Quantitative real-time PCR approaches for microbial community studies in wastewater treatment systems: Applications and considerations

Biotechnology Advances

Volumn 31, Issue 8, 2013, Pages 1358-1373

  Kim, Jaai ^a   Lim, Juntaek ^b   Lee, Changsoo ^a  

^a Ulsan National Institute of Science and Technology   (South Korea)

^b POSCO   (South Korea)

Author keywords

Absolute quantification; Microbial community analysis; Nucleic acids; Quantitative real time PCR (qPCR); Wastewater treatment

Indexed keywords

ABSOLUTE QUANTIFICATION; ACCURATE QUANTIFICATIONS; GROUP-SPECIFIC PRIMERS; MICROBIAL COMMUNITIES; MICROBIAL COMMUNITY ANALYSIS; MOLECULAR TECHNIQUES; QUANTITATIVE REAL TIME PCR; WASTEWATER TREATMENT SYSTEM;

BIOMOLECULES; DNA SEQUENCES; ECOLOGY; MICROORGANISMS; NUCLEIC ACIDS; RECLAMATION; WASTEWATER TREATMENT;

POLYMERASE CHAIN REACTION;

DATABASE; DNA; MICROBIAL COMMUNITY; MICROBIAL ECOLOGY; NUCLEIC ACID; POLYMERASE CHAIN REACTION; WASTEWATER; WATER TREATMENT;

BACTERIAL DNA; NUCLEIC ACID;

ABSOLUTE QUANTIFICATION; BACTERIUM; CLASSIFICATION; GENETICS; ISOLATION AND PURIFICATION; METHODOLOGY; MICROBIAL COMMUNITY ANALYSIS; MICROBIAL CONSORTIUM; MICROBIOLOGY; QUANTITATIVE REAL-TIME PCR (QPCR); REAL TIME POLYMERASE CHAIN REACTION; REVIEW; WASTE WATER; WASTE WATER MANAGEMENT;

ABSOLUTE QUANTIFICATION; MICROBIAL COMMUNITY ANALYSIS; NUCLEIC ACIDS; QUANTITATIVE REAL-TIME PCR (QPCR); WASTEWATER TREATMENT;

BACTERIA; DNA, BACTERIAL; MICROBIAL CONSORTIA; REAL-TIME POLYMERASE CHAIN REACTION; WASTE WATER;

EID: 84888016266     PISSN: 07349750     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.biotechadv.2013.05.010     Document Type: Review

References (168)

