Antonie van Leeuwenhoek

, Volume 86, Issue 1, pp 51–64 | Cite as

Improved resolution on the phylogenetic relationships among Pseudomonas by the combined analysis of atpD, carA, recA and 16S rDNA

  • Elena Hilario
  • Thomas R. Buckley
  • John M. Young
Article

Abstract

A study of representatives of the bacterial genus Pseudomonas, analysing a combined data set of four molecular sequences with completely different properties and evolutionary constraints, is reported. The best evolutionary model was obtained with a hierarchical hypothesis testing program to describe each data set and the combined data set is presented and analysed under the likelihood criterion. The resolution among Pseudomonas taxa based on the combined data set analysis of the different lineages increased due to a synergistic effect of the individual data sets. The unresolved fluorescens lineage, as well as other weakly supported lineages in the single data set trees, should be revised in detail at the biochemical and molecular level. The taxonomic status of biovars of P. putida is discussed.

Phylogenies 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Anzai Y., Kim H., Park J.-Y., Wakabayashi H. and Oyaizu H. 2000. Phylogenetic affiliation of the pseudomonads based on 16S rRNA sequence. Int. J. Syst. Evol. Microbiol. 50: 1563-1589.Google Scholar
  2. Ausubel F.M., Brent R., Kingston R.E., Moore D.D., Seidman J.G., Smith J.A. and Struhl K. (Eds.), 1994. Current Protocols in Molecular Biology. John Wiley and Sons Inc., USA.Google Scholar
  3. Cilia V., Lafay B. and Christen R. 1996. Sequence heterogeneities among 16S ribosomal RNA sequences, and their effect on phylogenetic analyses at the species level. Mol. Biol. Evol. 13: 451-461.Google Scholar
  4. Clayton R.A., Sutton G., Hinkle P.S., Bult C. and Fields C. 1995. Intraspecific variation in small-subunit rRNA sequences in Gen-Bank: Why single sequences may not adequately represent prokaryotic taxa. Int. J. Syst. Bacteriol. 45: 595-599.Google Scholar
  5. De Lajudie P., Willems A., Pot B., Dewettinck D., Maestrojuan G., Neyra M., Collins M.D., Dreyfus B., Kersters K. and Gillis M. 1994. Polyphasic taxonomy of rhizobia: emendation of the genus Sinorhizobium and description of Sinorhizobium meliloti comb. nov., Sinorhizobium saheli [sic: sahalense] sp. nov., and Sinorhizobium teranga [sic: terangae] sp. nov. Int. J. Syst. Bacteriol. 44: 715-733.Google Scholar
  6. De Vos P., Goor N., Gillis M. and de Ley J. 1985. Ribosomal ribonucleic acid cistron similarities of phytopathogenic Pseudomonas species. Int. J. Syst. Bacteriol. 35: 169-184.Google Scholar
  7. Eernisse D.J. and Kluge A.G. 1993. Taxonomic congruence versus total evidence, and amniote phylogeny inferred from fossils, molecules, and morphology. Mol. Biol. Evol. 10: 1170-1195.Google Scholar
  8. Farris J.S., Källersjö M., Kluge A.G. and Bult C. 1994. Testing significance of incongruence. Cladistics 10: 315-319.Google Scholar
  9. Gest H. 2003. Names of bacteria and their evolutionary relationships. Microbiol. 149: 1956-1958.Google Scholar
  10. Gutell R.R., Cannone J.J., Shang Z., Du Y. and Serra M.J. 2000. A Story: unpaired adenosine bases in ribosomal RNA. J. Mol. Biol. 304: 335-354.Google Scholar
  11. Hauben L., Moore E.R., Vauterin L., Steenackers M., Mergaert J., Verdonck L., Swings J. 1998. Phylogenetic position of phyto-pathogens within the Enterobacteriaceae. Syst. Appl. Microbiol. 21: 384-97.Google Scholar
  12. Hendy M.D. and Penny D. 1989. A framework for the quantitative study of evolutionary trees. Syst. Zool. 38: 297-309.Google Scholar
  13. Henikoff S. and Henikoff J.G. 1994. Protein family classification based on searching a database of blocks. Genomics 19: 97-107.Google Scholar
  14. Hofmann K., Bucher P., Falquet L. and Bairoch A. 1999. The PROSITE database, its status in 1999. Nucleic Acids Res. 27: 215-219.Google Scholar
  15. Johnson J.L. and Palleroni N.J. 1989. Deoxyribonucleic acid similarities among Pseudomonas species. Int. J. Syst. Bacteriol. 39: 230-235.Google Scholar
