Comparison of different DNA extraction methods for marine periphyton and its implications for ecotoxico-metagenomics
Conference poster, 2015
This is a time with unprecedented capacity of DNA sequencing technologies for metagenomic analysis (identifying new genes and species living in environmental samples) in natural communities. However, sequencing efforts on non-model organisms or communities, such as marine periphyton communities, are still scarce in ecotoxicology. Also, uncertainties in basic aspects, such as choice of appropriate DNA extraction method, are still not resolved. This study aims to compare the effects of different DNA extraction methods for marine periphyton in terms of DNA yield, purity and integrity, as well as eukaryotic and prokaryotic diversity. Cost-effectiveness among the methods was also assessed. Four different methods (the Plant DNAzol reagent (Invitrogen), the Fast DNA Spin kit for soil (MP Biomedicals), the PowerPlant and the PowerBiofilm DNA Isolation Kits (MoBio Laboratories)) commonly used for DNA extraction of eukaryotic and prokaryotic microorganisms from marine periphyton were compared. Results showed that the commercial method Plant DNAzol reagent and the Fast DNA Spin kit for soil appear to be the best to extract high quantities of DNA (> 50 ng/μL). DNA fragments obtained with these methods cover a wide range of sizes, from 250 to 15000 bp. With the PowerPlant and the PowerBiofilm DNA Isolation Kits, lower amounts of DNA were obtained (< 23 ng/μL), but the purity of these extractions, in terms of protein and polysaccharide contamination, was higher. Extractions from these latter kits also produced DNA size distributions with larger sizes, between 3000 and 15000 bp. Obtained DNA products were used for amplicon sequencing of the 18S rRNA and 16S rRNA genes, targeting eukaryotes and prokaryotes, respectively. Such DNA amplicon sequencing will be a powerful tool to compare community composition and biodiversity across samples, and to select DNA extraction method for further metagenomics of periphyton communities exposed to toxicants.