Comparison of DNA extraction methods for examining asteroid dermal microbiomes in the context of sea star wasting disease

There are various genomic approaches used to examine an organism's microbiome, including taking dermal swabs. However, there are few comparisons of how available DNA kits perform for extracting DNA from dermal swabs from organisms in the wild. Here, we carried out DNA extractions on dermal swabs from two intertidal sea star species - the ochre star (Pisaster ochraceus) and the leather star (Dermasterias imbricata) using five widely available extraction kits: the Qiagen PowerSoil, Qiagen PowerSoil Pro, Qiagen Blood and Tissue with and without QIAshredder tubes, and Zymo Research Quick-DNA Fungal/Bacterial Microprep kit. Prokaryotic communities were examined using 16S rRNA gene amplicon sequencing and compared among the five kits and two sea star species. DNA yields obtained from the swabs varied by kit, as did the ease of PCR amplification.