uu.seUppsala University Publications
Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Comparison of four DNA extraction methods for comprehensive assessment of 16S rRNA bacterial diversity in marine biofilms using high-throughput sequencing
Univ Gothenburg, Dept Biol & Environm Sci, Box 461, SE-40530 Gothenburg, Sweden..
Chalmers, Dept Math Sci, SE-41296 Gothenburg, Sweden..
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
Show others and affiliations
2017 (English)In: FEMS Microbiology Letters, ISSN 0378-1097, E-ISSN 1574-6968, Vol. 364, no 14, fnx139Article in journal (Refereed) Published
Abstract [en]

High-throughput DNA sequencing technologies are increasingly used for the metagenomic characterisation of microbial biodiversity. However, basic issues, such as the choice of an appropriate DNA extraction method, are still not resolved for non-model microbial communities. This study evaluates four commonly used DNA extraction methods for marine periphyton biofilms in terms of DNA yield, efficiency, purity, integrity and resulting 16S rRNA bacterial diversity. Among the tested methods, the Plant DNAzol (R) Reagent (PlantDNAzol) and the FastDNA (R) SPIN Kit for Soil (FastDNA Soil) methods were best suited to extract high quantities of DNA (77-130 mu g g wet wt(-1)). Lower amounts of DNA were obtained (<37 mu g g wet wt(-1)) with the Power Plant (R) Pro DNA Isolation Kit (PowerPlant) and the Power Biofilm (R) DNA Isolation Kit (PowerBiofilm) methods, but integrity and purity of the extracted DNA were higher. Results from 16S rRNA amplicon sequencing demonstrate that the choice of a DNA extraction method significantly influences the bacterial community profiles generated. A higher number of bacterial OTUs were detected when DNA was extracted with the PowerBiofilm and the PlantDNAzol methods. Overall, this study demonstrates the potential bias in metagenomic diversity estimates associated with different DNA extraction methods.

Place, publisher, year, edition, pages
OXFORD UNIV PRESS , 2017. Vol. 364, no 14, fnx139
Keyword [en]
DNA, extraction methods, bacteria, 16S amplicon sequencing, biofilms, metagenomics
National Category
Microbiology
Identifiers
URN: urn:nbn:se:uu:diva-335678DOI: 10.1093/femsle/fnx139ISI: 000410348600002OAI: oai:DiVA.org:uu-335678DiVA: diva2:1168165
Funder
Swedish Research Council Formas, 2011-1733Swedish Research Council Formas, 2015-1464
Available from: 2017-12-20 Created: 2017-12-20 Last updated: 2017-12-20Bibliographically approved

Open Access in DiVA

No full text

Other links

Publisher's full text

Authority records BETA

Sinclair, LucasEiler, Alexander

Search in DiVA

By author/editor
Sinclair, LucasEiler, Alexander
By organisation
LimnologyScience for Life Laboratory, SciLifeLab
In the same journal
FEMS Microbiology Letters
Microbiology

Search outside of DiVA

GoogleGoogle Scholar

doi
urn-nbn

Altmetric score

doi
urn-nbn
Total: 6 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf