Thomas I. Gibson
Environmental DNA metabarcoding for fish diversity assessment in a macrotidal estuary: A comparison with established fish survey methods
Gibson, Thomas I.; Carvalho, Gary; Ellison, Amy; Gargiulo, Enrica; Hatton-Ellis, Tristan; Lawson-Handley, Lori; Mariani, Stefano; Collins, Rupert A.; Sellers, Graham; Antonio Distaso, Marco; Zampieri, Carlo; Creer, Simon
Authors
Gary Carvalho
Amy Ellison
Enrica Gargiulo
Tristan Hatton-Ellis
Lori Lawson-Handley
Stefano Mariani
Rupert A. Collins
Graham Sellers
Marco Antonio Distaso
Carlo Zampieri
Simon Creer
Abstract
Fishes are a dominant component of the macrofauna in estuaries and are important for assessing the health of these threatened ecosystems. Several studies have applied environmental DNA (eDNA) metabarcoding to assess the biodiversity of fishes in estuaries. However, none have combined measurement of physicochemical variables with a spatially extensive sampling design across the full salinity gradient. This study aimed to compare spatial fish assemblage composition detected via eDNA metabarcoding of surface water samples with conventional fishing gear surveys in a macrotidal estuary (river Dee, North Wales, UK). In addition, eDNA assemblage composition across seasons was investigated. In autumn 2018, triplicate eDNA samples were taken at 13 stations in a spatially systematic design alongside seine, fyke and beam trawl sampling. In summer 2019, eDNA samples from eight of the 13 original stations were collected again in the upper and lower estuary. DNA was extracted from samples and subjected to metabarcoding analysis using an established assay targeting teleost fishes. The key findings were that in autumn, eDNA detected 17 of the 26 (71%) species caught by fishing gears, which included the most abundant species. Overall, eDNA detected a greater species richness, per 30 samples, than seine or fyke nets (but not beam trawling). Additionally, there was a clear correlation between salinity and assemblage composition, which was consistent across seasons. Overall, the study indicates that eDNA metabarcoding could enhance existing fish sampling methods, by generating a more comprehensive picture of estuarine fish biodiversity and providing additional information for ecological inference and management actions.
Citation
Gibson, T. I., Carvalho, G., Ellison, A., Gargiulo, E., Hatton-Ellis, T., Lawson-Handley, L., Mariani, S., Collins, R. A., Sellers, G., Antonio Distaso, M., Zampieri, C., & Creer, S. (2023). Environmental DNA metabarcoding for fish diversity assessment in a macrotidal estuary: A comparison with established fish survey methods. Estuarine, coastal and shelf science, 294, Article 108522. https://doi.org/10.1016/j.ecss.2023.108522
Journal Article Type | Article |
---|---|
Acceptance Date | Oct 1, 2023 |
Online Publication Date | Oct 10, 2023 |
Publication Date | Nov 5, 2023 |
Deposit Date | Apr 17, 2024 |
Publicly Available Date | Apr 23, 2024 |
Journal | Estuarine, Coastal and Shelf Science |
Print ISSN | 0272-7714 |
Publisher | Elsevier |
Peer Reviewed | Peer Reviewed |
Volume | 294 |
Article Number | 108522 |
DOI | https://doi.org/10.1016/j.ecss.2023.108522 |
Keywords | Estuaries; Fishes; Environmental DNA; Water framework directive; Metabarcoding; Biomonitoring |
Public URL | https://hull-repository.worktribe.com/output/4427112 |
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http://creativecommons.org/licenses/by/4.0
Copyright Statement
Crown Copyright © 2023 Published by Elsevier Ltd. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
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