分子生物学技术在环境微生物群落结构分析中的应用进展
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- 英文论文题名：Assessment of Microbial Community Structure of Environmental Samples by Molecular Techniques
- 论文作者：沈丹丹 ; 杨哲 ; 石娜 ; 孙迎雪 ; 田媛
- 英文论文作者：SHEN Dandan ; YANG Zhe ; SHI Na ; SUN Yingxue ; TIAN Yuan ; Department of environmental science and Engineering ; Beijing Technology and Business University
- 年：2015
- 作者机构：北京工商大学环境科学与工程系;
- 论文关键词：分子生物学技术 ; 微生物群落结构 ; T-RFLP ; 克隆文库 ; 高通量测序
- 英文论文关键词：Molecular biological technology ; microbial community structure ; T-RFLP ; clone library ; high-throughput sequencing
- 会议召开时间：2015-11-26
- 会议录名称：2015年水资源生态保护与水污染控制研讨会论文集
- 语种：中文
- 分类号：X172
- 学会代码：HJKP
- 会议名称：2015年水资源生态保护与水污染控制研讨会
- 会议地点：中国海南海口
- 主办单位：中国环境科学学会、哈尔滨师范大学
- 学会名称：中国环境科学学会
- 页数：5
- 文件大小：839k
- 原文格式：D
- 会议级别：全国
摘要
文献综述了分子生物学技术在环境微生物多样性方面的研究,并对末端限制性片段多态性(T-RFLP),克隆文库及高通量测序技术进行重点介绍介绍,指出这三种技术在环境微生物群落结构分析中以非传统纯培养的方法进行直接分析微生物的多样具有快速、准确等优势,可较为真实地反映环境样品中微生物群落结构组成。T-RFLP技术可提供微生物的种类和相对数量的信息;克隆文库技术在环境微生物群落分析中准确度高;高通量测序技术广泛的应用于宏基因组学,可对混合样品基因组直接测序,无需构建克隆文库。
The current molecular approaches on characterzing microbial community structure for environmental samples were summarized. Three methods as the terminal-restriction fragment length polymorphism, clone library and high-throughput sequencing were mainly described. Points out that these three kinds of technology are more fast and accurate than pure culture. And they can reflect the microbial community structure in environmental samples.T-RFLP analysis can provide the information of types and the relative quantity of microorganisms.Clone library may provide more comprehensive and exact information about microbial populations in environments.One of the most common application of high-throughput sequencing is metagenomics and it can directly sequence genome sequences of mixed samples without constructing clone libraries.
The current molecular approaches on characterzing microbial community structure for environmental samples were summarized. Three methods as the terminal-restriction fragment length polymorphism, clone library and high-throughput sequencing were mainly described. Points out that these three kinds of technology are more fast and accurate than pure culture. And they can reflect the microbial community structure in environmental samples.T-RFLP analysis can provide the information of types and the relative quantity of microorganisms.Clone library may provide more comprehensive and exact information about microbial populations in environments.One of the most common application of high-throughput sequencing is metagenomics and it can directly sequence genome sequences of mixed samples without constructing clone libraries.
引文
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[12]Porreca G J,Zhang K,Li J B,et al.Multiplex amplification of large sets of human exons.Nat Methods,2007,4(11):931-936.
[13]Ondov B D,Varadarajan A,Passalacqua K D,et al.Efficient mapping of Applied Biosystems SOLi D sequence data to a reference genome for functional genomic applications[J].Bioinformatics,2008,24(23):2776-2777.
[14]Harris TD,Buzby PR,Babcock H,et al.Single-molecule DNA sequencingof a viral genome.Science,2008,320(5872):106-109.
[15]姚粟.芝麻香型白酒高温大曲细菌群落多样性研究[D],2013.
[16]任红燕.油藏原位与实验室模拟系统中的微生物分子生态学研究[D],2011.
[17]Hiraishi A,Iwasaki M,Shinjo H.Terminal restriction pattern analysis of 16S r RNA genes for the characterization of bacterial communities of activated sludge[J].J.Biosci.Bioeng,2000,90(2):148-156.
[18]孙庆华,柏耀辉,赵翠,温东辉,唐孝炎.DGGE、T-RF LP、L H-PC R对两种活性污泥的微生物种群多样性分析的比较[J].环境工程学报,2009,3(8):1365-1370.
[19]柏耀辉,孙庆华,温东辉,唐孝炎.分子生态技术在微生物硝化及反硝化研究中的应用[J].北京大学学报(自然科学版),2011,47(2):378-384.
[20]任南琪,赵阳国,高崇洋,王爱杰.TRFLP在微生物群落结构与动态分析中的应用[J]..哈尔滨工业大学学报,2007,39(4).
[21]史青,柏耀辉,李宗逊,冯传平,温东辉.应用T-RFLP技术分析滇池污染水体的细菌群落[J]..环境科学,2011,32(6):1786-1792.
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[23]Mccaig A E,Glover L A,Prosser J I.Applied and Environmental Microbiology,1999,65:1727-1730.
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[25]刘卫国,梁存珍等,16 S r DNA克隆文库分析高含盐生物脱硫系统细菌多样性[J].环境科学,2013,34(2):767-772.
[26]窦娜莎,王琳.2011.16Sr DNA克隆文库法分析Biostyr曝气生物滤池处理城市污水的细菌多样性研究[J].环境科学学报,31(10):2117-2124.
[27]郑磊,熊铁,王前.新一代高通量测序技术一一检验医学发展的挑战与机遇[J].分子诊断与治疗杂志,2011,33(6):361-367.
[28]王兴春,王敏等.高通量测序技术及其应用[J].中国生物工程杂志,2012,32(1):109-114.
