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Applied and Environmental Microbiology, April 2003, p. 2377-2382, Vol. 69, No. 4
0099-2240/03/$08.00+0     DOI: 10.1128/AEM.69.4.2377-2382.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.

Direct Profiling of Environmental Microbial Populations by Thermal Dissociation Analysis of Native rRNAs Hybridized to Oligonucleotide Microarrays

Said El Fantroussi,1,{dagger} Hidetoshi Urakawa,1,{ddagger} Anne E. Bernhard,1 John J. Kelly,2 Peter A. Noble,1 H. Smidt,1,§ G. M. Yershov,3 and David A. Stahl1*

Department of Civil and Environmental Engineering, University of Washington, Seattle, Washington 98195,1 Department of Biology, Loyola University Chicago, Chicago, Illinois 60626,2 Biochip Technology Center, Argonne National Laboratory, Argonne, Illinois 604393

Received 29 July 2002/ Accepted 4 December 2002

Oligonucleotide microarrays were used to profile directly extracted rRNA from environmental microbial populations without PCR amplification. In our initial inspection of two distinct estuarine study sites, the hybridization patterns were reproducible and varied between estuarine sediments of differing salinities. The determination of a thermal dissociation curve (i.e., melting profile) for each probe-target duplex provided information on hybridization specificity, which is essential for confirming adequate discrimination between target and nontarget sequences.

* Corresponding author. Mailing address: Civil and Environmental Engineering, University of Washington, 302 More Hall, Box 352700, Seattle, WA 98195. Phone: (206) 685-3464. Fax: (206) 685-9185. E-mail: dastahl{at}u.washington.edu.

{dagger} Present address: Unit of Bioengineering, University of Louvain, B-1348 Louvain-la-Neuve, Belgium.

{ddagger} Present address: National Institute for Environmental Studies, Tsukuba-Shi, Ibaraki 305-8506, Japan.

§ Present address: Laboratory of Microbiology, Wageningen University, 6703 CT Wageningen, The Netherlands.

Applied and Environmental Microbiology, April 2003, p. 2377-2382, Vol. 69, No. 4
0099-2240/03/$08.00+0     DOI: 10.1128/AEM.69.4.2377-2382.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.



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