1887

Abstract

A Gram-stain-negative, aerobic, yellow-pigmented, rod-shaped bacterium, designated strain SC_3, was isolated from pesticide-contaminated soil sediment. The strain was able to mineralize 2-phenoxybenzoic acid. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SC_3 formed a monophyletic lineage in the genus , and showed highest similarity to the type strains of (97.0 %), followed by (96.8 %) and (96.7 %). The DNA–DNA relatedness between strain SC_3 and its closest phylogenetic neighbours was lower than 70 %. The major fatty acids (>5 % of the total) were summed feature 8 (comprising Cω7/Cω6), summed feature 3 (comprising Cω7/Cω6), C 2-OH, C and Cω6. The predominant quinone was ubiquinone Q-10, and the major polyamine was spermidine. The polar lipid profile contained diphosphatidylglycerol (DPG), sphingoglycolipid (SGL), phosphatidylethanolamine (PDME), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), phosphatidylmonomethylethanolamine (PMME), an unknown aminolipid (AL), two unknown lipids (L1, L2) and several unknown phospholipids (PL1–6). The genomic DNA G+C content of strain SC_3 was 62.9 mol%. On the basis of phenotypic, chemotaxonomic, phylogenetic and genotypic data, strain SC_3 represents a novel species of the genus , for which the name Sphingobium phenoxybenzoativorans sp. nov. is proposed. The type strain is SC_3 ( = CCTCC AB 2014349 = KACC 42448).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.000209
2015-06-01
2020-01-19
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/65/6/1986.html?itemId=/content/journal/ijsem/10.1099/ijs.0.000209&mimeType=html&fmt=ahah