1. Acinas S.G., Marcelino L.A., Klepac-Ceraj V., Polz M.F. Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons. J Bacteriol 2004, 186:2629-2635.
2. Agudelo R.M., Codony F., Adrados B., Fittipaldi M., Penuela G., Morato J. Monitoring bacterial faecal contamination in waters using multiplex real-time PCR assay for Bacteroides spp. and faecal enterococci. Water SA 2010, 36:127-132.
3. Ahn J.H., Yu R., Chandran K. Distinctive microbial ecology and biokinetics of autotrophic ammonia and nitrite oxidation in a partial nitrification bioreactor. Biotechnol Bioeng 2008, 100:1078-1087.
4. Akarsubasi A.T., Ince O., Kirdar B., Oz N.A., Orhon D., Curtis T.P., et al. Effect of wastewater composition on archaeal population diversity. Water Res 2005, 39:1576-1584.
5. Akerlund T., Nordstrom K., Bernander R. Analysis of cell size and DNA content in exponentially growing and stationary-phase batch cultures of Escherichia coli. J Bacteriol 1995, 177:6791-6797.
6. Amann R., Fuchs B.M. Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques. Nat Rev Microbiol 2008, 6:339-348.
7. Amann R.I., Ludwig W., Schleifer K. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 1995, 59:143-169.
8. Aoi Y., Shiramasa Y., Kakimoto E., Tsuneda S., Hirata A., Nagamune T. Single-stage autotrophic nitrogen-removal process using a composite matrix immobilizing nitrifying and sulfur-denitrifying bacteria. Appl Microbiol Biotechnol 2005, 68:124-130.
9. Asvapathanagul P., Huang Z., Gedalanga P.B., Baylor A., Olson B.H. Interaction of operational and physicochemical factors leading to Gordonia amarae-like foaming in an incompletely nitrifying activated sludge plant. Appl Environ Microbiol 2012, 78:8165-8175.
10. Auerbach E.A., Seyfried E.E., McMahon K.D. Tetracycline resistance genes in activated sludge wastewater treatment plants. Water Res 2007, 41:1143-1151.
11. Bae S., Wuertz S. Discrimination of viable and dead fecal Bacteroidales bacteria by quantitative PCR with propidium monoazide. Appl Environ Microbiol 2009, 75:2940-2944.
12. Bae H., Park K.-S., Chung Y.-C., Jung J.-Y. Distribution of anammox bacteria in domestic WWTPs and their enrichments evaluated by real-time quantitative PCR. Process Biochem 2010, 45:323-334.
13. Bai Y., Sun Q., Wen D., Tang X. Abundance of ammonia-oxidizing bacteria and archaea in industrial and domestic wastewater treatment systems. FEMS Microbiol Ecol 2012, 80:323-330.
14. Bendich A.J., Drlica K. Prokaryotic and eukaryotic chromosomes: what's the difference?. Bioessays 2000, 22:481-486.
15. Bessetti J. An introduction to PCR inhibitors. Profiles DNA 2007, 10:9-10.
16. Bitton G. Wastewater microbiology 2011, Wiley-Blackwell, Hoboken, NJ. 4th ed.
17. Bowers H.A., Tengs T., Glasgow H.B., Burkholder J.M., Rublee P.A., Oldach D.W. Development of real-Time PCR assays for rapid detection of Pfiesteria piscicida and related Dinoflagellates. Appl Environ Microbiol 2000, 66:4641-4648.
18. Braker G., Fesefeldt A., Witzel K. Development of PCR primer systems for amplification of nitrite reductase genes (nirK and nirS) to detect denitrifying bacteria in environmental samples. Appl Environ Microbiol 1998, 64:3769-3775.
19. Burggraf S., Olgemoller B. Simple technique for internal control of real-time amplification assays. Clin Chem 2004, 50:819-825.
20. Bustin S.A., Benes V., Garson J.A., Hellemans J., Huggett J., Kubista M., et al. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem 2009, 55:611-622.
21. Case R.J., Boucher Y., Dahllöf I., Holmström C., Doolittle W.F., Kjelleberg S. Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies. Appl Environ Microbiol 2007, 73:278-288.
22. Cawthorn D.M., Witthuhn R.C. Selective PCR detection of viable Enterobacter sakazakii cells utilizing propidium monoazide or ethidium bromide monoazide. J Appl Microbiol 2008, 105:1178-1185.
23. Cook K.L., Whitehead T.R., Spence C., Cotta M.A. Evaluation of the sulfate-reducing bacterial population associated with stored swine slurry. Anaerobe 2008, 14:172-180.
24. Crosby L.D., Criddle C.S. Understanding bias in microbial community analysis techniques due to rrn operon copy number heterogeneity. Biotechniques 2003, 34:2-9.
25. Curtis T.P., Sloan W.T. Prokaryotic diversity and its limits: microbial community structure in nature and implications for microbial ecology. Curr Opin Microbiol 2004, 7:221-226.
26. de los Reyes F.L. Challenges in determining causation in structure-function studies using molecular biological techniques. Water Res 2010, 44:4948-4957.
27. Derveaux S., Vandesompele J., Hellemans J. How to do successful gene expression analysis using real-time PCR. Methods 2010, 50:227-230.
