Metabarcoding analysis of the stomach contents of the Antarctic Toothfish (<i>Dissostichus mawsoni</i>) collected in the Antarctic Ocean

Yoon, Tae-Ho; Kang, Hye-Eun; Lee, Soo Rin; Lee, Jae-Bong; Baeck, Gun Wook; Park, Hyun; Kim, Hyun Woo

doi:10.7717/peerj.3977

Cited by 37 publications

(27 citation statements)

References 42 publications

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“…The value of the BOLD database is likely to increase even further with the development of metabarcoding studies. Recent approaches include for example the detection of tropical sharks (Bakker et al, 2017), large-scale larval fish ecology through efficient identification of thousands of larvae (Kimmerling et al, 2018), as well as Antarctic studies characterizing notothenioid fish assemblages (Cowart et al, 2017) and toothfish diet (Yoon et al, 2017). All these examples are fully dependent on a high quality reference database to match metabarcoding sequences, as the lack of identification can lead to reduced or biased results and interpretations.…”

Section: Extending and Using The Dna Barcode Library For Specimen Idementioning

confidence: 99%

Diversity of Mesopelagic Fishes in the Southern Ocean - A Phylogeographic Perspective Using DNA Barcoding

et al. 2018

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Section: Extending and Using The Dna Barcode Library For Specimen Idementioning

confidence: 99%

Diversity of Mesopelagic Fishes in the Southern Ocean - A Phylogeographic Perspective Using DNA Barcoding

et al. 2018

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“…(2019) compared the results of specific qPCR assays with bottom trawling in the Baltic Sea to detect G. morhua , Clupea harengus (Atlantic herring), Platichthys flesus (European flounder), Pleuronectes platessa (European plaice), Scomber scombrus (Atlantic mackerel), and Anguilla anguilla (European eel). Despite these recent and very promising advances, uncertainties and limitations associated with eDNA metabarcoding surveys that could lead to misinterpretation of the results must be investigated further, notably in different environments (Cristescu & Hebert, 2018; Darling & Mahon, 2011; Goldberg et al., 2016; Li et al., 2019; Seymour et al., 2018; Shaw et al., 2016; Taberlet, Coissac, Pompanon, Brochmann, & Willerslev, 2012; Yoon et al., 2017). In particular, a better understanding of the influence of environmental variables on eDNA production and persistence in the environment might facilitate comprehensive application of the method for conservation and management (Laporte et al, 2020;Stewart, 2019).…”

Section: Introductionmentioning

confidence: 99%

Comparing environmental metabarcoding and trawling survey of demersal fish communities in the Gulf of St. Lawrence, Canada

et al. 2020

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Biodiversity assessment is an important part of conservation management that ideally can be accomplished with noninvasive methods without influencing the structure and functioning of ecosystems. Environmental DNA (eDNA) metabarcoding has provided a promising tool to enable fast and comprehensive monitoring of entire ecosystems, but widespread adoption of this technique requires performance evaluations that compare it with conventional surveys. We compared eDNA metabarcoding and trawling data to evaluate their efficiency to characterize demersal fish communities in the Estuary and Gulf of Saint‐Lawrence, Canada. Seawater and bottom trawling samples were collected in parallel at 84 stations. For a subset of 30 of these stations, water was also collected at three different depths (15, 50, and 250 m) across the water column. An eDNA metabarcoding assay based on the 12S mitochondrial gene using the MiFish‐U primers was applied to detect fish eDNA. We detected a total of 88 fish species with both methods combined, with 72 species being detected by eDNA, 64 species detected by trawl, and 47 species (53%) overlapped between both methods. eDNA was more efficient for quantifying species richness, mainly because it detected species known to be less vulnerable to trawling gear. Our results indicated that the relative abundance estimated by eDNA and trawl is significantly correlated for species detected by both methods, while the relationship was also influenced by environmental variables (temperature, depth, salinity, and oxygen). Integrating eDNA metabarcoding to bottom trawling surveys could provide additional information on vertical fish distribution in the water column. Environmental DNA metabarcoding thus appears to be a reliable and complementary approach to trawling surveys for documenting fish biodiversity, including for obtaining relative quantitative estimates in the marine environment.

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“…Leray & Knowlton, 2015;Pearman, Anlauf, Irigoien, & Carvalho, 2016) and dietary samples (see e.g. Albaina, Aguirre, Abad, Santos, & Estonba, 2016;Yoon et al, 2017). Since then, DNA metabarcoding has been increasingly used worldwide in marine samples, as is demonstrated by projects such as the Genetic tools for Ecosystem health Assessment in the North Sea region (GEANS) and the Global ARMS Program with Autonomous Reef Monitoring Structures.…”

Section: Introductionmentioning

confidence: 99%

Biases in bulk: DNA metabarcoding of marine communities and the methodology involved

Loos

Nijland

2020

Preprint

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With the growing anthropogenic pressure on marine ecosystems, the need for efficient monitoring of biodiversity grows stronger. DNA metabarcoding of bulk samples is increasingly implemented in ecosystem assessments and is more cost-efficient and less time-consuming than monitoring based on morphology. However, before raw sequences are obtained from bulk samples, a profound number of methodological choices must be made. Here, we critically review the recent methods used for metabarcoding of marine bulk samples (including benthic, plankton and diet samples) and indicate how potential biases can be introduced throughout sampling, pre-processing, DNA extraction, marker and primer selection, PCR amplification and sequencing. From a total of 64 studies evaluated, our recommendations for best practices include to (a) consider DESS as a fixative instead of ethanol, (b) use the DNeasy PowerSoil kit for any samples containing traces of sediment, (c) not limit the marker selection to COI only, but preferably include multiple markers for higher taxonomic resolution, (d) avoid touchdown PCR profiles, (e) use a fixed annealing temperature for each primer pair when comparing across studies or institutes, (f) use a minimum of 3 PCR replicates and (g) include both negative and positive controls. Although the implementation of DNA metabarcoding still faces several technical complexities, we foresee wide-ranging advances in the near future, including improved bioinformatics for taxonomic assignment, sequencing of longer fragments, and the use of whole-genome information. Despite the bulk of biases involved in metabarcoding of bulk samples, it is clear that DNA metabarcoding provides a valuable tool in ecosystem assessments. Biases in bulk: DNA metabarcoding of marine communities and the methodology involved

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Metabarcoding analysis of the stomach contents of the Antarctic Toothfish (Dissostichus mawsoni) collected in the Antarctic Ocean

Cited by 37 publications

References 42 publications

Diversity of Mesopelagic Fishes in the Southern Ocean - A Phylogeographic Perspective Using DNA Barcoding

Diversity of Mesopelagic Fishes in the Southern Ocean - A Phylogeographic Perspective Using DNA Barcoding

Comparing environmental metabarcoding and trawling survey of demersal fish communities in the Gulf of St. Lawrence, Canada

Biases in bulk: DNA metabarcoding of marine communities and the methodology involved

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