DNA barcode reference libraries for the monitoring of aquatic biota in Europe: Gap-analysis and recommendations for future work

Weigand, Hannah; Beermann, Arne J.; Cĭampor, F; Costa, Filipe O.; Csabai, Zoltán; Duarte, Sofia Alexandra Ferreira; Geiger, Matthias F.; Grabowski, Michał; Rimet, Frédéric; Rulik, Björn; Strand, Malin; Szucsich, Nikolaus U.; Weigand, Alexander; Willassen, Endre; Wyler, Sofia; Bouchez, Agnès; Borja, Ángel; Čiamporová‐Zaťovičová, Zuzana; Ferreira, Sónia; Dijkstra, Klaas‐Douwe B.; Eisendle, Ursula; Freyhof, Jörg; Gadawski, Piotr; Graf, Wolfram; Haegerbaeumer, Arne; Hoorn, Berry B. van der; Japoshvili, Bella; Keresztes, Lujza; Keskin, Emre; Leese, Florian; Macher, Jan Niklas; Mamos, Tomasz; Paz, Guy; Pešić, Vladimir; Pfannkuchen, Daniela Marić; Pfannkuchen, Martin; Price, Benjamin W.; Rinkevich, B.; Teixeira, Marcos A. L.; Várbíró, Gábor; Ekrem, Torbjørn

doi:10.1016/j.scitotenv.2019.04.247

Cited by 358 publications

(315 citation statements)

References 110 publications

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“…Thanks to high-throughput sequencing technologies, molecular tools are being increasingly integrated in regular and large-scale biomonitoring initiatives (Leese et al, 2018;Pennisi, 2019). Together with the emergence of DNA metabarcoding and eDNA-based approaches for ecological and biological research (Deiner et al, 2018), the need to improve the DNA barcode reference library becomes even greater (Weigand et al, 2019). Not only for the already known species, but also for the remarkable hidden biodiversity, which has been continuously revealed with the support of molecular data.…”

Section: Discussionmentioning

confidence: 99%

Molecular and morphometric analyses identify new lineages within a large Eumida (Annelida) species complex

Teixeira

Vieira

Pleijel³

et al. 2019

Zoologica Scripta

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We report on two new lineages of the Eumida sanguinea complex from Great Britain and describe one of them as a new species using a multilocus approach, including the mitochondrial DNA COI‐5P and the nuclear markers ITS (ITS1, 5.8S rRNA and ITS2) and 28S rRNA. The molecular analysis placed Eumida mackiei sp. nov. in a monophyletic clade with 19.1% (COI), 10.1% (ITS) and 1.7% (28S) mean distance to its nearest neighbour. Molecular diagnoses were also applied to nine lineages within the E. sanguinea complex. This was complemented with morphometric data employing multivariate statistical analysis and the incorporation of statistical dissimilarities against three other described species from the complex. Eumida mackiei sp. nov. can be distinguished from E. notata and E. maia by the larger distance between the eyes and differences in morphometric proportions mainly in the dorsal and ventral cirri as well as in the prostomial appendages. E. sanguinea sensu stricto failed to produce a cluster of its own in the morphometric analysis, probably due to juvenile bias. Integrative taxonomy provided strong evidence to formally describe a new cryptic species that can now be used in biomonitoring or other relevant ecological research.

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Section: Discussionmentioning

confidence: 99%

Molecular and morphometric analyses identify new lineages within a large Eumida (Annelida) species complex

Teixeira

Vieira

Pleijel³

et al. 2019

Zoologica Scripta

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“…One main reason for this is that, in contrast to fish and amphibian eDNA analyses, the typically used metabarcoding fragment is the mitochondrial cytochrome c oxidase I (COI) gene. The big advantage of COI is its taxonomic resolution and the availability of extensive reference data (Ratnasingham and Hebert 2007, Clarke et al 2017, Andújar et al 2018, Weigand et al 2019. However, in contrast to 12S or 16S, COI as a proteincoding gene shows codon degeneracy that limits taxon-specific primer design (Clarke et al 2014, Deagle et al 2014, Sharma and Kobayashi 2014 making it almost impossible so far to design really target-specific primers for diverse groups such as 'invertebrates' but also fish and amphibians.…”

Section: Introductionmentioning

confidence: 99%

Improved freshwater macroinvertebrate detection from eDNA through minimized non-target amplification