28. Devers M., Soulas G., Martin-Laurent F. Real-time reverse transcription PCR analysis of expression of atrazine catabolism genes in two bacterial strains isolated from soil. J Microbiol Methods 2004, 56:3-15.
29. Drosten C., Gottig S., Schilling S., Asper M., Panning M., Schmitz H., et al. Rapid detection and quantification of RNA of Ebola and Marburg viruses, Lassa virus, Crimean-Congo hemorrhagic fever virus, Rift Valley fever virus, dengue virus, and yellow fever virus by real-time reverse transcription-PCR. J Clin Microbiol 2002, 40:2323-2330.
30. Dumonceaux T.J., Hill J.E., Pelletier C.P., Paice M.G., Van Kessel A.G., Hemmingsen S.M. Molecular characterization of microbial communities in Canadian pulp and paper activated slduge and quantification of a novel Thiothrix eikelboomii-like bulking filament. Can J Microbiol 2006, 52:494-500.
31. Fittipaldi M., Codony F., Adrados B., Camper A., Morat J. Viable real-time PCR in environmental samples: can all data be interpreted directly?. Microb Ecol 2011, 61:7-12.
32. Fleige S., Pfaffl M.W. RNA integrity and the effect on the real-time qRT-PCR performance. Mol Aspects Med 2006, 27:126-139.
33. Flowers J.J., He S., Yilmaz S., Noguera D.R., McMahon K.D. Denitrification capabilities of two biological phosphorus removal sludges dominated by different 'Candidatus Accumulibacter' clades. Environ Microbiol Rep 2009, 1:583-588.
34. Foerstner K.U., von Mering C., Hooper S.D., Bork P. Environments shape the nucleotide composition of genomes. EMBO Rep 2005, 6:1208-1213.
35. Fong T.-T., Phanikumar M.S., Xagoraraki I., Rose J.B. Quantitative detection of human adenoviruses in waste water and combined sewer overflows influencing a Michigan river. Appl Environ Microbiol 2010, 76:715-723.
36. Geets J., de Cooman M., Wittebolle L., Heylen K., Vanparys B., De Vos P., et al. Real-time PCR assay for the simultaneous quantification of nitrifying and denitrifying bacteria in activated sludge. Appl Microbiol Biotechnol 2007, 75:211-221.
37. Gentile A., Anastasopoulos F., McBrien N.A. High-resolution semi-quantitative real-time PCR without the use of a standard curve. Biotechniques 2001, 31:502-508.
38. Gilbride K.A., Lee D.Y., Beaudette L.A. Molecular techniques in wastewater: understanding microbial communities, detecting pathogens, and real-time process control. J Microbiol Methods 2006, 66:1-20.
39. Giovannoni S.J., Britschgi T.B., Moyer C.L., Field K.G. Genetic diversity in Sargasso Sea bacterioplankton. Nature 1990, 345:60-63.
40. Giulietti A., Overbergh L., Valckx D., Decallonne B., Bouillon R., Mathieu C. An overview of real-time quantitative PCR: applications to quantify cytokine gene expression. Methods 2001, 25:386-401.
41. Hall S.J., Hugenholtz P., Siyambalapitiya N., Keller J., Blackall L.L. The development and use of real-time PCR for the quantification of nitrifiers in activated sludge. Water Sci Technol 2002, 46:267-272.
42. Hamelers H., Ter Heijne A., Sleutels T., Jeremiasse A., Strik D., Buisman C. New applications and performance of bioelectrochemical systems. Appl Microbiol Biotechnol 2010, 85:1673-1685.
43. Harms G., Layton A.C., Dionisi H.M., Gregory I.R., Garrett V.M., Hawkins S.A., et al. Real-time PCR quantification of nitrifying bacteria in a municipal wastewater treatment plant. Environ Sci Technol 2003, 37:343-351.
44. He S., Gall D.L., McMahon K.D. "Candidatus Accumulibacter" population structure in enhanced biological phosphorus removal sludges as revealed by polyphosphate kinase genes. Appl Environ Microbiol 2007, 73:5865-5874.
45. Heid C.A., Stevens J., Livak K.J., Williams P.M. Real time quantitative PCR. Genome Res 1996, 6:986-994.
46. Hildenbrand C., Stock T., Lange C., Rother M., Soppa J. Genome copy numbers and gene conversion in methanogenic archaea. J Bacteriol 2011, 193:734-743.
47. Holmes D.E., Chaudhuri S.K., Nevin K.P., Mehta T., Methé B.A., Liu A., et al. Microarray and genetic analysis of electron transfer to electrodes in Geobacter sulfurreducens. Environ Microbiol 2006, 8:1805-1815.
48. Hrudey S.E., Payment P., Huck P.M., Gillham R.W., Hrudey E.J. A fatal waterborne disease epidemic in Walkerton, Ontario: comparison with other waterborne outbreaks in the developed world. Water Sci Technol 2003, 47:7-14.
49. Huang L., Cheng S., Chen G. Bioelectrochemical systems for efficient recalcitrant wastes treatment. J Chem Technol Biotechnol 2010, 86:481-491.
50. Huang Z., Gedalanga P.B., Asvapathanagul P., Olson B.H. Influence of physicochemical and operational parameters on Nitrobacter and Nitrospira communities in an aerobic activated sludge bioreactor. Water Res 2010, 44:4351-4358.
