环境微生物可培养性影响因素及培养方法研究进展
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摘要
目前,已知并能利用的微生物只是自然界微生物很小的缩影,过低的可培养效率使人类在认识和利用微生物上处于瓶颈阶段。现综述了微生物活的非可培养状态及其检测方法,阐述了微生物可培养性的影响因素,探讨了提高微生物可培养效率的培养策略和方法进展,以期为提高微生物的可培养性和菌种资源开发提供依据。
At present, only a small part of the environmental microorganisms can be recognized and utilized,and the culturable efficiency becomes a bottleneck in making use of the microbial resources. To provide a basis for improving the culturability of microorganisms in the environment, the viable but non-culturable(VBNC) state and the detection methods, and influence factors of the culturability of microorganisms were summarized; the methods for improving the culturable efficiency were discussed.
At present, only a small part of the environmental microorganisms can be recognized and utilized,and the culturable efficiency becomes a bottleneck in making use of the microbial resources. To provide a basis for improving the culturability of microorganisms in the environment, the viable but non-culturable(VBNC) state and the detection methods, and influence factors of the culturability of microorganisms were summarized; the methods for improving the culturable efficiency were discussed.
引文
[1]李昭,乔延路,范晓阳,等.南太平洋环流区底层水可培养细菌多样性研究[J].中国海洋大学学报(自然科学版)(Li Zhao,Qiao Yan-lu,Fan Xiao-yang,et al.Diversity of culturable bacteria in the bottom seawater of the South Pacific Gyre[J].Periodical of Ocean University of China),2014,44(6):52-59.
[2]王宁,包慧芳,崔卫东,等.比什凯克盐碱土壤可培养细菌的多样性[J].微生物学通报(Wang Ning,Bao Hui-fang,Cui Weidong,et al.Diversity of bacteria isolated from saline alkali soil of Bishkek region in Kyrgyzstan[J].Microbiology China),2014,41(9):1733-1740.
[3]Salma M,Rousseaux S,Sequeira-Le Grand A,et al.Characterization of the viable but nonculturable(VBNC)state in Saccharomyces cerevisiae[J].PLo S One,2013,8(10):e77600.
[4]彭伶俐,王琴,辛明秀.自然界中不可培养微生物的研究进展[J].微生物学杂志(Peng Ling-li,Wang Qin,Xin Ming-xiu.Advanced in uncultivable microorganisms in nature[J].Journal of Microbiology),2011,31(2):75-79.
[5]Chen H R,Shen J,Pan G S,et al.Correlations between cyanobacterial density and bacterial transformation to the viable but nonculturable(VBNC)state in four freshwater water bodies[J].Ecotoxicology,2015,24(7):1459-1466.
[6]Xu H S,Roberts N,Singleton F L,et al.Survival and viability of nonculturable Escherichia coli and Vibrio cholerae in the estuarine and marine environment[J].Microbial Ecology,1982,8(4):313-323.
[7]Um H Y,Kong H G,Lee H J,et al.Altered gene expression and intracellular changes of the viable but nonculturable state in Ralstonia solanacearum by copper treatment[J].Plant Pathology Journal,2013,29(4):374-385.
[8]Fu B,Jiang Q,Liu H B,et al.Occurrence and reactivation of viable but non-culturable E.coli in sewage sludge after mesophilic and thermophilic anaerobic digestion[J].Biotechnology Letters,2014,36(2):273-279.
[9]Magajna B A,Schraft H.Campylobacter jejuni biofilm cells become viable but non-culturable(VBNC)in low nutrient conditions at 4℃more quickly than their planktonic counterparts[J].Food Control,2015,50:45-50.
[10]Gin K Y,Goh S G.Modeling the effect of light and salinity on viable but non-culturable(VBNC)Enterococcus[J].Water Research,2013,47(10):3315-3328.
[11]Alleron L,Khemiri A,Koubar M,et al.VBNC Legionella pneumophila cells are still able to produce virulence proteins[J].Water Research,2013,47(17):6606-6617.
