Improvement of PCR Amplification Bias for Community Structure Analysis of Soil Bacteria by Denaturing Gradient Gel Electrophoresis

Denaturing gradient gel electrophoresis (DGGE) is one of the most frequently used methods for analysis of soil microbial community structure. Unbiased PCR amplification of target DNA templates is crucial for efficient detection of multiple microbial populations mixed in soil. In this study, DGGE pro...

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Veröffentlicht in:	Journal of microbiology and biotechnology 2006-10, Vol.16 (10), p.1561-1569
Hauptverfasser:	Ahn, J.H. (Seoul National University, Seoul, Republic of Korea), Kim, M.C. (Seoul National University, Seoul, Republic of Korea), Shin, H.C. (Seoul National University, Seoul, Republic of Korea), Choi, M.K. (Seoul National University, Seoul, Republic of Korea), Yoon, S.S. (Seoul National University, Seoul, Republic of Korea), Kim, T.S. (National Institute of Environmental Research, Incheon, Republic of Korea), Song, H.G. (Kangwon National University, Chuncheon, Republic of Korea), Lee, G.H. (Kunsan National University, Kunsan, Republic of Korea), Ka, J.O. (Seoul National University, Seoul, Republic of Korea), E-mail: joka@snu.ac.kr
Format:	Artikel
Sprache:	eng
Schlagworte:	16S rDNA sequence bacterial community structure Biological and medical sciences Biotechnology denaturing gradient gel electrophoresis Fundamental and applied biological sciences. Psychology PCR PCR amplification bias
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Zusammenfassung:	Denaturing gradient gel electrophoresis (DGGE) is one of the most frequently used methods for analysis of soil microbial community structure. Unbiased PCR amplification of target DNA templates is crucial for efficient detection of multiple microbial populations mixed in soil. In this study, DGGE profiles were compared using different pairs of primers targeting different hypervariable regions of thirteen representative soil bacteria and clones. The primer set (1070f-1392r) for the E. coli numbering 1,071-1,391 region could not resolve all the 16S rDNA fragments of the representative bacteria and clones, and moreover, yielded spurious bands in DGGE profiles.
ISSN:	1017-7825