- 作 者: ( "huahua jian" OR "hua-hua jian" )
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Reconstruction and Analysis of Thermodynamically Constrained Models Reveal Metabolic Responses of a Deep-Sea Bacterium to Temperature PerturbationsmSystems (IF 7.324) Pub Date : 2022-08-11 ,DOI:10.1128/msystems.00588-22Keith Dufault-Thompson, Chang Nie, Huahua Jian, Fengping Wang, Ying Zhang aDepartment of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Islandgrid.20431.34, Kingston, Rhode Island, USA bState Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai
mSystems, Ahead of Print.
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Reconstruction and analysis of thermodynamically-constrained models reveal metabolic responses of a deep-sea bacterium to temperature perturbationsbioRxiv - Systems Biology Pub Date : 2022-07-02 ,DOI:10.1101/2022.07.01.498526Keith Dufault-Thompson, Chang Nie, Huahua Jian, Fengping Wang, Ying Zhang
Microbial acclimation to different temperature conditions can involve broad changes in cell composition and metabolic efficiency. A systems-level view of these metabolic responses in non-mesophilic organisms, however, is currently missing. In this study, thermodynamically-constrained genome-scale models were applied to simulate the metabolic responses of a deep-sea psychrophilic bacterium, Shewanella
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A novel inovirus reprograms metabolism and motility of marine AlteromonasbioRxiv - Microbiology Pub Date : 2022-06-23 ,DOI:10.1101/2022.06.23.497286Kuntong Jia, Yongyi Peng, Xueji Chen, Huahua Jian, Min Jin, Zhiwei Yi, Ming Su, Xiyang Dong, Meisheng Yi
Members from the Inoviridae family with striking features are widespread, highly diverse and ecologically pervasive across multiple hosts and environments; however, very small amount of inoviruses have been isolated and studied. Here, a filamentous phage infecting Alteromonas abrolhosensis, designated ΦAFP1, was isolated from the South China Sea and represented as a novel genus of Inoviridae. ΦAFP1
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Composition and Ecological Roles of the Core Microbiome along the Abyssal-Hadal Transition Zone Sediments of the Mariana Trench.Microbiology Spectrum Pub Date : 2022-06-07 ,DOI:10.1128/spectrum.01988-21Hongmei Jing,Xiang Xiao,Yue Zhang,Zhiyong Li,Huahua Jian,Yingfeng Luo,Zhuang Han
The unique geological features of hadal trenches are known to influence both the structure and ecological function of microbial communities. It is also well known that heterotrophs and chemoautotrophs dominate the hadal and abyssal pelagic zones, respectively. Here, a metagenomic investigation was conducted on sediment samples obtained from the abyssal-hadal transition zone in the Mariana Trench to
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The effects of metabolism and temperature on carbon isotope composition of lipids in marine bacterium Shewanella piezotolerans WP3Chemical Geology (IF 4.685) Pub Date : 2022-06-02 ,DOI:10.1016/j.chemgeo.2022.120963Xin Chen, Liang Dong, Weishu Zhao, Huahua Jian, Jing Wang, Fengping WangThe carbon isotope composition of lipids has been widely used to decode the biogeochemical cycle and reconstruct paleo-environment and paleo-ecological changes over geologic time. However, up to now, little is known about the controls on the carbon isotope signatures of heterotrophic microbes with ecological functions in the ocean. Here, we investigate the carbon isotope fractionation between fatty ...
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Oxidative Stress and Autophagy Are Important Processes in Post Ripeness and Brown Film Formation in Mycelium of Lentinula edodesFrontiers in Microbiology (IF 6.064) Pub Date : 2022-02-24 ,DOI:10.3389/fmicb.2022.811673Lihua Tang, Ting Chu, Junjun Shang, Ruiheng Yang, Chunyan Song, Dapeng Bao, Qi Tan, Huahua Jian
Lentinula edodes (Berk.) Pegler, the shiitake mushroom, is one of the most important mushrooms in the global mushroom industry. Although mycelium post ripeness and brown film (BF) formation are crucial for fruiting body initiation, the underlying molecular mechanisms of BF formation are largely unknown. In this study, proteomic quantification (relative and absolute) and metabolomic profiling of L.
