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Applied and Environmental Microbiology, January 2002, p. 201-210, Vol. 68, No. 1
0099-2240/02/$04.00+0     DOI: 10.1128/AEM.68.1.201-210.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.

New Degenerate Cytophaga-Flexibacter-Bacteroides-Specific 16S Ribosomal DNA-Targeted Oligonucleotide Probes Reveal High Bacterial Diversity in River Taff Epilithon

Louise A. O’Sullivan, Andrew J. Weightman, and John C. Fry*

Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3TL, United Kingdom

Received 11 July 2001/ Accepted 5 September 2001

River microbial communities play an important role in global nutrient cycles, and aggregated bacteria such as those in epilithic biofilms may be major contributors. In this study the bacterial diversity of River Taff epilithon in South Wales was investigated. A 16S ribosomal DNA (rDNA) clone library was constructed and analyzed by partial sequencing of 76 of 347 clones and hybridization with taxon-specific probes. The epilithon was found to be very diverse, with an estimated 59.6% of the bacterial populations not accounted for by these clones. Members of the Cytophaga-Flexibacter-Bacteroides division (CFBs) were most abundant in the library, representing 25% of clones, followed by members of the {alpha} subdivision of the division Proteobacteria ({alpha}-Proteobacteria), {gamma}-Proteobacteria, gram-positive bacteria, Cyanobacteria, ß-Proteobacteria, {delta}-Proteobacteria, and the Prosthecobacter group. This study concentrated on the epilithic CFB populations, and a new set of degenerate 16S rDNA probes was developed to enhance their detection, namely, CFB560, CFB562, and CFB376. The commonly used probe CF319a/b may frequently lead to the underestimation of CFB populations in environmental studies, because it does not fully detect members of the division. CFB560 had exact matches to 95.6% of CFBs listed in the Ribosomal Database Project (release 8.0) small-subunit phylogenetic trees, compared to 60% for CF319a/b. The CFB probes detected 66 of 347 epilithon TAF clones, and 60 of these were partially sequenced. They affiliated with the RDP-designated groups Cytophaga, Sphingobacterium, Lewinella, and Cytophaga aurantiaca. CFB560 and CF319a/b detected 94% (62 of 66) and 48.5% (32 of 66) of clones, respectively, and therefore CFB560 is recommended for future use. Probe design in this study illustrated that multiple degenerate positions can greatly increase target range without adversely effecting specificity or experimental performance.

* Corresponding author. Mailing address: Cardiff School of Biosciences, Cardiff University, P.O. Box 915, Main Building, Park Pl., Cardiff CF10 3TL, United Kingdom. Phone: 44 029 20 874190. Fax: 44 029 20 874305. E-mail: Fry{at}Cardiff.ac.uk.

Applied and Environmental Microbiology, January 2002, p. 201-210, Vol. 68, No. 1
0099-2240/02/$04.00+0     DOI: 10.1128/AEM.68.1.201-210.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.



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