eDNA as a tool for identifying freshwater species in sustainable forestry: A critical review and potential future applications

Coble, Ashley A.; Flinders, Camille A.; Homyack, Jessica A.; Penaluna, Brooke E.; Cronn, Richard; Weitemier, Kevin

doi:10.1016/j.scitotenv.2018.08.370

Cited by 67 publications

(45 citation statements)

References 144 publications

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“…Much of the published eDNA literature highlights the use and applications of eDNA as an important conservation tool for the monitoring of animal populations and provides compelling evidence for eDNA analysis as a potential replacement for traditional genetic sampling methods, for example, physical handling, biopsying and tagging of individuals (Deiner et al, 2017;Harper et al, 2018;Minamoto et al, 2017;Stewart, Ma, Zheng, & Zhao, 2017;Thomsen & Willerslev, 2015). While there have been many reviews and studies on best practices for eDNA studies (Alberdi et al, 2018;Spens et al, 2017) and on the influence of abiotic and biotic factors on the persistence of eDNA in aquatic systems (Barnes et al, 2014;Coble et al, 2018), very little of the eDNA published literature contain studies with false-negative results for target DNA, and thus, there is a gap in the literature. Such studies yield key information regarding those species and environments where eDNA studies were not successful, providing an important reality check to inform conservationists, management bodies and researchers on potential pitfalls in their planned studies and help to work toward optimizing their workflow to ensure successful capture of target DNA.…”

Section: Edna and Conservationmentioning

confidence: 99%

False‐negative detections from environmental DNA collected in the presence of large numbers of killer whales (Orcinus orca)

et al. 2019

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While environmental DNA (eDNA) is becoming increasingly established in biodiversity monitoring of freshwater ecosystems, the use of eDNA surveys in the marine environment is still in its infancy. Here, we use two approaches: targeted quantitative PCR (qPCR) and whole-genome enrichment capture followed by shotgun sequencing in an effort to amplify killer whale DNA from seawater samples. Samples were collected in close proximity to killer whales in inshore and offshore waters, in varying sea conditions and from the surface and subsurface but none returned strongly positive detections of killer whale eDNA. We validated our laboratory methodologies by successfully amplifying a dilution series of a positive control of killer whale DNA. Furthermore, DNA of Atlantic mackerel, which was present at all sites during sampling, was successfully amplified from the same seawater samples, with positive detections found in ten of the eighteen eDNA extracts. We discuss the various eDNA collection and amplification methodologies used and the abiotic and biotic factors that influence eDNA detection. We discuss possible explanations for the lack of positive killer whale detections, potential pitfalls, and the apparent limitations of eDNA for genetic research on cetaceans, particularly in offshore regions. K E Y W O R D S eDNA, environmental DNA, metagenomics, Orcinus orca, PCR, Scomber scombrus, wholegenome enrichment | 317 PINFIELD Et aL. S U PP O RTI N G I N FO R M ATI O N Additional supporting information may be found online in the Supporting Information section at the end of the article. How to cite this article: Pinfield R, Dillane E, Runge AKW, et al. False-negative detections from environmental DNA collected in the presence of large numbers of killer whales (Orcinus orca).

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Section: Edna and Conservationmentioning

confidence: 99%

False‐negative detections from environmental DNA collected in the presence of large numbers of killer whales (Orcinus orca)

et al. 2019

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“…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].…”

Section: Introductionmentioning

confidence: 99%

“…eDNA from aquatic ecosystems is suitable for diversity assessment of contemporary aquatic species [7]. Furthermore, emerging eDNA technologies are non-invasive, sensitive, and cost-efficient compared to traditional survey approaches [2,5,8]. Target organisms can be detected at any life stage, including in the egg, larval, and juvenile forms from eDNA samples.…”

Section: Introductionmentioning

confidence: 99%

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Standards for Methods Utilizing Environmental DNA for Detection of Fish Species

Shu

Ludwig

Peng

2020

Genes

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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.

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“…Ogram et al introduced eDNA in the field of microbiology in 1987 [19]. eDNA is a valuable tool, and analysis of eDNA is increasingly being used to identify sensitive and invasive species or pathogens, detect low abundance or endangered species and estimate biodiversity [20,21] (Table S1). Furthermore, previous studies indicated that eDNA analysis could be more convenient, efficient and comprehensive than conventional methods for analyzing different taxa across spatial and temporal scales [22].…”

Section: Introductionmentioning

confidence: 99%

A Review and Perspective of eDNA Application to Eutrophication and HAB Control in Freshwater and Marine Ecosystems

Liu

Zhang

et al. 2020

Microorganisms

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Changing ecological communities in response to anthropogenic activities and climate change has become a worldwide problem. The eutrophication of waterbodies in freshwater and seawater caused by the effects of human activities and nutrient inputs could result in harmful algae blooms (HABs), decreases water quality, reductions in biodiversity and threats to human health. Rapid and accurate monitoring and assessment of aquatic ecosystems are imperative. Environmental DNA (eDNA) analysis using high-throughput sequencing has been demonstrated to be an effective and sensitive assay for detecting and monitoring single or multiple species in different samples. In this study, we review the potential applications of eDNA approaches in controlling and mitigating eutrophication and HABs in freshwater and marine ecosystems. We use recent studies to highlight how eDNA methods have been shown to be a useful tool for providing comprehensive data in studies of eutrophic freshwater and marine environments. We also provide perspectives on using eDNA techniques to reveal molecular mechanisms in biological processes and mitigate eutrophication and HABs in aquatic ecosystems. Finally, we discuss the feasible applications of eDNA for monitoring biodiversity, surveying species communities and providing instructions for the conservation and management of the environment by integration with traditional methods and other advanced techniques.

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eDNA as a tool for identifying freshwater species in sustainable forestry: A critical review and potential future applications

Cited by 67 publications

References 144 publications

False‐negative detections from environmental DNA collected in the presence of large numbers of killer whales (Orcinus orca)

False‐negative detections from environmental DNA collected in the presence of large numbers of killer whales (Orcinus orca)

Standards for Methods Utilizing Environmental DNA for Detection of Fish Species

A Review and Perspective of eDNA Application to Eutrophication and HAB Control in Freshwater and Marine Ecosystems

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