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Effects of DNA extraction and universal primers on 16S rRNA gene-based DGGE analysis of a bacterial community from fish farming water

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Abstract

Among many reports investigating microbial diversity from environmental samples with denaturing gradient gel electrophoresis (DGGE), limited attention has been given to the effects of universal primers and DNA extraction on the outcome of DGGE analysis. In this study, these effects were tested with 16S rRNA gene-based DGGE on a bacterial community from farming water samples. The results indicate that the number of discernable bands in the DGGE fingerprint differed with the primer pairs used; the bands produced by 63f/518r, 341f/926r and 933f/1387r primer pairs were obviously fewer than those by 968f/1401r. Also, we found that each DNA extraction method resulted in different community profiles, reflected by the number and intensity of bands in the DGGE fingerprint. Furthermore, the main bands (theoretically representing dominant bacteria) differed with the extraction methods applied. It is therefore believed that the effects of universal primers and DNA extraction should be given more attention and carefully chosen before performing an investigation into a new environment with DGGE.

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Authors and Affiliations

  1. The Key Laboratory of Applied Marine Biology of Guangdong Province and Chinese Academy of Sciences, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China

    Luo Peng  (罗鹏), Hu Chaoqun  (胡超群), Zhang Lüping  (张吕平), Ren Chunhua  (任春华) & Shen Qi  (沈琪)

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  1. Luo Peng  (罗鹏)
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  2. Hu Chaoqun  (胡超群)
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  3. Zhang Lüping  (张吕平)
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  4. Ren Chunhua  (任春华)
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  5. Shen Qi  (沈琪)
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Corresponding author

Correspondence to Hu Chaoqun  (胡超群).

Additional information

This work was funded by the Special Scientific Foundation of Guangdong Province (No. A305030301) and was partly supported by a grant from KLFEE, Ministry of Agriculture (2003-04).

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Luo, P., Hu, C., Zhang, L. et al. Effects of DNA extraction and universal primers on 16S rRNA gene-based DGGE analysis of a bacterial community from fish farming water. Chin. J. Ocean. Limnol. 25, 310–316 (2007). https://doi.org/10.1007/s00343-007-0310-7

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  • DOI: https://doi.org/10.1007/s00343-007-0310-7

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