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1. Revisiting the biogenic silica burial flux determinations : a case study for the East China seas

Author: Dongdong Zhu, Jill N. Sutton, Aude Leynaert, Paul J. Tréguer, Jonas Schoelynck, Morgane Gallinari, Yuwei Ma, Su Mei Liu, Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Qingdao National Laboratory for Marine Science and Technology, Université de Brest (UBO), University of Antwerp (UA), This study was funded by the Natural Sciences Foundation of China (NSFC: U1806211, 42176040), the Taishan Scholars Program of Shandong Province, Aoshan Talents Program Supported by the Qingdao National Laboratory for Marine Science and Technology (No. 2015ASTP-OS08), by the French National Research Agency (ANR 18-CEO1-0011-01), and the University of Antwerp Bijzonder Onderzoeksfonds (Project ID: 43171). This work was supported by ISblue project, Interdisciplinary graduate school for the blue planet (ANR-17-EURE-0015) and co-funded by a grant from the French government under the program 'Investissements d’Avenir' embedded in France 2030., and ANR-18-CEO1-0011,RadiCal,Radiolarian silicon stable isotope calibration
Subjects: [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Global and Planetary Change, burial flux, Ocean Engineering, Aquatic Science, Oceanography, alkaline digestion, marine silicon cycle, analytical methods, [SDU.STU.GC]Sciences of the Universe [physics]/Earth Sciences/Geochemistry, coastal and continental margin zones, biogenic silica, East China seas, Biology, Water Science and Technology
Abstract: The Coastal and Continental Margin Zones (CCMZs) contribute to 40% of the total burial flux of biogenic silica (bSi) of the world ocean. However, the accurate determination of the bSi content (bSiO2%) in marine sediments remains a challenge. The alkaline methods commonly used to quantitatively determine bSiO2% can completely digest the amorphous silica of diatoms but are less effective at digesting radiolarians and sponge spicules. In addition, the lithogenic silica (lSi) found in sediments is partly digested during these alkaline extractions, which can bias the accuracy of the determined bSiO2%. This is of importance in CCMZs where the lSi:bSi ratio is high. In this study, we examined sediments collected in the CCMZs of East China seas, an environment of peculiar interest given the large amount of lSi deposited by the Yellow River and the Yangtze River. The results show that alkaline digestions using stronger solutions and pretreatment steps resulted in an overestimate of the bSiO2% due to increased leaching of silica mainly from authigenic silicates and clays, whereas weak digestions underestimated the bSiO2% owing to incomplete digestion of sponge spicules. We found that the use of the Si/Al method accurately corrects for the lSi fraction in marine sediments, and thereby improves the determinations of bSiO2% in the sediments of East China seas CCMZs. Ensuring full digestion of all bSi remains challenging, in particular for sponge spicules, motivating both verifications via microscopy and longer extraction times. To emphasize the influence of these methodological differences, we revised the bSi burial flux in the East China seas and provide a new estimate of 253 (± 286) Gmol-SiO2 yr-1, which is one third of the previous estimates. We discuss the potential contribution from radiolarian and sponges and we propose a new general protocol for the determination of bSi in sediments that minimizes the methodological bias in bSi determination.
Published: 2023

2. Hotspots of Cenozoic Tropical Marine Biodiversity

Author: Moriaki Yasuhara, Huai-Hsuan May Huang, Markus Reuter, Skye Yunshu Tian, Jonathan D. Cybulski, Aaron O’Dea, Briony L. Mamo, Laura J. Cotton, Emanuela Di Martino, Ran Feng, Clay R. Tabor, Gabriel Reygondeau, Qianshuo Zhao, Mark T. Warne, Kyawt K. T. Aye, Jingwen Zhang, Anne Chao, Chih-Lin Wei, Fabien L. Condamine, Adam T. Kocsis, Wolfgang Kiessling, Mark J. Costello, Derek P. Tittensor., Chhaya Chaudhary, Marina C. Rillo, Hideyuki Doi, Yun-wei Dong, Thomas M. Cronin, Erin E. Saupe, Heike K. Lotze, Kenneth G. Johnson, Willem Renema, John M. Pandolfi, Mathias Harzhauser, Jeremy B. C. Jackson, Yuanyuan Hong, School of biological sciences (Hong Kong, Chine), The University of Hong Kong (HKU), Smithsonian Institution, Universität Greifswald - University of Greifswald, Smithsonian Tropical Research Institute, University of Bologna/Università di Bologna, Macquarie University, Natural History Museum of Denmark, Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), University of Oslo (UiO), University of Connecticut (UCONN), University of British Columbia (UBC), Ocean University of China (OUC), Deakin University [Burwood], National Tsing Hua University [Hsinchu] (NTHU), National Taiwan University [Taiwan] (NTU), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), MTA-MTM-ELTE Research Group for Paleontology, Eötvös Loránd University (ELTE)-Hungarian Academy of Sciences (MTA), Faculty of Biosciences and Aquaculture [Bodø], University of Nordland, Dalhousie University [Halifax], United Nations Environment Programme (UNEP) World Conservation Monitoring Center (WCMC) (UNEP WCMC), Alfred Wegener Institute [Potsdam], Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Carl Von Ossietzky Universität Oldenburg = Carl von Ossietzky University of Oldenburg (OFFIS), Center for Marine Environmental Sciences [Bremen] (MARUM), Universität Bremen, University of Hyogo, Qingdao National Laboratory for Marine Science and Technology, US Geological Survey [Salt Lake City], United States Geological Survey [Reston] (USGS), University of Oxford, The Natural History Museum [London] (NHM), Naturalis Biodiversity Center [Leiden], Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam [Amsterdam] (UvA), University of Queensland [Brisbane], Natural History Museum [Vienna] (NHM), American Museum of Natural History (AMNH), Nanjing Institute of Geology and Palaeontology (NIGPAS-CAS), Chinese Academy of Sciences [Nanjing Branch], This work is a product of the PSEEDS (Palaeobiology as the Synthetic Ecological, Evolutionary, and Diversity Sciences) project and is partly supported by grants from the Research Grants Council of the Hong Kong Special Administrative Region, China (project codes: HKU 17300821, HKU 17300720, HKU 17302518, C7050-18E, C7013-19G), the Marine Conservation Enhancement Fund (project code: MCEF20002_L01), the Marine Ecology Enhancement Fund (project code: MEEF2021001), the Small Equipment Grant of the University of Hong Kong, the Seed Funding Programme for Basic Research of the University of Hong Kong (project codes: 202011159122, 201811159076), the Faculty of Science RAE Improvement Fund of the University of Hong Kong, the Seed Funding of the HKU-TCL Joint Research Centre for Artificial Intelligence of the University of Hong Kong and the SKLMP Seed Collaborative Research Fund (SKLMP/SCRF/0031) (to M.Y.), by the Sistema Nacional de Investigadores (SENACYT) (to A.O), by the Australian Research Council Centre of Excellence for Coral Reef Studies (to J.M.P.), by the Austrian Science Fund (FWF, project code: P 29158-N29) (to M.R.), and by State Key Laboratory of Palaeobiology and Stratigraphy and Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences (project code: 203108) (to Y.H.)., Stephen J. Hawkins, A. Louise Allcock, Peter A. Todd, Stephen E. Swearer‬, Maria Byrne, Louise B. Firth, Anaëlle J. Lemasson, Cathy H. Lucas, Ezequiel M. Marzinelli, Peter J. Mumby, Bayden D. Russell, I. Philip Smith, and Hawkins, S. J.
Subjects: Species diversity gradients, Global patterns, [SDV]Life Sciences [q-bio], Tropics, Neogene, Paleobiology, Fossil records, Paleogene
Abstract: International audience; Hotspots of tropical marine biodiversity are areas that harbour disproportionately large numbers of species compared to surrounding regions. The richness and location of these hotspots have changed throughout the Cenozoic. Here, we review the global dynamics of Cenozoic tropical marine biodiversity hotspots, including the four major hotspots of the Indo-Australian Archipelago (IAA), western Tethys (present Mediterranean), Arabian Sea and Caribbean Sea. Our review supports the ‘Hopping Hotspots’ model, which proposes that the locations of peak biodiversity are related to Tethyan faunal elements and track broad-scale shallow-marine habitats and high coastal complexity created by the collision of tectonic plates. A null hypothesis is the ‘Whack-A-Mole’ model, which proposes that hotspots occur in habitats suitable for high diversity regardless of taxonomic identity or faunal elements. Earlier ‘Centre-of’ theories (e.g. centres of origin with diversity decreasing with distance from supposed areas of exceptionally high rates of speciation, for which easy connection to adjacent regions to the east and west is important) were based on the analysis of recent biotas with no palaeontological foundation, and may better explain diversity dynamics within a hotspot rather than those between hotspots. More recently, however, human disturbance is massively disrupting these natural patterns.
Published: 2022

3. East Asian monsoon intensification promoted weathering of the magnesium-rich southern China upper crust and its global significance

Author: Ran Zhang, Jian Zhang, Rongsheng Yang, Xiaomin Fang, Yudong Liu, Christian France-Lanord, Song Yang, Shiming Wan, Chengcheng Ye, Yibo Yang, Yunfa Miao, Albert Galy, Chinese Academy of Sciences [Beijing] (CAS), Centre de Recherches Pétrographiques et Géochimiques (CRPG), Institut national des sciences de l'Univers (INSU - CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), University of Chinese Academy of Sciences [Beijing] (UCAS), Institute of Oceanology [China], Qingdao National Laboratory for Marine Science and Technology, Institute of Atmospheric Physics [Beijing] (IAP), Northwest Institute of Eco-Environment and Resources, University of Chinese Academy of Sciences, and University of Chinese Academy of Sciences-University of Chinese Academy of Sciences
Subjects: 010504 meteorology & atmospheric sciences, Earth science, Silicate weathering, [SDU.STU]Sciences of the Universe [physics]/Earth Sciences, Weathering, 010502 geochemistry & geophysics, 01 natural sciences, chemistry.chemical_compound, [SDU.STU.GC]Sciences of the Universe [physics]/Earth Sciences/Geochemistry, Tibetan Plateau, East Asian Monsoon, East Asia, Water cycle, [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment, 0105 earth and related environmental sciences, geography, Oceanic Mg cycle, Plateau, geography.geographical_feature_category, Continental crust, Carbon cycle, 15. Life on land, Late Oligocene, Silicate, chemistry, 13. Climate action, Erosion, General Earth and Planetary Sciences, Geology
Abstract: International audience; The Oligocene-Miocene boundary Asian climatic reorganization linked to the northward migration of the East Asian monsoon into subtropical China is a potentially important but poorly constrained atmospheric CO2 consumption process. Here, we performed a first-order estimate of the CO2 consumption induced by silicate chemical weathering and organic carbon burial in subtropical China related to this climatic reorganization. Our results show that an increase in long-term CO2 consumption by silicate weathering varies from 0.06×1012 to 0.87×1012 mol yr−1 depending on erosion flux reconstructions, with an ~50% contribution of Mg-silicate weathering since the late Oligocene. The organic carbon burial flux is approximately 25% of the contemporary CO2 consumption by silicate weathering. The results highlight the significant role of weathering of the Mg-rich upper continental crust in East China, which would contribute to the rapid decline in atmospheric CO2 during the late Oligocene and the Neogene rise in the seawater Mg content. If this climatic reorganization was mainly induced by the Tibetan Plateau uplift, our study suggests that the growth of the Himalayan-Tibetan Plateau can lead to indirect modification of the global carbon and magnesium cycles by changing the regional hydrological cycle in areas of East Asia that are tectonically less active.
Published: 2021

4. Metagenomic and Microscopic Analysis of Magnetotactic Bacteria in Tangyin Hydrothermal Field of Okinawa Trough

Author: Chen, Si, Yu, Min, Zhang, Wenyan, He, Kuang, Pan, Hongmiao, Cui, Kaixuan, Zhao, Yicong, Zhang, Xiao-Hua, Xiao, Tian, Zhang, Wuchang, Wu, Long-Fei, Key Laboratory of Marine Ecology and Environmental Sciences, Qingdao National Laboratory for Marine Science and Technology, Ocean University of China (OUC), Laboratoire de chimie bactérienne (LCB), and Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Microbiology (medical), magnetosome genes, hydrothermal field, magnetotactic bacteria, 16S rRNA gene, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Microbiology, Magnetofossil
Abstract: International audience; Magnetotactic bacteria (MTB) have been found in a wide variety of marine habitats, ranging from intertidal sediments to deep-seaseamounts. Deep-sea hydrothermal fields are rich in metal sulfides, which are suitable areas for the growth of magnetotacticbacteria. However, magnetotactic bacteria in hydrothermal fields have never been reported. Here the occurrence of MTB insediments from the Tangyin hydrothermal field was analyzed by 16S rRNA gene amplicon analysis, metagenomics and transmissionelectron microscopy. Sequencing 16S rRNA gene yielded a total of 709 MTB sequences belonging to 20 OTUs, affiliated withDesulfobacterota, Alphaproteobacteria, and Nitrospirae. Three shapes of magnetofossil were identified by transmission electronmicroscopy: elongated-prismatic, bullet-shaped, and cuboctahedron. All of these structures were composed of Fe3O4. Totally 121sequences were found to be homologous to published MTB magnetosome-function-related genes, and relevant domains wereidentified. Further analysis revealed that diverse MTB are present in the Tangyin hydrothermal field, and that multicellularmagnetotactic prokaryotes (MMPs) might be the dominant MTB. And the MTB of Desulfobacterota and Nitrospirae here shownevolutionarily unique compared with known MTB.
Published: 2022

5. Global warming-induced Asian hydrological climate transition across the Miocene–Pliocene boundary

Author: Zhangdong Jin, Zhisheng An, Andrew P. Roberts, Jean-Baptiste Ladant, Zhonghui Liu, Qiang Sun, Christopher J. Poulsen, Peng Zhang, Xinxia Li, Qingsong Liu, Xianzhe Peng, Guoxiong Wu, Mark J. Dekkers, Xiaodong Liu, Xiaoke Qiang, Alexis Licht, Ran Zhang, Eelco J. Rohling, Guillaume Dupont-Nivet, John C. H. Chiang, Yong Xu, Feng Wu, Ann Holbourn, Chao Ma, Weijian Zhou, Wolfgang Kuhnt, Xinzhou Li, Hong Ao, Chinese Academy of Sciences [Xi’an], Australian National University (ANU), University of Southampton, Chinese Academy of Sciences [Beijing] (CAS), Christian-Albrechts University of Kiel, University of Michigan [Ann Arbor], University of Michigan System, Géosciences Rennes (GR), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), Utrecht University [Utrecht], Southern University of Science and Technology [Shenzhen] (SUSTech), The University of Hong Kong (HKU), China Geological Survey, Centre européen de recherche et d'enseignement des géosciences de l'environnement (CEREGE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Xi'an University of Science and Technology, University of California [Berkeley], University of California, Chengdu University of Technology (CDUT), China University of Geosciences [Wuhan] (CUG), Nanjing University (NJU), European Project: 649081,H2020,ERC-2014-CoG,MAGIC(2015), Department of Earth and Environmental Sciences [Ann Arbor], University of Michigan System-University of Michigan System, Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), University of Applied Sciences Potsdam (FHP), Institute of Earth Environment [Xi’an], Qingdao National Laboratory for Marine Science and Technology, Paleomagnetic Laboratory Fort Hoofddijk [Utrecht], Universiteit Utrecht, Southern University of Science and Technology (SUSTech), University of Washington [Seattle], University of California [Berkeley] (UC Berkeley), University of California (UC), This study was supported financially by the Chinese Academy of Sciences (CAS) Strategic Priority Research Program (XDB 40000000), the Second Tibetan Plateau Scientific Expedition and Research (STEP) program (2019QZKK0707), the Chinese Academy of Sciences Key Research Program of Frontier Sciences (QYZDB-SSW-DQC021), the National Natural Science Foundation of China, the Ministry of Science and Technology of China, Australian Research Council (ARC) Australian Laureate Fellowship grant FL120100050 to E.J.R., ARC grant DP120103952 to A.P.R., ERC consolidator grant MAGIC 649081 to G.D.-N., and Heising-Simons Foundation Grant #2016-05 to C.J.P., and Paleomagnetism
Subjects: 010504 meteorology & atmospheric sciences, Chemistry(all), Science, Population, General Physics and Astronomy, Late Miocene, Physics and Astronomy(all), 010502 geochemistry & geophysics, Monsoon, Palaeoclimate, 01 natural sciences, Biochemistry, General Biochemistry, Genetics and Molecular Biology, Article, Climate change, East Asia, education, 0105 earth and related environmental sciences, education.field_of_study, Multidisciplinary, Biochemistry, Genetics and Molecular Biology(all), Global warming, General Chemistry, 15. Life on land, 13. Climate action, Aridification, Climatology, [SDU.STU.ST]Sciences of the Universe [physics]/Earth Sciences/Stratigraphy, Aeolian processes, Climate model, Geology, Genetics and Molecular Biology(all)
Abstract: Across the Miocene–Pliocene boundary (MPB; 5.3 million years ago, Ma), late Miocene cooling gave way to the early-to-middle Pliocene Warm Period. This transition, across which atmospheric CO2 concentrations increased to levels similar to present, holds potential for deciphering regional climate responses in Asia—currently home to more than half of the world’s population— to global climate change. Here we find that CO2-induced MPB warming both increased summer monsoon moisture transport over East Asia, and enhanced aridification over large parts of Central Asia by increasing evaporation, based on integration of our ~1–2-thousand-year (kyr) resolution summer monsoon records from the Chinese Loess Plateau aeolian red clay with existing terrestrial records, land-sea correlations, and climate model simulations. Our results offer palaeoclimate-based support for ‘wet-gets-wetter and dry-gets-drier’ projections of future regional hydroclimate responses to sustained anthropogenic forcing. Moreover, our high-resolution monsoon records reveal a dynamic response to eccentricity modulation of solar insolation, with predominant 405-kyr and ~100-kyr periodicities between 8.1 and 3.4 Ma., Global warming drove ‘wet gets wetter and dry gets drier’ climate shifts in Asia ~5.3 million years ago with monsoon pacing by ~400,000 and ~ 100,000 year cycles. This could be a template for future Asian climate response to anthropogenic warming.
Published: 2021

