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Cultivation of Mesophilic Soil Crenarchaeotes in Enrichment Cultures from Plant Roots

Holly M. Simon,^1* Courtney E. Jahn,¹ Luke T. Bergerud,^1, Marek K. Sliwinski,^1, Paul J. Weimer,^2,3 David K. Willis,^1,3 and Robert M. Goodman^1,4

Department of Plant Pathology,¹ Department of Bacteriology,² Gaylord Nelson Institute for Environmental Studies, University of Wisconsin—Madison, Madison, Wisconsin 53706,⁴ Agricultural Research Service, U.S. Department of Agriculture, Madison, Wisconsin 53706³

Received 10 November 2004/ Accepted 14 February 2005

Because archaea are generally associated with extreme environments, detection of nonthermophilic members belonging to the archaeal division Crenarchaeota over the last decade was unexpected; they are surprisingly ubiquitous and abundant in nonextreme marine and terrestrial habitats. Metabolic characterization of these nonthermophilic crenarchaeotes has been impeded by their intractability toward isolation and growth in culture. From studies employing a combination of cultivation and molecular phylogenetic techniques (PCR-single-strand conformation polymorphism, sequence analysis of 16S rRNA genes, fluorescence in situ hybridization, and real-time PCR), we present evidence here that one of the two dominant phylotypes of Crenarchaeota that colonizes the roots of tomato plants grown in soil from a Wisconsin field is selectively enriched in mixed cultures amended with root extract. Clones recovered from enrichment cultures were found to group phylogenetically with sequences from clade C1b.A1. This work corroborates and extends our recent findings, indicating that the diversity of the crenarchaeal soil assemblage is influenced by the rhizosphere and that mesophilic soil crenarchaeotes are found associated with plant roots, and provides the first evidence for growth of nonthermophilic crenarchaeotes in culture.

Present address: Human Genome Sciences, Rockville, MD 20850.

Present address: Department of Botany, University of Wisconsin—Madison, Madison, WI 53706.

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