1887

Abstract

A non-sporulating, non-motile, catalase- and oxidase-positive, Gram-negative, rod-shaped bacterial strain, designated BA-3, was isolated from activated sludge of a wastewater treatment facility. The strain was able to degrade about 95 % of 100 mg 3-phenoxybenzoic acid l within 2 days of incubation. Growth occurred in the presence of 0–2 % (w/v) NaCl [optimum, 0.5 % (w/v) NaCl], at pH 5.5–9.0 (optimum, pH 7.0) and at 10–37 °C (optimum, 28 °C). Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain BA-3 was a member of the genus ; it showed highest gene sequence similarity to X23 (98.2 %), and similarities of <97.0 % with strains of other species. The polar lipid pattern, the presence of spermidine and ubiquinone Q-10, the predominance of summed feature 8 (Cω6 and/or Cω7) in the cellular fatty acid profile and the DNA G+C content also supported affiliation of the isolate to the genus . Strain BA-3 showed low DNA–DNA relatedness values (21.3±0.8 %) with X23. Based on phenotypic, genotypic and phylogenetic data, strain BA-3 represents a novel species of the genus , for which the name sp. nov. is proposed; the type strain is BA-3 ( = CCTCC AB 2010217 = KCTC 23196 = KACC 16433).

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2012-04-01
2020-01-17
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References

  1. Bala K. , Sharma P. , Lal R. . ( 2010; ). Sphingobium quisquiliarum sp. nov., a hexachlorocyclohexane (HCH)-degrading bacterium isolated from an HCH-contaminated soil. . Int J Syst Evol Microbiol 60:, 429–433. [CrossRef] [PubMed]
    [Google Scholar]
  2. Breznak J. A. , Costilow R. N. . ( 1994; ). Physicochemical factors in growth. . In Methods for General and Molecular Bacteriology, pp. 137–154. Edited by Gerhardt P. , Murray R. G. E. , Wood W. A. , Krieg N. R. . . Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  3. Buck J. D. . ( 1982; ). Nonstaining (KOH) method for determination of gram reactions of marine bacteria. . Appl Environ Microbiol 44:, 992–993.[PubMed]
    [Google Scholar]
  4. Busse H.-J. , Auling G. . ( 1988; ). Polyamine pattern as a chemotaxonomic marker within the Proteobacteria . . Syst Appl Microbiol 11:, 1–8.[CrossRef]
    [Google Scholar]
  5. Busse H. J. , Bunka S. , Hensel A. , Lubitz W. . ( 1997; ). Discrimination of members of the family Pasteurellaceae based on polyamine patterns. . Int J Syst Bacteriol 47:, 698–708. [CrossRef]
    [Google Scholar]
  6. Busse H. J. , Kämpfer P. , Denner E. B. M. . ( 1999; ). Chemotaxonomic characterisation of Sphingomonas . . J Ind Microbiol Biotechnol 23:, 242–251. [CrossRef] [PubMed]
    [Google Scholar]
  7. Chun J. , Lee J.-H. , Jung Y. , Kim M. , Kim S. , Kim B. K. , Lim Y. W. . ( 2007; ). EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. . Int J Syst Evol Microbiol 57:, 2259–2261. [CrossRef] [PubMed]
    [Google Scholar]
  8. Collins M. D. , Jones D. . ( 1980; ). Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2,4-diaminobutyric acid. . J Appl Bacteriol 48:, 459–470. [CrossRef]
    [Google Scholar]
  9. Collins M. D. , Pirouz T. , Goodfellow M. , Minnikin D. E. . ( 1977; ). Distribution of menaquinones in actinomycetes and corynebacteria. . J Gen Microbiol 100:, 221–230.[PubMed] [CrossRef]
    [Google Scholar]
  10. Dadhwal M. , Jit S. , Kumari H. , Lal R. . ( 2009; ). Sphingobium chinhatense sp. nov., a hexachlorocyclohexane (HCH)-degrading bacterium isolated from an HCH dumpsite. . Int J Syst Evol Microbiol 59:, 3140–3144. [CrossRef] [PubMed]
    [Google Scholar]
  11. 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]
  12. Felsenstein J. . ( 1981; ). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17:, 368–376. [CrossRef] [PubMed]
    [Google Scholar]
