Performance of eDNA assays to detect and quantify an elusive benthic fish in upland streams

Hinlo, Rheyda; Lintermans, Mark; Gleeson, Dianne; Broadhurst, Ben; Furlan, Elise M.

doi:10.1007/s10530-018-1760-x

Cited by 43 publications

(40 citation statements)

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“…As more projects seek to find or census fish within a particular reach (Hinlo et al, 2018;Pilliod et al, 2013;Tillotson et al, 2018), more attention will be paid to distance ~ detection rate and quantity relation- Figure 3), eDNA sampling for such permitted activities may F I G U R E 4 Simulated detection rates for various fish abundances and number of technical replicates, assuming evenly spaced streamlong sampling regimes. Using three technical replicates and a <400 m sampling distance nearly guarantees detection of any number of fish.…”

Section: Discussionmentioning

confidence: 99%

“…Understanding the outcome of eDNA production, transport, and loss processes is especially important for high-resolution studies, which may seek to detect or quantify organisms in very local areas, such as stream reaches (Hinlo et al, 2018;Pilliod et al, 2013;Tillotson et al, 2018). Attaining such high resolution in stream systems is complicated by how these time-dependent eDNA processes play out over a spatial scale.…”

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confidence: 99%

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Experimental assessment of optimal lotic eDNA sampling and assay multiplexing for a critically endangered fish

et al. 2020

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Detecting the environmental DNA (eDNA) of an organism can in principle be easier and more efficient than detecting the organism itself, particularly for rare or cryptic species (Hinlo et al., 2018; Jerde et al., 2011; Pfleger et al., 2016). eDNA detection is particularly valuable for threatened fishes, which are otherwise most often surveyed with labor-intensive capture surveys (e.g., electrofishing, netting), and might be harmed during the capture process (Dolan and

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Section: Discussionmentioning

confidence: 99%

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confidence: 99%

Experimental assessment of optimal lotic eDNA sampling and assay multiplexing for a critically endangered fish

et al. 2020

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“…Clavero et al 2006, Bies et al 2016; with boat electrofishing known to result in a high rate of false negative detections for Macquaria australasica (Lintermans 2016). Cryptic, benthic, fossorial species such as Misgurnus anguillicaudatus are also known to be difficult to capture by electrofishing (Hinlo et al 2018, Sigsgaard et al 2015, particularly in large stream habitats with elevated turbidity (Lintermans unpublished). The electrofishing data also failed to detect trout cod (Macquaria macquariensis) at three sites where both the experts and the metabarcoding survey indicated its presence, which could indicate that the current survey methods are inadequate to detect this rare threatened species (Ebner et al 2008).…”

Section: Discussionmentioning

confidence: 99%

Monitoring riverine fish communities through eDNA metabarcoding: determining optimal sampling strategies along an altitudinal and biodiversity gradient

Bylemans

Gleeson

Lintermans

et al. 2018

MBMG

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Monitoring aquatic biodiversity through DNA extracted from environmental samples (eDNA) combined with high-throughput sequencing, commonly referred to as eDNA metabarcoding, is increasing in popularity within the scientific community. However, sampling strategies, laboratory protocols and analytical pipelines can influence the results of eDNA metabarcoding surveys. While the impact of laboratory protocols and analytical pipelines have been extensively studied, the importance of sampling strategies on eDNA metabarcoding surveys has not received the same attention. To avoid underestimating local biodiversity, adequate sampling strategies (i.e. sampling intensity and spatial sampling replication) need to be implemented. This study evaluated the impact of sampling strategies along an altitudinal and biodiversity gradient in the upper section of the Murrumbidgee River (Murray-Darling Basin, Australia). An eDNA metabarcoding survey was used to determine the local fish biodiversity and evaluate the influence of sampling intensity and spatial sampling replication on the biodiversity estimates. The results show that optimal eDNA sampling strategies varied between sites and indicate that river morphology, species richness and species abundance affect the optimal sampling intensity and spatial sampling replication needed to accurately assess the fish biodiversity. While the generality of the patterns will need to be confirmed through future studies, these findings provide a basis to guide future eDNA metabarcoding surveys in river systems.

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“…Information about the ecology (e.g., feeding areas or spawning grounds) of target species should be used for sampling. Field sample replicates are necessary to enhance the efficiency of DNA collection and probability of target eDNA detection; at least three samples were collected from each site in most studies [38,[41][42][43][44][45]. When the number of samples is increased, to improve work efficiency and reduce analysis cost, researchers may consider pooling the water samples from multiple locations for subsequent processing.…”

Section: Sample Volume Depths and Amount Of Watermentioning

confidence: 99%

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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Performance of eDNA assays to detect and quantify an elusive benthic fish in upland streams

Cited by 43 publications

References 50 publications

Experimental assessment of optimal lotic eDNA sampling and assay multiplexing for a critically endangered fish

Experimental assessment of optimal lotic eDNA sampling and assay multiplexing for a critically endangered fish

Monitoring riverine fish communities through eDNA metabarcoding: determining optimal sampling strategies along an altitudinal and biodiversity gradient

Standards for Methods Utilizing Environmental DNA for Detection of Fish Species

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