Monitoring of environmental DNA from nonindigenous species of algae, dinoflagellates and animals in the North East Atlantic

Knudsen, Steen Wilhelm; Hesselsøe, Martin; Thaulow, Jens; Agersnap, Sune; Hansen, Brian Klitgaard; Jacobsen, Marianne; Bekkevold, Dorte; Jensen, Søren Krogh; Andersen, Jesper H.

doi:10.1016/j.scitotenv.2022.153093

Cited by 22 publications

(29 citation statements)

References 119 publications

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“…Application of qPCR eDNA detection approaches have already shown promise to serve as tools for understanding salmon as an invasive species, such as the establishment of Chinook Salmon and Coho Salmon in the Patagonia region of Argentina and Chile (Chalde et al 2019;Nardi et al 2019) and Coho Salmon on the Korean Peninsula (Fu'adil Amin et al 2021). Another investigation used a qPCR approach to corroborate evidence for the absence of Pink Salmon in Danish harbors, as previously inferred from snorkeling and fishing surveys (Knudsen et al 2022). Similar eDNA approaches may be useful for monitoring rivers in the Pacific Northwest region of Canada and the USA for Atlantic Salmon that may escape from aquaculture pens off the coast of British Columbia.…”

Section: Detection Of Distribution Changes For Salmon Their Pathogens...mentioning

confidence: 77%

Environmental DNA as a Tool for Better Understanding the Distribution, Abundance, And Health of Atlantic Salmon and Pacific Salmon

Ramey,

McKeeman,

Petrou

et al. 2024

Fisheries

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The development and application of approaches to detect and quantify environmental DNA (eDNA) have potential to improve our understanding of the distribution, abundance, and health of Atlantic Salmon Salmo salar and Pacific salmon Oncorhynchus spp. Here, we review 61 articles focusing on eDNA applications pertaining to salmon occupying natural habitat and aquaculture facilities in the context of advances, opportunities, and challenges. Given recent advances, eDNA now serves as a useful tool for detecting Atlantic Salmon and Pacific salmon and understanding threats to the health of fish and their habitats. Opportunities exist to apply sensitive and minimally invasive eDNA approaches to detect fish and assess fish habitat, assess range expansions of salmon and salmon pathogens, and detect invasive species that may threaten salmon health and abundance. Near real‐time eDNA detection and quantification approaches to inform fisheries management may be on the horizon. Challenges limiting the widespread application of eDNA approaches for informing salmon management include accounting for the many factors affecting detection and quantification of eDNA, limits of data for deriving inference, and expense. Through continued development and refinement, eDNA approaches are anticipated to become increasingly available to, and utilized by, managers of Atlantic Salmon and Pacific salmon fisheries.

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Section: Detection Of Distribution Changes For Salmon Their Pathogens...mentioning

confidence: 77%

Environmental DNA as a Tool for Better Understanding the Distribution, Abundance, And Health of Atlantic Salmon and Pacific Salmon

Ramey,

McKeeman,

Petrou

et al. 2024

Fisheries

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“…Concentrations of the purified dsPCR‐amplicons were measured on a Qubit 2.0 Fluorometer (ThermoFisher Scientific) using the QubitTM dsDNA High Sensitivity kit. The molecular weight of the target fragment was found with the OligoCalc calculator webpage (Kibbe, 2007) and used to calculate the number of copies per μL, as in previous studies where absolute standard dilution series are used as positive controls (Agersnap et al, 2017; Knudsen et al, 2022). For each assay, the dsPCR target fragment was stored at −20°C in a concentration of 1E+6 copies per uL and only thawed again when used for preparing a dilution series.…”

Section: Methodsmentioning

confidence: 99%

Detection of environmental DNA from amphibians in Northern Europe applied in citizen science

Knudsen,

Hesselsøe,

Rytter

et al. 2023

Environmental DNA

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Many species of amphibians in Northern Europe are threatened and the local distributions are rarely described in detail. Application of modern molecular methods provides an important supplementary tool for monitoring the distribution and diversity of amphibians. For this purpose, we designed, tested, validated, and optimized 14 species‐specific assays on genomic DNA extracted from tissue samples to use for quantitative polymerase chain reaction (qPCR) setups targeting mitochondrial DNA from amphibians in freshwater samples. The tests confirmed species specificity for all assays. Considering a systematic definition of the limit of detection for each of the assays, the presented qPCR assays are unlikely to return false positive detection from any co‐occurring species in northern Europe. For field validation, the qPCR assays were applied in a large‐scale nationwide citizen science project in which sampling and qPCR analysis was carried out by high school students. Data from the citizen science project returned the expected results when compared to the known regional distribution of the target species and confirmed the presence of nine out of 14 Danish species of amphibians in the collected freshwater samples. Four out of 2550 qPCR test sets carried out by the high school students required a professional reanalysis in multiple replicates due to initial unexpected results. This emphasizes that efforts from citizen science may generate large amounts of valuable data, as long as the results are carefully scrutinized by experts.

