| Traditionally protists have been described based on their morphology using what is often referred to as alpha taxonomy approaches. However, today it is all but certain that these approaches have not revealed the real scale of protistan diversity. The two main reasons are the current uncultivability of most of microbial eukaryotes, which often makes direct observations impossible, and the lack of a comprehensive concept of species. Today, the molecular based (beta) taxonomy of comparisons of DNA sequences is increasingly used to bypass the limitations of the alpha taxonomy. The challenge is that the two approaches are typically used separately, and with different units of diversity. For example, it is not known to what extent the genetic distance between two taxa corresponds to morphological differences between them, and it is not clear if morphologically defined species do or do not cluster as phylogenetically distinct genetic groups of rRNA gene sequences (Operational Taxonomic Units, or OTUs). In the end, there is little understanding whether traditionally defined species vs OTUs combine identical, similar, or entirely different populations. Since traditional morphology and molecular taxonomy will likely both be used for the foreseeable future, it is important to understand what a morphologically defined species means in terms of gene sequence variability among cells composing this species. Here we use marine ciliates as model representatives of protists to investigate the level of intra-- and interspecies heterogeneity in the most widely used genetic marker, the 18S rRNA gene. Using single-cell analysis and molecular cloning, we show that OTUs comprising 18S rRNA gene sequences that share ≥99% homology correspond well to species as defined by alpha taxonomy. Therefore, at least in ciliates, there appears to be a level of genetic variability in 18S rRNA gene sequences that could be used as a proxy for morphologically defined species. Merging alpha and beta taxonomy is very convenient for protistan diversity studies as this opens a way to assess this diversity faster and more objectively. Capitalizing on this, we surveyed ciliate diversity in several marine habitats, and statistically estimated the total ciliate richness in these habitats. The resulting throughput compares favorably to, and at times exceeds, what would have been achieved by more traditional alpha taxonomy approaches. |
