한국물환경학회지 (Journal of Korean Society on Water Environment)

  • 제22권2호
  • /
  • Pages.193-202
  • /
  • 2006
  • /
  • 2289-0971(pISSN)
  • /
  • 2289-098X(eISSN)
한국물환경학회 (Korean Society on Water Environment)
권호 표지

Real-time PCR 기술의 생물학적 폐수처리에서의 응용

Application of Real-time PCR Techniques for the Biological Wastewater Treatment

  • 엄호섭 (한국과학기술연구원 유해물질연구센터) ;
  • 이선미 (한국과학기술연구원 유해물질연구센터) ;
  • 상병인 (한국과학기술연구원 유해물질연구센터) ;
  • 정윤철 (한국과학기술연구원 유해물질연구센터)
  • Eom, Ho-Seop (Hazardous Substances Research Center, Korea Institute of Science and Technology) ;
  • Lee, Sun-Mi (Hazardous Substances Research Center, Korea Institute of Science and Technology) ;
  • Sang, Byoung-In (Hazardous Substances Research Center, Korea Institute of Science and Technology) ;
  • Chung, Yun-Chul (Hazardous Substances Research Center, Korea Institute of Science and Technology)
  • 투고 : 2005.11.15
  • 심사 : 2006.02.08
  • 발행 : 2006.03.30
PDF 다운로드
⟨ 이전 논문 다음 논문 ⟩

초록

About 99% of microorganisms in the environment are unculturable. However, advances in molecular biology techniques allow for the analysis of living microorganisms in the environment without any cultivation. With the advent of new technologies and the optimization of previous methods, various approaches to studying the analysis of living microorganisms in the environment are expanding the field of microbiology and molecular biology. In particular, real-time PCR provides methods for detecting and quantifying microorganisms in the environment. Through the use of the methods, researchers can study the influence of environmental factors such as nutrients, oxygen status, pH, pollutants, agro-chemicals, moisture and temperature on the performances of environmental processes and some of the mechanisms involved in the responses of cells to their environment. This review will also address information gaps in the analysis of the microorganisms using real-time PCR in the environmental process and possible future research to develop an understanding of microbial activities in the environment.

