Linking Environmental DNA and RNA for Improved Detection of the Marine Invasive Fanworm Sabella spallanzanii

Ammon, Ulla von; Wood, Susanna A.; Laroche, Olivier; Zaiko, Anastasija; Lavery, Shane; Inglis, Graeme J.; Pochon, Xavier

doi:10.3389/fmars.2019.00621

Cited by 61 publications

(53 citation statements)

References 84 publications

(113 reference statements)

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“…The marine realm is one of the richest and most diverse ecosystems on our planet, containing representatives from almost all the eukaryotic forms of life 10 . DNA metabarcoding in marine ecosystems has been used to assess environmental impacts 11 , undertake diet analysis 12 , understand trophic interactions 13 and to track invasive species 14 . Common to all of these applications of marine metabarcoding, has been the creation and/or use of a reference database to assist in the taxonomic assignment of sequences 15 .…”

Section: Background and Summarymentioning

confidence: 99%

MARES, a replicable pipeline and curated reference database for marine eukaryote metabarcoding

et al. 2020

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the use of DNa metabarcoding to characterise the biodiversity of environmental and community samples has exploded in recent years. However, taxonomic inferences from these studies are contingent on the quality and completeness of the sequence reference database used to characterise sample species-composition. In response, studies often develop custom reference databases to improve species assignment. the disadvantage of this approach is that it limits the potential for database re-use, and the transferability of inferences across studies. Here, we present the MaRine Eukaryote Species (MaRES) reference database for use in marine metabarcoding studies, created using a transparent and reproducible pipeline. MaRES includes all COI sequences available in GenBank and BOLD for marine taxa, unified into a single taxonomy. Our pipeline facilitates the curation of sequences, synonymization of taxonomic identifiers used by different repositories, and formatting these data for use in taxonomic assignment tools. Overall, MaRES provides a benchmark COI reference database for marine eukaryotes, and a standardised pipeline for (re)producing reference databases enabling integration and fair comparison of marine DNa metabarcoding results.

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Section: Background and Summarymentioning

confidence: 99%

MARES, a replicable pipeline and curated reference database for marine eukaryote metabarcoding

et al. 2020

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“…For instance, DNA metabarcoding employing 18S and COI, failed to detect several bryozoan taxa in a New Zealand's marina, despite several entries can been found for those species and markers on GenBank (von Ammon et al 2018b). In addition, in a study in a New Zealand harbour, DNA metabarcodingbased detection rates were low for the polychaete Sabella spallanzanii, although this species was highly abundant in the harbour and well represented by reference sequences in genetic databases (von Ammon et al 2019. These studies suggest that amplification may have failed due to mismatching primer binding sites or low primer affinity.…”

Section: Marker Loci and Primer Pairsmentioning

confidence: 99%

“…By combining this approach with a comprehensive sampling of different substrates, they were able to detect 12 NIS in Departure Bay, Pacific Canada, and 7 potential new records, across a wide taxonomic range. However, high intraspecific variation due to multiple sympatric lineages of NIS may lead to failed amplification with species-specific primers, but there is little to no empirical work to support this (von Ammon et al 2019). Thus, in the future, the use of metabarcoding in biosurveillance may be greatly improved by optimizing the tool for a particular biogeographic region and using a multi-marker approach, which may accelerate its implementation in regular monitoring of NIS worldwide (Westfall et al 2020).…”

Section: Marker Loci and Primer Pairsmentioning

confidence: 99%

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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“…Second, because functional shifts are likely to occur prior to compositional ones, as a response of the taxa present to the disturbance, the variation of functional profiles may constitute useful early warnings for a timelier ecosystem management, especially the ones detected by mean of metatranscriptomics. However, RNA molecules are reportedly less stable than DNA, which would add challenging practical constraints that could preclude their implementation in routine ecosystem monitoring programs (but see Fordyce et al, 2013;Pochon et al, 2017;Cristescu, 2019;von Ammon et al 2019). As a possible cost-effective "shortcut", bacterial 16S rRNA profiles can be used to predict functional community profiles, based on evolutionary models (Langille et al, 2013;Aßhauer et al, 2015).…”

Section: The Environmental Genomics Revolution For Biodiversity Reseamentioning

confidence: 99%

Ecosystems Monitoring Powered by Environmental Genomics: A Review of Current Strategies with An Implementation Roadmap

Cordier¹,

Sáez²,

Apothéloz-Perret-Gentil³

et al. 2020

Preprint

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A decade after environmental scientists integrated high-throughput sequencing technologies in their toolbox, the genomics-based monitoring of anthropogenic impacts on biodiversity and ecosystems is yet to be implemented by regulatory frameworks. Despite the broadly acknowledged potential of environmental DNA and RNA to cost-efficiently and accurately monitor biodiversity, technical limitations and conceptual issues still stand in the way of its routine application by end-users. In addition, the multiplicity of potential implementation strategies may contribute to a perception of the methodology as being premature or “in development”, hence restraining regulators from binding these tools into legal frameworks. This review focuses on the strengths and limitations of genomics-based strategies that have emerged over the past ten years and have been classified for this purpose into three broad strategies: (A) Taxonomy-based approaches that focus on known bio-indicators or the diversity of taxonomically described taxa, (B) De novo approaches that do not require well-established taxonomy, and (C) Function-based approaches that rely on community-wide metrics, where taxa are interchangeable, or on functional profiles instead of compositional turnovers. We finally propose a roadmap for the implementation of environmental genomics into routine monitoring programs that leverage recent analytical advancements, upon which some critical limitations are alleviated.

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Linking Environmental DNA and RNA for Improved Detection of the Marine Invasive Fanworm Sabella spallanzanii

Cited by 61 publications

References 84 publications

MARES, a replicable pipeline and curated reference database for marine eukaryote metabarcoding

MARES, a replicable pipeline and curated reference database for marine eukaryote metabarcoding

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

Ecosystems Monitoring Powered by Environmental Genomics: A Review of Current Strategies with An Implementation Roadmap

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