未培养微生物的限制因素及培养方法研究进展
Progress on the Research Pertinent to Cultivation Constraint Factors and Improved Cultivation Methods of Environmental Uncultured Microorganisms
DOI: 10.12677/AMB.2014.32003, PDF, HTML,  被引量 下载: 3,902  浏览: 17,155  国家自然科学基金支持
作者: 牛丽纯, 孙玉芳, 赵天琦, 宋福强:黑龙江大学修复生态研究室,哈尔滨
关键词: 未培养微生物限制因素培养方法Uncultured Microorganisms Limiting Factors Culture Method
摘要: 自然生境中存在许多独特的对人类有益却难以纯培养的未培养微生物,这些微生物蕴含着丰富的物种多样性,在整个地球上的物质循环和生命持续中占有重要的角色。本文简要介绍了未培养微生物以及目前不可将其分离培养的影响因素,重点阐述了未培养微生物分离培养的新颖方法和改进措施,在模拟自然条件维持微生物间相互关系的前提下,设计出促进微生物苏复因子的新型培养基,采用多种行之有效的技术相结合,使未培养微生物的纯培养成为可能,这对以后微生物领域的发展可以起到助推作用。
Abstract: A great deal of unique uncultured microorganisms exist in various kinds of habitats; they benefit humans but are difficult to be purely cultured and are rich in species diversity, playing a very important role on the matter cycle of the whole earth and life sustainability. The uncultured microorganisms as well as the factors attributing to their currently uncultured feature were briefly introduced in this review, and subsequently novel methods and improved measurements for isolating them were highlighted. Currently, novel medium containing microorganism recovery promoting factors was designed through simulating maintaining the relationships among microbes under natural conditions. Combination of a variety of proven technologies is employed to make the pure culture possible of uncultured microorganisms, which play a promoting role on the development of microbiological field.
文章引用:牛丽纯, 孙玉芳, 赵天琦, 宋福强. 未培养微生物的限制因素及培养方法研究进展[J]. 微生物前沿, 2014, 3(2): 17-28. http://dx.doi.org/10.12677/AMB.2014.32003

参考文献

[1] Boone, D.R., Castenholz, R.W. and Garrity, G.M. (2001) Bergey’s manual of systematic bacteriology (Vol. 1). Springer, New York.
[2] Newman, D.K. and Banfield, J.F. (2002) Geomicrobiology: How molecular-scale interactions underpin biogeochemical systems. Science, 296, 1071-1077.
[3] 朱允华, 李俭, 方俊, 田云, 卢向阳 (2011) 宏基因组技术在开发极端环境未培养微生物中的应用. 生物技术通报, 9, 52-58.
[4] Griffitt, K.J., Noriea, N.F., Johnson, C.N. and Grimes, D.J. (2011) Enumeration of Vibrio parahaemolyticus in the viable but nonculturable state using direct plate counts and recognition of individual gene fluorescence in situ hybridization. Journal of Microbiological Methods, 85, 114-118.
[5] 高鹤, 赵勇, 刘承初 (2014) 致病微生物应对环境胁迫形成的VBNC状态及其对风险评估的潜在影响. 微生物学通报, 1, 169-177.
[6] Cho, J.-C. and Giovannoni, S.J. (2004) Cultivation and growth characteristics of a diverse group of oligotrophic marine gammaproteobacteria. Applied and Environmental Microbiology, 70, 432-440.
[7] Zhang, X.M. and Zhang, X.H. (2009) New culture approaches of marine microorganisms. Marine Sciences, 33, 99-104. (in Chinese)
[8] 张秀明, 张晓华 (2009) 海洋微生物培养新技术的研究进展. 海洋科学, 6, 99-104.
[9] 蒋娜, 李健强, 罗来鑫 (2013) 植物病原细菌的VBNC状态研究进展. 植物病理学报, 3, 249-257.
[10] 潘虎, 卢向阳, 董俊德 (2012) 未培养微生物研究策略概述. 生物学杂志, 1, 79-83.
[11] 姜海琴, 范彩云, 李吕木, 程建波 (2011) 宏基因组技术在筛选未培养微生物中新型酶的研究进展. 湖北农业科学, 50, 3673-3676.
[12] Kolodkin-Gal, I. and Engelberg-Kulka, H. (2008) The extracellular death factor: Physiological and genetic factors influencing its production and response in Escherichia coli. Journal of Bacteriology, 190, 3169-3175.
[13] Pereira, C., Mc Auley, J.R., Taga, M.E., Xavier, K.B. and Miller, S.T. (2009) Sinorhizobium meliloti, a bacterium lacking the autoinducer-2(AI-2) synthase responds to AI-2 supplied by other bacteria. Molecular Microbiology, 70, 1223-1235.
[14] 周玥, 刘小锦, 朱晨光 (2004) 细菌中群体感应调节系统. 微生物学报, 1, 122-126.
[15] 彭伶俐, 王琴, 辛明秀 (2011) 自然界中不可培养微生物的研究进展. 微生物学杂志, 2, 75-79.
