Bacterial community analysis of activated sludge: an evaluation of four commonly used DNA extraction methods

Applied Microbiology and Biotechnology
Louise VanysackerPriscilla Declerck

Abstract

The effectiveness of three commercially available direct DNA isolation kits (Mobio, Fast, Qiagen) and one published direct DNA extraction protocol (Bead) for extracting bacterial DNA from different types of activated sludge was investigated and mutually compared. The DNA quantity and purity were determined using real-time PCR targeting the bacterial 16S rDNA gene. Microbial community fingerprints were assessed by automated ribosomal intergenic spacer analysis. The resulting community profiles were analyzed with canonical correspondence analysis. Our results clearly demonstrate that direct DNA extraction methods can significantly influence the DNA quantity, purity, and observed community patterns of microbiota in activated sludge. Fast and Mobio generated high amounts of good quality DNA compared to Bead and Qiagen. Mobio also resulted in the detection of the highest number of species while Fast scored the best in discriminating between the community patterns of different activated sludge types. With respect to the characterization of community profiles, our analyses demonstrated a strong sludge type dependent variability among methods. Taking into account our results, we recommend Fast as the most suitable DNA extraction method...Continue Reading

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Jul 5, 2012·Applied Microbiology and Biotechnology·Feng Guo, Tong Zhang
Dec 16, 2011·The ISME Journal·Mads AlbertsenKåre Lehmann Nielsen
May 7, 2014·Science & Justice : Journal of the Forensic Science Society·Jennifer M YoungAlan Cooper
Jun 12, 2013·Applied Microbiology and Biotechnology·Ya-juan XingAbbas Ghulam
Jul 22, 2017·Journal of Microbiological Methods·Connie WaldenWen Zhang

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