Development and validation of targeted environmental DNA (eDNA) metabarcoding for early detection of 69 invasive fishes and aquatic invertebrates
Abstract Invasive species are of concern due to their impacts on ecosystems and economies, but they pose significant control challenges. Environmental DNA (eDNA) is a powerful tool in the detection of aquatic organisms at low densities due to high detection sensitivity and relative ease of sample co...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2023-01-01
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| Series: | Environmental DNA |
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| Online Access: | https://doi.org/10.1002/edn3.359 |
| _version_ | 1797946796672024576 |
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| author | Yueyang Wu Scott F. Colborne Matthew R. Charron Daniel D. Heath |
| author_facet | Yueyang Wu Scott F. Colborne Matthew R. Charron Daniel D. Heath |
| author_sort | Yueyang Wu |
| collection | DOAJ |
| description | Abstract Invasive species are of concern due to their impacts on ecosystems and economies, but they pose significant control challenges. Environmental DNA (eDNA) is a powerful tool in the detection of aquatic organisms at low densities due to high detection sensitivity and relative ease of sample collection. Aquatic eDNA analyses have increased worldwide and are generally either applied to few target species (quantitative PCR), or for broad taxonomic applications (metabarcoding). Here, we describe the development and testing of a hybrid approach that utilized high‐sensitivity PCR primer sets and high‐throughput sequencing (HTS), referred to as targeted metabarcoding, to detect 69 fishes and invertebrates. We identified target species based on reports of globally important invasive species and developed two independent PCR primers for each species (CO1 and a second mtDNA region). We assessed sensitivity and eDNA interference for all 138 primers (2 per species and 69 species) using standard end‐point PCR and tested them on 10 eDNA samples spiked with various amounts of one or more of the target species DNA. The sensitivity of the 138 primer sets ranged between 1.5 × 10−5 and 2.64 ng template DNA (mean = 0.069 ng). Primers were also tested for interference effects using plankton eDNA to simulate field conditions. The inclusion of interfering plankton DNA reduced the sensitivity for most primer sets by one or more orders of magnitude (range 0–3). Overall, our targeted metabarcoding resulted in the detection of ~98% of species in the DNA spiked samples, and perhaps more importantly, the HTS read count was positively related to the quantity of spiked DNA (p < 0.002). We envision this technique being particularly useful for the early detection of species at low population densities; however, there are diverse applications of targeted metabarcoding for monitoring aquatic community composition and to quantify ecosystem change and health. |
| first_indexed | 2024-04-10T21:16:37Z |
| format | Article |
| id | doaj.art-ac59034095af420e96aae583cc019f62 |
| institution | Directory Open Access Journal |
| issn | 2637-4943 |
| language | English |
| last_indexed | 2024-04-10T21:16:37Z |
| publishDate | 2023-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | Environmental DNA |
| spelling | doaj.art-ac59034095af420e96aae583cc019f622023-01-20T12:18:11ZengWileyEnvironmental DNA2637-49432023-01-0151738410.1002/edn3.359Development and validation of targeted environmental DNA (eDNA) metabarcoding for early detection of 69 invasive fishes and aquatic invertebratesYueyang Wu0Scott F. Colborne1Matthew R. Charron2Daniel D. Heath3Great Lakes Institute for Environmental Research University of Windsor Windsor Ontario CanadaGreat Lakes Institute for Environmental Research University of Windsor Windsor Ontario CanadaGreat Lakes Institute for Environmental Research University of Windsor Windsor Ontario CanadaGreat Lakes Institute for Environmental Research University of Windsor Windsor Ontario CanadaAbstract Invasive species are of concern due to their impacts on ecosystems and economies, but they pose significant control challenges. Environmental DNA (eDNA) is a powerful tool in the detection of aquatic organisms at low densities due to high detection sensitivity and relative ease of sample collection. Aquatic eDNA analyses have increased worldwide and are generally either applied to few target species (quantitative PCR), or for broad taxonomic applications (metabarcoding). Here, we describe the development and testing of a hybrid approach that utilized high‐sensitivity PCR primer sets and high‐throughput sequencing (HTS), referred to as targeted metabarcoding, to detect 69 fishes and invertebrates. We identified target species based on reports of globally important invasive species and developed two independent PCR primers for each species (CO1 and a second mtDNA region). We assessed sensitivity and eDNA interference for all 138 primers (2 per species and 69 species) using standard end‐point PCR and tested them on 10 eDNA samples spiked with various amounts of one or more of the target species DNA. The sensitivity of the 138 primer sets ranged between 1.5 × 10−5 and 2.64 ng template DNA (mean = 0.069 ng). Primers were also tested for interference effects using plankton eDNA to simulate field conditions. The inclusion of interfering plankton DNA reduced the sensitivity for most primer sets by one or more orders of magnitude (range 0–3). Overall, our targeted metabarcoding resulted in the detection of ~98% of species in the DNA spiked samples, and perhaps more importantly, the HTS read count was positively related to the quantity of spiked DNA (p < 0.002). We envision this technique being particularly useful for the early detection of species at low population densities; however, there are diverse applications of targeted metabarcoding for monitoring aquatic community composition and to quantify ecosystem change and health.https://doi.org/10.1002/edn3.359CO1environmental DNAgenetic markersinvasive specieslaboratory validationmetabarcoding |
| spellingShingle | Yueyang Wu Scott F. Colborne Matthew R. Charron Daniel D. Heath Development and validation of targeted environmental DNA (eDNA) metabarcoding for early detection of 69 invasive fishes and aquatic invertebrates Environmental DNA CO1 environmental DNA genetic markers invasive species laboratory validation metabarcoding |
| title | Development and validation of targeted environmental DNA (eDNA) metabarcoding for early detection of 69 invasive fishes and aquatic invertebrates |
| title_full | Development and validation of targeted environmental DNA (eDNA) metabarcoding for early detection of 69 invasive fishes and aquatic invertebrates |
| title_fullStr | Development and validation of targeted environmental DNA (eDNA) metabarcoding for early detection of 69 invasive fishes and aquatic invertebrates |
| title_full_unstemmed | Development and validation of targeted environmental DNA (eDNA) metabarcoding for early detection of 69 invasive fishes and aquatic invertebrates |
| title_short | Development and validation of targeted environmental DNA (eDNA) metabarcoding for early detection of 69 invasive fishes and aquatic invertebrates |
| title_sort | development and validation of targeted environmental dna edna metabarcoding for early detection of 69 invasive fishes and aquatic invertebrates |
| topic | CO1 environmental DNA genetic markers invasive species laboratory validation metabarcoding |
| url | https://doi.org/10.1002/edn3.359 |
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