Biodiversity Monitoring in Remote Marine Environments: Advancing Purpose-Built Environmental DNA/RNA Sampling Workflows

This study compared simplified workflows for biodiversity assessment in remote coastal environments, requiring accurate and user-friendly molecular detection tools. It assessed streamlined eDNA/eRNA sampling-preservation workflows for eukaryotic marine biodiversity across trophic levels in three sounds within Fiordland National Park, Aotearoa New Zealand. Key questions included: Is there a difference in captured eDNA/eRNA biodiversity between two workflows considering sampling filtering methods (modified cod-end CSN and eDNA Citizen Scientist Sampler) and preservation methods (RNA Shield buffer and Smith-Root's self-preserving capsules)? Are these workflows equally efficient across eDNA and eRNA, and various metabarcoding markers?Water samples were collected aboard the MV Strannik in October 2021 from 12 sites spanning George (Te Houhou), Bligh (Hawea), and Milford (Piopiotahi) Sounds. Concentrated water samples were obtained using a cruising speed net (CSN) towed at approximately 2-3 knots for three to five minutes at about three meters below the water surface, including a modified cod-end featuring a 20 um nylon mesh insert, allowing active filtration while towing (modified cod-end filtration). After each tow, approximately 500 ml of concentrated plankton water was isolated into sterile bottles, and the 20 um filters from the modified cod-end were transferred into vials with DNA/RNA Shield buffer. Bottles were immediately processed onboard by filtering 500 ml through a self-preserving Smith-Root filter unit containing a 5 um PES membrane using the eDNA citizen science sampler. The filter membrane was halved, with one half retained in the Smith-Root self-preserving filter unit and the other half transferred into a vial with DNA/RNA Shield buffer. Metabarcoding used three primers: 18S rRNA for general eukaryotes and two mitochondrial 16S rRNA markers for fish and marine vertebrates.These findings are significant for monitoring remote coastal environments, such as fiords, providing essential knowledge for informed conservation and management strategies.