[12]王桢,李阳,车帅,等.北极海洋沉积物中可培养细菌及其多样性分析[J].海洋学报(中文版)(Wang Zhen,Li Yang,Che Shuai,et al.Diversity analysis of culturable bacteria isolated from marine sediments of Arctic[J].Acta Oceanologica Sinica(in Chinese)),2014,36(10):116-123.
[13]刘志培,刘双江.我国污染土壤生物修复技术的发展及现状[J].生物工程学报(Liu Zhi-pei,Liu Shuang-jiang.Development of bioremediation in China-a review[J].Chinese Journal of Biotechnology),2015,31(6):901-916.
[14]Aydin S,Shahi A,Ozbayram E G,et al.Use of PCR-DGGE based molecular methods to assessment of microbial diversity during anaerobic treatment of antibiotic combinations[J].Bioresource Technology,2015,192:735-740.
[15]Ravin N V,Mardanov A V,Skryabin K G.Metagenomics as a tool for the investigation of uncultured microorganisms[J].Russian Journal of Genetics,2015,51(5):431-439.
[16]李明源,陈芸,古丽巴哈尔·萨吾提.冰川微生物菌群分布及多样性研究技术进展[J].生命科学研究(Li Ming-yuan,Chen Yun,Sawut Gulbahar.Advance in community distribution of glacial microbe and research techniques for diversity[J].Life Science Research),2015,19(4):357-361.
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[18]许兵,徐怀恕.水生细菌荧光显微计数法的应用和发展[J].微生物学通报(Xu Bing,Xu Huai-shu.Application and development of fluorescence microscopic counting method for aquatic bacteria[J].Microbiology China),1993,20(6):357-362.
[19]Besnard V,Federighi M,Cappelier J M.Development of a direct viable count procedure for the investigation of VBNC state in Listeria monocytogenes[J].Letters in Applied Microbiology,2000,31:77-81.
[20]Parashar D,Paingankar M S,Sudeep A B,et al.Assessment of q PCR,nested RT-PCR and ELISA techniques in diagnosis of Chikungunya[J].Current Science,2014,107(12):2011-2013.
[21]Engvall E,Perlmann P.Enzyme-linked immunosorbent assay(ELISA).Quantitative assay of immunoglobulin G[J].Immunochemistry,1971,8(9):871-874.
[22]徐怀恕,黄备,祁自忠,等.霍乱弧菌(Vibrio cholerae)的细胞形态研究-活的非可培养状态细胞[J].青岛海洋大学学报:自然科学版(Xu Huai-shu,Huang Bei,Qi Zi-zhong,et al.Study on cell morphology of viable but nonculturable Vibrio cholerae[J].Journal of Ocean University of Qingdao),1997,27(2):187-190.
[23]Bellehumeur C,Boyle B,Charette S J.Propidium monoazide(PMA)and ethidium bromide monoazide(EMA)improve DNA array and high-throughput sequencing of porcine reproductive and respiratory syndrome virus identification[J].Journal of Virological Methods,2015,222(6):182-191.
[24]陈传,凌霄,郭震,等.LAMP技术在食源性病原微生物检测中的应用[J].生命科学研究(Chen Chuan,Ling Xiao,Guo Zhen,et al.The application of LAMP technology in detection for forborne pathogenic microorganisms[J].Life Science Research),2014,18(2):140-144.
[25]Zhong Q P,Tian J,Wang B,et al.PMA based real-time fluorescent LAMP for detection of Vibrio parahaemolyticus in viable but nonculturable state[J].Food Control,2016,63:230-238.
[26]邱玉兰,井晓欢,杨季芳,等.“非可培养细菌”培养策略研究进展[J].浙江万里学院学报(Qiu Yu-lan,Jing Xiao-huan,Yang Ji-fang,et al.The research progress in cultivation strategies of uncultivated bacteria[J].Journal of Zhejiang Wanli University),2014,27(3):78-88.
[27]Wu B,Liang W L,Kan B.Growth phase,oxygen,temperature,and starvation affect the development of viable but non-culturable state of Vibrio cholerae[J].Frontiers in Microbiology,2016,7:e1005145.
