Species-specific detection of hydrocarbon-utilizing bacteria

J Microbiol Methods. 1999 Dec;39(1):59-78. doi: 10.1016/s0167-7012(99)00098-6.


Rapid detection and quantitative assessment of specific microbial species in environmental samples is desirable for monitoring changes in ecosystems and for tracking natural or introduced microbial species during bioremediation of contaminated sites. In the interests of developing rapid tests for hydrocarbon-degrading bacteria, species-specific PCR primer sets have been developed for Pseudomonas aeruginosa, Stentrophomonas (Xanthomonas) maltophilia, and Serratia marsescens. Highly variable regions of the 16S rRNA gene were used to design these primer sets. The amplification products of these primer sets have been verified and validated with hemi-nested PCR and with ligase chain reaction (LCR) techniques, and have been applied to the analyses of environmental water samples. These species-specific primer sets were also chosen to amplify in conjunction with a universal set of PCR primers chosen from highly conserved neighboring sequences in the same gene. These multiplex or competitive PCR procedures enable testing with an internal marker and/or the quantitative estimation of the relative proportion of the microbial community that any one of these species occupies. In addition, this universal PCR primer set amplified the same size amplicon from a wide spectrum of procaryotic and eucaryotic organisms and may have potential in earth biota analyses.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Base Sequence
  • DNA, Bacterial / analysis
  • DNA, Ribosomal / analysis
  • Hydrocarbons / metabolism
  • Molecular Sequence Data
  • Polymerase Chain Reaction
  • Pseudomonas aeruginosa / classification*
  • Pseudomonas aeruginosa / metabolism
  • RNA, Ribosomal, 16S / analysis*
  • Random Amplified Polymorphic DNA Technique
  • Sequence Alignment
  • Serratia marcescens / classification*
  • Serratia marcescens / metabolism
  • Species Specificity
  • Stenotrophomonas maltophilia / classification*
  • Stenotrophomonas maltophilia / metabolism
  • Water Microbiology*


  • DNA, Bacterial
  • DNA, Ribosomal
  • Hydrocarbons
  • RNA, Ribosomal, 16S