6. Tensegrity system dynamics in fluids

Author: Muhao Chen, Jun Chen, Manoranjan Majji, Robert Skelton, Texas A&M University [College Station], Qingdao National Laboratory for Marine Science and Technology, and Chen, Muhao
Subjects: Fluid structure interaction, Flexible structures, [MATH.MATH-DS]Mathematics [math]/Dynamical Systems [math.DS], [MATH.MATH-DS] Mathematics [math]/Dynamical Systems [math.DS], [SPI.MECA.MEFL] Engineering Sciences [physics]/Mechanics [physics.med-ph]/Fluids mechanics [physics.class-ph], [PHYS.MECA.MSMECA] Physics [physics]/Mechanics [physics]/Materials and structures in mechanics [physics.class-ph], [MATH.MATH-CA]Mathematics [math]/Classical Analysis and ODEs [math.CA], [PHYS.MECA.MSMECA]Physics [physics]/Mechanics [physics]/Materials and structures in mechanics [physics.class-ph], [MATH.MATH-CA] Mathematics [math]/Classical Analysis and ODEs [math.CA], [SPI.MECA.MEFL]Engineering Sciences [physics]/Mechanics [physics.med-ph]/Fluids mechanics [physics.class-ph], Physics::Fluid Dynamics, Tensegrity systems, Nonlinear dynamics, Multibody dynamics
Abstract: International audience; This paper provides compact vector and matrix forms of the nonlinear dynamics of class-1 and class-k tensegrity systems with fluid forces incorporated. Firstly, the equation of motion (both translation and rotation) of a single rod is modeled. Then, the fluid forces by fluid particles interacting with the rod are modeled and added to the derived dynamic equations of the rod. Then, by stacking all the governing equations of motion for each rod, compact vector and matrix forms of class-1 and class-k tensegrity dynamics are formulated. Finally, three examples based on a three-dimensional prism model with and without considering fluid forces, with and without fluid inlet velocity, and landing to the ground with and without fluid influence are simulated and compared. Results show that the simulations match well with physics. The fluid provides significant damping to the dynamics of the structure. This work enables the ability to do fluid-structure interaction studies of any tensegrity structures. The principles developed here can also be used for analyzing various kinds of tensegrity structures operating in the air or underwater.
Published: 2021

7. The NanDeSyn database for $Nannochloropsis$ systems and synthetic biology

Author: Jian Xu, Yonghua Li-Beisson, Jong-Min Lim, Young Uk Kim, Byeong-ryool Jeong, Nam Kyu Kang, Yanhai Gong, Guanpin Yang, Kehou Pan, Li Wei, Yantao Li, Yi Xin, Qiang Hu, Wuxin You, Hee-Mock Oh, Yong K Chang, Zengbin Wang, Won-Joong Jeong, Eric Poliner, Youn-Il Park, Suk-Won Jeong, Eva M. Farré, Chen Shen, Qintao Wang, Ansgar Poetsch, University of Chinese Academy of Sciences [Beijing] (UCAS), Qingdao National Laboratory for Marine Science and Technology, Department of Electrical Engineering [Korea Advanced Institute of Science and Technology] (KAIST), Korea Advanced Institute of Science and Technology (KAIST), Chinese Academy of Sciences [Beijing] (CAS), Ruhr-Universität Bochum [Bochum], Korea Research Institute of Bioscience & Biotechnology (KRIBB), Chungnam National University (CNU), Ocean University of China (OUC), MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University [East Lansing], Michigan State University System-Michigan State University System, Michigan State University System, Environnement, Bioénergie, Microalgues et Plantes (EBMP), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), University of Maryland Center for Environmental Science (UMCES), University of Maryland System, Bioénergie et Microalgues (EBM), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Epigenomics, Proteomics, 0106 biological sciences, [SDV]Life Sciences [q-bio], Genomics, Plant Science, Genome browser, Biology, computer.software_genre, 01 natural sciences, Genome, 03 medical and health sciences, Synthetic biology, RNA, Small Cytoplasmic, Microalgae, Genetics, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Synteny, Internet, 0303 health sciences, Database, Cell Biology, Gene Annotation, biology.organism_classification, Databases as Topic, Synthetic Biology, Transcriptome, computer, Functional genomics, Metabolic Networks and Pathways, Nannochloropsis, 010606 plant biology & botany
Abstract: International audience; Nannochloropsis species, unicellular industrial oleaginous microalgae, are model organisms for microalgal systems and synthetic biology. To facilitate community-based annotation and mining of the rapidly accumulating functional genomics resources, we have initiated an international consortium and present a comprehensive multi-omics resource database named Nannochloropsis Design and Synthesis (NanDeSyn; http://nandesyn.single-cell.cn). Via the Tripal toolkit, it features user-friendly interfaces hosting genomic resources with gene annotations and transcriptomic and proteomic data for six Nannochloropsis species, including two updated genomes of Nannochloropsis oceanica IMET1 and Nannochloropsis salina CCMP1776. Toolboxes for search, Blast, synteny view, enrichment analysis, metabolic pathway analysis, a genome browser, etc. are also included. In addition, functional validation of genes is indicated based on phenotypes of mutants and relevant bibliography. Furthermore, epigenomic resources are also incorporated, especially for sequencing of small RNAs including microRNAs and circular RNAs. Such comprehensive and integrated landscapes of Nannochloropsis genomics and epigenomics will promote and accelerate community efforts in systems and synthetic biology of these industrially important microalgae.
Published: 2020

8. Doubling of the known set of RNA viruses by metagenomic analysis of an aquatic virome

Author: Michael J. Bocek, Andrew Fire, Yuri I. Wolf, Yongjie Wang, Mart Krupovic, Valerian V. Dolja, Shuang Wu, Darius Kazlauskas, Sukrit Silas, Eugene V. Koonin, National Library of Medicine (NLM), National Institutes of Health [Bethesda] (NIH)-National Center for Biotechnology Information (NCBI), Department of Cellular and Molecular Pharmacology [San Francisco] (CMP), University of California [San Francisco] (UCSF), University of California-University of California, College of Food Science and Technology [Shangai], Shanghai Ocean University, Qingdao National Laboratory for Marine Science and Technology, Institute of Biotechnology [Vilnius], Life Science Center [Vilnius], Vilnius University [Vilnius]-Vilnius University [Vilnius], Virologie des archées - Archaeal Virology, Institut Pasteur [Paris], Department of Pathology [Stanford], Stanford Medicine, Stanford University-Stanford University, Department of Botany and Plant Pathology, Oregon State University (OSU), Y.I.W. and E.V.K. are supported through the Intramural Research Program of the US National Institutes of Health (National Library of Medicine). S.S. is a Damon Runyon Fellow supported by the Damon Runyon Cancer Research Foundation (DRG-(2352-19)). A.F. was supported by National Institutes of Health awards R01GM37706 and R35GM130366. M.K. was supported by l’Agence Nationale de la Recherche grant ANR-17-CE15-0005-01 (ENVIRA). D.K. was funded by the European Social Fund under no. 09.3.3-LMT-K-712 ‘Development of Competences of Scientists, other Researchers and Students through Practical Research Activities’ measure. Y.W. was supported by the National Natural Science Foundation of China (nos. 41376135, 31570112 and 41876195)., We thank N. Yutin for providing protein multiple-sequence analysis for DNA virus search., ANR-17-CE15-0005,ENVIRA,Remodelage de la membrane cytoplasmique par les virus enveloppés d'archées(2017), University of California [San Francisco] (UC San Francisco), University of California (UC)-University of California (UC), and Institut Pasteur [Paris] (IP)
Subjects: Microbiology (medical), Water microbiology, China, viruses, Immunology, Genome, Viral, Applied Microbiology and Biotechnology, Microbiology, Article, Evolution, Molecular, Microbial ecology, 03 medical and health sciences, chemistry.chemical_compound, Viral Proteins, Capping enzyme, Plant virus, RNA polymerase, Gene Order, Genetics, RNA Viruses, Human virome, Amino Acid Sequence, Phylogeny, 030304 developmental biology, 0303 health sciences, biology, single-stranded-DNA, genome organization, nucleotide-sequence, diversity, discovery, plant, identification, virosphere, phylogeny, evolution, 030306 microbiology, Potyviridae, RNA, Computational Biology, RNA virus, Cell Biology, Biodiversity, biology.organism_classification, Marnaviridae, Computational biology and bioinformatics, chemistry, Evolutionary biology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Metagenome, Metagenomics
Abstract: RNA viruses in aquatic environments remain poorly studied. Here, we analysed the RNA virome from approximately 10 l water from Yangshan Deep-Water Harbour near the Yangtze River estuary in China and identified more than 4,500 distinct RNA viruses, doubling the previously known set of viruses. Phylogenomic analysis identified several major lineages, roughly, at the taxonomic ranks of class, order and family. The 719-member-strong Yangshan virus assemblage is the sister clade to the expansive class Alsuviricetes and consists of viruses with simple genomes that typically encode only RNA-dependent RNA polymerase (RdRP), capping enzyme and capsid protein. Several clades within the Yangshan assemblage independently evolved domain permutation in the RdRP. Another previously unknown clade shares ancestry with Potyviridae, the largest known plant virus family. The ‘Aquatic picorna-like viruses/Marnaviridae’ clade was greatly expanded, with more than 800 added viruses. Several RdRP-linked protein domains not previously detected in any RNA viruses were identified, such as the small ubiquitin-like modifier (SUMO) domain, phospholipase A2 and PrsW-family protease domain. Multiple viruses utilize alternative genetic codes implying protist (especially ciliate) hosts. The results reveal a vast RNA virome that includes many previously unknown groups. However, phylogenetic analysis of the RdRPs supports the previously established five-branch structure of the RNA virus evolutionary tree, with no additional phyla., Metagenomic analysis of a single RNA virome from the Yangshan Deep-Water Harbour in China enabled the recovery of more than 4,500 distinct RNA viruses, doubling the known set of RNA viruses to date, and provided insights into their biology.
Published: 2020

9. Carbon nanotubes accelerate acetoclastic methanogenesis: From pure cultures to anaerobic soils

Author: Min Luo, Yang Tan, Leilei Xiao, Fanghua Liu, Eric Lichtfouse, Shiling Zheng, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences [Beijing] (CAS), Centre européen de recherche et d'enseignement des géosciences de l'environnement (CEREGE), Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Collège de France (CdF (institution))-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD), Fuzhou University, Qingdao National Laboratory for Marine Science and Technology, Center for Ocean Mega-Science [Qingdao], Chinese Academy of Sciences [Changchun Branch] (CAS), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: Anaerobic soils, Proteome, Methanogenesis, ved/biology.organism_classification_rank.species, Soil Science, Methanogenic archaea, Carbon nanotube, [SDV.SA.SDS]Life Sciences [q-bio]/Agricultural sciences/Soil study, Microbiology, Methane, law.invention, [SPI.MAT]Engineering Sciences [physics]/Materials, chemistry.chemical_compound, Electron transfer, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Biogas, law, [SDU.STU.GC]Sciences of the Universe [physics]/Earth Sciences/Geochemistry, [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment, biology, Chemistry, ved/biology, [SDE.IE]Environmental Sciences/Environmental Engineering, Direct interspecies electron transfer, [SPI.NRJ]Engineering Sciences [physics]/Electric power, 04 agricultural and veterinary sciences, Methanosarcina, [CHIM.CATA]Chemical Sciences/Catalysis, [CHIM.MATE]Chemical Sciences/Material chemistry, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Acetoclastic methanogenesis, [SPI.ELEC]Engineering Sciences [physics]/Electromagnetism, Isotopes of carbon, Environmental chemistry, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Methanosarcina barkeri, [SDV.EE.BIO]Life Sciences [q-bio]/Ecology, environment/Bioclimatology, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: International audience; Direct interspecies electron transfer (DIET) between electricigens and methanogens has been shown to favour CO2 reduction to produce biomethane. Furthermore, DIET is accelerated by conductive materials. However, whether conductive materials can promote other methanogenic pathways is unclear due to a lack of detailed experimental data and the poor mechanistic studies. Here, we hypothesized that conductive carbon nanotubes (CNTs) stimulate acetoclastic methanogenesis independently of electricigens in pure cultures of Methanosarcina spp. and anaerobic wetland soil. We found a significant increase in the methane production rate during the growth phase, e.g. from 0.169 mM to 0.241 mM after addition of CNTs on the 3rd day. CNTs did not increase the abundance of electromicroorganisms or the electron transfer rate in anaerobic soils, using via microbial diversity and electrochemical analysis. 13 C-CH3COOH labelling, stable carbon isotope fractionation and the CH3F inhibitor of acetoclastic methanogenesis were used to distinguish methanogenic pathways. CNTs mainly accelerated acetoclastic methanogenesis rather than CO 2 reduction in both pure cultures and anaerobic soils. Furthermore, the presence of CNTs slightly alleviate the inhibition of CH3F on acetoclastic methanogenesis during the pure culture of Methanosarcina barkeri and Methanosarcina mazei with the production of more than 0.3 mM methane. CNTs closely attached to the cell surface were observed by transmission electron microscopy. Proteome analysis revealed a stimulation of protein synthesis with about twice the improvement involved in COOH oxidation and electron transfer. Overall, our findings demonstrate that conducting CNTs favor methane production and that the mechanism involved is acetoclastic methanogenesis via acetate dismutation, at least partly, rather than classical CO2 reduction.
Published: 2020

10. Virioplankton distribution in the tropical western Pacific Ocean in the vicinity of a seamount

Author: Li Zhao, Yanchu Zhao, Yuan Zhao, Gérald Grégori, Xuegang Li, Tian Xiao, Shan Zheng, Wuchang Zhang, Institute of Information Science and Engineering [Shandong], Shandong Agricultural University (SDAU), Zhejiang University, Department of Polymer Science and Engineering, Zhejiang University, Qingdao National Laboratory for Marine Science and Technology, Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), CAS Institute of Oceanology (IOCAS), Chinese Academy of Sciences [Beijing] (CAS), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, virioplankton, Range (biology), Seamount, lcsh:QR1-502, viral subclusters, 01 natural sciences, Microbiology, Pacific ocean, Fluorescence, lcsh:Microbiology, 03 medical and health sciences, Water column, Abundance (ecology), Photic zone, 14. Life underwater, Ecosystem, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, 0303 health sciences, geography, Deep chlorophyll maximum, Pacific Ocean, geography.geographical_feature_category, 010604 marine biology & hydrobiology, flow cytometry, Biodiversity, Original Articles, Plankton, Oceanography, [SDU]Sciences of the Universe [physics], Viruses, Caroline Seamount, Original Article, seamount effect, Geology
Abstract: The shallow Caroline Seamount is located in the tropical western Pacific Ocean. Its summit is 57 m below the surface and penetrates the euphotic zone. Therefore, it is ideal for the study of the influence of seamount on plankton distribution. Here, virioplankton abundance and distribution were investigated by flow cytometry (FCM) in the Caroline Seamount in August and September 2017. The total abundance of virus‐like particles (VLP) was in the range of 0.64 × 106–18.77 × 106 particles/ml and the average was 5.37 ± 3.75 × 106 particles/ml. Three to four distinct viral subclusters with similar side scatter but different green fluorescence intensities were identified. Above the deep chlorophyll maximum (DCM), two medium fluorescence virus (MFV) subclusters were discriminated. Between the DCM and the deeper layers, only one MFV subcluster was resolved. In general, low fluorescence viruses (LFV) comprised the most abundant subclusters. In the 75–150 m water column, however, the MFV abundance was higher than the LFV abundance. High fluorescence viruses (HFV) constituted the least abundant subcluster throughout the entire water column. Virioplankton abundance was significantly enhanced at the seamount stations. Environmental factors including water temperature and nitrate concentration were the most correlated with the variation in virioplankton abundance at the seamount stations. Interactions between shallow seamounts and local currents can support large virus standing stocks, causing a so‐called indirect “seamount effect” on the virioplankton., The abundance and distribution of virioplankton were investigated in the Caroline seamount of Western Pacific. Three to four distinct viral subclusters with similar side scatter but different green fluorescence intensity were identified. The interactions of shallow seamount and local current could sustain a significant enhancement of virus standing stock, causing a so‐called “seamount effect” for virioplankton.
Published: 2020

