OprF polymorphism as a marker of ecological niche in Pseudomonas

Environmental Microbiology

Volumn 8, Issue 9, 2006, Pages 1544-1551

  Bodilis, Josselin ^a,b,d   Hedde, Mickaël ^c   Orange, Nicole ^a   Barray, Sylvie ^a,b  

^a UNIVERSITÉ DE ROUEN   (France)

^b UNIVERSITÉ DE ROUEN   (France)

^c UNIVERSITÉ DE ROUEN   (France)

^d DEPARTMENT OF PLANT SYSTEMS BIOLOGY   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

OUTER MEMBRANE PROTEIN;

ARTICLE; CLASSIFICATION; ECOSYSTEM; GENETIC POLYMORPHISM; GENETIC SELECTION; GENETICS; MICROBIOLOGY; MOLECULAR EVOLUTION; PSEUDOMONAS;

BACTERIAL OUTER MEMBRANE PROTEINS; ECOSYSTEM; EVOLUTION, MOLECULAR; POLYMORPHISM, GENETIC; PSEUDOMONAS; SELECTION (GENETICS); SELECTION, GENETIC; SOIL MICROBIOLOGY;

LINUM USITATISSIMUM; PSEUDOMONAS; PSEUDOMONAS FLUORESCENS; TRITICUM AESTIVUM;

EID: 33746712371     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2006.01045.x     Document Type: Article

References (57)