  16. Kersters K., Ludwig W., Vancanneyt M., de Vos P., Gillis M. and Schleifer K.-H. 1996. Recent changes in the classification of the pseudomonads: an overview. Syst. Appl. Microbiol. 19: 465-477.Google Scholar
  17. Kishino H. and Hasegawa M. 1989. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order of Hominoidea. J. Mol. Evol. 29: 170-179.Google Scholar
  18. López-Gómez R. and Gómez-Lin M.A. 1992. A method for extracting intact RNA from fruits rich in polysaccharides using ripe mango mesocarp. HortScience 27: 440-442.Google Scholar
  19. Moore E.R.B., Mau M., Arnscheidt A., Böttger E.C., Hutson R.A., Collins M.D., van de Peer Y., de Wachter R. and 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.Google Scholar
  20. Nicholas K.B., Nicholas H.B. Jr. and Deerfield D.W. II 1997. GeneDoc: Analysis and Visualisation of Genetic Variation, EM-BNEW. News. 4: 14.Google Scholar
  21. Palleroni N.J. 1984. Genus I. Pseudomonas Migula 1894, 237,. pp. 141-199. In: Krieg N.J. and Jolt J.G. (eds), Bergey's Manual of Systematic Bacteriology Vol. 1. Williams and Wilkins, Baltimore, Maryland, USA.Google Scholar
  22. Palleroni N.J. 1993. Pseudomonas classification: a new case history in the taxonomy of Gram-negative bacteria. Antonie Leeuwenhoek 64: 231-251.Google Scholar
  23. Palleroni N.J., Ballard R.W., Ralston E. and Doudoroff M. 1972. Deoxyribonucleic acid homologies among some Pseudomonas species. J. Bacteriol. 110: 1-11.Google Scholar
  24. Palleroni N.J., Kunisawa R., Contopoulu R. and Doudoroff M. 1973. Nucleic acid homologies in the genus Pseudomonas. Int. J. Syst. Bacteriol. 23: 333-339.Google Scholar
  25. Posada D. and Crandall K.A. 1998. MODELTEST: testing the model of DNA substitution. Bioinformatics 14: 817-818.Google Scholar
  26. Rodríguez F.J., Oliver J.L., Marín A. and Medina J.R. 1990. The general stochastic model of nucleotide substitution. J. Theor. Biol. 142: 485-501.Google Scholar
  27. Shimodaira H. and Hasegawa M. 1999. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 16: 1114-1116.Google Scholar
  28. Spiers A.J., Buckling A. and Rainey P.B. 2000. The causes of Pseudomonas diversity. Microbiology 146: 2345-2350.Google Scholar
  29. Stanier R., Palleroni N.J. and Doudoroff M. 1966. The aerobic pseudomonads: a taxonomic study. J. Gen. Microbiol. 43: 159-271.Google Scholar
  30. Su X. and Gibor A. 1988. A method for RNA isolation from marine macro-algae. Anal. Chem. 174: 650-657.Google Scholar
  31. Swofford D.L. 2001. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sinauer Associates, Sunderland, Massachusetts, USA.Google Scholar
  32. Tamura K. and Nei M. 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10: 512-526.Google Scholar
  33. Templeton A.R. 1983. Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the humans and apes. Evolution 37: 221-244.Google Scholar
  34. Thompson J.D., Higgins D.G. and Gibson T.J. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680.Google Scholar
  35. Vancanneyt M., Torck U., Dewettinck D., Vaerewijck M. and Kersters K. 1996. Grouping of pseudomonads by SDS-PAGE of whole cell proteins. Syst. Appl. Microbiol. 19: 556-568.Google Scholar
  36. 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: 407-38.Google Scholar
  37. Weiller G.F. 1998. Phylogenetic Profiles: a graphical method for detecting genetic recombinations in homologous sequences. Mol. Biol. Evol. 15: 326-335.Google Scholar
  38. Woese C.R. 1987. Bacterial evolution. Microbiol. Rev. 51: 221-71.Google Scholar
  39. Wolf Y.I., Rogozin I.B., Grishin N.V. and Koonin E.V. 2002. Ge-nome trees and the Tree of Life. Trends Genet. 18: 472-479.Google Scholar
  40. Yamamoto S., Kasai H., Arnold D.L., Jackson R.W., Vivian A. and Harayama S. 2000. Phylogeny of the genus Pseudomonas: in-trageneric structure reconstructed from the nucleotide sequences of gyrB and rpoD genes. Microbiology 146: 2385-2394.Google Scholar

Copyright information

© Kluwer Academic Publishers 2004

Authors and Affiliations

  • Elena Hilario
    • 1
    • 2
  • Thomas R. Buckley
    • 1
  • John M. Young
    • 1
  1. 1.Landcare ResearchAucklandNew Zealand
  2. 2.Horticulture and Food Research Institute of New ZealandAucklandNew Zealand

Personalised recommendations