Estimating prokaryotic diversity: When are 16S rDNA libraries large enough?

Paul F. Kemp, Josephine Y. Aller

Limnol. Oceanogr. Methods 2:114-125 (2004) | DOI: 10.4319/lom.2004.2.114

ABSTRACT: As a necessary step in the study of prokaryotic diversity using 16S rDNA libraries, authors should evaluate how well their libraries represent diversity in the source environment. Phylotype–richness estimates can be used to judge whether a library represents diversity sufficiently for its intended purpose. We have argued that richness estimates are most useful if libraries are first shown to be large enough to yield stable estimates. In this article, we (1) evaluate two potentially suitable, non-parametric richness estimators (SACE and SChao1), tested against model libraries and libraries drawn from natural prokaryotic communities; (2) evaluate whether stable richness estimates are also unbiased; and (3) examine characteristics of prokaryotic libraries that influence the usefulness of richness estimators. Richness estimates consistently reached a stable asymptotic value for libraries that sampled diversity exhaustively. Stable estimates appear to be unbiased or minimally biased estimates of phylotype richness. The SACE estimator was often undefined, sometimes overestimated phylotype richness at intermediate sampling efforts, and sometimes stabilized at a larger library size than the SChao1 estimator. The SChao1 estimator appears well suited for estimating phylotype richness from prokaryotic 16S rDNA libraries. Libraries judged too small to yield a stable richness estimate typically had a highly uneven frequency distribution of phylotypes, with a preponderance of phylotypes that occurred only once in the library. Libraries considered large enough typically had a more even frequency distribution of phylotypes. A software tool is provided to aid others in assessing whether their libraries are large enough to yield stable phylotype–richness estimates.