Detecting aquatic invasive species in bait and pond stores with targeted environmental (e)DNA high-throughput sequencing metabarcode assays: Angler, retailer, and manager implications

Snyder, Matthew R.; Stepien, Carol A.; Marshall, Nathaniel T.; Scheppler, Hannah B.; Black, Christopher L.; Czajkowski, Kevin

doi:10.1016/j.biocon.2020.108430

Cited by 19 publications

(25 citation statements)

References 52 publications

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“…Three metabarcoding assays designed by our lab (Stepien et al 2019, Snyder et al 2020 were used, which targeted the mtDNA cytochrome (cyt) b gene to identify and differentiate fish species (native and introduced/invasive) from the Great Lakes and upper Wabash River regions (Table 1, Suppl. material 1: Fig.…”

Section: Metabarcoding Assays Employedmentioning

confidence: 99%

“…The FishCytb assay was a general assay designed to detect all fishes in these ecosystems (Snyder et al 2020), which amplified a 154 nucleotide (NT) region of the cyt b gene, beginning at NT 855. The CarpCytb assay was formulated for invasive carps (Stepien et al 2019), amplifying 136 NTs beginning at NT 114, and the GobyCytb assay (Snyder et al 2020) was designed to distinguish invasive gobies, amplifying 167 NTs beginning at NT 42. Another general fish assay for part of the mt 12S RNA gene (MiFish; Miya et al 2015) also was used, for comparison (Table 1).…”

Section: Metabarcoding Assays Employedmentioning

confidence: 99%

“…Spacer inserts were from Klymus et al (2017). Assay publications: CarpCytb (Stepien et al 2019), GobyCytb and FishCytb (Snyder et al 2020), and 12S RNA MiFish (Miya et al 2015). or traditional population genetics sampling and data collection ( †) were conducted and compared to eDNA metabarcoding assay results.…”

Section: Metabarcoding Assays Employedmentioning

confidence: 99%

“…Water samples from turbid habitats often clog filters (Williams et al 2017) and thus genetic material was captured using centrifugation (per Stepien et al 2019;Snyder et al 2020). The DNA was extracted from the pellets using Qiagen DNeasy kits (Hilden, Germany) (detailed in Suppl.…”

Section: Dna Capture Extraction and Library Preparationmentioning

confidence: 99%

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Increasing confidence for discerning species and population compositions from metabarcoding assays of environmental samples: case studies of fishes in the Laurentian Great Lakes and Wabash River

Snyder¹,

Stepien²

2020

MBMG

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Community composition data are essential for conservation management, facilitating identification of rare native and invasive species, along with abundant ones. However, traditional capture-based morphological surveys require considerable taxonomic expertise, are time consuming and expensive, can kill rare taxa and damage habitats, and often are prone to false negatives. Alternatively, metabarcoding assays can be used to assess the genetic identity and compositions of entire communities from environmental samples, comprising a more sensitive, less damaging, and relatively time- and cost-efficient approach. However, there is a trade-off between the stringency of bioinformatic filtering needed to remove false positives and the potential for false negatives. The present investigation thus evaluated use of four mitochondrial (mt) DNA metabarcoding assays and a customized bioinformatic Bioinformatic pipeline to increase confidence in species identifications by removing false positives, while achieving high detection probability. Positive controls were used to calculate sequencing error, and results that fell below those cutoff values were removed, unless found with multiple assays. The performance of this approach was tested to discern and identify North American freshwater fishes using lab experiments (mock communities and aquarium experiments) and processing of a bulk ichthyoplankton sample. The method then was applied to field environmental (e) DNA water samples taken concomitant with electrofishing surveys and morphological identifications. This protocol detected 100% of species present in concomitant electrofishing surveys in the Wabash River and an additional 21 that were absent from traditional sampling. Using single 1 L water samples collected from just four locations, the metabarcoding assays discerned 73% of the total fish species that were discerned during four months of an extensive electrofishing river survey in the Maumee River, along with an additional nine species. In both rivers, total fish species diversity was best resolved when all four metabarcoding assays were used together, which identified 35 additional species missed by electrofishing. Ecological distinction and diversity levels among the fish communities also were better resolved with the metabarcoding assays than with morphological sampling and identifications, especially using all four assays together. At the population-level, metabarcoding analyses targeting the invasive round goby Neogobius melanostomus and the silver carp Hypophthalmichthys molitrix identified all population haplotype variants found using Sanger sequencing of morphologically sampled fish, along with additional intra-specific diversity, meriting further investigation. Overall findings demonstrated that the use of multiple metabarcoding assays and custom bioinformatics that filter potential error from true positive detections improves confidence in evaluating biodiversity.

