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

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

Research output: Contribution to journalArticlepeer-review

Abstract

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.

Original languageEnglish
Pages (from-to)499-524
Number of pages26
JournalScience of the Total Environment
Volume678
DOIs
StatePublished - 15 Aug 2019
Externally publishedYes

Bibliographical note

Funding Information:
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 Council of Norway . BR, FL and MFG contributed through support from the GBOL project, which is generously funded by the German Federal Ministry 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).

Funding Information:
The Austrian Barcode of Life ( ABOL ) is an initiative with the main aim to generate and provide DNA barcodes for all species of animals, plants and fungi recorded from Austria. The main purpose of the pilot phase (2014–2017) was to build up a network of biodiversity experts and conduct four pilot studies. Currently DNA barcodes are generated in a number of independently funded projects. The pilot phase and the continued coordination of ABOL is funded by the Ministry of Education, Science and Research and located at the Natural History Museum Vienna. Apart from building up the reference library, ABOL aims to stimulate biodiversity research by acquiring funds, fostering diverse applications of DNA barcoding, building up and exchanging skills within the network, and increasing public awareness for biodiversity.

Funding Information:
The Norwegian Barcode of Life Network ( NorBOL ) started in 2008 as a consortium of biodiversity institutions in formal agreement of advancing DNA barcoding in Norway. The four university museums in Bergen, Oslo, Tromsø and Trondheim have been hubs in the network since then, and together with the Biodiversity Institute of Ontario, Canada, the main partners in a national research infrastructure project that received funding from the Research Council of Norway and the Norwegian Biodiversity Information Centre (NBIC) in 2014. The major goal of the NorBOL-project was to database DNA barcodes of 20,000 Norwegian, Scandinavian or Polar species in BOLD by the end of 2018. However, also knowledge transfer, building expertise, and curation of specimen reference collections have been important tasks of the network. Close collaboration with the Norwegian Taxonomy Initiative, run by NBIC, has been crucial in this process as it has provided identified specimens of many organism groups available for DNA analysis. Several applied research and management projects have originated through collaboration in NorBOL.

Funding Information:
Among various DNA barcoding initiatives in Portugal, one of the most prominent contributions has been provided by the network for barcoding marine life. This network was activated in 2008 through a research grant (LusoMarBoL - Lusitanian Marine Barcode of Life) from the national science funding body (Fundação para a Ciência e a Tecnologia - FCT), and has been active ever since through subsequent research grants. Core reference libraries for Portuguese marine life have been created, published and made available in BOLD, with particular focus on marine fish ( Costa et al., 2012 ; Oliveira et al., 2016 ), annelids ( Lobo et al., 2016 ), crustaceans (e.g. Lobo et al., 2017 ) and molluscs ( Borges et al., 2016 ).

Funding Information:
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 Council of Norway. BR, FL and MFG contributed through support from the GBOL project, which is generously funded by the German Federal Ministry 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).

Publisher Copyright:
© 2019 The Authors

Keywords

  • Biological monitoring
  • DNA barcoding
  • Freshwater
  • Marine
  • Quality assurance
  • Reference library

ASJC Scopus subject areas

  • Pollution
  • Waste Management and Disposal
  • Environmental Engineering
  • Environmental Chemistry

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