Are Oligotypes Meaningful Ecological and Phylogenetic Units? A Case Study ofMicrocystisin Freshwater Lakes.
Oligotyping is a computational method used to increase the resolution of marker gene microbiome 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 marker gene. 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 cyanobacteriumMicrocystis. We identified threeMicrocystisoligotypes from a western Lake Erie bacterial 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 46Microcystiscultures isolated from Michigan inland lakes spanning a trophic gradient. In Lake Erie, shifts inMicrocystisoligotypes 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 Erie did 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.
Department of Ecology and Evolutionary Biology, University of Michigan Ann Arbor, MI, USA.
Michelle A
MA
Berry
Department of Biology, Framingham State University Framingham, MA, USA.
Jeffrey D
JD
White
NOAA Great Lakes Environmental Research Laboratory Ann Arbor, MI, USA.
Timothy W
TW
Davis
Department of Earth and Environmental Sciences, University of Michigan Ann Arbor, MI, USA.
Sunit
S
Jain
Cooperative Institute for Limnology and Ecosystems Research, University of Michigan Ann Arbor, MI, USA.
Thomas H
TH
Johengen
Department of Earth and Environmental Sciences, University of Michigan Ann Arbor, MI, USA.
Gregory J
GJ
Dick
Department of Fisheries and Wildlife, Michigan State University East Lansing, MI, USA.
Orlando
O
Sarnelle
Department of Ecology and Evolutionary Biology, University of Michigan Ann Arbor, MI, USA.
Vincent J
VJ
Denef
16S rRNA gene sequencing; Microcystis; dada2; ecotypes; microbial species; oligotypes