Environmental <scp>DNA</scp> metabarcoding of lake fish communities reflects long‐term data from established survey methods

Hänfling, Bernd; Handley, Lori Lawson; Read, Daniel S.; Hahn, Christoph; Li, Jianlong; Nichols, Paul; Blackman, Rosetta C.; Oliver, Anna; Winfield, Ian J.

doi:10.1111/mec.13660

Cited by 437 publications

(682 citation statements)

References 48 publications

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“…To circumvent this problem, we suggest here a method based on abundance ranks. The semiquantitative or rank-level value of metabarcoding data has been shown in several contexts (e.g., Kelly et al, 2014b;Sun et al, 2015;Abad et al, 2016;Albaina et al, 2016, Hänfling et al, 2016. Our method is expected to filter out potential biases, at the cost of partially sacrificing the quantitative information present.…”

Section: Discussionmentioning

confidence: 96%

Under the canopy: Community-wide effects of invasive algae in Marine Protected Areas revealed by metabarcoding

Wangensteen

Cebrián

Palacín

et al. 2018

Marine Pollution Bulletin

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Running title: community-wide effects of invasive algae in MPAs Highlights  Hard-bottom communities dominated by invasive algae were studied with metabarcoding  A size-fractionation method is developed for the metabarcoding of complex samples  A modified primer set is used for the amplification of a COI fragment  A semiquantitave abundance index is proposed for statistical analyses  Results show effects of canopy-forming invasive algae on the underlying communities AbstractWe analysed with multigene (18S and COI) metabarcoding the effects of the proliferation of invasive seaweeds on rocky littoral communities in two Spanish Marine Protected Areas. The invasive algae studied were Caulerpa cylindracea, Lophocladia lallemandii and Asparagopsis armata. They are canopy-forming, landscape-dominant seaweeds, and we were interested in their effects on the underlying communities of meiobenthos and macrobenthos, separated in two size fractions through sieving. A new semiquantitative treatment of metabarcoding data is introduced. The results for both markers showed that the presence of the invasive seaweed had a significant effect on the understory communities for Lophocladia lallemandii and Asparagopsis armata but not for Caulerpa cylindracea. Likewise, changes in MOTU richness and diversity with invasion status varied in magnitude and direction depending on the alga considered. Our results showed that metabarcoding allows monitoring of the less conspicuous, but not least important, effects of the presence of dominant invasive seaweeds.

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Section: Discussionmentioning

confidence: 96%

Under the canopy: Community-wide effects of invasive algae in Marine Protected Areas revealed by metabarcoding

Wangensteen

Cebrián

Palacín

et al. 2018

Marine Pollution Bulletin

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“…Similarly, Valentini et al (2016) detected at least as many fish as traditional sampling methods in 89% of 23 aquatic sampling sites that included ponds, rivers, mountain lakes, streams, and ditches. Likewise, using eDNA metabarcoding, Hänfling et al (2016) detected 14 of 16 historically known fish species in a 1480 ha natural lake. Lastly, using eDNA metabarcoding, Shaw et al (2016) detected all fish species captured with fyke nets in each of two Australian river systems.…”

Section: Introductionmentioning

confidence: 99%

Fish community assessment with eDNA metabarcoding: effects of sampling design and bioinformatic filtering

Evans

Renshaw

et al. 2017

Can. J. Fish. Aquat. Sci.

163

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Species richness is a metric of biodiversity that represents the number of species present in a community. Traditional fisheries assessments that rely on capture of organisms often underestimate true species richness. Environmental DNA (eDNA) metabarcoding is an alternative tool that infers species richness by collecting and sequencing DNA present in the ecosystem. Our objective was to determine how spatial distribution of samples and "bioinformatic stringency" affected eDNA-metabarcoding estimates of species richness compared with capture-based estimates in a 2.2 ha reservoir. When bioinformatic criteria required species to be detected only in a single sample, eDNA metabarcoding detected all species captured with traditional methods plus an additional 11 noncaptured species. However, when we required species to be detected with multiple markers and in multiple samples, eDNA metabarcoding detected only seven of the captured species. Our analysis of the spatial patterns of species detection indicated that eDNA was distributed relatively homogeneously throughout the reservoir, except near the inflowing stream. We suggest that interpretation of eDNA metabarcoding data must consider the potential effects of water body type, spatial resolution, and bioinformatic stringency.Résumé : La richesse spécifique est une mesure de la biodiversité qui représente le nombre d'espèces présentes dans une communauté. Les évaluations traditionnelles des ressources halieutiques qui reposent sur la capture d'organismes sousestiment souvent la richesse spécifique réelle. Les méta-codes à barres d'ADN environnemental) (ADNe) constituent un autre outil qui permet d'inférer la richesse spécifique en recueillant et en séquençant l'ADN présent dans l'écosystème. Notre objectif consistait à déterminer comment la répartition spatiale des échantillons et la « rigueur bioinformatique » influent sur les estimations de la richesse spécifique reposant sur les méta-codes à barres d'ADNe par rapport aux estimations reposant sur la capture, dans un réservoir de 2,2 ha. Quand les critères bioinformatiques exigeaient la détection d'une espèce dans un seul échantillon, la méthode des méta-codes à barres d'ADNe a détecté toutes les espèces capturées par les méthodes traditionnelles en plus de 11 autres espèces non capturées. Toutefois, quand il fallait que les espèces soient détectées sur la base de plus d'un marqueur et dans plus d'un échantillon, les méta-codes à barres d'ADNe n'ont détecté que sept des espèces capturées. Notre analyse de la répartition spatiale de la détection d'espèces indique que l'ADNe était réparti de manière assez uniforme dans tout le réservoir, sauf près de l'embouchure du cours d'eau qui l'alimente. Nous proposons que l'interprétation des données obtenues par la méthode des méta-codes à barres d'ADNe doit tenir compte des effets potentiels du type de plan d'eau, de la résolution spatiale et de la rigueur bioinformatique. [Traduit par la Rédaction]

