Are oligotypes meaningful ecological and phylogenetic units? A case study of Microcystis in Freshwater lakes

Oligotyping is a computational method used to increase the resolution of marker genemicrobiome studies. Although oligotyping can distinguish highly similar sequence variants, the resulting units are not necessarily phylogenetically and ecologically informative due to limitations of the selected markergene. In this perspective, we examine how oligotyping data is interpreted in recent literature, and we illustrate some of the method’s constraints with a case study of the harmful bloom-forming cyanobacterium Microcystis. We identified three Microcystisoligotypes from a western Lake Eriebacterial community 16S rRNA gene (V4 region) survey that had previously clustered into one OTU. We found the same three oligotypes and two additional sequence variants in 46 Microcystiscultures isolated from Michigan inland lakes spanning a trophic gradient. In Lake Erie, shifts in Microcystisoligotypes corresponded to spatial nutrient gradients and temporal transitions in bloom toxicity. In the cultures, Microcystisoligotypes showed preferential distributions for different trophic states, but genomic data revealed that the oligotypes identified in Lake Eriedid not correspond to toxin gene presence. Thus, oligotypes could not be used for inferring toxic ecotypes. Most strikingly, Microcystisoligotypes were not monophyletic. Our study supports the utility of oligotyping for distinguishing sequence types along certain ecological features, while it stresses that 16S rRNA gene sequence types may not reflect ecologically or phylogenetically cohesive populations. Therefore, we recommend that studies employing oligotyping or related tools consider these caveats during data interpretation.