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Advancements in prokaryotic systematics and the role of Bergey's International Society for Microbial Systematics in addressing challenges in the meta-data era

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National Science Review 2024年第7期11卷 292-304页

作者： Jian-Yu Jiao Rashidin Abdugheni Dao-Feng Zhang Iftikhar Ahmed Mukhtiar Ali Maria Chuvochina Svetlana N.Dedysh xiuzhu dong Markus G?ker Brian P.Hedlund Philip Hugenholtz Kamlesh Jangid Shuang-Jiang Liu Edward R.B.Moore Manik Prabhu Narsing Rao Aharon Oren Ramon Rossello-Mora Bhagwan Narayan Rekadwad Nimaichand Salam Wensheng Shu Iain C.Sutcliffe Wee Fei Aaron Teo Martha E.Trujillo Stephanus N.Venter William B.Whitman Guoping Zhao Wen-Jun Li State Key Laboratory of Biocontrol Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai) School of Life Sciences Sun Yat-Sen University State Key Laboratory of Desert and Oasis Ecology Key Laboratory of Ecological Safety and Sustainable Development in Arid LandsXinjiang Institute of Ecology and Geography Chinese Academy of Sciences Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization&College of Oceanography Hohai University National Culture Collection of Pakistan(NCCP) Land Resources Research Institute(LRRI) National Agricultural Research Centre(NARC) The University of Queensland School of Chemistry and Molecular Biosciences Australian Centre for Ecogenomics Winogradsky Institute of Microbiology Research Center of BiotechnologyRussian Academy of Sciences State Key Laboratory of Microbial Resources Institute of Microbiology Chinese Academy of Sciences Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures School of Life Sciences University of Nevada Nevada Institute of Personalized Medicine University of Nevada Bioenergy Group MACS Collection of Microorganisms Agharkar Research Institute State Key Laboratory of Microbial Technology Shandong University Department of Infectious Disease Institute for Biomedicine and Culture Collection University of Gothenburg(CCUG) Institute for BiomedicineSahlgrenska AcademyUniversity of Gothenburg Instituto de Ciencias Aplicadas Facultad de Ingeniería Universidad Autónoma de Chile The Alexander Silberman Institute of Life Sciences The Edmond J.Safra Campus The Hebrew University of Jerusalem Marine Microbiology Group Department of Animal and Microbial Biodiversity Mediterranean Institute for Advanced Studies(IMEDEA CSIC-UIB) MicrobeAI Lab Division of Microbiology and Biotechnology Yenepoya Research Centre Yenepoya(Deemed to be University) National Agri-Food Biotechnology Institute Institute of Ecological Science Sch

Prokaryotes are ubiquitous in the biosphere, important for human health and drive diverse biological and environmental processes. Systematics of prokaryotes, whose origins can be traced to the discovery of microorganisms in the 17th century, has transitioned from a phenotype-based classification to a more comprehensive polyphasic taxonomy and eventually to the current genome-based taxonomic *** transition aligns with a foundational shift from studies focused on phenotypic traits that have limited comparative value to those using genome sequences. In this context, Bergey's Manual of Systematics of Archaea and Bacteria(BMSAB) and Bergey's International Society for Microbial Systematics(BISMiS) play a pivotal role in guiding prokaryotic systematics. This review focuses on the historical development of prokaryotic systematics with a focus on the roles of BMSAB and BISMiS. We also explore significant contributions and achievements by microbiologists, highlight the latest progress in the field and anticipate challenges and opportunities within prokaryotic systematics. Additionally, we outline five focal points of BISMiS that are aimed at addressing these challenges. In conclusion, our collaborative effort seeks to enhance ongoing advancements in prokaryotic systematics, ensuring its continued relevance and innovative characters in the contemporary landscape of genomics and bioinformatics.

关键词： prokaryotic systematics Bergey's Manual of Systematics of Archaea and Bacteria (BMSAB) Bergey's International Society for Microbial Systematics (BISMiS) meta-data era

Psychrotolerant methanogenic archaea:Diversity and cold adaptation mechanisms

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Science China(Life Sciences) 2012年第5期55卷 415-421页

作者： dong xiuzhu CHEN ZiJuan State Key Laboratory of Microbial Resources Institute of Microbiology Chinese Academy of Sciences Beijing 100101 China

Because of their diversity and abundance in a wide range of environments, particularly in cold regions, cold-adaptive archaea are expected to play a pivotal role in material recycling in cold environments. Methanogenic archaea are ubiquitous on earth and produce a large amount of methane （CH4） as their main carbon metabolite. Methanogens are the most laboratory amenda- ble archaea. The few psychrophilic archaea that have been cultured to date are mainly affiliated with methanogens, thus make them a good model for investigating mechanisms of archaeal cold adaptation. Studies of psychrotolerant methanogens have been ongoing since the 1990s. Using Methanocoecoides burtonii, a methanogen isolated from Ace Lake in Antarctica, exten- sive studies on the genomic characteristics associated with cold adaptation have been carried out by the Cavicchioli laboratory. We recently analyzed the genome of another psychrophilic methanogen and identified the gene repertoire associated with cold adaptation. This review summarizes recent studies of psychroactive methanogens, particularly their diversity, the genomics and proteomics associated with their cold adaptation, and the cellular components and proteins likely involved in their cold protec- tion.

