Enhancing metabarcoding efficiency and ecological insights through integrated taxonomy and DNA reference barcoding: a case study on beach meiofauna
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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Affiliation as printed
Naturalis Biodiversity Center
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Affiliation as printed
Water Research Institute National Research Council Verbania Branch
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Affiliation as printed
Naturalis Biodiversity Center
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Affiliation as printed
Naturalis Biodiversity Center
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CMMI – Cyprus Marine & Maritime Institute (Cyprus)
Affiliation as printed
Cyprus Marine and Maritime Institute
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Affiliation as printed
University of Sassari
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Affiliation as printed
Naturalis Biodiversity Center
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Universidad Complutense de Madrid
Affiliation as printed
Universidad Complutense de Madrid
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Swedish Museum of Natural History
Affiliation as printed
Swedish Museum of Natural History
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Affiliation as printed
Naturalis Biodiversity Center
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University of Tennessee at Chattanooga
Affiliation as printed
The University of Tennessee at Chattanooga
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Affiliation as printed
Water Research Institute National Research Council Verbania Branch
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Universidad Complutense de Madrid
Affiliation as printed
Universidad Complutense de Madrid Facultad de Ciencias Biologicas
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University of Copenhagen · Natural History Museum of Denmark
Affiliation as printed
University of Copenhagen Natural History Museum of Denmark
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University of Modena and Reggio Emilia
Affiliation as printed
University of Modena and Reggio Emilia
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Affiliation as printed
Naturalis Biodiversity Center
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Affiliation as printed
CNR-Institute of Ecosystem Study
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