Rapid and Efficient Identification of Agrobacterium Species by recA Allele Analysis

Microbial Ecology

Volumn 60, Issue 4, 2010, Pages 862-872

  Costechareyre, Denis ^a   Rhouma, Ali ^b   Lavire, Céline ^a   Portier, Perrine ^a,c   Chapulliot, David ^a   Bertolla, Franck ^a   Boubaker, Ali ^d   Dessaux, Yves ^e   Nesme, Xavier ^a  

^a UNIVERSITÉ LYON 1   (France)

^b Olive Tree Institute   (Tunisia)

^c UNIVERSITÉ D'ANGERS   (France)

^d INSTITUT NATIONAL AGRONOMIQUE DE TUNISIE   (Tunisia)

^e CNRS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

AGROBACTERIUM; AGROBACTERIUM LARRYMOOREI; AGROBACTERIUM RHIZOGENES; AGROBACTERIUM RUBI; AGROBACTERIUM SP. NCPPB1650; AGROBACTERIUM TUMEFACIENS; AGROBACTERIUM VITIS; RHIZOBIUM; VITACEAE;

EID: 78149466102     PISSN: 00953628     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00248-010-9685-7     Document Type: Article

References (41)

1. Bouzar H, Jones JB (2001) Agrobacterium larrymoorei sp. nov., a pathogen isolated from aerial tumours of Ficus benjamina. Int J Syst Evol Microbiol 51: 1023-1026.
2. Bouzar H, Moore LW (1987) Isolation of different Agrobacterium biovars from a natural oak savanna and tall grass prairie. Appl Environ Microbiol 53: 717-721.
3. Bruce KD, Hiorns WD, Hobman JL, Osborn AM, Strike P, Ritchie DA (1992) Amplification of DNA from native populations of soil bacteria by using the polymerase chain reaction. Appl Environ Microbiol 58: 3413-3416.
4. de Lajudie P, Laurent-Fulele E, Willems A, Torck U, Coopman R, Collins D, Kersters K, Dreyfus B, Gillis M (1998) Allorhizobium undicola gen. nov., sp. nov., nitrogen-fixing bacteria that efficiently nodulate Neptunia natans in Senegal. Int J Syt Bacteriol 48: 1277-1290.
5. De Ley J (1974) Phylogeny of procaryotes. Taxon 23: 291-300.
6. De Ley J, Tijtgat R, De Smedt J, Michiels M (1973) Thermal stability of DNA: DNA hybrids within the genus Agrobacterium. J Gen Microbiol 78: 241-252.
7. Farrand SK, van Berkum PB, Oger P (2003) Agrobacterium is a definable genus of the family Rhizobiaceae. Int J Syst Evol Microbiol 53: 1681-1687.
8. Gaunt MW, Turner SL, Rigottier-Gois L, Lloyd-Macgilp SA, Young JPW (2001) Phylogenies of atpD and recA support the small subunit rRNA-based classification of rhizobia. Int J Syst Evol Microbiol 51: 2037-2048.
9. Genetello C, van Larebeke N, Holsters M, De Picker A, van Montagu M, Schell J (1977) Ti plasmids of Agrobacterium tumefaciens as conjugative plasmids. Nature 265: 561-563.
10. Gouy M, Guindon S, Gascuel O (2010) SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol 27: 221-224.
11. Holmes B, Roberts P (1981) The classification, identification and nomenclature of agrobacteria. J Appl Bacteriol 50: 443-467.
12. Keane PJ, Kerr A, New PB (1970) Crown gall of stone fruit. II. Identification and nomenclature of Agrobacterium isolates. Austral J Biol Sci 23: 585-595.
13. Kersters K, De Ley J (1984) Agrobacterium Conn 1942. In: Krieg NR, Holt JG (eds) Bergey's manual of systematic bacteriology, vol. 1. Williams & Wilkins, Baltimore, pp 244-254.
14. Krimi Z, Petit A, Mougel C, Dessaux Y, Nesme X (2002) Seasonal fluctuations and long-term persistence of pathogenic populations of Agrobacterium spp. in soils. Appl Environ Microbiol 68: 3358-33654.
15. Krimi Z, Raio A, Petit A, Nesme X, Dessaux Y (2006) Eucalyptus (E occidentalis) plantlets may be naturally infected by pathogenic Agrobacterium tumefaciens. Eur J Plant Pathol 116: 237-246.
16. Llop P, Lastra B, Marsal H, Murillo J, Lopez MM (2003) Tracking Agrobacterium strains by a RAPD system to identify single colonies from plant tumours. Eur J Plant Pathol 109: 381-389.
17. Maiden MC, Bygraves JA, Feil E, Morelli G, Russell JE, Urwin R, Zhang Q, Zhou J, Zurth K, Caugant DA, Feavers IM, Achtman M, Spratt BG (1998) Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci USA 95: 3140-3145.
18. Martens M, Delaere M, Coopman R, De Vos P, Gillis M, Willems A (2007) Multilocus sequence analysis of Ensifer and related taxa. Int J Syst Evol Microbiol 57: 489-503.
19. Moore LW, Cooksey DA (1981) Biology of Agrobacterium tumefaciens: plant interactions. Int Rev Cytol 13(Suppl): 15-46.
20. Mougel C, Cournoyer B, Nesme X (2001) Novel tellurite-amended media and specific chromosomal Ti plasmid probes for direct analysis of soil populations of Agrobacterium biovars 1 and 2. Appl Environ Microbiol 67: 65-74.
