A manager's guide to using eDNA metabarcoding in marine ecosystems

A manager's guide to using eDNA metabarcoding in marine ecosystems

Environmental DNA (eDNA) metabarcoding is a powerful tool that can enhance marine ecosystem/biodiversity monitoring programs. Here we outline five important steps managers and researchers should consider when developing eDNA monitoring program: (1) select genes and primers to target taxa; (2) assemb...

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Bibliographic Details
Published in:PeerJ (San Francisco, CA) Vol. 10; p. e14071
Main Authors: Gold, Zachary, Wall, Adam R, Schweizer, Teia M, Pentcheff, N Dean, Curd, Emily E, Barber, Paul H, Meyer, Rachel S, Wayne, Robert, Stolzenbach, Kevin, Prickett, Kat, Luedy, Justin, Wetzer, Regina
Format: Journal Article
Language:English
Published: United States PeerJ. Ltd 15-11-2022
PeerJ, Inc
PeerJ Inc
Subjects:
Assessment
Bar codes
Biodiversity
Biological monitoring
Biomonitoring
Case studies
Climate change
Conservation Biology
Decontamination
DNA barcoding
DNA Barcoding, Taxonomic - methods
DNA, Environmental - genetics
Ecosystem
Ecosystem Science
eDNA
Endangered species
Environmental DNA
Environmental Impacts
Environmental Monitoring - methods
Gene mapping
Genes
Genetic analysis
Genetic resources
Introduced species
Invasive species
Laboratories
Management
Marine Biology
Marine ecosystems
Metabarcoding
Nonnative species
Science Policy
Taxonomy
Trawling
Metabarcoding
Biomonitoring
Site occupancy
Marine
Assessment
Primer set
Management
Biodiversity
Protocol
eDNA
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Description
Summary:Environmental DNA (eDNA) metabarcoding is a powerful tool that can enhance marine ecosystem/biodiversity monitoring programs. Here we outline five important steps managers and researchers should consider when developing eDNA monitoring program: (1) select genes and primers to target taxa; (2) assemble or develop comprehensive barcode reference databases; (3) apply rigorous site occupancy based decontamination pipelines; (4) conduct pilot studies to define spatial and temporal variance of eDNA; and (5) archive samples, extracts, and raw sequence data. We demonstrate the importance of each of these considerations using a case study of eDNA metabarcoding in the Ports of Los Angeles and Long Beach. eDNA metabarcoding approaches detected 94.1% (16/17) of species observed in paired trawl surveys while identifying an additional 55 native fishes, providing more comprehensive biodiversity inventories. Rigorous benchmarking of eDNA metabarcoding results improved ecological interpretation and confidence in species detections while providing archived genetic resources for future analyses. Well designed and validated eDNA metabarcoding approaches are ideally suited for biomonitoring applications that rely on the detection of species, including mapping invasive species fronts and endangered species habitats as well as tracking range shifts in response to climate change. Incorporating these considerations will enhance the utility and efficacy of eDNA metabarcoding for routine biomonitoring applications.
ISSN:2167-8359
2167-8359
DOI:10.7717/peerj.14071