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Applied and Environmental Microbiology, August 1998, p. 3110-3113, Vol. 64, No. 8
0099-2240/98/$04.00+0
Copyright © 1998, American Society for Microbiology. All rights reserved.

Specific Ribosomal DNA Sequences from Diverse Environmental Settings Correlate with Experimental Contaminants

Michael A. Tanner, Brett M. Goebel,dagger Michael A. Dojka, and Norman R. Pace*

Departments of Plant and Microbial Biology and Molecular and Cell Biology, University of California, Berkeley, California 94720-3102

Received 23 April 1998/Accepted 10 June 1998

Phylogenetic analysis of 16S ribosomal DNA (rDNA) clones obtained by PCR from uncultured bacteria inhabiting a wide range of environments has increased our knowledge of bacterial diversity. One possible problem in the assessment of bacterial diversity based on sequence information is that PCR is exquisitely sensitive to contaminating 16S rDNA. This raises the possibility that some putative environmental rRNA sequences in fact correspond to contaminant sequences. To document potential contaminants, we cloned and sequenced PCR-amplified 16S rDNA fragments obtained at low levels in the absence of added template DNA. 16S rDNA sequences closely related to the genera Duganella (formerly Zoogloea), Acinetobacter, Stenotrophomonas, Escherichia, Leptothrix, and Herbaspirillum were identified in contaminant libraries and in clone libraries from diverse, generally low-biomass habitats. The rRNA sequences detected possibly are common contaminants in reagents used to prepare genomic DNA. Consequently, their detection in processed environmental samples may not reflect environmentally relevant organisms.

* Corresponding author. Mailing address: Departments of Plant and Microbial Biology and Molecular and Cell Biology, 111 Koshland Hall, University of California, Berkeley, CA 94720-3102. Phone: (510) 643-2571. Fax: (510) 642-4995. E-mail: nrpace{at}nature.berkeley.edu.

dagger Present address: Australian Magnesium Corporation, Toowong, Queensland, 4066 Australia.

Applied and Environmental Microbiology, August 1998, p. 3110-3113, Vol. 64, No. 8
0099-2240/98/$04.00+0
Copyright © 1998, American Society for Microbiology. All rights reserved.


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