Skip to main content
SpringerLink
Log in

Relationships within the Proteobacteria of plant pathogenic Acidovorax species and subspecies, Burkholderia species, and Herbaspirillum rubrisubalbicans by sequence analysis of 16S rDNA, numerical analysis and determinative tests

  • Published:
Antonie van Leeuwenhoek Aims and scope Submit manuscript

Abstract

Sequence data for 16S rDNA of the type strains of Acidovorax avenae subsp. avenae, A. avenae subsp. cattleyae, A. avenae subsp. citrulli, A. konjaci and Herbaspirillum rubrisubalbicans were compared with GenBank library accessions of Burkholderiaspp., Comamonas sp., Ralstonia solanacearum and Variovorax sp. Maximum Parsimony analysis produced two clusters: 1. Acidovoraxspp., Comamonas sp., and Variovorax sp. (all in the Comamonadaceae), and 2. Burkholderia spp., Ralstonia solanacearum,and Herbaspirillum rubrisubalbicans.Maximum Likelihood analysis produced only one cluster (of the Comamonadaceae). Using nutritional and laboratory tests, all Acidovorax spp., Burkholderiaspp., and Herbaspirillum rubrisubalbicans were discriminated in distinct clusters at the species level, and could be identified by selected determinative tests. There were no phenotypic tests constituted as a circumscription of the genera and which permitted the allocation of strains to genera. Strain identification as species allowed allocation to genera only by inference. The nomenclatural implications of these data are discussed.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • Baldani JI, Pot B, Kirchhof G, Falsen E, Baldani VLD, Olivares FL, Hoste B, Kersters K, Hartmann K, Gillis M, & Döbereiner J (1996) Emended description of Herbaspirillum; inclusion of [Pseudomonas] rubrisubalbicans, a mild plant pathogen, as Herbaspirillum rubrisubalbicans comb. nov.; and classification of a group of clinical isolates (EF Group 1) as Herbaspirillum species 3. Int. J. Syst. Bacteriol. 46: 802-810.

    Google Scholar 

  • Colwell RR (1970) Polyphasic taxonomy and the genus Vibrio: numerical taxonomy of Vibrio cholerae, Vibrio parahaemolyticus, and related Vibrio species. J. Bacteriol. 104: 410-433.

    Google Scholar 

  • Cowan ST (1978) In: Hill LR (Ed) A Dictionary of Microbial Taxonomy. Cambridge University Press, London, UK. 285pp.

    Google Scholar 

  • De Vos P, Goor M, Gillis M & De Ley J (1985) Ribosomal ribonucleic acid cistron similarities of phytopathogenic Pseudomonas species. Int. J. Syst. Bacteriol. 35: 169-184.

    Google Scholar 

  • Feng D-F & Doolittle R F (1987) Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J. Mol. Evol. 25: 351-360.

    Google Scholar 

  • Gillis M, Van Van T, Bardin R, Goor M, Hebbar P, Willems A, Segers P, Kersters K, Heulin T & Fernandez MP (1995) Polyphasic taxonomy in the genus Burkholderia leading to an emended description of the genus and proposition of Burkholderia vietnamiensis sp. nov. for N2-fixing isolates from rice in Vietnam. Int. J. Syst. Bacteriol. 45: 274-289.

    Google Scholar 

  • Goodfellow M, Manfio GP & Chun J (1997) Towards a practical species concept for cultivable bacteria. In: Claridge MF, Dawah HA & Wilson MR (Eds) Species: The Units of Biodiversity, (pp 25-59). Chapman Hall, London.

    Google Scholar 

  • Goodfellow M & O'Donnell AG (1993) The roots of bacterial systematics. In: Goodfellow M. & O'Donnell AG (Eds) Handbook of New Bacterial Systematics, (pp. 3-54). Academic Press, London.

    Google Scholar 

  • Hasegawa M, Kishino H & Yano T (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 21: 160-174.