51. Hughes J.B., Hellmann J.J., Ricketts T.H., Bohannan B.J.M. Counting the uncountable: statistical approaches to estimating microbial diversity. Appl Environ Microbiol 2001, 67:4399-4406.
52. Ibekwe A.M., Watt P.M., Grieve C.M., Sharma V.K., Lyons S.R. Multiplex fluorogenic real-Time PCR for detection and quantification of Escherichia coli O157:H7 in dairy wastewater wetlands. Appl Environ Microbiol 2002, 68:4853-4862.
53. Jenkins D., Richard M. Manual on the causes and control of activated sludge bulking and foaming 2003, IWA Publishing, London.
54. Jiang B., Parshina S.N., van Doesburg W., Lomans B.P., Stams A.J.M. Methanomethylovorans thermophila sp. nov., a thermophilic, methylotrophic methanogen from an anaerobic reactor fed with methanol. Int J Syst Evol Microbiol 2005, 55:2465-2470.
55. Jiang J., Li J., Kwan H.S., Au C.H., Law P.T.W., Li L., et al. A cost-effective and universal strategy for complete prokaryotic genomic sequencing proposed by computer simulation. BMC Res Notes 2012, 5:80.
56. Jin T., Zhang T., Yan Q. Characterization and quantification of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in a nitrogen-removing reactor using T-RFLP and qPCR. Appl Microbiol Biotechnol 2010, 87:1167-1176.
57. Kaetzke A., Jentzsch D., Eschrich K. Quantification of Microthrix parvicella in activated sludge bacterial communities by real-time PCR. Lett Appl Microbiol 2005, 40:207-211.
58. Kanto Oqvist C., Kurola J., Pakarinen J., Ekman J., Ikavalko S., Simell J., et al. Prokaryotic microbiota of recycled paper mills with low or zero effluent. J Ind Microbiol Biotechnol 2008, 35:1165-1173.
59. Kim J., Shin S.G., Han G., O'Flaherty V., Lee C., Hwang S. Common key acidogen populations in anaerobic reactors treating different wastewaters: molecular identification and quantitative monitoring. Water Res 2011, 45:2539-2549.
60. Kindaichi T., Kawano Y., Ito T., Satoh H., Okabe S. Population dynamics and in situ kinetics of nitrifying bacteria in autotrophic nitrifying biofilms as determined by real-time quantitative PCR. Biotechnol Bioeng 2006, 94:1111-1121.
61. Klein D. Quantification using real-time PCR technology: applications and limitations. Trends Mol Med 2002, 8:257-260.
62. Kobayashi H., Oethinger M., Tuohy M.J., Hall G.S., Bauer T.W. Unsuitable distinction between viable and dead Staphylococcus aureus and Staphylococcus epidermis by ethidium bromide monoazide. Lett Appl Microbiol 2009, 48:633-638.
63. Könneke M., Bernhard A.E., de la Torre J.R., Walker C.B., Waterbury J.B., Stahl D.A. Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 2005, 437:543-546.
64. Kuhnert P., Boerlin P., Frey J. Target genes for virulence assessment of Escherichia coli isolates from water, food and the environment. FEMS Microbiol Rev 2000, 24:107-117.
65. Kumari S.K.S., Marrengane Z., Bux F. Application of quantitative RT-PCR to determine the distribution of Microthrix parvicella in full-scale activated sludge treatment systems. Appl Microbiol Biotechnol 2009, 83:1135-1141.
66. La Rosa G., Pourshaban M., Iaconelli M., Muscillo M. Quantitative real-time PCR of enteric viruses in influent and effluent samples from wastewater treatment plants in Italy. Ann Ist Super Sanita 2010, 46:266-273.
67. Layton A.C., Dionisi H., Kuo H.W., Robinson K.G., Garrett V.M., Meyers A., et al. Emergence of competitive dominant ammonia-oxidizing bacterial populations in a full-scale industrial wastewater treatment plant. Appl Environ Microbiol 2005, 71:1105-1108.
68. Le Cann P., Ranarijaona S., Monpoeho S., Le Guyader F., Ferre V. Quantification of human astroviruses in sewage using real-time RT-PCR. Res Microbiol 2004, 155:11-15.
69. Lee J.-L., Levin R.E. Use of ethidium bromide monoazide for quantification of viable and dead mixed bacterial flora from fish fillets by polymerase chain reaction. J Microbiol Methods 2006, 67:456-462.
70. Lee D.-Y., Shannon K., Beaudette L.A. Detection of bacterial pathogens in municipal wastewater using an oligonucleotide microarray and real-time quantitative PCR. J Microbiol Methods 2006, 65:453-467.
71. Lee C., Kim J., Shin S.G., Hwang S. Monitoring bacterial and archaeal community shifts in a mesophilic anaerobic batch reactor treating a high-strength organic wastewater. FEMS Microbiol Ecol 2008, 65:544-554.
72. Lee C., Kim J., Hwang K., O'Flaherty V., Hwang S. Quantitative analysis of methanogenic community dynamics in three anaerobic batch digesters treating different wastewaters. Water Res 2009, 43:157-165.
73. Lee C., Kim J., Shin S.G., O'Flaherty V., Hwang S. Quantitative and qualitative transitions of methanogen community structure during the batch anaerobic digestion of cheese-processing wastewater. Appl Microbiol Biotechnol 2010, 87:1963-1973.