11. Relationship between well pattern density and variation function of stochastic modelling and database establishment

Author: Kai Zhao, Jun Xie, Zhaoxun Yan, Jinkai Wang, Yuxiang Fu, College of Earth Science and Engineering, Shandong University of Science and Technology, and Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology
Subjects: Stochastic modelling, 020209 energy, General Chemical Engineering, media_common.quotation_subject, Minor (linear algebra), Energy Engineering and Power Technology, 02 engineering and technology, Type (model theory), lcsh:Chemical technology, lcsh:HD9502-9502.5, 010502 geochemistry & geophysics, computer.software_genre, 01 natural sciences, Adaptability, Convergence (routing), 0202 electrical engineering, electronic engineering, information engineering, Range (statistics), lcsh:TP1-1185, Variogram, 0105 earth and related environmental sciences, media_common, Mathematics, [PHYS]Physics [physics], Database, Function (mathematics), Condensed Matter::Mesoscopic Systems and Quantum Hall Effect, lcsh:Energy industries. Energy policy. Fuel trade, Fuel Technology, computer
Abstract: International audience; For 3D geological modelling of oil and gas reservoirs, well pattern density is directly related to the number of samples involved in the calculation, which determines the variation function of stochastic modelling and has great impacts on the results of reservoir modelling. This paper focuses on the relationship between well pattern density and the variogram of stochastic modelling, selects the large Sulige gas field with many well pattern types as the research object, and establishes a variogram database of stochastic models for different well pattern densities. First, the well pattern in the study area is divided into three different types (well patterns A, B, and C) according to well and row space. Several different small blocks (model samples) are selected from each type of well pattern to establish the model, and their reasonable variogram values (major range, minor range and vertical range) are obtained. Then, the variogram values of all model samples with similar well pattern densities are analysed and counted, and the variogram database corresponding to each type of well pattern is established. Finally, the statistical results are applied to the modelling process of other blocks with similar well pattern density to test their accuracy. The results show that the reservoir model established by using the variation function provided in this paper agrees well with the actual geological conditions and that the random model has a high degree of convergence. This database has high adaptability, and the model established is reliable.
Published: 2020

12. The rise and fall of the ancient northern pike master sex-determining gene

Author: Mike Tringali, Hongxia Hu, Amaury Herpin, Patrick W. DeHaan, Eric Rondeau, Louis Bernatchez, Wesley A. Larson, Manfred Schartl, Elodie Jouanno, E. A. Interesova, Yann Guiguen, Eric Saillant, Stephen S. Curran, Hugo Verreycken, Gaël P.J. Denys, Roger A. Tabor, Vladimir A. Trifonov, Hugo Darras, Christophe Klopp, Hugues Parrinello, Frederick W. Goetz, John H. Postlethwait, Qiaowei Pan, Céline Roques, J. Andrés López, Camille Eché, Jérôme Lluch, Laurent Journot, Frank A. von Hippel, Krista M. Nichols, Konrad Ocalewicz, Romain Feron, René Guyomard, Song-Lin Chen, Ben F. Koop, Laboratoire de Physiologie et Génomique des Poissons (LPGP), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Ecology and Evolution [Lausanne], Université de Lausanne (UNIL), Swiss Institute of Bioinformatics [Lausanne] (SIB), Department of Biology, University of Victoria, Northwest Fisheries Science Center (NWFSC), NOAA National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA)-National Oceanic and Atmospheric Administration (NOAA), Alaska Pacific University, Institut de Biologie Intégrative et des Systèmes [Québec] (IBIS), Florida Marine Research Institute, Florida Fish and Wildlife Conservation Commission, School of Ocean Science and Technology [Mississippi] (SOST), University of Southern Mississippi (USM), Gulf Coast Research Laboratory, Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), Patrimoine naturel (PatriNat), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Office français de la biodiversité (OFB), Department of Biological Sciences [Flagstaff], Northern Arizona University [Flagstaff], Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, College of Fisheries and Ocean Sciences (CFOS), University of Alaska [Fairbanks] (UAF), Research Institute for Nature and Forest (INBO), Department of Marine Biology and Ecology, University of Gdansk, Génétique Animale et Biologie Intégrative (GABI), Université Paris-Saclay-AgroParisTech-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Beijing Fisheries Research Institute, U.S. Fish and Wildlife Service, Institut de Génomique Fonctionnelle (IGF), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Système d'Information des GENomes des Animaux d'Elevage (SIGENAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Tomsk State University [Tomsk], Siberian Branch of the Russian Academy of Sciences (SB RAS), Developmental Biochemistry, Biocenter, Julius-Maximilians-Universität Würzburg [Wurtzbourg, Allemagne] (JMU), Institute of Neuroscience, University of Oregon, Eugene, Oregon, University of Oregon [Eugene], This work was supported by the Agence Nationale de la Recherche, the Deutsche Forschungsgemeinschaft (ANR/DFG, PhyloSex project, 2014–2016, SCHA 408/10–1, to YG and MS), and the U.S. National Institutes of Health (R01GM085318 to JHP). The MGX and Get-Plage core sequencing facilities were supported by France Genomique National infrastructure, funded as part of the ‘Investissement d’avenir’ program managed by the Agence Nationale pour la Recherche (contract ANR-10-INBS-09)., ANR-13-ISV7-0005,PhyloSex,Evolution des déterminants majeurs du sexe chez les poissons.(2013), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), Université de Lausanne = University of Lausanne (UNIL), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Toulouse III - Paul Sabatier (UT3), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), University of Victoria [Canada] (UVIC), Qingdao National Laboratory for Marine Science and Technology, University of Gdańsk (UG), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Texas State University, Agence Nationale de la Recherche, Deutsche Forschungsgemeinschaft (ANR/DFG, PhyloSex project, 2014–2016, SCHA 408/10–1, to YG and MS), U.S. National Institutes of Health (R01GM085318 to JHP), France Genomique National infrastructure, funded as part of the ‘Investissement d’avenir’ program managed by the Agence Nationale pour la Recherche (contract ANR-10-INBS-09), Julius-Maximilians-Universität Würzburg (JMU), Corvaisier, Maryse, Blanc – Accords bilatéraux 2013 - Evolution des déterminants majeurs du sexe chez les poissons. - - PhyloSex2013 - ANR-13-ISV7-0005 - Blanc – Accords bilatéraux 2013 - VALID, Organisation et montée en puissance d'une Infrastructure Nationale de Génomique - - France-Génomique2010 - ANR-10-INBS-0009 - INBS - VALID, and Przeworski, Molly (ed.)
Subjects: Male, 0106 biological sciences, 0301 basic medicine, Evolution of sexual reproduction, Lineage (evolution), [SDV]Life Sciences [q-bio], sex determination, 01 natural sciences, mudminnows, Gene Duplication, Gene duplication, Biology (General), Clade, master sex determining gene, Phylogeny, северная щука, computer.programming_language, гены, определяющие пол, 0303 health sciences, education.field_of_study, Sex Chromosomes, biology, umbridae, General Neuroscience, General Medicine, [SDV] Life Sciences [q-bio], Medicine, Female, Research Article, QH301-705.5, Demographic history, Science, Population, esocidae, Y chromosome, 010603 evolutionary biology, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Animals, education, Esox, pikes, 030304 developmental biology, Pike, fish, General Immunology and Microbiology, evolutionary biology, Sex Determination Processes, biology.organism_classification, esociforms, Sexual reproduction, 030104 developmental biology, Evolutionary biology, Other, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, computer, Sex linkage
Abstract: Sexual reproduction is a ubiquitous basic feature of life and genetic sex determination is thus widespread, at least among eukaryotes. Understanding the remarkable diversity of sex determination mechanisms, however, is limited by the paucity of empirical studies. Here, we traced back the evolution of sex determination in an entire clade of vertebrates and uncovered that the northern pike (Esox lucius) master sex-determining gene initiated from a 65 to 90 million-year-old gene duplication and remained sex-linked on undifferentiated sex chromosomes for at least 56 million years. Contrasting with its ancient origin, we identified several independent species- or population-specific transitions of sex determination mechanisms in this lineage, including an unexpected complete and recent Y-chromosome loss in some North American northern pike populations. These findings highlight the diversity of the evolutionary fates of master sex-determining genes and raise the importance of careful considerations of population demographic history in sex determination studies. Our study also puts forward the hypothesis that occasional sex reversals and genetic bottlenecks provide a non-adaptive explanation for sex determination transitions.
Published: 2020

13. Compatible solutes profiling and carbohydrate feedstock from diversified cyanobacteria

Author: Muriel Gugger, Xuefeng Lu, Nitin Keshari, Tao Zhu, Qingdao Institute of Bioenergy and Bioprocess Technology [Qingdao, China], Chinese Academy of Sciences, Collection des Cyanobactéries, Institut Pasteur [Paris], Qingdao National Laboratory for Marine Science and Technology, This work was supported by the National Science Fund for Distinguished Young Scholars of China (Grant 31525002 to XL), the National Natural Science Foundation of China (Grant 31570068 to TZ), the Talented Young Scientist Program of Chinese Ministry of Science and Technology (Grant IND-16-001 to NK), Shandong Key Basic Research Project (XL) and Qingdao Innovative Leading Talent project (15-10-3-15-(31)-zch)., and Institut Pasteur [Paris] (IP)
Subjects: Cyanobacteria, Sucrose, [SDV]Life Sciences [q-bio], Glucosylglycerol (GG), 03 medical and health sciences, chemistry.chemical_compound, Bioproducts, Botany, Sugar, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, biology, 030306 microbiology, Compatible solutes, Trehalose, biology.organism_classification, 6. Clean water, Multicellular organism, Metabolic pathway, chemistry, Osmoprotectant, Agronomy and Crop Science, Glycogen
Abstract: International audience; Cyanobacteria are promising cell factories for producing high-value bioproducts. They accumulate low molecular mass organic molecules under salinity stress conditions, which are known as compatible solutes, e.g. sucrose, trehalose, and glucosylglycerol (GG). The physiological properties of compatible solutes sort them as the potential bioproducts for applications in the field of health, pharmacy, and cosmetic sectors. During last few decades, mostly model cyanobacterial strains (unicellular from freshwater and marine habitats) have been targeted for the biochemical and molecular characterization of compatible solutes accumulation, while, the study on other cyanobacteria from extreme/stressful habitats are scanty. The advantage for selecting multicellular cyanobacteria in the present study is their easier harvesting mode over unicellular strains which are one of the primary concerns for the cost-effective production of desired products at pilot scale. Therefore, five cyanobacterial strains with diverse morphotypes belonging to subsection I (Unicellular), II (Baeocytous), III (Filamentous), and V (Ramified) isolated from extreme/stressful habitats (sewage pond and hot spring including freshwater strain as a reference) were screened for salt tolerance, compatible solutes profiling, and sugar feedstock production. High GG, sucrose, and glycogen production were found in Leptolyngbya sp. PCC 8913, Chroogloeocystis siderophila NIES-1031 and Fischerella major NIES-592, respectively. Under salt stress, Leptolyngbya sp. PCC 8913 showed a GG production of 101 ± 12 mg/L/OD 730 , which is significantly higher than that of the model strain Synechocystis sp. PCC 6803. Fischerella major NIES-592 and Oscillatoria laetevirens NIES-31 were identified as novel trehalose-producing cyanobacteria. The key genes involved in production of compatible solutes among these cyanobacteria were also studied. Thus, the results not only displayed the potential cyanobacteria for production of GG, sucrose, trehalose and glycogen but also address the metabolic pathways for the compatible solutes biosynthesis in diversified cyanobacteria, which can be further targeted for the in-depth study to enhance the production using molecular approaches.
Published: 2019

14. Frontiers in Fine-Scale in situ Studies: Opportunities During the SWOT Fast Sampling Phase

Author: Francesco d’Ovidio, Ananda Pascual, Jinbo Wang, Andrea M. Doglioli, Zhao Jing, Sebastien Moreau, Gérald Grégori, Sebastiaan Swart, Sabrina Speich, Frédéric Cyr, Benoit Legresy, Yi Chao, Lee Fu, Rosemary Anne Morrow, Processus et interactions de fine échelle océanique (PROTEO), Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU), Instituto Mediterráneo de Estudios Avanzados (CSIC-UIB) (IMEDEA), Jet Propulsion Laboratory (JPL), NASA-California Institute of Technology (CALTECH), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Qingdao National Laboratory for Marine Science and Technology, Norwegian Polar Institute, Department of Oceanography [Cape Town], University of Cape Town, Department of Marine Sciences [Gothenburg], University of Gothenburg (GU), Laboratoire de Météorologie Dynamique (UMR 8539) (LMD), Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-École des Ponts ParisTech (ENPC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Département des Géosciences - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Fisheries and Oceans Canada (DFO), CSIRO Marine and Atmosphere Research [Hobart], Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Remote Sensing Solutions, Laboratoire d'études en Géophysique et océanographie spatiales (LEGOS), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), Spanish Research Agency and the European Regional Development Fund (Award no. CTM2016-78607-P/PRE-SWOT), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), European Research Council, Ministerio de Economía y Competitividad (España), National Aeronautics and Space Administration (US), and Direction Générale de l'Armement (France)
Subjects: 0106 biological sciences, lcsh:QH1-199.5, 010504 meteorology & atmospheric sciences, Ocean Engineering, submesoscale, lcsh:General. Including nature conservation, geographical distribution, Aquatic Science, Oceanography, energy cascade, 01 natural sciences, remote sensing, Marine energy, 14. Life underwater, lcsh:Science, SWOT analysis, 0105 earth and related environmental sciences, Water Science and Technology, Remote sensing, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Global and Planetary Change, 010604 marine biology & hydrobiology, Sampling (statistics), Biogeochemial processes, mesoscale, Earth system science, Ocean dynamics, Ocean surface topography, Temporal resolution, ocean dynamics, Environmental science, lcsh:Q, Satellite
Abstract: Conceived as a major new tool for climate studies, the Surface Water and Ocean Topography (SWOT) satellite mission will launch in late 2021 and will retrieve the dynamics of the oceans upper layer at an unprecedented resolution of a few kilometers. During the calibration and validation (CalVal) phase in 2022, the satellite will be in a 1- day-repeat fast sampling orbit with enhanced temporal resolution, sacrificing the spatial coverage. This is an ideal opportunity - unique for many years to come - to coordinate in situ experiments during the same period for a focused study of fine scale dynamics and their broader roles in the Earth system. Key questions to be addressed include the role of fine scales on the ocean energy budget, the connection between their surface and internal dynamics, their impact on plankton diversity, and their biophysical dynamics at the ice margin., AP acknowledges support from the Spanish Research Agency and the European Regional Development Fund (Award no. CTM2016-78607-P/PRE-SWOT). Part of the research for this paper was carried out at the Jet Propulsion Laboratory, California Institute of Technology, under a contract with the National Aeronautics and Space Administration. JW and L. L. Fu acknowledge the support from SWOT mission. We thank the “Délégation Générale de l’Armement” which funded through the “Programme d’Etudes Amont Protevs II” the 2018 PROTEVSBIOSWOT campaign (PI Franck Dumas from the Service hydrographique et océanographique de la Marine) and makes a fruitful collaboration with the SWOT Science Team possible.
Published: 2019

