Development and evaluation of a quantitative real-time PCR assay for the detection of saltwater Bacteriovorax

Environ Microbiol. 2008 Oct;10(10):2515-26. doi: 10.1111/j.1462-2920.2008.01676.x. Epub 2008 Jul 9.

Abstract

Bdellovibrio-and-like-organisms (BALOs) are small, Gram-negative predatory bacteria with the ability to prey on a wide variety of Gram-negative bacteria, and which may have a significant ecological role. Detection and quantification of BALOs by culture-dependent methods are complicated, as their reproduction is dependent upon the use of appropriate prey. For this reason, a sensitive and specific molecular detection method was developed. This paper describes a SYBR Green-based real-time PCR (quantitative PCR) assay that combines the use of a specific 16S rDNA primer with a universal primer for quantitative detection of halophilic Bacteriovorax. 16S rDNA sequences from 174 BALO strains, including both halophilic and freshwater, were aligned and a consensus region was identified that is unique to the halophilic Bacteriovorax strains. A specific primer was designed and analysed for specificity. The PCR conditions were optimized to obtain high specificity and sensitivity. The specificity was evaluated by testing a series of halophilic Bacteriovorax samples and prey specimens, including both pure cultures and environmental saltwater samples. A linear and reproducible standard curve was obtained over a range of 10(1)-10(6) gene copies and the detection limit was determined to be 10 copies of 16S rRNA gene per reaction. The results presented in this study validate the procedure as a rapid, sensitive and accurate method for the detection and quantification of halophilic Bacteriovorax in environmental saltwater samples. It is anticipated that this culture-independent method will facilitate future investigations of the distribution and population dynamics of these interesting predatory bacteria, leading to a better understanding of their ecological role.

Publication types

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

MeSH terms

  • Benzothiazoles
  • DNA Primers / genetics
  • DNA, Bacterial / genetics
  • DNA, Ribosomal / genetics
  • Deltaproteobacteria / isolation & purification*
  • Diamines
  • Organic Chemicals / metabolism
  • Polymerase Chain Reaction / methods*
  • Quinolines
  • RNA, Ribosomal, 16S / genetics
  • Reproducibility of Results
  • Sensitivity and Specificity
  • Water Microbiology*

Substances

  • Benzothiazoles
  • DNA Primers
  • DNA, Bacterial
  • DNA, Ribosomal
  • Diamines
  • Organic Chemicals
  • Quinolines
  • RNA, Ribosomal, 16S
  • SYBR Green I