分子生物学技术在土壤微生物多样性中的应用
Molecular Biology Technology and Its Application in Soil Microbial Diversity
DOI: 10.12677/BP.2013.33004, PDF, HTML, XML,  被引量    国家自然科学基金支持
作者: 曹万举：吉林省白河林业局；隋 心：中国科学院沈阳应用生态研究所；中国科学院大学；韩士杰：中国科学院沈阳应用生态研究所；王 云, 李金功, 王洁：吉林省长白山自然保护管理中心
关键词: 微生物多样性；研究方法；分子生物学；生态系统；Microbial Diversity; Research Method; Molecular Biology; Ecosystems
摘要: 微生物在生态系统中占据着很重要的作用，其结构和功能的多样性及变化在一定程度上反映了生态系统的基本状态。传统的微生物培养和鉴定方法得到的微生物信息很片面，不足以代表微生物在生态系统中的真实情况。近几十年发展起来的分子生物技术突破了传统方法的限制，极大地促进了微生物学和生态学的发展。本文介绍了现在常用的几种分子生物学方法在微生物多样性研究中的应用现状。
Abstract: Microorganism plays a key role in ecosystem, the structure and function of microbial diversity, to a certain extent, reflects the status of ecosystem. It is unilateral to study microorganism with traditional cultural method, which could not reflect the real situation of microorganism in ecosystem. Recently, the molecular biology technology breaks the limitation of traditional cultural method and tremendously promotes the development of microbiology and ecology. So, this paper introduces several molecular biology methods which they’re applied in microbial diversity research.

文章引用：曹万举, 隋心, 韩士杰, 王云, 李金功, 王洁. 分子生物学技术在土壤微生物多样性中的应用[J]. 生物过程, 2013, 3(3): 23-28. http://dx.doi.org/10.12677/BP.2013.33004

参考文献

[1] 孙波, 赵其国. 土壤质量与持续环境: Ⅲ. 土壤质量评价的生物学指标[J]. 土壤, 1997, 29(5): 225-234.
[2] D. R. Zak, et al. Plant diversity, soil microbial communities, and ecosystem function: Are there any links? Ecology, 2003, 84(8): 2042-2050.
[3] S. G. Fischer, L. S. Lerman. Length-independent separation of DNA restriction fragments in two-dimensional gel electrophoresis. Cell, 1979, 16(1): 191-200.
[4] D. Ercolini. PCR-DGGE fingerprinting: Novel strategies for de- tection of microbes in food. Journal of Microbiological Methods, 2004, 56(3): 297-314.
[5] E. Lyautey, et al. Analysis of bacterial diversity in river biofilms using 16S rDNA PCR-DGGE: Methodological settings and fingerprints interpretation. Water Research, 2005, 39(2): 380-388.
[6] M. Miletto, P. L. Bodelier and H. J. Laanbroek. Improved PCR- DGGE for high resolution diversity screening of complex sul- fate-reducing prokaryotic communities in soils and sediments. Journal of Microbiological Methods, 2007, 70(1): 103-111.
[7] G.-H. Wang, et al. Bacterial community structure in a mollisol under long-term natural restoration, cropping, and bare fallow history estimated by PCR-DGGE. Pedosphere, 2009, 19(2): 156- 165.
[8] M. Manzano, et al. A PCR-TGGE (Temperature Gradient Gel Electrophoresis) technique to assess differentiation among enological Saccharomyces cerevisiae strains. International Journal of Food Microbiology, 2005, 101(3): 333-339.
[9] D. Mikkelsen, et al. Probing the archaeal diversity of a mixed thermophilic bioleaching culture by TGGE and FISH. Systematic and Applied Microbiology, 2009, 32(7): 501-513.
[10] K. Leung, E. Topp. Bacterial community dynamics in liquid swine manure during storage: Molecular analysis using DGGE/ PCR of 16S rDNA. Fems Microbiology Ecology, 2001, 38(2-3): 169-177.
