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Updated: May 10, 2026

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles
Published on: July 11, 2025
Delimiting operational taxonomic units for assessing ciliate environmental diversity using small-subunit rRNA gene
Markus Nebel1, Cornelia Pfabel, Alexandra Stock
1Departments of Informatics Ecology, University of Kaiserslautern, Kaiserslautern, Germany.
Abstract:
Delineating operational taxonomic units (OTUs) is a central element in any culture-independent analysis of environmental microbial eukaryotic diversity. Previous studies either have not justified their choice in sequence distance used to bin small-subunit ribosomal RNA (SSU rRNA) gene sequences amplified from environmental samples into OTUs, or have used a value based on the average across a broad sampling of microbial eukaryotes. Here, we analyse distances (320 922 pairwise comparisons) among sequences just from identified ciliates, and compare these with their taxonomic hierarchy. Our results show that no single sequence similarity value can always and unambiguously delineate species boundaries and higher taxa. Nevertheless, we suggest the use of 98% similarity to delineate ciliate OTUs because this threshold at least accounts for intra-specific polymorphism among multiple rRNA cistron copies. However, we suggest refraining from reconciling SSU rRNA gene-based OTUs and ciliate morphotypes; these OTUs should be used to analyse ciliate phylotype diversity, not ciliate species diversity.
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