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Transcriptomic Analysis Reveals that Changes in Gene Expression Contribute to Microbacterium sediminis YLB-01 Adaptation at Low Temperature Under High Hydrostatic PressureCurrent Microbiology (IF 2.343) Pub Date : 2022-02-12 ,DOI:10.1007/s00284-022-02786-9Xu Qiu, Xiaorong Cao, Huahua Jian, Huangming Wu, Guangxin Xu, Xixiang TangMicrobes living in extreme environments often adopt strategies for survival, however, only a few studies have examined the adaptive mechanism of deep-sea bacteria in in-situ environments. In this study, transcriptomic data of the deep-sea piezotolerant and psychrotolerant actinomycete Microbacterium sediminis YLB-01 under the conditions of NPNT (normal temperature and pressure: 28 °C, 0.1 MPa), HPNT ...
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Isolation and characterization of a novel linear-plasmid phage from the sediment of the Mariana TrenchVirologica Sinica (IF 6.947) Pub Date : 2022-01-28 ,DOI:10.1016/j.virs.2022.01.022Yali Hao, Siyuan Wang, Mujie Zhang, Qingxue Tang, Canxing Meng, Liping Wang, Qilian Fan, Yaxian Yan, Xiang Xiao, Huahua Jian
Abstract not available
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Novel Viral Communities Potentially Assisting in Carbon, Nitrogen, and Sulfur Metabolism in the Upper Slope Sediments of Mariana TrenchmSystems (IF 7.324) Pub Date : 2022-01-04 ,DOI:10.1128/msystems.01358-21Jiulong Zhao, Hongmei Jing, Zengmeng Wang, Long Wang, Huahua Jian, Rui Zhang, Xiang Xiao, Feng Chen, Nianzhi Jiao, Yongyu Zhang
The Mariana Trench harbors a substantial number of infective viral particles. However, very little is known about the identity, survival strategy, and potential functions of viruses in the trench sediments.
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The origin and impeded dissemination of the DNA phosphorothioation system in prokaryotesNature Communications (IF 17.694) Pub Date : 2021-11-04 ,DOI:10.1038/s41467-021-26636-7Huahua Jian, Guanpeng Xu, Yi Yi, Yali Hao, Yinzhao Wang, Lei Xiong, Siyuan Wang, Shunzhang Liu, Canxing Meng, Jiahua Wang, Yue Zhang, Chao Chen, Xiaoyuan Feng, Haiwei Luo, Hao Zhang, Xingguo Zhang, Lianrong Wang, Zhijun Wang, Zixin Deng, Xiang Xiao
Phosphorothioate (PT) modification by the dnd gene cluster is the first identified DNA backbone modification and constitute an epigenetic system with multiple functions, including antioxidant ability, restriction modification, and virus resistance. Despite these advantages for hosting dnd systems, they are surprisingly distributed sporadically among contemporary prokaryotic genomes. To address this
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Characterization of two novel psychrophilic and piezotolerant strains, Shewanella psychropiezotolerans sp. nov. and Shewanella eurypsychrophilus sp. nov, adapted to an extreme deep-sea environmentSystematic and Applied Microbiology (IF 4.064) Pub Date : 2021-09-24 ,DOI:10.1016/j.syapm.2021.126266Libo Yu, Huahua Jian, Yingbao Gai, Zhiwei Yi, Ying Feng, Xu Qiu, Zongze Shao, Xixiang TangThree marine bacterial strains designated YLB-06T, YLB-08T and YLB-09 were isolated under high hydrostatic pressure from deep-sea sediment samples collected from the Southwest Indian Ocean. They were Gram-stain-negative, oxidase- and catalase-positive, facultative anaerobic and motile. In addition, the strains were capable of growing at 0–20 °C (optimum 4–10 °C) and 0.1–40 MPa (optimum 0.1 MPa), were ...
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Diversity and distribution of viruses inhabiting the deepest ocean on EarthThe ISME Journal (IF 11.217) Pub Date : 2021-05-10 ,DOI:10.1038/s41396-021-00994-yHuahua Jian, Yi Yi, Jiahua Wang, Yali Hao, Mujie Zhang, Siyuan Wang, Canxing Meng, Yue Zhang, Hongmei Jing, Yinzhao Wang, Xiang XiaoAs the most abundant biological entities on the planet, viruses significantly influence the overall functioning of marine ecosystems. The abundance, distribution, and biodiversity of viral communities in the upper ocean have been relatively well studied, but our understanding of viruses in the hadal biosphere remains poor. Here, we established the oceanic trench viral genome dataset (OTVGD) by analysing ...
