Environmental DNA (eDNA) detection of marine aquatic invasive species (AIS) in Eastern Canada using a targeted species-specific qPCR approach

Leblanc, F.; Belliveau, Valérie; Watson, Erica D.; Coomber, Chantal; Simard, Nathalie; DiBacco, Claudio; Bernier, Renée; Gagné, Nellie

doi:10.3391/mbi.2020.11.2.03

Cited by 36 publications

(23 citation statements)

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“…Specificity testing of the brook floater assay against a congener ( Alasmidonta undulata ) also found in New Brunswick rivers showed no cross‐amplification of this species. Based on the in vitro validation results, field results were classified as (i) not detected, (ii) inconclusive (detection was only obtained in one of the two technical replicates of the qPCR assay performed), (iii) suspected (detection was obtained in two of the two technical replicates of the qPCR assay performed, but the value was below the LOD) or (iv) detected (detection was obtained in two of the two technical replicates of the qPCR assay performed and the value was above the LOD; LeBlanc et al, 2020).…”

Section: Resultsmentioning

confidence: 99%

Detecting the brook floater, a freshwater mussel species at risk, using environmental DNA

Leblanc

Steeves

Belliveau

et al. 2021

Aquatic Conservation

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The use of environmental DNA (eDNA) is a promising approach for the detection of aquatic species, including species at risk. One freshwater mussel species of interest in Atlantic Canada, the brook floater (Alasmidonta varicosa), is listed as being of Special Concern under the Species at Risk Act in Canada and as Vulnerable on the International Union for Conservation of Nature Red List. Further scientific data regarding species distribution and critical habitat is needed for the protection and conservation of this species. The aim of this study was to design, optimize, and apply a species‐specific quantitative polymerase chain reaction assay for the detection of brook floater from eDNA samples, and to assess temporal variability in brook floater eDNA quantities. Through an eDNA survey performed in New Brunswick rivers in 2017 and 2018, brook floater DNA was found at a total of 16 out of 56 sites sampled. The amount of brook floater DNA detected at all 16 sites was always below the theoretical limit of detection of the assay, and, as such, results were classified as either ‘inconclusive’ or ‘suspected’. The co‐detection of eastern pearlshell (Margaritifera margaritifera), a more abundant freshwater mussel species in Atlantic Canada, was successfully used as a natural positive control. Temporal variability in the amount of eDNA found in the water was also assessed at a site with a known brook floater population and minimal variability in eDNA quantities was observed from May to September. These results provide researchers and managers with a new tool for the detection of the brook floater in support of conservation and monitoring efforts.

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Section: Resultsmentioning

confidence: 99%

Detecting the brook floater, a freshwater mussel species at risk, using environmental DNA

Leblanc

Steeves

Belliveau

et al. 2021

Aquatic Conservation

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“…DNA extraction from filters was conducted using half of each filter with the MN NucleoSpin Tissue Kit (Macherey-Nagel, PA, United States) following a modified protocol (LeBlanc et al, 2020). The resulting DNA extracts were stored at −20 • C and the second half of the filter was kept as a back-up.…”

Section: Dna Extraction and Species-specific Qpcr Testingmentioning

confidence: 99%

Spatial Heterogeneity of eDNA Transport Improves Stream Assessment of Threatened Salmon Presence, Abundance, and Location

et al. 2021

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The integration of environmental DNA (eDNA) within management strategies for lotic organisms requires translating eDNA detection and quantification data into inferences of the locations and abundances of target species. Understanding how eDNA is distributed in space and time within the complex environments of rivers and streams is a major factor in achieving this translation. Here we study bidimensional eDNA signals in streams to predict the position and abundance of Atlantic salmon (Salmo salar) juveniles. We use data from sentinel cages with a range of abundances (3–63 juveniles) that were deployed in three coastal streams in New Brunswick, Canada. We evaluate the spatial patterns of eDNA dispersal and determine the effect of discharge on the dilution rate of eDNA. Our results show that eDNA exhibits predictable plume dynamics downstream from sources, with eDNA being initially concentrated and transported in the midstream, but eventually accumulating in stream margins with time and distance. From these findings we developed a fish detection and distribution prediction model based on the eDNA ratio in midstream versus bankside sites for a variety of fish distribution scenarios. Finally, we advise that sampling midstream at every 400 m is sufficient to detect a single fish at low velocity, but sampling efforts need to be increased at higher water velocity (every 100 m in the systems surveyed in this study). Studying salmon eDNA spatio-temporal patterns in lotic environments is essential to developing strong quantitative population assessment models that successfully leverage eDNA as a tool to protect salmon populations.