15. Pantropical climate interactions

Author: Marta Martín-Rey, Benjamin Ng, Yun Yang, Bolan Gan, Xiaopei Lin, Malte F. Stuecker, Guojian Wang, Jing-Jia Luo, Yan Du, Dietmar Dommenget, Noel Keenlyside, Wenju Cai, Fan Jia, Yoo-Geun Ham, Sarah M. Kang, Jeong-Hwan Kim, Agus Santoso, Ping Chang, Jun-Young Choi, Jules B. Kajtar, Tim Li, Jin-Yi Yu, Sun-Young Kim, Matthieu Lengaigne, Xichen Li, Geon-Il Kim, Shayne McGregor, Jong-Seong Kug, Michael J. McPhaden, Yoshimitsu Chikamoto, Lixin Wu, Chang Eun Kim, Shang-Ping Xie, Yohan Ruprich-Robert, Barcelona Supercomputing Center, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Qingdao National Laboratory for Marine Science and Technology, Océan et variabilité du climat (VARCLIM), Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU), School of Ocean and Earth Science and Technology (SOEST), University of Hawai‘i [Mānoa] (UHM), Pohang University of Science and Technology (POSTECH), Department of Atmospheric Sciences [Seattle], University of Washington [Seattle], Climate Change Research Centre, ARC Centre of Excellence for Climate System Science, University of New South Wales, Level 4 Matthews Bldg., Kensington, NSW 2052, Australia, Department of Plants, Soils and Climate, Utah State University (USU), NOAA Pacific Marine Environmental Laboratory [Seattle] (PMEL), National Oceanic and Atmospheric Administration (NOAA), South China Sea Institute of Oceanology, School of Earth, Atmosphere and Environment, Monash University, Monash University [Clayton], University of Chinese Academy of Sciences [Beijing] (UCAS), Key Laboratory of Ocean Circulation and Waves, CAS Institute of Oceanology (IOCAS), Chinese Academy of Sciences [Beijing] (CAS)-Chinese Academy of Sciences [Beijing] (CAS), College of Engineering, Mathematics and Physical Sciences [Exeter] (EMPS), University of Exeter, Nansen-Tutu Center for Marine Environmental Research, University of Cape Town, Key Laboratory of Meteorological Disaster [Nanjing University] (KLME - NUIST), Nanjing University of Information Science and Technology (NUIST), CSIC Instituto de Ciencias del Mar, Barcelona Supercomputing Center - Centro Nacional de Supercomputacion (BSC - CNS), Climate, Atmospheric Science and Physical Oceanography Department [La Jolla] (CASPO), Scripps Institution of Oceanography (SIO), University of California [San Diego] (UC San Diego), University of California-University of California-University of California [San Diego] (UC San Diego), University of California-University of California, Ulsan National Institute of Science and Technology (UNIST), University of Regina, Okinawa Institute of Science and Technology Graduate University (OIST), ANR-15-JCLI-0004,GOTHAM,Globally Observed Teleconnections and their role and representation in Hierarchies of Atmospheric Models(2015), Ministerio de Ciencia, Innovación y Universidades (España), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), School of Earth, Atmosphere and Environment, Scripps Institution of Oceanography (SIO - UC San Diego), University of California (UC)-University of California (UC)-University of California [San Diego] (UC San Diego), and University of California (UC)-University of California (UC)
Subjects: Tropical interconnections, Desenvolupament humà i sostenible::Degradació ambiental [Àrees temàtiques de la UPC], 010504 meteorology & atmospheric sciences, Atmospheric circulation, Surface warming, Pantropical, [PHYS.PHYS.PHYS-GEO-PH]Physics [physics]/Physics [physics]/Geophysics [physics.geo-ph], Forcing (mathematics), Tropical Atlantic, Hiatus, 010502 geochemistry & geophysics, El Niño Current, 01 natural sciences, Tropical climate, 14. Life underwater, Ocean-atmosphere interaction, Climate variability, 0105 earth and related environmental sciences, Atmospheric bridge, Climatology, Multidisciplinary, Climatic changes, Atlantic Multidecadal Variability (AMV), El Niño–Southern Oscillation (ENSO), El Niño Southern Oscillation, Tropics -- Clima Meteorología, 13. Climate action, Climatologia, Environmental science, pantropic, Canvis climàtics
Abstract: 12 pages, 5 figures, 1 box, The El Niño–Southern Oscillation (ENSO), which originates in the Pacific, is the strongest and most well-known mode of tropical climate variability. Its reach is global, and it can force climate variations of the tropical Atlantic and Indian Oceans by perturbing the global atmospheric circulation. Less appreciated is how the tropical Atlantic and Indian Oceans affect the Pacific. Especially noteworthy is the multidecadal Atlantic warming that began in the late 1990s, because recent research suggests that it has influenced Indo-Pacific climate, the character of the ENSO cycle, and the hiatus in global surface warming. Discovery of these pantropical interactions provides a pathway forward for improving predictions of climate variability in the current climate and for refining projections of future climate under different anthropogenic forcing scenarios, W.C. is supported by National Key R&D Program of China (2018YFA0605700). L.W., Xia.L., and B.G. are supported by the National Natural Science Foundation of China (NSFC) projects (41490643, 41490640, U1606402, and 41521091). W.C., G.W., B.N., and A.S. are supported by CSHOR and the Earth System and Climate Change Hub of the Australian Government’s National Environment Science Program. CSHOR is a joint research Centre for Southern Hemisphere Oceans Research between QNLM and CSIRO. M.L. is supported by the GOTHAM Belmont project (ANR-15-JCLI-0004-01) and the ARiSE ANR project. T.L. is supported by NSFC 41630423 and NSF AGS-1565653 grants. S.M. is supported by the Australian Research Council (ARC) through grant number FT160100162. J.-S.K. was supported by a National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) (NRF-2018R1A5A1024958). J.-Y.Y. is supported by NSF AGS-1505145 and AGS-1833075 grants. M.F.S is supported by the Institute for Basic Science (project code IBS-R028-D1). Y.-G.H. is funded by the Korea Meteorological Administration Research and Development Program under grant KMI2018-03214. M.J.M is supported by NOAA and PMEL contribution number 4838. Y.D. is supported by the National Natural Science Foundation of China (41525019, 41830538, and 41521005) and the State Oceanic Administration of China (GASI-IPOVAI-02). D.D. is supported by ARC grant number CE170100023. M.M.-R. has been supported by the MORDICUS grant under contract ANR-13-762 SENV-0002-01 and CGL2017-86415-R. Y.R.-R. is supported by an 800154-INADEC individual MSCA-IF-EF-ST grant. S.-P.X. is supported by the NSF. J.B.K. was supported by the National Environment Research Council (NE/N005783/1)
Published: 2019
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16. Sea level-controlled sediment transport to the eastern Arabian Sea over the past 600 kyr: Clay minerals and Sr Nd isotopic evidence from IODP site U1457

Author: YU, Zhaojie, Colin, Christophe, WAN, Shiming, Saraswat, Rajeev, Song, Lina, XU, Zhaokai, Clift, Peter, Lu, Huayu, Lyle, Mitchell, Kulhanek, Denise, Hahn, Annette, Tiwari, Manish, Mishra, Ravi, Miska, Serge, Kumar, Anil, CRINON, Evelyne, Institute of Oceanology [China], Géosciences Paris Sud (GEOPS), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Qingdao National Laboratory for Marine Science and Technology, Key Laboratory of Ocean Circulation and Waves, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China, Université Paris Diderot - Paris 7 (UPD7), Key Laboratory of Marine Geology and Environment [China, Louisiana State University (LSU), and BITS Pilani, K. K. Birla Campus, Goa (India)
Subjects: [SDU] Sciences of the Universe [physics], [SDU]Sciences of the Universe [physics], [SDU.STU] Sciences of the Universe [physics]/Earth Sciences, [SDU.STU]Sciences of the Universe [physics]/Earth Sciences, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2019

17. Planktonic ciliates in different water masses in open waters near Prydz Bay (East Antarctica) during austral summer, with an emphasis on tintinnid assemblages

Author: Zhencheng Tao, Wuchang Zhang, Gérald Grégori, Yi Dong, Chaolun Li, Haibo Li, Chen Liang, Yuan Zhao, Qingdao National Laboratory for Marine Science and Technology, Institute of Information Science and Engineering [Shandong], Shandong Agricultural University (SDAU), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Water mass, 010504 meteorology & atmospheric sciences, Temperature salinity diagrams, 01 natural sciences, Prydz, Abundance, Circumpolar deep water, 14. Life underwater, 0105 earth and related environmental sciences, biology, Planktonic ciliates, 010604 marine biology & hydrobiology, Pelagic zone, Plankton, biology.organism_classification, Oceanography, Bay, [SDE]Environmental Sciences, Upwelling, Antarctica, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, General Agricultural and Biological Sciences, Tintinnid
Abstract: International audience; Planktonic ciliates are important microzooplankton in pelagic ecosystems. Previous studies in Antarctic waters have only investigated ciliate assemblages in different habitats without considering water masses. In this article, we report the characteristics of ciliate assemblages in different water masses in open waters near Prydz Bay (East Antarctica) during austral summer. Three water masses were identified according to temperature and salinity: Summer Surface Water (SSW), Winter Water (WW), and Circumpolar Deep Water (CDW). SSW was further divided into SSW Chl a < 3 (in vivo Chlorophyll a > 3 mg m −3) and SSW Chl a < 3 (in vivo Chlorophyll a < 3 mg m −3). Ciliate abundance and biomass in water masses decreased in the order: SSW > WW > CDW. SSW Chl a > 3 had a higher proportion (38.2%) of tintinnids to the total ciliate abundance and larger aloricate ciliates (ciliates in the 10-20 µm size class were < 15% of the total aloricate ciliate abundance) than in other water masses. WW had a higher proportion (> 30%) of Southern Ocean endemic tintinnid species in total tintinnid abundance than in other water masses. Each water mass had the following indigenous tintinnid species: SSW, Salpingella sp., Codonellopsis gaussi; WW, Salpingella costata, S. faurei, Cymatocylis affinis/convallaria forma drygalskii, and C. vanhoeffeni. Laackman-niella naviculaefera and C. affinis/convallaria forma cristallina were present at high abundance in both WW and SSW Chl a > 3. Upwelling caused discontinuity of the ciliate distribution. Our results will help predict the spatial and temporal variations of ciliate assemblages and other plankton according to the dynamics of water masses in Antarctic waters.
Published: 2018

18. Increased seasonality and aridity drove the C4 plant expansion in Central Asia since the Miocene–Pliocene boundary

Author: Christophe Colin, Wenqiang Pei, Shiming Wan, Xuefa Shi, Xingyan Shen, Yang Tan, Xuejun Jiang, Ryuji Tada, Anchun Li, Key Laboratory of Marine Geology and Environment [China, Institute of Oceanology [China], University of Chinese Academy of Sciences [Beijing] (UCAS), Qingdao National Laboratory for Marine Science and Technology, Géosciences Paris Sud (GEOPS), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Department of Earth and Planetary Science [Tokyo], The University of Tokyo (UTokyo), SOA, Inst Oceanog 1, Key Lab Marine Sedimentol & Environm Geol, Qingdao, Peoples R China., Institut des Systèmes Intelligents et de Robotique (ISIR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Qingdao Institute of Marine Geology, China Geological Survey, Qingdao 266071, China, Université Paris Diderot - Paris 7 (UPD7), State Key Laboratory of Marine Geology [Shanghai], Tongji University, Graduate School of Science [Tokyo], and The University of Tokyo (UTokyo)-The University of Tokyo (UTokyo)
Subjects: Biomass (ecology), 010504 meteorology & atmospheric sciences, [SDU.STU]Sciences of the Universe [physics]/Earth Sciences, Westerlies, Vegetation, 15. Life on land, Seasonality, Late Miocene, 010502 geochemistry & geophysics, medicine.disease, 01 natural sciences, Arid, Geophysics, 13. Climate action, Space and Planetary Science, Geochemistry and Petrology, Isotopes of carbon, [SDU]Sciences of the Universe [physics], Earth and Planetary Sciences (miscellaneous), medicine, Physical geography, Precipitation, Geology, 0105 earth and related environmental sciences
Abstract: Continuous and high-resolution records of the content, mass accumulation rate (MAR) and δ 13 C values of black carbon obtained from Integrated Ocean Drilling Program (IODP) Site U1430 in the southwestern Japan Sea have been established and combined with previous results obtained from Central Asia. The main objective of this work is to reconstruct the historical changes in vegetation types (C3–C4), and to constrain the driving force of C4 plant expansion over the last 13 Ma. The stable carbon isotope value of black carbon ( δ 13 CBC) shows a major shift since the Miocene–Pliocene boundary (∼5.3 Ma), suggesting significant expansion of C4 plants in broad areas of Central Asia, including the inland basins of northwestern China and the Loess Plateau. However, a decline in the content and MAR of black carbon reveals the absence of any link between fire and C4 plant expansion in Central Asia, due to the dramatic decrease in biomass under a drying regime. On a global scale, asynchronous expansion of C4 plants suggests that regional hydroclimatic change, rather than decline in CO2 concentration, was the most important factor to influence C4 expansion. We propose that the increased seasonality and the enhanced long-term aridity driven by the concurrent decline in winter westerly vapor, and increase in East Asian summer monsoon precipitation, were the main driving forces of C4 plant expansion in broad areas of Central Asia. Variations in winter westerly moisture have played a significant role in changes of regional climate and vegetation in Central Asia since the late Miocene.
Published: 2018

19. Antarctic Intermediate Water penetration into the Northern Indian Ocean during the last deglaciation

Author: Christophe Colin, Arnaud Dapoigny, Zhaojie Yu, F. Bassinot, Shiming Wan, Qiong Wu, Laure Meynadier, Ruifang Ma, Nejib Kallel, Sophie Sépulcre, Géosciences Paris Sud (GEOPS), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Key Laboratory of Marine Geology and Environment [China, Institute of Oceanology [China], Center for Ocean Mega-Science, Chinese Academy of Sciences, Institut de Physique du Globe de Paris (IPGP), Centre National de la Recherche Scientifique (CNRS)-Université de La Réunion (UR)-Université Paris Diderot - Paris 7 (UPD7)-IPG PARIS-Institut national des sciences de l'Univers (INSU - CNRS), College of Oceanography, Hohai University, Unité GEOGLOB, Faculté des Sciences de Sfax, Université de Sfax - University of Sfax-Université de Sfax - University of Sfax, Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Géochrononologie Traceurs Archéométrie (GEOTRAC), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Paléocéanographie (PALEOCEAN), This work was supported by the National Natural Science Foundation of China (41622603 and 41576034), National Programme on Global Change and Air–Sea Interaction (GASI-GEOGE-03), Innovation Project (2016ASKJ13) and Aoshan Talents programme (2017ASTCP-ES01) of Qingdao National Laboratory for Marine Science and Technology and CAS Interdisciplinary Innovation Team, Open Fund of the Key Laboratory of Marine Geology and Environment, Chinese Academy of Sciences (No. MGE2018KG01). Z. Yu acknowledges the China Scholarship Council for providing funding for his study in France. This study was supported by the Labex L-IPSL and the MONOPOL projects, which are funded by the ANR (grant nos. ANR-10-LABX-0018 and ANR 2011 Blanc SIMI 5-6 024 04), ANR-10-LABX-0018,L-IPSL,LabEx Institut Pierre Simon Laplace (IPSL): Understand climate and anticipate future changes(2010), ANR-11-BS56-0024,MONOPOL,Paléo-variabilité de la mousson indienne(2011), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Institut de Physique du Globe de Paris (IPG Paris)-Centre National de la Recherche Scientifique (CNRS), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Centre National de la Recherche Scientifique (CNRS), and ANR-10-LABX-0018/10-LABX-0018,L-IPSL,LabEx Institut Pierre Simon Laplace (IPSL): Understand climate and anticipate future changes(2010)
Subjects: 010504 meteorology & atmospheric sciences, Climate change, [SDU.STU]Sciences of the Universe [physics]/Earth Sciences, 010502 geochemistry & geophysics, 01 natural sciences, Panoply, law.invention, Foraminifera, Geochemistry and Petrology, law, Earth and Planetary Sciences (miscellaneous), Deglaciation, 14. Life underwater, Radiocarbon dating, 0105 earth and related environmental sciences, Carbon dioxide in Earth's atmosphere, Antarctic Intermediate Water, biology, Northern Hemisphere, biology.organism_classification, Geophysics, Oceanography, 13. Climate action, Space and Planetary Science, [SDU]Sciences of the Universe [physics], Upwelling, Geology
Abstract: The two-stage increase in atmospheric carbon dioxide (CO2), and the associated decrease in radiocarbon (14C) during the last deglaciation, are thought to have been linked to enhanced Southern Ocean upwelling and the rapid release of sequestered 14C-depleted CO2. Antarctic Intermediate Water (AAIW), originating from the Southern Ocean, reflects variations in the Southern Ocean and, crucially, mirrors the chemical signature of upwelling deep water. However, the penetration of AAIW into the Northern Indian Ocean and its relationship with deglacial climate changes have not been thoroughly elucidated to date. Here, we present the neodymium isotopic composition ( e Nd ) of mixed planktonic foraminifera from core MD77-176 from an intermediate depth in the Northern Indian Ocean to reconstruct the past evolution of intermediate water during deglaciation. The e Nd record in the Northern Indian Ocean displays two pulse-like shifts towards more radiogenic Southern Ocean values during the deglaciation, and these shifts coincide with excursions in Δ 14 C and e Nd records in the Pacific and Atlantic Oceans. These results suggest invasion of AAIW into the Northern Hemisphere oceans associated with enhanced Southern Ocean ventilation during deglaciation. Our new e Nd record strongly supports the close linkage of AAIW propagation and atmospheric CO2 rise through Southern Ocean ventilation during deglaciation.
Published: 2018