키워드

과제정보

연구 과제 주관 기관 : 환경부

참고문헌

  1. 기초기술연구회, 생명공학 TRM 및 전략분야 연구 (2003)
  2. Aguilar, M. I., Sa'ez, J., Llorens, M., Soler, A. and Ortuno, J. F., Nutrient Removal and Sludge Production in the Coagulation-Flocculation Process, Water Research, 36, pp. 2910-2919 (2002) https://doi.org/10.1016/S0043-1354(01)00508-5
  3. Aoi, Y., Masaki, Y., Tsuneda, S. and Hirata, A., Quantitative Analysis of amoA mRNA Expression as a New Biomarker of Ammonia Oxidation Activities in a Complex Microbial Community, Letters in Applied Microbiology, 39, pp. 477482 (2004) https://doi.org/10.1111/j.1472-765X.2004.01585.x
  4. Avrahami, S., Conrad, R. and Braker, G., Effect of Soil Ammonium Concentration on $N_2O$Release and on the Community Structure of Ammonia Oxidizers and Denitrifiers, Appl. Environ. Microbiol., 68, pp. 5685-5692 (2003)
  5. Bach, H. J., Tomanova, J., Schloter, M. and Munch, J. C., Enumeration of Total Bacteria and Bacteria with Genes for Proteolytic Activity in Pure Cultures and in Environmental Samples by Quantitative PCR Mediated Amplification, J. Microbio!. Methods, 49, pp. 235-245 (2002) https://doi.org/10.1016/S0167-7012(01)00370-0
  6. Bange, H. W., Global change. It's not a gas, Nature, 16, pp. 301-302 (2000) https://doi.org/10.1038/016301a0
  7. Becker-Andre, M. and Hahlbrock, K., Absolute mRNA Quantification Using the Polymerase Chain Reaction, A Novel Approach by a PCR Aided Transcript Titration Assay PATTY, Nucleic Acids Research, 17, pp. 9437-9446 (1989) https://doi.org/10.1093/nar/17.22.9437
  8. Bradford, D., Christensson, C, Jakab, N. and Blackall, L. L., Microthrix parvicella and to Determine its Abundance in Activated Sludge, Molecular Bological Methods to Detect, Water Science and Technology, 37, pp. 37-45 (1998)
  9. Braker, G., Ayala-del-Rio, H. L., Devol, A. H., Fesefeldt, A. and Tiedje, J. M., Community Structure of Denitrifiers, Bacteria, and Archaea along Redox Gradients in Pacific Northwest Marine Sediments by Terminal Restriction Fragment Length Polymorphism Analysis of Amplified Nitrite Reductase (nirS) and 16S rRNA Genes, Appl. Environ. Microbiol., 67, pp. 1893-1901 (2001) https://doi.org/10.1128/AEM.67.4.1893-1901.2001
  10. Connell, C. R. and Bloch, W., Allelic Discrimination by Nicktranslation PCR with Fluorogenic Probes., Nucleic Acids Research, 21(16), pp. 3761-3766 (1993) https://doi.org/10.1093/nar/21.16.3761
  11. David, J. S. and Lee, .J. K., Nitrous Oxide Reductase (nosZ) Gene-specific PCR Primers for Detection of Denitrifiers and three nosZ Genes from Marine Sediments, FEMS Microbiology Letters, 162, pp. 61-68 (1998) https://doi.org/10.1111/j.1574-6968.1998.tb12979.x
  12. de los Reyes, M. F., de los Reyes, F. L. III, Hernandez, M. and Raskin, Quantification of Gordona Amarae Strains in Foaming Activated Sludge and Anaerobic Digester Systems with Oligonucleotide Hybridization Probes, L. Applied and Environmental Microbiology, 64, pp. 2503-2512 (1998)
  13. Dionisi, H. M., Layton, A. C., Harms, G., Gregory, I. R., Robinson, K. G. and Sayler, G. S., Quantification of Nitrosomonas Oligotropha-like Ammonia-oxidizing Bacteria and Nitrospira spp. from Full-scale Wastewater Treatment Plants by Competitive PCR, Applied and Environmental Microbiology, 68(1), pp. 245-253 (2002) https://doi.org/10.1128/AEM.68.1.245-253.2002
  14. Gamble, T. N., Bctlach, M. R. and Tiedje, J. M., Numerically Dominant Denitrifying Bacteria From World Soils, Appl. Environ. Microbiol., 33, pp. 926-939 (1977)
  15. Gilliand, G., Perrin, S., Blanchard, K. and Bunn, F., Analysis of Cytokine mRNA and DNA: Detection and Quantitation by Competitive Polymerase Chain Reaction, Proceedings of the National Academy of Sciences, 87, pp. 2725-2729 ( 1990)
