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Journal of Bacteriology, October 1998, p. 5003-5009, Vol. 180, No. 19
0021-9193/98/$04.00+0
Copyright © 1998, American Society for Microbiology. All rights reserved.

Genomic Analysis Reveals Chromosomal Variation in Natural Populations of the Uncultured Psychrophilic Archaeon Cenarchaeum symbiosum

Christa Schleper,1,dagger Edward F. DeLong,1,Dagger Christina M. Preston,1 Robert A. Feldman,2 Ke-Ying Wu,1 and Ronald V. Swanson2,*

Marine Science Institute, University of California, Santa Barbara, California 93106,1 and Diversa Corporation, San Diego, California 921212

Received 27 May 1998/Accepted 21 July 1998

Molecular phylogenetic surveys have recently revealed an ecologically widespread crenarchaeal group that inhabits cold and temperate terrestrial and marine environments. To date these organisms have resisted isolation in pure culture, and so their phenotypic and genotypic characteristics remain largely unknown. To characterize these archaea, and to extend methodological approaches for characterizing uncultivated microorganisms, we initiated genomic analyses of the nonthermophilic crenarchaeote Cenarchaeum symbiosum found living in association with a marine sponge, Axinella mexicana. Complex DNA libraries derived from the host-symbiont population yielded several large clones containing the ribosomal operon from C. symbiosum. Unexpectedly, cloning and sequence analysis revealed the presence of two closely related variants that were consistently found in the majority of host individuals analyzed. Homologous regions from the two variants were sequenced and compared in detail. The variants exhibit >99.2% sequence identity in both small- and large-subunit rRNA genes and they contain homologous protein-encoding genes in identical order and orientation over a 28-kbp overlapping region. Our study not only indicates the potential for characterizing uncultivated prokaryotes by genome sequencing but also identifies the primary complication inherent in the approach: the widespread genomic microheterogeneity in naturally occurring prokaryotic populations.

* Corresponding author. Mailing address: Diversa Corporation, 10665 Sorrento Valley Rd., San Diego, CA 92121. Phone: (619) 623-5156. Fax: (619) 623-5120. E-mail: rswanson{at}diversa.com.

dagger Present address: Institute for Microbiology, Technical University of Darmstadt, 64287 Darmstadt, Germany.

Dagger Present address: Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039.

Journal of Bacteriology, October 1998, p. 5003-5009, Vol. 180, No. 19
0021-9193/98/$04.00+0
Copyright © 1998, American Society for Microbiology. All rights reserved.


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