Use of artificial DNA with multiple probe sites as reference DNA templates for quantitative real-time PCR to examine methanogen communities

Journal of Environmental Science and Health - Part A Toxic/Hazardous Substances and Environmental Engineering

Volumn 48, Issue 4, 2013, Pages 417-421

  Kim, Tae Gwan ^a   Yi, Taewoo ^a   Cho, Kyung Suk ^a  

^a Ewha Womans University   (South Korea)

Author keywords

artificial DNA; mcrA; methanogens; Quantitative PCR

Indexed keywords

ANAEROBIC DIGESTER; DNA-TEMPLATE; MCRA; METHYL-COENZYME M REDUCTASE; PCR AMPLIFICATION; QUANTITATIVE PCR; QUANTITATIVE REAL TIME PCR;

DNA; METHANOGENS; PROBES;

POLYMERASE CHAIN REACTION;

DNA; MESNA;

ARTICLE; DNA PROBE; DNA SEQUENCE; DNA TEMPLATE; FLUORESCENCE; INTERMETHOD COMPARISON; METHANOBACTERIACEAE; METHANOCORPUSCULACEAE; METHANOGEN; METHANOSAETACEAE; METHANOSARCINA; METHANOSPIRILLACEAE; METHANOTHERMOBACTER THERMAUTOTROPHICUS; NONHUMAN; QUANTITATIVE ASSAY; REAL TIME POLYMERASE CHAIN REACTION;

BASE SEQUENCE; DNA PRIMERS; EURYARCHAEOTA; METHANOBACTERIUM; MOLECULAR SEQUENCE DATA; OXIDOREDUCTASES; REAL-TIME POLYMERASE CHAIN REACTION; SEWAGE; WASTE DISPOSAL, FLUID;

EID: 84873577112     PISSN: 10934529     EISSN: 15324117     Source Type: Journal    
DOI: 10.1080/10934529.2013.728915     Document Type: Article

References (12)

1. Kim, T.G.; Knudsen, G.R. Quantitative real-time PCR effectively detects and quantifies colonization of sclerotia of Sclerotinia sclerotiorum by Trichoderma spp. Appl. Soil Ecol. 2008, 40(1), 100- 108.
2. Dionisi, H.M.; Harms, G.; Layton, A.C.; Gregory, I.R.; Parker, J.; Hawkins, S.A.;Robinson, K.G.; Sayler, G.S. Power analysis for realtime PCR quantification of genes in activated sludge and analysis of the variability itroduced by DNA extraction. Appl. Environ. Microbiol. 2003, 69(11), 6597-6604.
3. Higuchi, R.; Fockler, C.; Dollinger, G.; Watson, R. Kinetic PCR analysis: Real-time monitoring of DNA amplification reactions. Nat. Biotechnol. 1993, 11(9), 1026-1030.
4. Steinberg, L.M.; Regan, J.M. mcrA-targeted real-time quantitative PCR method to examine methanogen communities. Appl. Environ. Microbiol. 2009, 75(13), 4435-4442.
5. Jones, W.J.; Nagle, D.P.J.; Whitman, W.B. Methanogens and the diversity of archaebacteria. Microbial Rev. 1987, 51, 135-177.
6. Cakir, F. Y.; Stenstrom, M. K. Greenhouse gas production: A comparison between aerobic and anaerobic wastewater treatment technology. Water Res. 2005, 39(17), 4197-4203.
7. Demirel, B.; Scherer, P. The roles of acetotrophic and hydrogenotrophic methanogens during anaerobic conversion of biomass to methane: A review. Rev. Environ. Sci. Biotechnol. 2008, 7(2), 173-190.
8. Rittmann, B.E. Microbial ecology to manage processes in environmental biotechnology. Trends Biotechnol. 2006, 24(6), 261- 266.
9. Hedrick, D.B.; Richards, B.; Jewell, W.; Guckert, J.B.; White, D.C. Disturbance, starvation, and overfeeding stresses detected by microbial lipid biomarkers in high-solids high-yield methanogenic reactors. J. Ind. Microbiol. Biotechnol. 1991, 8(2), 91-98.
10. Luton, P.E.; Wayne, J.M.; Sharp, R.J.; Riley, P.W. The mcrA gene as an alternative to 16S rRNA in the phylogenetic analysis of methanogen populations in landfill. Microbiology 2002, 148(11), 3521-3530.
11. Markham, N.R.; Zuker, M. DINAMelt web server for nucleic acid melting prediction. Nucl. Acids Res. 2005, 33 (2), W577-W581.
12. Ramakers, C.; Ruijter, J.M.; Deprez, R.H.L.; Moorman, A.F.M. Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data. Neurosci. Lett. 2003, 339(1), 62- 66.