Abstract
Metagenomics approaches and recent improvements in the next‐generation sequencing methods, have become a method of choice in establishing a microbial population structure. Many commercial soil DNA extraction kits are available and due to their efficiency they are replacing traditional extraction protocols. However, differences in the physicochemical properties of soil samples require optimization of DNA extraction techniques for each sample separately. The aim of this study was to compare the efficiency, quality, and diversity of genetic material extracted with the use of commonly used kits. The comparative analysis of microbial community composition, displayed differences in microbial community structure depending on which kit was used. Statistical analysis indicated significant differences in recovery of the genetic material for 24 out of 32 analyzed phyla, and the most pronounced differences were seen for Actinobacteria. Also, diversity indexes and reproducibility of DNA extraction with the use of a given kit, varied among the tested methods. As the extraction protocol may influence the apparent structure of a microbial population, at the beginning of each project many extraction kits should be tested in order to choose one that would yield the most representative results and present the closest view to the actual structure of microbial population.
Highlights
Due to the lack of ability to culture almost 99% of bacteria using traditional microbiology methods, extraction of bacterial DNA directly from environmental samples has become a method of choice in the environmental microbiology studies
It has been shown that due to differences in the bacterial cell wall and membrane structures, the effectiveness of DNA extraction can depend on the procedure used (Carrigg, Rice, Kavanagh, Collins, & O’Flaherty, 2007; Felczykowska, Krajewska, Zileińska, & Łoś, 2015; Krsek & Wellington, 1999), while successful application of molecular techniques relies on an efficient recovery of nucleic acids from environmental samples (Hurt, Qiu, Wu, Roh, & Palumbo, 2001)
We evaluated DNA extraction kits according to the convenience of their use, time spent on extraction, and cost per sample
Summary
Due to the lack of ability to culture almost 99% of bacteria using traditional microbiology methods, extraction of bacterial DNA directly from environmental samples has become a method of choice in the environmental microbiology studies This kind of approach allows obtaining previously unknown bacterial DNA and it can lead to discovery of novel genes, e.g., encoding proteins with a desired function, such as resistance to antibiotics or involved in pollutant degradation (Handelsman et al, 2007). This is a useful tool when it comes to estimating a population diversity in a particular environment (Daniel, 2005; Zhou, Bruns, & Tiedje, 1996), as vast majority of bacteria may be omitted when using traditional cultivation methods.
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