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Biodiversity of Estuarine Species: Comparing Multi-depth eDNA Sampling to Four Traditional Sampling Gears

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Title:Biodiversity of Estuarine Species: Comparing Multi-depth eDNA Sampling to Four Traditional Sampling Gears
Authors:Gonzalez, Aurelia Ruby
Contributors:TSANG, YINPHAN (advisor)
Natural Resources and Environmental Management (department)
Keywords:Aquatic sciences
Bioinformatics
Ecology
biodiversity
environmental DNA
show 4 moreestuary
fish
methods
sampling
show less
Date Issued:2020
Publisher:University of Hawai'i at Manoa
Abstract:Estuaries are physically and biologically complex habitats which demand higher sampling efforts in either freshwater or marine systems to fully document aquatic species and understand ecological relationships. A lack in sampling effort for estuarine biota is typical which may lead to negligent resource management decisions and a limited view of estuarine systems. Environmental DNA (eDNA) metabarcoding is a developing method used to detect multiple taxonomic groups in a single water sample, reshaping biodiversity surveys in aquatic systems. However, sampling methodologies for eDNA surveying in estuaries and their operational constraints remain ambiguous. Previous comparative studies examined solely surface water eDNA samples with a single traditional sampling gear. These studies did not address the need for more diverse traditional sampling methods and the additional possible bias of taking only surface samples in relatively physiochemically complex water columns, e.g., salt wedges. With an aim to provide reliable estimates of biodiversity and best practices of eDNA surveying methodologies in estuaries, this study compared four manual sampling gears, i.e., underwater baited camera, cast net, minnow trap, and angling, to multi-depth eDNA sampling using two targeted genetic regions (COI, 12S) across five stream mouths of the Pearl Harbor estuary on the island of O‘ahu in the Hawaiian Archipelago. In doing so, this study compared alpha and beta biodiversity estimates between methods, identified unique and overlapping species of each sampling component, measured the agreement of species detected between methods, and assessed the need to take eDNA samples at multiple depths. This study found that sampling multiple locations in an estuarine water column offers a more efficient means of capturing rare species than extended sampling at surface waters. Both traditional and eDNA methods revealed similar spatial and temporal patterns of species composition between surveys in Pearl Harbor but had conflicting views of total alpha diversity for stream sites. Inverse relationships for streams between methods were due to differences in each method’s ability to capture species richness, rare species, and dominant species, affecting computations of diversity. The exclusive use of one method can give incomplete views of species composition and estimates of diversity, which can alter management perspectives of estuarine ecosystems.
Pages/Duration:84 pages
URI:http://hdl.handle.net/10125/73364
Rights:All UHM dissertations and theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission from the copyright owner.
Appears in Collections: M.S. - Natural Resources and Environmental Management


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