Enhancing metabarcoding efficiency and ecological insights through integrated taxonomy and DNA reference barcoding: a case study on beach meiofauna
bioRxiv (Cold Spring Harbor Laboratory)
Abstract
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 Institute of Environmental Sciences (CML) Naturalis Biodiversity Center
Leiden University · Naturalis Biodiversity Center
Affiliation as printed
Naturalis Biodiversity Center; Institute of Environmental Sciences (CML), Leiden University;
Institute of Environmental Sciences (CML), Leiden University
Naturalis Biodiversity Center
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Affiliation as printed
National Research Council of Italy;
National Research Council of Italy
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Affiliation as printed
Naturalis Biodiversity Center;
Naturalis Biodiversity Center
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Affiliation as printed
Naturalis Biodiversity Center;
Naturalis Biodiversity Center
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Cyprus University of Technology · CMMI – Cyprus Marine & Maritime Institute (Cyprus)
Affiliation as printed
Cyprus Marine and Maritime Institute; Cyprus University of Technology;
Cyprus Marine and Maritime Institute
Cyprus University of Technology
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Affiliation as printed
Dipartimento di Medicina Veterinaria, Universita di Sassari; National Biodiversity Future Center (NBFC);
Dipartimento di Medicina Veterinaria, Universita di Sassari
National Biodiversity Future Center (NBFC)
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Affiliation as printed
Naturalis Biodiversity Center;
Naturalis Biodiversity Center
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Universidad Complutense de Madrid
Affiliation as printed
Department of Biodiversity, Ecology and Evolution, Universidad Complutense de Madrid;
Department of Biodiversity, Ecology and Evolution, Universidad Complutense de Madrid
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Swedish Museum of Natural History
Affiliation as printed
Swedish Museum of Natural History;
Swedish Museum of Natural History
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Affiliation as printed
Naturalis Biodiversity Center;
Naturalis Biodiversity Center
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University of Tennessee at Chattanooga
Affiliation as printed
Department of Biology, Geology, and Environmental Science. University of Tennessee at Chattanooga;
Department of Biology, Geology, and Environmental Science. University of Tennessee at Chattanooga
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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
National Research Council of Italy (CNR), Water Research Institute (IRSA; Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences; Department of Ecology, Charles University, Faculty of Science;
Department of Ecology, Charles University, Faculty of Science
Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences
National Research Council of Italy (CNR), Water Research Institute (IRSA
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Universidad Complutense de Madrid
Affiliation as printed
Department of Biodiversity, Ecology and Evolution, Universidad Complutense de Madrid;
Department of Biodiversity, Ecology and Evolution, Universidad Complutense de Madrid
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University of Copenhagen · Natural History Museum of Denmark
Affiliation as printed
Natural History Museum of Denmark, University of Copenhagen;
Natural History Museum of Denmark, University of Copenhagen
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University of Modena and Reggio Emilia
Affiliation as printed
National Biodiversity Future Center (NBFC); Department of Life Sciences, University of Modena and Reggio Emilia;
Department of Life Sciences, University of Modena and Reggio Emilia
National Biodiversity Future Center (NBFC)
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Naturalis Biodiversity Center · University of Amsterdam
Affiliation as printed
Naturalis Biodiversity Center; Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam;
Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam
Naturalis Biodiversity Center
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Affiliation as printed
CNR-IRSA
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