20. El Niño–Southern Oscillation complexity

Author: Ken Takahashi, Matthieu Lengaigne, Guomin Wang, Tim Li, Antonietta Capotondi, Tobias Bayr, Michael J. McPhaden, Axel Timmermann, WonMoo Kim, Wenju Cai, Malte F. Stuecker, Sunyong Kim, Ruihuang Xie, Harun Rashid, Fei-Fei Jin, Alexander Todd, Jong-Seong Kug, Boris Dewitte, Sang-Wook Yeh, Yoo-Geun Ham, Kim M. Cobb, Elke Zeller, Agus Santoso, Scott B. Power, Dietmar Dommenget, Daehyun Kang, Michiya Hayashi, Soon Il An, Kyung-Sook Yun, Pamela R. Grothe, Guojian Wang, June-Yi Lee, Karl Stein, Jing-Jia Luo, Shayne McGregor, Eric Guilyardi, Yoshimitsu Chikamoto, Xuebin Zhang, Sarah Ineson, Andrew T. Wittenberg, Woo Hyun Yang, Han Ching Chen, Jin-Ho Yoon, Yann Planton, Hong Li Ren, Institute of Basic Science (IBS), Pusan National University, Department of Atmospheric Sciences, Yonsei University, Pohang University of Science and Technology (POSTECH), School of Ocean and Earth Science and Technology (SOEST), University of Hawai‘i [Mānoa] (UHM), Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Qingdao National Laboratory for Marine Science and Technology, NOAA Earth System Research Laboratory (ESRL), National Oceanic and Atmospheric Administration (NOAA), Cooperative Institute for Research in Environmental Sciences (CIRES), University of Colorado [Boulder]-National Oceanic and Atmospheric Administration (NOAA), School of Earth and Atmospheric Sciences [Atlanta], Georgia Institute of Technology [Atlanta], Océan et variabilité du climat (VARCLIM), Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU), NOAA Pacific Marine Environmental Laboratory [Seattle] (PMEL), Department of Atmospheric Sciences [Seattle], University of Washington [Seattle], NOAA Geophysical Fluid Dynamics Laboratory (GFDL), Helmholtz Centre for Ocean Research [Kiel] (GEOMAR), National Taiwan University [Taiwan] (NTU), Department of Plants, Soils and Climate, Utah State University (USU), Centro de Estudios Avanzados en Zonas Aridas (CEAZA), Laboratoire d'études en Géophysique et océanographie spatiales (LEGOS), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), School of Earth, Atmosphere and Environment, Monash University, Monash University [Clayton], NCAS-Climate [Reading], Department of Meteorology [Reading], University of Reading (UOR)-University of Reading (UOR), Met Office Hadley Centre for Climate Change (MOHC), United Kingdom Met Office [Exeter], Centre for Australian Weather and Climate Research (CAWCR), Centre national de recherches météorologiques (CNRM), Institut national des sciences de l'Univers (INSU - CNRS)-Météo France-Centre National de la Recherche Scientifique (CNRS), ARC Centre of Excellence for Climate System Science, University of New South Wales [Sydney] (UNSW)-Australian Research Council [Canberra] (ARC), Instituto Geofísico del Perú (IGP), Exeter Climate Systems, College of Engineering, Mathematics and Physical Science, University of Exeter, Exeter, United Kingdom, Korean Ocean Research and Development Institute (KORDI), Gwangju Institute of Science and Technology (GIST), CSIRO, Oceans and Atmosphere, Hobart, TAS, Australia, Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), School of Earth, Atmosphere and Environment, Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), and University of Exeter
Subjects: El Nino-Southern Oscillation, Tropical Climate, Multidisciplinary, 010504 meteorology & atmospheric sciences, Climate Change, Equator, Climate change, [PHYS.PHYS.PHYS-GEO-PH]Physics [physics]/Physics [physics]/Geophysics [physics.geo-ph], 15. Life on land, 010502 geochemistry & geophysics, 01 natural sciences, Earth system science, Sea surface temperature, La Niña, El Niño, 13. Climate action, Climatology, Tropical climate, Water Movements, Environmental science, Terrestrial ecosystem, 14. Life underwater, 0105 earth and related environmental sciences
Abstract: El Niño events are characterized by surface warming of the tropical Pacific Ocean and weakening of equatorial trade winds that occur every few years. Such conditions are accompanied by changes in atmospheric and oceanic circulation, affecting global climate, marine and terrestrial ecosystems, fisheries and human activities. The alternation of warm El Niño and cold La Niña conditions, referred to as the El Niño–Southern Oscillation (ENSO), represents the strongest year-to-year fluctuation of the global climate system. Here we provide a synopsis of our current understanding of the spatio-temporal complexity of this important climate mode and its influence on the Earth system.
Published: 2018

21. Terminal Olefin Profiles and Phylogenetic Analyses of Olefin Synthases of Diverse Cyanobacterial Species

Author: Nathalie Sassoon, Thibault Scalvenzi, Tao Zhu, Muriel Gugger, Xuefeng Lu, Chinese Academy of Sciences [Beijing] (CAS), Collection des Cyanobactéries, Institut Pasteur [Paris], Qingdao National Laboratory for Marine Science and Technology, This work was supported by the National Natural Science Foundation of China (grant 31570068 and 31200001 to T.Z.), the National Science Fund for Distinguished Young Scholars of China (grant 31525002 to X.L.), the Shandong Taishan Scholarship (to X.L.), and the Qingdao Innovative Leading Talent [15-10-3-15-(31)-zch to X.L.]., and Institut Pasteur [Paris] (IP)
Subjects: 0301 basic medicine, Cyanobacteria, In silico, Alkenes, Applied Microbiology and Biotechnology, cyanobacteria, Substrate Specificity, Ligases, 03 medical and health sciences, chemistry.chemical_compound, Biosynthesis, Bacterial Proteins, Protein Domains, Amino Acid Sequence, Phylogeny, chemistry.chemical_classification, DNA ligase, olefin synthase, Ecology, biology, ATP synthase, Fatty Acids, Substrate (chemistry), Fatty acid, Computational Biology, biology.organism_classification, Hydrocarbons, biofuels, Biosynthetic Pathways, terminal olefins, fatty acyl-adenylate ligase, 030104 developmental biology, Enzyme, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, chemistry, Biochemistry, biology.protein, Polyketide Synthases, Sequence Alignment, Food Science, Biotechnology
Abstract: Cyanobacteria can synthesize alkanes and alkenes, which are considered to be infrastructure-compatible biofuels. In terms of physiological function, cyanobacterial hydrocarbons are thought to be essential for membrane flexibility for cell division, size, and growth. The genetic basis for the biosynthesis of terminal olefins (1-alkenes) is a modular type I polyketide synthase (PKS) termed olefin synthase (Ols). The modular architectures of Ols and structural characteristics of alkenes have been investigated only in a few species of the small percentage (approximately 10%) of cyanobacteria that harbor putative Ols pathways. In this study, investigations of the domains, modular architectures, and phylogenies of Ols in 28 cyanobacterial strains suggested distinctive pathway evolution. Structural feature analyses revealed 1-alkenes with three carbon chain lengths (C 15 , C 17 , and C 19 ). In addition, the total cellular fatty acid profile revealed the diversity of the carbon chain lengths, while the fatty acid feeding assay indicated substrate carbon chain length specificity of cyanobacterial Ols enzymes. Finally, in silico analyses suggested that the N terminus of the modular Ols enzyme exhibited characteristics typical of a fatty acyl-adenylate ligase (FAAL), suggesting a mechanism of fatty acid activation via the formation of acyl-adenylates. Our results shed new light on the diversity of cyanobacterial terminal olefins and a mechanism for substrate activation in the biosynthesis of these olefins. IMPORTANCE Cyanobacterial terminal olefins are hydrocarbons with promising applications as advanced biofuels. Despite the basic understanding of the genetic basis of olefin biosynthesis, the structural diversity and phylogeny of the key modular olefin synthase (Ols) have been poorly explored. An overview of the chemical structural traits of terminal olefins in cyanobacteria is provided in this study. In addition, we demonstrated by in vivo fatty acid feeding assays that cyanobacterial Ols enzymes might exhibit substrate carbon chain length specificity. Furthermore, by performing bioinformatic analyses, we observed that the substrate activation domain of Ols exhibited features typical of a fatty acyl-adenylate ligase (FAAL), which activates fatty acids by converting them to fatty acyl-adenylates. Our results provide further insight into the chemical structures of terminal olefins and further elucidate the mechanism of substrate activation for terminal olefin biosynthesis in cyanobacteria.
Published: 2018

22. ENSO-Like Modulated Tropical Pacific Climate Changes Since 2.36 Myr and Its Implication for the Middle Pleistocene Transition

Author: Zhaojie Yu, Shiming Wan, Tiegang Li, Hanjie Sun, Debo Zhao, Jie Huang, Christophe Colin, Zhaokai Xu, Lina Song, Anchun Li, Institute of Oceanology [China], Géosciences Paris Sud (GEOPS), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Qingdao National Laboratory for Marine Science and Technology, Key Laboratory of Ocean Circulation and Waves, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China, Université Paris Diderot - Paris 7 (UPD7), Key Laboratory of Marine Geology and Environment [China, State Key Laboratory of Marine Geology [Shanghai], and Tongji University
Subjects: Early Pleistocene, 010504 meteorology & atmospheric sciences, Pleistocene, Middle Pleistocene Transition, Climate change, West Philippine Sea, [SDU.STU]Sciences of the Universe [physics]/Earth Sciences, 010502 geochemistry & geophysics, 01 natural sciences, Geochemistry and Petrology, ENSO‐like system, 14. Life underwater, ENSO-like system, 0105 earth and related environmental sciences, grain size, myr, East Asian monsoon precipitation, Sea surface temperature, Geophysics, Oceanography, 13. Climate action, [SDU]Sciences of the Universe [physics], Upwelling, Walker circulation, Quaternary, Geology
Abstract: International audience; El Niño/Southern Oscillation (ENSO) activity and the Pacific Walker Circulation are controlled by the zonal sea surface temperature (SST) gradient between the western and Eastern Equatorial Pacific (EEP) and the corresponding barometric difference. Variations in the zonal SST gradient since the early Pleistocene have primarily been triggered by changes in the SST in the Eastern Equatorial Pacific. However, the response of the ENSO‐like long‐term state to the cooling of the EEP and its coupling role with tropical Pacific climate changes are still not well established. Here we present a high‐resolution grain‐size record spanning the last 2.36 Myr, obtained from marine core sediment located in the West Philippine Sea in order to decipher the tropical pacific climate changes and reveal its controlling mechanism. By combining our data with other long‐term climatic records from the Equatorial Pacific, we demonstrate that the cooling of SST and enhanced upwelling in the EEP resulted in the development of the Walker Circulation and increased monsoon precipitation in Luzon from 2.2 to 1.6 Myr, from 1.2 to 0.8 Myr, and since 0.2 Myr ago. The progressive cooling of the high‐latitudes in the Quaternary may be responsible for our observation here. A newly identified 100 kyr dominant period between 2.2 and 1.6 Myr in the ENSO‐like modulated Pacific climate records indicates that the ENSO‐like system may play a key role in facilitating or responding to the global climate changes.
Published: 2018

23. Distinct control mechanism of fine-grained sediments from Yellow River and Kyushu supply in the northern Okinawa Trough since the last glacial

Author: Hanchao Jiang, Yoshimi Kubota, Sidonie Révillon, Xuefa Shi, Xufeng Zheng, Zhaokai Xu, Ryuji Tada, Debo Zhao, Shiming Wan, Peter D. Clift, Zhaojie Yu, Samuel Toucanne, Anchun Li, Jie Huang, Institute of Oceanology [China], Qingdao National Laboratory for Marine Science and Technology, Qingdao Natl Lab Marine Sci & Technol, Lab Marine Geol, Qingdao, Peoples R China, Centre de Recherches Pétrographiques et Géochimiques (CRPG), Institut national des sciences de l'Univers (INSU - CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Environnements et Paléoenvironnements OCéaniques (EPOC), Observatoire aquitain des sciences de l'univers (OASU), Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), IFREMER, Unite Rech Geosci Marines, Lab Geophys & Enregistrements Sedimentaires, Plouzane, France., Louisiana State University (LSU), Department of Earth and Planetary Science [Tokyo], The University of Tokyo (UTokyo), Laboratoire Géosciences Océan (LGO), Institut Français de Recherche pour l'Exploitation de la Mer - Brest (IFREMER Centre de Bretagne), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Natl Museum Nat & Sci, Dept Geol, Ibaraki, Japan., Chinese Acad Sci, South China Sea Inst Oceanol, Key Lab Marginal Sea Geol, Guangzhou, Guangdong, Peoples R China., Géosciences Paris Sud (GEOPS), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), China Earthquake Adm, Inst Geol, State Key Lab Earthquake Dynam, Beijing, Peoples R China., Key Laboratory of Marine Geology and Environment [China, SOA, Inst Oceanog 1, Key Lab Marine Sedimentol & Environm Geol, Qingdao, Peoples R China., State Key Laboratory of Marine Geology [Shanghai], Tongji University, Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Graduate School of Science [Tokyo], and The University of Tokyo (UTokyo)-The University of Tokyo (UTokyo)
Subjects: Provenance, 010504 meteorology & atmospheric sciences, Tsushima Warm Current, Trough (geology), Fluvial, [SDU.STU]Sciences of the Universe [physics]/Earth Sciences, Yellow River, 010502 geochemistry & geophysics, 01 natural sciences, chemistry.chemical_compound, Okinawa Trough, Geochemistry and Petrology, River mouth, 14. Life underwater, Glacial period, 0105 earth and related environmental sciences, Kyushu Island, geography, geography.geographical_feature_category, clay-sized sediments, Sediment, Silicate, sea-level change, Geophysics, Oceanography, chemistry, 13. Climate action, [SDU]Sciences of the Universe [physics], Kuroshio Current, Sediment transport, Geology
Abstract: High-resolution multi-proxy records, including clay minerals and Sr-Nd-Pb isotopes of the clay-sized silicate fraction of sediments from IODP Site U1429 in the northern Okinawa Trough, provide reliable evidence for distinct control mechanism on fine-grained sediments input from the Yellow River and the southern Japanese Islands to the northern Okinawa Trough since 34 ka BP. Provenance analysis indicates that the sediments were mainly derived from the Yellow River and the island of Kyushu. Since the last glacial, clay-sized sediments transported from the Yellow River to the study site were strongly influenced by sea-level fluctuation. During low sea-level stage (∼34‒14 ka BP), the paleo-Yellow River mouth was positioned closer to the northern Okinawa Trough, favoring large fluvial discharge or even direct input of detrital sediments, which resulted about four times more flux of clay-sized sediments supply to the study area as during the relatively high sea-level stage (∼14‒0 ka BP). The input of Kyushu-derived clay-sized sediments to the study site was mainly controlled by the Kuroshio Current and Tsushima Warm Current intensity, with increased input in phase with weakened Kuroshio Current/Tsushima Warm Current. Our study suggests that the Kuroshio Current was very likely flowed into the Okinawa Trough and thus influenced the fine-grained sediment transport in the area throughout the last glacial and deglacial. During ∼34‒11 ka BP, the Kyushu clay-sized sediment input was mainly controlled by the Kuroshio Current. Since ∼11 ka BP, the occurrence of Tsushima Warm Current became important in influencing the Kyushu fine-grained sediment input to the northern Okinawa Trough.
Published: 2017

24. Magnetotactic Coccus Strain SHHC-1 Affiliated to Alphaproteobacteria Forms Octahedral Magnetite Magnetosomes

Author: Heng Zhang, Nicolas Menguy, Fuxian Wang, Karim Benzerara, Eric Leroy, Peiyu Liu, Wenqi Liu, Chunli Wang, Yongxin Pan, Zhibao Chen, Jinhua Li, Institute of Geology and Geophysics [Beijing] (IGG), Chinese Academy of Sciences [Beijing] (CAS), Heilongjiang Bayi Agricultural University, Qingdao National Laboratory for Marine Science and Technology, Institut de minéralogie, de physique des matériaux et de cosmochimie (IMPMC), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de recherche pour le développement [IRD] : UR206-Centre National de la Recherche Scientifique (CNRS), France-China Biomineralization and Nano-structures Laboratory, Institut de Chimie et des Matériaux Paris-Est (ICMPE), and Institut de Chimie du CNRS (INC)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Greigite, Microbiology (medical), coordinated FISH-SEM, Magnetotactic bacteria, 030106 microbiology, Magnetosome, lcsh:QR1-502, Biology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Microbiology, lcsh:Microbiology, 03 medical and health sciences, chemistry.chemical_compound, Lipid bilayer, magnetosome, Magnetite, magnetotactic cocci, Strain (chemistry), Alphaproteobacteria, biology.organism_classification, biomineralization, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, octahedron, 030104 developmental biology, chemistry, Biophysics, TEM, Biomineralization
Abstract: International audience; Magnetotactic bacteria (MTB) are morphologically and phylogenetically diverse prokaryotes. They can form intracellular chain-assembled magnetite (Fe3O4) or greigite (Fe3S4) nanocrystals each enveloped by a lipid bilayer membrane called a magnetosome. Magnetotactic cocci have been found to be the most abundant morphotypes of MTB in various aquatic environments. However, knowledge on magnetosome biomineralization within magnetotactic cocci remains elusive due to small number of strains that have been cultured. By using a coordinated fluorescence and scanning electron microscopy method, we discovered a unique magnetotactic coccus strain (tentatively named SHHC-1) in brackish sediments collected from the estuary of Shihe River in Qinhuangdao city, eastern China. It phylogenetically belongs to the Alphaproteobacteria class. Transmission electron microscopy analyses reveal that SHHC-1 cells formed many magnetite-type magnetosomes organized as two bundles in each cell. Each bundle contains two parallel chains with smaller magnetosomes generally located at the ends of each chain. Unlike most magnetotactic alphaproteobacteria that generally form magnetosomes with uniform crystal morphologies, SHHC-1 magnetosomes display a more diverse variety of crystal morphology even within a single cell. Most particles have rectangular and rhomboidal projections, whilst others are triangular, or irregular. High resolution transmission electron microscopy observations coupled with morphological modeling indicate an idealized model—elongated octahedral crystals, a form composed of eight {111} faces. Furthermore, twins, multiple twins and stack dislocations are frequently observed in the SHHC-1 magnetosomes. This suggests that biomineralization of strain SHHC-1 magnetosome might be less biologically controlled than other magnetotactic alphaproteobacteria. Alternatively, SHHC-1 is more sensitive to the unfavorable environments under which it lives, or a combination of both factors may have controlled the magnetosome biomineralization process within this unique MTB.
Published: 2017