[16] Sanmee, R., Lumyong, P., Dell, B. and Lumyong, S. (2010) In vitro cultivation and fruit body formation of the black bolete, Phlebopus portentosus, a popular edible ectomycorrhizal fungus in Thailand. Mycoscience, 51, 15-22.
[17] Santander, R.D., Catala-Senent, J.F., Marco-Noales, E. and Biosca, E.G. (2012) In planta recovery of Erwinia amylovora viable but nonculturable cell. Trees, 26, 75-82.
[18] 徐怀恕, 黄备, 祁自忠 (1997) 霍乱弧菌(V. cholerae)的细胞形态研究—活的非可培养状态细胞. 青岛海洋大学学报, 2, 187-190.
[19] Besnard, V., Federighi, M. and Cappelier, J.M. (2011) Evidence of viable but non-culturable state in Listeria monocytogenes by direct viable count and CTC-DAPI double staining. Food Microbiology, 17, 697-704.
[20] 鄂佳, 梁景平 (2011) 活的非可培养状态下的粪肠球菌的研究进展. 国际口腔医学杂志, 4, 430-432.
[21] 李伦, 李元, 白婧, 许崇波 (2010) 细菌复苏促进因子. 动物医学进展, 4, 103-106.
[22] Olsen, R.A. and Bakken, L.R. (1987) Viability of soil bacteria: Optimization of plate-counting technic and comparison between total counts and plate within different size groups. Microbial Ecology, 13, 59-74.
[23] Ferrari, B.C., Binnerup, S.J. and Gillings, M. (2005) Microcolony cultivation on a soil substrate membrane system selects for previously uncultured soil bacteria. Applied and Environmental Microbiology, 71, 8714-8720.
[24] Bollmann, A., Lewis, K. and Epstein, S.S. (2007) Incubation of environmental samples in a diffusion chamber increases the diversity of recovered isolates. Applied and Environmental Microbiology, 73, 6386-6390.
[25] 史立君, 徐丽娟, 刘润进 (2011) 与植物共生的难培养菌物及其培养特性研究进展. 微生物学通报, 1, 110-117.
[26] Stott, M.B., Crowe, M.A., Mountain, B.W., Smirnova, A.V., Hou, S., Alam, M. and Dunfield, P.F. (2008) Isolation of novel bacteria, including a candidate division, from geothermal soils in New Zealand. Environmental Microbiology, 10, 2030-2041.
[27] 袁静, 李清明 (2012) 未培养微生物筛选高纤维素酶活性基因的研究进展. 农产品加工, 3, 11-13.
[28] Davis, K.E.R., Joseph, S.J. and Janssen, P.H. (2005) Effects of growth medium, inoculum size, and incubation time on culturability and isolation of soil bacteria. Applied and Environmental Microbiology, 71, 826-834.
[29] Button, D.K., Schut, F., Quang, P., Martin, R. and Robertson, B.R. (1993) Vialibity and isolation of marine bacteria by dilution culture: Theory, procedures, and initial results. Applied and Environmental Microbiology, 59, 881-891.
[30] 刘新星, 霍转转, 云慧, 杨英杰 (2014) 流式细胞术在细菌快速检测中的应用. 微生物学通报, 1, 161-168.
[31] Kenters, N., Henderson, G., Jeyanathan, J., Kittelmann, S. and Janssen, P.H. (2010) Isolation of previously uncultured rumen bacteria by dilution to extinction using a new liquid culture medium. Journal of Microbiological Methods, 84, 52-60.
[32] 田甜, 李冬梅, 戴世鲲 (2009) 海洋环境中难培养微生物的寡营养培养. 微生物学通报, 7, 1031-1039.
[33] Connon, S.A. and Giovannoni, S.J. (2002) High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates. Applied and Environmental Microbiology, 68, 3878-3885.
[34] Nichols, D., Cahoon, N., Trakhtenberg, E.M., Pham, L., Mehta, A., Belanger, A., Kanigan, T., Lewis, K. and Epstein, S.S. (2010) Use of ichip for highthrough put in Situ cultivation of “uncultiva-ble”microbial species. Applied and Environmental Microbiology, 76, 2445-2450.
[35] Bruns, A., Cypionka, H. and Overmann, J. (2002) Cyclic AMP and acyl homoserine lactones increase the cultivation efficiency of heterotrophic bacteria from the central Baltic sea. Applied and Environmental Microbiology, 68, 39783987.
[36] Hirakawa, H. (2013) Tomita H: A new class of Acyl-homoserine lactone quorum sensing signals. Nihon Saikingaku Zasshi, 68, 325-335.
[37] Upfoff, H.U., Felske, A., Fehr, W. and Wagner-Döbler, I. (2001) The microbial diversity in picoplankton enrichment cultures: A molecular screening of marine isolates. FEMS Microbiology Ecology, 35, 249-258.
[38] Coates, J.D., Cole, K.A., Chakraborty, R., O’Connor, S.M. and Achenbach, L.A. (2002) Diversity and ubiquity of bacteria capable of utilizing humic substances as electron donors for anaerobic respiration. Applied and Environmental Microbiology, 68, 2445-2452.