1. Aagot, N., Nybroe, O., Nielsen, P., and Johnsen, K. (2001) An altered Pseudomonas diversity is recovered from soil by using nutrient-poor Pseudomonas-selective soil extract media. Appl Environ Microbiol 67: 5233-5239.
2. AFES (1998) A Sound Reference Basis for Soils: the Réfé rential Pédologique. Paris, France: INRA Editions.
3. Ait Tayeb, L., Ageron, E., Grimont, F., and Grimont, P.A.D. (2005) Molecular phylogeny of the genus Pseudomonas based on rpoB sequences and application for the identification of isolates. Res Microbiol 156: 763-773.
4. Alonso, A., Rojo, F., and Martinez, J. (1999) Environmental and clinical isolates of Pseudomonas aeruginosa show pathogenic and biodegradative properties irrespective of their origin. Environ Microbiol 1: 421-430.
5. Anzai, Y., Kim, H., Park, J., Wakabayashi, H., and Oyaizu, H. (2000) Phylogenetic affiliation of the pseudomonads based on 16S rRNA sequence. Int J Syst Evol Microbiol 50: 1563-1589.
6. Bodilis, J., and Barray, S. (2006) Molecular evolution of the major outer-membrane protein gene (oprF) of Pseudomonas. Microbiology 52: 1075-1088.
7. Bodilis, J., Calbrix, R., Guerillon, J., Mérieau, A., Pawlak, B., Orange, N., and Barray, S. (2004) Phylogenetic relationships between environmental and clinical isolates of Pseudomonas fluorescens and related species deduced from 16S rRNA gene and OprF protein sequences. Syst Appl Microbiol 27: 93-108.
8. Bossis, E., Lemanceau, P., Latour, X., and Gardan, L. (2000) The taxonomy of Pseudomonas fluorescens and Pseudomonas putida: current status and need for revision. Agronomie 20: 51-63.
9. Buck, K.J., Harris, R.A., and Sikela, J.M. (1991) A general method for quantitative PCR analysis of mRNA levels for members of gene families: application to GABAa receptor subunits. Biotechniques 11: 636-641.
10. Buckling, A., Wills, M., and Colegrave, N. (2003) Adaptation limits diversification of experimental bacterial populations. Science 302: 2107-2109.
11. Cho, J.-C., and Tiedje, J.M. (2000) Biogeography and degree of endemicity of fluorescent Pseudomonas strains in soil. Appl Environ Microbiol 66: 5448-5456.
12. Cohan, F.M. (2002) What are bacterial species. Annu Rev Microbiol 56: 457-487.
13. De, E., De Mot, R., Orange, N., Saint, N., and Molle, G. (1995) Channel-forming properties and structural homology of major outer membrane proteins from Pseudomonas fluorescens MFO and OE 28.3. FEMS Microbiol Lett 127: 267-272.
14. Duffy, B.K., and Defago, G. (1997) Zinc improves biocontrol of Fusarium crown and root rot of tomato by Pseudomonas fluorescens and represses the production of pathogen metabolites inhibitory to bacterial antibiotic biosynthesis. Phytopathology 87: 1250-1257.
15. Duffy, B.K., and Defago, G. (2000) Controlling instability in gacS-gacA regulatory genes during inoculant production of Pseudomonas fluorescens biocontrol strains. Appl Environ Microbiol 66: 3142-3150.
16. Felske, A., Akkermans, A.D.L., and De Vos, W.M. (1998) Quantification of 16S rRNAs in complex bacterial communities by multiple competitive reverse transcription-PCR in temperature gradient gel electrophoresis fingerprints. Appl Environ Microbiol 64: 4581-4587.
17. Gamalero, E., Lingua, G., Tombolini, R., Avidano, L., Pivato, B., and Berta, G. (2005) Colonization of tomato root seedling by Pseudomonas fluorescens 92rkG5: spatio-temporal dynamics, localization, organization, viability, and culturability. Microb Ecol 50: 289-297.
18. Gevers, D., Cohan, F.M., Lawrence, J.G., Spratt, B.G., Coenye, T., Feil, E.J., et al. (2005) Opinion: re-evaluating prokaryotic species. Nat Rev Microbiol 3: 733-739.
19. Haas, D., and Défago, G. (2005) Biological control of soilborne pathogens by fluorescent pseudomonads. Nat Rev Microbiol 3: 307-319.
20. Handelsman, J., and Stabb, E.V. (1996) Biocontrol of soilborne plante pathogens. Plant Cell 8: 1855-1869.
21. Hilario, E., Buckley, T., and Young, J. (2004) Improved resolution on the phylogenetic relationships among Pseudomonas by the combined analysis of atpD, carA, recA and 16S rDNA. Antonie Van Leeuwenhoek 86: 51-64.
22. Jaouen, T., De, E., Chevalier, S., and Orange, N. (2004) Pore size dependence on growth temperature is a common characteristic of the major outer membrane protein OprF in psychrotrophic and mesophilic Pseudomonas species. Appl Environ Microbiol 70: 6665-6669.
23. Johnsen, K., and Nielsen, P. (1999) Diversity of Pseudomonas strains isolated with King's B and Gould's S1 agar determined by repetitive extragenic palindromic-polymerase chain reaction, 16S rDNA sequencing and Fourier transform infrared spectroscopy characterisation. FEMS Microbiol Lett 173: 155-162.
24. Kimura, M. (1983) The Neutral Theory of Molecular Evolution. Cambridge, UK: Cambridge University Press.
25. Klein, D. (2002) Quantification using real-time PCR technology: applications and limitations. Trends Mol Med 8: 257-260.
26. Lugtenberg, B.J.J., de Weger, L.A., and Bennett, J.W. (1991) Microbial stimulation of plant growth and protection from disease. Curr Opin Biotechnol 2: 457-464.
27. Mazzola, M., Fujimoto, D., Thomashow, L., and Cook, R. (1995) Variation in sensitivity of Gaeumannomyces graminis to antibiotics produced by fluorescent Pseudomonas spp. & effect on biological control of take-all of wheat. Appl Environ Microbiol 61: 2554-2559.
28. Misko, A.L., and Germida, J.J. (2002) Taxonomic and functional diversity of pseudomonads isolated from the roots of field-grown canola. FEMS Microbiol Ecol 42: 399-407.