[28]袁志辉,王健,杨文蛟,等.土壤微生物分离新技术的研究进展[J].土壤学报(Yuan Zhi-hui,Wang Jian,Yang Wen-jiao,et al.Progress in cultivation research on soil microbes[J].Acta Pedologica Sinica),2014,51(6):1183-1191.
[29]Sturbelle R T,Avila L F,Roos T B,et al.The role of quorum sensing in Escherichia coli(ETEC)virulence factors[J].Veterinary Microbiology,2015,180(3):245-252.
[30]徐芳,李军,段云飞,等.细菌群体感应信号网络及其应用[J].生物学杂志(Xu Fang,Li Jun,Duan Yun-fei,et al.Quorum sensing signaling networks in bacteria and the potential application[J].Journal of Biology),2014,31(4):77-81.
[31]王保军,刘双江.环境微生物培养新技术的研究进展[J].微生物学通报(Wang Bao-jun,Liu Shuang-jiang.Perspectives on the cultivability of environmental microorganisms[J].Microbiology China),2013,40(1):6-17.
[32]Su X M,Chen X,Hu J X,et al.Exploring the potential environment functions of viable but non-culturable bacteria[J].World Journal of Microbiology and Biotechnology,2013,29(12):2213-2218.
[33]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].济南:中国海洋大学(Ji Shi-qi.The Establishment and Applications of High-throughput Cultivating and Sorting Method for Marine Microorganisms[D].Jinan:Ocean University of China),2011.
[34]吴月红,韩正兵,张心齐,等.南极普里兹湾可培养浮游细菌群落结构研究[J].极地研究(Wu Yue-hong,Han Zheng-bin,Zhang Xin-qi,et al.Community composition of Antarctic bacterioplankton isolated from the Prydz Bay,Antarctica[J].Chinese Journal of Polar Research),2014,26(2):222-229.
[35]Jallouli W,Zouari N,Jaoua S.Involvement of oxidative stress and growth at high cell density in the viable but nonculturable state of Photorhabdus temperate ssp.temperata strain K122[J].Process Biochemistry,2010,45(5):706-713.
[36]Morishige Y,Fujimori K,Amano F.Differential resuscitative effect of pyruvate and its analogues on VBNC(viable but nonculturable)Salmonella[J].Microbes and Environments,2013,28(2):180-186.
[37]陈丽媛,徐冲.微生物培养技术研究进展[J].微生物学杂志(Chen Li-yuan,Xu Chong.Advanced in microbial technology on cultivation[J].Journal of Microbiology),2013,33(6):93-95.
[38]Connon S A,Giovannoni S J.High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates[J].Applied and Environmental Microbiology,2002,68(8):3878-3885.
[39]Olabisi R M.Cell microencapsulation with synthetic polymers[J].Journal of Biomedical Materials Research.Part A,2015,103(2):846-859.
[40]Ge Z F,Girguis P R,Buie C R.Nanoporous microscale microbial incubators[J].Lab on A Chip,2016,16(3):480-488.
[41]Steinert G,Whitfield S,Taylor M W,et al.Application of diffusion growth chambers for the cultivation of marine sponge-associated bacteria[J].Marine Biotechnology,2014,16(5):594-603.
[42]Kaeberlein T,Lewis K,Epstein S S.Isolating“uncultivable”microorganisms in pure culture in a simulated natural environment[J].Science,2002,296(5570):1127-1129.
[43]Jung D,Seo E Y,Epstein S S,et al.Application of a new cultivation technology,I-tip,for studying microbial diversity in freshwater sponges of Lake Baikal,Russia[J].FEMS Microbiology Ecology,2014,90(2):417-423.
[44]周楠,姜成英,刘双江.从环境中分离培养微生物:培养基营养水平至关重要[J].微生物学通报(Zhou Nan,Jiang Chengying,Liu Shuang-jiang.Cultivation of microorganisms from environments:nutrient level of the culture medium is of great importance[J].Microbiology China),2016,43(5):1057-1081.
[45]Cellini L.Helicobacter pylori:a chameleon-like approach to life[J].World Journal of Gastroenterology,2014,20(19):5575-5582.
