Probable synonymy of the nitrogen-fixing genus Azotobacter and the genus Pseudomonas

International Journal of Systematic and Evolutionary Microbiology

Volumn 57, Issue 12, 2007, Pages 2894-2901

  Young, J M ^a   Park, D C ^a  

^a LANDCARE RESEARCH   (New Zealand)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; BACTERIAL RNA; CARBAMOYL PHOSPHATE SYNTHASE; CONCATENATED DNA; GENOMIC DNA; NITROGEN; PROTON TRANSPORTING ADENOSINE TRIPHOSPHATE SYNTHASE; RNA 16S;

ARTICLE; AZOMONAS MACROCYTOGENES; AZOSPIRILLUM; AZOTOBACTER; BACTERIAL GENE; BACTERIAL STRAIN; BACTERIUM IDENTIFICATION; GENE SEQUENCE; HORIZONTAL GENE TRANSFER; MICROMORPHOLOGY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PRIORITY JOURNAL; PSEUDOMONAS; PSEUDOMONAS AERUGINOSA; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SPECIES COMPARISON; STAINING;

AZOTOBACTER; BACTERIAL PROTEINS; CARBON-NITROGEN LIGASES; DNA, BACTERIAL; DNA, RIBOSOMAL; EVOLUTION, MOLECULAR; GENE TRANSFER, HORIZONTAL; GENES, RRNA; MOLECULAR SEQUENCE DATA; NITROGEN FIXATION; PHYLOGENY; PROTON-TRANSLOCATING ATPASES; PSEUDOMONAS; REC A RECOMBINASES; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID;

AZOMONAS; AZOMONAS MACROCYTOGENES; AZOTOBACTER; BACTERIA (MICROORGANISMS); PSEUDOMONAS; PSEUDOMONAS AERUGINOSA;

EID: 37449030371     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.64969-0     Document Type: Article

References (51)