  16. Guan, Y., Kurisu, F., Satoh, H. and Mino, T., A Quantitative Method for Measuring the Mass Concentration of the Filamentous Bacterium Type 021N in Activated Sludge using Fluorescence In Situ Hybridization, Letters in Applied Microbiology, 37, pp. 100-104 (2003) https://doi.org/10.1046/j.1472-765X.2003.01356.x
  17. Hall, G., Nitrification in Lakes. In J. I. Prosser (cd.), Nitrification. IRL Press, Oxford, pp. 127-156 (1986)
  18. Harms, G., Layton, A. C, Dionisi, H. M., Gregory, I. R., Garrett, V. M., Hawkins, S. A., Robinson, K. G. and Sayler, G. S., Real-Time PCR Quantification of Nitrifying Bacteria in a Municipal Wastewater Treatment Plant, Environ. Sci. Technol., 37(2), pp. 343-351 (2003) https://doi.org/10.1021/es0257164
  19. Haugland, R. A., Vesper, S. J. and Wymer, L. .J., Quantitative Measurement of Stachybotrys Chartarum Conidia using Real time Detection of PCR Products with the $TaqMan^{TM}$ Fluorogenic Probe System, Mol. Cell. Probes, 13, pp. 329340 (1999) https://doi.org/10.1006/mcpr.1999.0258
  20. Henrya. S., Baudoinb, E., Lopez-Gutierreza, .J. C., MartinLaurenta, F., Braumanb, A. and Philippot, L., Quantification of Denitrifying Bacteria in Soils by nirK Gene Targeted Real-time PCR, Journal of Microhiological Methods, 59, pp. 327-335 (2004) https://doi.org/10.1016/j.mimet.2004.07.002
  21. Hermansson, A. and Lindgren, P. E., Quantification of Ammonia-oxidizing Bacteria in Arable Soil by Real-time PCR, Applied and Environmental Microbiology, 67(2), pp. 972-976 (2001) https://doi.org/10.1128/AEM.67.2.972-976.2001
  22. Higuchi, R., Dollinger, G., Walsh, P. S. and Griffith, R., Simultaneous Amplification and Detection of Specific DNA Sequences, Biotechnology(NY), 10(4), pp. 413-417 (1992) https://doi.org/10.1038/nbt0492-413
  23. Higuchi, R., Fockler, C., Dollinger, G. and Watson, R., Kinetic PCR Analysis: Real-time Monitoring of DNA Amplification Reactions, Biotechnology(NY), 11(9), pp. 1026-1030 (1993) https://doi.org/10.1038/nbt0993-1026
  24. John, S. and Georgina, F., The Common Thread, Black Swan press, 2nd edition, chapter 2. (2003)
  25. Kaetzke, A., Jentzsch, D. and Eschrich, K., Quantification of Microthrix Parvicella in Activated Sludge Bacterial Communities by Real-time PCR, Letters in Applied Microbioogyl, 40(3) pp. 207-211 (2005) https://doi.org/10.1111/j.1472-765X.2005.01656.x
  26. Kawai, A., Sugiyama, M., Shiozaki, R. and Sugahara, I., Microbiological Studies on the Nitrogen Cycle in Aquatic Environments, Mem. Res. lnst. Food Sci. Kyoto Univ., 32, pp. 7-15 (1971)
  27. Killham, K., Heterotrophic Nitrification, In J. I. Prosser (ed.), Nitrification. IRL Press, Oxford, pp. 117-126 (1986)
  28. Kimura, H., Morita, M., Yabuta, Y., Kuzushima, K., Kato, K., Kojima, S., Matsuyama, T. and Morishima, T., Quantitative Analysis of Epstein-Barr Virus Load by using a Real-time PCR Assay, J. Clin. Microbiol., 37, pp. 132-136 (1999)
  29. Kirstein, K. and Bock, E., Close Genetic Relationship between Nitrobacter Hamburgensis Nitrobacter Hamburgensis Nitrite Oxidoreductase and Escherichia Coli Escherichia Coli Nitrate Reductases, Arch. Microbiol, 160, pp. 447-453 (1993) https://doi.org/10.1007/BF00245305
  30. Kolb, S., Knief, C., Stubner, S. and Conrad, R., Quantitative Detection of Metanotrophs in Soil by Novel pmoA Targeted Real-time PCR Assays, Appl. Environ Microbiol., 69, pp. 2423-2429 (2003). https://doi.org/10.1128/AEM.69.5.2423-2429.2003
  31. Lashof, D. A. and Lashof, D. R., Relative Contributions of Greenhouse Gas Emissions to Global Warming, Nature, 3, pp. 529-531 (1995) https://doi.org/10.1038/nmat1163