    Google Scholar 

  • Hu F-P, Young JM & Triggs CM (1991) Numerical analysis and determinative tests for non-fluorescent plant-pathogenic Pseudomonas spp. and genomic analysis and reclassification of species related to Pseudomonas avenae Manns 1909. Int. J. Syst. Bacteriol. 41: 516-525.

    Google Scholar 

  • Kersters K, Ludwig W, Vancanneyt M, De Vos P, Gillis M & Schleifer KH (1996) Recent changes in the classification of pseudomonads: an overview. Syst. Appl. Microbiol. 9: 465-477.

    Google Scholar 

  • Kishino H & Hasegawa M (1989) Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from sequence data and the branching order in the Hominoidea. J. Mol. Evol. 29: 170-179.

    Google Scholar 

  • Lelliott RA (1972) The genus Xanthomonas. In: Maas Geesteranus HP (Ed) Plant Pathogenic Bacteria 1971, Proceedings of the 3rd International Conference on Plant Pathogenic Bacteria, Wageningen, 14-21 April, 1971, (pp 269-272). Pudoc, Wageningen.

  • Li X & Hayward AC (1994) Bacterial whole cell protein profiles of the rRNA group II pseudomonads. J. Appl. Bacteriol. 77: 308-318.

    Google Scholar 

  • Li X, Dorsch M, Del Dot T, Sly LI, Stackebrandt E & Hayward AC (1993) Phylogenetic studies of the rRNA group II pseudomonads based on 16srRNA gene sequences. J. Appl. Bacteriol. 74: 324-329.

    Google Scholar 

  • Murray RGE, Brenner DJ, Colwell RR, De Vos P, Goodfellow M, Grimont PAD, Pfenning N, Stackebrandt E & Zavarzin GA (1990) Report of the ad hoc committee on approaches to taxonomy within the Proteobacteria. Int. J. Syst. Bacteriol. 40: 213-215.

    Google Scholar 

  • Palleroni NJ (1984) Genus Pseudomonas Migula 1894. In: Krieg NR & Holt JG (Eds) Bergey's Manual of Systematic Bacteriology, Vol 1. (pp 141-199). Williams & Wilkins, Baltimore. pp 964.

    Google Scholar 

  • Sambrook J, Fritsch EF & Maniatis T (1989) Molecular Cloning-a Laboratory Manual. Second Edition. Cold Spring Harbour Laboratory Press, USA.

    Google Scholar 

  • Sneath PHA (1984) Numerical taxonomy. In: Krieg NR & Holt JG (Eds) Bergey's Manual of Systematic Bacteriology, Vol 1 (pp 5-7). Williams & Wilkins, Baltimore.

    Google Scholar 

  • Stackebrandt E & Goebel BM (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.

    Google Scholar 

  • Stead DE (1992) Grouping of plant-pathogenic and some other Pseudomonas spp. by using cellular fatty acid profiles. Int. J. Syst. Bacteriol. 42: 281-295.

    Google Scholar 

  • Swofford DL (1999) PAUP*. Phylogenetic Analysis Using Parsimony (* and Other Methods). Version 4. Sinauer Associates, Sunderland, Massachusetts.

    Google Scholar 

  • Urakami T, Ito-Yoshida C, Araki H, Kijima T, Suzuki K-I & Komagata K (1994) Transfer of Pseudomonas plantarii and Pseudomonas glumae to Burkholderia as Burkholderia spp. and description of Burkholderia vandii sp. nov. Int. J. Syst. Bacteriol. 44: 235-245.

    Google Scholar 

  • 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 

  • Wayne LG, Brenner DJ, Colwell RR., Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E, Starr MP & Trüper HG (1987) Report of the ad hoc committee on the reconciliation of approaches to bacterial systematics. Int. J. Syst. Bacteriol. 37: 463-64.