关键词： psychrotolerant methanogens diversity cold adaptation mechanisms

Microbiome:from community metabolism to host diseases

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Science China(Life Sciences) 2018年第7期61卷 741-743页

作者： Nan Qin xiuzhu dong Liping Zhao Shanghai Tenth People's Hospital Affiliated to Tongji University Shanghai 200072China Realbio Genomies Institute Shanghai 200050China State Key Laboratory of Microbial Resources Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China State Key Laboratory of Microbial Metabolism and Minstry of Education Key Laboratory of Systems Biomedicine School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai 200240China Department of Biochemistry and Microbiology and New Jersey Institute for Food Nutritionand HealthSchool of Environmental and Biological SciencesRutgers UniversityNew BrunswickNJ 08901USA

Microorganisms live in almost every habitat on the earth from the poles to the equator,from forest to desert,from mountain to deep sea,from geysers to karst structures,as well as the body of almost all multicellular organisms from plants to ***,species among the microbial populations interact in different ways,as predators and prey,or as symbionts in the form of communities.

关键词：新陈代谢社区疾病石灰岩地区地形结构食肉动物微生物有机体

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居瘤胃解纤维素菌细胞密度与纤维素酶的合成

微生物学报 2012年第9期52卷 1069-1074页

作者：王璨东秀珠中国科学院微生物研究所微生物资源前期开发国家重点实验室北京100101

居瘤胃解纤维素菌(Cellulosilyticum ruminicola)H1是本实验室分离自青海牦牛瘤胃的一株新的纤维素降解细菌。前期研究发现,菌株H1在滤纸纤维素上连续传代数次后无法生长,只有在纤维素降解产物纤维二糖中培养后方能继续在纤维素中生长,... 详细信息

居瘤胃解纤维素菌(Cellulosilyticum ruminicola)H1是本实验室分离自青海牦牛瘤胃的一株新的纤维素降解细菌。前期研究发现,菌株H1在滤纸纤维素上连续传代数次后无法生长,只有在纤维素降解产物纤维二糖中培养后方能继续在纤维素中生长,并恢复其纤维素降解活性。这与纤维素酶合成受"代谢产物抑制"的传统认识相悖。【目的】证明菌株H1的纤维素酶合成受细胞密度调控。【方法】检测菌株H1的纤维素酶活和转录水平在高和低密度细胞培养物中差异,并检测高密度细胞培养物中的寡肽对低密度细胞纤维素酶活和转录水平的促进作用。【结果】菌株H1的高密度细胞培养物的纤维素酶活和转录水平比低密度细胞的高3-10倍;并且高密度细胞培养液能显著提高低密度细胞纤维素酶活和转录水平。【结论】居瘤胃解纤维素菌(Cellulosilyticum ruminicola)H1纤维素酶的合成受细胞密度调控。

关键词：纤维素降解细菌纤维素酶合成细胞密度

岩石中微生物学研究的分子生物学技术——中国大陆科学钻探(CCSD)微生物研究

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岩石学报 2006年第7期22卷 2107-2111页

作者：李光玉王远亮董海良东秀珠董志扬中国科学院微生物研究所微生物资源前期开发国家重点实验室北京100080 美国迈阿密大学地质系

本文介绍了中国大陆科学钻探(CCSD)微生物学研究中所建立起来的分子生物学技术,即环境基因组DNA提取、16S rDNA分析、Real-time PCR技术和磷脂酸分析技术。另外探索了防污染的手段以及监测方法,并介绍了我们以这种方法时CCSD的微生物学... 详细信息

本文介绍了中国大陆科学钻探(CCSD)微生物学研究中所建立起来的分子生物学技术,即环境基因组DNA提取、16S rDNA分析、Real-time PCR技术和磷脂酸分析技术。另外探索了防污染的手段以及监测方法,并介绍了我们以这种方法时CCSD的微生物学研究所得到的一些初步结果。

关键词：中国大陆科学钻探微生物学分子生物学方法

中国大陆科学钻探(CCSD)地下岩心样品中的细菌群落分析

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岩石学报 2005年第2期21卷 533-539页

作者：王远亮夏颖董海良东秀珠杨克迁黄力董志扬中国科学院微生物研究所微生物资源前期开发国家重点实验室北京100080 迈阿密大学地质系

通过建立高效率的微生物未培养DNA提取技术和16SrDNA分析技术,在中国大陆钻探深层岩芯中发现微生物存在的证据。从地下430.00米(S1)与1033.77米(S13)深度岩芯中分别提取到微生物DNA,进行16SrDNAPCR扩增,通过对S13样品DNA中克隆得到的54... 详细信息

