Methods in Ecology and Evolution (Jan 2024)
Filter no more: A modified plankton sampler for rapid in‐water eDNA capture
Abstract
Abstract The combination of an efficient sampling method and high‐throughput analysis of environmental DNA (eDNA) can be a powerful approach for characterising biodiversity across aquatic ecosystems. Plankton net tows are one of the oldest, simplest, and least expensive methods for seston and eDNA collection, but require laborious filtration steps which often lead to clogging and/or the introduction of contaminants. In this study, we used a cruising speed net (CSN) device enabling the collection of seston‐derived eDNA at 5 knots speed combined with a novel modified cod‐end with 20 μm nylon mesh inserts enabling eDNA capture while towing. We compared the performance of the CSN sampling protocol with the original conventional filtration of water sample versus the modified cod‐end. Samples were collected in parallel horizontal tows along New Zealand's North‐Eastern coastline. Concentrated water was filtered on conventional 5 μm cellulose acetate membranes, while the 20 μm nylon mesh inserts were immediately isolated post‐towing. Metabarcoding of bacterial 16S rRNA, eukaryotic nuclear 18S rRNA and mitochondrial COI genes, revealed no significant difference in alpha diversity between filtration techniques. In terms of community composition, a clear and significant shift could be observed between sampling sites and environments. Significant differences could be detected between filtration methods for 16S and COI markers, likely driven by fine‐scale differences at more turbid sheltered sites. Nonetheless, each technique could detect shifts in communities between sites and environments with similar sensitivity. Our results demonstrate the promising potential of the modified cod‐end to enable practical and cost‐effective isolation of eDNA‐derived biodiversity data from any vessel types (at ≤5 knots) across a large range of aquatic ecosystems and biogeographic scales.
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