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Genomic analysis of Microbacterium sediminis YLB-01T reveals backgrounds related to its deep-sea environment adaptationMarine Genomics (IF 2.143) Pub Date : 2020-09-15 ,DOI:10.1016/j.margen.2020.100818Zhiwei Yi, Xiaorong Cao, Hong Li, Huahua Jian, Xiashutong Xu, Libo Yu, Xixiang TangMicrobacterium sediminis YLB-01T, a piezotolerant and psychrotolerant actinomycete, was isolated from deep-sea sediment of the South-West Indian Ocean and could be a good model for understanding the adaptation of extremophiles to the benthic piezosphere. Here, we report the analysis of the complete genome sequence of strain YLB-01T. The genome sequence consists of a single circular chromosome comprising ...
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Cross-Stress Adaptation in a Piezophilic and Hyperthermophilic Archaeon From Deep Sea Hydrothermal VentFrontiers in Microbiology (IF 6.064) Pub Date : 2020-08-07 ,DOI:10.3389/fmicb.2020.02081Weishu Zhao, Xiaopan Ma, Xiaoxia Liu, Huahua Jian, Yu Zhang, Xiang Xiao
Hyperthermophiles, living in environments above 80°C and usually coupling with multi-extreme environmental stresses, have drawn great attention due to their application potential in biotechnology and being the primitive extant forms of life. Studies on their survival and adaptation mechanisms have extended our understanding on how lives thrive under extreme conditions. During these studies, the “cross-stress”
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Phylogenomic analysis reveals a two‐stage process of the evolutionary transition of Shewanella from the upper ocean to the hadal zoneEnvironmental Microbiology (IF 5.476) Pub Date : 2020-07-13 ,DOI:10.1111/1462-2920.15162Xixiang Tang, Libo Yu, Yi Yi, Jiahua Wang, Siyuan Wang, Canxing Meng, Shunzhang Liu, Yali Hao, Yue Zhang, Xiaorong Cao, Huahua Jian, Xiang XiaoShewanella strains are characterized by versatile metabolic capabilities, resulting in their wide distribution in the ocean at different depths. Considering that particle sedimentation is an important dynamic process in the ocean, we hypothesized that hadal Shewanella species evolved from the upper ocean. In this study, we isolated three novel Shewanella strains from deep‐sea sediments in the Southwest ...
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Genomic analysis of Brevundimonas mediterranea D151-2-6 isolated from hadal sediment of the Pacific Ocean.Marine Genomics (IF 2.143) Pub Date : 2020-06-16 ,DOI:10.1016/j.margen.2020.100787Siyuan Wang,Libo Yu,Xiaoli Tan,Xiaorong Cao,Xixiang Tang,Huahua JianBrevundimonas mediterranea D151-2-6 is a marine bacterium that has been isolated from 6582-m hadal sediment of the Pacific Ocean. Here, we present the complete genome sequence of B. mediterranea D151-2-6. The genome of strain D151-2-6 is 3,383,373 base pairs in size. It contains one circular chromosome with an average G + C content of 67.41%, 53 tRNAs, and 3270 protein-coding genes. Genomic analysis ...
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The thermo-regulated genetic switch of deep-sea filamentous phage SW1 and its distribution in the Pacific Ocean.FEMS Microbiology Letters (IF 2.82) Pub Date : 2020-06-08 ,DOI:10.1093/femsle/fnaa094Canxing Meng,Site Li,Qilian Fan,Rouke Chen,Yang Hu,Xiang Xiao,Huahua JianViruses, especially bacteriophages are thought to have important functions in the deep-sea ecosystem, but little is known about the induction mechanism of benthic phages towards environmental change. Our prior work characterized a cold-active filamentous phage SW1 which infects the deep-sea bacterium Shewanella piezotolerans WP3; however, the underlying mechanism of this putative thermo-regulated genetic ...