74. Lee I.-S., Parameswaran P., Rittmann B.E. Effects of solids retention time on methanogenesis in anaerobic digestion of thickened mixed sludge. Bioresour Technol 2011, 102:10266-10272.
75. Li W.-W., Yu H.-Q. From wastewater to bioenergy and biochemicals via two-stage bioconversion processes: a future paradigm. Biotechnol Adv 2011, 29:972-982.
76. Licence K., Oates K.R., Synge B.A., Reid T.M.S. An outbreak of E. coli O157 infection with evidence of spread from animals to man through contamination of a private water supply. Epidemiol Infect 2001, 126:135-138.
77. Lim J., Do H., Shin S.G., Hwang S. Primer and probe sets for group-specific quantification of the genera Nitrosomonas and Nitrosospira using real-time PCR. Biotechnol Bioeng 2008, 99:1374-1383.
78. Lim J., Shin S.G., Lee S., Hwang S. Design and use of group-specific primers and probes for real-time quantitative PCR. Front Environ Sci Eng China 2011, 5:28-39.
79. Limpiyakorn T., Shinohara Y., Kurisu F., Yagi O. Communities of ammonia-oxidizing bacteria in activated sludge of various sewage treatment plants in Tokyo. FEMS Microbiol Ecol 2005, 54:205-217.
80. Limpiyakorn T., Sonthiphand P., Rongsayamanont C., Polprasert C. Abundance of amoA genes of ammonia-oxidizing archaea and bacteria in activated sludge of full-scale wastewater treatment plants. Bioresour Technol 2011, 102:3694-3701.
81. Lin M.-H., Chen T.-C., Kuo T.-t., Tseng C.-C., Tseng C.-P. Real-Time PCR for quantitative detection of Toxoplasma gondii. J Clin Microbiol 2000, 38:4121-4125.
82. Liu W., Saint D.A. A new quantitative method of real-time reverse transcription polymerase chain reaction assay based on simulation of polymerase chain reaction kinetics. Anal Biochem 2002, 302:52-59.
83. Liu B., Zhang F., Feng X., Liu Y., Yan X., Zhang X., et al. Thauera and Azoarcus as functionally important genera in a denitrifying quinoline-removal bioreactor as revealed by microbial community structure comparison. FEMS Microbiol Ecol 2006, 55:274-286.
84. -δδCT method. Methods 2001, 25:402-408.
85. Ma K., Liu X., Dong X. Methanosaeta harundinacea sp. nov., a novel acetate-scavenging methanogen isolated from a UASB reactor. Int J Syst Evol Microbiol 2006, 56:127-131.
86. Ma B., Peng Y., Zhang S., Wang J., Gan Y., Chang J., et al. Performance of anammox UASB reactor treating low strength wastewater under moderate and low temperatures. Bioresour Technol 2013, 129:606-611.
87. Malandrin L., Huber H., Bernander R. Nucleoid structure and partition in Methanococcus jannaschii: an archaeon with multiple copies of the chromosome. Genetics 1999, 152:1315-1323.
88. Maldonado R., Jimenez J., Casadesus J. Changes of ploidy during the Azotobacter vinelandii growth cycle. J Bacteriol 1994, 176:3911-3919.
89. Malinen E., Kassinen A., Rinttila T., Palva A. Comparison of real-time PCR with SYBR Green I or 5'-nuclease assays and dot-blot hybridization with rDNA-targeted oligonucleotide probes in quantification of delected faecal bacteria. Microbiology 2003, 149:269-277.
90. Marrengane Z., Kumar S.K.S., Pillay L., Bux F. Rapid quantification and analysis of genetic diversity among Gordonia populations in foaming activated sludge plants. J Basic Microbiol 2011, 51:415-423.
91. Mileyko Y., Joh R.I., Weitz J.S. Small-scale copy number variation and large-scale changes in gene expression. Proc Natl Acad Sci 2008, 105:16659-16664.
92. Mori K., Iino T., Suzuki K.-i., Yamaguchi K., Kamagata Y. Aceticlastic and NaCl-requiring methanogen "Methanosaeta pelagica" sp. nov., isolated from marine tidal flat sediment. Appl Environ Microbiol 2012, 78:3416-3423.
93. Mulder A., van de Graaf A.A., Robertson L.A., Kuenen J.G. Anaerobic ammonium oxidation discovered in a denitrifying fluidized bed reactor. FEMS Microbiol Ecol 1995, 16:177-184.
94. Munir M., Wong K., Xagoraraki I. Release of antibiotic resistant bacteria and genes in the effluent and biosolids of five wastewater utilities in Michigan. Water Res 2011, 45:681-693.
95. Ni S.-Q., Gao B.-Y., Wang C.-C., Lin J.-G., Sung S. Fast start-up, performance and microbial community in a pilot-scale anammox reactor seeded with exotic mature granules. Bioresour Technol 2011, 102:2448-2454.
96. Nittami T., Magura T., Imai Y., Matsumoto K. Influence of the electron acceptor on nitrite reductase gene (nir) diversity in an activated sludge community. J Biosci Bioeng 2009, 108:394-399.
97. Nocker A., Camper A.K. Selective removal of DNA from dead cells of mixed bacterial communities by use of ethidium monoazide. Appl Environ Microbiol 2006, 72:1997-2004.
98. Nocker A., Camper A.K. Novel approaches toward preferential detection of viable cells using nucleic acid amplification techniques. FEMS Microbiol Lett 2009, 291:137-142.
