Comparison of four DNA extraction methods for comprehensive assessment of 16S rRNA bacterial diversity in marine biofilms using high-throughput sequencing
Journal article, 2017

High-throughput DNA sequencing technologies are increasingly used for the metagenomic characterization 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® Reagent (PlantDNAzol) and the Fast DNATM SPIN Kit for Soil (FastDNA Soil) methods were best suited to extract high quantities of DNA (77 - 130 μg g wet wt-1). Lower amounts of DNA were obtained (< 37 μg g wet wt-1) with the Power Plant® Pro DNA Isolation Kit (PowerPlant) and the Power Biofilm® 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.

bacteria

16S amplicon sequencing

biofilms

extraction methods

DNA

metagenomics

Author

Natàlia Corcoll

University of Gothenburg

Tobias Österlund

Chalmers, Mathematical Sciences, Applied Mathematics and Statistics

University of Gothenburg

Lucas Sinclair

Uppsala University

Alexander Eiler

Uppsala University

Erik Kristiansson

Chalmers, Mathematical Sciences, Applied Mathematics and Statistics

University of Gothenburg

Thomas Backhaus

University of Gothenburg

Martin Eriksson

Mechanics and Maritime Sciences (M2)

FEMS Microbiology Letters

0378-1097 (ISSN) 1574-6968 (eISSN)

Vol. 364 14 fnx139

Driving Forces

Sustainable development

Areas of Advance

Transport

Life Science Engineering (2010-2018)

Subject Categories

Ecology

Microbiology

Bioinformatics and Systems Biology

Other Natural Sciences

Infrastructure

Facility for Computational Systems Biology

DOI

10.1093/femsle/fnx139

PubMed

28673033

More information

Latest update

2/28/2018