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Microbially-mediated formation of Ca-Fe carbonates during dissimilatory ferrihydrite reduction:Implications for the origin of sedimentary ankerite

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Science China Earth Sciences 2024年第1期67卷 208-221页

作者： Deng LIU Jinpeng CAO Shanshan YANG Yating YIN Pengcong wang Dominic PAPINEAU Hongmei wang Xuan QIU Genming LUO Zongmin ZHU fengping wang State Key Laboratory of Biogeology and Environmental Geology China University of GeosciencesWuhan 430074China School of Environmental Studies China University of GeosciencesWuhan 430074China London Centre for Nanotechnology University College LondonLondon WC1H 0AHUK Department of Earth Sciences University College LondonLondon WC1E 6BTUK Center for Planetary Sciences University College London and Birkbeck College LondonLondon WC1E 6BTUK State Key Laboratory of Microbial Metabolism State Key Laboratory of Ocean EngineeringShanghai Jiao Tong UniversityShanghai 200240China

The origin of sedimentary dolomite has become a long-standing problem in the Earth *** carbonate minerals like ankerite have the same crystal structure as dolomite,hence their genesis may provide clues to help solving the dolomite *** purpose of this study was to probe whether microbial activity can be involved in the formation of ***-carbonation experiments associated with microbial iron reduction were performed in batch systems with various concentrations of Ca^(2+)(0–20 mmol/L),with a marine iron-reducing bacterium Shewanella piezotolerans WP3 as the reaction mediator,and with lactate and ferrihydrite as the respective electron donor and *** biomineralization data showed that Ca-amendments expedited microbially-mediated ferrihydrite reduction by enhancing the adhesion between WP3 cells and ferrihydrite *** bioreduction,siderite occurred as the principal secondary mineral in the Ca-free ***,Ca-Fe carbonates were formed when Ca^(2+)ions were *** CaCO_(3) content of microbially-induced Ca-Fe carbonates was positively correlated with the initial Ca2+*** Ca-Fe carbonate phase produced in the 20 mmol/L Ca-amended biosystems had a chemical formula of Ca_(0.8)Fe_(1.2)(CO_(3))_(2),which is close to the theoretical composition of *** ankeritelike phase was nanometric in size and spherical,Ca-Fe disordered,and structurally *** simulated diagenesis experiments further demonstrated that the resulting ankerite-like phase could be converted into ordered ankerite under hydrothermal *** introduced the term“proto-ankerite”to define the Ca-Fe phases that possess near-ankerite stoichiometry but disordered cation *** the basis of the present study,we proposed herein that microbial activity is an important contributor to the genesis of sedimentary ankerite by providing the metastable Ca-Fe carbonate precursors.

关键词： Ankerite Proto-ankerite Microbial iron reduction Dolomite problem Mineral transformation

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Why and how to use the SeqCode

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mLife 2024年第1期3卷 1-13页

作者： Wiliam B.Whitman Maria Chuvochina Brian P.Hedlund Konstantinos T.Konstantinidis Marike Palmer Luis M.Rodriguez-R lain Sutcliffe fengping wang Deparment of Microbioogy University of GeorgiaAthensGeorgiaUAA Schoolof Chemistry and Molecular Biosciences Australian CentreforEogenomicsThe Universty of QueenslandSt LuciaAustralia University of Nevada Las Vegas Las VegasNevadaUSA Schol of Civil and Environmental Engineering and School of Biological SciencesGeorgia Institute of TechnologyAtlantaGeorgiaUSA Department of Microbiology University of ManitobaWinnipegManitobaCanada School of Life Sciences University of Nevada Las VegasLas VegasNevadaUSA Department of Microbiology and Digital Science Center(DiSC) University of InnsbruckInnsbruckAustria Faculty of Health&Life Sciences Northumbria UniversityNewcastle upon TyneUK School of Oceanography International Center for Deep Life InvestigationShanghai Jiao Tong UniversityShanghaiChina