    Google Scholar 

  • Wen A, Fegan M, Hayward AC, Chakraborty S & Sly Li, 1999. Phylogenetic relationships among members of the Comamonadaceae, and description of Delftia acidovorans (den Dooren de Jong 1926 and Tamaoka et al. 1987) gen. nov., comb. nov. Int. J. Syst. Bacteriol. 49: 567-576.

    Google Scholar 

  • Willems A, Busse J, Goor M. & Kersters K (1991) Comamonadaceae, a new family encompassing the acidovorans rRNA complex, including Variovorax paradoxus gen. nov., comb. nov., for Alcaligenes paradoxus (Davis 1969). Int. J. Syst. Bacteriol. 41: 445-450.

    Google Scholar 

  • Willems A, Goor M, Thielemans S, Gillis M, Kersters K & De Ley J (1992) Transfer of several phytopathogenic Pseudomonas species to Acidovorax as Acidovorax avenae subsp.avenae subsp. nov., comb. nov., Acidovorax avenae subsp. citrulli, Acidovorax avenae subsp. cattleyae, and Acidovorax konjaci. Int. J. Syst. Bacteriol. 42: 107-119.

    Google Scholar 

  • Yabuuchi E, Kosako Y, Oyaizu H, Yano I, Hotta H, Hashimoto Y, Ezaki T & Arakawa M (1992) Proposal of Burkholderia gen. nov. and transfer of seven species of the genus Pseudomonas homology group II to the new genus, with the type species Burkholderia cepacia (Palleroni & Holmes 1981) comb. nov. Microbiol. Immunol. 36: 1251-1275.

    Google Scholar 

  • Yabuuchi E, Kosako Y, Yano I, Hotta H & Nishiuchi Y (1995) Transfer of two Burkholderia and an Alcaligenes species to Ralstonia gen. nov.: proposal of Ralstonia pickettii (Ralston, Palleroni and Doudoroff 1973) comb. nov., Ralstonia solanacearum (Smith 1896) comb. nov. and Ralstonia eutropha (Davis 1969) comb. nov. Microbiol. Immunol. 39: 897-904.

    Google Scholar 

  • Young JM (1999) Recent systematics developments and implications for plant pathogenic bacteria. In: Priest FG & Goodfellow M (Eds) Applied Microbial Systematics, (pp 133-160). Chapman Hall.

  • Young JM, Takikawa Y, Gardan L & Stead DE (1992) Changing concepts in the taxonomy of plant pathogenic bacteria. Annu. Rev. Phytopathol. 30: 67-105.

    Google Scholar 

  • Young JM, Jones DS & Gillings M (1996) Relationships between populations of Pseudomonas syringae pv. persicae determined by restriction analysis. Pl. Pathol. 45: 350-357.

    Google Scholar 

  • Young JM, Gardan L, Ren X-Z & Hu F-P (1997) Genomic and phenotypic characterization of the bacterium causing blight of kiwifruit in New Zealand. Pl. Pathol. 46: 857-864.

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Landcare Research, Auckland, New Zealand

    F.-P. Hu, J.M. Young & D.-C. Park

  2. Department of Plant Protection, Fujian Agricultural University, Fuzhou, Fujian, People's Republic of China

    F.-P. Hu & J.M. Young

  3. Statistics Department, University of Auckland, Auckland, New Zealand

    C.M. Triggs

  4. School of Biological Sciences, University of Auckland, Auckland, New Zealand

    D.J. Saul

Authors
  1. F.-P. Hu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. J.M. Young
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. C.M. Triggs
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. D.-C. Park
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. D.J. Saul
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to J.M. Young.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Hu, FP., Young, J., Triggs, C. et al. Relationships within the Proteobacteria of plant pathogenic Acidovorax species and subspecies, Burkholderia species, and Herbaspirillum rubrisubalbicans by sequence analysis of 16S rDNA, numerical analysis and determinative tests. Antonie Van Leeuwenhoek 80, 201–213 (2001). https://doi.org/10.1023/A:1013066912814

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1023/A:1013066912814

Keywords

Search

Navigation