Quantitative improvement of 16S rDNA DGGE analysis for soil bacterial community using real-time PCR

Journal of Microbiological Methods

Volumn 78, Issue 2, 2009, Pages 216-222

  Ahn, Jae Hyung ^a   Kim, Yoo Jeong ^a   Kim, Taesung ^b   Song, Hong Gyu ^c   Kang, ChulHee ^d   Ka, Jong Ok ^a  

^a Seoul National University   (South Korea)

^b National Institute of Environmental Research   (South Korea)

^c Kangwon National University   (South Korea)

^d WASHINGTON STATE UNIVERSITY   (United States)

Author keywords

16S rDNA DGGE; Bacterial community structure; PCR bias; Real time PCR

Indexed keywords

ACRYLAMIDE; DNA 16S; DNA POLYMERASE;

ACCURACY; ANALYTICAL ERROR; ARTICLE; BASE MISPAIRING; CONCENTRATION (PARAMETERS); CONTROLLED STUDY; DENATURING GRADIENT GEL ELECTROPHORESIS; DNA DETERMINATION; DNA TEMPLATE; GENE AMPLIFICATION; HIGH TEMPERATURE; LOW TEMPERATURE; MELTING POINT; MICROBIAL COMMUNITY; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROCESS OPTIMIZATION; PROTEIN SECONDARY STRUCTURE; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; SOIL MICROFLORA;

BACTERIA; BIODIVERSITY; DNA, BACTERIAL; DNA, RIBOSOMAL; ELECTROPHORESIS, POLYACRYLAMIDE GEL; MOLECULAR SEQUENCE DATA; NUCLEIC ACID DENATURATION; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SOIL MICROBIOLOGY;

BACTERIA (MICROORGANISMS);

EID: 67650131351     PISSN: 01677012     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mimet.2009.06.001     Document Type: Article

References (25)

1. Ahn J.H., Kim M.C., Shin H.C., Choi M.K., Yoon S.S., Kim T.S., Song H.G., Lee G.H., and Ka J.O. Improvement of PCR amplification bias for community structure analysis of soil bacteria by denaturing gradient gel electrophoresis. J. Microbiol. Biotechnol. 16 (2006) 1561-1569
2. Chan O.C., Yang X.D., Fu Y., Feng Z.L., Sha L.Q., Casper P., and Zou X.M. 16S rRNA gene analyses of bacterial community structures in the soils of evergreen broad-leaved forests in south-west China. FEMS Microbiol. Ecol. 58 (2006) 247-259
3. Cole J.R., Chai B., Farris R.J., Wang Q., Kulam S.A., McGarrell D.M., Garrity G.M., and Tiedje J.M. The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res. 33 (2005) Database issue D294-D296
4. Crump B.C., Hopkinson C.S., Sogin M.L., and Hobbie J.E. Microbial biogeography along an estuarine salinity gradient: combined influences of bacterial growth and residence time. Appl. Environ. Microbiol. 70 (2003) 1494-1505
5. Eckert K.A., and Kunkel T.A. High fidelity DNA synthesis by the Thermus aquaticus DNA polymerase. Nucleic Acids Res. 18 (1990) 3739-3744
6. Ferris M.J., and Ward D.M. Seasonal distribution of dominant 16S rRNA-defined populations in a hot spring microbial mat examined by denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 63 (1997) 1375-1381
7. Hartmann M., and Widmer F. Community structure analyses are more sensitive to differences in soil bacterial communities than anonymous diversity indices. Appl. Environ. Microbiol. 72 (2006) 7804-7812
8. Henke W., Herdel K., Jung K., Schnorr D., and Loening S.A. Betaine improves the PCR amplification of GC-rich DNA sequences. Nucleic Acids Res. 25 (1997) 3957-3958
9. Hongoh Y., Yuzawa H., Ohkuma M., and Kudo T. Evaluation of primers and PCR conditions for the analysis of 16S rRNA genes from a natural environment. FEMS Microbiol. Lett. 221 (2003) 299-304
10. Janse I., Bok J., and Zwart G. A simple remedy against artifactual double bands in denaturing gradient gel electrophoresis. J. Microbiol. Methods 57 (2004) 279-281
11. Keohavong P., and Thilly W.G. Fidelity of DNA polymerase in DNA amplification. Proc. Natl. Acad. Sci. 86 (1989) 9253-9257
12. Kim M.S., Ahn J.H., Jung M.K., Yu J.H., Joo D.H., Kim M.C., Shin H.C., Kim T.S., Ryu T.H., Kweon S.J., Kim T.S., Kim D.H., and Ka J.O. Molecular and cultivation-based characterization of bacterial structure in rice field soil. J. Microbiol. Biotechnol. 15 (2005) 1087-1093
13. Lerman L.S., and Silverstein K. Computational simulation of DNA melting and its application to denaturing gradient gel electrophoresis. Methods Enzymol. 155 (1987) 482-501
14. 2 affects soil microbial diversity associated with trembling aspen. Environ. Microbiol. 10 (2008) 926-941
15. Loewen P.C., and Switala J. Template secondary structure can increase the error frequency of the DNA polymerase from Thermus aquaticus. Gene 164 (1995) 59-63
16. Niederberger T.D., McDonald I.R., Hacker A.L., Soo R.M., Barrett J.E., Wall D.H., and Cary S.C. Microbial community composition in soils of Northern Victoria Land, Antarctica. Environ. Microbiol. 10 (2008) 1713-1724
17. Polz M.F., and Cavanaugh C.M. Bias in template-to-product rations in multitemplate PCR. Appl. Environ. Microbiol. 64 (1998) 3724-3730
18. Rees W.A., Yager T.D., Korte J., and Vonhippel P.H. Betaine can eliminate the base pair composition dependence of DNA melting. Biochemistry 32 (1993) 137-144
19. Sambrook J., and Russell D.W. Molecular Cloning: A Laboratory Manual. 3rd ed. (2001), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
20. Shen W.H., and Hohn B. DMSO improves PCR amplification of DNA with complex secondary structure. Trends Genet. 8 (1992) 227
21. Speksnijder A., Kowalchuk G.A., De Jong S., Kline E., Stephen J.R., and Laanbroek H.J. Microvariation artifacts introduced by PCR and cloning of closely related 16S rDNA gene sequences. Appl. Environ. Microbiol. 67 (2001) 469-472
22. Suzuki M.T., and Giovannoni S.J. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl. Environ. Microbiol. 62 (1996) 625-630
23. Vallaeys T., Topp E., Muyzer G., Macheret V., Laguerre G., Rigaud A., and Soulas G. Evaluation of denaturing gradient gel electrophoresis in the detection of 16S rDNA sequence variation in rhizobia and methanotrophs. FEMS Microbiol. Ecol. 24 (1997) 279-285
24. Wu Y., Hayes V.M., Osinga J., Mulder I.M., Looman M.W.G., Buys C., and Hofstra R.M.W. Improvement of fragment and primer selection for mutation detection by denaturing gradient gel electrophoresis. Nucleic Acids Res. 26 (1998) 5432-5440
25. Zhu D., Zhou J.S., and Keohavong P. Taq-amplified fragments appear as doublets in denaturing gradient gels. Anal. Biochem. 244 (1997) 404-406