[11] M. Sakurai, et al. Analysis of bacterial communities in soil by PCR-DGGE targeting protease genes. Soil Biology and Bio-chemistry, 2007, 39(11): 2777-2784.
[12] 章家恩. 土壤微生物多样性实验研究方法概述[J]. 土壤, 2004, 36(4): 346-350.
[13] J. L. Kirk, et al. Methods of studying soil microbial diversity. Journal of Microbiological Methods, 2004, 58(2): 169-188.
[14] G. P. Gafan, D. A. Spratt. Denaturing gradient gel electrophore- sis gel expansion (DGGEGE)—An attempt to resolve the limitations of co-migration in the DGGE of complex polymicrobial communities. Fems Microbiology Letters, 2005, 253(2): 303- 307.
[15] L. Kerkhof, M. Santoro and J. Garland. Response of soybean rhizosphere communities to human hygiene water addition as determined by community level physiological profiling (CLPP) and terminal restriction fragment length polymorphism (T-RFLP) analysis. Fems Microbiology Letters, 2000, 184(1): 95-101.
[16] T. Harder, et al. A bacterial culture-independent method to in- vestigate chemically mediated control of bacterial epibiosis in marine invertebrates by using TRFLP analysis and natural bac- terial populations. Fems Microbiology Ecology, 2004, 47(1): 93- 99.
[17] D. J. Burke, et al. Ectomycorrhizal fungi identification in single and pooled root samples: Terminal restriction fragment length polymorphism (TRFLP) and morphotyping compared. Soil Bi- ology and Biochemistry, 2005, 37(9): 1683-1694.
[18] F. Li, M. A. Hullar and J. W. Lampe. Optimization of terminal restriction fragment polymorphism (T-RFLP) analysis of human gut microbiota. Journal of Microbiological Methods, 2007, 68(2): 303.
[19] S. A. Wakelin, et al. Pasture management clearly affects soil mi- crobial community structure and N-cycling bacteria. Pedobiologia, 2009, 52(4): 237-251.
[20] T. L. Marsh, et al. Terminal restriction fragment length poly- morphism analysis program, a web-based research tool for mi- crobial community analysis. Applied and environmental micro- biology, 2000, 66(8): 3616-3620.
[21] S. M. Tiquia, et al. Effects of mulching and fertilization on soil nutrients, microbial activity and rhizosphere bacterial commu- nity structure determined by analysis of TRFLPs of PCR-ampli- fied 16S rRNA genes. Applied Soil Ecology, 2002, 21(1): 31-48.
[22] 王洪媛, 管华诗, 江晓路. 微生物生态学中分子生物学方法及 T-RFLP技术研究[J]. 中国生物工程杂志, 2004, 24(8): 42-47.
[23] E. Schwartz, K. L. Adair and E.A. Schuur. Bacterial community structure correlates with decomposition parameters along a Ha- waiian precipitation gradient. Soil Biology and Biochemistry, 2007, 39(8): 2164-2167.
[24] J. Handelsman, et al. Molecular biological access to the chemis- try of unknown soil microbes: a new frontier for natural products. Chemistry & Biology, 1998, 5(10): 245-249.
[25] H. L. Steele, W. R. Streit. Metagenomics: Advances in ecology and biotechnology. Fems Microbiology Letters, 2005, 247(2): 105-111.
[26] J. Dupré, M. A. O’Malley. Metagenomics and biological ontol- ogy. Studies in History and Philosophy of Science Part C: Stud- ies in History and Philosophy of Biological and Biomedical Sci- ences, 2007, 38(4): 834-846.
[27] M. Schaechter, Encyclopedia of microbiology. Maltham, Aca- demic Press, 2009.
[28] J. H. Kima, T. L. Simmonsa and S. F. Bradya. Unlocking envi- ronmental DNA derived gene clusters using a metagenomics ap- proach. Chemistry and Biology, 2010, 2: 455-474.