1. Ait Tayeb, L., Ageron, E., Grimont, F. & Grimont P. A. D. (2005). Molecular phylogeny of the genus Pseudomonas based on rpoB sequences and application for identification of isolates. Res Microbiol 156, 763-773.
2. Anzal, Y., Kim, H., Park, J.-Y., Wakabayashi, H. & Oyaizu, H. (2000). Phylogenetic affiliation of the pseudomonads based on 16S rRNA sequence. Int J Syst Evol Microbiol 50, 1563-1589.
3. Ausubel, F. M., Brent, B., Kingston, R. E., Moore, D. D., Seidman, J. G., Smith, J. A. & Struhl, K. (1987). Current Protocols in Molecular Biology. New York: John Wiley.
4. Barraquio, W. L., Parde, B. C., Jr, Watanabe, I. & Knowles, R. (1986). Nitrogen fixation by Pseudomonas, saccharophila Doudoroff ATCC 15946. J Gen Microbiol 132, 237-241.
5. Brosch, R., Lefèvre, M., Grimont, F. & Grimont, P. A. D. (1996). Taxonomic diversity of pseudomonads revealed by computer interpretation of ribotyping data. Syst Appl Microbiol 19, 541-555.
6. Castresana, J. (2000). Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17, 540-552.
7. 2-fixing pseudomonads and related soil bacteria. FEMS Microbiol Rev 13, 93-118.
8. Davis, P. H. & Hayward, V. H. (1963). Principles of Angiosperm Taxonomy. Edinburgh: Oliver & Boyd.
9. Doolittle, W. F. (1999). Phylogenetic classification and the universal tree. Science 284, 2124-2128.
10. Euzéby, J. P. (1997). List of Bacterial Names with Standing in Nomenclature: a folder available on the Internet (updated: March, 2007; revised URL: http://www.bacterio.cict.fr/). Int J Syst Bacteriol 47, 590-592.
11. Gaunt, M. W., Turner, S. L., Rigottier-Gois, L., Lloyd-Macgilp, S. A. & Young, J. P. W. (2001). Phylogenies of atpD and recA support the small subunit rRNA-based classification of rhizobia. Int J Syst Evol Microbiol 51, 2037-2048.
12. Gevers, D., Cohan, F. M., Lawrence, J. G., Spratt, B. G., Coenye, T., Fell, E. J., Stackebrandt, E., Van de Peer, Y., Vandamme, P. & other authors (2005). Re-evaluating prokaryotic species. Nat Rev Microbiol 3, 733-739.
13. Guindon, S., Lethiec, F., Duroux, P. & Gascuel, O. (2005). PHYML Online - a web server for fast maximum likelihood-based phylogenetic inference. Nucleic Acids Res 33, W557-W559.
14. Hilario, E. M., Buckley, T. R. & Young, J. M. (2004). Improved resolution on the phylogenetic relationships among Pseudomonas species by the combined analysis of atpD, carA, recA and 16S rDNA. Antonie Van Leeuwenhoek 86, 51-64.
15. Jenni, B., Isch, C. & Aragno, M. (1989). Nitrogen fixation by new strains of Pseudomonas pseudoflava and related bacteria. J Gen Microbiol 135, 461-467.
16. Karlin, S., Mrazek, J. & Campbell, A. M. (1997). Compositional biases of bacterial genomes and evolutionary implications. J Bacteriol 179, 3899-3913.
17. AL. In Bergey's Manual of Systematic Bacteriology - The Proteobacteria, 2nd edn, vol. 2, part B, pp. 379-384. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
18. AL. In Bergey's Manual of Systematic Bacteriology - The Proteobacteria, 2nd edn, vol. 2, part B, pp. 384-402. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
19. Kersters, K., Ludwig, W., Vancanneyt, M., De Vos, P., Gillis, M. & Schleifer, K. H. (1996). Recent changes in the classification of the pseudomonads: an overview, Syst Appl Microbiol 19, 465-477.
20. Kulakov, L. A., McAlister, M. B., Kimberley, L. O., Larkin, M. J. & O'Hanlon, J. F. (2002). Analysis of bacteria contaminating ultrapure water in industrial systems. Appl Environ Microbiol 68, 1548-1555.
21. Line, M. A. (1997). A nitrogen-fixing consortia associated with the bacterial decay of a wooden pipeline. Lett Appl Microbiol 25, 220-224.
22. Ludwig, W. & Schleifer, K. H. (1999). Phylogeny of bacteria beyond the 16S rRNA standard. ASM News 65, 752-757.
23. Maiden, M. C. J., Bygraves, J. A., Feil, E., Morelli, G., Russell, J. E., Urwin, R., Zhang, O., Zhou, J., Zurth, K. & other authors (1998). Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci U S A 95, 3140-3145.
24. Mindell, D. P. & Thacker, C. E. (1996). Rates of molecular evolution: phylogenetic issues and applications. Annu Rev Ecol Syst 27, 279-303.
25. Moore, E. R. B., Mau, M., Arnscheidt, A., Böttger, E C., Hutson, R. A., Collins, M. D., van de Peer, Y., de Wachter, R. & Timmis, K. N. (1996). The determination and comparison of the 16S rRNA gene sequences of species of the genus Pseudomonas (sensu stricto) and estimation of the natural intrageneric relationships. Syst Appl Microbiol 19, 478-492.
