Relationships of plant pathogenic enterobacteria based on partial atpD, carA, and recA as individual and concatenated nucleotide and peptide sequences

Systematic and Applied Microbiology

Volumn 30, Issue 5, 2007, Pages 343-354

  Young, J M ^a   Park, D C ^a  

^a LANDCARE RESEARCH   (New Zealand)

Author keywords

Brenneria; Dickeya; Enterobacter; Erwinia; Multilocus sequence typing (MLST); Pantoea; Pectobacterium; Samsonia; Taxonomy

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; COMPARATIVE STUDY; ENTEROBACTERIACEAE; ERWINIA; NONHUMAN; NUCLEOTIDE SEQUENCE; PANTOEA; PECTOBACTERIUM; PLANT; PRIORITY JOURNAL; TAXONOMY;

BRENNERIA; BRENNERIA QUERCINA; DICKEYA; ENTEROBACTER; ENTEROBACTERIACEAE; ERWINIA; PANTOEA; PECTOBACTERIUM; PECTOBACTERIUM CYPRIPEDII; SAMSONIA;

EID: 34250704824     PISSN: 07232020     EISSN: 16180984     Source Type: Journal    
DOI: 10.1016/j.syapm.2007.03.002     Document Type: Article

References (44)

1. Ausubel F.M., Brent B., Kingston R.E., Moore D.D., Seidman J.G., Smith J.A., and Struhl K. Current Protocols in Molecular Biology (1987), Wiley, New York
2. Brenner D.J., Fanning G.R., and Steigerwalt A.G. Deoxyribonucleic acid relatedness among Erwinia and other Enterobacteriaceae: the gall, wilt, and dry-necrosis organisms (genus Erwinia Winslow et al., sensu stricto). Int. J. Syst. Bacteriol. 24 (1974) 197-204
3. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17 (2000) 540-552
4. Brenner D.J., McWhorter A.C., Kai A., Steigerwalt A.G., and Farmer J.J. Enterobacter asburiae sp. nov., a new species found in clinical specimens, and reassignment of Erwinia dissolvens and Erwinia nimipressuralis to the genus Enterobacter as Enterobacter dissolvens comb. nov. and Enterobacter nimipressuralis comb. nov. J. Clin. Microbiol. 23 (1986) 1114-1120
5. Dickey R.S., and Zumoff C.H. Emended description of Enterobacter cancerogenus comb. nov. (formerly Erwinia cancerogena). Int. J. Syst. Bacteriol. 38 (1988) 371-374
6. Dye D.W. A numerical taxonomic study of the genus Erwinia. NZ J. Agric. Res. 24 (1981) 223-229
7. J.P. Euzéby, List of bacterial names with standing in nomenclature: a folder available on the Internet (updated: March 2006; revised URL: http://www.bacterio.cict.fr/). Int. J. Syst. Evol. Microbiol. 47 (1997-2006) 590-592.
8. Gardan L., Gouy C., Christen R., and Samson R. Elevation of three subspecies of Pectobacterium carotovorum to species level: Pectobacterium atrosepticum sp. nov., Pectobacterium betavasculorum sp. nov. and Pectobacterium wasabiae sp. nov. Int. J. Syst. Evol. Microbiol. 53 (2003) 381-391
9. Gaunt M.W., Turner S.L., Rigottier-Gois L., Lloyd-Macgilp S.A., and Young J.P.W. Phylogenies of atpD and recA support the small subunit rRNA-based classification of rhizobia. Int J. Syst. Evol. Microbiol. 51 (2001) 2037-2048
10. Gavini F., Mergaert J., Beji A., Mielcarek C., Izard D., and Kersters K. J. De Ley. Transfer of Enterobacter agglomerans (Beijerinck 1888) Ewing & Fife 1972 to Pantoea gen. nov. as Pantoea agglomerans comb. nov. and description of Pantoea dispersa sp. nov. Int. J. Syst. Bact. 39 (1989) 337-345
11. P.A.D. Grimont, F. Grimont, Genus XXIII. Pantoea Gavini, Mergaert, Beji, Mielcarek, Izard, Kersters, and De Ley 1989 343VP emend. Mergaert, Verconck and Kersters 1993, 171, in: D.J. Brenner, N.R. Krieg, J.T. Staley, G.M. Garrity (Eds.), Bergey's Manual of Systematic Bacteriology, The Proteobacteria, vol. 2C, second ed., Springer, New York, USA, 2005, pp. 340-345.
