1887

Abstract

Five isolates, designated TA2, TA4, TA25, KOx and NS15 were isolated in previous studies by enrichment in mineral medium with potassium oxalate as the sole carbon source and were characterized using a polyphasic approach. The isolates were Gram-reaction-negative, aerobic, non-spore-forming rods. Phylogenetic analyses based on 16S rRNA and DNA gyrase B subunit () gene sequences confirmed that the isolates belonged to the genus and were most closely related to and (97.2–99.7 % 16S rRNA gene sequence similarity). The isolates could be differentiated from their closest relatives on the basis of several phenotypic characteristics. The major cellular fatty acid profiles of the isolates comprised C, Cω7, C cyclo and summed feature 3 (Cω7 and/or iso-C 2-OH). On the basis of DNA–DNA hybridization studies and phylogenetic analyses, the isolates represent three novel species within the genus , for which the names sp. nov. (TA25  = NBRC 106091  = CCM 7677  = DSM 23570), sp. nov. (KOx  = NBRC 106092  = CCM 2766  = DSM 23572) and sp. nov. (NS15  = NBRC 106088  = CCM 7667  = DSM 23571) are proposed.

Funding
This study was supported by the:
  • Ministry of Education, Youth and Sports of the Czech Republic (Award MSM0021622416)
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2011-09-01
2024-12-05
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References