通过建立高效率的微生物未培养DNA提取技术和16SrDNA分析技术,在中国大陆钻探深层岩芯中发现微生物存在的证据。从地下430.00米(S1)与1033.77米(S13)深度岩芯中分别提取到微生物DNA,进行16SrDNAPCR扩增,通过对S13样品DNA中克隆得到的54个16SrDNA的序列测定,初步构建了该深度地下微生物群落的系统进化树,发现了23种不同的微生物序列存在。通过DAPI染色证明在地下1033.77米的微生物数量约为1×104个/克岩石,采用实时定量PCR分析分析,发现了其中两种微生物(CCSD1305与CCSD1307)的数量为6.6×104+/g岩石与2.18×106个/g岩石。

关键词：超高压变质岩中国大陆科学钻探微生物 16SrDNA

中国大陆科学钻探(CCSD)深部地层微生物研究——两株未培养地下微生物菌株原位含量的分析

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岩石学报 2006年第7期22卷 2103-2106页

作者：王远亮夏莹东秀珠董海良杨克迁董志扬黄力中国科学院微生物研究所微生物资源前期开发国家重点实验室北京100080 迈阿密大学地质系

从地下1033．77米深处岩芯中提取微生物DNA,经PCR扩增,获得16S rDNA序列。选取其中两个序列(CCSD1305与CCSD1307),根据其16S rDNA可变区设计PCR引物,通过实时定量PCR分析,确定这两株未培养微生物在岩芯中的生物量。结果表明,CCSD1305与C... 详细信息

从地下1033．77米深处岩芯中提取微生物DNA,经PCR扩增,获得16S rDNA序列。选取其中两个序列(CCSD1305与CCSD1307),根据其16S rDNA可变区设计PCR引物,通过实时定量PCR分析,确定这两株未培养微生物在岩芯中的生物量。结果表明,CCSD1305与CCSD1307在该岩芯中的数量分别约为6．6×104和2．18×106个／克岩石。

关键词：深层地下微生物 16S rDNA 实时定量PCR 定量

中国大陆科学钻探(CCSD)微生物研究——地下3900米一株细菌的分离与鉴定

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岩石学报 2005年第2期21卷 540-544页

作者：王远亮李光玉东秀珠董海良杨克迁董志扬中国科学院微生物研究所微生物资源国家重点实验室北京100080 迈阿密大学地质系

在中国大陆科学钻探科钻一井的3911.28米处利用厌氧培养基分离到一株细菌CCSDFL3900,该菌的最适生长温度为65℃,兼性厌氧,革兰氏染色为阴性,端生芽孢,不运动,电镜观察无鞭毛。利用细菌16SrDNA通用引物对其16SrRNA进行PCR扩增,16SrRNA序... 详细信息

在中国大陆科学钻探科钻一井的3911.28米处利用厌氧培养基分离到一株细菌CCSDFL3900,该菌的最适生长温度为65℃,兼性厌氧,革兰氏染色为阴性,端生芽孢,不运动,电镜观察无鞭毛。利用细菌16SrDNA通用引物对其16SrRNA进行PCR扩增,16SrRNA序列及其进化树分析结果显示,该菌为芽孢杆菌或地杆菌。生化试验检测显示,该菌株能够利用多种糖类发酵产酸,最终鉴定为热坚芽孢杆菌。

关键词：中国大陆科学钻探热坚芽孢杆菌鉴定分离

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波浪荷载作用下砂土变形特性的模拟试验研究

地震工程与工程振动 2005年第2期25卷 155-159页

作者：张晨明董秀竹郭莹栾茂田同济大学地下建筑与工程系上海200092 大连理工大学海岸和近海工程国家重点工程实验室辽宁大连116024

利用新研制的“土工静力-动力液压三轴-扭转多功能剪切仪”模拟波浪荷载作用,对福建标准砂进行了4组三轴-扭转耦合振动剪切试验,以研究海床砂土在波浪荷载作用下的变形特性及其对砂土初始密度和固结压力的依赖性。试验结果表明,应力-应... 详细信息

利用新研制的“土工静力-动力液压三轴-扭转多功能剪切仪”模拟波浪荷载作用,对福建标准砂进行了4组三轴-扭转耦合振动剪切试验,以研究海床砂土在波浪荷载作用下的变形特性及其对砂土初始密度和固结压力的依赖性。试验结果表明,应力-应变呈现出良好的双曲线关系,与等效线性模型理论相吻合;阻尼比和模量随应变幅值的变化规律均依赖于土体的初始密度和固结压力;归一化后的E/Emax-ε及G/Gmax-γ曲线对相对密度和固结压力仍具有明显的依赖性;但完全归一化后的E/Emax-ε/εr及G/Gmax-γ/γr的关系曲线则与固结压力无关。

关键词：波浪荷载三轴-扭转耦合振动剪切试验变形特性阻尼比模量