Validity, sensitivity and resolution limit of the PCR-RFLP analysis of the rrs (16S rRNA gene) as a tool to identify soil-borne and plant- associated bacterial populations

Genetics Selection Evolution

Volumn 30, Issue SUPPL., 1998, Pages

  Oger, Phil ^a   Dessaux, Yves ^a   Petit, Annick ^a   Gardan, Louis ^b   Manceau, Charles ^b   Chomel, Cécil ^c   Nesme, Xavier ^c  

^a INSTITUT DES SCIENCES DU VÉGÉTAL   (France)

^b CEMAGREF   (France)

^c UNIVERSITÉ LYON 1   (France)

Author keywords

16S; Agrobacterium; PCR RFLP; Pseudomonas; Rrs; Xanthomonas

Indexed keywords

RNA 16S;

BACTERIUM; IDENTIFICATION METHOD; METHODOLOGY; PERFORMANCE ASSESSMENT; POLYMERASE CHAIN REACTION;

AGROBACTERIUM; BACTERIUM IDENTIFICATION; BACTERIUM ISOLATION; BIODIVERSITY; CONFERENCE PAPER; DNA SEQUENCE; ECOSYSTEM; NONHUMAN; OPERON; POLYMERASE CHAIN REACTION; PSEUDOMONAS SYRINGAE; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; RHIZOBIACEAE; RIBOTYPING; SEQUENCE ANALYSIS; STENOTROPHOMONAS MALTOPHILIA; XANTHOMONAS;

AGROBACTERIUM; BACTERIA (MICROORGANISMS); PSEUDOMONAS; PSEUDOMONAS SYRINGAE; RHIZOBIACEAE; STENOTROPHOMONAS; STENOTROPHOMONAS MALTOPHILIA; XANTHOMONAS;

EID: 0031793449     PISSN: 0999193X     EISSN: None     Source Type: Journal    
DOI: 10.1051/gse:19980719     Document Type: Conference Paper

References (57)