References

  1. Bala G. , Caldeira K. , Nemani R. . ( 2010;). Fast versus slow response in climate change: implications for the global hydrological cycle. Clim Dyn 35: 423–434 doi:10.1007/s00382-009-0583-y .[CrossRef]
    [Google Scholar]
  2. Bernardet J.F. , Bowman J. . ( 2006;). The genus Flavobacterium . . In The Prokaryotes: A Handbook on the Biology of Bacteria vol. 7, pp. 481–531. Edited by Dworkin M. , Falkow S. , Rosenberg E. , Schleifer K. H. , Stackebrandt E. . , 3rd edn.., New York: Springer; doi:10.1007/0-387-30747-8_17 .
    [Google Scholar]
  3. Busse H.J. , Auling G. . ( 1988;). Polyamine pattern as a chemotaxonomic marker within the Proteobacteria . Syst Appl Microbiol 11: 1–8 doi:10.1016/S0723-2020(88)80040-7 .[CrossRef]
    [Google Scholar]
  4. 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 doi:10.1099/00207713-47-3-698 .[CrossRef]
    [Google Scholar]
  5. Busse H.J. , Kämpfer P. , Denner E.B.M. . ( 1999;). Chemotaxonomic characterisation of Sphingomonas . J Ind Microbiol Biotechnol 23: 242–251 10.1038/sj.jim.2900745 [PubMed].[CrossRef]
    [Google Scholar]
  6. Cashion P. , Holder-Franklin M.A. , McCully J. , Franklin M. . ( 1977;). A rapid method for the base ratio determination of bacterial DNA. Anal Biochem 81: 461–466 10.1016/0003-2697(77)90720-5 [PubMed].[CrossRef]
    [Google Scholar]
  7. Collins M.D. . ( 1985;). Isoprenoidquinone analyses in classification and identification. . In Chemical Methods in Bacterial Systematics, pp. 267–287. Edited by Goodfellow M. , Minnikin D. E. . Orlando, FL: Academic Press;.
    [Google Scholar]
  8. 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 10.1099/ijs.0.005553-0 [PubMed].[CrossRef]
    [Google Scholar]
  9. De Ley, J., Cattoir, H. and Reynaerts A. . ( 1970;). The quantitative measurement of DNA hybridization from renaturation rates. Europ. J. Biochem. 12: 133–142.[CrossRef]
    [Google Scholar]
  10. Fitch W.M. . ( 1971;). Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20: 406–416 doi:10.2307/2412116 .[CrossRef]
    [Google Scholar]
  11. Fujii K. , Urano N. , Ushio H. , Satomi M. , Kimura S. . ( 2001;). Sphingomonas cloacae sp. nov., a nonylphenol-degrading bacterium isolated from wastewater of a sewage-treatment plant in Tokyo. Int J Syst Evol Microbiol 51: 603–610 [PubMed].
    [Google Scholar]
  12. Garg N. , Bala K. , Lal R. . ( 2012;). Sphingobium lucknowense sp. nov., a hexachlorocyclohexane (HCH)-degrading bacterium isolated from HCH-contaminated soil. Int J Syst Evol Microbiol 62: 618–623 10.1099/ijs.0.028886-0 [PubMed].[CrossRef]
    [Google Scholar]
  13. Gerhardt P. , Murray R.G.E. , Wood W.A. , Krieg N.R. . ( 1994;). Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology;.
    [Google Scholar]
  14. 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 doi:10.1016/j.ibiod.2009.09.008 .[CrossRef]
    [Google Scholar]
  15. 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 10.1099/ijs.0.009795-0 [PubMed].[CrossRef]
    [Google Scholar]
  16. Huss V.A.R. , Festl H. , Schleifer K.H. . ( 1983;). Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 4: 184–192 10.1016/S0723-2020(83)80048-4 [PubMed].[CrossRef]
    [Google Scholar]
  17. Kim O.S. , Cho Y.J. , Lee K. , Yoon S.H. , Kim M. , Na H. , Park S.C. , Jeon Y.S. , Lee J.H. , other authors . ( 2012;). Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62: 716–721 10.1099/ijs.0.038075-0 [PubMed].[CrossRef]
    [Google Scholar]
  18. 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 10.1099/ijs.0.004739-0 [PubMed].[CrossRef]
    [Google Scholar]
  19. 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 10.1099/ijs.0.008144-0 [PubMed].[CrossRef]
    [Google Scholar]
  20. Mesbah M. , Premachandran U. , Whitman W.B. . ( 1989;). Precise measurement of the G+C content of deoxyribonucleic acid by highperformance liquid chromatography. Int J Syst Bacteriol 39: 159–167 doi:10.1099/00207713-39-2-159 .[CrossRef]
    [Google Scholar]
  21. Minnikin D.E. , Collins M.D. , Goodfellow M. . ( 1979;). Fatty acid and polar lipid composition in the classification of Cellulomonas Oerskovia and related taxa. J Appl Bacteriol 47: 87–95 doi:10.1111/j.1365-2672.1979.tb01172.x .[CrossRef]
    [Google Scholar]
  22. Nohynek L.J. , Nurmiaho-Lassila E.-L. , Suhonen E.L. , Busse H.J. , Mohammadi M. , Hantula J. , Rainey F. , Salkinoja-Salonen M.S. . ( 1996;). Description of chlorophenol-degrading Pseudomonas sp. strains KF1T, KF3, and NKF1 as a new species of the genus Sphingomonas Sphingomonas subarctica sp. nov. Int J Syst Bacteriol 46: 1042–1055 10.1099/00207713-46-4-1042 [PubMed].[CrossRef]
    [Google Scholar]
  23. 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 10.1099/ijs.0.63201-0 [PubMed].[CrossRef]
    [Google Scholar]
  24. 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 10.1099/ijs.0.64080-0 [PubMed].[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 [PubMed].
    [Google Scholar]
  26. Sambrook J.andRussel,D.W. . ( 2007;). Molecular cloning: A laboratory manual Cold Spring Harbor Laboratory Press Cold Spring Harbor: NY;.
    [Google Scholar]
  27. Sasser M. . ( 1990;). Identification of bacteria by gas chromatography of cellular fatty acids MIDI Technical Note 101 Newark, DE: MIDI Inc;.
    [Google Scholar]
  28. 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 10.1099/ijs.0.65712-0 [PubMed].[CrossRef]
    [Google Scholar]
  29. 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]
  30. Stolz A. , Schmidt-Maag C. , Denner E.B.M. , Busse H.J. , Egli T. , Kämpfer P. . ( 2000;). Description of Sphingomonas xenophaga sp. nov. for strains BN6T and N,N which degrade xenobiotic aromatic compounds. Int J Syst Evol Microbiol 50: 35–41 10.1099/00207713-50-1-35 [PubMed].[CrossRef]
    [Google Scholar]
  31. Takeuchi M. , Hamana K. , Hiraishi A. . ( 2001;). Proposal of the genus Sphingomonas sensu stricto and three new genera, Sphingobium Novosphingobium Sphingopyxis, on the basis of phylogenetic and chemotaxonomic analyses. Int J Syst Evol Microbiol 51: 1405–1417 [PubMed].
    [Google Scholar]
  32. 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 10.1093/molbev/msr121 [PubMed].[CrossRef]
    [Google Scholar]
  33. 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 10.1093/nar/25.24.4876 [PubMed].[CrossRef]
    [Google Scholar]
  34. 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 10.1099/ijs.0.016949-0 [PubMed].[CrossRef]
    [Google Scholar]
  35. 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 10.1099/ijs.0.02581-0 [PubMed].[CrossRef]
    [Google Scholar]
  36. 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 10.1099/ijs.0.023309-0 [PubMed].[CrossRef]
    [Google Scholar]
  37. 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 doi:10.1099/00207713-37-4-463 .[CrossRef]
    [Google Scholar]
  38. 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 10.1099/ijs.0.64433-0 [PubMed].[CrossRef]
    [Google Scholar]
  39. 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 10.1099/ijs.0.020362-0 [PubMed].[CrossRef]
    [Google Scholar]
  40. Zhang J. , Lang Z.F. , Zheng J.W. , Hang B.J. , Duan X.Q. , He J. , Li S.P. . ( 2012;). Sphingobium jiangsuense sp. nov., a 3-phenoxybenzoic acid-degrading bacterium isolated from a wastewater treatment system. Int J Syst Evol Microbiol 62: 800–805 10.1099/ijs.0.029827-0 [PubMed].[CrossRef]
    [Google Scholar]
  41. Zipper C. , Nickel K. , Angst W. , Kohler H.-P.E. . ( 1996;). Complete microbial degradation of both enantiomers of the chiral herbicide mecoprop [(RS)-2-(4-chloro-2-methylphenoxy)propionic acid] in an enantioselective manner by Sphingomonas herbicidovorans sp. nov. Appl Environ Microbiol 62: 4318–4322 [PubMed].
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.000209
Loading
/content/journal/ijsem/10.1099/ijs.0.000209
Loading

Data & Media loading...

Supplements

Supplementary Data



PDF

Most cited articles

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error