Early detection of a highly invasive bivalve based on environmental DNA (eDNA)

Xia, Ziqiang; Zhan, Aibin; Gao, Yangchun; Zhang, Lei; Haffner, G. Douglas; MacIsaac, Hugh J.

doi:10.1007/s10530-017-1545-7

Cited by 67 publications

(70 citation statements)

References 45 publications

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“…A total of 10 replicates for each concentration was applied, and the LoD was defined as the lowest concentration returning at least one positive replicate (Agersnap et al, ). We Sanger‐sequenced four random positive amplicons of the field samples to confirm specificity of our primers, which was identified as species‐specific in a previous study (Xia et al, ).…”

Section: Methodsmentioning

confidence: 89%

“…We observed a higher detection rate of qPCR than cPCR, suggesting that the former should be embraced in rare species management since it was more sensitive and less prone to false negatives. A number of avenues exist to reduce false negatives including judicious deployment of replicates in field sampling and in the laboratory (Pedersen et al, ; Piaggio et al, ) and the use of highly sensitive PCR methods (Doi et al, ; Xia et al, ). We found that the false negative rate was inversely related to the number of replicates used per time‐point/site (Figure ).…”

Section: Discussionmentioning

confidence: 99%

“…Many studies have focused on the former to improve detection rate (e.g. Renshaw, Olds, Jerde, Mcveigh, & Lodge, 2014;Takahara, Minamoto, & Doi, 2014;Deiner et al, 2015;Spens et al, 2016;Hinlo, Gleeson, Lintermans, & Furlan, 2017;Xia et al, 2018), while attention has rarely been paid to the latter. Given that eDNA is often found in trace amounts (Furlan, Gleeson, Hardy, & Duncan, 2016), robust PCR methods are essential to eDNA-based studies.…”

Section: Introductionmentioning

confidence: 99%

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Conventional versus real‐time quantitative PCR for rare species detection

Xia

Johansson

Gao

et al. 2018

Ecology and Evolution

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Detection of species in nature at very low abundance requires innovative methods. Conventional PCR (cPCR) and real‐time quantitative PCR (qPCR) are two widely used approaches employed in environmental DNA (eDNA) detection, though lack of a comprehensive comparison of them impedes method selection. Here we test detection capacity and false negative rate of both approaches using samples with different expected complexities. We compared cPCR and qPCR to detect invasive, biofouling golden mussels (Limnoperna fortunei), in samples from laboratory aquaria and irrigation channels where this mussel was known to occur in central China. Where applicable, the limit of detection (LoD), limit of quantification (LoQ), detection rate, and false negative rate of each PCR method were tested. Quantitative PCR achieved a lower LoD than cPCR (1 × 10−7 vs. 10−6 ng/μl) and had a higher detection rate for both laboratory (100% vs. 87.9%) and field (68.6% vs. 47.1%) samples. Field water samples could only be quantified at a higher concentration than laboratory aquaria and total genomic DNA, indicating inhibition with environmental samples. The false negative rate was inversely related to the number of sample replicates. Target eDNA concentration was negatively related to distance from sampling sites to the water (and animal) source. Detection capacity difference between cPCR and qPCR for genomic DNA and laboratory aquaria can be translated to field water samples, and the latter should be prioritized in rare species detection. Field environmental samples may involve more complexities—such as inhibitors—than laboratory aquaria samples, requiring more target DNA. Extensive sampling is critical in field applications using either approach to reduce false negatives.