1. Bouzar H., Request for a judicial opinion concerning the type species of Agrobacterium, Int. J. Syst. Bacteriol. 44 (1994) 373-374.
2. Bouzar H., Chilton W.S., Nesme X., Dessaux Y., Vaudequin V., Petit A., Jones J.B., Hodge N.C., A new Agrobacterium strain isolated from aerial tumors on Ficus benjamina L., Appl. Environ. Microb. 61 (1995) 65-73.
3. Dessaux Y., Elasri M., Glickmann E., Oger P., Petit A., Vaudequin-Dransart V., The use of digoxigenin-labelled probes to detect DNA sequences specific for plant pathogenic bacteria, Cell Mol. Biol. 41 (1995) 933-943.
4. Dubnau D., Cirigliano C., Fate of transforming deoxyribonucleic acid after uptake by competent Bacillus subtilis: size and distribution of the integrated donor sequence, J. Bacteriol. 111 (1972) 488-494.
5. Felsenstein J., Phylogenesis from restriction sites: a maximum-likelihood approach, Evolution 46 (1992) 159-173.
6. Felsenstein J., Phylip (Phylogeny Inference Package) version 3.5 c. Distributed by the author, Department of Genetics, University of Washington, Seattle, WA, USA, 1993.
7. Gardan L., Shafik H.L., Grimont P.A.D., DNA relatedness among pathovars of P. syringae and related bacteria, in: Rudolf K., Burr T.J., Mansfield J.W., Stead D., Vivian A., von Kietzel J. (Eds.), Proceedings of the 5th International Conference on P. syringae pathovars and related pathogens, Kluwer Academic Publishers, Dordrecht, (1997) 445-447.
8. Grimont F., Grimont P.A., Ribosomal ribonucleic acid gene restriction pattern as potential taxonomic tools, Ann. I. Pasteur Microbiol. 137b (1986) 165-175.
9. Gurtler V., Wilson V.A., Mayall B.C., Classification of medically important clostridia using restriction endonuclease site differences of PCR-amplified 16S rDNA, J. Gen. Microbiol. 137 (1991) 2673-2679.
10. Hauben L., Vauterin L., Swings J., Moore E.R.B., Comparison of 16S ribosomal DNA sequences of all Xanthomonas species, Int. J. Syst. Bacteriol. 47 (1997) 328-335.
11. Heberlein G.T., De Ley J., Tijtgat R., Deoxyribonucleic acid homology and taxonomy of Agrobacterium, Rhizobium, and Chromobacterium. J. Bacteriol. 94 (1967) 116-124.
12. Holmes B., Roberts P., The classification, identification and nomenclature of agrobacteria. Incorporating revised descriptions for each of Agrobacterium tumefaciens (Smith & Townsend) Conn 1942. Agrobacterium rhizogenes (Riker et al.) Conn 1942, and Agrobacterium rubi (Hildebrand) Starr & Weiss 1943, J. Appl. Bacteriol. 50 (1981) 443-467.
13. Keane P.J., Kerr A., New P.B., Crown gall on stone fruit. II. Identification and nomenclature of Agrobacterium isolates, Aust. J. Biol. Sci. 23 (1970) 585-595.
14. Kerr A., Panagopoulos C.G., Biotypes of Agrobacterium radiobacter var tumefaciens and their biological control, Phytopathol. Z. 90 (1977) 172-179.
15. Kersters K., De Ley J., Genus III Agrobacterium Conn 1942, in: Kieg N.R., Holt J.G (Eds.), Bergeys Manual of Systematic Bacteriology, Williams & Wilkins Co., Baltimore, 1984, pp. 244-254.
16. Kersters K., De Ley J., Sneath P.H.A., Sackin M., Numerical taxonomic analysis of Agrobacterium, J. Gen. Microbiol. 78 (1973) 227-239.
17. Laguerre G., Rigottier-Gois L., Lemanceau P., Fluorescent Pseudomonas species categorized by using polymerase chain reaction (PCR) restriction fragment analysis of 16S rDNA, Mol. Ecol. 3 (1996a) 479-487.
18. Laguerre G., Mavingui P., Allard R., Charnay M.P., Louvrier P., Mazurier S.I., Rigottier-Gois L., Amarger N., Typing of rhizobia by PCR-DNA fingerprinting and PCR-restriction fragment length polymorphism analysis of chromosomal and symbiotic gene regions, application to Rhizobium leguminosarum and its different biovars, Appl. Environ. Microb. 62 (1996b) 2029-2036.