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“…The eDNA approach promises information about bioindicators and commercially important or protected species without the need to collect tissue or trawl through sensitive habitats (Foote et al, 2012;Bohmann et al, 2014;Thomsen and Willerslev, 2015;Evans et al, 2016;Lacoursière-Roussel et al, 2016;Shelton et al, 2016). Some studies show promising results with regard to abundance estimates (Hänfling et al, 2016;Port et al, 2016), but others show significant differences between eDNA results and traditional tows for epibenthic macroinvertebrates (Kelly et al, 2017) and zooplankton (Hirai et al, 2015b), suggesting that these methods require further research.…”

Section: Applications Of Dna Sequencing To Marine Assessment Programsmentioning

confidence: 99%

“…Lack of intercalibration between morphological and molecular methods presents an additional issue, and transferability across taxa is a concern, particularly if the initial assessment used to establish the database is limited to one or two taxonomic groups (Kelly, 2016). Although comparable molecular and traditional approaches are reported (Lejzerowicz et al, 2015;Aylagas et al, 2016Aylagas et al, , 2017Hänfling et al, 2016;Valentini et al, 2016), other studies show discrepancies (Cowart et al, 2015;Hirai et al, 2015b;Mohrbeck et al, 2015;Giner et al, 2016;Kelly et al, 2017); therefore, it has been advised to use both approaches in a complementary fashion rather than outright substitution of morphotaxonomic approaches (Borja et al, 2008;Pedersen et al, 2015;Thomsen and Willerslev, 2015). Although such an approach may deliver a holistic perspective of marine ecological status, it would not produce the desired effect of streamlining monitoring efforts, which is needed to transition research into practice (de Jonge et al, 2006).…”

Section: Taxonomic Classification and Quantificationmentioning

confidence: 99%

DNA Sequencing as a Tool to Monitor Marine Ecological Status

et al. 2017

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Many ocean policies mandate integrated, ecosystem-based approaches to marine monitoring, driving a global need for efficient, low-cost bioindicators of marine ecological quality. Most traditional methods to assess biological quality rely on specialized expertise to provide visual identification of a limited set of specific taxonomic groups, a time-consuming process that can provide a narrow view of ecological status. In addition, microbial assemblages drive food webs but are not amenable to visual inspection and thus are largely excluded from detailed inventory. Molecular-based assessments of biodiversity and ecosystem function offer advantages over traditional methods and are increasingly being generated for a suite of taxa using a "microbes to mammals" or "barcodes to biomes" approach. Progress in these efforts coupled with continued improvements in high-throughput sequencing and bioinformatics pave the way for sequence data to be employed in formal integrated ecosystem evaluation, including food web assessments, as called for in the European Union Marine Strategy Framework Directive. DNA sequencing of bioindicators, both traditional (e.g., benthic macroinvertebrates, ichthyoplankton) and emerging (e.g., microbial assemblages, fish via eDNA), promises to improve assessment of marine biological quality by increasing the breadth, depth, and throughput of information and by reducing costs and reliance on specialized taxonomic expertise.

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Environmental DNA metabarcoding of lake fish communities reflects long‐term data from established survey methods

Cited by 437 publications

References 48 publications

Under the canopy: Community-wide effects of invasive algae in Marine Protected Areas revealed by metabarcoding

Under the canopy: Community-wide effects of invasive algae in Marine Protected Areas revealed by metabarcoding

Fish community assessment with eDNA metabarcoding: effects of sampling design and bioinformatic filtering

DNA Sequencing as a Tool to Monitor Marine Ecological Status

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