Metabarcoding and post-sampling strategies to discover non-indigenous species: A case study in the estuaries of the central south Bay of Biscay

Borrell, Yaisel J.; Miralles, Laura; Mártinez-Marqués, Adrián; Semeraro, Alexia; Arias, Andrés; Carleos, Carlos; García‐Vázquez, Eva

doi:10.1016/j.jnc.2017.07.002

Cited by 17 publications

(20 citation statements)

References 55 publications

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“…A similar result was also reported by Borrell, et al . 64 who investigated the applicability of these two markers to detect NIS in estuaries. The most likely explanation for this result is that the rate of evolution in the COI gene is much faster than in the 18S rRNA and therefore there is greater sequence variability between species 65 .…”

Section: Discussionmentioning

confidence: 99%

Combining morpho-taxonomy and metabarcoding enhances the detection of non-indigenous marine pests in biofouling communities

Ammon

Wood

Laroche

et al. 2018

Sci Rep

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Marine infrastructure can favor the spread of non-indigenous marine biofouling species by providing a suitable habitat for them to proliferate. Cryptic organisms or those in early life stages can be difficult to distinguish by conventional morphological taxonomy. Molecular tools, such as metabarcoding, may improve their detection. In this study, the ability of morpho-taxonomy and metabarcoding (18S rRNA and COI) using three reference databases (PR2, BOLD and NCBI) to characterize biodiversity and detect non-indigenous species (NIS) in biofouling was compared on 60 passive samplers deployed over summer and winter in a New Zealand marina. Highest resolution of metazoan taxa was identified using 18S rRNA assigned to PR2. There were higher assignment rates to NCBI reference sequences, but poorer taxonomic identification. Using all methods, 48 potential NIS were identified. Metabarcoding detected the largest proportion of those NIS: 77% via 18S rRNA/PR2 and NCBI and 35% via COI/BOLD and NCBI. Morpho-taxonomy detected an additional 14% of all identified NIS comprising mainly of bryozoan taxa. The data highlight several on-going challenges, including: differential marker resolution, primer biases, incomplete sequence reference databases, and variations in bioinformatic pipelines. Combining morpho-taxonomy and molecular analysis methods will likely enhance the detection of NIS from complex biofouling.

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Section: Discussionmentioning

confidence: 99%

Combining morpho-taxonomy and metabarcoding enhances the detection of non-indigenous marine pests in biofouling communities

Ammon

Wood

Laroche

et al. 2018

Sci Rep

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“…This means that false negatives (i.e., failure to detect a species when it is present) are a much greater concern for traditional methods, and significant investment of time and effort will be required to confidently detect species at low densities. eDNA surveys can complement traditional surveys by guiding subsequent unambiguous surveys in a targeted, site‐specific, species‐specific and cost‐efficient manner (e.g., Borrell et al., 2017).…”

Section: Discussionmentioning

confidence: 99%

Identifying error and accurately interpreting environmental DNA metabarcoding results: A case study to detect vertebrates at arid zone waterholes

Furlan

Davis

Duncan

2020

Molecular Ecology Resources

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Environmental DNA (eDNA) metabarcoding surveys enable rapid, noninvasive identification of taxa from trace samples with wide‐ranging applications from characterizing local biodiversity to identifying food‐web interactions. However, the technique is prone to error from two major sources: (a) contamination through foreign DNA entering the workflow, and (b) misidentification of DNA within the workflow. Both types of error have the potential to obscure true taxon presence or to increase taxonomic richness by incorrectly identifying taxa as present at sample sites, but multiple error sources can remain unaccounted for in metabarcoding studies. Here, we use data from an eDNA metabarcoding study designed to detect vertebrate species at waterholes in Australia's arid zone to illustrate where and how in the workflow errors can arise, and how to mitigate those errors. We detected the DNA of 36 taxa spanning 34 families, 19 orders and five vertebrate classes in water samples from waterholes, demonstrating the potential for eDNA metabarcoding surveys to provide rapid, noninvasive detection in remote locations, and to widely sample taxonomic diversity from aquatic through to terrestrial taxa. However, we initially identified 152 taxa in the samples, meaning there were many false positive detections. We identified the sources of these errors, allowing us to design a stepwise process to detect and remove error, and provide a template to minimize similar errors that are likely to arise in other metabarcoding studies. Our findings suggest eDNA metabarcoding surveys need to be carefully conducted and screened for errors to ensure their accuracy.

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“…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%

“…We found that most of the studies have sampled multiple ports or marinas (e.g. Brown et al 2016, Leduct et al 2019, or estuaries (Borrell et al 2018), and multiple sites within each port/marina/estuary (Abad et al 2016, Leduc et al 2019, Rey et al 2020. 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.…”

Section: Sampling Designmentioning

confidence: 99%

“…Possibly the metabarcoding primers differed from the primers used to generate the full-length reference sequences. Thus, the characterization of diverse eukaryotic NIS communities will greatly benefit with the application of multiple marker approaches (Borrell et al 2018, Stefanni et al 2018, von Ammon et al 2018b, Westfall et al 2020, multiple primer pairs targeting the same genetic regions (Pagenkopp Lohan et al 2016 or by designing NISspecific primers (Ardura et al 2017, Westfall et al 2020.…”

Section: Marker Loci and Primer Pairsmentioning

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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Metabarcoding and post-sampling strategies to discover non-indigenous species: A case study in the estuaries of the central south Bay of Biscay

Abstract: Metabarcoding and post-sampling strategies to discover non-indigenous species: a case study in the estuaries of the central south Bay of Biscay.

Cited by 17 publications

References 55 publications

Combining morpho-taxonomy and metabarcoding enhances the detection of non-indigenous marine pests in biofouling communities

Combining morpho-taxonomy and metabarcoding enhances the detection of non-indigenous marine pests in biofouling communities

Identifying error and accurately interpreting environmental DNA metabarcoding results: A case study to detect vertebrates at arid zone waterholes

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

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