The SeqCode,formally called the Code of Nomenclature of Prokaryotes Described from Sequence Data,is a new code of nomenclature in which genome sequences are the nomenclatural types for the names of prokaryotic *** similar to the International Code of Nomenclature of Prokaryotes(ICNP)in structure and rules of priority,it does not require the deposition of type strains in international culture ***,it allows for the formation of permanent names for uncultured prokaryotes whose nearly complete genome sequences have been obtained directly from environmental DNA as well as other prokaryotes that cannot be deposited in culture *** the diversity of uncultured prokaryotes greatly exceeds that of readily culturable prokaryotes,the SeqCode is the only code suitable for naming the majority of prokaryotic *** start date of the SeqCode was January 1,2022,and the online Registry(https://***)was created to ensure valid publication of *** SeqCode recognizes all names validly published under the ICNP before *** that date,names validly published under the SeqCode compete with ICNP names for *** a result,species can have only one name,either from the SeqCode or ICNP,enabling effective communication and the creation of unified taxonomies of uncultured and cultured *** SeqCode is administered by the SeqCode Committee,which is comprised of the SeqCode Community and elected administrative *** with an interest in the systematics of prokaryotes is encouraged to join the SeqCode Community and participate in the development of this resource.

关键词： genome sequences metagenome-assembled genomes nomenclature SeqCode

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大跨径斜拉桥施工阶段临时抗风措施对比分析

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铁道工程学报 2024年第1期41卷 39-44,52页

作者：刘旭政曾健峰王丰平华东交通大学轨道交通基础设施性能监测与保障国家重点实验室南昌330013 中国市政工程中南设计研究总院有限公司武汉430010 浙江数智交院科技股份有限公司杭州310006

研究目的:大跨径斜拉桥在最大双悬臂施工状态下结构刚度较小,对风荷载引起的结构风致振动响应较为敏感。本文以受沿海台风影响区域的一座主跨316 m斜拉桥为研究对象,根据风洞试验确定主梁的气动三分力系数,对比分析不同风缆布置方案与... 详细信息

研究目的:大跨径斜拉桥在最大双悬臂施工状态下结构刚度较小,对风荷载引起的结构风致振动响应较为敏感。本文以受沿海台风影响区域的一座主跨316 m斜拉桥为研究对象,根据风洞试验确定主梁的气动三分力系数,对比分析不同风缆布置方案与不同临时墩布置方式对大桥风致响应控制效果的影响。研究结论:(1)增设临时风缆可使主梁竖弯基频提高22.0%~32.5%,对结构自身的扭转基频影响效果不显著;临时风缆对主梁竖向位移和主塔顺桥向位移控制有一定作用,固定位置在主梁最大悬臂长度的80%~90%范围内效果较好;(2)临时墩的抗风减振效果显著优于临时风缆,临时墩的设置使主梁悬臂端竖向位移响应降低了53.5%~65.5%,对主梁悬臂根部的顺桥向弯矩与横桥向弯矩的控制效果较为明显,降幅11.7%~58.8%;(3)在选择桥梁临时抗风措施时,需综合考虑抗风需求、施工条件、施工风险和经济性;(4)本研究成果可为大跨度斜拉桥临时抗风措施的选择提供参考。

关键词：斜拉桥最大双悬臂施工状态临时墩临时风缆风致响应

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Determination of carbon-fixing potential of Bathyarchaeota in marine sediment by DNA stable isotope probing analysis

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Science China Earth Sciences 2023年第4期66卷 910-917页

作者： Wenyue LIANG Tiantian YU Liang DONG Zhongjun JIA fengping wang State Key Laboratory of Microbial Metabolism School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai 200240China School of Oceanography Shanghai Jiao Tong UniversityShanghai 200240China State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil ScienceChinese Academy of SciencesNanjing 210008China

