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Parallel characterization of anaerobic toluene- and ethylbenzene-degrading microbial consortia by PCR-denaturing gradient gel electrophoresis, RNA-DNA membrane hybridization, and DNA microarray technologyA mesophilic toluene-degrading consortium (TDC) and an ethylbenzene-degrading consortium (EDC) were established under sulfate-reducing conditions. These consortia were first characterized by denaturing gradient gel electrophoresis (DGGE) fingerprinting of PCR-amplified 16S rRNA gene fragments, followed by sequencing. The sequences of the major bands (T-1 and E-2) belonging to TDC and EDC, respectively, were affiliated with the family Desulfobacteriaceae. Another major band from EDC (E-1) was related to an uncultured non-sulfate-reducing soil bacterium. Oligonucleotide probes specific for the 16S rRNAs of target organisms corresponding to T-1, E-1, and E-2 were designed, and hybridization conditions were optimized for two analytical formats, membrane and DNA microarray hybridization. Both formats were used to characterize the TDC and EDC, and the results of both were consistent with DGGE analysis. In order to assess the utility of the microarray format for analysis of environmental samples, oil-contaminated sediments from the coast of Kuwait were analyzed. The DNA microarray successfully detected bacterial nucleic acids from these samples, but probes targeting specific groups of sulfate-reducing bacteria did not give positive signals. The results of this study demonstrate the limitations and the potential utility of DNA microarrays for microbial community analysis.
Document ID
20040088245
Acquisition Source
Legacy CDMS
Document Type
Reprint (Version printed in journal)
Authors
Koizumi, Yoshikazu
(Graduate School of Science, Tokyo Metropolitan University 1-1 Minami-Ohsawa, Hachioji, Tokyo 192-0397, Japan)
Kelly, John J.
Nakagawa, Tatsunori
Urakawa, Hidetoshi
El-Fantroussi, Said
Al-Muzaini, Saleh
Fukui, Manabu
Urushigawa, Yoshikuni
Stahl, David A.
Date Acquired
August 21, 2013
Publication Date
July 1, 2002
Publication Information
Publication: Applied and environmental microbiology
Volume: 68
Issue: 7
ISSN: 0099-2240
Subject Category
Life Sciences (General)
Distribution Limits
Public
Copyright
Other
Keywords
Non-NASA Center
NASA Discipline Life Sciences Technologies

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