Synthetic Statistical Approach Reveals a High Degree of Richness of Microbial Eukaryotes in an Anoxic Water Column
- 1 October 2006
- journal article
- Published by American Society for Microbiology in Applied and Environmental Microbiology
- Vol. 72 (10), 6578-6583
- https://doi.org/10.1128/aem.00787-06
Abstract
Molecular surveys suggest that communities of microbial eukaryotes are remarkably rich, because even large clone libraries seem to capture only a minority of species. This provides a qualitative picture of protistan richness but does not measure its real extent either locally or globally. Statistical analysis can estimate a community's richness, but the specific methods used to date are not always well grounded in statistical theory. Here we study a large protistan molecular survey from an anoxic water column in the Cariaco Basin (Caribbean Sea). We group individual 18S rRNA gene sequences into operational taxonomic units (OTUs) using different cutoff values for sequence similarity (99 to 50%) and systematically apply parametric models and nonparametric estimators to the OTU frequency data to estimate the total protistan diversity. The parametric models provided statistically sound estimates of protistan richness, with biologically meaningful standard errors, maximal data usage, and extensive model diagnostics and were preferable to the available nonparametric tools. Our clone library exceeded 700 clones but still covered only a minority of species and less than half of the larger protistan clades. Our estimates of total protistan richness portray the target community as very rich at all OTU levels, with hundreds of different populations apparently co-occurring in the small (3-liter) volume of our sample, as well as dozens of clades of the highest taxonomic order. These estimates are among the first for microbial eukaryotes that are obtained using state-of-the-art statistical methods and can serve as benchmark numbers for the local diversity of protists.Keywords
This publication has 33 references indexed in Scilit:
- Microeukaryote Community Patterns along an O2/H2S Gradient in a Supersulfidic Anoxic Fjord (Framvaren, Norway)Applied and Environmental Microbiology, 2006
- A Penalized Nonparametric Maximum Likelihood Approach to Species Richness EstimationJournal of the American Statistical Association, 2005
- Introducing DOTUR, a Computer Program for Defining Operational Taxonomic Units and Estimating Species RichnessApplied and Environmental Microbiology, 2005
- Picoeukaryotic diversity in an oligotrophic coastal site studied by molecular and culturing approachesFEMS Microbiology Ecology, 2004
- Type I errors and power of the parametric bootstrap goodness-of-fit test: Full and limited informationBritish Journal of Mathematical and Statistical Psychology, 2003
- Annual cycle of primary production in the Cariaco Basin: Response to upwelling and implications for vertical exportJournal of Geophysical Research: Oceans, 2001
- Divergent Perspectives on Protist Species RichnessProtist, 1999
- CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choiceNucleic Acids Research, 1994
- Estimating the Number of Classes via Sample CoverageJournal of the American Statistical Association, 1992
- The characterization of enzymatically amplified eukaryotic 16S-like rRNA-coding regionsGene, 1988