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“…In contrast, DNA-based tools can performed well, with the ease of collecting water samples offering the potential for scaling up monitoring efforts. In some countries progress toward incorporating eDNA into routine surveillance programs has already been initiated, demonstrating how these tools can contribute to improved monitoring of marine non-native species (Roux et al, 2020;Wood et al, 2019;LeBlanc et al, 2020). Performance and ability of targeted tools such as qPCR to support marine biosecurity scored high in a review conducted by Zaiko et al (2018).…”

Section: Discussionmentioning

confidence: 99%

“…In addition to the specificity of the eDNA assay, clear definitions of the limit of detection (LOD) and quantification (LOQ) are essential to generate robust and accurate data. Different templates are used to generate the LOD and LOQ calibration plots with either target species genomic DNA (Gillum et al, 2014;Miralles et al, 2016Miralles et al, , 2019Mauvisseau et al, 2019;LeBlanc et al, 2020), synthetic DNA constructs (Larson et al, 2017;Harper et al, 2018;Mirimin et al, 2019;Roux et al, 2020), or a PCR product of the target gene (Wood et al, 2019) being commonly utilized. The standards in calculating and reporting these parameters continue to vary widely in the published literature and consequently the LOD and LOQ are reported either as a copy number or concentration of a given target per reaction or microliter.…”

Section: Sensitivity Of Didemnum Vexillum Qpcr Assaymentioning

confidence: 99%

“…The second, multi-species detection approach by metabarcoding uses generic primer pairs and high throughput sequencing (see review by Zaiko et al, 2018). Recent studies have demonstrated that the detection of invasive non-native species by targeting their eDNA can be incorporated into routine marine biosecurity surveillance either at species (Simpson et al, 2017;Wood et al, 2019;LeBlanc et al, 2020) or community level (Holman et al, 2019;Rey et al, 2019). This study presents the results of a D. vexillum monitoring program carried out between 2017 and 2019 in selected recreational marinas and shellfish aquaculture farms in Scotland based on detection of target species eDNA by qPCR and describes the assay validation process for the use of this assay in the Northern Hemisphere.…”

Section: Introductionmentioning

confidence: 99%

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Environmental DNA Based Surveillance for the Highly Invasive Carpet Sea Squirt Didemnum vexillum: A Targeted Single-Species Approach

et al. 2021

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The presence and diversity of marine non-native species, the number of new invasions, and the impact on native communities and habitats are important metrics used to assess the health of marine ecosystems. Monitoring for marine non-native species, using traditional approaches such as rapid assessment surveys (RASs), requires taxonomic expertise and may still fail to detect rare or inconspicuous species. This study reports a validation process for a quantitative PCR (qPCR) assay based on the cytochrome oxidase 1 gene, designed to detect highly invasive tunicate Didemnum vexillum by targeting environmental DNA (eDNA) present in water samples. The D. vexillum qPCR assay showed high sensitivity, with the threshold limit of detection (LOD) and modeled LOD3 (based on triplicate qPCR reactions) estimated as 9.187 and 1.117 copies reaction–1, respectively and the limit of quantification (LOQ) was calculated as 18 copies reaction–1. Analyses of water samples collected from selected Pacific oyster farms and recreational marinas in Scotland showed 100% concordance between the historical data on presence of D. vexillum from RASs and detection of D. vexillum eDNA. Consistency of detection of D. vexillum eDNA among different sampling points within each infected sampling site varied, ranging between 100% positive throughout the site to some sampling points testing “negative” or only as “suspected” for D. vexillum. Sites with lower within-site detection consistency included sites with a low density of D. vexillum as reported by RASs or were sites undergoing D. vexillum management. The present pilot monitoring program demonstrates the potential to generate important data on presence of D. vexillum. This program will be scaled up across large geographic regions and used in the first instance to focus and target the traditional RASs to D. vexillum eDNA-positive sites in a cost-effective way, with an aim to verify the species presence by visual observation and direct Sanger sequencing of positive qPCR products.

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Environmental DNA (eDNA) detection of marine aquatic invasive species (AIS) in Eastern Canada using a targeted species-specific qPCR approach

Cited by 36 publications

References 0 publications

Detecting the brook floater, a freshwater mussel species at risk, using environmental DNA

Detecting the brook floater, a freshwater mussel species at risk, using environmental DNA

Spatial Heterogeneity of eDNA Transport Improves Stream Assessment of Threatened Salmon Presence, Abundance, and Location

Environmental DNA Based Surveillance for the Highly Invasive Carpet Sea Squirt Didemnum vexillum: A Targeted Single-Species Approach

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