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Open AccessFeature PaperReview

Standards for Methods Utilizing Environmental DNA for Detection of Fish Species

by 1, 2,3,* and 1,*
1
Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing 400715, China
2
Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, 10315 Berlin, Germany
3
Albrecht Daniel Thaer-Institute, Faculty of Life Sciences, Humboldt University Berlin, 10115 Berlin, Germany
*
Authors to whom correspondence should be addressed.
Genes 2020, 11(3), 296; https://doi.org/10.3390/genes11030296
Received: 20 January 2020 / Revised: 13 February 2020 / Accepted: 7 March 2020 / Published: 11 March 2020
(This article belongs to the Section Technologies and Resources for Genetics)
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. View Full-Text
Keywords: environmental DNA; water sampling; eDNA capture; eDNA extraction; eDNA detection; genetic marker; detection error environmental DNA; water sampling; eDNA capture; eDNA extraction; eDNA detection; genetic marker; detection error
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MDPI and ACS Style

Shu, L.; Ludwig, A.; Peng, Z. Standards for Methods Utilizing Environmental DNA for Detection of Fish Species. Genes 2020, 11, 296. https://doi.org/10.3390/genes11030296

AMA Style

Shu L, Ludwig A, Peng Z. Standards for Methods Utilizing Environmental DNA for Detection of Fish Species. Genes. 2020; 11(3):296. https://doi.org/10.3390/genes11030296

Chicago/Turabian Style

Shu, Lu; Ludwig, Arne; Peng, Zuogang. 2020. "Standards for Methods Utilizing Environmental DNA for Detection of Fish Species" Genes 11, no. 3: 296. https://doi.org/10.3390/genes11030296

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