A new approach to molecular biosurveillance of invasive species using DNA metabarcoding

Westfall, Kristen M.; Therriault, Thomas W.; Abbott, Cathryn L.

doi:10.1111/gcb.14886

Cited by 45 publications

(62 citation statements)

References 51 publications

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“…However, studies employing both eDNA and bulk organismal samples suggest that eDNA alone cannot replace organismal sampling (e.g. Leduc et al 2019, Huhn et al 2020, Rey et al 2020, Westfall et al 2020). Currently, it would probably work best as an early alert system or exploratory method to be used as a complement to conventional approaches such as in situ visual confirmation (Borrell et al 2018, Holman et al 2019, Rey et al 2020, specimen collection (Leduc et al 2019, Huhn et al 2020 or followed by active surveillance with digital drop PCR (ddPCR) or quantitative PCR (qPCR) (Wood et al 2019).…”

Section: Sampled Locations Substrates and Biological Targetsmentioning

confidence: 99%

“…1B). Zooplankton sampling has been conducted in ships ballast water (Zaiko et al 2015a,b, Ghabooli et al 2016, Darling et al 2018, Lin et al 2020, boats bilge water (Fletcher et al 2017), and in sea water in ports and marinas or nearby natural habitats , Zaiko et al 2015c, Abad et al 2016, Stefanni et al 2018, Couton et al 2019, Leduc et al 2019, Rey et al 2020, Westfall et al 2020. The monitoring of larvae in plankton samples in ports or in the close vicinities, may provide key information about NIS introduction status or detect their presence at an earlier stage (Couton et al 2019).…”

Section: Sampled Locations Substrates and Biological Targetsmentioning

confidence: 99%

“…In order to detect the majority of taxa in a given location, in particular rare and/or patchy species, biodiversity surveys require comprehensive spatial and temporal sampling and screening of different types of substrates (e.g. water, sediment, bulk samples; Koziol et al 2018, Huhn et al 2020, Rey et al 2020, Westfall et al 2020. However, the sampling design varied significantly across studies and very few have compared the effects of the sampling effort or the use of different substrates in NIS detection (see Zaiko et al 2016, Koziol et al 2018, Rey et al 2020, Westfall et al 2020 (Table S2).…”

Section: Sampling Designmentioning

confidence: 99%

“…For instance, based on an extensive survey conducted in the port of Bilbao (Spain), Rey et al (2020) found a strong influence of the sampling site in the recovered biodiversity, suggesting that spatially comprehensive sampling was crucial to recover biodiversity, and to increase the success of NIS detection. Also, higher sampling frequency has been shown to increase the diversity recovered, as well as the ability to detect NIS (Chain et al 2016, Couton et al 2019, Rey et al 2020, Westfall et al 2020).…”

Section: Sampling Designmentioning

confidence: 99%

“…Despite the great potential of DNA metabarcoding to improve NIS monitoring in marine and coastal ecosystems (Pochon et al 2013, Ardura et al 2015, Zaiko et al 2015a,b,c, Borrell et al 2018, Westfall et al 2020, the widespread and routine implementation of this method is still highly dependent on reliable and cost-effective standardization (Leese et al 2016, Rey et al 2020. In this study, we carried out a comprehensive compilation and evaluation of methodologies employed across the full workflow (e.g.…”

Section: Introductionmentioning

confidence: 99%

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Status and prospects of marine NIS detection and monitoring through (e)DNA metabarcoding

Duarte

Vieira

Lavrador

et al. 2020

Preprint

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17In coastal ecosystems, non-indigenous species (NIS) are recognized as a major threat to 18 biodiversity, ecosystem functioning and socio-economic activities. Here we present a systematic 19 review on the use of metabarcoding for NIS surveillance in marine and coastal ecosystems, 20 through the analysis of 42 publications. Metabarcoding has been mainly applied to environmental 21 DNA (eDNA) from water samples, but also to DNA extracted from bulk organismal samples. 22 2 seeking the best approach for detecting the broadest range of species, while minimizing the 38 chances of false positives and false negatives detection. 39 40 Keywords: Marine and coastal ecosystems; non-indigenous species; biosurveillance; (e)DNA 41 metabarcoding 42 43

