On the effectiveness of two universal metabarcoding primer pairs in amplifying Arctic gelatinous zooplankton DNA from tissue and environmental samples

Abstract

Gelatinous zooplankton (GZP) comprise a highly diverse group of marine taxa that play key ecological roles throughout the world’s oceans. However, their fragile bodies make them difficult to effectively study using traditional sampling methods such as net and optical surveys. While the recent advancements of non-invasive DNA metabarcoding techniques have become valuable tools in GZP biodiversity research, the performance of commonly used metabarcoding markers for these taxa remains poorly understood. In this study, we evaluated two universal primer pairs targeting the 18S rRNA V1–V2 and mitochondrial COI Leray gene regions for detecting key Arctic GZP species. Primer performance was assessed using in silico PCRs, then in vitro PCRs and sequencing of tissue-derived DNA, and environmental DNA collected from a controlled mock community experiment. The COI primers provided high species-level taxonomic resolution but failed to amplify several hydrozoan species and the cydippid ctenophores. In contrast, the 18S primers amplified a broader range of taxa but lacked sufficient resolution to discriminate among closely related genera and species. We also identified substantial gaps in public reference databases that limit the accurate identification of Arctic GZP and finally, we provide additional barcodes to expand the existing coverage in public databases. These findings demonstrate the complementary strengths and limitations of commonly-used COI and 18S markers and provide guidance for marker and exploration of new genetic markers to support DNA-based monitoring of Arctic GZP. This is essential in surveying these elusive organisms in light of their climate-change driven observed and projected distributional shifts.