Comparison of four DNA extraction methods for comprehensive assessment of 16S rRNA bacterial diversity in marine biofilms using high-throughput sequencing
Artikel i vetenskaplig tidskrift, 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

Författare

Natàlia Corcoll

Göteborgs universitet

Tobias Österlund

Chalmers, Matematiska vetenskaper, Tillämpad matematik och statistik

Göteborgs universitet

Lucas Sinclair

Uppsala universitet

Alexander Eiler

Uppsala universitet

Erik Kristiansson

Chalmers, Matematiska vetenskaper, Tillämpad matematik och statistik

Göteborgs universitet

Thomas Backhaus

Göteborgs universitet

Martin Eriksson

Mekanik och maritima vetenskaper

FEMS Microbiology Letters

0378-1097 (ISSN)

Vol. 364 14 fnx139

Drivkrafter

Hållbar utveckling

Styrkeområden

Transport

Livsvetenskaper och teknik

Ämneskategorier

Ekologi

Mikrobiologi

Bioinformatik och systembiologi

Annan naturvetenskap

Infrastruktur

Beräkningsinfrastruktur för systembiologi

DOI

10.1093/femsle/fnx139

PubMed

28673033