[29]张彩霞.新一代高通量测序技术研究土壤微生物群落结构对环境条件的响应[D],2012.
[30]冀世奇.海洋微生物高通量培养和分选技术的建立及应用[D],2011.
[31]夏围围,贾仲君.高通量测序和DGGE分析土壤微生物群落的技术评价[J].微生物学报,2014,54(12):1489-1499
[32]何伟娜,王中华等.基于454测序技术研究宁波沿海陆源排污口希瓦氏菌属的时空分布[J].2014,33(6):896-901
[2]Lin W T,Marsh T L,Cheng H,et al.Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S r RNA[J].Applied and Environmental Microbiology,1997,63(11):4516-4522.
[3]余素林,吴晓磊,钱易.环境微生物群落分析的T-RFLP技术及其优化措施[J].应用与环境生物学报,2006,12(6):861一868.
[4]沈萍,陈向东.微生物学(第二版)[M].北京:高等教育出版社,2006,90.
[5]Collins,M.D.,T.Pirouz,M.Goodfellow,and D.E.Minnikin.Distribution of menaquinones in actinomycetes and corynebacteria.J.Gen[J].Microbiol.1977,100:221-230.
[6]De Long,E.F.,G.S.Wickham,and N.R.Pace.Phylogehetic stains:ribosomal RNA-based probes for the identification of single cells[J].Science,1989.243(4896):1360-1363.
[7]Giovannoni,S.J.,T.B.Britschgi,C.L.Moyer,et al.Genetic diversity in Sargasso Sea bacterioplahktoh.1990.345(3):60-63.
[8]Fodor S P A,Read J I,Pirning M C,et al.Light-directed,spatially addressable parallel chemical synthesis[J].Science,1991,251(4):767一773.
[9]Muyzer G,Wall E C D,Uitterlindem A G.Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction--amplified genes coding for16S r RNA[J].Applied and Environmental Microbiology,1993(59):695一700.
[10]Lin W T,Marsh T L,Cheng H,et al.Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S r RNA[J].Applied and Environmental Microbiology,1997,63(11):4516-4522.
[11]Margulies M,Egholn M,Altman W E,Attiya S,Bader JS,Bemben LA,et al.Genome sequencing in microfabricated high-density picolitre reactors[J].Nature 2005;437:376-380.
[12]Porreca G J,Zhang K,Li J B,et al.Multiplex amplification of large sets of human exons.Nat Methods,2007,4(11):931-936.
[13]Ondov B D,Varadarajan A,Passalacqua K D,et al.Efficient mapping of Applied Biosystems SOLi D sequence data to a reference genome for functional genomic applications[J].Bioinformatics,2008,24(23):2776-2777.
[14]Harris TD,Buzby PR,Babcock H,et al.Single-molecule DNA sequencingof a viral genome.Science,2008,320(5872):106-109.
[15]姚粟.芝麻香型白酒高温大曲细菌群落多样性研究[D],2013.
[16]任红燕.油藏原位与实验室模拟系统中的微生物分子生态学研究[D],2011.
[17]Hiraishi A,Iwasaki M,Shinjo H.Terminal restriction pattern analysis of 16S r RNA genes for the characterization of bacterial communities of activated sludge[J].J.Biosci.Bioeng,2000,90(2):148-156.
[18]孙庆华,柏耀辉,赵翠,温东辉,唐孝炎.DGGE、T-RF LP、L H-PC R对两种活性污泥的微生物种群多样性分析的比较[J].环境工程学报,2009,3(8):1365-1370.
[19]柏耀辉,孙庆华,温东辉,唐孝炎.分子生态技术在微生物硝化及反硝化研究中的应用[J].北京大学学报(自然科学版),2011,47(2):378-384.
[20]任南琪,赵阳国,高崇洋,王爱杰.TRFLP在微生物群落结构与动态分析中的应用[J]..哈尔滨工业大学学报,2007,39(4).
[21]史青,柏耀辉,李宗逊,冯传平,温东辉.应用T-RFLP技术分析滇池污染水体的细菌群落[J]..环境科学,2011,32(6):1786-1792.
[22]杨苏声,周俊初.微生物生物学.北京:科学出版社.2004,291-292.
[23]Mccaig A E,Glover L A,Prosser J I.Applied and Environmental Microbiology,1999,65:1727-1730.
[24]罗艳,谢作明,周义芳等.16S r DNA克隆文库解析江汉平原高砷地下水系统中的细菌多样性[J].生态毒理学报,2013,8(2)::194-200.
[25]刘卫国,梁存珍等,16 S r DNA克隆文库分析高含盐生物脱硫系统细菌多样性[J].环境科学,2013,34(2):767-772.
[26]窦娜莎,王琳.2011.16Sr DNA克隆文库法分析Biostyr曝气生物滤池处理城市污水的细菌多样性研究[J].环境科学学报,31(10):2117-2124.
[27]郑磊,熊铁,王前.新一代高通量测序技术一一检验医学发展的挑战与机遇[J].分子诊断与治疗杂志,2011,33(6):361-367.
[28]王兴春,王敏等.高通量测序技术及其应用[J].中国生物工程杂志,2012,32(1):109-114.
[29]张彩霞.新一代高通量测序技术研究土壤微生物群落结构对环境条件的响应[D],2012.
[30]冀世奇.海洋微生物高通量培养和分选技术的建立及应用[D],2011.
[31]夏围围,贾仲君.高通量测序和DGGE分析土壤微生物群落的技术评价[J].微生物学报,2014,54(12):1489-1499
[32]何伟娜,王中华等.基于454测序技术研究宁波沿海陆源排污口希瓦氏菌属的时空分布[J].2014,33(6):896-901