COI metabarcoding with a curated reference database and optimized protocol provides a reliable species-level diversity assessment of tardigrades
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Abstract
DNA metabarcoding is revolutionizing biodiversity research by providing rapid and efficient ways of collecting species occurrence data. However, it has not yet been effectively applied to many taxonomic groups, mainly due to a significant lack of reference sequences and dedicated protocols. One such group is the tardigrades - a charismatic phylum of microinvertebrates known for their extremophilic and cryptobiotic capabilities. In this study, we provide the first curated database of 3,194 tardigrade COI sequences sourced from public databases and supplemented with newly produced barcodes. We demonstrate tardigrade metabarcoding in action with optimized PCR primers and a sample processing protocol using 78 samples collected in Poland and Italy. The metabarcoding revealed the presence of more than a hundred operational taxonomic units classified as Tardigrada, representing 23 genera. We compared the metabarcoding results with a morphological survey, which revealed the presence of the same genera, but a lower number of species-level taxa identified morphologically. We observed congruent patterns of tardigrade species richness and taxonomic composition between metabarcoding and morphological surveys. The metabarcoding had a higher discriminatory power, revealing cryptic diversity, and distinguishing species belonging to taxonomically challenging species complexes. By combining metabarcoding with morphological study we were able to find rare taxa, including novel biogeographic records and putative species new to science, showing also that this approach can be extremely powerful and effective in meiofauna research.
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Abstract
DNA metabarcoding is revolutionizing biodiversity research by providing rapid and efficient ways of collecting species occurrence data. However, it has not yet been effectively applied to many taxonomic groups, mainly due to a significant lack of reference sequences and dedicated protocols. One such group is the tardigrades - a charismatic phylum of microinvertebrates known for their extremophilic and cryptobiotic capabilities. In this study, we provide the first curated database of 3,194 tardigrade COI sequences sourced from public databases and supplemented with newly produced barcodes. We demonstrate tardigrade metabarcoding in action with optimized PCR primers and a sample processing protocol using 78 samples collected in Poland and Italy. The metabarcoding revealed the presence of more than a hundred operational taxonomic units classified as Tardigrada, representing 23 genera. We compared the metabarcoding results with a morphological survey, which revealed the presence of the same genera, but a lower number of species-level taxa identified morphologically. We observed congruent patterns of tardigrade species richness and taxonomic composition between metabarcoding and morphological surveys. The metabarcoding had a higher discriminatory power, revealing cryptic diversity, and distinguishing species belonging to taxonomically challenging species complexes. By combining metabarcoding with morphological study we were able to find rare taxa, including novel biogeographic records and putative species new to science, showing also that this approach can be extremely powerful and effective in meiofauna research.
DOI
https://doi.org/10.32942/X2NH0P
Subjects
Zoology
Keywords
Tardigrada, biodiversity, invertebrates, DNA barcoding, metabarcoding, meiofauna
Dates
Published: 2025-03-18 01:21
Last Updated: 2025-03-18 01:21
License
CC BY Attribution 4.0 International
Additional Metadata
Conflict of interest statement:
None
Data and Code Availability Statement:
All supplementary materials associated with this study are publicly available in FigShare repository (https://doi.org/10.6084/m9.figshare.27048157.v1), and the reference database is available as version 1 of the Tardi-COI database stored at the GitHub repository https://github.com/bsurmacz/Tardi-COI. The newly obtained barcode references are deposited in GenBank with accession numbers PQ140616- PQ140659.
Language:
English
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