Practical eDNA sampling methods inferred from particle size distribution and comparison of capture techniques for a Critically Endangered elasmobranch

Cooper, Madalyn K., Villacorta-Rath, Cecilia, Burrows, Damien, Jerry, Dean R., Carr, Leah, Barnett, Adam, Huveneers, Charlie, and Simpfendorfer, Colin A. (2022) Practical eDNA sampling methods inferred from particle size distribution and comparison of capture techniques for a Critically Endangered elasmobranch. Environmental DNA. (In Press)

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Abstract

Environmental DNA (eDNA) methods are increasingly applied in the marine environment to identify species and community structure. To establish widely applicable eDNA techniques for elasmobranchs, we used the Critically Endangered largetooth sawfish (Pristis pristis Linnaeus, 1758) as a model species for: (1) assessing eDNA particle size distribution; (2) assessing the efficiency of long-term preservation of water samples; and (3) comparing the efficiency and detection sensitivity of filtration and precipitation methods. Water samples (1 L) collected from a tank containing one largetooth sawfish specimen were sequentially filtered through five filter membranes of decreasing pore size (20, 10, 5, 1.2, and 0.45 μm). The proportion of sawfish eDNA retained within each size class was determined through quantitative real-time PCR (qPCR) using a species-specific TaqMan probe assay. A linear mixed-effects model (lme) showed that the 1.2 and 20 μm filters captured most of the eDNA particles present in the sampled water. Additionally, whole water samples (0.375 L) were preserved in Longmire's buffer, stored at tropical ambient temperatures (26.3°C ± 3.0 SD) and extracted at five time points: immediately, one, two, and three months after collection, as well as frozen and extracted three months later, to assess the preservation efficiency of Longmire's buffer via qPCR analysis. A linear mixed-effects model showed that samples maintained maximal eDNA yield for at least three months after collection at ambient storage. Lastly, when comparing the filtration and precipitation methods, filtration using 0.45 μm pore size was more sensitive to capture of large-tooth sawfish eDNA than filtration with 20 μm filter or water precipitation. However, water precipitation was more efficient when accounting for volume of water processed. These results provide options for best capture and preservation of elasmobranch eDNA.

Item ID: 72725
Item Type: Article (Research - C1)
ISSN: 2637-4943
Keywords: ecology of eDNA, eDNA sampling methods, elasmobranch eDNA, non-invasive surveys, threatened species, marine species monitoring
Copyright Information: This is an open access article under the terms of the Creative Commons Attribution-NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes. © 2022 The Authors. Environmental DNA published by John Wiley & Sons Ltd.
Funders: Save Our Seas Foundation (SOSF), National Environmental Science Program (NESP), Fisheries Research and Development Corporation (FRDC)
Date Deposited: 17 Mar 2022 01:11
FoR Codes: 31 BIOLOGICAL SCIENCES > 3105 Genetics > 310599 Genetics not elsewhere classified @ 30%
31 BIOLOGICAL SCIENCES > 3103 Ecology > 310305 Marine and estuarine ecology (incl. marine ichthyology) @ 30%
41 ENVIRONMENTAL SCIENCES > 4104 Environmental management > 410401 Conservation and biodiversity @ 40%
SEO Codes: 18 ENVIRONMENTAL MANAGEMENT > 1802 Coastal and estuarine systems and management > 180299 Coastal and estuarine systems and management not elsewhere classified @ 50%
18 ENVIRONMENTAL MANAGEMENT > 1805 Marine systems and management > 180504 Marine biodiversity @ 50%
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