Tracing European eel in the diet of mesopelagic fishes from the Sargasso Sea using DNA from fish stomachs

Jensen, Mads Radmer; Knudsen, Steen Wilhelm; Munk, Peter; Thomsen, Philip Francis

doi:10.1007/s00227-018-3390-3

Cited by 21 publications

(17 citation statements)

References 67 publications

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“…We performed TaqMan qPCRs for S. glanis and A. anguilla using previously published protocols (Jensen, Knudsen, Munk, Thomsen, & Møller, ; Roy, Belliveau, Mandrak, & Gagné, ). Sampling sites which either represent suitable habitat for target species or for which recent sightings were reported were identified (Figure ).…”

Section: Re‐evaluation Of a Metabarcoding Study In The Volga Headwatersmentioning

confidence: 99%

Reference databases, primer choice, and assay sensitivity for environmental metabarcoding: Lessons learnt from a re‐evaluation of an eDNA fish assessment in the Volga headwaters

Schenekar

Schletterer

Lecaudey

et al. 2020

River Research & Apps

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Biodiversity monitoring via environmental DNA, particularly metabarcoding, is evolving into a powerful assessment tool for riverine systems. However, for metabarcoding to be fully integrated into standardized monitoring programmes, some current challenges concerning sampling design, laboratory workflow, and data analysis need to be overcome. Here, we review some of these major challenges and potential solutions. We further illustrate three potential pitfalls, namely the choice of suitable metabarcoding primers, the necessity of complete reference databases, and varying assay sensitivities, by a reappraisal of our‐own recently carried out metabarcoding study in the Volga headwaters. TaqMan qPCRs had detected catfish (Silurus glanis) and European eel (Anguilla anguilla), whereas metabarcoding had not, in the same samples. Furthermore, after extending the genetic reference database by 12 additional species and re‐analysing the metabarcoding data, we additionally detected the Siberian spiny loach (Cobitis sibirica) and Ukrainian brook lamprey (Eudontomyzon mariae) and reassigned the operational taxonomic units previously assigned to Misgurnus fossilis to Cobitis sibirica. In silico analysis of metabarcoding primer efficiencies revealed considerable variability among primer pairs and among target species, which could lead to strong primer bias and potential false‐negatives in metabarcoding studies if not properly compensated for. These results highlight some of the pitfalls of eDNA‐metabarcoding as a means of monitoring fish biodiversity in large rivers, which need to be considered in order to fully unleash the full potential of these approaches for freshwater biodiversity monitoring.

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Section: Re‐evaluation Of a Metabarcoding Study In The Volga Headwatersmentioning

confidence: 99%

Reference databases, primer choice, and assay sensitivity for environmental metabarcoding: Lessons learnt from a re‐evaluation of an eDNA fish assessment in the Volga headwaters

Schenekar

Schletterer

Lecaudey

et al. 2020

River Research & Apps

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“…There are two types of molecular prey detection data: (a) presence/absence data and (b) quantitative data. Independent of the way the data were obtained ( via diagnostic PCR, real‐time qPCR or metabarcoding), presence/absence data always require a detection threshold to be set, i.e ., a measurable parameter such as a fluorescence threshold (Jensen et al ., 2018; Thalinger et al ., 2016), or an absolute or relative number of target reads (Deagle et al ., 2019; Thomas et al ., 2017). Presence/absence data are generally used to calculate frequency of occurrence ( i.e ., the number of samples containing a specific prey taxon; FOO), which is often displayed in percent (F% or %FOO) or rescaled to per cent of occurrence (POO), providing a summed up occurrence rate of 100% across all prey taxa (Baker et al ., 2014; Deagle et al ., 2019).…”