99. Nocker A., Cheung C.Y., Camper A.K. Comparison of propidium monoazide and ethidium monoazide for differentiation of live vs. dead bacteria by selective removal of DNA from dead cells. J Microbiol Methods 2006, 67:310-320.
100. Nogva H.K., Dromtorp S.M., Nissen H., Rudi K. Ethidium monoazide for DNA-based differentiation of viable and dead bacteria by 5'-nuclease PCR. Biotechniques 2003, 34:804-813.
101. Obata K., Segawa O., Yakabe M., Ishida Y., Kuroita T., Ikeda K., et al. Development of a novel method for operating magnetic particles, magtration technology, and its use for automating nucleic acid purification. J Biosci Bioeng 2001, 91:500-503.
102. Olsen S.J., Miller G., Breuer T., Kennedy M., Higgins C., Walford J., et al. A waterborne outbreak of Escherichia coli O157:H7 infections and hemolytic uremic syndrome: implications for rural water systems. Emerg Infect Dis 2002, 8:370-375.
103. O'Reilly J., Lee C., Collins G., Chinalia F., Mahony T., O'Flaherty V. Quantitative and qualitative analysis of methanogenic communities in mesophilically and psychrophilically cultivated anaerobic granular biofilims. Water Res 2009, 43:3365-3374.
104. Parameswaran P., Torres C.I., Lee H.-S., Krajmalnik-Brown R., Rittmann B.E. Syntrophic interactions among anode respiring bacteria (ARB) and non-ARB in a biofilm anode: electron balances. Biotechnol Bioeng 2009, 103:513-523.
105. Park H.-D., Wells G.F., Bae H., Criddle C.S., Francis C.A. Occurrence of ammonia-oxidizing archaea in wastewater treatment plant bioreactors. Appl Environ Microbiol 2006, 72:5643-5647.
106. Peirson S.N., Butler J.N., Foster R.G. Experimental validation of novel and conventional approaches to quantitative real-time PCR data analysis. Nucleic Acids Res 2003, 31:e73.
107. Pfaffl M.W. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 2001, 29:2002-2007.
108. Pisz J.M., Lawrence J.R., Schafer A.N., Siciliano S.D. Differentiation of genes extracted from nonviable versus viable micro-organisms in environmental samples using ethidium monoazaide bromide. J Microbiol Methods 2007, 71:312-318.
109. Powell S., Ferguson S., Bowman J., Snape I. Using real-time PCR to assess changes in the hydrocarbon-degrading microbial community in antarctic soil during bioremediation. Microb Ecol 2006, 52:523-532.
110. Qi Y., Patra G., Liang X., Williams L.E., Rose S., Redkar R.J., et al. Utilization of the rpoB gene as a specific chromosomal marker for real-time PCR detection of Bacillus anthracis. Appl Environ Microbiol 2001, 67:3720-3727.
111. Radonic A., Thulke S., Mackay I.M., Landt O., Siegert W., Nitsche A. Guideline to reference gene selection for quantitative real-time PCR. Biochem Biophys Res Commun 2004, 313:856-862.
112. Rasmussen R. Quantification on the LightCycler. Rapid cycle real-time PCR: methods and applications 2001, 21-34. Springer-Verlag, Berlin, Germany. S. Meuer, C. Wittwer, K. Nakagawara (Eds.).
113. Ren Z., Steinberg L.M., Regan J.M. Electricity production and microbial biofilm characterization in cellulose-fed microbial fuel cells. Water Sci Technol 2008, 58:617-622.
114. Ririe K.M., Rasmussen R.P., Wittwer C.T. Product differentiation by analysis of DNA melting curves during the polymerase chain reaction. Anal Biochem 1997, 245:154-160.
115. Rizzo L., Manaia C., Merlin C., Schwartz T., Dagot C., Ploy M.C., et al. Urban wastewater treatment plants as hotspots for antibiotic resistant bacteria and genes spread into the environment: a review. Sci Total Environ 2013, 447:345-360.
116. Rudi K., Moen B., Dromtorp S.M., Holck A.L. Use of ethidium monoazide and PCR in combination for quantification of viable and dead cells in complex samples. Appl Environ Microbiol 2005, 71:1018-1024.
117. Saikaly P.E., Hicks K., Barlaz M.A., de los Reyes F.L. Transport behavior of surrogate biological warfare agents in a simulated landfill: effect of leachate recirculation and water infiltration. Environ Sci Technol 2010, 44:8622-8628.
118. Sakai S., Takaki Y., Shimamura S., Sekine M., Tajima T., Kosugi H., et al. Genome sequence of a mesophilic hydrogenotrophic methanogen Methanocella paludicola, the first cultivated representative of the order Methanocellales. PLoS One 2011, 6:e22898.
119. Sanz J.L., Kochling T. Molecular biology techniques used in wastewater treatment: an overview. Process Biochem 2007, 42:119-133.
120. Sawayama S., Tsukahara K., Yagishita T. Phylogenetic description of immobilized methanogenic community using real-time PCR in a fixed-bed anaerobic digester. Bioresour Technol 2006, 97:69-76.
121. Schriewer A., Wehlmann A., Wuertz S. Improving qPCR efficiency in environmental samples by selective removal of humic acids with DAX-8. J Microbiol Methods 2011, 85:16-21.
