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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,
Edward F.
DeLong,1,
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.

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

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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