Species-specific detection of hydrocarbon-utilizing bacteria

Rapid detection and quantitative assessment of specific microbial species i n environmental samples is desirable for monitoring changes in ecosystems a nd for tracking natural or introduced microbial species during bioremediati on of contaminated sites. In the interests of developing rapid tests for hy drocarbon-degrading bacteria, species-specific PCR primer sets have been de veloped for Pseudomonas aeruginosa, Stentrophomonas (Xanthomonas) maltophil ia, and Serratia marescens. Highly variable regions of the 16S rRNA gene we re used to design these primer sets. The amplification products of these pr imer sets have been verified and validated with hemi-nested PCR and with li gase chain reaction (LCR) techniques, and have been applied to the analyses of environmental water samples. These species-specific primer sets were al so chosen to amplify in conjunction with a universal set of PCR primers cho sen from highly conserved neighboring sequences in the same gene. These mul tiplex or competitive PCR procedures enable testing with an internal marker and/or the quantitative estimation of the relative proportion of the micro bial community that any one of these species occupies. In addition, this un iversal PCR primer set amplified the same size amplicon from a wide spectru m of procaryotic and eucaryotic organisms and may have potential in earth b iota analyses. (C) 1999 Elsevier Science B.V. All rights reserved.