DNA extraction bias is more pronounced for microbial eukaryotes than for prokaryotes

In this study, we compared the effect of two DNA preservation methods and six  DNA extraction methods on the community profiles of both eukaryotes and prokaryotes in phototrophic biofilms on seagrass (Zostera marina) leaves from the Baltic Sea. We found that, whereas both DNA preservation and extraction method caused significant bias in perceived community composition for both eukaryotes and prokaryotes, extraction bias was more pronounced for eukaryotes than for prokaryotes. In particular, soft-bodied and hard-shelled eukaryotes like nematodes and diatoms, respectively, were differentially abundant depending on the extraction method. We conclude that careful consideration of DNA preservation and extraction methodology is crucial to achieving representative community profiles of eukaryotes in marine biofilms and likely all other habitats containing diverse eukaryotic microbial communities.

Source: MicrobiologyOpen - September 30, 2022 Category: Microbiology Authors: Anne Brauer, Mia M. Bengtsson Tags: COMMENTARY Source Type: research