DNA metabarcoding on repeat: Sequencing data of marine macrobenthos are reproducible and robust across labs and protocols

Ecological Indicators, vol. 150, pp. 110207

Abstract

DNA metabarcoding can be used in marine environmental monitoring if results are reproducible between labs and robust against modifications to the lab protocol. In this interlaboratory study, we conducted a ring test where subsamples of blended macrobenthos samples were distributed to four laboratories located in Belgium, the Netherlands, Germany and Denmark. Samples were processed by a standardized lab protocol and by an adapted protocol, and the resulting datasets were analyzed with the same bioinformatics pipeline. Different biodiversity indicators were calculated. Our results show that bulkDNA metabarcoding of marine macrobenthos offers a highly reproducible assessment of alpha diversity patterns when using a standardized protocol, since comparable species numbers, Shannon indices and Inverse Simpson indices were found between laboratories. Especially high abundant species and species with large body sizes were shared between the laboratories. The need for using a standardized protocol to enhance comparability in alpha diversity between different studies was shown. Beta diversity patterns are less subjected to changes in the metabarcoding protocol and were almost identical between different laboratories, as the main clustering was always based on the macrobenthic community, independent of the used protocol or the laboratory that conducted the work. We conclude that DNA metabarcoding for marine environmental monitoring is an appropriate method when the aim is to study changes in community patterns and advocate its implementation in routine monitoring programs of national and European authorities, providing that a standardized protocol is implemented and/or a detailed description of the protocol is available.

Authors 12

1. Laure Van den Bulcke corresponding

   Ghent University

   Affiliation as printed

   Flanders Research Institute for Agriculture, Fisheries and Food – Marine Research, Jacobsenstraat 1, 8400 Oostende, Belgium

   University of Ghent, Department of Data Analysis and Mathematical Modelling - Knowledge-based Systems Research Group, Coupure Links 653, 9000 Gent, Belgium

2. Annelies De Backer
   Affiliation as printed

   Flanders Research Institute for Agriculture, Fisheries and Food – Marine Research, Jacobsenstraat 1, 8400 Oostende, Belgium

3. Jan Wittoeck
   Affiliation as printed

   Flanders Research Institute for Agriculture, Fisheries and Food – Marine Research, Jacobsenstraat 1, 8400 Oostende, Belgium

4. Kevin K. Beentjes Aachen Naturalis Biodiversity Center

   Naturalis Biodiversity Center

   Affiliation as printed

   Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands

5. Sara Maes
   Affiliation as printed

   Flanders Research Institute for Agriculture, Fisheries and Food – Marine Research, Jacobsenstraat 1, 8400 Oostende, Belgium

6. Magdalini Christodoulou

   Senckenberg am Meer · OÖ Landes-Kultur GmbH (Austria)

   Affiliation as printed

   OÖ Landes-Kultur GmbH, Biologiezentrum, Johann-Wilhelm-Klein-Straße 73, 4040 Linz, Austria

   Senckenberg am Meer, German Centre for Marine Biodiversity Research, Südstrand 44, 26382 Wilhelmshaven, Germany

7. Pedro Martínez Arbizu

   Senckenberg am Meer

   Affiliation as printed

   Senckenberg am Meer, German Centre for Marine Biodiversity Research, Südstrand 44, 26382 Wilhelmshaven, Germany

8. Rumakanta Sapkota

   Aarhus University

   Affiliation as printed

   Aarhus University, Department of Environmental Science, Frederiksborgvej 399, 4000 Roskilde, Denmark

9. Berry van der Hoorn Aachen Naturalis Biodiversity Center

   Naturalis Biodiversity Center · Inholland University of Applied Sciences

   Affiliation as printed

   Inholland University of Applied Sciences, Landscape and Environment Management, Rotterdamseweg 141, 2628 AL Delf, The Netherlands

   Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands

10. Anne Winding

    Aarhus University

    Affiliation as printed

    Aarhus University, Department of Environmental Science, Frederiksborgvej 399, 4000 Roskilde, Denmark

11. Kris Hostens
    Affiliation as printed

    Flanders Research Institute for Agriculture, Fisheries and Food – Marine Research, Jacobsenstraat 1, 8400 Oostende, Belgium

12. Sofie Derycke

    Ghent University

    Affiliation as printed

    Flanders Research Institute for Agriculture, Fisheries and Food – Marine Research, Jacobsenstraat 1, 8400 Oostende, Belgium

    University of Ghent, Department of Biology - Marine Biology Research Group, Krijgslaan 281, 9000 Gent, Belgium