Bathyarchaeota is believed to play a crucial role in the global carbon cycle due to its vast biomass,broad distribution,and diverse ***,its physiological and metabolic features are hard to determine without pure *** metagenomic analyses have shown that Bathyarchaeota has a complete inorganic carbon fixation(Wood-Ljungdahl,WL)pathway,no direct functional confirmation has been *** explore the inorganic carbon fixation ability of Bathyarchaeota,we used lignin and sodium bicarbonate-^(13)C(NaH^(13)CO_(3))in the long-term incubation of marine sediment *** found that Bathyarchaeota grew continuously in the cultivation system with lignin,and its abundance increased up to 15.3 times after10 months,increasing its fraction of all archaea from 30%to 80%.We monitored theδ^(13)C of total organic carbon to identify microbial carbon fixation in the cultivation systems,finding that it increased in the first month while NaH^(13)CO_(3)was present but only increased continuously afterward when lignin was also ***,ultracentrifugation was performed on DNA extracted from samples at different cultivation stages to separate DNA of different buoyant densities,and bathyarchaeotal and bacterial 16S ribosomal RNA(r RNA)gene abundance were quantified using *** to bacteria,bathyarchaeotal 16S rRNA tended to be concentrated in heavy layers after 4 months of incubation with lignin and NaH^(13)CO_(3),indicating that Bathyarchaeota DNA contained^(13)C through proliferation based on lignin utilization and NaH^(13)CO_(3)assimilation,proving the carbon fixation capacity of Bathyarchaeota.

关键词： Bathyarchaeota Reductive acetyl-CoA pathway Carbon fixation DNA-SIP

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Refractory humic-like dissolved organic matter fuels microbial communities in deep energy-limiting marine sediments

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Science China Earth Sciences 2023年第8期66卷 1738-1756页

作者： Yunru CHEN Weikang SUI Jing wang Ding HE Liang DONG Joanna JWANIEK fengping wang State Key Laboratory of Microbial Metabolism School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai 200240China School of Oceanography Shanghai Jiao Tong UniversityShanghai 200240China Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai) Zhuhai 519000China Department of Ocean Science and the Southern Marine Science and Engineering Guangdong Laboratory(Guangzhou) The Hong Kong University of Science and TechnologyHong Kong 999077China School of Earth Sciences Zhejiang UniversityHangzhou 310027China Leibniz Institute for Baltic Sea Research WarnemündeRostock 18119Germany

Humic-like dissolved organic matter(DOM),usually regarded as refractory,is a major component of DOM in marine sediment pore ***,its bio-reactivity remains poorly explored in natural environments,which makes its roles in supporting subsurface microbial communities and regulating long-term carbon cycling ***,the bio-reactivity of humiclike DOM was evaluated by modeled reaction rates together with its interactions with microbial communities in five sediment cores collected from the eutrophic Pearl River Estuary to the oligotrophic deep-sea basin in the northern South China *** revealed contrasting relationships between humic-like DOM and microbes in the coastal and deep-sea *** eutrophic coastal sediments,specific microbial groups enriched in the deep layers co-varied with humic-like DOM,while most microbial groups were significantly correlated with protein-like DOM,microbial transformation of which likely resulted in the production of humic-like *** the contrary,in energy-limiting deep-sea sediments,over 70%of the microbial groups were found closely correlated with humic-like DOM,a net consumption of which was demonstrated in deep *** consumption of humic-like DOM in deep-sea sediments reduced its total production flux in the uppermost~5-meter layer to about one-tenth of that in coastal sediments,which could consequently decrease the refractory DOM flux to the overlying seawater and influence long-term oceanic carbon cycling.

关键词： Fluorescent dissolved organic matter Subsurface microbial communities Marine sediments Microbial transformation Oceanic carbon cycling

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Expanding Asgard members in the domain of Archaea sheds new light on the origin of eukaryotes

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Science China(Life Sciences) 2022年第4期65卷 818-829页

作者： Ruize Xie Yinzhao wang Danyue Huang Jialin Hou Liuyang Li Haining Hu Xiaoxiao Zhao fengping wang School of Oceanography Shanghai Jiao Tong UniversityShanghai200030China State Key Laboratory of Microbial Metabolism School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai200240China Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai) Zhuhai519082China

