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Microorganisms 2015, 3(4), 695-706; doi:10.3390/microorganisms3040695

How to Show the Real Microbial Biodiversity? A Comparison of Seven DNA Extraction Methods for Bacterial Population Analyses in Matrices Containing Highly Charged Natural Nanoparticles

1
Department of Medical Sciences, Clinical Microbiology, Uppsala University, Dag Hammarskjöldsväg 17, Uppsala 75185, Sweden
2
Chemistry of Oxydic and Organic Interfaces, Institute of Functional Interfaces (IFG), Karlsruhe Institute of Technology (KIT), Herrmann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen 76131, Germany
*
Author to whom correspondence should be addressed.
Academic Editor: David W. Ussery
Received: 31 August 2015 / Revised: 25 September 2015 / Accepted: 13 October 2015 / Published: 20 October 2015
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Abstract

A DNA extraction that comprises the DNA of all available taxa in an ecosystem is an essential step in population analysis, especially for next generation sequencing applications. Many nanoparticles as well as naturally occurring clay minerals contain charged surfaces or edges that capture negatively charged DNA molecules after cell lysis within DNA extraction. Depending on the methodology of DNA extraction, this phenomenon causes a shift in detection of microbial taxa in ecosystems and a possible misinterpretation of microbial interactions. With the aim to describe microbial interactions and the bio-geo-chemical reactions during a clay alteration experiment, several methods for the detection of a high number of microbial taxa were examined in this study. Altogether, 13 different methods of commercially available DNA extraction kits provided by seven companies as well as the classical phenol-chloroform DNA extraction were compared. The amount and the quality of nucleic acid extracts were determined and compared to the amplifiable amount of DNA. The 16S rRNA gene fragments of several taxa were separated using denaturing gradient gel electrophoresis (DGGE) to determine the number of different species and sequenced to get the information about what kind of species the microbial population consists of. A total number of 13 species was detected in the system. Up to nine taxa could be detected with commercially available DNA extraction kits while phenol-chloroform extraction lead to three detected species. In this paper, we describe how to combine several DNA extraction methods for the investigation of microbial community structures in clay. View Full-Text
Keywords: bacteria; biodiversity; DNA-extraction; ecology bacteria; biodiversity; DNA-extraction; ecology
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Kaden, R.; Krolla-Sidenstein, P. How to Show the Real Microbial Biodiversity? A Comparison of Seven DNA Extraction Methods for Bacterial Population Analyses in Matrices Containing Highly Charged Natural Nanoparticles. Microorganisms 2015, 3, 695-706.

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