[46]郭慧玲,邵玉宇,高姝冉,等.细菌活的非可培养状态研究[J].中国乳品工业(Guo Hui-ling,Shao Yu-yu,Gao Shu-ran,et al.Research on the viable but non-culturable(VBNC)state of bacteria[J].China Dairy Industry),2014,42(1):31-36.
[47]Su X M,Liu Y D,Hu J X,et al.Optimization of protein production by Micrococcus luteus for exploring pollutant-degrading uncultured bacteria[J].Springer Plus,2014,3:117.
[48]Senoh M,Ghosh-Banerjee J,Mizuno T,et al.Isolation of viable but nonculturable Vibrio cholerae O1 from environmental water samples in Kolkata,India,in a culturable state[J].Microbiology Open,2014,3(2):239-246.
[49]Ayrapetyan M,Williams T C,Oliver J D.Interspecific quorum sensing mediates the resuscitation of viable but nonculturable Vibrios[J].Applied and Environmental Microbiology,2014,80(8):2478-2483.
[50]Kong H G,Bae J Y,Lee H J,et al.Induction of the viable but nonculturable state of Ralstonia solanacearum by low temperature in the soil microcosm and its resuscitation by catalase[J].PLo S One,2014,9(10):e109792.
[2]王宁,包慧芳,崔卫东,等.比什凯克盐碱土壤可培养细菌的多样性[J].微生物学通报(Wang Ning,Bao Hui-fang,Cui Weidong,et al.Diversity of bacteria isolated from saline alkali soil of Bishkek region in Kyrgyzstan[J].Microbiology China),2014,41(9):1733-1740.
[3]Salma M,Rousseaux S,Sequeira-Le Grand A,et al.Characterization of the viable but nonculturable(VBNC)state in Saccharomyces cerevisiae[J].PLo S One,2013,8(10):e77600.
[4]彭伶俐,王琴,辛明秀.自然界中不可培养微生物的研究进展[J].微生物学杂志(Peng Ling-li,Wang Qin,Xin Ming-xiu.Advanced in uncultivable microorganisms in nature[J].Journal of Microbiology),2011,31(2):75-79.
[5]Chen H R,Shen J,Pan G S,et al.Correlations between cyanobacterial density and bacterial transformation to the viable but nonculturable(VBNC)state in four freshwater water bodies[J].Ecotoxicology,2015,24(7):1459-1466.
[6]Xu H S,Roberts N,Singleton F L,et al.Survival and viability of nonculturable Escherichia coli and Vibrio cholerae in the estuarine and marine environment[J].Microbial Ecology,1982,8(4):313-323.
[7]Um H Y,Kong H G,Lee H J,et al.Altered gene expression and intracellular changes of the viable but nonculturable state in Ralstonia solanacearum by copper treatment[J].Plant Pathology Journal,2013,29(4):374-385.
[8]Fu B,Jiang Q,Liu H B,et al.Occurrence and reactivation of viable but non-culturable E.coli in sewage sludge after mesophilic and thermophilic anaerobic digestion[J].Biotechnology Letters,2014,36(2):273-279.
[9]Magajna B A,Schraft H.Campylobacter jejuni biofilm cells become viable but non-culturable(VBNC)in low nutrient conditions at 4℃more quickly than their planktonic counterparts[J].Food Control,2015,50:45-50.
[10]Gin K Y,Goh S G.Modeling the effect of light and salinity on viable but non-culturable(VBNC)Enterococcus[J].Water Research,2013,47(10):3315-3328.
[11]Alleron L,Khemiri A,Koubar M,et al.VBNC Legionella pneumophila cells are still able to produce virulence proteins[J].Water Research,2013,47(17):6606-6617.
[12]王桢,李阳,车帅,等.北极海洋沉积物中可培养细菌及其多样性分析[J].海洋学报(中文版)(Wang Zhen,Li Yang,Che Shuai,et al.Diversity analysis of culturable bacteria isolated from marine sediments of Arctic[J].Acta Oceanologica Sinica(in Chinese)),2014,36(10):116-123.
[13]刘志培,刘双江.我国污染土壤生物修复技术的发展及现状[J].生物工程学报(Liu Zhi-pei,Liu Shuang-jiang.Development of bioremediation in China-a review[J].Chinese Journal of Biotechnology),2015,31(6):901-916.