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Section: Methodsmentioning

confidence: 89%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Conventional versus real‐time quantitative PCR for rare species detection

Xia

Johansson

Gao

et al. 2018

Ecology and Evolution

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“…Since then, many invasive fish have been targeted, and eDNA has been used for determining the efficiency of fish eradication efforts [38][39][40][41][42][43]. Amphibian species have also been targeted [30,44,45], as have crustaceans [41,[46][47][48][49], reptiles [50,51], and molluscs [19,52,53]. The rapid adoption of eDNA for invasive aquatic species paved the way for developing eDNA-based tools for other systems and continues to motivate advancing this method for further genetic monitoring.…”

Section: Introductionmentioning

confidence: 99%

A Brief Review of Non-Avian Reptile Environmental DNA (eDNA), with a Case Study of Painted Turtle (<em>Chrysemys picta</em>) eDNA under Field Conditions

Adams¹,

Hoekstra²,

Muell³

et al. 2019

Preprint

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Environmental DNA (eDNA) is an increasingly used non-invasive molecular tool for detecting species presence and monitoring populations. In this article, we review the current state of non-avian reptile eDNA work in aquatic systems, as well as present a field experiment on detecting the presence of painted turtle (Chrysemys picta) eDNA. Thus far, turtle and snake eDNA studies have been successful mostly in detecting the presence of these animals in field conditions. However, some instances of low detection rates and non-detection occur for these non-avian reptiles, especially for squamates. We explored this matter by sampling lentic ponds with different densities (0 kg/ha, 6 kg/ha, 9 kg/ha, and 13 kg/ha) of painted turtles over three months, attempting to detect differences in eDNA accumulation using a qPCR assay. Only one sample of the highest density pond readily amplified eDNA. Yet, estimates of eDNA concentration from pond eDNA were rank-order correlated with turtle density. We present a “shedding hypothesis”–the possibility that animals with hard, keratinized integument do not shed as much DNA as mucus-covered organisms–as a potential challenge for turtle eDNA studies. Despite challenges with eDNA inhibition and availability in water samples, we remain hopeful that eDNA can be used to detect freshwater turtles in the field. We provide key recommendations for biologists wishing to use eDNA methods for detecting non-avian reptiles.

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“…In addition, it can be difficult to directly observe these facilities because water cannot be withdrawn easily from irrigation ponds and reservoirs while the irrigation facilities are in use. Molecular biological techniques that have been advanced in recent years (such as those using environmental DNA), are thought to be effective for detecting the presence or absence of invasive aquatic organisms, although these methods are not yet able to provide quantitative data (Pie et al 2017;Xia et al, 2017). In addition, the density of larvae that can be used as an indicator of the abundance of the mussel fluctuates drastically during the reproductive season (e.g.…”

Section: Introductionmentioning

confidence: 99%

The effect of tube trap structure on sampling efficacy and accuracy for golden mussel, <i>Limnoperna fortunei</i>

Ito

Inoue

2018

Plankton Benthos Res

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The study was conducted to identify the effect of different types of tube traps on the sampling efficacy and accuracy for invasive golden mussels, Limnoperna fortunei (Dunker, 1857), at four sites in Japan. The traps consisted of PVC tubes (diameter: 5.5 cm; length: 20 cm) inside which a PVC plate was fixed horizontally as settlement substrate, and we examined two trap characteristics: mesh covering at the tube ends (present or not) and substrate texture (even or uneven). Mesh covering had a negative effect (P<0.001) and uneven substrate had a marginally positive effect (P=0.08) on mussel settlement density. A positive relationship was found between larval and settlement density in traps without mesh. These results imply that the most effective type of tube trap had no mesh covering and used uneven substrate. The settlement density of the mussels was also examined on several surfaces of the tube trap and the rope used to suspend the trap. The mussel density on the rope was higher than that on the PVC plates and tubes. The best correlation between settlement density and larval density occurred on the outside of the PVC tubes.

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Early detection of a highly invasive bivalve based on environmental DNA (eDNA)

Cited by 67 publications

References 45 publications

Conventional versus real‐time quantitative PCR for rare species detection

Conventional versus real‐time quantitative PCR for rare species detection

A Brief Review of Non-Avian Reptile Environmental DNA (eDNA), with a Case Study of Painted Turtle (<em>Chrysemys picta</em>) eDNA under Field Conditions

The effect of tube trap structure on sampling efficacy and accuracy for golden mussel, <i>Limnoperna fortunei</i>

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