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

Autor: Emre Keskin, Vladimir Pešić, Fedor Čiampor, Sonia Maria Soares Ferreira, Arne J. Beermann, Michał Grabowski, Berry van der Hoorn, Filipe O. Costa, Agnès Bouchez, Sofia A. Wyler, Björn Rulik, Nikolaus U. Szucsich, Florian Leese, Guy Paz, Piotr Gadawski, Gábor Várbíró, Jörg Freyhof, Benjamin W. Price, Zoltán Csabai, Sofia Alexandra Ferreira Duarte, Lujza Keresztes, Marcos A. L. Teixeira, Tomasz Mamos, Hannah Weigand, Arne Haegerbaeumer, Martin Pfannkuchen, Zuzana Čiamporová-Zaťovičová, Ángel Borja, Malin Strand, Daniela Marić Pfannkuchen, Wolfram Graf, Klaas-Douwe B. Dijkstra, Alexander M. Weigand, Jan Macher, Bella Japoshvili, B. Rinkevich, Matthias F. Geiger, Frédéric Rimet, Torbjørn Ekrem, Endre Willassen, Ursula Eisendle
Přispěvatelé: Universidade do Minho, Musée National d'Histoire Naturelle de Luxembourg (MNHN), University of Duisburg-Essen, Centre of Molecular and Environmental Biology (CBMA), University of Minho, University of Pecs, Leibniz Institute for Animal Biodiversity, Partenaires INRAE, University of Lódź, Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques (CARRTEL), Institut National de la Recherche Agronomique (INRA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])
Jazyk: angličtina
Rok vydání: 2019
Předmět:
0106 biological sciences
Aquatic Organisms
010504 meteorology & atmospheric sciences
[SDV]Life Sciences [q-bio]
Ciências Biológicas [Ciências Naturais]
Aquatic biomonitoring
010501 environmental sciences
Barcode
01 natural sciences
DNA barcoding
law.invention
Marine Strategy Framework Directive
law
Environmental monitoring
Taxonomic rank
Waste Management and Disposal
0303 health sciences
Environmental resource management
Gap analysis (conservation)
Pollution
Biota
Quality assurance
Europe
Biological monitoring
Geography
Water Framework Directive
Biologie
Environmental Monitoring
Environmental Engineering
Context (language use)
010603 evolutionary biology
03 medical and health sciences
Freshwater
Environmental Chemistry
DNA Barcoding
Taxonomic
14. Life underwater
030304 developmental biology
0105 earth and related environmental sciences
Gene Library
Ciências Naturais::Ciências Biológicas
Science & Technology
Marine
business.industry
reference library
biological monitoring
freshwater
marine
quality assurance
Reference library
15. Life on land
13. Climate action
business
Zdroj: Science of the Total Environment
Science of the Total Environment, Elsevier, 2019, 678, pp.499-524. ⟨10.1016/j.scitotenv.2019.04.247⟩
Repositório Científico de Acesso Aberto de Portugal
Repositório Científico de Acesso Aberto de Portugal (RCAAP)
instacron:RCAAP
ISSN: 0048-9697
1879-1026
Popis: Effective identification of species using short DNA fragments (DNA barcoding and DNA metabarcoding) requires reliable sequence reference libraries of known taxa. Both taxonomically comprehensive coverage and content quality are important for sufficient accuracy. For aquatic ecosystems in Europe, reliable barcode reference libraries are particularly important if molecular identification tools are to be implemented in biomonitoring and reports in the context of the EU Water Framework Directive (WFD) and the Marine Strategy Framework Directive (MSFD). We analysed gaps in the two most important reference databases, Barcode of Life Data Systems (BOLD) and NCBI GenBank, with a focus on the taxa most frequently used in WFD and MSFD. Our analyses show that coverage varies strongly among taxonomic groups, and among geographic regions. In general, groups that were actively targeted in barcode projects (e.g. fish, true bugs, caddisflies and vascular plants) are well represented in the barcode libraries, while others have fewer records (e.g. marine molluscs, ascidians, and freshwater diatoms). We also found that species monitored in several countries often are represented by barcodes in reference libraries, while species monitored in a single country frequently lack sequence records. A large proportion of species (up to 50%) in several taxonomic groups are only represented by private data in BOLD. Our results have implications for the future strategy to fill existing gaps in barcode libraries, especially if DNA metabarcoding is to be used in the monitoring of European aquatic biota under the WFD and MSFD. For example, missing species relevant to monitoring in multiple countries should be prioritized for future collaborative programs. We also discuss why a strategy for quality control and quality assurance of barcode reference libraries is needed and recommend future steps to ensure full utilisation of metabarcoding in aquatic biomonitoring.
This paper is a deliverable of the European Cooperation in Science and Technology (COST) Action DNAqua-Net (CA15219) Working Group 1, led by Torbjørn Ekrem and Fedor Čiampor. Thanks to the University of Minho and University of Pécs for hosting workshops and working group meetings. We also thank staff at National Environment Agencies and others that provided national checklists of taxa used in biomonitoring, and otherwise assisted with checklist proof-reading: Jarmila Makovinská and Emília Mišíková Elexová (Slovakia); Steinar Sandøy and Dag Rosland (Norway); Mišel Jelič (Croatia); Marlen Vasquez (Cyprus); Adam Petrusek (Czech Republic); Kristel Panksep (Estonia); Panagiotis Kaspiditis (Greece); Matteo Montagna (Italy); Marija Katarzyte (Lithuania); Ana Rotter (Slovenia); Rosa Trabajo (Spain); Florian Altermatt (Switzerland); Kristian Meissner (Finland), Rigers Bakiu (Albania), Valentina Stamenkovic and Jelena Hinic (Macedonia); Patricia Mergen (Belgium); Gael Denys & the French Biodiversity Agency (France); Mary Kelly-Quinn (Ireland); Piotr Panek and Andrzej Zawal (Poland); Cesare Mario Puzzi (Italy); Carole Fitzpatrick (United Kingdom); Simon Vitecek (Austria); Ana Filipa Filipe (Portugal); Peter Anton Stæhr & Anne Winding (Denmark); Michael Monaghan (Germany); Alain Dohet, Lionel L'Hoste, Nora Welschbillig & Luc Ector (Luxembourg), Lujza Keresztes, (Romania). The authors also want to thank Dirk Steinke for providing the original European ERMS list for marine taxa and Florian Malard for comments on the manuscript. The preparation of the AMBI checklist was carried out in the scope of a Short-term Scientific Mission (ECOST-STSM-CA15219-150217- 082111) granted to SD visiting AZTI, Spain. ZC was supported by grants EFOP-3.6.1.-16-2016-00004 and 20765-3/2018/FEKUTSTRAT. TE was supported by the NorBOL-grant (226134/F50) from the Research Coun cil of Norway. BR, FL and MFG contributed through support from the GBOL project, which is generously funded by the German Federal Min istry of Education and Research (FKZ 01LI1101 and 01LI1501). MG contributed through support of the Polish National Science Centre, grants N N303 5794 39 and 2014/15/B/NZ8/00266. SF was funded by the project PORBIOTA - Portuguese E-Infrastructure for Information and Research on Biodiversity (POCI-01-0145-FEDER-022127), supported by Operational Thematic Program for Competitiveness and Internationalization (POCI), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (FEDER).
Databáze: OpenAIRE
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