12. Hauben L., Moore E.R.B., Vauterin L., Steenackers M., Mergaert J., Verdonck L., and Swings J. Phylogenetic position of phytopathogens within the Enterobacteriaceae. Syst. Appl. Microbiol. 21 (1998) 384-397
13. Hoffmann H., Stindl S., Ludwig W., Stumpf A., Mehlen A., Heesemann J., Monget D., Schleifer K.-H., and Roggenkamp A. Reassignment of Enterobacter dissolvens to Enterobacter cloacae as E. cloacae subspecies dissolvens comb. nov. and emended description of Enterobacter asburiae and Enterobacter kobei. Syst. Appl. Microbiol. 28 (2005) 196-205
14. Hwang M.S.H., Morgan R.L., Sarkar S.F., Wang P.W., and Guttman D.S. Phylogenetic characterization of virulence and resistance phenotypes of Pseudomonas syringae. Appl. Environ. Microbiol. 71 (2005) 5182-5191
15. Kwon S.-W., Park J.-Y., Kim J.-S., Kang J.-W., Cho Y.-H., Lim C.-K., Parker M.A., and Lee G.-B. Phylogenetic analysis of the genera Bradyrhizobium, Mesorhizobium, Rhizobium and Sinorhizobium on the basis of 16S rRNA gene and internally transcribed spacer region sequences. Int. J. Syst. Evol. Microbiol. 55 (2005) 263-270
16. Lelliott R.A., and Dickey R.S. Genus XII. Erwinia Winslow, Broadhurst, Buchanan, Krumwiede, Rogers & Smith 1920, 209AL. In: Krieg N.R., and Holt J.G. (Eds). Bergey's Manual of Systematic Bacteriology. seventh ed. (1984), The Williams & Wilkins Co., Baltimore 235-242
17. Lindström K., and Martínez-Romero M.E. International Committee on Systematics of Prokaryotes; Subcommittee on the taxonomy of Agrobacterium and Rhizobium. Minutes of the Meeting, 26 July 2004, Toulouse, France. Int. J. Syst. Evol. Microbiol. 55 (2005) 1383
18. Maiden M.C.J., Bygraves J.A., Feil E., Morelli G., Russell J.E., Urwin R., Zhang Q., Zhou J., Zurth K., Caugant D.A., Feavers I.M., Achtman M., and Spratt B.G. Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc. Natl. Acad. Sci. USA 95 (1998) 3140-3145
19. Mergaert J., Verdonck L., and Kersters K. Transfer of Erwinia ananas (synonym, Erwinia uredovora) and Erwinia stewartii to the genus Pantoea emend. as Pantoea ananas (Serrano 1928) comb. nov. and Pantoea stewartii (Smith 1898) comb. nov., respectively, and description of Pantoea stewartii subsp. indologenes subsp. nov. Int. J. Syst. Bacteriol. 43 (1993) 162-173
20. Michener C.D., and Sokal R.R. A quantitative approach to a problem in classification. Evolution 11 (1957) 130-162
21. Page R.D.M. TREEVIEW: an application to display phylogenetic trees on personal computers. Comput. Appl. Biosci. 12 (1996) 357-358
22. Ronquist F., and Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19 (2003) 1572-1574
23. Samson R., Legendre J.B., Christen R., Fischer-Le Saux M., Achouak W., and Gardan L. Transfer of Pectobacterium chrysanthemi (Burkholder et al. 1953) Brenner et al. 1973 and Brenneria paradisiaca to the genus Dickeya gen. nov. as Dickeya chrysanthemi comb. nov. and Dickeya paradisiaca comb. nov. and delineation of four novel species, Dickeya dadantii sp. nov., Dickeya dianthicola sp. nov.Dickeya dieffenbachiae sp. nov. and Dickeya zeae sp. nov. Int. J. Syst. Evol. Microbiol. 55 (2005) 1415-1427
24. Sarkar S.F., and Guttman D.S. Evolution of the core genome of Pseudomonas syringae, a highly clonal, endemic plant pathogen. Appl. Environ. Microbiol. 70 (2004) 1999-2012