The hypothesis that eukaryotes originated from within the domain Archaea has been strongly supported by recent phylogenomic analyses placing Heimdallarchaeota-Wukongarchaeota branch from the Asgard superphylum as the closest known archaeal sister-group to eukaryotes. However, our understanding is still limited in terms of the relationship between eukaryotes and archaea, as well as the evolution and ecological functions of the Asgard archaea. Here, we describe three previously unknown phylum-level Asgard archaeal lineages, tentatively named Sigyn-, Freyr-and Njordarchaeota. Additional members in Wukongarchaeota and Baldrarchaeota from distinct environments are also reported here, further expanding their ecological roles and metabolic capacities. Comprehensive phylogenomic analyses further supported the origin of eukaryotes within Asgard archaea and a new lineage Njordarchaeota was supposed as the known closest branch with the eukaryotic nuclear host lineage. Metabolic reconstruction suggests that Njordarchaeota may have a heterotrophic lifestyle with capability of peptides and amino acids utilization, while Sigynarchaeota and Freyrarchaeota also have the potentials to fix inorganic carbon via the Wood-Ljungdahl pathway and degrade organic matters. Additionally, the Ack/Pta pathway for homoacetogenesis and de novo anaerobic cobalamin biosynthesis pathway were found in Freyrarchaeota and Wukongrarchaeota,respectively. Some previously unidentified eukaryotic signature proteins for intracellular membrane trafficking system, and the homologue of mu/sigma subunit of adaptor protein complex, were identified in Freyrarchaeota. This study expands the Asgard superphylum, sheds new light on the evolution of eukaryotes and improves our understanding of ecological functions of the Asgard archaea.

关键词： Asgard archaea eukaryotic origin metagenome

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Widespread Bathyarchaeia encode a novel methyltransferase utilizing lignin-derived aromatics

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mLife 2023年第3期2卷 272-282页

作者： Tiantian Yu Haining Hu Xianhong Zeng Yinzhao wang Donald Pan Longhui Deng Lewen Liang Jialin Hou fengping wang School of Oceanography Shanghai Jiao Tong UniversityShanghaiChina State Key Laboratory of Microbial Metabolism School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai)ZhuhaiChina

Lignin degradation is a major process in the global carbon cycle across both terrestrial and marine ***,which are among the most abundant microorganisms in marine sediment,have been proposed to mediate anaerobic lignin ***,the mechanism of bathyarchaeial lignin degradation remains ***,we report an enrichment culture of Bathy-archaeia,named Candidatus Baizosediminiarchaeum ligniniphilus DL1YTT001(***),from coastal sediments that can grow with lignin as the sole organic carbon source under mesophilic anoxic *** possesses and highly expresses novel methyltransferase 1(MT1,mtgB)for transferring methoxyl groups from lignin monomers to cob(I)*** have no homology with known microbial methyltransferases and are present only in bathyarchaeial *** expression of the mtgB gene confirmed O-demethylation *** mtgB genes were identified in metagenomic data sets from a wide range of coastal sediments,and they were highly expressed in coastal sediments from the East China *** findings suggest that Bathyarchaeia,capable of O-demethylation via their novel and specific methyltransferases,are ubiquitous in coastal sediments.

关键词： Bathyarchaeia coastal sediments lignin-degrading lignin-derived aromatics specific methyltransferase

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Nonlinear Impact Damage Evolution of Charpy Type and Analysis of Its Key Influencing Factors

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Chinese Journal of Mechanical Engineering 2024年第1期37卷 254-264页

作者： Jianfeng Mao Qian Xu Jiadong Yang Chi Cao Dasheng wang fengping Zhong Mingya Chen Institute of Process Equipment and Control Engineering Zhejiang University of TechnologyHangzhou 310032China Taizhou Key Laboratory of Advanced Manufacturing Technology Taizhou InstituteZhejiang University of TechnologyTaizhou 318014China State Key Laboratory of Nuclear Power Safety Monitoring Technology and Equipment Shenzhen 518172China Zhejiang Academy of Special Equipment Science Hangzhou 310020China Suzhou Nuclear Power Research Institute Suzhou 215004China

