Ecological patterns are robust to use of exact sequence variants versus operational taxonomic units

Recent controversy focuses on the best method for delineating microbial taxa, based on either traditional operational taxonomic units (OTUs) or exact sequence variants (ESVs) of marker gene sequences. We sought to test if the binning approach (ESVs versus OTUs) affected the ecological conclusions of a large field study. The dataset included sequences of both bacteria (16S) and fungi (ITS), across multiple environments diverging markedly in abiotic conditions, over three collection times. Despite quantitative differences in microbial richness, we found that all alpha- and beta-diversity metrics were highly positively correlated (r > 0.90) between samples analyzed with both approaches. Moreover, the community composition of the dominant taxa did not vary between approaches. Consequently, statistical inferences were nearly indistinguishable. Thus, we conclude that for typical alpha- and beta-diversity analyses, OTU or ESV methods will likely reveal similar ecological results and determining which method to employ will depend on the question at hand.