  32. Lebek, M. and Rosenwinkel, K. H., Control of the Growth of Microthrix parvicella by using an Aerobic Selector - Results of Pilot and Full Scale Plant Operation, Water Science and Technology, 46, pp. 491-494 (2002) https://doi.org/10.2166/wst.2002.0522
  33. Lee, Y. and Oleszkiewicz, J. A., Bench-scale Assessment of the Effectiveness of an Anaerobic Selector in Controlling Filamentous Bulking, Environmental Technology, 25, pp. 751-755 (2004) https://doi.org/10.1080/09593330.2004.9619365
  34. Liu, X., Tiquia, S. M., Holguin, G., Wu, L.., Nold, S. C, Devol, A. H., Luo, K., Palumbo, A. V., Tiedje, J. M. and Zhou, J., Molecular Diversity of Denitrifying Genes in Continental Marine Sediments within the Oxygen-deficient Zone off the Pacific Coast of Mexico, Appl. Environ. Microbiol., 69, pp. 3549-3560 (2003) https://doi.org/10.1128/AEM.69.6.3549-3560.2003
  35. Livak, K. J., Flood, S. .J., Marmaro, J., Giusti, W. and Deetz, K., Oligonucleotides with Fluorescent Dyes at Opposite Ends Provide a Quenched Probe System Useful for Detecting PCR Product and Nucleic Acid Hybridization, PCR Methods, 4(6), pp. 357-362 (1995) https://doi.org/10.1101/gr.4.6.357
  36. Lopez-Gutierrez, J. C., Henry, S., Hallet, S., Martin-Laurent, F., Catroux, G. and Philippot, L., Quantification of a Novel Group of Nitrate-reducing Bacteria in the Environment by Real-time PCR, J. Microbiol. Methods, 57, pp. 399-407 (2004) https://doi.org/10.1016/j.mimet.2004.02.009
  37. Oerther, D. B., de los Reyes, F. L. IIl, de los Reyes, M. F. and Raskin, L., Quantifying Filamentous Microorganisms in Activated Sludge before, during, and after an Incident of Foaming by Oligonucleotide Probe Hybridizations and Antibody Staining, Water Research, 35, pp. 3325-3336 (2001) https://doi.org/10.1016/S0043-1354(01)00057-4
  38. Painter, H. A., Nitrification in the Treatment of Sewage and Waste-water, In .J. I. Prosser (ed.), Nitrification. IRL Press, Oxford, pp. 185-211 (1986)
  39. Philippot, L.., Denitrifying Genes in Bacterial and Archeal Genomes, Biochim. Biophys. Acta, 1577, pp. 355-376 (2002) https://doi.org/10.1016/S0167-4781(02)00420-7
  40. Piatak, M., Luk, K. C, Williams, B. and Lifson, .J. D., Quantitative Competitive Polymerase Chain Reaction for Accurate Quantitation of HIV DNA and RNA Species, Bio'Techniques, 14, pp. 70-80 (1993)
  41. Purkhold, U., Pommerening-Roser, A., Juretschko, S., Schmid, M. C., Koops, H. P. and Wagner, M., Phylogeny of all Recognized Species of Ammonia Oxidizers Based on Comparative 16S rRNA and amoA Sequence Analysis: Implications for Molecular Diversity Surveys., Appl. Environ. Microbiol., 66, pp. 5368-5382 (2000) https://doi.org/10.1128/AEM.66.12.5368-5382.2000
  42. Raskin, L., Poulsen, L. K., Noguera, D. R., Rittmann, B. E. and Stahl, D. A., Quantification of Methanogenic Groups in Anaerobic Biological Reactors by Oligonucleotide Probe Hybridization, Applied and Environmental Microbiology, 60, pp. 1241-1248 (1994)
  43. Rittmann, B. E., McCarty, P. L., Environmental biotechnology .' Principles and applications, Mew York, NY : McGraw-Hill, New York, pp. 470-496 (2001)
  44. Rocls, T., Dauwe, F., Van Damme, S., De Wilde, K. and Roelandt, F., The Influences of PAX-14 on Activated Sludge Systems and in Particular on Microthrix Parvicella Roels, Water Science and Technology, 46, pp. 487-490 (2002) https://doi.org/10.2166/wst.2002.0521
  45. Sawayama, S., Tada, C; Tshukahara, K. and Yagishita, T., Effect of ammonium addition on methanogenic community in a fluidized bed anaerobic digestion, Journal of Bioscience and Bioengineering, 97(1), pp. 64-70 (2004)