Leese

Sander

Buchner

et al. 2020

Preprint

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Acknowledgments:We would like to thank Marlen Mährlein, Nathalie Kaffenberger, Cristina Hartmann-Fatu and Arne Beermann for help with sample collection or processing. Furthermore, we thank Jan-Niklas Macher for helpful discussions, Beatrice Kulawig for compiling the taxonomic data from the Rhine-Main-Observatory, and Martina Weiss for valuable comments on the structure of the manuscript. This work has been funded by a grant of the Bode Foundation to FL. This work has been conducted as part of COST (European Cooperation in Science and Technology) Action DNAqua-Net (CA15219). AbstractDNA metabarcoding of freshwater communities typically relies on PCR amplification of a fragment of the mitochondrial cytochrome c oxidase (COI) gene with degenerate primers. The advantage of COI is its taxonomic resolution and the availability of an extensive reference database.However, when universal primers are used on environmental DNA (eDNA) isolated from stream water, macroinvertebrate read and OTU numbers are typically "watered down", i.e. diluted, compared to whole specimen 'bulk samples' due to greater co-amplification of abundant nontarget taxa such as algae and bacteria. Because stream macroinvertebrate taxa are of prime importance for regulatory biomonitoring, more effective ways to capture their diversity via eDNA isolated from water are important. In this study, we aimed to improve macroinvertebrate assessment from eDNA by minimizing non-target amplification. Therefore, we generated data using universal primers BF2/BR2 throughout 15 months from a German Long-Term Ecological Research (LTER) site, the River Kinzig, to identify most abundant non-target taxa. Based on these data, we designed a new reverse primer (EPTDr2n) with 3'-specificity towards macrozoobenthic taxa and validated its specificity in silico together with universal forward primer fwhF2 using available data from GenBank and BOLD. We then performed in vitro tests using 20 eDNA samples taken in the Kinzig catchment. We found that the percentage of target reads was much higher for the new primer combination compared to two universal macrozoobenthic primer pairs, BF2/BR2 and fwhF2/fwhR2n (>99 % vs. 21.4 % and 41.25 %, respectively). Likewise, number of detected macroinvertebrate taxa was substantially higher (351 vs. 46 and 170, respectively) and exceeded the number of 257 taxa identified by expert taxonomists at nearby sites across two decades of sampling. While few taxa such as Turbellaria were not detected, we show that the optimized primer avoids the dilution problem and thus significantly improves macroinvertebrate detection for bioassessment and -monitoring.

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“…The range of laboratory methods (Dopheide, Xie, Buckley, Drummond, & Newcomb, 2019) and different pipelines used for bioinformatics can determine the results (Pauvert et al, 2019). Weigand et al (2019) did find large gaps in current Barcode databases for macroinvertebrates, and their coverage varies among aquatic taxonomic groups and regions in Europe. Weigand et al (2019) did find large gaps in current Barcode databases for macroinvertebrates, and their coverage varies among aquatic taxonomic groups and regions in Europe.…”

Section: Introductionmentioning

confidence: 99%

“…The still incomplete status of reference databases is other of the debated issues for application of metabarcoding in studies of aquatic biodiversity (Deiner et al, 2017). Weigand et al (2019) did find large gaps in current Barcode databases for macroinvertebrates, and their coverage varies among aquatic taxonomic groups and regions in Europe. It is also worthy to mention eDNA degradation rate and transport in freshwater ecosystems need to be considered to interpret the results (Goldberg, Strickler, & Pilliod, 2015).…”

Section: Introductionmentioning

confidence: 99%

How can eDNA contribute in riverine macroinvertebrate assessment? A metabarcoding approach in the Nalón River (Asturias, Northern Spain)

et al. 2019

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Background: Bioassessment of rivers is a fundamental method to determine surface water quality. One of the groups most commonly employed as bioindicators of aquatic ecosystems are benthic macroinvertebrates. Their conventional assessment is based on morphological identification and entails several limitations, such as being time-consuming and requires trained experts for taxonomic identification. The use of genetic tools to solve these limitations offers an alternative way to evaluate rivers status. The use of environmental DNA (eDNA) metabarcoding has increased in recent years for different purposes, but its use in water quality evaluation is yet to be tested. Here, morphological and eDNA based inventories of macroinvertebrates were compared from the same seven sampling sites in the Upper Nalón River Basin (Asturias, Spain). Materials & Methods:High-Throughput Sequencing (HTS) of the cytochrome oxidase subunit 1 (COI) gene was carried out on DNA from water samples using an Ion Torrent platform. Biotic water quality indices were calculated from morphological and molecular data and compared with independent physico-chemical habitat assessment to validate eDNA based approach.Results: Highly positive and significant correlation was found between eDNA metabarcoding and morphological methods (Morphological and eDNA indices, r = 0.798, 5 degrees of freedom d.f., P = 0.031;) and a highly significant negative correlation was found between molecular and habitat quality indices (Stress score & eDNA, ρ = -0.878 and P = 0.009; Stress score & Visual, ρ = -0.949 and P = 0.0002). Discussion:The similarity of results from the two approaches and the correlation of eDNA metabarcoding data with the habitat quality indices, suggest that eDNA performs as well as conventional methods for calculating biotic indices in this system, positioning eDNA metabarcoding of macroinvertebrate communities to transform how river bioassessment can be achieved.

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DNA barcode reference libraries for the monitoring of aquatic biota in Europe: Gap-analysis and recommendations for future work

Cited by 358 publications

References 110 publications

Molecular and morphometric analyses identify new lineages within a large Eumida (Annelida) species complex

Molecular and morphometric analyses identify new lineages within a large Eumida (Annelida) species complex

Improved freshwater macroinvertebrate detection from eDNA through minimized non-target amplification

How can eDNA contribute in riverine macroinvertebrate assessment? A metabarcoding approach in the Nalón River (Asturias, Northern Spain)

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