21. Mougel C, Thioulouse J, Perrière G, Nesme X (2002) A mathematical method for determining genome divergence and species delineation using AFLP. Int J Syst Evol Microbiol 52: 573-586.
22. Nesme X, Ponsonnet C, Picard C, Normand P (1992) Chromosomal and pTi genotypes of Agrobacterium strains isolated from Populus tumors in two nurseries. FEMS Microbiol Ecol 101: 189-196.
23. Oger P, Dessaux Y, Petit A, Gardan L, Manceau C, Chomel C, Nesme X (1998) Validity, sensitivity and resolution limit of the PCR-RFLP analysis of the rrs (16 rRNA gene) as a tool to identify soil-borne and plant associated bacterial population. Genet Select Evol 30(Suppl 1): S311-S332.
24. Ophel K, Kerr A (1990) Agrobacterium vitis sp. nov. for strains of Agrobacterium biovar 3 from grapevines. Int J Syst Bacteriol 40: 236-241.
25. Panagopoulos CG, Psallidas PG (1973) Characteristics of Greek isolates of Agrobacterium tumefaciens (E F Smith & Townsend) Conn. J Appl Bacteriol 36: 233-240.
26. Ponsonnet C, Nesme X (1994) Identification of Agrobacterium strains by PCR-RFLP analysis of pTi and chromosomal regions. Arch Microbiol 161: 300-309.
27. Popoff MY, Kersters K, Kiredjian M, Miras I, Coynault C (1984) Position systématique de souches de Agrobacterium d'origine hospitalière. Ann Microbiol 135: 427-442.
28. Portier P, Fischer-Le Saux M, Mougel C, Lerondelle C, Chapulliot D, Thioulouse J, Nesme X (2006) Identification of genomic species from Agrobacterium biovar 1 by AFLP genomic markers. Appl Environ Microbiol 72: 123-7131.
29. Rhouma A, Boubaker A, Nesme X, Dessaux Y (2005) Susceptibility of some stone and pome fruit rootstocks to crown gall. Phytopathol Mediterr 44: 275-284.
30. Rhouma A, Boubaker A, Nesme X, Dessaux Y (2006) Plasmid and chromosomal diversity of a Tunisian collection of Agrobacterium tumefaciens strains. Tunis J Plant Protect 1: 73-84.
31. Sawada H, Ieki H, Oyaizu H, Matsumoto S (1993) Proposal for rejection of Agrobacterium tumefaciens and revised descriptions for the genus Agrobacterium and for Agrobacterium radiobacter and Agrobacterium rhizogenes. Int J Syst Bacteriol 43: 694-702.
32. Stackebrandt E, Frederiksen W, Garrity GM, Grimont PA, Kampfer P, Maiden MC, Nesme X, Rossello-Mora R, Swings J, Truper HG, Vauterin L, Ward AC, Whitman WB (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.
33. Tenover FC, Arbeit RD, Goering RV, Mickelsen PA, Murray BE, Persing DH, Swaminathan B (1995) Interpreting chromosomal DNA restriction patterns produced by pulsed-field gel electrophoresis: criteria for bacterial strain typing. J Clin Microbiol 33: 2233-2239.
34. Teyssier-Cuvelle S, Oger P, Mougel C, Groud K, Farrand S, Nesme X (2004) A highly selectable and highly transferable Ti plasmid to study conjugal host range and Ti plasmid dissemination in complex ecosystems. Microbial Ecol 48: 10-18.
35. van Larebeke N, Engler G, Holsters M, van den Elsacker S, Zaenen I, Schilperoort RA, Schell J (1974) Large plasmid in Agrobacterium tumefaciens essential for crown gall-inducing ability. Nature 252: 169-170.
36. Vinuesa P, Silva C, Lorite MJ, Izaguirre-Mayoral ML, Bedmar EJ, Martinez-Romero E (2005) Molecular systematics of rhizobia based on maximum likelihood and Bayesian phylogenies inferred from rrs, atpD, recA and nifH sequences, and their use in the classification of Sesbania microsymbionts from Venezuelan wetlands. Syst Appl Microbiol 8: 702-716.
37. Vos P, Hogers R, Bleeker M, Reijans M, van De Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23: 4407-4414.
38. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevisky MI, Moore LH, Moore WEC, Murray GRE, Stackebrandt E, Starr MP, Truper HG (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37: 463-464.
39. Yanagi M, Yamasato K (1993) Phylogenetic analysis of the family Rhizobiaceae and related bacteria by sequencing of 16S rRNA gene using PCR and DNA sequencer. FEMS Microbiol Lett 107: 115-120.
40. Young JM, Kuykendall LD, Martinez-Romero E, Kerr A, Sawada H (2001) A revision of Rhizobium Frank 1889, with an emended description of the genus, and the inclusion of all species of Agrobacterium Conn 1942 and Allorhizobium undicola De Lajudie et al. 1998 as new combinations: Rhizobium radiobacter, R. rhizogenes, R. rubi, R. undicola and R. vitis. Int J Syst Env Microbiol 51: 89-103.
41. Young JM, Pennycook SR, Watson DRW (2006) Proposal that Agrobacterium radiobacter has priority over Agrobacterium tumefaciens. Request for an opinion. Int J Syst Env Microbiol 56: 491-493.