Publication Date:
2022-05-25
Description:
Author Posting. © The Author(s), 2009. This is the author's version of the work. It is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 75 (2009): 5797-5808, doi:10.1128/AEM.00298-09.
Description:
DNA sequence information has been increasingly used in ecological research on
microbial eukaryotes. Sequence-based approaches have included studies of the total
diversity of selected ecosystems, the autecology of ecologically relevant species, and the
identification and enumeration of species of interest to 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 partly a
consequence of the limited amount of sequence information presently available for many
free-living microbial eukaryotes, and partly the problematic nature 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 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
approximate species-level distinctions. The 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
ribosomal RNA (18S) gene sequences and partial gene sequences obtained from
GenBank for morphologically described protistan species. The program was tested using
environmental 18S data sets from two oceanic ecosystems. A total of 388 operational
taxonomic units were observed among 2,207 sequences obtained from samples collected
in the western North Atlantic and eastern North Pacific.
Description:
Support for this manuscript
was provided by National Science Foundation grants MCB-0732066, MCB-0703159 and
OCE-0550829 and a grant from the Gordon and Betty Moore Foundation.
Repository Name:
Woods Hole Open Access Server
Type:
Preprint
Format:
application/pdf
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