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.