122. Sekido T., Bodelier P.L.E., Shoji T., Suwa Y., Laanbroek H.J. Limitations of the use of group-specific primers in real-time PCR as appear from quantitative analyses of closely related ammonia-oxidising species. Water Res 2008, 42:1093-1101.
123. Seviour R.J., Mino T., Onuki M. The microbiology of biological phosphorus removal in activated sludge systems. FEMS Microbiol Rev 2003, 27:99-127.
124. Shanks O.C., Sivaganesan M., Peed L., Kelty C.A., Blackwood A.D., Greene M.R., et al. Interlaboratory comparison of real-time PCR protocols for quantification of general fecal indicator bacteria. Environ Sci Technol 2011, 46:945-953.
125. Shen L.-D., Hu A.-H., Jin R.-C., Cheng D.-Q., Zheng P., Xu X.-Y., et al. Enrichment of anammox bacteria from three sludge sources for the startup of monosodium glutamate industrial wastewater treatment system. J Hazard Mater 2012, 199-200:193-199.
126. Shin S.G., Zhou B.W., Lee S., Kim W., Hwang S. Variations in methanogenic population structure under overloading of pre-acidified high-strength organic wastewaters. Process Biochem 2011, 46:1035-1038.
127. Sievert S.M., Brinkhoff T., Muyzer G., Ziebis W., Kuever J. Spatial heterogeneity of bacterial populations along an environmental gradient at a shallow submarine hydrothermal vent near Milos Island (Greece). Appl Environ Microbiol 1999, 65:3834-3842.
128. Silkie S.S., Nelson K.L. Concentrations of host-specific and generic fecal markers measured by quantitative PCR in raw sewage and fresh animal feces. Water Res 2009, 43:4860-4871.
129. Simmons F.J., Xagoraraki I. Release of infectious human enteric viruses by full-scale wastewater utilities. Water Res 2011, 45:3590-3598.
130. Smith C.J., Osborn A.M. Advantages and limitations of quantitative PCR (Q-PCR)-based approaches in microbial ecology. FEMS Microbiol Ecol 2009, 67:6-20.
131. Souaze F., Ntodou-Thome A., Tran C.Y., Rostene W., Forgez P. Quantitative RT-PCR: limits and accuracy. Biotechniques 1996, 21:280-285.
132. Spano G., Beneduce L., Terzi V., Stanca A.M., Massa S. Real-time PCR for the detection of Escherichia coli O157:H7 in dairy and cattle wastewater. Lett Appl Microbiol 2005, 40:164-171.
133. Stordeur P., Poulin L.F., Craciun L., Zhou L., Schandene L., de Lavareille A., et al. Cytokine mRNA quantification by real-time PCR. J Immunol Methods 2002, 259:55-64.
134. Strous M., Heijnen J.J., Kuenen J.G., Jetten M.S.M. The sequencing batch reactor as a powerful tool for the study of slowly growing anaerobic ammonium-oxidizing microorganisms. Appl Microbiol Biotechnol 1998, 50:589-596.
135. Stults J.R., Snoeyenbos-West O., Methe B., Lovley D.R., Chandler D.P. Application of the 5' fluorogenic exonuclease assay (TaqMan) for quantitative ribosomal DNA and rRNA analysis in sediments. Appl Environ Microbiol 2001, 67:2781-2789.
136. Suzuki M.T., Taylor L.T., DeLong E.F. Quantitative analysis of small-subunit rRNA genes in mixed microbial populations via 5'-nuclease assays. Appl Environ Microbiol 2000, 66:4605-4614.
137. Talbot G., Topp E., Plalin M.F., Masse D.I. Evaluation of molecular methods used for establishing the interactions and functions of microorganisms in anaerobic bioreactors. Water Res 2008, 42:513-537.
138. Tang Y., Ontiveros-Valencia A., Feng L., Zhou C., Krajmalnik-Brown R., Rittmann B.E. A biofilm model to understand the onset of sulfate reduction in denitrifying membrane biofilm reactors. Biotechnol Bioeng 2013, 110:763-772.
139. Tatara M., Makiuchi T., Ueno Y., Goto M., Sode K. Methanogenesis from acetate and propionate by thermophilic down-flow anaerobic packed-bed reactor. Bioresour Technol 2008, 99:4786-4795.
140. Torsvik V., Ovreas L., Thingstad T.F. Prokaryotic diversity - magnitude, dynamics, and controlling factors. Science 2002, 296:1064-1066.
141. Traversi D., Villa S., Acri M., Pietrangeli B., Degan R., Gilli G. The role of different methnogen groups evaluated by real-time qPCR as high-efficiency bioindicators of wet anaerobic co-digestion of organic waste. AMB Express 2011, 1:28.
142. Tsushima I., Kindaichi T., Okabe S. Quantification of anaerobic ammonium-oxidizing bacteria in enrichment cultures by real-time PCR. Water Res 2007, 41:785-794.
143. US EPA Prepublication of the ground water rule federal register notice. National primary drinking water regulations: ground water rule. 40 CFR Parts, 9, 141, and 142. EPA-HQ-OW-2002-0061 FRL RIN 2040-AA97 2006, US EPA, Washington, DC.
144. Valasek M.A., Repa J.J. The power of real-time PCR. Adv Physiol Educ 2005, 29:151-159.
