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Volume 61, Issue 2

sp. nov., a bacterium isolated from acidic forest soil that catabolizes (+)-catechin and its putative aromatic derivatives Free

Abstract

A novel bacterium, designated strain OX-01, was isolated from acidic soil, taxonomically investigated and identified as an agent that catabolizes (+)-catechin into taxifolin. Strain OX-01 is a Gram-reaction-negative, aerobic, non-sporulating, non-motile and rod-shaped bacterium. 16S rRNA gene sequence analysis identified this strain as a member of the genus and occupying a phylogenetic position closest to, but clearly distinct from, . Strain OX-01 does not have any genes, which are required for N-fixation, in its genome, a feature that is similar to , which lacks , but is distinct from the N-fixing features of many other phylogenetically related taxa, such as , , , , , and . Strain OX-01 has the following chemotaxonomic characteristics: the major ubiquinone is Q-8, the DNA G+C content is 64 mol% and the major fatty acids are C, C cyclo and C 7. It also has a unique profile of carbohydrate utilization among other species of the genus . The strain cannot assimilate many pentoses, hexoses and oligosaccharides, whereas it can catabolize (+)-catechin and its putative aromatic derivatives, such as 4-hydroxy-3-methoxycinnamic acid, protocatechuic acid, -hydroxybenzoic acid, --coumaric acid and vanillic acid. Based on its morphological, physiological and chemotaxonomic characteristics, together with DNA–DNA relatedness values and 16S rRNA gene sequence comparison data, we show that strain OX-O1 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is OX-01 (=NBRC 105797 =DSM 22550).

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2011-02-01
2024-04-25
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References

