An rpoD-based PCR procedure for the identification of Pseudomonas species and for their detection in environmental samples

Molecular and Cellular Probes

Volumn 23, Issue 3-4, 2009, Pages 140-147

  Mulet, Magdalena ^a   Bennasar, Antonio ^a   Lalucat, Jorge ^a,b   García Valdés, Elena ^a,b  

^a UNIVERSITAT DE LES ILLES BALEARS   (Spain)

^b INSTITUTO MEDITERRÁNEO DE ESTUDIOS AVANZADOS   (Spain)

Author keywords

PCR; Pseudomonas detection; rpoD; Species identification

Indexed keywords

BACTERIAL PROTEIN; DNA 16S; DNA POLYMERASE; NUCLEOTIDE; PRIMER DNA; RPOD PROTEIN; UNCLASSIFIED DRUG;

AMPLICON; ARTICLE; BACTERIAL STRAIN; BACTERIUM DETECTION; BACTERIUM IDENTIFICATION; DNA SEQUENCE; ENVIRONMENT; GAMMAPROTEOBACTERIA; GENE AMPLIFICATION; GENE CLUSTER; GENE SEQUENCE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PSEUDOMONAS; UNINDEXED SEQUENCE;

DNA PRIMERS; DNA, RIBOSOMAL; DNA, RIBOSOMAL SPACER; PHYLOGENY; POLYMERASE CHAIN REACTION; PSEUDOMONAS; SIGMA FACTOR;

GAMMAPROTEOBACTERIA; PSEUDOMONAS;

EID: 67349145928     PISSN: 08908508     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mcp.2009.02.001     Document Type: Article

References (17)

1. Bennasar A., Guasp C., and Lalucat J. Molecular methods for the detection and identification of Pseudomonas stutzeri in pure culture and environmental samples. Microb Ecol 35 (1998) 22-33
2. Burton Z., Burgess R.R., Lin J., Moore D., Holder S., and Gross C.A. The nucleotide sequence of the cloned rpoD gene for the RNA polymerase sigma subunit from E. coli K12. Nucleic Acids Res 9 (1981) 2889-2903
3. Case R.J., Boucher Y., Dahllo I., Holmström C., Doolittle W.F., and Kjellebergl S. Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies. Appl Environ Microbiol 73 (2007) 278-288
4. Chun J., Lee J.-H., Jung Y., Kim M., Kim S., Kim B.K., et al. EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol 7 (2007) 2259-2261
5. Cladera A.M., Bennasar A., Barceló M., Lalucat J., and García-Valdés E. Comparative genetic diversity of Pseudomonas stutzeri genomovars, clonal structure, and phylogeny of the species. J Bacteriol 186 (2004) 5239-5248
6. Felsenstein J. PHYLIP - phylogeny inference package, version 3.63. Distributed by the author (2004), Department of Genome Sciences, University of Washington, Seattle
7. Ginard M., Lalucat J., Tümmler B., and Römling U. Genome organization of Pseudomonas stutzeri and resulting taxonomic and evolutionary considerations. Int J Syst Bacteriol 47 (1997) 132-143
8. Guasp C., Moore E.R.B., Lalucat J., and Bennasar A. Utility of internally-transcribed 16S-23S rDNA spacer regions for the definition of Pseudomonas stutzeri genomovars and other Pseudomonas species. Int J Syst Evol Microbiol 50 (2000) 1629-1639
9. Jukes T.H., and Cantor C.R. Evolution of protein molecules. In: Munro H.N. (Ed). Mammalian protein metabolism (1969), Academic Press, Inc., New York, NY 21-132
10. Klappenbach J.A., Saxman P.R., Cole J.R., and Schmidt T.M. rrndb: the ribosomal RNA operon copy number database. Nucleic Acids Res 29 (2001) 181-184
11. Locatelli L., Tarnawski S., Hamelin J., Rossi P., Aragno M., and Fromin N. Specific PCR amplification for the genus Pseudomonas targeting the 3′ half of 16S rDNA and the whole 16S-23S rDNA spacer. Syst Appl Microbiol 25 (2002) 220-227
12. Mulet M., Gomila M., Gruffaz C., Meyer J.-M., Palleroni N.J., Lalucat J., et al. Phylogenetic analysis and siderotyping as useful tools in the taxonomy of Pseudomonas stutzeri: description of a novel genomovar. Int J Syst Evol Microbiol 58 (2008) 2309-2315
13. Tayeb L.A., Ageron E., Grimont F., and Grimont P.A.D. Molecular phylogeny of the genus Pseudomonas based on rpoB sequences and application for the identification of isolates. Res Microbiol 156 (2005) 763-773
14. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., and Higgins D.G. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25 (1997) 4876-4882
15. Widmer F., Seidler R.J., Gillevet P.M., Watrud L.S., and DiGiovanni G.D. A highly selective PCR protocol for detecting 16S rRNA genes of the genus Pseudomonas (sensu stricto) in environmental samples. Appl Environ Microbiol 64 (1998) 2545-2553
16. Yamamoto S., and Harayama S. Phylogenetic relationships of Pseudomonas putida strains deduced from the nucleotide sequences of gyrB, rpoD and 16S rRNA genes. Int J Syst Bacteriol 48 (1998) 813-819
17. Yamamoto S., Ksai H., Arnold D.L., Jackson R.W., Vivian A., and Harayama S. Phylogeny of the genus Pseudomonas: intrageneric structure reconstructed from the nucleotide sequences of gyrB and rpoD genes. Microbiology 146 (2000) 2385-2394