145. van der Star W.R.L., Abma W.R., Blommers D., Mulder J.-W., Tokutomi T., Strous M., et al. Startup of reactors for anoxic ammonium oxidation: experiences from the first full-scale anammox reactor in Rotterdam. Water Res 2007, 41:4149-4163.
146. VanGuilder H.D., Vrana K.E., Freeman W.M. Twenty-five years of quantitative PCR for gene expression analysis. Biotechniques 2008, 44:619-626.
147. Varma M., Field R., Stinson M., Rukovets B., Wymer L., Haugland R. Quantitative real-time PCR analysis of total and propidium monoazide-resistant fecal indicator bacteria in wastewater. Water Res 2009, 43:4790-4801.
148. Venter J.C., Remington K., Heidelberg J.F., Halpern A.L., Rusch D., Eisen J.A., et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science 2004, 304:66-74.
149. Vervaeren H., De Wilde K., Matthys J., Boon N., Raskin L., Verstraete W. Quantification of an Eikelboom type 021N bulking event with fluorescence in situ hybridization and real-time PCR. Appl Microbiol Biotechnol 2005, 68:695-704.
150. Viau E., Peccia J. Survey of wastewater indicators and human pathogen genomes in biosolids produced by Class A and Class B stabilization treatments. Appl Environ Microbiol 2009, 75:164-174.
151. Volkmann H., Schwartz T., Bischoff P., Kirchen S., Obst U. Detection of clinically relevant antibiotic-resistance genes in municipal wastewater using real-time PCR (TaqMan). J Microbiol Methods 2004, 56:277-286.
152. Wagner M., Horn M., Daims H. Fluorescence in situ hybridization for the identification and characterization of prokaryotes. Curr Opin Microbiol 2003, 6:302-309.
153. Wagner A.O., Malin C., Knapp B.A., Illmer P. Removal of free extracellular DNA from environmental samples by ethidium monoazaide and propidium monoazide. Appl Environ Microbiol 2008, 74:2537-2539.
154. Wells G.F., Park H.-D., Yeung C.-H., Eggleston B., Francis C.A., Criddle C.S. Ammonia-oxidizing communities in a highly aerated full-scale activated sludge bioreactor: betaproteobacterial dynamics and low relative abundance of Crenarchaea. Environ Microbiol 2009, 11:2310-2328.
155. Whelan J.A., Russel N.B., Whelan M.A. A method for the absolute quantification of cDNA using real time PCR. J Immunol Methods 2003, 278:261-269.
156. White H.K., Reimers C.E., Cordes E.E., Dilly G.F., Girguis P.R. Quantitative population dynamics of microbial communities in plankton-fed microbial fuel cells. ISME J 2009, 3:635-646.
157. Winkler M., Coats E.R., Brinkman C.K. Advancing post-anoxic denitrification for biological nutrient removal. Water Res 2011, 45:6119-6130.
158. Wittwer C.T., Herrmann M.G., Moss A.A., Rasmussen R.P. Continuous fluorescence monitoring of rapid cycle DNA amplification. Biotechniques 1997, 22:130-138.
159. Wong M.L., Medrano J.F. Real-time PCR for mRNA quantitation. Biotechniques 2005, 39:75-85.
160. Wong K., Onan B.M., Xagoraraki I. Quantification of enteric viruses, pathogen indicators, and Salmonella bacteria in Class B anaerobically digested biosolids by culture and molecular methods. Appl Environ Microbiol 2010, 76:6441-6448.
161. Xia S., Jia R., Feng F., Xie K., Li H., Jing D., et al. Effect of solids retention time on antibiotics removal performance and microbial communities in an A/O-MBR process. Bioresour Technol 2012, 106:36-43.
162. Yang Q., Wang J., Wang H., Chen X., Ren S., Li X., et al. Evolution of the microbial community in a full-scale printing and dyeing wastewater treatment system. Bioresour Technol 2012, 117:155-163.
163. Yang Y., Zhang T., Zhang X.-X., Liang D.-W., Zhang M., Gao D.-W., et al. Quantification and characterization of β-lactam resistance genes in 15 sewage treatment plants from East Asia and North America. Appl Microbiol Biotechnol 2012, 95:1351-1358.
164. Ye L., Zhang T. Ammonia-oxidizing bacteria dominates over ammonia-oxidizing archaea in a saline nitrification reactor under low DO and high nitrogen loading. Biotechnol Bioeng 2011, 108:2544-2552.
165. Yu Y., Lee C., Kim J., Hwang S. Group-specific primer and probe sets to detect methanogenic communities using quantitative real-time polymerase chain reaction. Biotechnol Bioeng 2005, 89:670-679.
166. Yu Y., Kim J., Hwang S. Use of real-time PCR for group-specific quantification of aceticlastic methanogens in anaerobic processes: population dynamics and community structures. Biotechnol Bioeng 2006, 93:424-433.
167. Zhang T., Fang H.H.P. Applications of real-time polymerase chain reaction for quantification of microorganisms in environmental samples. Appl Microbiol Biotechnol 2006, 70:281-289.
168. Zhang T., Zhang M., Zhang X., Fang H.H. Tetracycline resistance genes and tetracycline resistant lactose-fermenting Enterobacteriaceae in activated sludge of sewage treatment plants. Environ Sci Technol 2009, 43:3455-3460.