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

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)
Publication Information
Journal of Korean Society on Water Environment / v.22, no.2, 2006 , pp. 193-202 More about this Journal
Abstract
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.
Keywords
Biological wastewater treatment; Real-time PCR;
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1 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)   DOI   ScienceOn
2 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)   DOI
3 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)   DOI   ScienceOn
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 Bange, H. W., Global change. It's not a gas, Nature, 16, pp. 301-302 (2000)   DOI
6 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)   DOI   ScienceOn
7 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)   DOI   ScienceOn
8 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)   DOI   ScienceOn
9 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)
10 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)   DOI   ScienceOn
11 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)
12 Killham, K., Heterotrophic Nitrification, In J. I. Prosser (ed.), Nitrification. IRL Press, Oxford, pp. 117-126 (1986)
13 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)
14 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)   DOI   ScienceOn
15 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)
16 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)
17 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)
18 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)   DOI   ScienceOn
19 Ward, B. B., Nitrification in Marine Environments, In, J. l. Prosser (ed.), Nitrification. IRL Press, Oxford, pp. 157-184 (1986)
20 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)
21 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)
22 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)   DOI
23 기초기술연구회, 생명공학 TRM 및 전략분야 연구 (2003)
24 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)
25 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)   DOI
26 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)   DOI   ScienceOn
27 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)   DOI   ScienceOn
28 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)   DOI
29 Speece, R. E., Ammonia Inhibition in High-solids Biogasfication : an Overview and Practical Solutions, Environ. Technol., 20, pp. 355-365 (1999)   DOI   ScienceOn
30 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)   DOI   ScienceOn
31 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)   DOI   ScienceOn
32 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)   DOI   ScienceOn
33 Connell, C. R. and Bloch, W., Allelic Discrimination by Nicktranslation PCR with Fluorogenic Probes., Nucleic Acids Research, 21(16), pp. 3761-3766 (1993)   DOI   ScienceOn
34 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)   DOI   ScienceOn
35 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)   DOI   ScienceOn
36 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)   DOI   ScienceOn
37 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)
38 Speece, R. E., Anaerobic Biotechnology for Industrial Wastewaters, Nashvile, TN : Archae Press (1996)
39 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)   DOI   ScienceOn
40 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)   DOI   ScienceOn
41 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)
42 John, S. and Georgina, F., The Common Thread, Black Swan press, 2nd edition, chapter 2. (2003)
43 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)   DOI   ScienceOn
44 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)
45 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)
46 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)   DOI   ScienceOn
47 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)   DOI   ScienceOn
48 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).   DOI   ScienceOn
49 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)
50 Philippot, L.., Denitrifying Genes in Bacterial and Archeal Genomes, Biochim. Biophys. Acta, 1577, pp. 355-376 (2002)   DOI   ScienceOn
51 Wagner, M. and Loy, A., Bacterial Community Composition and Function In Sewage Treatment Systems Wagner, Current Opinion in Biotechnology, 13, pp. 218-227 (2002)   DOI   ScienceOn
52 Zumft, W. G., Cell Biology and Molecular Basis of Denitrification, Microbial. Mol. BioI. Rev., 61, pp. 533-536 (1997)
53 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)
54 Hall, G., Nitrification in Lakes. In J. I. Prosser (cd.), Nitrification. IRL Press, Oxford, pp. 127-156 (1986)
55 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)   DOI   ScienceOn
56 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)
57 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)   DOI
58 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)
59 Rittmann, B. E., McCarty, P. L., Environmental biotechnology .' Principles and applications, Mew York, NY : McGraw-Hill, New York, pp. 470-496 (2001)
60 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)
61 Lashof, D. A. and Lashof, D. R., Relative Contributions of Greenhouse Gas Emissions to Global Warming, Nature, 3, pp. 529-531 (1995)   DOI
62 Verstraete, W. and Alexander, M., Heterotrophic Nitrification in Samples of Natural Ecosystems, Envir. Sci. Technol., 7(1), pp. 39-43 (1973)   DOI   ScienceOn