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Applied and Environmental Microbiology, September 2009, p. 5797-5808, Vol. 75, No. 18
0099-2240/09/$08.00+0     doi:10.1128/AEM.00298-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

Defining DNA-Based Operational Taxonomic Units for Microbial-Eukaryote Ecology{triangledown}

David A. Caron,1* Peter D. Countway,1 Pratik Savai,1 Rebecca J. Gast,2 Astrid Schnetzer,1 Stefanie D. Moorthi,1,{dagger} Mark R. Dennett,2 Dawn M. Moran,2 and Adriane C. Jones1

Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, California 90089-0371,1 Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 025432

Received 5 February 2009/ Accepted 6 July 2009

DNA sequence information has increasingly been used in ecological research on microbial eukaryotes. Sequence-based approaches have included studies of the total diversity of selected ecosystems, studies of the autecology of ecologically relevant species, and identification and enumeration of species of interest for human health. It is still uncommon, however, to delineate protistan species based on their genetic signatures. The reluctance to assign species-level designations based on DNA sequences is in part a consequence of the limited amount of sequence information presently available for many free-living microbial eukaryotes and in part a consequence of the problematic nature of and debate surrounding the microbial species concept. Despite the difficulties inherent in assigning species names to DNA sequences, there is a growing need to attach meaning to the burgeoning amount of sequence information entering the literature, and there is a growing desire to apply this information in ecological studies. We describe a computer-based tool that assigns DNA sequences from environmental databases to operational taxonomic units at approximately species-level distinctions. This approach provides a practical method for ecological studies of microbial eukaryotes (primarily protists) by enabling semiautomated analysis of large numbers of samples spanning great taxonomic breadth. Derivation of the algorithm was based on an analysis of complete small-subunit (18S) rRNA gene sequences and partial gene sequences obtained from the GenBank database for morphologically described protistan species. The program was tested using environmental 18S rRNA data sets for two oceanic ecosystems. A total of 388 operational taxonomic units were observed for 2,207 sequences obtained from samples collected in the western North Atlantic and eastern North Pacific oceans.

* Corresponding author. Mailing address: Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA 90089-0371. Phone: (2143) 740-0203. Fax: (2130) 740-8123. E-mail: dcaron{at}usc.edu

{triangledown} Published ahead of print on 10 July 2009.

{dagger} Present address: Carl-von-Ossietzky Universität Oldenburg, ICBM-Terramare, Schleusenstr. 1, D-26382 Wilhelmshaven, Germany.

Applied and Environmental Microbiology, September 2009, p. 5797-5808, Vol. 75, No. 18
0099-2240/09/$08.00+0     doi:10.1128/AEM.00298-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.





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