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Applied and Environmental Microbiology, August 1998, p. 3110-3113, Vol. 64, No. 8
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.
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

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