Section: Interpretation Of Molecular Trophic Datamentioning

confidence: 99%

“…Quantitative or semiquantitative data provide absolute or relative measures of target DNA. They can be received from both quantitative types of diagnostic PCR (Table 2) in the form of (absolute) target DNA copies per microlitre (Bowles et al ., 2011; Deagle and Tollit, 2007; Jensen et al ., 2018) or (relative) quantification of CE‐PCR signal strength between taxa (Thalinger et al . 2016), and metabarcoding in the form of relative read abundance (RRA) accounting for varying sequencing depths between samples (Ford et al ., 2016; McInnes et al ., 2017b; Thomas et al ., 2017).…”

Section: Interpretation Of Molecular Trophic Datamentioning

confidence: 99%

Fish as predators and prey: DNA‐based assessment of their role in food webs

Traugott

Thalinger

Wallinger

et al. 2020

Journal of Fish Biology

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Fish are both consumers and prey, and as such part of a dynamic trophic network. Measuring how they are trophically linked, both directly and indirectly, to other species is vital to comprehend the mechanisms driving alterations in fish communities in space and time. Moreover, this knowledge also helps to understand how fish communities respond to environmental change and delivers important information for implementing management of fish stocks. DNA‐based methods have significantly widened our ability to assess trophic interactions in both marine and freshwater systems and they possess a range of advantages over other approaches in diet analysis. In this review we provide an overview of different DNA‐based methods that have been used to assess trophic interactions of fish as consumers and prey. We consider the practicalities and limitations, and emphasize critical aspects when analysing molecular derived trophic data. We exemplify how molecular techniques have been employed to unravel food web interactions involving fish as consumers and prey. In addition to the exciting opportunities DNA‐based approaches offer, we identify current challenges and future prospects for assessing fish food webs where DNA‐based approaches will play an important role.

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“…The remarkable migrations and fossorial life styles make it difficult to observe them in aquatic environments and monitor their presence or absence. A species-specific method to detect DNA from fish stomachs and eDNA has been already used for A. anguilla 25,26 and A. japonica 27 to begin to overcome these difficulties.…”

Section: Introductionmentioning

confidence: 99%

New PCR primers for metabarcoding environmental DNA from freshwater eels, genus Anguilla

Takeuchi¹,

Sadõ²,

Gotoh³

et al. 2019

Sci Rep

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Freshwater eels of the genus Anguilla comprise 16 species that include three subspecies and are characterized by their unique catadromous life cycles. Their life histories and nocturnal life styles make it difficult to observe them in freshwater and marine habitats. To investigate their distribution and ecology in aquatic environments, we developed new PCR primers for metabarcoding environmental DNA (eDNA) from Anguilla . The new primers (MiEel) were designed for two conserved regions of the mitochondrial ATP6 gene, which amplify a variable region with sufficient interspecific variations ranging from five to 22 nucleotide differences (one to three nucleotide differences between three subspecies pairs). We confirmed the versatility of the MiEel primers for all freshwater eels using tissue DNA extracts when analyzed separately. The metabarcoding combined with the MiEel primers using mock communities enabled simultaneous detection of Anguilla at the species level. Analysis of eDNA samples from aquarium tanks, a controlled pond and natural rivers demonstrated that the MiEel metabarcoding could successfully detect the correct Anguilla species from water samples. These results suggested that eDNA metabarcoding with MiEel primers would be useful for non-invasively monitoring the presence of the endangered anguillid eels in aquatic environments where sampling surveys are difficult.

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Tracing European eel in the diet of mesopelagic fishes from the Sargasso Sea using DNA from fish stomachs

Cited by 21 publications

References 67 publications

Reference databases, primer choice, and assay sensitivity for environmental metabarcoding: Lessons learnt from a re‐evaluation of an eDNA fish assessment in the Volga headwaters

Reference databases, primer choice, and assay sensitivity for environmental metabarcoding: Lessons learnt from a re‐evaluation of an eDNA fish assessment in the Volga headwaters

Fish as predators and prey: DNA‐based assessment of their role in food webs

New PCR primers for metabarcoding environmental DNA from freshwater eels, genus Anguilla

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