1887

Abstract

The relationships of the genus , and the genus were revealed by comparative analysis of partial 16S rRNA and , and gene sequences and as concatenated nucleotide and peptide sequences. Sequence similarities of species and indicated that these may be considered to be synonyms at the molecular level. In addition, these species show an intimate relationship with species of , especially . (the type species of the genus). In terms of the current circumscription of the genus , and should be considered for amalgamation with . and comprise nitrogen-fixing strains with large pleomorphic cells that form cysts, and peritrichous flagella insertion; characteristics not included in the current circumscription of . The data are discussed in the light of whether lateral transfer of genes could be involved in the determination of significant morphological characteristics, thus leading to a problem that may be encountered more frequently: how to resolve classification of taxa based on conserved sequences with those based on their phenotype. More fundamentally, the results illuminate problems that will increasingly be encountered: by what criteria can taxa be delineated, what are the most appropriate methods for classification, and what are the proper assumptions of bacterial classification?

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2007-12-01
2024-10-14
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References

  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 [CrossRef]
    [Google Scholar]
  2. Anzai 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 [CrossRef]
    [Google Scholar]
  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;
    [Google Scholar]
  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
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  6. Castresana J. 2000; Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17:540–552 [CrossRef]
    [Google Scholar]
  7. Chan Y.-K., Barraquio W. L., Knowles R. 1994; N2-fixing pseudomonads and related soil bacteria. FEMS Microbiol Rev 13:93–118
    [Google Scholar]
  8. Davis P. H., Hayward V. H. 1963 Principles of Angiosperm Taxonomy Edinburgh: Oliver & Boyd;
    [Google Scholar]
  9. Doolittle W. F. 1999; Phylogenetic classification and the universal tree. Science 284:2124–2128 [CrossRef]
    [Google Scholar]
  10. Euzéby J. P. 1997; List of Bacterial Names with Standing in Nomenclature: a folder available on the Internet (updated: March, 2007; revised URL:). Int J Syst Bacteriol 47:590–592 http://www.bacterio.cict.fr/ [CrossRef]
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  12. Gevers D., Cohan F. M., Lawrence J. G., Spratt B. G., Coenye T., Feil E. J., Stackebrandt E., Van de Peer Y., Vandamme P. & other authors; 2005; Re-evaluating prokaryotic species. Nat Rev Microbiol 3:733–739
    [Google Scholar]
  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
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  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
    [Google Scholar]
  16. Karlin S., Mrazek J., Campbell A. M. 1997; Compositional biases of bacterial genomes and evolutionary implications. J Bacteriol 179:3899–3913
    [Google Scholar]
  17. Kennedy C., Rudnick P., Brenner D. J. 2005; Genus II. Azomonas Winogradsky 1938, 391AL.. In Bergey's Manual of Systematic Bacteriology The Proteobacteria 2nd edn vol 2 part B Edited by Krieg N. R., Staley J. T., Garrity G. M. pp 379–384 New York: Springer;
    [Google Scholar]
  18. Kennedy C., Rudnick P., MacDonald M. L., Melton T., Brenner D. J. 2005; Genus III. Azotobacter Beijerinck 1901, 567AL . In Bergey's Manual of Systematic Bacteriology – The Proteobacteria , 2nd edn. vol 2 part B Edited by Krieg N. R., Staley J. T., Garrity G. M. pp 384–402 New York: Springer;
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  21. Line M. A. 1997; A nitrogen-fixing consortia associated with the bacterial decay of a wooden pipeline. Lett Appl Microbiol 25:220–224 [CrossRef]
    [Google Scholar]
  22. Ludwig W., Schleifer K. H. 1999; Phylogeny of bacteria beyond the 16S rRNA standard. ASM News 65:752–757
    [Google Scholar]
  23. Maiden M. C. J., Bygraves J. A., Feil E., Morelli G., Russell J. E., Urwin R., Zhang Q., 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 [CrossRef]
    [Google Scholar]
  24. Mindell D. P., Thacker C. E. 1996; Rates of molecular evolution: phylogenetic issues and applications. Annu Rev Ecol Syst 27:279–303 [CrossRef]
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  27. Palleroni N. J. 1984; Genus I. Pseudomonas Migula 1894, 237AL . In Bergey's Manual of Systematic Bacteriology vol. 1 pp 141–199 Edited by Krieg N. R., Holt J. G. Baltimore: Williams & Wilkins;
    [Google Scholar]
  28. Palleroni N. J. 2005; Genus I. Pseudomonas Migula 1894, 237AL. In Bergey's Manual of Systematic Bacteriology – The Proteobacteria . , 2nd edn. vol. 2, part B pp 323–379 Edited by Brenner D. J., Krieg N. R., Staley J. T., Garrity G. M. New York: Springer;
  29. Pfennig N., Trüper H. 2005; Family 1. Rhodospirillaceae Pfennig and Trüper 1971, 17AL . In Bergey's Manual of Systematic Bacteriology – The Proteobacteria , 2nd edn. vol 2 part C p– 17 Edited by Brenner D. J., Krieg N. R., Staley J. T., Garrity G. M. New York: Springer;
    [Google Scholar]
  30. Rediers H., Vanderleyden J., De Mot R. 2004; Azotobacter vinelandii : a Pseudomonas in disguise?. Microbiology 150:1117–1119 [CrossRef]
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  34. Stackebrandt E., Woese C. R. 1984; The phylogeny of the prokaryotes. Microbiol Sci 1:117–122
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  38. Thompson J. P., Skerman V. B. D. 1981 Azotobacteraceae: the Taxonomy and Ecology of the Aerobic Nitrogen-fixing Bacteria London: Academic Press;
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  40. Vancanneyt M., Torck U., Dewettinck D., Vaerewijck M., Kersters K. 1996b; Grouping of pseudomonads by SDS-PAGE of whole-cell proteins. Syst Appl Microbiol 19:556–568 [CrossRef]
    [Google Scholar]
  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
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  44. Wilkins A. S. 2002 The Evolution of Developmental Pathways Sunderland, MA: Sinauer Associates;
    [Google Scholar]
  45. Woese C. R. 1987; Bacterial evolution. Microbiol Rev 51:221–271
    [Google Scholar]
  46. Xie C.-H., Yokota A. 2005; Reclassification of Alcaligenes latus strains IAM 12599T 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 [CrossRef]
    [Google Scholar]
  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
    [Google Scholar]
  48. Young J. M. 2001; Implications of alternative classifications and horizontal gene transfer for bacterial taxonomy. Int J Syst Evol Microbiol 51:945–953 [CrossRef]
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  51. Zeigler D. R. 2003; Gene sequences useful for predicting relatedness of whole genomes in bacteria. Int J Syst Evol Microbiol 53:1893–1900 [CrossRef]
    [Google Scholar]
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