[39] Santini, J.M., Sly, L.I., Schnagl, R.D. and Macy, J.M. (2000) A new chemolitho-autotrophic arsenite-oxidizing bacterium isolated from a gold mine: Phylogenetic, physiological, and preliminary biochemical studies. Applied and Environmental Microbiology, 66, 92-97.
[40] Oremland, R.S., Hoeft, S.E., Santini, J.M., Bano, N., Hollibaugh, R.A. and Hollibaugh, J.T. (2002) Anaerobic oxidation of arsenite in Mono Lake water and by a facultative, arsenite-oxidizing chemoautotroph, strain MIHE-1. Applied and Environmental Microbiology, 68, 4795-4802.
[41] Schink, B. and Friedrich, M. (2000) Phosphite oxidation by sulfate reduction. Nature, 6, 37-43.
[42] Schink, B., Thiemann, V., Laue, H. and Friedrich, M.W. (2002) Desulfotigenum phosphitoxidans sp.nov., a new marine sulfate reducer that oxidizes phosphite to phosphate. Archives of Microbiology, 177, 381-391.
[43] Coates, J.D., Chakraborty, R., Lack, J.D., O’Connor, S.M., Cole, K.A., Bender, K.S. and Achenbach, L.A. (2001) Anaerobic benzene oxidation coupled to nitrate reduction in pure culture by two strains of Dechloromonas. Nature, 411, 1039-1043.
[44] Sanford, R.A., Cole, J.R. and Tiedje, J.M. (2002) Characterization and description of Anaeromyxobacter dehalogenans gen. nov., sp. nov., an aryl-halorespiring facultative anaerobic Myxobacterium. Applied and Environmental Microbiology, 68, 893-900.
[45] Achenbach, L.A., Michaelidou, U., Bruce, R.A., Fryman, J. and Coates, J.D. (2001) Dechloromonas agitala gen. nov., sp. nov. and Dechlorosoma suillum gen. nov., sp. nov., two novel environmentally dominant (per) chlorate-reducing bacteria and their phylogenetlc position. International Journal of Systematic and Evolutionary Microbiology, 51, 527533.
[46] Emerson, D. and Moyer, C.L. (2002) Neutrophilic Fe-oxidizing bacteria are abundant at the Loihi Seamount hydrothermal vents and play a major role in Fe oxide deposition. Applied and Environmental Microbiology, 68, 3085-3093.
[47] D’Onofrio, A., Crawford, J.M., Witt, K., Gavrish, E., Epstein, S., Clardy, J. and Lewis, K. (2010) Siderophores from neighboring organisms promote the growth of uncultured bacteria. Chemistry & Biology, 17, 254-264.
[48] Plugge, C.M. and Stams, A.J. (2002) Enrichment of thermophilic syntrophic anaerobic glutamate-degrading consortia using a dialysis membrane reactor. Microbial Ecology, 43, 379-387.
[49] Zengler, K., Walcher, M., Clark, G., Haller, I., Toledo, G., Holland, T., Mathur, E.J., Woodnutt, G., Short, J.M. and Keller, M. (2005) High-throughput cuhivation of microorganisms using microcapsules. Methods in Enzymology, 397, 124-130.
[50] 高秀珍 (2010) 微包埋培养技术的建立及其在粘细菌分离纯化中的应用. 硕士学位论文, 山东大学, 济南.
[51] Kaeberlein, T., Lewis, K. and Epstein, S.S. (2002) Isolating “uncultivable” microorganisms in pure culture in a simulated natural environment. Science, 296, 1127-1129.
[52] 丁林贤, 张萍华, 洪华嫦, 林红军, 横田明 (2012) 藤黄微球菌Rpf活性蛋白的制取及其对红球菌VBNC菌体的复苏作用. 微生物学报, 1, 77-82.
[53] Bollmann, A., Palumbo, A.V., Lewis, K. and Epstein, S.S. (2010) Isolation and physiology of bacteria from contaminated subsurface sediments. Applied and Environmental Microbiology, 76, 7413-7419.
[54] 曾建民, 曾振顺, 原红娟 (2012) 难培养微生物培养方法的研究进展. 生物技术进展, 3, 165-170.
[55] Stevenson, B.S., Eichorst, S.A., Wertz, J.T., Schmidt, T.M. and Breznak, J.A. (2004) New strategies for cultivation and detection of previously uncultured microbes. Applied and Environmental Microbiology, 70, 4748-4755.
[56] Nichols, D., Lewis, K., Orjala, J., Mo, S., Ortenberg, R., O’Connor, P., Zhao, C., Vouros, P., Kaeberlein, T. and Epstein, S.S. (2008) Short peptide induces an “uncultivable” microorganism to grow in Vitro. Applied and Environmental Microbiology, 74, 4889-4897.
[57] Gavrish, E., Bollmann, A., Epstein, S. and Lewis, K. (2008) A trap for in Situ cultivation of filamentous Actinobacteria. Journal of Microbiological Methods, 72, 257-262.
[58] Alain, K. and Querellon, J. (2009) Cultivating the uncultured: Limits, advances and future challenges. Extremophiles, 13, 583-594.