29. de Mot, R., Proost, P., van Damme, J., and Vanderleyden, J. (1992) Homology of the root adhesin of Pseudomonas fluorescens OE 28.3 with porin F of P. aeruginosa and P. syringae. Mol Gen Genet 231: 489-493.
30. de Mot, R., Schoofs, G., Roelandt, A., Declerck, P., Proost, P., van Damme, J., and Vanderleyden, J. (1994) Molecular characterization of the major outer-membrane protein OprF from plant root-colonizing Pseudomonas fluorescens. Microbiology 140: 1377-1387.
31. Nikaido, H. (2003) Molecular basis of bacterial outer membrane permeability revisited. Microbiol Mol Biol Rev 67: 593-656.
32. Orange, N. (1994) Growth temperature regulates the induction of β-lactamase in Pseudomonas fluorescens through modulation of the outer membrane permeation of a beta-lactam-inducing antibiotic. Microbiology 140: 3125-3130.
33. Palleroni, N., and Moore, E.R.B. (2004) Taxonomy of pseudomonads: experimental approaches. In Pseudomonas. Ramos, J.L. (ed.) New York, USA: Plenum Publishers, pp. 3-44.
34. Palys, T., Nakamura, L., and Cohan, F. (1997) Discovery and classification of ecological diversity in the bacterial world: the role of DNA sequence data. Int J Syst Bacteriol 47: 1145-1156.
35. Palys, T., Berger, E., Mitrica, I., Nakamura, L., and Cohan, F. (2000) Protein-coding genes as molecular markers for ecologically distinct populations: the case of two Bacillus species. Int J Syst Evol Microbiol 50: 1021-1028.
36. Pirnay, J.-P., Matthijs, S., Colak, H., Chablain, P., Bilocq, F., Van Eldere, J., et al. (2005) Global Pseudomonas aeruginosa biodiversity as reflected in a Belgian river. Environ Microbiol 7: 969-980.
37. Ramette, A., Moenne-Loccoz, Y., and Défago, G. (2003) Prevalence of fluorescent pseudomonads producing antifungal phloroglucinols and/or hydrogen cyanide in soils naturally suppressive or conducive to tobacco black root rot. FEMS Microbiol Ecol 44: 35-43.
38. Rawling, E.G., Martin, N.L., and Hancock, R.E. (1995) Epitope mapping of the Pseudomonas aeruginosa major outer membrane porin protein OprF. Infect Immun 63: 38-42.
39. Rawling, E.G., Brinkman, F.S., and Hancock, R.E. (1998) Roles of the carboxy-terminal half of Pseudomonas aeruginosa major outer membrane protein OprF in cell shape, growth in low-osmolarity medium, and peptidoglycan association. J Bacteriol 180: 3556-3562.
40. Rediers, H., Vanderleyden, J., and de Mot, R. (2004) Azotobacter vinelandii: a Pseudomonas in disguise? Microbiology 150: 1117-1119.
41. Rossello-Mora, R., and Amann, R. (2001) The species concept for prokaryotes. FEMS Microbiol Rev 25: 39-67.
42. Schippers, B., Bakker, A.W., and Bakker, P.A.H.M. (1987) Interactions of deleterious and beneficial rhizosphere microorganisms and the effect of cropping practices. Annu Rev Phytopathol 25: 339-358.
43. Schippers, B., Bakker, A.W., Bakker, P.A.H.M., and van Peer, R. (1990) Beneficial and deleterious effects of HCN-producing pseudomonads on rhizosphere interactions. Plant Soil 129: 75-83.
44. Schneeberger, C., Speiser, P., Kury, F., and Zellinger, R. (1995) Quantitative detection of reverse transcriptase-PCR products by means of a novel and sensitive DNA stain. PCR Methods Applic 4: 234-238.
45. de Smedt, H., Missiaen, L., Parys, J.-B., Bootman, M.D., Mertens, L., van den Bosch, L., and Casteels, R. (1994) Determination of relative amounts of inositol trisphosphate receptor mRNA isoforms by ratio polymerase chain reaction. J Biol Chem 269: 21691-21698.
46. Smith, C., Nedwell, D., Dong, L., and Osborn, M. (2006) Evaluation of quantitative polymerase chain reaction-based approaches for determining gene copy and gene transcript numbers in environmental samples. Environ Microbiol 8: 804-815.
47. Smith, K.P., Handelsman, J., and Goodman, R.M. (1999) Genetic basis in plants for interactions with disease-suppressive bacteria. Proc Natl Acad Sci USA 96: 4786-4790.
48. Stackebrandt, E., Frederiksen, W., Garrity, G.M., Grimont, P., Kampfer, P., Maiden, M., et al. (2002) Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52: 1043-1047.
49. Tamber, S., and Hancock, R. (2004) The outer membranes of pseudomonads. In: Pseudomonas. Ramos, J.L. (ed.) New York, USA: Plenum Publishers, pp. 575-601.
50. Torsvik, V. (1990) High diversity of DNA of soil bacteria. Appl Environ Microbiol 56: 782-787.
51. Vandamme, P., Pot, B., Gillis, M., de Vos, P., Kersters, K., and Swings, J. (1996) Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev 60: 407-438.
52. Vermeiren, H., Willems, A., Schoofs, G., de Mot, R., Keijers, V., Hai, W., and Vanderleyden, J. (1999) The rice inoculant strain Alcaligenes faecalis A15 is a nitrogen-fixing Pseudomonas stutzeri. Syst Appl Microbiol 22: 215-224.
53. Weller, D.M. (1986) Effects of wheat genotype on root colonization by a take-all suppressive strain of Pseudomonas fluorescens. Phytopathology 76: 1059.
54. Weller, D.M. (1988) Biological control of soilborne plant pathogens in the rhizosphere with bacteria. Annu Rev Phytopathol 26: 379-407.
55. Worgall, S., Krause, A., Rivara, M., Hee, K.K., Vintayen, E.V., Hackett, N.R., et al. (2005) Protection against P. aeruginosa with an adenovirus vector containing an OprF epitope in the capsid. J Clin Invest 115: 1281-1289.
56. Wu, L., Estrada, O., Zaborina, O., Bains, M., Shen, L., Kohler, J.E., et al. (2005) Recognition of host immune activation by Pseudomonas aeruginosa. Science 309: 774-777.
57. Yamamoto, S., Kasai, H., Arnold, D.L., Jackson, R.W., Vivian, A., and Harayama, S. (2000) Phylogeny of the genus Pseudomonas: intrageneric structure reconstructed from the nucleotide sequences of gyrB and rpoD genes. Microbiology 146: 2385-2394.