  13. Felsenstein J. . ( 1985; ). Confidence limits on phylogenies: an approach using the bootstrap. . Evolution 39:, 783–791. [CrossRef]
    [Google Scholar]
  14. Gregersen T. . ( 1978; ). Rapid method for distinction of Gram-negative from Gram-positive bacteria. . Eur J Appl Microbiol Biotechnol 5:, 123–127. [CrossRef]
    [Google Scholar]
  15. Guo P. , Wang B. , Hang B. , Li L. , Ali S. W. , He J. , Li S. . ( 2009; ). Pyrethroid-degrading Sphingobium sp. JZ-2 and the purification and characterization of a novel pyrethroid hydrolase. . Int Biodeterior Biodegradation 63:, 1107–1112. [CrossRef]
    [Google Scholar]
  16. Guo P. , Wang B. Z. , Hang B. J. , Li L. , Li S. P. , He J. . ( 2010; ). Sphingobium faniae sp. nov., a pyrethroid-degrading bacterium isolated from activated sludge treating wastewater from pyrethroid manufacture. . Int J Syst Evol Microbiol 60:, 408–412. [CrossRef] [PubMed]
    [Google Scholar]
  17. 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] [PubMed]
    [Google Scholar]
  18. Kroppenstedt R. M. . ( 1982; ). Separation of bacterial menaquinones by HPLC using reverse phase (RP-18) and a silver loaded ion exchanger. . J Liq Chromatogr 5:, 2359–2367. [CrossRef]
    [Google Scholar]
  19. Kumari H. , Gupta S. K. , Jindal S. , Katoch P. , Lal R. . ( 2009; ). Sphingobium lactosutens sp. nov., isolated from a hexachlorocyclohexane dump site and Sphingobium abikonense sp. nov., isolated from oil-contaminated soil. . Int J Syst Evol Microbiol 59:, 2291–2296. [CrossRef] [PubMed]
    [Google Scholar]
  20. 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]
  21. Liang Q. , Lloyd-Jones G. . ( 2010; ). Sphingobium scionense sp. nov., an aromatic hydrocarbon-degrading bacterium isolated from contaminated sawmill soil. . Int J Syst Evol Microbiol 60:, 413–416. [CrossRef] [PubMed]
    [Google Scholar]
  22. Mandel M. , Marmur J. . ( 1968; ). Use of ultraviolet absorbance-temperature profile for determining the guanine plus cytosine content of DNA. . Methods Enzymol 12B:, 195–206. [CrossRef]
    [Google Scholar]
  23. Minnikin D. E. , O’Donnell A. G. , Goodfellow M. , Alderson G. , Athalye M. , Schaal A. , Parlett J. H. . ( 1984; ). An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. . J Microbiol Methods 2:, 233–241. [CrossRef]
    [Google Scholar]
  24. Ohta H. , Hattori T. . ( 1983; ). Agromonas oligotrophica gen. nov., sp. nov., a nitrogen-fixing oligotrophic bacterium. . Antonie van Leeuwenhoek 49:, 429–446.[PubMed]
    [Google Scholar]
  25. Pal R. , Bala S. , Dadhwal M. , Kumar M. , Dhingra G. , Prakash O. , Prabagaran S. R. , Shivaji S. , Cullum J. . & other authors ( 2005; ). Hexachlorocyclohexane-degrading bacterial strains Sphingomonas paucimobilis B90A, UT26 and Sp+, having similar lin genes, represent three distinct species, Sphingobium indicum sp. nov., Sphingobium japonicum sp. nov. and Sphingobium francense sp. nov., and reclassification of [Sphingomonas] chungbukensis as Sphingobium chungbukense comb. nov.. Int J Syst Evol Microbiol 55:, 1965–1972. [CrossRef] [PubMed]
    [Google Scholar]
  26. Prakash O. , Lal R. . ( 2006; ). Description of Sphingobium fuliginis sp. nov., a phenanthrene-degrading bacterium from a fly ash dumping site, and reclassification of Sphingomonas cloacae as Sphingobium cloacae comb. nov.. Int J Syst Evol Microbiol 56:, 2147–2152. [CrossRef] [PubMed]
    [Google Scholar]
  27. Saitou N. , Nei M. . ( 1987; ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4:, 406–425.[PubMed]
    [Google Scholar]
  28. Sambrook J. , Russell D. W. . ( 2001; ). Molecular cloning: a Laboratory Manual, , 3rd edn.. Cold Spring Harbor, NY:: Cold Spring Harbor Laboratory;.
    [Google Scholar]
  29. Sasser M. . ( 1990; ). Identification of bacteria by gas chromatography of cellular fatty acids. . USFCC Newsl 20:, 16.