  1. Anandham R., Indiragandhi P., Kwon S. W., Sa T. M., Jeon C. O., Kim Y. K., Jee H. J. 2010; Pandoraea thiooxydans sp. nov., a facultatively chemolithotrophic, thiosulfate-oxidizing bacterium isolated from rhizosphere soils of sesame (Sesamum indicum L.). Int J Syst Evol Microbiol 60:21–26 [View Article][PubMed]
    [Google Scholar]
  2. Chandra T. S., Shethna Y. I. 1975; Isolation and characterization of some new oxalate-decomposing bacteria. Antonie van Leeuwenhoek 41:101–111 [View Article][PubMed]
    [Google Scholar]
  3. Coenye T., LiPuma J. J. 2002; Use of the gyrB gene for the identification of Pandoraea species. FEMS Microbiol Lett 208:15–19 [View Article][PubMed]
    [Google Scholar]
  4. Coenye T., Falsen E., Hoste B., Ohlén M., Goris J., Govan J. R. W., Gillis M., Vandamme P. 2000; Description of Pandoraea gen. nov. with Pandoraea apista sp. nov., Pandoraea pulmonicola sp. nov., Pandoraea pnomenusa sp. nov., Pandoraea sputorum sp. nov. and Pandoraea norimbergensis comb. nov.. Int J Syst Evol Microbiol 50:887–899 [View Article][PubMed]
    [Google Scholar]
  5. Daneshvar M. I., Hollis D. G., Steigerwalt A. G., Whitney A. M., Spangler L., Douglas M. P., Jordan J. G., MacGregor J. P., Hill B. C. et al. 2001; Assignment of CDC weak oxidizer group 2 (WO-2) to the genus Pandoraea and characterization of three new Pandoraea genomospecies. J Clin Microbiol 39:1819–1826 [View Article][PubMed]
    [Google Scholar]
  6. Ezaki T., Hashimoto Y., Yabuuchi E. 1989; Fluorometric deoxyribonucleic acid deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane-filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 39:224–229 [View Article]
    [Google Scholar]
  7. Felsenstein J. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791 [View Article]
    [Google Scholar]
  8. Graff A., Stubner S. 2003; Isolation and molecular characterization of thiosulfate-oxidizing bacteria from an Italian rice field soil. Syst Appl Microbiol 26:445–452 [View Article][PubMed]
    [Google Scholar]
  9. Jenni B., Realini M., Aragno M., Tamer A. U. 1988; Taxonomy of non H2-lithotrophic, oxalate-oxidizing bacteria related to Alcaligenes eutrophus . Syst Appl Microbiol 10:126–133 [CrossRef]
    [Google Scholar]
  10. Jeon Y. S., Chung H. W., Park S., Hur I., Lee J. H., Chun J. 2005; jphydit: a java-based integrated environment for molecular phylogeny of ribosomal RNA sequences. Bioinformatics 21:3171–3173 [View Article][PubMed]
    [Google Scholar]
  11. Jiang X. W., Liu H., Xu Y., Wang S. J., Leak D. J., Zhou N. Y. 2009; Genetic and biochemical analyses of chlorobenzene degradation gene clusters in Pandoraea sp. strain MCB032. Arch Microbiol 191:485–492 [View Article][PubMed]
    [Google Scholar]
  12. Kimura M. 1980; A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120 [View Article][PubMed]
    [Google Scholar]
  13. Lane D. J. 1991; 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics pp. 115–175 Edited by Stackebrandt E., Goodfellow M. Chichester: Wiley;
    [Google Scholar]
  14. Larkin M. A., Blackshields G., Brown N. P., Chenna R., McGettigan P. A., McWilliam H., Valentin F., Wallace I. M., Wilm A. et al. 2007; clustal w and clustal_x version 2.0. Bioinformatics 23:2947–2948 [View Article][PubMed]
    [Google Scholar]
  15. Liz J. A. Z. E., Jan-Roblero J., de la Serna J. Z. D., de León A. V. P., Hernández-Rodríguez C. 2009; Degradation of polychlorinated biphenyl (PCB) by a consortium obtained from a contaminated soil composed of Brevibacterium, Pandoraea and Ochrobactrum . World J Microbiol Biotechnol 25:165–170 [View Article]
    [Google Scholar]
  16. Maidak B. L., Cole J. R., Lilburn T. G., Parker C. T. Jr, Saxman P. R., Farris R. J., Garrity G. M., Olsen G. J., Schmidt T. M., Tiedje J. M. 2001; The RDP-II (Ribosomal Database Project). Nucleic Acids Res 29:173–174 [View Article][PubMed]
    [Google Scholar]
  17. Marmur J. 1961; A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 3:208–218 [View Article]
    [Google Scholar]
  18. Myers E. W., Miller W. 1988; Optimal alignments in linear space. Comput Appl Biosci 4:11–17[PubMed]
    [Google Scholar]
  19. Okeke B. C., Siddique T., Arbestain M. C., Frankenberger W. T. 2002; Biodegradation of γ-hexachlorocyclohexane (lindane) and α-hexachlorocyclohexane in water and a soil slurry by a Pandoraea species. J Agric Food Chem 50:2548–2555 [View Article][PubMed]
    [Google Scholar]
  20. Owen R. J., Lapage S. P. 1976; The thermal denaturation of partly purified bacterial deoxyribonucleic acid and its taxonomic applications. J Appl Bacteriol 41:335–340[PubMed] [CrossRef]
    [Google Scholar]
  21. Ozaki S., Kishimoto N., Fujita T. 2007; Change in the predominant bacteria in a microbial consortium cultured on media containing aromatic and saturated hydrocarbons as the sole carbon source. Microbes Environ 22:128–135 [View Article]
    [Google Scholar]
  22. Sahin N. 2003; Oxalotrophic bacteria. Res Microbiol 154:399–407 [View Article][PubMed]
    [Google Scholar]
  23. Saitou N., Nei M. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–426
    [Google Scholar]
  24. Sasser M. 1990; Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 20:16
    [Google Scholar]
  25. Siddique T., Okeke B. C., Arshad M., Frankenberger W. T. Jr 2003; Enrichment and isolation of endosulfan-degrading microorganisms. J Environ Qual 32:47–54 [View Article][PubMed]
    [Google Scholar]
  26. Smibert R. M., Krieg N. R. 1994; Phenotypic characterization. In Methods for General and Molecular Bacteriology pp. 607–654 Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  27. Tabacchioni S., Ferri L., Manno G., Mentasti M., Cocchi P., Campana S., Ravenni N., Taccetti G., Dalmastri C. et al. 2008; Use of the gyrB gene to discriminate among species of the Burkholderia cepacia complex. FEMS Microbiol Lett 281:175–182 [View Article][PubMed]
    [Google Scholar]
  28. Tamer A. U., Aragno M. 1980; [Isolement, charactérization et essai d’identification de bactéries capables d’utiliser l’oxalate comme seule source de carbone et d’énergie.]. Bull Soc Neuchâtel Sci Nat 103:91–104 (in French)
    [Google Scholar]
  29. Wayne L. G., Brenner D. J., Colwell R. R., Grimont P. A. D., Kandler O., Krichevsky M. I., Moore L. H., Moore W. E. C., Murray R. G. E. et al. 1987; Report of the ad-hoc-committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464 [View Article]
    [Google Scholar]
  30. Wittke R., Ludwig W., Peiffer S., Kleiner D. 1997; Isolation and characterisation of Burkholderia norimbergensis sp. nov., a mildly alkaliphilic sulfur oxidizer. Syst Appl Microbiol 20:549–553 [CrossRef]
    [Google Scholar]
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