[29] R. Daniel. The soil metagenome—A rich resource for the dis- covery of novel natural products. Current Opinion in Biotech- nology, 2004, 15(3): 199-204.
[30] M. R. Rondon, et al. Cloning the soil metagenome: A strategy for accessing the genetic and functional diversity of uncultured microorganisms. Applied and Environmental Microbiology, 2000, 66(6): 2541-2547.
[31] 黄循柳. 宏基因组学研究进展[J]. 微生物学通报, 2009, 36(7): 1058-1066.
[32] E. M. Wellington, A. Berry and M. Krsek. Resolving functional diversity in relation to microbial community structure in soil: Exploiting genomics and stable isotope probing. Current Opinion in Microbiology, 2003, 6(3): 295-301.
[33] O. Uhlík, et al. DNA-based stable isotope probing: A link be- tween community structure and function. Science of the Total Environment, 2009, 407(12): 3611-3619.
[34] Y. Chen, J. C. Murrell. When metagenomics meets stable-iso- tope probing: Progress and perspectives. Trends in Microbiology, 2010, 18(4): 157-163.
[35] E. L. Madsen. The use of stable isotope probing techniques in bioreactor and field studies on bioremediation. Current Opinion in Biotechnology, 2006, 17(1): 92-97.
[36] D. R. Singleton, et al. Stable-isotope probing with multiple growth substrates to determine substrate specificity of uncultivated bac-teria. Journal of Microbiological Methods, 2007, 69(1): 180-187.
[37] D. H. Buckley, et al. 15N2-DNA-stable isotope probing of diazotrophic methanotrophs in soil. Soil Biology and Biochemistry, 2008, 40(6): 1272-1283.
[38] Y. Lu, R. Conrad. In situ stable isotope probing of methanogenic archaea in the rice rhizosphere. Science, 2005, 309(5737): 1088- 1090.
[39] I. R. McDonald, S. Radajewski and J. C. Murrell. Stable isotope probing of nucleic acids in methanotrophs and methylotrophs: A review. Organic Geochemistry, 2005, 36(5): 779-787.
[40] 葛源. 稳定性同位素探测技术在微生物生态学研究中的应用[J]. 生态学报, 2006, 26(5): 1574-1582.
[41] G. Jurgens, et al. Identification of novel Archaea in bacterio- plankton of a boreal forest lake by phylogenetic analysis and fluorescent in situ hybridization1. Fems Microbiology Ecology, 2000, 34(1): 45-56.
[42] R. Araya, et al. Bacterial activity and community composition in stream water and biofilm from an urban river determined by fluorescent in situ hybridization and DGGE analysis. Fems Mi- crobiology Ecology, 2003, 43(1): 111-119.
[43] K.-J. Chae, et al. Analysis of the nitrifying bacterial community in BioCube sponge media using fluorescent in situ hybridization (FISH) and microelectrodes. Journal of Environmental Management, 2008, 88(4): 1426-1435.
[44] J. Liu, L. Leff. Temporal changes in the bacterioplankton of a Northeast Ohio (USA) River. Hydrobiologia, 2002, 489(1-3): 151-159.
[45] M. Domlnaues, et al. Evaluation of thermophilic anaerobic mi- crobial consortia using fluorescence in situ hybridization (FISH). Water Science and Technology, 2002, 45(10): 27-33.
[46] 李华芝, 李秀艳, 徐亚同. 荧光原位杂交技术在微生物群落结构研究中的应用[J]. 中国生物学文摘, 2007, 21(9): 48-49.
[47] M. Hernández, et al. Development of real-time PCR systems based on SYBR® Green I, Amplifluor™ and TaqMan® technologies for specific quantitative detection of the transgenic maize event GA21. Journal of Cereal Science, 2004, 39(1): 99- 107.
[48] K. C. McGrath, et al. Isolation and analysis of mRNA from environmental microbial communities. Journal of Microbiological Methods, 2008, 75(2): 172-176.