  46. Shigematsu, T., Tang, Y., Kawaguchi, H., Ninomiya, K., Kinjima, .J., Kobayashi, T., Morirnura, S. and Kida, K., Effect of Dilution Rate on Structure of a Mesophilic Acetate-Degrading Methanogenic Community during Continuous Cultivation, Journal of Bioscience and Bioengineering, 94(6), pp. 547-558 (2003)
  47. Speece, R. E., Anaerobic Biotechnology for Industrial Wastewaters, Nashvile, TN : Archae Press (1996)
  48. Speece, R. E., Ammonia Inhibition in High-solids Biogasfication : an Overview and Practical Solutions, Environ. Technol., 20, pp. 355-365 (1999) https://doi.org/10.1080/09593332008616828
  49. Stubner, S., Enumeration of 16S rDNA of Desulfotomaculum Lineage I in Rice Field Soil by Real-time PCR with SyberGreen Detection, J. Microbiol. Methods, 50, pp. 155164 (2002)
  50. Veronica, G., Stepheb, C. N., Jizhong, Z. and James, M. T., Pseudomonas Sutzeri Nitrite Reductase Gene Abundance in Environmental Samples Measured by Real-Time PCR, Appl. Environ. Microbiol., 67, pp. 760-768 (2001) https://doi.org/10.1128/AEM.67.2.760-768.2001
  51. Verstraete, W. and Alexander, M., Heterotrophic Nitrification in Samples of Natural Ecosystems, Envir. Sci. Technol., 7(1), pp. 39-43 (1973) https://doi.org/10.1021/es60073a007
  52. Wagner, M. and Loy, A., Bacterial Community Composition and Function In Sewage Treatment Systems Wagner, Current Opinion in Biotechnology, 13, pp. 218-227 (2002) https://doi.org/10.1016/S0958-1669(02)00315-4
  53. Wang, A. M., Doyle, M. V. and Mark, D. F., Quantitation of mRNA by the Polymerase Chain Reaction, Proceedings of the National Academy of Sciences, 86, pp. 9717-9721 (1989)
  54. Ward, B. B., Nitrification in Marine Environments, In, J. l. Prosser (ed.), Nitrification. IRL Press, Oxford, pp. 157-184 (1986)
  55. Ward, B. B. and Cockcroft, A. R., Immunofluorescence Detection of the Denitrifying Strain Pseudomonas stutzeri(ATCC 14405) in Seawater and Intertidal Sediment Environments, Microb. Ecol., 25, pp. 233-246 (1993)
  56. Watson, S. W., Valos, F. W. and Waterbury, J. B., The Family Nitrobacteraceae, In the Prokaryotes, Edited by M.P. Starr et al. Berlin: Springer-Verlag (1981)
  57. Wolfe, R. L., Nancy, I. L, George, I. and Edward, G. M., Ammonia-oxidizing Bacteria in a Chloraminated Distribution System: Seasonal Occurrence, Distribution, and Disinfection Resistance, Appl. Environ. Microbiol., 56(2), pp. 451-462 (1990)
  58. Yang, K., Yu, Y. and Hwang, S., Selective Optimization in Thermophilic Acidogenesis of Cheese-whey Wastewater to Acetic and Butyric Acids : Partial Acidification and Methanation, Water Res., 37(10), pp. 277-286 (2003)
  59. Yang, Y., Tada, C., Tsukahara, K. and Sawayarna, S., Methanogenic Community and Performance of Fixed- and Fluidized-bed Reactors with Reticular Polyurethane Foam with Different Pore Size, Materials Science and Engineering, 24, pp. 803-813 (2004) https://doi.org/10.1016/j.msec.2004.08.022
  60. Yoshie, S., Noda, T., Tsuneda, S., Hirata, A. and Inamori, Y., Salinity Decreases Nitrite Reductase Diversity in Denitrifying Bacteria of Wastewater Treatment Systems, Appl. Environ. Microbiol., 70, pp. 3152-3157 (2004) https://doi.org/10.1128/AEM.70.5.3152-3157.2004
  61. Yu, Y., Kim, J. and Hwang, S., Use of Real-time PCR for Group-specific Quantification of Aceticlastic Methanogens in Anaerobic Processes : Population Dynamics and Community Structures, Biotechnology and bioengineering, accepted, (2005)
  62. Zumft, W. G., Cell Biology and Molecular Basis of Denitrification, Microbial. Mol. BioI. Rev., 61, pp. 533-536 (1997)