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Section: Sampled Locations Substrates and Biological Targetsmentioning

confidence: 99%

Section: Sampled Locations Substrates and Biological Targetsmentioning

confidence: 99%

Section: Sampling Designmentioning

confidence: 99%

Section: Sampling Designmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Status and prospects of marine NIS detection and monitoring through (e)DNA metabarcoding

Duarte

Vieira

Lavrador

et al. 2020

Preprint

View full text Add to dashboard Cite

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Trust your guts? The effect of gut section on diet composition and impact of Mus musculus on islands using metabarcoding

Pinho

Lopes

Paupério

et al. 2022

Ecology and Evolution

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DNA metabarcoding is widely used to characterize the diet of species, and it becomes very relevant for biodiversity conservation, allowing the understanding of trophic chains and the impact of invasive species. The need for cost‐effective biodiversity monitoring methods fostered advances in this technique. One question that arises is which sample type provides a better diet representation. Therefore, with this study, we intended to evaluate if there were differences in diet estimates according to the section of the gastrointestinal tract analysed and which section(s) provided the best diet representation. Additionally, we intended to infer the ecological/economic impacts of an invader as a model of the potential effects in an originally mammal‐free ecosystem. We examined the gut contents of the house mouse Mus musculus introduced to Cabo Verde, considering three sections: stomach, small intestine, and large intestine. We applied a DNA‐metabarcoding approach using two genetic markers, one specific for plants and another for invertebrates. We showed that this invader consumed 131 taxa (73 plants and 58 invertebrates). We obtained significant differences in the composition of two of the three sections, with a higher incidence of invertebrates in the stomach and plants in the intestines. This may be due to stomach inhibitors acting on plants and/or to faster absorption of soft‐body invertebrates compared to the plant fibers in the intestines. We verified that the impact of this invader in the ecosystem is predominantly negative, as at least 50% of the ingested items were native, endemic, or economically important taxa, and only 19% of the diet items were exotics. Overall, results showed the need to analyse only two gastrointestinal tract sections to obtain robust diet data, increasing the cost‐effectiveness of the method. Furthermore, by uncovering the native taxa most frequently preyed on by mice, this DNA‐metabarcoding approach allowed us to evaluate efficiently which are at the highest risk.

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Targeted next‐generation sequencing of environmental DNA improves detection of invasive European green crab (Carcinus maenas)

2021

Self Cite

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In the northeast Pacific Ocean, there is high interest in developing eDNA‐based survey methods to aid management of invasive populations of European green crab (Carcinus maenas). Expected benefits are improved sensitivity for early detection of secondary spread and to assess the outcome of eradication efforts. A new eDNA‐based approach we term “targeted next‐generation sequencing (tNGS)” is introduced here and shown to improve detection relative to qPCR at sites with lower green crab CPUE values measured by trapping. DNA standards (gBlock) with starting molecule copies that were 10 to 100 times lower than the qPCR limit of detection returned significant numbers of sequencing reads, which in our field assessments translated to a 7%–10% increase in detection probability from tNGS relative to qPCR at sites with lower CPUE. We also found the number of sequencing reads from tNGS was significantly correlated with green crab CPUE whereas Ct values from qPCR were not. When sources of variation were partitioned for each assay, we found the difference between mean within‐site and mean between‐site variation was much larger and had non‐overlapping confidence intervals for tNGS relative to qPCR, suggesting the former may offer more power for detecting spatial variation in eDNA availability. Results presented here indicate this approach is suitable for species of known low abundances where a positive detection has high economic or environmental consequences, or for labs doing eDNA surveys for whom NGS‐based workflows are operationally more efficient than qPCR given its upward scalability. Any species with an existing qPCR assay can be easily tested with a tNGS assay using the approach presented here. We conclude with a discussion on the fitness for purpose of tNGS vs. qPCR for various applications and on how to best apply molecular surveys in management programs.

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A new approach to molecular biosurveillance of invasive species using DNA metabarcoding

Cited by 45 publications

References 51 publications

Status and prospects of marine NIS detection and monitoring through (e)DNA metabarcoding

Status and prospects of marine NIS detection and monitoring through (e)DNA metabarcoding

Trust your guts? The effect of gut section on diet composition and impact of Mus musculus on islands using metabarcoding

Targeted next‐generation sequencing of environmental DNA improves detection of invasive European green crab (Carcinus maenas)

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