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Multiple Mechanisms Are Involved in Repression of Filamentous Phage SW1 Transcription by the DNA-Binding Protein FpsRJournal of Molecular Biology (IF 6.151) Pub Date : 2019-02-07 ,DOI:10.1016/j.jmb.2019.01.040Huahua Jian,Guanpeng Xu,Shunzhang Liu,Yali Hao,Canxing Meng,Jianrong Xu,Yue Zhang,Xipeng Liu,Xiang XiaoSW1 is the first filamentous phage isolated from a deep-sea environment. Nevertheless, the mechanism by which the SW1 genetic switch is controlled is largely unknown. In this study, the function of the phage-encoded FpsR protein was characterized by molecular biological and biochemical analyses. The deletion of fpsR increased the copy number of SW1 ssDNA and mRNA, indicating that FpsR functions as ...
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Pressure-Regulated Gene Expression and Enzymatic Activity of the Two Periplasmic Nitrate Reductases in the Deep-Sea Bacterium Shewanella piezotolerans WP3.Frontiers in Microbiology (IF 6.064) Pub Date : 2019-01-10 ,DOI:10.3389/fmicb.2018.03173Xue-Gong Li,Wei-Jia Zhang,Xiang Xiao,Hua-Hua Jian,Ting Jiang,Hong-Zhi Tang,Xiao-Qing Qi,Long-Fei Wu
Shewanella species are widely distributed in marine environments, from the shallow coasts to the deepest sea bottom. Most Shewanella species possess two isoforms of periplasmic nitrate reductases (NAP-α and NAP-β) and are able to generate energy through nitrate reduction. However, the contributions of the two NAP systems to bacterial deep-sea adaptation remain unclear. In this study, we found that
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Validation of reference genes for reverse transcription real-time quantitative PCR analysis in the deep-sea bacterium Shewanella psychrophila WP2.FEMS Microbiology Letters (IF 2.82) Pub Date : 2018-03-13 ,DOI:10.1093/femsle/fny048Shunzhang Liu,Canxing Meng,Guanpeng Xu,Huahua Jian,Fengping Wang
Reference genes are critical to obtain reliable results of reverse transcription real-time quantitative PCR (RT-qPCR), which is widely used for relative quantification of gene expression. In this study, we evaluated the validity of seven candidate reference genes for normalization in RT-qPCR analysis in the deep-sea bacterium Shewanella psychrophila WP2 under different environmental conditions. Among
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Enhancing the Adaptability of the Deep-Sea Bacterium Shewanella piezotolerans WP3 to High Pressure and Low Temperature by Experimental Evolution under H2O2 Stress.Applied and Environmental Microbiology (IF 5.005) Pub Date : 2017-12-23 ,DOI:10.1128/aem.02342-17Zhe Xie,Huahua Jian,Zheng Jin,Xiang Xiao
Oxidative stresses commonly exist in natural environments, and microbes have developed a variety of defensive systems to counteract such events. Although increasing evidence has shown that high hydrostatic pressure (HHP) and low temperature (LT) induce antioxidant defense responses in cells, there is no direct evidence to prove the connection between antioxidant defense mechanisms and the adaptation
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Deep-Sea Bacterium Shewanella piezotolerans WP3 Has Two Dimethyl Sulfoxide Reductases in Distinct Subcellular Locations.Applied and Environmental Microbiology (IF 5.005) Pub Date : 2017-07-09 ,DOI:10.1128/aem.01262-17Lei Xiong,Huahua Jian,Xiang Xiao
Dimethyl sulfoxide (DMSO) acts as a substantial sink for dimethyl sulfide (DMS) in deep waters and is therefore considered a potential electron acceptor supporting abyssal ecosystems. Shewanella piezotolerans WP3 was isolated from west Pacific deep-sea sediments, and two functional DMSO respiratory subsystems are essential for maximum growth of WP3 under in situ conditions (4°C/20 MPa). However, the
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Microbial Community Structure of Deep-sea Hydrothermal Vents on the Ultraslow Spreading Southwest Indian Ridge.Frontiers in Microbiology (IF 6.064) Pub Date : 2017-07-01 ,DOI:10.3389/fmicb.2017.01012Jian Ding,Yu Zhang,Han Wang,Huahua Jian,Hao Leng,Xiang Xiao
Southwest Indian Ridge (SWIR) is a typical oceanic ultraslow spreading ridge with intensive hydrothermal activities. The microbial communities in hydrothermal fields including primary producers to support the entire ecosystem by utilizing geochemical energy generated from rock-seawater interactions. Here we have examined the microbial community structures on four hydrothermal vents from SWIR, representing