25. Coastal upwelling areas as safe havens during climate warming

Author: Zi-Min Hu, Marie-Laure Guillemin, Key Laboratory of Experimental Marine Biology [Qingdao], Chinese Academy of Sciences [Qingdao], Qingdao National Laboratory for Marine Science and Technology, Instituto de Ciencias ambientales y evolutivas, Universidad Austral de Chile, Evolutionary Biology and Ecology of Algae (EBEA), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Pontificia Universidad Católica de Chile (UC)-Universidad Austral de Chile-Centre National de la Recherche Scientifique (CNRS), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Universidad Austral de Chile-Centre National de la Recherche Scientifique (CNRS)-Pontificia Universidad Católica de Chile (UC)
Subjects: 0106 biological sciences, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Ecology, Range (biology), 010604 marine biology & hydrobiology, Effects of global warming on oceans, Global warming, Carbon sink, 15. Life on land, Coastal community, 010603 evolutionary biology, 01 natural sciences, Ecosystem engineer, Oceanography, 13. Climate action, Environmental science, Upwelling, Marine ecosystem, 14. Life underwater, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Ecology, Evolution, Behavior and Systematics
Abstract: International audience; Seaweeds have long been recognized as “ecosystem engineers” and carbon sinks in coastal marine ecosystems. However, recent ocean warming has had drastic eco-physiological impacts on seaweed assemblages and hence coastal community structure (Wernberg et al., 2011, 2013). Seaweeds, particularly species that prefer lower water temperatures, are facing imminent threat and will experience strong population-size reductions at low-latitude range limits (Wernberg et al., 2011, 2013).
Published: 2016

26. Ciliates - Protists with complex morphologies and ambiguous early fossil record

Author: Michaela C. Strüder-Kypke, Thorsten Stoeck, Miroslav Macek, Wuchang Zhang, John C. Clamp, Alan Warren, Joong Ki Choi, George G. McManus, Eleni Gentekaki, Hongan Long, Takashi Kamiyama, Sabine Agatha, Adriana Vallesi, Peter Vd'acny, Geoffrey Odhiambo Ong'ondo, Laura R. P. Utz, Jere H. Lipps, William A. Bourland, Barbara Kammerlander, Diane K. Stoecker, Sun Young Kim, Diana L. Lipscomb, David J. S. Montagnes, Thomas Weisse, Mercedes Martín-Cereceda, Helmut Berger, Matthew D. Johnson, Bettina Sonntag, Christopher S. Lobban, David J. Patterson, Weibo Song, Stephen A. Wickham, Xiaozhong Hu, Mary Doherty, Zifeng Zhan, Blanca Pérez-Uz, Micah Dunthorn, Young-Ok Kim, Maria Sonia Barria de Cao, Pablo Quintela-Alonso, Erna Aescht, Marie Abboud-Abi Saab, Michele Laval-Peuto, Luciana F. Santoferrara, Rebecca A. Zufall, Robert I. Mansergh, Jun Gong, Jie Huang, Charles Bachy, Feng Gao, Isabelle Trautmann, Denis H. Lynn, Antonietta La Terza, John R. Dolan, Zhenzhen Yi, Pierangelo Luporini, Lúcia S. L. Safi, Department of ecology, Universität Kaiserslautern, Observatoire océanologique de Villefranche-sur-mer (OOVM), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Austrian Museum, Ecologie Systématique et Evolution (ESE), Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Mecanique des Fluides et d'Acoustique (LMFA), École Centrale de Lyon (ECL), Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), School of Energy and Power Engineering [Beijing], Beihang University (BUAA), Faculty of Computer Science, Dalhousie University [Halifax], Yantai Institute of Coastal Zone Research for Sustainable Development, Chinese Academy of Sciences [Beijing] (CAS), Institute of Oceanology [China], Woods Hole Oceanographic Institution (WHOI), University of Guelph, School of Biological Sciences [Sydney], The University of Sydney, Ecology, University of Innsbruck, University of Maryland Center for Environmental Science, Horn Point Laboratory, National History Museum of London, Institutions et Dynamiques Historiques de l'Économie et de la Société (IDHES), Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Nanterre (UPN)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris 1 Panthéon-Sorbonne (UP1), Qingdao National Laboratory for Marine Science and Technology, Universität Salzburg, and Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Ciliate, 0303 health sciences, Fossil Record, Ecology, Paleontology, Acritarch, Biology, Oceanography, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Incertae sedis, Devonian, 03 medical and health sciences, Taxonomy (biology), Clade, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, 030304 developmental biology, Tintinnid
Abstract: International audience; Since ciliates rarely possess structures that easily fossilize, we are limited in our ability to use paleontological studies to reconstruct the early evolution of this large and ecologically important clade of protists. Tintinnids, a group of loricate (house-forming) planktonic ciliates, are the only group that has a significant fossil record. Putative tintinnid fossils from rocks older than Jurassic, however, possess few to no characters that can be found in extant ciliates; these fossils are best described as `incertae sedis eukaryotes'. Here, we review the Devonian fossil Nassacysta reticulata and propose that it is likewise another `incertae sedis eukaryote due to the lack of any unambiguous ciliate characters. Future tintinnid fossil descriptions would be most helpful if: (i) neutral terminology is used in the descriptions but ciliate-specific terminology in the interpretations; (ii) the current ciliate classification is used, although fossil data may expand or modify classifications based on modem forms; (iii) close collaboration with specialists studying extant ciliates is done; and (iv) editors include an expert of extant ciliates in the review process. (C) 2015 Elsevier B.V. All rights reserved.
Published: 2015

27. Co-encapsulation of curcumin and fucoxanthin in solid-in-oil-in-water multilayer emulsions: Characterization, stability and programmed sequential release.

Author: Wang L, Wei Z, and Xue C
Subjects: Drug Compounding, Nanoparticles chemistry, Particle Size, Drug Stability, Water chemistry, Drug Delivery Systems, Drug Carriers chemistry, Emulsions chemistry, Curcumin chemistry, Xanthophylls chemistry
Abstract: To enhance the bioavailability of bioactives with varying efficacy in the gastrointestinal tract (GIT), a co-delivery system of solid-in-oil-in-water (S/O/W) emulsion was designed for the co-encapsulation of two bioactives in this paper. S/O/W emulsions were fabricated utilizing fucoxanthin (FUC)-loaded nanoparticles (NPs) as the solid phase, coconut oil containing curcumin (Cur) as the oil phase, and carboxymethyl starch (CMS)/propylene glycol alginate (PGA) complex as the aqueous phase. The high entrapment efficiency of Cur (82.3-91.3%) and FUC (96.0-96.1%) was found in the CMS/PGA complex-stabilized S/O/W emulsions. Encapsulation of Cur and FUC within S/O/W emulsions enhanced their UV and thermal stabilities. In addition, S/O/W emulsions prepared with CMS/PGA complexes displayed good stability. More importantly, the formed S/O/W emulsion possessed programmed sequential release characteristics, delivering Cur and FUC to the small intestine and colon, respectively. These results contributed to designing co-delivery systems for the programmed sequential release of two hydrophobic nutrients in the GIT., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)
Published: 2024
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28. Discovery, Total Synthesis, and Anti-Inflammatory Evaluation of Naturally Occurring Naphthopyrone-Macrolide Hybrids as Potent NLRP3 Inflammasome Inhibitors.

Author: Sun C, Jiang Y, Li C, Sun S, Lin J, Wang W, Zhou L, Li L, Shah M, Che Q, Zhang G, Wang, Zhu T, and Li D
Subjects: Humans, Mice, Anti-Inflammatory Agents pharmacology, Anti-Inflammatory Agents chemical synthesis, Anti-Inflammatory Agents chemistry, Animals, Molecular Structure, Pyrones pharmacology, Pyrones chemistry, Pyrones chemical synthesis, Drug Discovery, Naphthalenes pharmacology, Naphthalenes chemistry, Naphthalenes chemical synthesis, Anti-Inflammatory Agents, Non-Steroidal pharmacology, Anti-Inflammatory Agents, Non-Steroidal chemistry, Anti-Inflammatory Agents, Non-Steroidal chemical synthesis, NLR Family, Pyrin Domain-Containing 3 Protein antagonists & inhibitors, NLR Family, Pyrin Domain-Containing 3 Protein metabolism, Inflammasomes metabolism, Inflammasomes antagonists & inhibitors, Macrolides pharmacology, Macrolides chemistry, Macrolides chemical synthesis
Abstract: Numerous clinical disorders have been linked to the etiology of dysregulated NLRP3 (NACHT, LRR, and PYD domain-containing protein 3) inflammasome activation. Despite its potential as a pharmacological target, modulation of NLRP3 activity remains challenging. Only a sparse number of compounds have been reported that can modulate NLRP3 and none of them have been developed into a commercially available drug. In this research, we identified three potent NLRP3 inflammasome inhibitors, gymnoasins A-C (1-3), with unprecedented pentacyclic scaffolds, from an Antarctic fungus Pseudogymnoascus sp. HDN17-895, which represent the first naturally occurring naphthopyrone-macrolide hybrids. Additionally, biomimetic synthesis of gymnoasin A (1) was also achieved validating the chemical structure and affording ample amounts of material for exhaustive bioactivity assessments. Biological assays indicated that 1 could significantly inhibited in vitro NLRP3 inflammasome activation and in vivo pro-inflammatory cytokine IL-1β release, representing a valuable new lead compound for the development of novel therapeutics with the potential to inhibit the NLRP3 inflammasome., (© 2024 Wiley-VCH GmbH.)
Published: 2024
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29. Trophic effects of jellyfish blooms on fish populations in ecosystems of the coastal waters of China.

Author: Wang P, Zhang F, Guo D, Chi X, Feng S, and Sun S
Subjects: Animals, China, Scyphozoa physiology, Environmental Monitoring, Biomass, Fisheries, Fishes, Food Chain, Ecosystem, Eutrophication
Abstract: Jellyfish play an important role in the material cycling and energy flow of food webs, and massive aggregations may have deleterious consequences for local fisheries; yet a theoretical framework of the trophic effects of jellyfish blooms on coastal fisheries is unclear. To address this knowledge gap, we assessed the trophic interactions between cooccurring bloom jellyfish and dominant fish groups (omnivorous fish and piscivorous fish) in the coastal waters of China (CWC) via stable isotope analysis; we subsequently discussed how jellyfish blooms may affect energy flow through coastal ecosystems. Our results indicate a considerable degree of trophic overlap (mean ratio > 65 %) between jellyfish and small omnivorous fish (< 10 cm), highlighting a similarity in feeding habits, while the overlap ratio decreased to <55 % of the large omnivorous fish group (> 10 cm). Relatively higher trophic levels and smaller overlaps of large omnivorous fish were found in the ecosystem with high jellyfish biomass, which suggested that they may reinforce the ontogenetic trophic shift pattern to alleviate the potential for resource competition with jellyfish under conditions of jellyfish explosion. The smallest trophic overlap (< 20 %) highlighted the strong trophic differentiation between jellyfish and piscivorous fish. Additionally, our study suggested that a massive aggregation of jellyfish can negatively influence zooplankton but may not transfer energy further up efficiently, implying a weak trophic coupling between jellyfish and upper-trophic levels in CWC ecosystems. Thus, we speculate that jellyfish play an important role in shaping pathways involved in the energy transfer of food webs and that large blooms may negatively affect fisheries through bottom-up control affecting prey availability. In general, these results hold strong potential to further improve the understanding of the trophic interactions between jellyfish and fish populations. Furthermore, this study provides valuable data for predicting the consequences of jellyfish blooms on ecosystems, and is crucial for ecosystem-based management of coastal fisheries., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)
Published: 2024
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30. Integrated global proteomic and phosphoproteomic analysis of cisplatin-induced apoptosis in A549 cells.

Author: Qi L, Zhu J, Cheng Z, Yuan Z, Qi W, Wu J, Qin Y, Yang J, Luo T, Wang M, Weng Y, and Shao J
Abstract: Protein phosphorylation, a widely occurring and significant post-translational modification, is integral to various biological processes. We previously utilized a protein affinity probe to identify genes damaged by cisplatin, revealing that it inflicts substantial damage on protein kinase and protein phosphatase genes. In this study, we investigated cisplatin-induced alterations in the global proteome and phosphoproteome of A549 cells. Employing Fe-IMAC beads and tyrosine phosphorylation enrichment antibodies, we identified 6944 protein groups and 18,274 phosphorylation sites on 4915 proteins across three biological replicates of both cisplatin-treated A549 cells and control cells. Among these, 730 tyrosine phosphorylation sites were identified-marking the most substantial discovery of such sites in A549 cells following cisplatin treatment. Bioinformatics analysis indicated that the proteins exhibiting significant phosphorylation level changes predominantly involved in RNA processing, modification, transcription, translation, and the spliceosome. This suggests that cisplatin-induced damage to protein kinases and phosphatases may disrupt the normal function of these proteins, consequently impairing DNA replication, RNA translation, and shearing, ultimately culminating in tumor cell death. Moreover, we cross-referenced our proteomic data with our previously obtained cisplatin-damaged genes, observing that the majority of down-regulated proteins derived from cisplatin-induced gene damage. The data are available on ProteomeXchange under the identifier PXD053902., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Inc. All rights reserved.)
Published: 2024
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31. Spirophosphine-Catalyzed Enantioselective [3 + 2] Cycloaddition of Allenoates and Unsaturated α-Ketimine Esters.

Author: Hao L, Zhu F, Liu X, and Wang
Abstract: A novel chiral spiro-monophosphine, OUC-Phos, was synthesized and utilized for the first time in the asymmetric Lu's [3 + 2] cycloaddition reaction of β,γ-unsaturated α-ketimine ester with allenoate. OUC-Phos, featuring a 3,3'-diphenyl-modified spirobiindane skeleton, demonstrated exceptional catalytic efficiency in the [3 + 2] cycloaddition to achieve high yields, enantioselectivities, and diastereoselectivities for the targeted products. The broad substrate scope encompassing diverse functional groups demonstrated the versatility of this methodology. Furthermore, the reaction was successfully scaled up, and the products were easily converted into their corresponding functionalized derivatives.
Published: 2024
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32. Effects of dietary succinic acid supplementation on growth performance, digestive ability, intestinal development and immunity of large yellow croaker (Larimichthys crocea) larvae.

Author: Zhang C, Liu Y, Shi Z, Yao C, Zhang J, Wang Y, Liu J, Mai K, and Ai Q
Abstract: The application of artificial micro-diet is an effective way to improve and standardize the quality of aquatic animal larvae. However, the widespread adoption of micro-diet faces a bottleneck due to the limited utilization capacity of the larvae. A 30-day feeding experiment was carried out to investigate the effect of dietary succinic acid (SA) on the growth performance, digestive ability, intestinal development, and immunity of large yellow croaker larvae (initial body weight 11.33 ± 0.57 mg). Four isonitrogenous and isolipidic diets were formulated, incorporating 0.00%, 0.01%, 0.02% and 0.03% SA separately. The results showed that a diet with 0.02% SA significantly increased both the final body weight and the specific growth rate of the larvae. Regarding digestive ability, 0.01% SA supplementation significantly enhanced trypsin activity in both intestinal and pancreatic segments. In addition, 0.01% SA supplementation notably improved amylase activity in the intestinal segment, while diets with 0.01%-0.02% SA significantly improved lipase activity in the pancreatic segment. In terms of intestinal development, 0.01% SA supplementation remarkably boosted the activities of alkaline-phosphatase and leucine-aminopeptidase on brush border membrane in intestine. Furthermore, 0.03% SA supplementation significantly increased the expression of occludin. In terms of immunity, larvae fed diets with 0.01%-0.02% SA exhibited significantly higher lysozyme activity compared to the control group. Supplementation with 0.01% SA also significantly increased both iNOS activity and NO content. In summary, the findings of this study suggested that adding 0.02% SA can improve the growth performance of large yellow croaker larvae by improving digestive enzymes activities, promoting intestinal development, and enhancing nonspecific immunity., (Copyright © 2024. Published by Elsevier Ltd.)
Published: 2024
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33. Intestinal-Target and Glucose-Responsive Smart Hydrogel toward Oral Delivery System of Drug with Improved Insulin Utilization.

