Enhancing metabarcoding efficiency and ecological insights through integrated taxonomy and DNA reference barcoding: A case study on beach meiofauna
Molecular Ecology Resources, vol. 24, pp. e13997
Abstract
Molecular techniques like metabarcoding, while promising for exploring diversity of communities, are often impeded by the lack of reference DNA sequences available for taxonomic annotation. Our study explores the benefits of combining targeted DNA barcoding and morphological taxonomy to improve metabarcoding efficiency, using beach meiofauna as a case study. Beaches are globally important ecosystems and are inhabited by meiofauna, microscopic animals living in the interstitial space between the sand grains, which play a key role in coastal biodiversity and ecosystem dynamics. However, research on meiofauna faces challenges due to limited taxonomic expertise and sparse sampling. We generated 775 new cytochrome c oxidase I DNA barcodes from meiofauna specimens collected along the Netherlands' west coast and combined them with the NCBI GenBank database. We analysed alpha and beta diversity in 561 metabarcoding samples from 24 North Sea beaches, a region extensively studied for meiofauna, using both the enriched reference database and the NCBI database without the additional reference barcodes. Our results show a 2.5-fold increase in sequence annotation and a doubling of species-level Operational Taxonomic Units (OTUs) identification when annotating the metabarcoding data with the enhanced database. Additionally, our analyses revealed a bell-shaped curve of OTU richness across the intertidal zone, aligning more closely with morphological analysis patterns, and more defined community dissimilarity patterns between supralittoral and intertidal sites. Our research highlights the importance of expanding molecular reference databases and combining morphological taxonomy with molecular techniques for biodiversity assessments, ultimately improving our understanding of coastal ecosystems.
Authors 17
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Jan‐Niklas Macher corresponding Aachen Department of Environmental Biology Institute of Environmental Sciences (CML) Leiden University Leiden The Netherlands Naturalis Biodiversity Center Marine Biodiversity Leiden The Netherlands Institute of Environmental Sciences (CML) Naturalis Biodiversity Center
Leiden University · Naturalis Biodiversity Center
Affiliation as printed
Department of Environmental Biology, Institute of Environmental Sciences (CML) Leiden University Leiden The Netherlands
Naturalis Biodiversity Center Marine Biodiversity Leiden The Netherlands
Department of Environmental Biology, Institute of Environmental Sciences (CML), Leiden University, Leiden, The Netherlands
Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands
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Water Research Institute · National Research Council
Affiliation as printed
National Research Council of Italy (CNR) Water Research Institute (IRSA) Verbania Pallanza Italy
National Research Council of Italy (CNR), Water Research Institute (IRSA), Verbania Pallanza, Italy
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Sude Çakir Aachen Naturalis Biodiversity Center Marine Biodiversity Leiden The Netherlands Naturalis Biodiversity Center
Affiliation as printed
Naturalis Biodiversity Center Marine Biodiversity Leiden The Netherlands
Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands
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Pierre‐Etienne Cholley Aachen Naturalis Biodiversity Center Marine Biodiversity Leiden The Netherlands Naturalis Biodiversity Center
Affiliation as printed
Naturalis Biodiversity Center Marine Biodiversity Leiden The Netherlands
Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands
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Cyprus University of Technology · CMMI – Cyprus Marine & Maritime Institute (Cyprus)
Affiliation as printed
Cyprus Marine and Maritime Institute, CMMI House Larnaca Cyprus
Department of Chemical Engineering Cyprus University of Technology Limassol Cyprus
Cyprus Marine and Maritime Institute, CMMI House, Larnaca, Cyprus
Department of Chemical Engineering, Cyprus University of Technology, Limassol, Cyprus
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University of Sassari · University of Palermo
Affiliation as printed
Dipartimento di Medicina Veterinaria Università di Sassari Sassari Italy
National Biodiversity Future Center (NBFC) Palermo Italy
Dipartimento di Medicina Veterinaria Università di Sassari Sassari Italy
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Lotte van Galen Aachen Naturalis Biodiversity Center Marine Biodiversity Leiden The Netherlands Naturalis Biodiversity Center
Affiliation as printed
Naturalis Biodiversity Center Marine Biodiversity Leiden The Netherlands
Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands
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Universidad Complutense de Madrid
Affiliation as printed
Department of Biodiversity, Ecology and Evolution Universidad Complutense de Madrid Madrid Spain
Department of Biodiversity, Ecology and Evolution, Universidad Complutense de Madrid, Madrid, Spain
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Swedish Museum of Natural History
Affiliation as printed
Department of Zoology Swedish Museum of Natural History Stockholm Sweden
Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
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Daphne de Jong Aachen Naturalis Biodiversity Center Marine Biodiversity Leiden The Netherlands Naturalis Biodiversity Center
Affiliation as printed
Naturalis Biodiversity Center Marine Biodiversity Leiden The Netherlands
Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands
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University of Tennessee at Chattanooga
Affiliation as printed
Department of Biology, Geology, and Environmental Science University of Tennessee at Chattanooga Chattanooga Tennessee USA
Department of Biology, Geology, and Environmental Science, University of Tennessee at Chattanooga, Chattanooga, Tennessee, USA
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Czech Academy of Sciences · Charles University · Water Research Institute · Czech Academy of Sciences, Institute of Microbiology · National Research Council
Affiliation as printed
Department of Ecology, Faculty of Science Charles University Prague 2 Czech Republic
Laboratory of Environmental Microbiology Institute of Microbiology of the Czech Academy of Sciences Prague Czech Republic
National Research Council of Italy (CNR) Water Research Institute (IRSA) Verbania Pallanza Italy
Department of Ecology, Faculty of Science, Charles University, Prague 2, Czech Republic
Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
National Research Council of Italy (CNR), Water Research Institute (IRSA), Verbania Pallanza, Italy
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Universidad Complutense de Madrid
Affiliation as printed
Department of Biodiversity, Ecology and Evolution Universidad Complutense de Madrid Madrid Spain
Department of Biodiversity, Ecology and Evolution, Universidad Complutense de Madrid, Madrid, Spain
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University of Copenhagen · Natural History Museum of Denmark
Affiliation as printed
Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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University of Modena and Reggio Emilia · University of Palermo
Affiliation as printed
Department of Life Sciences University of Modena and Reggio Emilia Modena Italy
National Biodiversity Future Center (NBFC) Palermo Italy
Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
National Biodiversity Future Center (NBFC), Palermo, Italy
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Willem Renema Aachen Naturalis Biodiversity Center Marine Biodiversity Leiden The Netherlands Naturalis Biodiversity Center
Naturalis Biodiversity Center · University of Amsterdam
Affiliation as printed
Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam Amsterdam The Netherlands
Naturalis Biodiversity Center Marine Biodiversity Leiden The Netherlands
Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands
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Water Research Institute · National Research Council · University of Palermo
Affiliation as printed
National Biodiversity Future Center (NBFC) Palermo Italy
National Research Council of Italy (CNR) Water Research Institute (IRSA) Verbania Pallanza Italy
National Biodiversity Future Center (NBFC), Palermo, Italy
National Research Council of Italy (CNR), Water Research Institute (IRSA), Verbania Pallanza, Italy
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