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“…The DNA left in the surrounding environment can be retrieved and analyzed to deduce the species' identity. Environmental DNA has been studied in different environments, including water (Ficetola et al, 2008; Knudsen et al, 2022; Stoeckle et al, 2021; Thomsen et al, 2012; Thomsen et al, 2016), air (Clare et al, 2022; Roger et al, 2022), and soil (Buxton et al, 2018; Ryan et al, 2022). Typically, it is used to assess the presence of either a single target species (Ficetola et al, 2008; Knudsen et al, 2022; Yates et al, 2021) or the composition of species from larger taxonomic groups, that is, biodiversity (Bakker et al, 2019; Boussarie et al, 2018; Hongo et al, 2021; Roger et al, 2022; Russo et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

“…Environmental DNA has been studied in different environments, including water (Ficetola et al, 2008; Knudsen et al, 2022; Stoeckle et al, 2021; Thomsen et al, 2012; Thomsen et al, 2016), air (Clare et al, 2022; Roger et al, 2022), and soil (Buxton et al, 2018; Ryan et al, 2022). Typically, it is used to assess the presence of either a single target species (Ficetola et al, 2008; Knudsen et al, 2022; Yates et al, 2021) or the composition of species from larger taxonomic groups, that is, biodiversity (Bakker et al, 2019; Boussarie et al, 2018; Hongo et al, 2021; Roger et al, 2022; Russo et al, 2021). Because eDNA allows for easier, cheaper, and faster species monitoring compared to the labor‐intensive traditional visual methods (Fediajevaite et al, 2021; Goldberg et al, 2013; Lugg et al, 2018; Thomsen et al, 2012), there is an ongoing effort to explore the potential of eDNA studies beyond species detection toward estimation of biomass and abundance (Russo et al, 2021; Stoeckle et al, 2021; Thomsen et al, 2012; Yates et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

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Using eDNA to estimate biomass of bycatch in pelagic fisheries

et al. 2022

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In recent years, the analysis of environmental DNA (eDNA) has significantly improved, allowing for high‐resolution species identification and possible biomass quantification from water samples. Fisheries management typically requires monitoring of catches, including precise information about bycatch quantities to make sound assessments of exploitation rates. Bycatch assessment is particularly challenging in large catches (>500 T), and the current practice of visual assessment of subsampled catches is time‐consuming, requires extensive labor, and often has low precision. We explored the feasibility for applying eDNA‐based methods for studying catch composition using the pelagic North Sea herring fishery with bycatch of mackerel as a case. First, we experimentally simulate a series of catches using a range of herring and mackerel weight proportions to establish relationships under real fisheries scenarios. The relationship is subsequently used to estimate the biomass of mackerel bycatch from eDNA from three herring catches, by sampling and comparing processing water both onboard ships and at the processing factory. All samples are analyzed using species‐specific quantitative PCR (qPCR). The experiments reveled a strong correlation between DNA and weight fractions characterized by a constant overrepresentation of mackerel DNA compared to expected mackerel weight. We found that eDNA‐based and visual methods applied to the same landing reflect the within catch variability in species composition alike, however, the methods can show disparity in total estimates of mackerel biomass. Accounting for haul mixing within total landed catches increases the precision of the factory and ship eDNA‐based estimates for the same catch. We show that eDNA‐based bycatch estimates provide coherent quantitative data, and likely improve quality and reduce costs of collecting fisheries‐dependent data and thereby contribute to securing sustainable fisheries.

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Monitoring of environmental DNA from nonindigenous species of algae, dinoflagellates and animals in the North East Atlantic

Cited by 22 publications

References 119 publications

Environmental DNA as a Tool for Better Understanding the Distribution, Abundance, And Health of Atlantic Salmon and Pacific Salmon

Environmental DNA as a Tool for Better Understanding the Distribution, Abundance, And Health of Atlantic Salmon and Pacific Salmon

Detection of environmental DNA from amphibians in Northern Europe applied in citizen science

Using eDNA to estimate biomass of bycatch in pelagic fisheries

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