Standards for Methods Utilizing Environmental DNA for Detection of Fish Species.

Lu Shu,Arne Ludwig,Zuogang Peng

doi:10.3390/genes11030296

Abstract

Environmental DNA (eDNA) techniques are gaining attention as cost-effective, non-invasive strategies for acquiring information on fish and other aquatic organisms from water samples. Currently, eDNA approaches are used to detect specific fish species and determine fish community diversity. Various protocols used with eDNA methods for aquatic organism detection have been reported in different eDNA studies, but there are no general recommendations for fish detection. Herein, we reviewed 168 papers to supplement and highlight the key criteria for each step of eDNA technology in fish detection and provide general suggestions for eliminating detection errors. Although there is no unified recommendation for the application of diverse eDNA in detecting fish species, in most cases, 1 or 2 L surface water collection and eDNA capture on 0.7-μm glass fiber filters followed by extraction with a DNeasy Blood and Tissue Kit or PowerWater DNA Isolation Kit are useful for obtaining high-quality eDNA. Subsequently, species-specific quantitative polymerase chain reaction (qPCR) assays based on mitochondrial cytochrome b gene markers or eDNA metabarcoding based on both 12S and 16S rRNA markers via high-throughput sequencing can effectively detect target DNA or estimate species richness. Furthermore, detection errors can be minimized by mitigating contamination, negative control, PCR replication, and using multiple genetic markers. Our aim is to provide a useful strategy for fish eDNA technology that can be applied by researchers, advisors, and managers.

Highlights

Environmental DNA is a newly developed and promising resource for species detection [1,2]
Species detection using Environmental DNA (eDNA) has many advantages, this method cannot fully substitute classical monitoring, if information on population demography is needed for conservation management
EDNA methods have been increasingly utilized in fish detection for monitoring and conserving fish diversity

Summary

Introduction

Environmental DNA (eDNA) is a newly developed and promising resource for species detection [1,2]. In contrast to DNA collected directly from organisms, eDNA is obtained from water, sediments, soil, or ice of various environmental samples [3,4,5] and reveals important information about past and present biodiversity [6]. EDNA from aquatic ecosystems is suitable for diversity assessment of contemporary aquatic species [7]. Target organisms can be detected at any life stage, including in the egg, larval, and juvenile forms from eDNA samples. EDNA was used to detect the critically endangered Mekong giant catfish Pangasianodon gigas [9] and rare green sturgeon Acipenser medirostris, demonstrating that the method is applicable for detecting rare fish species even in large river systems [10,11].

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