25. Scally M., Schuenzel E.L., Stouthamer R., and Nunney L. Multilocus sequence type system for the plant pathogen Xylella fastidiosa and relative contributions of recombination and point mutation to clonal diversity. Appl. Environ. Microbiol. 71 (2005) 8491-8499
26. V.B.D. Skerman, V. McGowan, P.H.A. Sneath (Eds.), Approved lists of bacterial names. Int. J. Syst. Bacteriol. 30 (1980) 225-420.
27. Sneath P.H.A. Analysis and interpretation of sequence data for bacterial systematics: the view of a numerical taxonomist. Syst. Appl. Microbiol. 12 (1989) 15-31
28. Spröer C., Mendrock U., Swiderski J., Lang E., and Stackebrandt E. The phylogenetic position of Serratia, Buttiauxella and some other genera of the family Enterobacteriaceae. Int. J. Syst. Bacteriol. 49 (1999) 1433-1438
29. Stackebrandt E., and Goebel G.M. Taxonomic note: a place for DNA-DNA-reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int. J. Syst. Bacteriol. 44 (1994) 846-849
30. Stackebrandt E., and Woese C.R. The phylogeny of the prokaryotes. Microbiol. Sci. 1 (1984) 117-122
31. Starr M.P., and Chatterjee A.K. The genus Erwinia: enterobacteria pathogenic to plants and animals. Annu. Rev. Microbiol. 26 (1972) 389-426
32. Starr M.P., and Mandel M. DNA base composition and taxonomy of phytopathogenic and other enterobacteria. J. Gen. Microbiol. 56 (1969) 113-123
33. Sutra L., Christen R., Bollet C., Simoneau P., and Gardan L. Samsonia erythrinae gen. nov., sp. nov., isolated from bark necrotic lesions of Erythrina sp., and discrimination of plant-pathogenic Enterobacteriaceae by phenotypic features. Int. J. Syst. Evol. Microbiol. 51 (2001) 1291-1304
34. Swofford D.L. PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4 (2001), Sinauer Associates, Sunderland, MA
35. Tettelin H., Masignani V., Cieslewicz M.J., and and 43 others. Genomic analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial pan-genome. Proc. Natl. Acad. Sci. 102 (2005) 13950-13955
36. Vauterin L., and Swings J. Are classifications and phytopathological diversity compatible in Xanthomonas?. J. Ind. Microbiol. Biotechnol. 19 (1997) 77-82
37. Waldee E.L. Comparative studies of some peritrichous phytopathogenic bacteria. Iowa State College, J. Sci. 19 (1945) 435-484
38. Weir B.S., Turner S.J., Silvester W.B., and Young J.M. Unexpectedly diverse Mesorhizobium strains and Rhizobium leguminosarum nodulate native legume genera of New Zealand, while introduced legume weeds are nodulated by Bradyrhizobium species. Appl. Environ. Microbiol. 70 (2004) 5980-5987
39. White J.N., and Starr M.P. Glucose fermentation end products of Erwinia spp. and other Enterobacteria. J. Appl. Bacteriol. 34 (1971) 459-475
40. Woese C.R. Bacterial evolution. Microbiol. Rev. 51 (1987) 221-271
41. Young J.M. Recent systematics developments and implications for plant pathogenic bacteria. In: Priest F.G., and Goodfellow M. (Eds). Applied Microbial Systematics (2000), Kluwer, Dordrecht 133-160
42. Young J.M. Implications of alternative classifications and horizontal gene transfer for bacterial taxonomy. Int. J. Syst. Evol. Microbiol. 51 (2001) 945-953
43. Young J.M., Takikawa Y., Gardan L., and Stead D.E. Changing concepts in the taxonomy of plant pathogenic bacteria. Annu. Rev. Phytopathol. 30 (1992) 67-105
44. Zeigler D.R. Gene sequences useful for predicting relatedness of whole genomes in bacteria. Int. J. Syst. Evol. Microbiol. 53 (2003) 1893-1900