Moving environmental DNA (eDNA) technologies from bench top to the field using passive sampling and PDQeX extraction

Introduction: Environmental DNA (eDNA) metabarcoding surveys have shown great promise as an effective, non-invasive monitoring method for marine biomes. However, long vacuum filtration times and the need for state-of-the-art, PCR-free laboratories are restricting sample replication and in situ species detections. Methodological innovations, such as passive filtration and self-contained DNA extraction protocols, have the potential to alleviate these issues within the eDNA workflow. Methods: Here, we explored the implementation of both passive sampling and a self-contained DNA extraction protocol into the eDNA workflow by comparing fish diversity obtained from active filtration (1L; 0.45 um cellulose nitrate [CN] filters) to five passive capture substrates, including 0.45 um CN filters, 5 um nylon filters, 0.45 um positively charged nylon filters, artificial sponges, and fishing net. In addition, fish diversity was compared between the novel PDQeX Nucleic Acid Extractor and the conventional Qiagen DNeasy Blood & Tissue protocol. Comparative experiments were conducted in both a controlled mesocosm and in situ in the harbor adjacent to the Portobello Marine Laboratory, Otago, New Zealand.Results: No significant differences in fish alpha and beta diversity were observed among active filtration and more porous passive materials (artificial sponges and fishing net) for both the mesocosm and harbor waters. For the in situ harbor comparison, all passive capture filter membranes detected a significantly lower number of fish species, resulting from partial sample drop-out. While no significant differences in fish eDNA signal diversity were observed between either DNA extraction methods in the mesocosm, the PDQeX system was less effective at detecting fish for the in situ harbor comparison.Conclusion: Our results demonstrate that a passive sampling approach using porous substrates can be effectively implemented to capture eDNA from seawater, thereby potentially eliminating vacuum filtration processing. The large variation in efficiency observed among the five substrate types, however, warrants further optimization of the passive sampling approach for routine eDNA applications. The PDQeX system can extract high abundance DNA and is able to obtain similar results to Qiagen extractions in a mesocosm. However, further optimization is required to detect low abundance eDNA from the marine environment.