Author: Ying R, Wang W, Chen R, Zhou R, and Mao X
Abstract: An intelligent insulin delivery system targeting intestinal absorption and glucose responsiveness can enhance the bioavailability through oral insulin therapy, offering promising diabetes treatment. In this paper, a glucose and pH dual-response polymer hydrogel using carboxymethyl agarose modified with 3-amino-phenylboronic acid and l-valine (CPL) was developed as an insulin delivery carrier, exhibiting excellent biocompatibility and effective insulin encapsulation. The insulin encapsulated in the hydrogel (Ins-CPL) was released in a controlled manner in response to the in vivo stimulation of blood glucose and pH levels with higher levels of intracellular uptake and utilization of insulin in the intestinal environment simultaneously. Notably, the Ins-CPL hydrogel effectively regulated blood sugar in diabetic rats over a long period by simulating endogenous insulin, responding to changes in plasma pH and glucose levels, and overcoming the intestinal epithelium barrier. This indicates a significant boost in oral insulin bioavailability and broadens its application prospects.
Published: 2024
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34. The application of marine polysaccharides to antitumor nanocarriers.

Author: Wang H, Hunter R, Zhang Q, Yu H, Wang J, Yue Y, Geng L, and Wu N
Subjects: Humans, Animals, Aquatic Organisms chemistry, Alginates chemistry, Chitosan chemistry, Neoplasms drug therapy, Liposomes chemistry, Micelles, Carrageenan chemistry, Polysaccharides chemistry, Polysaccharides pharmacology, Antineoplastic Agents chemistry, Antineoplastic Agents pharmacology, Antineoplastic Agents therapeutic use, Drug Carriers chemistry, Nanoparticles chemistry
Abstract: Nanotechnology has revolutionized the diagnosis, monitoring and treatment of biomedical diseases, in which nanocarriers have greatly improved the targeting and bioavailability of antitumor drugs. The marine natural polysaccharides fucoidan, chitosan, alginate, carrageenan and porphyran have broad-spectrum bioactivities and unique physicochemical properties such as excellent non-toxicity, biocompatibility, biodegradability and reproducibility, which have placed them as a principal focus in the nanocarrier field. Nanocarriers based on different types of marine polysaccharides are distinctive in addressing antitumor therapeutic challenges such as targeting, environmental responsiveness, drug resistance, tissue toxicity, enhancing diagnostic imaging, overcoming the first-pass effect and innovative 3D binding. Additionally, they all share the possibility of relatively easy chemical modification, while their separation into well-defined derivatives provide innovative structure-activity relationship possibilities. Liposomes, nanoparticles and polymer-micelles constructed from them can efficiently deliver drugs such as paclitaxel, gemcitabine, siRNA and others, which are widely used in radiotherapy, chemotherapy, immunotherapy, nucleic acid therapy and photothermal therapy, yet there are still infinite possibilities for innovation and exploration. This article reviews the recent advances and challenges of marine polysaccharide-based delivery systems as oncology drug nanocarriers., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier Ltd.)
Published: 2024
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35. Chitosan-Based Charge-Controllable Supramolecular Carrier for Universal Immobilization of Enzymes with Different Isoelectric Points.

Author: Wang W, Huang WC, He Y, Zhang Y, and Mao X
Abstract: Electrostatic adsorption is an enzyme immobilization method that effectively maintains enzyme activity and exhibits considerable binding efficiency. However, enzymes carry different charges at their respective reaction pH levels, which prevents the use of the same carrier to immobilize enzymes with different charges. In this study, we employed a template-mediated polysaccharide-enzyme coupling self-assembly strategy to develop a charge-controllable supramolecular immobilization carrier by regulating the charge properties of carboxymethyl chitosan, enabling the universal immobilization of enzymes with different charge levels across a range of reaction pH values. By using silica nanoparticles of certain sizes as templates, the size of the carrier can be precisely controlled and the hollow network structure formed after removing the template can effectively reduce mass transfer resistance. Trypsin and papain are used as model enzymes, and the experimental results show that the supramolecular self-assembly immobilization strategy does not disrupt the secondary structure of the enzyme molecules. After 2 h of reaction, the enzyme activities of immobilized papain and immobilized trypsin are 13.2% and 7.7% higher than those of the free enzymes, respectively. After 10 consecutive reactions, the enzyme activities of immobilized papain and immobilized trypsin retained 56.3% and 64.3% of their initial values, respectively.
Published: 2024
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36. Understanding metabolic resistance strategy of clinically isolated antibiotic-resistant bacteria by proteomic approach.

Author: Peng B, Li H, and Peng X
Abstract: Introduction: Understanding the metabolic regulatory mechanisms leading to antibacterial resistance is important to develop effective control measures., Areas Covered: In this review, we summarize the progress on metabolic mechanisms of antibiotic resistance in clinically isolated bacteria, as revealed using proteomic approaches., Expert Opinion: Proteomic approaches are effective tools for uncovering clinically significant bacterial metabolic responses to antibiotics. Proteomics can disclose the associations between metabolic proteins, pathways, and networks with antibiotic resistance, and help identify their functional impact. The mechanisms by which metabolic proteins control the four generally recognized resistance mechanisms (decreased influx and targets, and increased efflux and enzymatic degradation) are particularly important. The proposed mechanism of reprogramming proteomics via key metabolites to enhance the killing efficiency of existing antibiotics needs attention.
Published: 2024
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37. Unveiling the immunogenicity of allogeneic mesenchymal stromal cells: Challenges and strategies for enhanced therapeutic efficacy.

Author: Li Y, Jin M, Guo D, Shen S, Lu K, Pan R, Sun L, Zhang H, Shao J, and Pan G
Abstract: Mesenchymal stromal cells (MSCs) exhibit significant potential in the context of cell therapy because of their capacity to perform a range of interconnected functions in damaged tissues, including immune modulation, hematopoietic support, and tissue regeneration. MSCs are hypoimmunogenic because of their diminished expression of major histocompatibility molecules, absence of costimulatory molecules, and presence of coinhibitory molecules. While autologous MSCs reduce the risk of rejection and infection, variability in cell numbers and proliferation limits their potential applications. Conversely, allogeneic MSCs (allo-MSCs) possess broad clinical applications unconstrained by donor physiology. Nonetheless, preclinical and clinical investigations highlight that transplanted allo-MSCs are subject to immune attack from recipients. These cells exhibit anti-inflammatory and proinflammatory phenotypes contingent on the microenvironment. Notably, the proinflammatory phenotype features enhanced immunogenicity and diminished immunosuppression, potentially triggering allogeneic immune reactions that impede long-term clinical efficacy. Consequently, preserving the low immunogenicity of allo-MSCs in vivo and mitigating immune rejection in diverse microenvironments represent crucial challenges for the widespread clinical application of MSCs. In this review, we elucidate the immune regulation of allo-MSCs, specifically focusing on two distinct subgroups, MSC1 and MSC2, that exhibit varying polarization states and immunogenicity. We discuss the factors and underlying mechanisms that induce MSC immunogenicity and polarization, highlighting the crucial role of major histocompatibility complex class I/II molecules in rejection post-transplantation. Additionally, we summarize the immunogenic regulatory targets and applications of allo-MSCs and outline strategies to address challenges in this promising field, aiming to enhance allo-MSC therapeutic efficacy for patients., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Masson SAS.. All rights reserved.)
Published: 2024
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38. Recovery of intestinal microbial community in Penaeus vannamei after florfenicol perturbation.

Author: Luo K, Yang Z, Wen X, Wang D, Liu J, Wang L, Fan R, and Tian X
Abstract: The concept and application of probiotic intervention for restoring intestinal microbial dysbiosis induced by antibiotics in aquaculture are still in early stages. This study aimed to investigate potential responses of various recovery strategies, including natural recovery and probiotic intervention, in restoring the growth and intestinal microbial community of Penaeus vannamei following florfenicol perturbation. The basal diet (control, CN) was supplemented with florfenicol (FC) or Lactobacillus plantarum W2 (LM) throughout the entire feeding trial. Meanwhile, the basal diet was supplemented with florfenicol for 7 days, followed by a period without florfenicol (natural recovery, FB), or with live strain W2 (probiotic recovery, FM), for a duration of 35 days. Results indicated that dietary supplementation of strain W2, whether continuous or following florfenicol perturbation, along with continuous florfenicol supplementation, significantly enhanced the growth performance of shrimp. Early natural recovery and probiotic intervention did not induce significant alterations in microbial diversity and community structure. Florfenicol perturbation resulted in a decrease in the abundance of potentially beneficial bacteria in intestinal microbial community of shrimp. However, both probiotic intervention and natural recovery strategies gradually reduced the abundance of potentially pathogenic bacteria while increasing the abundance of potentially beneficial ones. The robustness of microbial network decreased during florfenicol perturbation, showed gradual improvement during probiotic recovery, and remained relatively low during natural recovery and continuous florfenicol supplementation. Moreover, the microbial community composition in intestinal habitat significantly differed under various recovery strategies compared to the control. Notably, the microbial community composition of intestinal habitat following probiotic recovery exhibited greater similarity to that of continuous strain W2 supplementation without florfenicol perturbation. In summary, dietary supplementation of florfenicol perturbed intestinal microbial community stability of shrimp, whereas probiotic intervention and natural recovery facilitated the attainment of new stable states by altering keystone taxa. Considering intestinal microbial community stability of shrimp, the recovery of microbial community through probiotic intervention appears to be more effective than natural recovery., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)
Published: 2024
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39. The marine environmental microbiome mediates physiological outcomes in host nematodes.

Author: Xue Y, Xie Y, Cao X, and Zhang L
Subjects: Animals, Nematoda physiology, Nematoda microbiology, Bacteria genetics, Bacteria classification, Bacteria isolation & purification, Bacteria metabolism, Ecosystem, Microbiota physiology, Caenorhabditis elegans physiology, Caenorhabditis elegans microbiology
Abstract: Background: Nematodes are the most abundant metazoans in marine sediments, many of which are bacterivores; however, how habitat bacteria affect physiological outcomes in marine nematodes remains largely unknown. RESULTS: Here, we used a Litoditis marina inbred line to assess how native bacteria modulate host nematode physiology. We characterized seasonal dynamic bacterial compositions in L. marina habitats and examined the impacts of 448 habitat bacteria isolates on L. marina development, then focused on HQbiome with 73 native bacteria, of which we generated 72 whole genomes sequences. Unexpectedly, we found that the effects of marine native bacteria on the development of L. marina and its terrestrial relative Caenorhabditis elegans were significantly positively correlated. Next, we reconstructed bacterial metabolic networks and identified several bacterial metabolic pathways positively correlated with L. marina development (e.g., ubiquinol and heme b biosynthesis), while pyridoxal 5'-phosphate biosynthesis pathway was negatively associated. Through single metabolite supplementation, we verified CoQ 10 , heme b, acetyl-CoA, and acetaldehyde promoted L. marina development, while vitamin B6 attenuated growth. Notably, we found that only four development correlated metabolic pathways were shared between L. marina and C. elegans. Furthermore, we identified two bacterial metabolic pathways correlated with L. marina lifespan, while a distinct one in C. elegans. Strikingly, we found that glycerol supplementation significantly extended L. marina but not C. elegans longevity. Moreover, we comparatively demonstrated the distinct gut microbiota characteristics and their effects on L. marina and C. elegans physiology., Conclusions: Given that both bacteria and marine nematodes are dominant taxa in sedimentary ecosystems, the resource presented here will provide novel insights to identify mechanisms underpinning how habitat bacteria affect nematode biology in a more natural context. Our integrative approach will provide a microbe-nematodes framework for microbiome mediated effects on host animal fitness., (© 2024. The Author(s).)
Published: 2024
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40. In Situ Synthesis and Visualization of Membrane SNAP25 Nano-Organization.

Author: Cheng S, Zhang J, Zhang Y, Wang H, and Wang H
Subjects: Humans, HEK293 Cells, Cryoelectron Microscopy, Electron Microscope Tomography methods, Synaptosomal-Associated Protein 25 metabolism, Synaptosomal-Associated Protein 25 chemistry, Gold chemistry, Metal Nanoparticles chemistry, Cell Membrane chemistry, Cell Membrane metabolism
Abstract: Cryo-electron tomography (cryo-ET) can provide insights into the structure and states of natural membrane environments to explore the role of SNARE proteins at membrane fusion and understand the relationship between their subcellular localization/formation and action mechanism. Nevertheless, the identification of individual molecules in crowded and low signal-to-noise ratio membrane environments remains a significant challenge. In this study, cryo-ET is employed to image near-physiological state 293T cell membranes, specifically utilizing in situ synthesized gold nanoparticles (AuNPs) bound with cysteine-rich protein tags to single-molecularly labeled synaptosomal-associated protein 25 (SNAP25) on the membrane surface. The high-resolution images reveal that SNAP25 is predominantly located in regions of high molecular density within the cell membrane and aggregates into smaller clusters, which may increase the fusion efficiency. Remarkably, a zigzag arrangement of SNAP25 is observed on the cell membrane. These findings provide valuable insights into the functional mechanisms of SNARE proteins.
Published: 2024
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41. SENP1 mediates zinc-induced ZnT6 deSUMOylation at Lys-409 involved in the regulation of zinc metabolism in Golgi apparatus.

Author: Song CC, Liu T, Hogstrand C, Zhong CC, Zheng H, Sun LH, and Luo Z
Subjects: Animals, Humans, Male, Mice, Carrier Proteins, DNA-Binding Proteins metabolism, DNA-Binding Proteins genetics, Liver metabolism, Mice, Inbred C57BL, Protein Processing, Post-Translational, SUMO-1 Protein metabolism, Transcription Factor MTF-1, Transcription Factors metabolism, Transcription Factors genetics, Cation Transport Proteins metabolism, Cation Transport Proteins genetics, Cysteine Endopeptidases metabolism, Cysteine Endopeptidases genetics, Golgi Apparatus metabolism, Sumoylation, Zinc metabolism
Abstract: Zinc (Zn) transporters contribute to the maintenance of intracellular Zn homeostasis in vertebrate, whose activity and function are modulated by post-translational modification. However, the function of small ubiquitin-like modifier (SUMOylation) in Zn metabolism remains elusive. Here, compared with low Zn group, a high-Zn diet significantly increases hepatic Zn content and upregulates the expression of metal-response element-binding transcription factor-1 (MTF-1), Zn transporter 6 (ZnT6) and deSUMOylation enzymes (SENP1, SENP2, and SENP6), but inhibits the expression of SUMO proteins and the E1, E2, and E3 enzymes. Mechanistically, Zn triggers the activation of the MTF-1/SENP1 pathway, resulting in the reduction of ZnT6 SUMOylation at Lys 409 by small ubiquitin-like modifier 1 (SUMO1), and promoting the deSUMOylation process mediated by SENP1. SUMOylation modification of ZnT6 has no influence on its localization but reduces its protein stability. Importantly, deSUMOylation of ZnT6 is crucial for controlling Zn export from the cytosols into the Golgi apparatus. In conclusion, for the first time, we elucidate a novel mechanism by which SUMO1-catalyzed SUMOylation and SENP1-mediated deSUMOylation of ZnT6 orchestrate the regulation of Zn metabolism within the Golgi apparatus., (© 2024. The Author(s).)
Published: 2024
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42. Novel antifungal talaroenamine L with unusual leptosphaeronyl moiety from marine-derived Talaromyces sp. HDN17-428 via HDACi elicitation.

Author: Anjum K, Zhou L, Hayyat K, Huang X, Wang J, Zhang G, Zhu T, Che Q, and Li D
Abstract: Vorinostat elicitation of the deep-sea fungus Talaromyces sp. HDN17-428 resulted in the isolation of one new compound, talaroenamine L ( 1 ) with unusual leptosphaeronyl moiety and three known compounds ( 2 - 4 ). Structures of 1 - 4 were confirmed by extensive NMR, HRESIMS and OR calculations. Antimicrobial activities of all compounds were tested in which compounds 1 - 4 showed substantial antifungal activities with MIC values ranged from 3.1 to 12.5 μ M.
Published: 2024
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43. Marine thermal fluctuation induced gluconeogenesis by the transcriptional regulation of CgCREBL2 in Pacific oysters.