  1. Aizawa T., Ve N. B., Nakajima M., Sunairi M. 2010; Burkholderia heleia sp. nov., a nitrogen-fixing bacterium isolated from an aquatic plant, Eleocharis dulcis , that grows in highly acidic swamps in actual acid sulfate soil areas of Vietnam. Int J Syst Evol Microbiol 60:1152–1157 [CrossRef]
     [Google Scholar]
  2. Aspray T. J., Frey-Klett P., Jones J. E., Whipps J. M., Barbaye J., Bending G. D. 2006; Mycorrhization helper bacteria: a case of specificity for altering ectomycorrhiza architecture but not ectomycorrhiza formation. Mycorrhiza 16:533–541 [CrossRef]
     [Google Scholar]
  3. Brämer C. O., Vandamme P., da Silva L. F., Gomez J. G. C., Steinbuchel A. 2001; Burkholderia sacchari sp. nov., a polyhydroxyalkanoate-accumulating bacterium isolated from soil of a sugar-cane plantation in Brazil. Int J Syst Evol Microbiol 51:1709–1713 [CrossRef]
     [Google Scholar]
  4. Caballero-Mellado J., Martínez-Aguilar L., Paredes-Valdez G., Estrada-de los Santos P. 2004; Burkholderia unamae sp. nov., an N2-fixing rhizospheric and endophytic species. Int J Syst Evol Microbiol 54:1165–1172 [CrossRef]
     [Google Scholar]
  5. Chen W.-M., James E. K., Coenye T., Chou J.-H., Barrios E., de Faria S. M., Elliott G. N., Sheu S.-Y., Sprent J. I., Vandamme P. 2006; Burkholderia mimosarum sp. nov., isolated from root nodules of Mimosa spp. from Taiwan and South America. Int J Syst Evol Microbiol 56:1847–1851 [CrossRef]
     [Google Scholar]
  6. Chen W.-M., de Faria S. M., James E. K., Elliott G. N., Lin K.-Y., Chou J.-H., Sheu S.-Y., Cnockaert M., Sprent J. I., Vandamme P. 2007; Burkholderia nodosa sp. nov., isolated from root nodules of the woody Brazilian legumes Mimosa bimucronata and Mimosa scabrella . Int J Syst Evol Microbiol 57:1055–1059 [CrossRef]
     [Google Scholar]
  7. Coenye T., Vandamme P. 2003; Diversity and significance of Burkholderia species occupying diverse ecological niches. Environ Microbiol 5:719–729 [CrossRef]
     [Google Scholar]
  8. Estrada-de los Santos P., Bustillos-Cristales R., Caballero-Mellado J. 2001; Burkholderia , a genus rich in plant-associated nitrogen fixers with wide environmental and geographic distribution. Appl Environ Microbiol 67:2790–2798 [CrossRef]
     [Google Scholar]
  9. 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 [CrossRef]
     [Google Scholar]
  10. Felsenstein J. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791 [CrossRef]
     [Google Scholar]
  11. Gutell R. R., Larsen N., Woese C. R. 1994; Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective. Microbiol Rev 58:10–26
     [Google Scholar]
  12. Izumi H., Anderson I. C., Alexander I. J., Killham K., Moore E. R. 2006; Endobacteria in some ectomycorrhiza of Scots pine ( Pinus sylvestris . FEMS Microbiol Ecol 56:34–43 [CrossRef]
     [Google Scholar]
  13. Johnston J. L. 1994; Similarity analysis of rRNAs. In Methods for General and Molecular Bacteriology. pp 683–700 Edited by Gerhardt P., Murray R. G. E., Wood W. A. Washington, DC: American Society for Microbiology;
  14. 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 [CrossRef]
     [Google Scholar]
  15. Lehning A., Fock U., Wittich R.-M., Timmis K. N., Pieper D. H. 1997; Metabolism of chlorotoluenes by Burkholderia sp. strain PS12 and toluene dioxygenase of Pseudomonas putida F1: evidence for monooxygenation by toluene and chlorobenzene dioxygenases. Appl Environ Microbiol 63:1974–1979
     [Google Scholar]
  16. Levy A., Chang B. J., Abbott L. K., Kuo J., Harnett G., Inglis T. J. J. 2003; Invasion of spores of the arbuscular mycorrhizal fungus Gigaspora decipiens by Burkholderia spp. Appl Environ Microbiol 69:6250–6256 [CrossRef]
     [Google Scholar]
  17. Lim Y. W., Baik K. S., Han S. K., Kim S. B., Bae K. S. 2003; Burkholderia sordidicola sp. nov., isolated from the white-rot fungus Phanerochaete sordida . Int J Syst Evol Microbiol 53:1631–1636 [CrossRef]
     [Google Scholar]
  18. Martínez-Aguilar L., Díaz R., Peña-Cabriales J. J., Estrada-de los Santos P., Dunn M. F., Caballero-Mellado J. 2008; Multichromosomal genome structure and confirmation of diazotrophy in novel plant-associated Burkholderia species. Appl Environ Microbiol 74:4574–4579 [CrossRef]
     [Google Scholar]
  19. Miller J. H. 1972 Experiments in Molecular Genetics Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
     [Google Scholar]
  20. Minerdi D., Fani R., Gallo R., Boarino A., Bonfante P. 2001; Nitrogen fixation genes in an endosybiotic Burkholderia strain. Appl Environ Microbiol 67:725–732 [CrossRef]
     [Google Scholar]
  21. Nishijima M., Araki-Sakai M., Sano H. 1997; Identification of isoprenoid quinones by frit-FAB liquid chromatography–mass spectrometry for the chemotaxonomy of microorganisms. J Microbiol Methods 28:113–122 [CrossRef]
     [Google Scholar]
  22. Otsuka Y., Nakamura M., Shigehara K., Sugimura K., Masai E., Ohara S., Katayama Y. 2006; Efficient production of 2-pyrone 4,6-dicarboxylic acid as a novel polymer-based material from protocatechuate by microbial function. Appl Microbiol Biotechnol 71:608–614 [CrossRef]
     [Google Scholar]
  23. Perin L., Martínez-Aguilar L., Paredes-Valdez G., Baldani J. I., Estrada-de los Santos P., Reis V. M., Caballero-Mellado J. 2006; Burkholderia silvatlantica sp. nov., a diazotrophic bacterium associated with sugar cane and maize. Int J Syst Evol Microbiol 56:1931–1937 [CrossRef]
     [Google Scholar]
  24. Reis V. M., Estrada-de los Santos P., Tenorio-Salgado S., Vogel J., Stoffels M., Guyon S., Mavingui P., Baldani V. L. D., Schmid M. other authors 2004; Burkholderia tropica sp. nov., a novel nitrogen-fixing, plant-associated bacterium. Int J Syst Evol Microbiol 54:2155–2162 [CrossRef]
     [Google Scholar]
  25. Saitou N., Nei M. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
     [Google Scholar]
  26. Seigle-Murandi F., Guiraud P., Croizê J., Falsen E., Eriksson K.-E. L. 1996; Bacteria are omnipresent on Phanerochaete chrysosporium Burdsall. Appl Environ Microbiol 62:2477–2481
     [Google Scholar]
  27. Staskawicz B. J., Dahlbeck D., Keen N. T. 1984; Cloned avirulence gene of Pseudomonas syringae pv. glycinea determines race-specific incompatibility on Glycine max (L.). Merr. Proc Natl Acad Sci U S A 81:6024–6028 [CrossRef]
     [Google Scholar]
  28. Takagi H., Shida O., Kadowaki K., Komagata K., Udaka S. 1993; Characterization of Bacillus brevis with descriptions of Bacillus migulanus sp.nov., Bacilluschoshinensis sp. nov., Bacillus parabrevis sp. nov., and Bacillus galactophilus sp. nov. Int J Syst Bacteriol 43:221–231 [CrossRef]
     [Google Scholar]
  29. Thompson J. D., Gibson T. J., Plewniak F., Jeanmougin F., Higgins D. G. 1997; The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882 [CrossRef]
     [Google Scholar]
  30. Valverde A., Delvasto P., Peix A., Velázquez E., Santa-Regina I., Ballester A., Rodríguez-Barrueco C., García-Balboa C., Igual J. M. 2006; Burkholderia ferrariae sp. nov., isolated from an iron ore in Brazil. Int J Syst Evol Microbiol 56:2421–2425 [CrossRef]
     [Google Scholar]
  31. Vandamme P., Govan J. R. W., LiPuma J. J. 2007; Diversity and role of Burkholderia spp. In Burkholderia: Molecular Microbiology and Genomics pp 1–28 Edited by Coenye T., Vandamme P. Wymondham, UK: Horizon Bioscience;
     [Google Scholar]
  32. Yano K., Nishi T. 1980; pKJ, a naturally occurring conjugative plasmid coding for toluene degradation and resistance to streptomycin and sulfonamides. J Bacteriol 143:552–560
     [Google Scholar]
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Burkholderia oxyphila sp. nov., a bacterium isolated from acidic forest soil that catabolizes (+)-catechin and its putative aromatic derivatives
Int J Syst Evol Microbiol 61, 249 (2011); https://doi.org/10.1099/ijs.0.017368-0
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