The choice of the DNA extraction method may influence the outcome of the soil microbial community structure analysis

Sylwia Zielińska , Piotr Radkowski , Aleksandra Blendowska , Agnieszka Ludwig-Gałęzowska , Joanna Monika Łoś , Marcin Łoś

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.
Author Sylwia Zielińska KGMB
Sylwia Zielińska,,
- Department of Molecular Genetics of Bacteria
, Piotr Radkowski
Piotr Radkowski,,
-
, Aleksandra Blendowska WB
Aleksandra Blendowska,,
- Faculty of Biology
, Agnieszka Ludwig-Gałęzowska
Agnieszka Ludwig-Gałęzowska,,
-
, Joanna Monika Łoś KGMB
Joanna Monika Łoś,,
- Department of Molecular Genetics of Bacteria
, Marcin Łoś KGMB
Marcin Łoś,,
- Department of Molecular Genetics of Bacteria
Journal seriesMicrobiologyOpen, ISSN 2045-8827
Issue year2017
Vol6
No4
Pages1-11
Publication size in sheets0.5
Keywords in English16S rDNA, commercial kits, DNA extraction, microbial community, NGS library, soil sample
DOIDOI:10.1002/mbo3.453
URL http://onlinelibrary.wiley.com/doi/10.1002/mbo3.453/epdf
Languageen angielski
LicenseJournal (articles only); published final; Uznanie Autorstwa (CC-BY); with publication
Score (nominal)20
ScoreMinisterial score = 20.0, 20-12-2017, ArticleFromJournal
Ministerial score (2013-2016) = 20.0, 20-12-2017, ArticleFromJournal
Publication indicators WoS Impact Factor: 2016 = 2.747 (2) - 2016=2.638 (5)
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* presented citation count is obtained through Internet information analysis and it is close to the number calculated by the Publish or Perish system.
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