Combined use of 16S ribosomal DNA and 16S rRNA to study the bacterial community of polychlorinated biphenyl-polluted soil

The bacterial diversity assessed from clone libraries prepared from rRNA (t wo libraries) and ribosomal DNA (rDNA) (one library) from polychlorinated b iphenyl (PCB)-polluted soil has been analyzed. A good correspondence of the community composition found in the two types of library was observed. Near ly 29% of the cloned sequences in the rDNA library were identical to sequen ces 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 clone s]) represented in both types of libraries. Some of those phylogenetic grou ps, mostly represented by a single (or pair) of cloned sequence type(s), we re observed in only one of the types of library. An important difference be tween the libraries was the lack of clones representative of the Actinobact eria in the rDNA library. The PCB-polluted soil exhibited a high bacterial diversity which included representatives of two novel lineages. The apparen t abundance of bacteria affiliated to the beta-subclass of the Proteobacter ia, and to the genus Burkholderia in particular, was confirmed by fluoresce nce in situ hybridization analysis. The possible influence on apparent dive rsity of low template concentrations was assessed by dilution of the RNA te mplate prior to amplification by reverse transcription-PCR. Although differ ences in the composition of the two rRNA libraries obtained from high and l ow RNA concentrations were observed, the main components of the bacterial c ommunity were represented in both libraries, and therefore their detection was not compromised by the lower concentrations of template used in this st udy.