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

PeerJ

article

Zachary Gold¹  Adam R. Wall²  Teia M. Schweizer³  N. Dean Pentcheff²  Emily E. Curd⁴  Paul H. Barber¹  Rachel S. Meyer¹  Robert Wayne¹  Kevin Stolzenbach⁵  Kat Prickett⁶  Justin Luedy⁷  Regina Wetzer² 

[1]Department of Ecology and Evolutionary Biology, University of California

[2]Diversity Initiative for the Southern California Ocean

[3]Department of Fish and Wildlife Conservation Biology, Colorado State University

[4]Department of Natural Sciences, Landmark College

[5]Wood Environment and Infrastructure, Inc.

[6]Port of Los Angeles

[7]Port of Long Beach

关键词: eDNA;    Metabarcoding;    Management;    Biomonitoring;    Assessment;    Biodiversity;    Marine;    Protocol;    Primer set;    Site occupancy;   

DOI  :  10.7717/peerj.14071

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

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.

【 授权许可】

CC BY