[14]Aydin S,Shahi A,Ozbayram E G,et al.Use of PCR-DGGE based molecular methods to assessment of microbial diversity during anaerobic treatment of antibiotic combinations[J].Bioresource Technology,2015,192:735-740.
[15]Ravin N V,Mardanov A V,Skryabin K G.Metagenomics as a tool for the investigation of uncultured microorganisms[J].Russian Journal of Genetics,2015,51(5):431-439.
[16]李明源,陈芸,古丽巴哈尔·萨吾提.冰川微生物菌群分布及多样性研究技术进展[J].生命科学研究(Li Ming-yuan,Chen Yun,Sawut Gulbahar.Advance in community distribution of glacial microbe and research techniques for diversity[J].Life Science Research),2015,19(4):357-361.
[17]Kogure K,Simidu U,Taga N.A tentative direct microscopic method for counting living marine bacteria[J].Canadian Journal of Microbiology,1979,25(3):415-420.
[18]许兵,徐怀恕.水生细菌荧光显微计数法的应用和发展[J].微生物学通报(Xu Bing,Xu Huai-shu.Application and development of fluorescence microscopic counting method for aquatic bacteria[J].Microbiology China),1993,20(6):357-362.
[19]Besnard V,Federighi M,Cappelier J M.Development of a direct viable count procedure for the investigation of VBNC state in Listeria monocytogenes[J].Letters in Applied Microbiology,2000,31:77-81.
[20]Parashar D,Paingankar M S,Sudeep A B,et al.Assessment of q PCR,nested RT-PCR and ELISA techniques in diagnosis of Chikungunya[J].Current Science,2014,107(12):2011-2013.
[21]Engvall E,Perlmann P.Enzyme-linked immunosorbent assay(ELISA).Quantitative assay of immunoglobulin G[J].Immunochemistry,1971,8(9):871-874.
[22]徐怀恕,黄备,祁自忠,等.霍乱弧菌(Vibrio cholerae)的细胞形态研究-活的非可培养状态细胞[J].青岛海洋大学学报:自然科学版(Xu Huai-shu,Huang Bei,Qi Zi-zhong,et al.Study on cell morphology of viable but nonculturable Vibrio cholerae[J].Journal of Ocean University of Qingdao),1997,27(2):187-190.
[23]Bellehumeur C,Boyle B,Charette S J.Propidium monoazide(PMA)and ethidium bromide monoazide(EMA)improve DNA array and high-throughput sequencing of porcine reproductive and respiratory syndrome virus identification[J].Journal of Virological Methods,2015,222(6):182-191.
[24]陈传,凌霄,郭震,等.LAMP技术在食源性病原微生物检测中的应用[J].生命科学研究(Chen Chuan,Ling Xiao,Guo Zhen,et al.The application of LAMP technology in detection for forborne pathogenic microorganisms[J].Life Science Research),2014,18(2):140-144.
[25]Zhong Q P,Tian J,Wang B,et al.PMA based real-time fluorescent LAMP for detection of Vibrio parahaemolyticus in viable but nonculturable state[J].Food Control,2016,63:230-238.
[26]邱玉兰,井晓欢,杨季芳,等.“非可培养细菌”培养策略研究进展[J].浙江万里学院学报(Qiu Yu-lan,Jing Xiao-huan,Yang Ji-fang,et al.The research progress in cultivation strategies of uncultivated bacteria[J].Journal of Zhejiang Wanli University),2014,27(3):78-88.
[27]Wu B,Liang W L,Kan B.Growth phase,oxygen,temperature,and starvation affect the development of viable but non-culturable state of Vibrio cholerae[J].Frontiers in Microbiology,2016,7:e1005145.
[28]袁志辉,王健,杨文蛟,等.土壤微生物分离新技术的研究进展[J].土壤学报(Yuan Zhi-hui,Wang Jian,Yang Wen-jiao,et al.Progress in cultivation research on soil microbes[J].Acta Pedologica Sinica),2014,51(6):1183-1191.
