Comparison of swab DNA extraction methods for examining sea star dermal microbiomes

Abstract

Marine invertebrates are surrounded by and interact with an array of microbes, yet their microbiomes remain largely unexplored. With a seemingly endless choice of nucleic acid extraction kits, there is a need to assess the compatibility across approaches to determine whether microbiome results are comparable across studies employing different extraction methods. In this study, 5 kits were compared for extracting DNA from dermal swabs from 2 sea star species: Pisaster ochraceus and Dermasterias imbricata. DNA yield varied by kit, as did the ease of PCR amplification. Using 16S rRNA amplicon sequencing, differences in microbial richness and diversity were observed between sea star species, but not among extraction kits. Relative abundances of the most abundant prokaryotic phyla were largely attributed to sea star species rather than kit: the D. imbricata microbiome was dominated by Proteobacteria, whereas P. ochraceous had more even representation of Proteobacteria, Spirochaetota and Bacteroidota. Our results suggest that, despite some differences in ease of amplification, all 5 extraction kits examined here provide comparable and suitable results for characterizing sea star dermal microbiomes.