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Applied and Environmental Microbiology, January 2002, p. 335-345, Vol. 68, No. 1
0099-2240/02/$04.00+0     DOI: 10.1128/AEM.68.1.335-345.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.

Comparative Genomic Analysis of Archaeal Genotypic Variants in a Single Population and in Two Different Oceanic Provinces

Oded Béjà,1,{dagger} Eugene V. Koonin,2 L. Aravind,2 Lance T. Taylor,1 Heidi Seitz,3,{ddagger} Jefferey L. Stein,4,§ Daniel C. Bensen,4,§ Robert A. Feldman,4,|| Ronald V. Swanson,4,# and Edward F. DeLong1*

Monterey Bay Aquarium Research Institute, Moss Landing, California 95039,1 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894,2 Marine Science Institute, University of California, Santa Barbara, California 93106,3 Diversa Corporation, San Diego, California 921214

Received 30 May 2001/ Accepted 1 October 2001

Planktonic crenarchaeotes are present in high abundance in Antarctic winter surface waters, and they also make up a large proportion of total cell numbers throughout deep ocean waters. To better characterize these uncultivated marine crenarchaeotes, we analyzed large genome fragments from individuals recovered from a single Antarctic picoplankton population and compared them to those from a representative obtained from deeper waters of the temperate North Pacific. Sequencing and analysis of the entire DNA insert from one Antarctic marine archaeon (fosmid 74A4) revealed differences in genome structure and content between Antarctic surface water and temperate deepwater archaea. Analysis of the predicted gene products encoded by the 74A4 sequence and those derived from a temperate, deepwater planktonic crenarchaeote (fosmid 4B7) revealed many typical archaeal proteins but also several proteins that so far have not been detected in archaea. The unique fraction of marine archaeal genes included, among others, those for a predicted RNA-binding protein of the bacterial cold shock family and a eukaryote-type Zn finger protein. Comparison of closely related archaea originating from a single population revealed significant genomic divergence that was not evident from 16S rRNA sequence variation. The data suggest that considerable functional diversity may exist within single populations of coexisting microbial strains, even those with identical 16S rRNA sequences. Our results also demonstrate that genomic approaches can provide high-resolution information relevant to microbial population genetics, ecology, and evolution, even for microbes that have not yet been cultivated.

* Corresponding author. Mailing address: Monterey Bay Aquarium Research Institute, 7700 Sandholdt Rd., P.O. Box 628, Moss Landing, CA 95039-0628. Phone: (831) 775-1843. Fax: (831) 775-1646. E-mail: delong{at}mbari.org.

{dagger} Present address: Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel.

{ddagger} Present address: Institut für Mikrobiologie und Weinforschung, Universität Mainz, 55099 Mainz, Germany.

§ Present address: Quorex Pharmaceuticals Inc., Carlsbad, CA 92009.

|| Present address: Molecular Dynamics Inc., Amersham Pharmacia Biotech, Sunnyvale, CA 94086.

# Present address: Syrrx Inc., San Diego, CA 92121.

Applied and Environmental Microbiology, January 2002, p. 335-345, Vol. 68, No. 1
0099-2240/02/$04.00+0     DOI: 10.1128/AEM.68.1.335-345.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.



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