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Applied and Environmental Microbiology, October 2006, p. 6578-6583, Vol. 72, No. 10
0099-2240/06/$08.00+0     doi:10.1128/AEM.00787-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

Synthetic Statistical Approach Reveals a High Degree of Richness of Microbial Eukaryotes in an Anoxic Water Column{dagger}

S.-O. Jeon,1,4 J. Bunge,2 T. Stoeck,3 K. J.-A. Barger,2 S.-H. Hong,1,4 and S. S. Epstein1,5*

Department of Biology, Northeastern University, Boston, Massachusetts 02115,1 Marine Science Center, Northeastern University, Nahant, Massachusetts 01908,5 Department of Statistical Science, Cornell University, Ithaca, New York 14853,2 Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany,3 Department of Environment Science, Kangwon National University, Kangwon-Do, Korea4

Received 4 April 2006/ Accepted 29 July 2006

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.

* Corresponding author. Mailing address: Department of Biology, Northeastern University, Boston, MA 02115. Phone: (617) 373-4048. Fax: (617) 373-3724. E-mail: s.epstein{at}neu.edu.

{dagger} Contribution 254 of the Marine Science Center of Northeastern University, Boston, Mass.

Applied and Environmental Microbiology, October 2006, p. 6578-6583, Vol. 72, No. 10
0099-2240/06/$08.00+0     doi:10.1128/AEM.00787-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.





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