19. Latour X., Corberand T., Laguerre G., Allard F., Lemanceau P., The composition of fluorescent pseudomonad populations associated with roots is influenced by plant and soil type, Appl. Environ. Microb. 62 (1996) 2449-2456.
20. Manceau C., Horvais A., Assessment of genetic diversity among strains of Pseudomonas syringae by PCR-restrict ion fragment length polymorphism analysis of rRNA operons with special emphasis on P. syringae pv. tomato, Appl. Environ. Microb. 63 (1997) 498-505.
21. Marmur J., A procedure for the isolation of DNA from microorganisms, J. Mol. Biol. 3 (1961) 208-218.
22. Mevarech M., Hirsch-Twizer S., Goldman S., Yakobson E., Eisenberg H., Dennis P.P., Isolation and characterization of the rRNA gene clusters of Halobacterium marismortui, J. Bacteriol. 171 (1989) 3479-3485.
23. Navarro E., Simonet P., Normand P., Bardin R., Characterization of natural populations of Nitrobacter spp. using PCR/RFLP analysis of the ribosomal intergenic spacer. Arch. Microbiol. 157 (1992) 107-115.
24. Nei M., Li W.H., Mathematical model for studying genetic variation in terms of restriction endonucleases, Proc. Natl. Acad. Sci. USA 79 (1979) 5269-5273.
25. Nesme X., Vaneechoutte M., Orso S., Hoste B., Swings J., Diversity and genetic relatedness within genera Xanthomonas and Stenotrophomonas using restriction endonuclease site differences of PCR amplified 16S rRNA gene, Syst. Appl. Microbiol. 18 (1995) 127-135.
26. Normand P., Cournoyer B., Simonet P., Nazaret S., Analysis of a ribosomal operon in the actinomycete Frankia, Gene 111 (1992) 119-124.
27. Oger P., Petit A., Dessaux Y., Genetically engineered plants producing opines alter their biological environment, Nature/Biotechnol. 15 (1997) 369-372.
28. Ophel K., Kerr A., Agrobacterium vitis sp. nov. for strains of Agrobacterium biovar 3 from grapevines, Int. J. Syst. Bacteriol. 40 (1990) 236-241.
29. Palleroni N.J., Bradbury J.F., Stenotrophomonas, a new bacterial genus for Xanthomonas maltophilia (Hugh, 1980) Swings et al., 1983, Int. J. Syst. Bacteriol. 43 (1993) 606-609.
30. Pionnat S., Dessaux Y., Nesme X., Poncet C., Detection and determination of pathogenic Agrobacterium of roses with PCR, Acta Horticulturae 424 (1996) 227-232.
31. Ponsonnet C., Nesme X., Characterisation of Agrobacterium biotypes by RFLP analysis of PCR-amplified 16S gene, in: Lemattre M., Freigoun S., Rudolph K., Swings J.G. (Eds.), Plant Pathogenic Bacteria, Les Colloques, Éditions Inra, Paris, 66 1994a, pp. 377-381.
32. Ponsonnet C., Nesme X., Identification of Agrobacterium strains by PCR-RFLP analysis of pTi and chromosomal regions, Arch. Microbiol. 161 (1994b) 300-309.
33. Popoff M.Y., Kersters K., Kiredjian M., Miras I., Coynault C., Position taxonomique de souches de Agrobacterium d'origine hospitalière, Ann. Microbiol. (I. Pasteur) 135A (1984) 427-442.
34. Ream W., Agrobacterium tumefaciens and interkingdom genetic exchange, Ann. Rev. Phytopathol. 27 (1989) 583-618.
35. Riley M., Functions of the gene products of Escherichia coli, Microbiol. Rev. 57 (1993) 862-952.
36. Sawada H., Ieki H., Oyaizu H., Matsumoto S., Proposal for rejection of Agrobacterium tumefaciens and revised description for genus Agrobacterium and for Agrobacterium radiobacter and Agrobacterium rhizogenes. Int. J. Syst. Bacteriol. 43 (1993) 694-702.
37. Schaad N.W., How phytopathogenic bacteria are classified, in: Mount M.S., Lacy G.H. (Eds.), Phytopathogenic Bacteria, vol. 1, Academic Press, San Diego, CA, 1982, pp. 19-29.
38. Sneath P.H.A., Sokal R.R., Numerical Taxonomy. The Principles and Practice of Numerical Classification, Freeman, San Francisco, CA, 1973.
39. Stackebrandt E., Liesack W., Goebel B.M., Bacterial diversity in a soil sample from subtropical Australian environment as determined by 16S rDNA analysis, FASEB J. 7 (1993) 232-236.
