou University, Bachelor.
Publications:
[1] Zhang, Y., Jing, H., & Liu, H. (2024). Geographical distribution and driving force of microbial communities in the sediments of Diamantina and Kermadec trenches. Frontiers in Microbiology, 15, 1474645.
[2] Zhang, Y., & Jing, H. (2024). Metagenome sequencing and 107 microbial genomes from seamount sediments along the Yap and Mariana trenches. Scientific Data, 11(1), 887.
[3] Zhang, Y., & Jing, H. (2024). Deterministic process controlling the prokaryotic community assembly across seamounts along in the Yap and Mariana trenches. Ecological Indicators, 158, 111538.
[4] Zhang, Y., Liu, H., Huang, N., Peng, X., & Jing, H. (2023). Geographical distribution and driving force of micro-eukaryotes in the seamount sediments along the island arc of the Yap and Mariana trenches. Microbiology Spectrum, 11(6), e02069-23.
[5] Zhang, Y., Xia, X., Wan, L., Han, B. P., Liu, H., & Jing, H. (2023). Microbial Communities Are Shaped by Different Ecological Processes in Subtropical Reservoirs of Different Trophic States. Microbial Ecology, 86(3), 2073-2085.
[6] Zhang, Y., Huang, N., & Jing, H. (2022). Biogeography and Population Divergence of Microeukaryotes Associated with Fluids and Chimneys in the Hydrothermal Vents of the Southwest Indian Ocean. Microbiology Spectrum, 10(5), e02632-21.
[7] Zhang, Y., Huang, N., Wang, M., Liu, H., & Jing, H. (2021). Microbial eukaryotes associated with sediments in deep-sea cold seeps. Frontiers in Microbiology, 12, 782004.
[8] Zhang, Y., Jing, H., & Peng, X. (2020). Vertical shifts of particle-attached and free-living prokaryotes in the water column above the cold seeps of the South China Sea. Marine Pollution Bulletin, 156, 111230.
[9] Jing, H., Zhang, Y., Li, Y., Zhu, W., & Liu, H. (2018). Spatial variability of picoeukaryotic communities in the Mariana Trench. Scientific reports, 8(1), 15357.
Name and position: Yang Zhou, Assistant Professor
Email: zhouy@idsse.ac.cn
Research interests:
Genomics, The adaptation mechanisms of deep-sea invertebrates, and Population genetics.
Education and Employment History:
PhD, Marine Biology, University of Chinese Academy of Sciences
Publications:
[1] Zhou, Y., Feng, C., Pu, Y., Liu, J., Liu, R., & Zhang, H. (2021). The first draft genome of a cold-water coral Trachythela sp. (Alcyonacea: Stolonifera: Clavulariidae). Genome Biology and Evolution, 13(2), evaa265.
[2] Zhou, Y., Liu, H., Feng, C., Lu, Z., Liu, J., Huang, Y., ... & Zhang, H. (2023). Genetic adaptations of sea anemone to hydrothermal environment. Science Advances, 9(42), eadh0474.
[3] Liu, J., Zhou, Y., Pu, Y., & Zhang, H. (2023). A chromosome-level genome assembly of a deep-sea starfish (Zoroaster cf. ophiactis). Scientific Data, 10(1), 506.
[4] Zhang, H., Zhou, Y., & Yang, Z. (2024). Genetic adaptations of marine invertebrates to hydrothermal vent habitats. Trends in Genetics.40 (12), 1047 – 1059
[5] Pu, Y., Zhou, Y., Liu, J., & Zhang, H. (2024). A high-quality chromosomal genome assembly of the sea cucumber Chiridota heheva and its hydrothermal adaptation. GigaScience, 13, giad107.
[6] Huang, Y., Liu, H., Zhou, Y., Lu, Z., Pu, Y., & Zhang, H. (2024). Cloning and functional characterization of the oxidative squalene cyclase gene in the deep-sea holothurian Chiridota sp. Gene, 894, 147971.
Name and position: Yunmeng Chu, Postdoctor
Email: chuym@idsse.ac.cn
Research interests:
Focuses on microbial ecology, mainly on the biodiversity of deep-sea viruses, the role and influence of viruses on microbial ecosystem structure and biogeochemical cycles, and the virus-host interaction mechanism.
Education and Employment History:
2024.10 – present, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Postdoctor
2022.06 - 2024.07, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Postdoctor
2018.04 - 2022.05, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, PhD (Visiting Scholar)
2017.09 - 2021.12, Huaqiao University, Docter
Publications:
[1] Chu, Y., Zhao, Z., Cai, L., & Zhang, G. (2022). Viral diversity and biogeochemical potential revealed in different prawn-culture sediments by virus-enriched metagenome analysis. Environmental research, 210, 112901.
[2] Chu, Y., Guo, S., Cui, D., Fu, X., & Ma, Y. (2022). DeephageTP: a convolutional neural network framework for identifying phage-specific proteins from metagenomic sequencing data. PeerJ, 10, e13404.
Name and position: Lulu Guo, Experimentalist, Assistant to the Director
Email: guolulu112@idsse.ac.cn
Research interests:
Microbiology, Bioactive Enzyme
Research funding and awards:
The National Key R&D Program of China, The mutualistic relationship between the intestinal symbiotic microorganisms of hadal macrobiota and their hosts, The Person In Charge of sub-Project
Education and Employment History:
Dec. 2015- present, Experimentalist, The Institute of Deep-sea Science and Engineering, CAS
Dec. 2013-Dec. 2015, Research Assistant, The Institute of Deep-sea Science and Engineering, CAS
Sep. 2010- Jul. 2013, Aquaculture, Hainan University, Master degree
Sep. 2006- Jul. 2010, Aquaculture, Hainan University, Bachelor degree
Publications:
Guo L.L., Wang S.L., Zhu F.C, Xue F., He L.S.* (2021) Characteristics of two crustins from Alvinocaris longirostris in Hydrothermal Vents. Marine Drugs, 19(11), 600; https://doi.org/10.3390/md19110600
Name and position: Kun Shang, Experimentalist
Email: shangk@idsse.ac.cn
Research interests:
Antibacterials, Natural Products, Marine Ecology , Microorganisms
Education and Employment History:
2024.01 – Present, Experimenter, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences
2020.12 – 2023.12, Assistant Experimenter, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences
2019.07-2020.11, Research Assistant, Institute of Hydrobiology, Chinese Academy of Sciences & Qingdao Agricultural University
2016.09-2019.07, Master's Student in Microbiology, Dalian Ocean University & First Institute of Oceanography, Ministry of Natural Resources.
Publications:
[1] Bai, SJ., Shang, K., Zeng, SQ., Huang, ZM., Han, Z*. (2024) Genome analysis of Salinimicrobium sp. 3283s, a deep-sea bacterium isolated from the sediments of South China Sea, China, Marine Genomics. Volume 76,2024,101125, ISSN 1874-7787
[2] Zhu, BY., Cen, ZY., Chen, YQ., Shang, K., Zhai, JA., Han, MG., Wang, JW., Chen, ZY., Wei, TS., Han, Z*. (2024）α-Pyrone mediates quorum sensing through the conservon system in Nocardiopsis sp.. Microbiological Research. 285, 127767.
[3] Wang, JW., Shang, K., Wu, SY., Zhu, BY., Han, MG., Zhao, Y., Chen, YQ., Xie, J., Huang, B., Han, Z*. Complete genome sequence of piezotolerant Stutzerimonas kunmingensis 7850S isolated from the sediment of the Mariana Trench. (2022) Marine Genomics. 66:100996.
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