This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrowReprints and Permissions
Right arrow Copyright Information
Right arrow Books from ASM Press
Right arrow MicrobeWorld
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Schleper, C.
Right arrow Articles by Swanson, R. V.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Schleper, C.
Right arrow Articles by Swanson, R. V.

 Previous Article  |  Next Article 

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.


This article has been cited by other articles:

  • Grzymski, J. J., Murray, A. E., Campbell, B. J., Kaplarevic, M., Gao, G. R., Lee, C., Daniel, R., Ghadiri, A., Feldman, R. A., Cary, S. C. (2008). Metagenome analysis of an extreme microbial symbiosis reveals eurythermal adaptation and metabolic flexibility. Proc. Natl. Acad. Sci. USA 105: 17516-17521 [Abstract] [Full Text]  
  • Taylor, M. W., Radax, R., Steger, D., Wagner, M. (2007). Sponge-Associated Microorganisms: Evolution, Ecology, and Biotechnological Potential. Microbiol. Mol. Biol. Rev. 71: 295-347 [Abstract] [Full Text]  
  • Konstantinidis, K. T, Ramette, A., Tiedje, J. M (2006). The bacterial species definition in the genomic era. Phil Trans R Soc B 361: 1929-1940 [Abstract] [Full Text]  
  • Hallam, S. J., Konstantinidis, K. T., Putnam, N., Schleper, C., Watanabe, Y.-i., Sugahara, J., Preston, C., de la Torre, J., Richardson, P. M., DeLong, E. F. (2006). Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum. Proc. Natl. Acad. Sci. USA 103: 18296-18301 [Abstract] [Full Text]  
  • Grzymski, J. J., Carter, B. J., DeLong, E. F., Feldman, R. A., Ghadiri, A., Murray, A. E. (2006). Comparative Genomics of DNA Fragments from Six Antarctic Marine Planktonic Bacteria. Appl. Environ. Microbiol. 72: 1532-1541 [Abstract] [Full Text]  
  • Schirmer, A., Gadkari, R., Reeves, C. D., Ibrahim, F., DeLong, E. F., Hutchinson, C. R. (2005). Metagenomic Analysis Reveals Diverse Polyketide Synthase Gene Clusters in Microorganisms Associated with the Marine Sponge Discodermia dissoluta. Appl. Environ. Microbiol. 71: 4840-4849 [Abstract] [Full Text]  
  • Cubonova, L., Sandman, K., Hallam, S. J., DeLong, E. F., Reeve, J. N. (2005). Histones in Crenarchaea. J. Bacteriol. 187: 5482-5485 [Abstract] [Full Text]  
  • Whitaker, R. J., Banfield, J. F. (2005). Population Dynamics Through the Lens of Extreme Environments. Reviews in Mineralogy and Geochemistry 59: 259-277 [Full Text]  
  • Handelsman, J. (2004). Metagenomics: Application of Genomics to Uncultured Microorganisms. Microbiol. Mol. Biol. Rev. 68: 669-685 [Abstract] [Full Text]  
  • Schmeisser, C., Stockigt, C., Raasch, C., Wingender, J., Timmis, K. N., Wenderoth, D. F., Flemming, H.-C., Liesegang, H., Schmitz, R. A., Jaeger, K.-E., Streit, W. R. (2003). Metagenome Survey of Biofilms in Drinking-Water Networks. Appl. Environ. Microbiol. 69: 7298-7309 [Abstract] [Full Text]  
  • Beja, O., Koonin, E. V., Aravind, L., Taylor, L. T., Seitz, H., Stein, J. L., Bensen, D. C., Feldman, R. A., Swanson, R. V., DeLong, E. F. (2002). Comparative Genomic Analysis of Archaeal Genotypic Variants in a Single Population and in Two Different Oceanic Provinces. Appl. Environ. Microbiol. 68: 335-345 [Abstract] [Full Text]  
  • Kähler, M., Antranikian, G. (2000). Cloning and Characterization of a Family B DNA Polymerase from the Hyperthermophilic Crenarchaeon Pyrobaculum islandicum. J. Bacteriol. 182: 655-663 [Abstract] [Full Text]  
  • DeLong, E. F., Taylor, L. T., Marsh, T. L., Preston, C. M. (1999). Visualization and Enumeration of Marine Planktonic Archaea and Bacteria by Using Polyribonucleotide Probes and Fluorescent In Situ Hybridization. Appl. Environ. Microbiol. 65: 5554-5563 [Abstract] [Full Text]  
  • Vetriani, C., Jannasch, H. W., MacGregor, B. J., Stahl, D. A., Reysenbach, A.-L. (1999). Population Structure and Phylogenetic Characterization of Marine Benthic Archaea in Deep-Sea Sediments. Appl. Environ. Microbiol. 65: 4375-4384 [Abstract] [Full Text]  


Copyright © 2009 by the American Society for Microbiology.   For an alternate route to Journals.ASM.org, visit: http://intl-journals.asm.org | More Info»