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Section: Metabarcoding Assays Employedmentioning

confidence: 99%

Section: Metabarcoding Assays Employedmentioning

confidence: 99%

Section: Metabarcoding Assays Employedmentioning

confidence: 99%

Section: Dna Capture Extraction and Library Preparationmentioning

confidence: 99%

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Increasing confidence for discerning species and population compositions from metabarcoding assays of environmental samples: case studies of fishes in the Laurentian Great Lakes and Wabash River

Snyder¹,

Stepien²

2020

MBMG

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“…However, because sequences from different species can be parsed within HTS, the presence of QM-ZM could still be discerned, with the HTS eDNA effort still outperforming visual surveys. Snyder et al (2020) later used HTS and MOL16S to successfully monitor for QM-ZM in holding-tank waters in bait shops in the Great Lakes Region. Prié et al (2020) also developed bivalve-specific HTS metabaroding primers, targeting 16S in the orders Unionida (Unio01) and Venerida (Vene01).…”

Section: High-throughput Sequencingmentioning

confidence: 99%

Advanced molecular-based surveillance of quagga and zebra mussels: A review of environmental DNA/RNA (eDNA/eRNA) studies and considerations for future directions

Feist¹,

Lance²

2021

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Sensitive methods, capable of rapidly and accurately detecting aquatic invasive species, are in demand. Molecular-based approaches, such as environmental DNA (eDNA) surveys, satisfy these requirements and have grown in popularity. As such, eDNA surveys could aid the effort to combat the colonisation and spread of two notoriously invasive freshwater mussel species, the quagga mussel (Dreissena rostriformis bugensis) and zebra mussel (D. polymorpha), through improved surveillance ability. Here, we provide a review of dreissenid eDNA literature (both grey and published), summarising efforts involved in the development of various assays for use in multiple different technologies (e.g. quantitative PCR, high-throughput sequencing and loop-mediated isothermal amplification) and sampling scenarios. We discuss important discoveries made along the way, including novel revelations involving environmental RNA (eRNA), as well as the advantages and limitations of available methods and instrumentation. In closing, we highlight critical remaining gaps, where further investigation could lead to advancements in dreissenid monitoring capacity.

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eDNA metabarcoding reveals riverine fish community structure and climate associations in northeastern Canada

Crowley,

Bentzen,

Kess

et al. 2024

Environmental DNA

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Climate change is a critical threat to northern freshwater ecosystems, yet many remote areas are data deficient in terms of biodiversity information. Generating community composition data through collection of environmental DNA (eDNA) is less labor‐intensive than traditional sampling methods and is being increasingly used in areas that have been historically difficult to sample such as northern freshwater habitats. Here, we employed eDNA metabarcoding using three mitochondrial markers at 174 coastal river sites, sampled over three years (2019–2021) across a broad region in northeastern North America, Newfoundland and Labrador. We characterized current riverine fish community composition, compared it to traditional sampling records, and quantified the influence of climate on variation in fish community composition. The analysis detected 33 fish species across the region (1–13 per location), including three non‐native species, as well as several new possible range expansions. Variance partitioning with redundancy analysis indicated ~56% of the variation in community composition could be explained by spatial and climate factors (~21% and ~7%, respectively, with an additional ~28% shared). A temporal comparison across a subset of locations with both eDNA and historical records (1965–1985) revealed that more species were detected on average with eDNA sampling, and that sampling method explained a small portion of the variation (~4%) in comparison with space (~10%) and climate (~7%). Ultimately, this work is the most complete survey of freshwater and diadromous fishes present in Newfoundland and Labrador to date, highlights new detections of non‐native species including previously unknown diversity for the region, and provides future direction for the application of eDNA analysis in northern riverine habitats.

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Detecting aquatic invasive species in bait and pond stores with targeted environmental (e)DNA high-throughput sequencing metabarcode assays: Angler, retailer, and manager implications

Cited by 19 publications

References 52 publications

Increasing confidence for discerning species and population compositions from metabarcoding assays of environmental samples: case studies of fishes in the Laurentian Great Lakes and Wabash River

Increasing confidence for discerning species and population compositions from metabarcoding assays of environmental samples: case studies of fishes in the Laurentian Great Lakes and Wabash River

Advanced molecular-based surveillance of quagga and zebra mussels: A review of environmental DNA/RNA (eDNA/eRNA) studies and considerations for future directions

eDNA metabarcoding reveals riverine fish community structure and climate associations in northeastern Canada

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