[29]Sturbelle R T,Avila L F,Roos T B,et al.The role of quorum sensing in Escherichia coli(ETEC)virulence factors[J].Veterinary Microbiology,2015,180(3):245-252.
[30]徐芳,李军,段云飞,等.细菌群体感应信号网络及其应用[J].生物学杂志(Xu Fang,Li Jun,Duan Yun-fei,et al.Quorum sensing signaling networks in bacteria and the potential application[J].Journal of Biology),2014,31(4):77-81.
[31]王保军,刘双江.环境微生物培养新技术的研究进展[J].微生物学通报(Wang Bao-jun,Liu Shuang-jiang.Perspectives on the cultivability of environmental microorganisms[J].Microbiology China),2013,40(1):6-17.
[32]Su X M,Chen X,Hu J X,et al.Exploring the potential environment functions of viable but non-culturable bacteria[J].World Journal of Microbiology and Biotechnology,2013,29(12):2213-2218.
[33]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].济南:中国海洋大学(Ji Shi-qi.The Establishment and Applications of High-throughput Cultivating and Sorting Method for Marine Microorganisms[D].Jinan:Ocean University of China),2011.
[34]吴月红,韩正兵,张心齐,等.南极普里兹湾可培养浮游细菌群落结构研究[J].极地研究(Wu Yue-hong,Han Zheng-bin,Zhang Xin-qi,et al.Community composition of Antarctic bacterioplankton isolated from the Prydz Bay,Antarctica[J].Chinese Journal of Polar Research),2014,26(2):222-229.
[35]Jallouli W,Zouari N,Jaoua S.Involvement of oxidative stress and growth at high cell density in the viable but nonculturable state of Photorhabdus temperate ssp.temperata strain K122[J].Process Biochemistry,2010,45(5):706-713.
[36]Morishige Y,Fujimori K,Amano F.Differential resuscitative effect of pyruvate and its analogues on VBNC(viable but nonculturable)Salmonella[J].Microbes and Environments,2013,28(2):180-186.
[37]陈丽媛,徐冲.微生物培养技术研究进展[J].微生物学杂志(Chen Li-yuan,Xu Chong.Advanced in microbial technology on cultivation[J].Journal of Microbiology),2013,33(6):93-95.
[38]Connon S A,Giovannoni S J.High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates[J].Applied and Environmental Microbiology,2002,68(8):3878-3885.
[39]Olabisi R M.Cell microencapsulation with synthetic polymers[J].Journal of Biomedical Materials Research.Part A,2015,103(2):846-859.
[40]Ge Z F,Girguis P R,Buie C R.Nanoporous microscale microbial incubators[J].Lab on A Chip,2016,16(3):480-488.
[41]Steinert G,Whitfield S,Taylor M W,et al.Application of diffusion growth chambers for the cultivation of marine sponge-associated bacteria[J].Marine Biotechnology,2014,16(5):594-603.
[42]Kaeberlein T,Lewis K,Epstein S S.Isolating“uncultivable”microorganisms in pure culture in a simulated natural environment[J].Science,2002,296(5570):1127-1129.
[43]Jung D,Seo E Y,Epstein S S,et al.Application of a new cultivation technology,I-tip,for studying microbial diversity in freshwater sponges of Lake Baikal,Russia[J].FEMS Microbiology Ecology,2014,90(2):417-423.
[44]周楠,姜成英,刘双江.从环境中分离培养微生物:培养基营养水平至关重要[J].微生物学通报(Zhou Nan,Jiang Chengying,Liu Shuang-jiang.Cultivation of microorganisms from environments:nutrient level of the culture medium is of great importance[J].Microbiology China),2016,43(5):1057-1081.
[45]Cellini L.Helicobacter pylori:a chameleon-like approach to life[J].World Journal of Gastroenterology,2014,20(19):5575-5582.
[46]郭慧玲,邵玉宇,高姝冉,等.细菌活的非可培养状态研究[J].中国乳品工业(Guo Hui-ling,Shao Yu-yu,Gao Shu-ran,et al.Research on the viable but non-culturable(VBNC)state of bacteria[J].China Dairy Industry),2014,42(1):31-36.
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