The current research of Charpy impact mainly focuses on obtaining the ductile brittle transition temperature of materials by *** with experiments,numerical simulation can study many problems with harsh ***,there are still few studies on the influence of geometric factors such as side *** this paper,the geometry of standard Charpy impact test is *** with different widths and side grooves are *** finite element model of Charpy impact was established by ABAQUS *** test results and simulation results to verify each *** effects of sample width,side groove depth and side groove bottom fillet on the impact fracture resistance of the sample were *** results show that the specimen width is positively correlated with the impact toughness of the *** side groove greatly reduces the impact toughness of the material;the toughness of side groove decreases with the increase of depth;the fracture toughness of side groove decreases with the increase of fillet at the bottom of side *** proportion of toughness energy to impact energy of samples was *** results show that the toughness energy accounts for about 70%of the impact energy of the sample,which has little to do with the geometric characteristics of the *** study presents a reliable method for studying Charpy impact *** influence of geometric parameters is obtained,which provides a reference method for the study of impact toughness of high toughness materials.

关键词： Johnson-Cook model Impact toughness Charpy impact

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Methane biotransformation in the ocean and its effects on climate change: A review

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Science China Earth Sciences 2018年第12期61卷 1697-1713页

作者： Mingyang NIU Wenyue LIANG fengping wang State Key Laboratory of Microbial Metabolism School of Life Sciences and Biotechnology Shanghai Jiao Tong University State Key Laboratory of Ocean Engineering School of Naval Architecture Ocean and Civil Engineering Shanghai Jiao Tong University

Methane is a potent greenhouse gas. Continental margins contain large reservoirs of methane as solid gas hydrate and the dissolved and gaseous forms of methane. Submarine methane seeps along the global continental margins, including the coastal seas, have been estimated to contribute 0.01 to 0.05 Gt of carbon to the atmosphere annually, accounting for between 1%and 5% of the global methane emissions to the atmosphere. Much of this methane is exhausted via microbial anaerobic methane oxidation. Methane biotransformation in the ocean has effects on global climate change. This review mainly introduces the mechanisms of methanogenesis and methane oxidation and describes new findings that will provide information that will improve the understanding of the balance in terms of the generation, migration and consumption of methane in marine environments. Moreover, this review provides new insights into methane biogeochemical cycles and the effects of marine methane budgets on global climate.

关键词： Methane production Methane oxidization Marine Sediment Climate

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Metal-dependent anaerobic methane oxidation in marine sediment:insights from marine settings and other systems

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Science China(Life Sciences) 2019年第10期62卷 1287-1295页

作者： Lewen Liang Yinzhao wang Orit Sivan fengping wang State Key Laboratory of Microbial Metabolism School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai 200240 China Joint International Research Laboratory of Metabolic & Developmental Sciences Shanghai Jiao Tong UniversityShanghai 200240China Department of Geological and Environmental Sciences Ben-Gurion University of the NegevBeer-Sheva 84105Israel

Anaerobic oxidation of methane(AOM) plays a crucial role in controlling global methane emission. This is a microbial process that relies on the reduction of external electron acceptors such as sulfate, nitrate/nitrite, and transient metal ions. In marine settings, the dominant electron acceptor for AOM is sulfate, while other known electron acceptors are transient metal ions such as iron and manganese oxides. Despite the AOM process coupled with sulfate reduction being relatively well characterized,researches on metal-dependent AOM process are few, and no microorganism has to date been identified as being responsible for this reaction in natural marine environments. In this review, geochemical evidences of metal-dependent AOM from sediment cores in various marine environments are summarized. Studies have showed that iron and manganese are reduced in accordance with methane oxidation in seeps or diffusive profiles below the methanogenesis zone. The potential biochemical basis and mechanisms for metal-dependent AOM processes are here presented and discussed. Future research will shed light on the microbes involved in this process and also on the molecular basis of the electron transfer between these microbes and metals in natural marine environments.

关键词： anaerobic methane oxidation metal-AOM marine sediment archaea electron transfer

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