40. Stackebrandt E., Goebel B.M., Taxonomic note: a place for DNA. DNA reassociation study and 16S RNA sequence analysis in the present species definition in bacteriology, Int. J. Syst. Bacteriol. 44 (1994) 846-849.
41. Vaneechoutte M., Rossau R., De Vos P., Gillis M., Janssens D., Paepe N., De Rouck A., Fiers T., Claeys G., Kersters K., Rapid identification of bacteria of the Comamonadaceae with amplified ribosomal DNA-restriction analysis (ARDRA), FEMS Microbiol. Lett. 93 (1992) 227-234.
42. Vaneechoutte M., De Beenhouwer H., Claeys G., Verschraegen G., De Rouck A., Paepe N., Elaichouni A., Portaels F., Identification of Mycobacterium species by using amplified ribosomal DNA restriction analysis, J. Clin. Microbiol. 31 (1993) 2061-2065.
43. Van Larebeke N., Genetello C., Schell J., Schilperoot R.A., Hermans A.K., Van Montagu M., Hernalsteens J.-P., Acquisition of tumor-inducing ability by non-oncogenic agrobactria as a result of plasmid transfer, Nature 255 (1975) 742-743.
44. Vaudequin-Dransart V., Petit A., Poncet C., Ponsonnet C., Nesme X., Jones J.J., Bouzar H., Chilton W.S., Dessaux Y., Novel Ti plasmids in Agrobacterium tumefaciens strains isolated from fig trees and chrysanthemum tumors and their opine-like molecules, Mol. Plant-Microbe Interact. 8 (1995) 311-321.
45. Vauterin L., Swings J., Kersters K., Gillis M., Mew T.W., Schroth M.N., Palleroni N.J., Hildebrand D.C., Stead D.E., Civerolo E.L., Hayward A.C., Maraite H., Stall R.E., Vidaver A.K., Bradbury J.F., Toward an improved taxonomy of Xanthomonas, Int. J. Syst. Bacteriol. 40 (1990) 312-316.
46. Vauterin L., Hoste B., Kersters K., Swings J., Reclassification of Xanthomonas, Int. J. Syst. Bacteriol. 45 (1995) 472-489.
47. Ward D.M., Weller R., Bateson M.M., 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature 345 (1990) 63-65.
48. Wayne L.G., Brenner D.J., Colwell R.R., Grimont P.A.D., Kandler O., Krichevsky M.I., Moore L.H., Murray R.G.E., Stackebrandt E., Starr M.P., Truper H.G., Report of the ad hoc committee on reconciliation of approaches to bacterial systematics, Int. J. Syst. Bacteriol. 37 (1987) 463.
49. Weisburg W.G., Barns S.M., Pelletier D.A., Lane D.J., 16S ribosomal DNA amplification for phylogenetic study, J. Bacteriol. 173 (1991) 697-703.
50. Wells J.M., Raju B.C., Hung H.Y., Weisburg W.G., Mandelco-Paul L., Brenner D.J., Xylella fastidiosa gen nov, sp nov, Gram-negative, xylem-limited, fastidious plant bacteria related to Xanthomonas spp., Int. J. Syst. Bacteriol. 37 (1987) 136-143.
51. Willems A., Collins M.D., Phylogenetic analysis of rhizobia and agrobacteria based on 16S rRNA gene sequences, Int. J. Syst. Bacteriol. 43 (1993) 305-313.
52. Woese C.R., Bacterial evolution, Microbiol. Rev. 51 (1987) 221-271.
53. Woese C.R., Stackebrandt E., Weisburg W.G., Pater B.J., Madigan M.T., Fowler V.J., Hahn C.M., Blanz P., Gupta R., Nealson K.H., Fox G.E., The phylogeny of purple bacteria, the alpha subdivision, Syst. Appl. Microbiol. 5 (1984a) 315-326.
54. Woese C.R., Blanz P., Hahn C.M., What isn't a pseudomonad, the importance of nomenclature in bacterial classification? Syst. Appl. Microbiol. 5 (1984b) 179-195.
55. Yanagi M., Yamasato K., Phylogenetic analysis of the family Rhizobiaceae and related bacteria by sequencing of 16S rRNA gene using PCR and DNA sequencer, FEMS Microbiol. Lett. 107 (1993) 115-120.
56. Young J.M., Takikawa Y., Gardan L., Stead D.E., Changing concepts in the taxonomy of plant pathogenic bacteria, Annu. Rev. Phytopathol. 30 (1992) 67-105.
57. Young J.M., Saddler G.S., Takikawa Y., De Boer S.H., Vauterin L., Gardan L., Gvozdak R.I., Stead D.E., Names of plant pathogenic bacteria 1864-1995, Rev. Plant Pathol. 75 (1996) 721-763.