26. Murray, R. G. E., Brenner, D. J., Colwell, R. R., De Vos, P., Goodfellow, M., Grimont, P. A. D., Pfennig, N., Stackebrandt, E. & Zavarzin, G. A. (1990). Report of the ad hoc committee on approaches to taxonomy within the Proteobacteria. Int J Syst Bacteriol 40, 213-215.
27. AL. In Bergey's Manual of Systematic Bacteriology, vol. 1, pp. 141-199. Edited by N. R. Krieg & J. G. Holt. Baltimore: Williams & Wilkins.
28. AL. In Bergey's Manual of Systematic Bacteriology - The Proteobacteria, 2nd edn, vol. 2, part B, pp. 323-379. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
29. AL. In Bergey's Manual of Systematic Bacteriology - The Proteobacteria, 2nd edn, vol. 2, part C, p. 17. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
30. Rediers, H., Vanderleyden, J. & De Mot, R. (2004). Azotobacter vinelandii: a Pseudomonas in disguise? Microbiology 150, 1117-1119.
31. Rivera, M. C., Jain, R., Moore, J. E. & Lake, J. A. (1998). Genomic evidence for two functionally distinct genome classes. Proc Natl Acad Sci U S A 95, 6239-6244.
32. Sneath, P. H. A. (1989). Analysis and interpretation of sequence data for bacterial systematics: the view of a numerical taxonomist. Syst Appl Microbiol 12, 15-31.
33. Stackebrandt, E. & Goebel, G. M. (1994). 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, 846-849.
34. Stackebrandt, E. & Woese, C. R. (1984). The phylogeny of the prokaryotes. Microbiol Sci 1, 117-122.
35. Stackebrandt, E., Frederiksen, W., Garrity, G. M., Grimont, P. A. D., Kämpfer, P., Maiden, M. C. J., Nesme, X., Rosselló-Mora, R., Swings, J. & other authors (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.
36. Stead, D. E. (1992). Grouping of plant-pathogenic and some other Pseudomonas spp. by using cellular fatty acid profiles. Int J Syst Bacteriol 42, 281-295.
37. Tesar, M., Hoch, C., Moore, E. R. B. & Timmis, K. N. (1996). Westprinting: development of a rapid immunochemical identification for species within the genus Pseudomonas sensu stricto. Syst Appl Microbiol 19, 577-588.
38. Thompson, J. P. & Skerman, V. B. D. (1981). Azotobacteraceae: the Taxonomy and Ecology of the Aerobic Nitrogen-fixing Bacteria. London: Academic Press.
39. Vancanneyt, M., Witt, S., Abraham, W.-R., Kersters, K. & Fredrickson, H. L. (1996a). Fatty acid content in whole-cell hydrolysates; and phospholipid fractions of pseudomonads: a taxonomic evaluation. Syst Appl Microbiol 19, 528-540.
40. Vancanneyt, M., Torck, U., Dewettinck, b., Vaerewijck M. & Kersters, K. (1996b). Grouping of pseudomonads by SDS-PAGE of whole-cell proteins. Syst Appl Microbiol 19, 556-568.
41. Vandamme, P., Pot, B., Gillis, M., De Vos, P., Kersters, K. & Swings, J. (1996). Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev 60, 407-438.
42. Vermeiren, H., Willems, A., Schoofs, G., de Mot R., Keijers, V. & Hai, W. (1999). The rice inoculant strain Alcaligenes faecalis A15 is a nitrogen-fixing Pseudomonas stutzeri. Syst Appl Microbiol 22, 215-224.
43. Weir, B. S., Turner, S. J., Silvester, W. B. & Young, J. M. (2004). 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, 5980-5987.
44. Wilkins, A. S. (2002). The Evolution of Developmental Pathways. Sunderland, MA: Sinauer Associates.
45. Woese, C. R. (1987). Bacterial evolution. Microbiol Rev 51, 221-271.
46. and IAM 12664 and Pseudomonas saccharophila as Azohydromonas lata gen. nov., comb. nov., Azohydromonas australica sp. nov. and Pelomonas saccharophila gen. nov., comb. nov., respectively. Int J Syst Evol Microbiol 55, 2419-2425.
47. Yamamoto, S., Kasai, H., Arnold, D. L., Jackson, R. W., Vivian, A. & Harayama, S. (2000). Phylogeny of the genus Pseudomonas: intrageneric structure reconstructed from the nucleotide sequences of gyrB and rpoD genes. Microbiology 146, 2385-2394.
48. Young, J. M. (2001). Implications of alternative classifications and horizontal gene transfer for bacterial taxonomy. Int J Syst Evol Microbiol 51, 945-953.
49. Young, J. M. & Park, D.-C. (2007). Relationships of plant pathogenic enterobacteria based on partial atpD, carA, and recA as individual and concatenated nucleotide and peptide sequences. Syst Appl Microbiol 30, 343-354.
50. Young, J. M., Takikawa, Y., Gardan, L. & Stead, D. E. (1992). Changing concepts in the taxonomy of plant pathogenic bacteria. Annu Rev Phytopathol 30, 67-105.
51. Zeigler, D. R. (2003). Gene sequences useful for predicting relatedness of whole genomes in bacteria. Int J Syst Evol Microbiol 53, 1893-1900.