Author: Li Q, Gao L, Liu L, Wang L, Hu L, Wang L, and Song L
Subjects: Animals, Hot Temperature, Crassostrea genetics, Crassostrea physiology, Gluconeogenesis genetics, Gene Expression Regulation
Abstract: Marine thermal fluctuation profoundly influences energy metabolism, physiology, and survival of marine life. In the present study, short-term and long-term high-temperature stresses were found to affect gluconeogenesis by inhibiting PEPCK activity in the Pacific oyster (Crassostrea gigas), which is a globally distributed species that encounters significant marine thermal fluctuations in intertidal zones worldwide. CgCREBL2, a key molecule in the regulation of gluconeogenesis, plays a critical role in the transcriptional regulation of PEPCK in gluconeogenesis against high-temperature stress. CgCREBL2 was able to increase the transcription of CgPEPCK by either binding the promoter of CgPEPCK gene or activating CgPGC-1α and CgHNF-4α after short-term (6 h) high-temperature stress, while only by binding CgPEPCK after long-term (60 h) high-temperature stress. These findings will further our understanding of the effect of marine thermal fluctuation on energy metabolism on marine organisms., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)
Published: 2024
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44. The phytoplankton community affects the energy metabolism and immunomodulation strategy of oyster during breeding seasons.

Author: Liu Z, Kong N, Zhang Y, Zheng Y, Yang C, Fu Q, Zhang Z, Li F, Liu R, Wang L, and Song L
Subjects: Animals, Phytoplankton immunology, Immunomodulation, Seasons, Immunity, Innate, Diatoms immunology, Aquaculture, Reproduction immunology, Crassostrea immunology, Crassostrea microbiology, Crassostrea genetics, Energy Metabolism
Abstract: The mass mortality of Pacific oyster Crassostrea gigas has become a severe ecological and economic concern to Chinese aquaculture, which is proposed to be linked to the phytoplankton community in the farming waters. In the present study, both field and laboratory experiments were conducted to identify the phytoplankton taxa associated with oyster mortality and explore the molecular mechanism by which they affect the physiological health of oysters. The field experiment showed that more serious mortality of oysters was observed in the North Yellow Sea from July to September in 2018 (average survival rate of 75.11 %) than in 2019 (average survival rate of 85.78 %), with the proportion of Bacillariophyta (diatoms) in the phytoplankton community in 2018 lower than that in 2019. In comparison to 2019, reduced dry weight, lower glycogen and triglyceride contents in hepatopancreas, lower 17β-estradiol and testosterone concentrations in gonad, as well as a generally weaker immune response against Vibrio splendidus stimulation were detected in the oysters sampled in 2018. The treatment of oysters with either starvation (starvation group) or Nitzschia closterium f. minutissima feeding (N. closterium group) was conducted to verify the field findings, with individuals reared in natural seawater as control. After 40 days of N. closterium feeding, dry weight, glycogen and triglyceride contents in hepatopancreas significantly increased, as well as the biosynthesis of sex hormones and gonadal maturation were promoted compared to the control and starvation groups. Moreover, a much stronger immune response against V. splendidus stimulation was observed in the oysters of N. closterium group, with the fold-changes of norepinephrine content in serum, SOD activity in hepatopancreas, and the mRNA expression level of IL17-5 and HSP70 in haemocytes higher than those in the control and starvation groups. Collectively, these results suggested that lack of diatoms in the farming waters suppressed the energy storage and gonadal maturation of adult oysters, and also resulted in a compromised immune response against bacterial infection, which may be a leading cause of the mass mortality of oysters living in diatom-deficient waters during breeding seasons., Competing Interests: Declaration of competing interest The authors declare no competing interests which may be perceived to influence the conduct or analysis of the data., (Copyright © 2024 Elsevier Ltd. All rights reserved.)
Published: 2024
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45. A novel lectin with a distinct Gal_Lectin and CUB domain mediates haemocyte phagocytosis in oyster Crassostrea gigas.

Author: Yang W, Sun J, Leng J, Li Y, Guo Q, Wang L, and Song L
Subjects: Animals, Mannans metabolism, Mannans immunology, Protein Domains genetics, Peptidoglycan immunology, Peptidoglycan metabolism, Galactose metabolism, Galactose immunology, Vibrio Infections immunology, Phagocytosis, Hemocytes immunology, Hemocytes metabolism, Crassostrea immunology, Vibrio immunology, Vibrio physiology, Immunity, Innate, Lectins metabolism, Lectins genetics, Lectins immunology
Abstract: Invertebrate lectins exhibit structural diversity and play crucial roles in the innate immune responses by recognizing and eliminating pathogens. In the present study, a novel lectin containing a Gal_Lectin, a CUB and a transmembrane domain was identified from the Pacific oyster Crassostrea gigas (defined as CgGal-CUB). CgGal-CUB mRNA was detectable in all the examined tissues with the highest expression in adductor muscle (11.00-fold of that in haemocytes, p < 0.05). The expression level of CgGal-CUB mRNA in haemocytes was significantly up-regulated at 3, 24, 48 and 72 h (8.37-fold, 12.13-fold, 4.28-fold and 10.14-fold of that in the control group, respectively) after Vibrio splendidus stimulation. The recombinant CgGal-CUB (rCgGal-CUB) displayed binding capability to Mannan (MAN), peptidoglycan (PGN), D-(+)-Galactose and L-Rhamnose monohydrate, as well as Gram-negative bacteria (Escherichia coli, V. splendidus and Vibrio anguillarum), Gram-positive bacteria (Micrococcus luteus, Staphylococcus aureus, and Bacillus sybtilis) and fungus (Pichia pastoris). rCgGal-CUB was also able to agglutinate V. splendidus, and inhibit V. splendidus growth. Furthermore, rCgGal-CUB exhibited the activities of enhancing the haemocyte phagocytosis towards V. splendidus, and the phagocytosis rate of haemocytes was descended in blockage assay with CgGal-CUB antibody. These results suggested that CgGal-CUB served as a pattern recognition receptor to bind various PAMPs and bacteria, and enhanced the haemocyte phagocytosis towards V. splendidus., (Copyright © 2024 Elsevier Ltd. All rights reserved.)
Published: 2024
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46. CgIκB2 negatively regulates the expression of interferon-like protein by Rel/NF-κB signal in Crassostrea gigas.

Author: Niu J, Wang S, Qiao X, Yu S, Yu Z, Jin Y, Huang M, Wang L, and Song L
Subjects: Animals, Immunity, Innate genetics, I-kappa B Proteins genetics, I-kappa B Proteins metabolism, Hemocytes immunology, Hemocytes metabolism, Crassostrea genetics, Crassostrea immunology, Signal Transduction, Poly I-C pharmacology, NF-kappa B genetics, NF-kappa B metabolism, Gene Expression Regulation immunology, Interferons genetics, Interferons immunology, Interferons metabolism
Abstract: Inhibitors of NF-κB (IκBs) have been implicated as major components of the Rel/NF-κB signaling pathway, playing an important negative regulatory role in host antiviral immunity such as in the activation of interferon (IFN) in vertebrates. In the present study, the immunomodulatory effect of IκB (CgIκB2) on the expression of interferon-like protein (CgIFNLP) was evaluated in Pacific oyster (Crassostrea gigas). After poly (I:C) stimulation, the mRNA expression level of CgIκB2 in haemocytes was significantly down-regulated at 3-12 h while up-regulated at 48-72 h. The mRNA expression of CgIκB2 in haemocytes was significantly up-regulated at 3 h after rCgIFNLP stimulation. In the CgIκB2-RNAi oysters, the mRNA expression of CgIFNLP, interferon regulatory factor-8 (CgIRF8) and NF-κB subunit (CgRel), the abundance of CgIFNLP and CgIRF8 protein in haemocytes, as well as the abundance of CgRel protein in nucleus were significantly increased after poly (I:C) stimulation. Immunofluorescence assay showed that nuclear translocation of CgIRF8 and CgRel protein was promoted in CgIκB2-RNAi oysters compared with that in EGFP-RNAi group. In the CgRel-RNAi oysters, the mRNA and protein expression level of CgIFNLP significantly down-regulated after poly (I:C) stimulation. The collective results indicated that CgIκB2 plays an important role in regulating CgIFNLP expression through its effects on Rel/NF-κB and IRF signaling pathways., Competing Interests: Declaration of competing interest The authors declare that they have no conflict of interests., (Copyright © 2024 Elsevier Ltd. All rights reserved.)
Published: 2024
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47. BmfR, a novel GntR family regulator, regulates biofilm formation in marine-derived, Bacillus methylotrophicus B-9987.

Author: Xu S, Liu Z, Ren P, Liu Y, Xiao F, and Li W
Subjects: Transcription Factors genetics, Transcription Factors metabolism, Polysaccharides, Bacterial metabolism, Aquatic Organisms genetics, Repressor Proteins genetics, Repressor Proteins metabolism, Biofilms growth & development, Gene Expression Regulation, Bacterial, Bacterial Proteins genetics, Bacterial Proteins metabolism, Bacillus genetics, Bacillus physiology, Bacillus metabolism
Abstract: Biofilms are common living states for microorganisms, allowing them to adapt to environmental changes. Numerous Bacillus strains can form complex biofilms that play crucial roles in biocontrol processes. However, our current understanding of the molecular mechanisms of biofilm formation in Bacillus is mainly based on studies of Bacillus subtilis. Knowledge regarding the biofilm formation of other Bacillus species remains limited. In this study, we identified a novel transcriptional regulator, BmfR, belonging to the GntR family, that regulates biofilm formation in marine-derived Bacillus methylotrophicus B-9987. We demonstrated that BmfR induces biofilm formation by activating the extracellular polysaccharide structural genes epsA-O and negatively regulating the matrix gene repressor, SinR; of note it positively affects the expression of the master regulator of sporulation, Spo0A. Furthermore, database mining for BmfR homologs has revealed their widespread distribution among many bacterial species, mainly Firmicutes and Proteobacteria. This study advances our understanding of the biofilm regulatory network of Bacillus strains, and provides a new target for exploiting and manipulating biofilm formation., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier GmbH.)
Published: 2024
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48. Calreticulin from Apostichopus japonicus relieves endoplasmic reticulum stress induced by Vibrio splendidus through autophagy.

Author: Liang W, Hu L, Dai F, Shi Y, Yang L, and Li C
Subjects: Animals, Gene Expression Regulation immunology, Amino Acid Sequence, Phylogeny, Gene Expression Profiling veterinary, Sequence Alignment veterinary, Immunity, Innate genetics, Calreticulin genetics, Calreticulin immunology, Vibrio physiology, Autophagy, Stichopus immunology, Stichopus genetics, Stichopus microbiology, Endoplasmic Reticulum Stress
Abstract: When organisms are exposed to external stimuli, misfolded proteins accumulate continuously, resulting in endoplasmic reticulum (ER) stress. Autophagy is of great significance for eliminating aggregated proteins and maintaining cellular homeostasis. However, the molecular mechanism of activating autophagy in response to ER stress in sea cucumber is remain unclear. In the current study, we demonstrated that the pathogen Vibrio splendidus can cause ER stress in Apostichopus japonicus coelomocytes and identified a Ca 2+ binding partner calreticulin (designated as AjCRT), which increased with the occurrence of ER stress. The nucleotide sequence analysis showed that the open reading frame of AjCRT was 1242 bp and encoded a 413-amino-acid residue polyprotein with calreticulin domains. The spatial expression analysis revealed that AjCRT was ubiquitously expressed in all examined tissues with large magnitude in the coelomocytes and was minimally expressed in muscle. Furthermore, silencing AjCRT in vivo could significantly exacerbate ER stress induced by V. splendidus and resulted in the signiﬁcant reduction of coelomocyte autophagy. These findings indicate a calreticulin-based mechanism that positively regulates autophagy in response to ER stress induced by pathogen infection. The results will provide a basis for understanding the way of host alleviating ER stress through autophagy, and pharmacological approaches may have potential for managing ER stress induced by pathogen and related cellular disorders., (Copyright © 2024 Elsevier Ltd. All rights reserved.)
Published: 2024
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49. Characterization of c-Jun N-terminal kinase (JNK) gene reveals involvement of immune defense against Vibrio splendidus infection in Apostichopus japonicus.

Author: Tao W, Xu W, Li X, Zhang X, Li C, and Guo M
Subjects: Animals, Sequence Alignment veterinary, Gene Expression Profiling veterinary, Base Sequence, Gene Expression Regulation immunology, Vibrio Infections immunology, Vibrio Infections veterinary, Stichopus immunology, Stichopus genetics, Stichopus microbiology, Vibrio physiology, Immunity, Innate genetics, Amino Acid Sequence, Phylogeny, JNK Mitogen-Activated Protein Kinases genetics, JNK Mitogen-Activated Protein Kinases immunology, JNK Mitogen-Activated Protein Kinases metabolism
Abstract: The c-Jun N-terminal kinase (JNK) constitutes an evolutionarily conserved family of serine/threonine protein kinases, pivotal in regulating various physiological processes in vertebrates, encompassing apoptosis and antibacterial immunity. Nevertheless, the involvement of JNK in the innate immune response remains largely unexplored in pathogen-induced echinoderms. We isolated and characterized the JNK gene from Apostichopus japonicus (AjJNK) in our investigation. The full-length cDNA sequences of AjJNK spanned 1806 bp, comprising a 1299 bp open reading frame (ORF) encoding 432 amino acids, a 274 bp 5'-untranslated region (UTR), and a 233 bp 3'-UTR. Structural analysis revealed the presence of a classical S_TKc domain (37-335 amino acids) within AjJNK and contains several putative immune-related transcription factor-binding sites, including Elk-1, NF-κB, AP-1, and STAT5. Spatial expression analysis indicated ubiquitous expression of AjJNK across all examined tissues, with the highest expression noted in coelomocytes. The mRNA, protein, and phosphorylation levels of AjJNK were obviously induced in coelomocytes upon V. splendidus challenge and lipopolysaccharide stimulation. Immunofluorescence analysis demonstrated predominant cytoplasmic localization of AjJNK in coelomocytes with subsequent nuclear translocation following the V. splendidus challenge in vivo. Moreover, siRNA-mediated knockdown of AjJNK led to a significant increase in intracellular bacterial load, as well as elevated levels of Ajcaspase 3 and coelomocyte apoptosis post V. splendidus infection. Furthermore, the phosphorylation levels of AjJNK inhibited by its specific inhibitor SP600125 and also significantly suppressed the expression of Ajcaspase 3 and coelomocyte apoptosis during pathogen infection. Collectively, these data underscored the pivotal role of AjJNK in immune defense, specifically in the regulation of coelomocyte apoptosis in V. splendidus-challenged A. japonicus., (Copyright © 2024 Elsevier Ltd. All rights reserved.)
Published: 2024
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50. Norepinephrine regulates TNF expression via the A1AR-p38 MAPK-Relish pathway in granulocytes of oyster Crassostrea gigas.

Author: Liu Z, Wang W, Zong Y, Li M, Gao Y, Xin X, Zhu T, Wang L, and Song L
Subjects: Animals, Apoptosis, Signal Transduction, Phagocytosis, Cells, Cultured, Tumor Necrosis Factor-alpha metabolism, Gene Expression Regulation, MAP Kinase Signaling System immunology, Tumor Necrosis Factors metabolism, Tumor Necrosis Factors genetics, Crassostrea immunology, Norepinephrine metabolism, Norepinephrine pharmacology, Granulocytes immunology, Granulocytes metabolism, p38 Mitogen-Activated Protein Kinases metabolism, Immunity, Innate, Lipopolysaccharides immunology
Abstract: Norepinephrine (NE) is involved in regulating cytokine expression and phagocytosis of immune cells in the innate immunity of vertebrates. In the present study, the modulation mechanism of NE on the biosynthesis of TNFs in oyster granulocytes was explored. The transcripts of CgTNF-1, CgTNF-2 and CgTNF-3 were highly expressed in granulocytes, and they were significantly up-regulated after LPS stimulation, while down-regulated after NE treatment. The phagocytic rate and apoptosis index of oyster granulocytes were also triggered by LPS stimulation and suppressed by NE treatment. The mRNA expressions of CgMAPK14 and CgRelish were significantly induced after NE treatment, and the translocation of CgRelish from cytoplasm to nucleus was observed. The concentration of intracellular Ca 2+ in granulocytes was significantly up-regulated upon NE incubation, and this trend reverted after the treatment with DOX (specific antagonist for NE receptor, CgA1AR-1). No obvious significance was observed in intracellular cAMP concentrations in the PBS, NE and NE + DOX groups. Once CgA1AR-1 was blocked by DOX, the mRNA expressions of CgMAPK14 and CgRelish were significantly inhibited, and the translocation of CgRelish from cytoplasm to nucleus was also dramatically suppressed, while the mRNA expression of CgTNF-1 and the apoptosis index increased significantly to the same level with those in LPS group, respectively. These results collectively suggested that NE modulated TNF expression in oyster granulocyte through A1AR-p38 MAPK-Relish signaling pathway., (Copyright © 2024 Elsevier Ltd. All rights reserved.)
Published: 2024
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