    [Google Scholar]
  30. Singh A. , Lal R. . ( 2009; ). Sphingobium ummariense sp. nov., a hexachlorocyclohexane (HCH)-degrading bacterium, isolated from HCH-contaminated soil. . Int J Syst Evol Microbiol 59:, 162–166. [CrossRef] [PubMed]
    [Google Scholar]
  31. Skerman V. B. D. . ( 1967; ). A Guide to the Identification of the Genera of Bacteria, , 2nd edn.. Baltimore:: Williams & Wilkins;.
    [Google Scholar]
  32. Takeuchi M. , Kawai F. , Shimada Y. , Yokota A. . ( 1993; ). Taxonomic study of polyethylene glycerol-utilizing bacteria: emended description of the genus Sphingomonas and new descriptions of Sphingomonas macrogoltabidus sp. nov., Sphingomonas sanguis sp. nov. and Sphingomonas terrae sp. nov.. Syst Appl Microbiol 16:, 227–238. [CrossRef]
    [Google Scholar]
  33. Takeuchi M. , Hamana K. , Hiraishi A. . ( 2001; ). Proposal of the genus Sphingomonas sensu stricto and three new genera, Sphingobium, Novosphingobium and Sphingopyxis, on the basis of phylogenetic and chemotaxonomic analyses. . Int J Syst Evol Microbiol 51:, 1405–1417.[PubMed]
    [Google Scholar]
  34. Tamura K. , Peterson D. , Peterson N. , Stecher G. , Nei M. , Kumar S. . ( 2011; ). mega5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. . Mol Biol Evol 28:, 2731–2739.[PubMed] [CrossRef]
    [Google Scholar]
  35. 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] [PubMed]
    [Google Scholar]
  36. Tindall B. J. , Rosselló-Móra R. , Busse H.-J. , Ludwig W. , Kämpfer P. . ( 2010; ). Notes on the characterization of prokaryote strains for taxonomic purposes. . Int J Syst Evol Microbiol 60:, 249–266. [CrossRef] [PubMed]
    [Google Scholar]
  37. Ushiba Y. , Takahara Y. , Ohta H. . ( 2003; ). Sphingobium amiense sp. nov., a novel nonylphenol-degrading bacterium isolated from a river sediment. . Int J Syst Evol Microbiol 53:, 2045–2048. [CrossRef] [PubMed]
    [Google Scholar]
  38. Wang B. Z. , Guo P. , Hang B. J. , Li L. , He J. , Li S. P. . ( 2009; ). Cloning of a novel pyrethroid-hydrolyzing carboxylesterase gene from Sphingobium sp. strain JZ-1 and characterization of the gene product. . Appl Environ Microbiol 75:, 5496–5500. [CrossRef] [PubMed]
    [Google Scholar]
  39. Wang B.-Z. , Guo P. , Zheng J.-W. , Hang B.-J. , Li L. , He J. , Li S.-P. . ( 2011; ). Sphingobium wenxiniae sp. nov., a synthetic pyrethroid (SP)-degrading bacterium isolated from activated sludge in an SP-manufacturing wastewater treatment facility. . Int J Syst Evol Microbiol 61:, 1776–1780. [CrossRef] [PubMed]
    [Google Scholar]
  40. 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. . & other authors ( 1987; ). International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. . Int J Syst Bacteriol 37:, 463–464. [CrossRef]
    [Google Scholar]
  41. Wittich R.-M. , Busse H.-J. , Kämpfer P. , Tiirola M. , Wieser M. , Macedo A. J. , Abraham W.-R. . ( 2007; ). Sphingobium aromaticiconvertens sp. nov., a xenobiotic-compound-degrading bacterium from polluted river sediment. . Int J Syst Evol Microbiol 57:, 306–310. [CrossRef] [PubMed]
    [Google Scholar]
  42. Yabuuchi E. , Yano I. , Oyaizu H. , Hashimoto Y. , Ezaki T. , Yamamoto H. . ( 1990; ). Proposals of Sphingomonas paucimobilis gen. nov. and comb. nov., Sphingomonas parapaucimobilis sp. nov., Sphingomonas yanoikuyae sp. nov., Sphingomonas adhaesiva sp. nov., Sphingomonas capsulata comb. nov., and two genospecies of the genus Sphingomonas . . Microbiol Immunol 34:, 99–119.[PubMed] [CrossRef]
    [Google Scholar]
  43. Yan Q.-X. , Wang Y.-X. , Li S.-P. , Li W.-J. , Hong Q. . ( 2010; ). Sphingobium qiguonii sp. nov., a carbaryl-degrading bacterium isolated from a wastewater treatment system. . Int J Syst Evol Microbiol 60:, 2724–2728. [CrossRef] [PubMed]
    [Google Scholar]
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