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Genome-Wide Detection of Small Regulatory RNAs in Deep-Sea Bacterium Shewanella piezotolerans WP3.Frontiers in Microbiology (IF 6.064) Pub Date : 2017-07-01 ,DOI:10.3389/fmicb.2017.01093Muhammad Z Nawaz,Huahua Jian,Ying He,Lei Xiong,Xiang Xiao,Fengping Wang
Shewanella are one of the most abundant Proteobacteria in the deep-sea and are renowned for their versatile electron accepting capacities. The molecular mechanisms involved in their adaptation to diverse and extreme environments are not well understood. Small non-coding RNAs (sRNAs) are known for modulating the gene expression at transcriptional and posttranscriptional levels, subsequently playing
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A Genome-Scale Model of Shewanella piezotolerans Simulates Mechanisms of Metabolic Diversity and Energy Conservation.mSystems (IF 7.324) Pub Date : 2017-04-07 ,DOI:10.1128/msystems.00165-16Keith Dufault-Thompson,Huahua Jian,Ruixue Cheng,Jiefu Li,Fengping Wang,Ying Zhang
Shewanella piezotolerans strain WP3 belongs to the group 1 branch of the Shewanella genus and is a piezotolerant and psychrotolerant species isolated from the deep sea. In this study, a genome-scale model was constructed for WP3 using a combination of genome annotation, ortholog mapping, and physiological verification. The metabolic reconstruction contained 806 genes, 653 metabolites, and 922 reactions
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Complete genome sequence of Shewanella psychrophila WP2, a deep-sea bacterium isolated from west Pacific sedimentMarine Genomics (IF 2.143) Pub Date : 2017-03-27 ,DOI:10.1016/j.margen.2017.03.004Guanpeng Xu, Huahua Jian, Xiang Xiao, Fengping WangShewanella psychrophila WP2 is a psychrophilic and piezophilic bacterium, isolated from west Pacific deep-sea sediment at depth of 1914 m. Here we report the 6,353,406-bp complete genome sequence of S. psychrophila WP2, which is the largest genome among the reported genomes of the Shewanella genus. The genome consists of one circular chromosome with GC content of 44.3%. The provided genomic information ...
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Time-series transcriptomic analysis of the deep-sea bacterium Shewanella piezotolerans WP3 in response to high salinity stressMarine Genomics (IF 2.143) Pub Date : 2017-03-11 ,DOI:10.1016/j.margen.2017.03.001Huahua Jian, Shengkang Li, Xixiang Tang, Xiang XiaoOsmoregulatory mechanisms have been investigated in different groups of bacteria. Nevertheless, the molecular processes of deep-sea microorganism in response to salt stress have not been investigated. In this study, the temporal gene expression patterns of the deep-sea bacterium Shewanella piezotolerans WP3 in response to high salinity stress were evaluated through whole-genome microarray analysis ...
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Microarray analysis of the benthic bacterium Shewanella piezotolerans WP3 at low temperatureMarine Genomics (IF 2.143) Pub Date : 2017-02-08 ,DOI:10.1016/j.margen.2017.01.005Huahua Jian, Shengkang Li, Xixiang Tang, Xiang XiaoLow temperature is one of the most critical environmental factors influencing the microbial diversity and functioning of deep-sea ecosystem. In the present study, the global gene expression patterns of the deep-sea bacterium Shewanella piezotolerans WP3 at different temperatures (4 °C and 25 °C) were evaluated through DNA microarray analysis. We identified 185 and 183 genes in WP3 whose expression ...
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Characterisation of the regulatory function of the H-NS protein in the benthic bacterium Shewanella piezotolerans WP3 under cold conditions.FEMS Microbiology Letters (IF 2.82) Pub Date : 2017-01-29 ,DOI:10.1093/femsle/fnx021Huahua Jian,Guanpeng Xu,Fengping Wang,Xiang Xiao
The histone-like nucleoid structuring (H-NS) protein is conserved in Gram-negative bacteria and plays important roles as a multifunctional bacterial modulator. However, its roles in deep-sea microorganisms warrant investigation. In this study, the relationship between temperature and the regulatory function of H-NS was characterised in the benthic bacterium Shewanella piezotolerans WP3. Comparative
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