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Applied and Environmental Microbiology, September 2008, p. 5422-5428, Vol. 74, No. 17
0099-2240/08/$08.00+0     doi:10.1128/AEM.00410-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Novelty and Uniqueness Patterns of Rare Members of the Soil Biosphere ^,

Department of Microbiology and Molecular Genetics, Oklahoma State University, 1110 S. Innovation Way, Stillwater, Oklahoma 74074,¹ Department of Botany and Microbiology and Institute for Energy and The Environment, University of Oklahoma, 770 Van Vleet Oval, Norman, Oklahoma 73019,² Department of Chemistry and Biochemistry and the Advanced Center for Genome Technology, University of Oklahoma, 101 David L. Boren Blvd., Norman, Oklahoma 73019,³ Department of Microbiology, University of Massachusetts, 639 North Pleasant Street, Amherst, Massachusetts 01003,⁴ Microbiology Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington 99354⁵

Received 18 February 2008/ Accepted 26 June 2008

Soil bacterial communities typically exhibit a distribution pattern in which most bacterial species are present in low abundance. Due to the relatively small size of most culture-independent sequencing surveys, a detailed phylogenetic analysis of rare members of the community is lacking. To gain access to the rarely sampled soil biosphere, we analyzed a data set of 13,001 near-full-length 16S rRNA gene clones derived from an undisturbed tall grass prairie soil in central Oklahoma. Rare members of the soil bacterial community (empirically defined at two different abundance cutoffs) represented 18.1 to 37.1% of the total number of clones in the data set and were, on average, less similar to their closest relatives in public databases when compared to more abundant members of the community. Detailed phylogenetic analyses indicated that members of the soil rare biosphere either belonged to novel bacterial lineages (members of five novel bacterial phyla identified in the data set, as well as members of multiple novel lineages within previously described phyla or candidate phyla), to lineages that are prevalent in other environments but rarely encountered in soil, or were close relatives to more abundant taxa in the data set. While a fraction of the rare community was closely related to more abundant taxonomic groups in the data set, a significant portion of the rare biosphere represented evolutionarily distinct lineages at various taxonomic cutoffs. We reason that these novelty and uniqueness patterns provide clues regarding the origins and potential ecological roles of members of the soil's rare biosphere.

Published ahead of print on 7 July 2008.

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