Data from: Testing the waters: A comparison of DNA extraction methods for the metabarcoding of microbial communities

DNA metabarcoding is an emerging technique for enhancing microbial
community monitoring programs that assess water quality and environmental
health. However, comparability between studies is limited by a lack of
standardized laboratory protocols. To contribute to protocol optimization
and decision making, we compare seven commercially available DNA
extraction kits and evaluate their impact on DNA yield, PCR inhibitor
removal, and taxonomic resolution of microplankton, microalgae, and
particle-associated bacterial communities using 18S V9 and 16S V3-V4
amplicon sequencing of samples from two contrasting estuarine environments
varying in salinity and productivity. We observed greater DNA yields and
detected PCR inhibition at the higher productivity, lower salinity site.
The Qiagen DNeasy PowerSoil Pro and Omega E.Z.N.A. Tissue DNA kits both
yielded greater amounts of DNA, but only the soil- and plant-specific kits
effectively removed PCR inhibitors. Notably, differences in taxonomic
richness between kits were statistically significant but small (often
<10 taxa). Additionally, beta diversity was more strongly
influenced by abundance than by the presence/absence of taxa. All
extraction methods shared 84-90% of resolved taxa and detected all major
eukaryotic divisions/phyla identified by microscopy, as well as
cyanobacteria. Furthermore, all kits detected several potentially harmful
taxa, including Akashiwo sanguinea and Vibrio sp. These results suggest
that DNA extraction methods should be chosen based on environmental
conditions, and we recommend the Qiagen PowerSoil Kit for obtaining high
yields of uninhibited DNA from productive estuarine water samples. While
alpha- and beta-diversity are largely similar between extraction methods,
pilot studies should be performed to confirm the resolution of taxa of
interest.