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Applied and Environmental Microbiology, April 2001, p. 1874-1884, Vol. 67, No. 4
0099-2240/01/$04.00+0   DOI: 10.1128/AEM.67.4.1874-1884.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.

Combined Use of 16S Ribosomal DNA and 16S rRNA To Study the Bacterial Community of Polychlorinated Biphenyl-Polluted Soil

Balbina Nogales,1,2,* Edward R. B. Moore,1 Enrique Llobet-Brossa,3 Ramon Rossello-Mora,3,dagger Rudolf Amann,3 and Kenneth N. Timmis1,2

Division of Microbiology, GBF-National Research Centre for Biotechnology, Braunschweig,1 and Molecular Ecology Group, Max-Planck-Institut für Marine Mikrobiologie, Bremen,3 Germany, and Department of Biological Sciences, University of Essex, Colchester, United Kingdom2

Received 18 September 2000/Accepted 9 January 2001

The bacterial diversity assessed from clone libraries prepared from rRNA (two libraries) and ribosomal DNA (rDNA) (one library) from polychlorinated biphenyl (PCB)-polluted soil has been analyzed. A good correspondence of the community composition found in the two types of library was observed. Nearly 29% of the cloned sequences in the rDNA library were identical to sequences in the rRNA libraries. More than 60% of the total cloned sequence types analyzed were grouped in phylogenetic groups (a clone group with sequence similarity higher than 97% [98% for Burkholderia and Pseudomonas-type clones]) represented in both types of libraries. Some of those phylogenetic groups, mostly represented by a single (or pair) of cloned sequence type(s), were observed in only one of the types of library. An important difference between the libraries was the lack of clones representative of the Actinobacteria in the rDNA library. The PCB-polluted soil exhibited a high bacterial diversity which included representatives of two novel lineages. The apparent abundance of bacteria affiliated to the beta-subclass of the Proteobacteria, and to the genus Burkholderia in particular, was confirmed by fluorescence in situ hybridization analysis. The possible influence on apparent diversity of low template concentrations was assessed by dilution of the RNA template prior to amplification by reverse transcription-PCR. Although differences in the composition of the two rRNA libraries obtained from high and low RNA concentrations were observed, the main components of the bacterial community were represented in both libraries, and therefore their detection was not compromised by the lower concentrations of template used in this study.

* Corresponding author. Mailing address: Departament of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom. Phone: 44-1206-872547. Fax: 44-1206 872592. E-mail: bnogales{at}essex.ac.uk.

dagger Present address: Area de Microbiologia, Department de Biologia, Universitat de les Illes Balears, Palma de Mallorca, Spain.

Applied and Environmental Microbiology, April 2001, p. 1874-1884, Vol. 67, No. 4
0099-2240/01/$04.00+0   DOI: 10.1128/AEM.67.4.1874-1884.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.


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