1887

Abstract

A yellow-pigmented, Gram-negative, aerobic, non-motile, non-spore-forming, rod-shaped-bacterium, LE124, was isolated from a hexachlorocyclohexane (HCH) dumpsite located in Lucknow, India. The type strain LE124 grew well with hexachlorocyclohexane as a sole carbon source, degrading it within 24 h of incubation. Phylogenetic analysis of strain LE124 showed highest 16S rRNA gene sequence similarity to LL02 (98.5 %), SM16 (98.1 %), CC-TPE-1 (97.9 %), TUT562 (97.6 %), SM117 (97.5 %) and NCIMB 8767 (97.5 %) and lower sequence similarity (<97 %) to all other members of the genus Novosphingobium. The DNA–DNA relatedness between strain LE124 and LL02 and other related type strains was found to vary from 15 % to 45 % confirming that it represents a novel species. The genomic DNA G+C content of strain LE124 was 60.7 mol%. The predominant fatty acids were summed feature 8 (Cω7, 49.1 %), summed feature 3 (Cω7/Cω6, 19.9 %), C (6.7 %), Cω6 (4.9 %) and a few hydroxyl fatty acids, C 2-OH (9.4 %) and C 2-OH (2.1 %). Polar lipids consisted mainly of phosphatidyldimethylethanolamine, phosphatidylcholine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, sphingoglycolipid and some unidentified lipids. The major respiratory quinone was ubiquinone Q-10. Spermidine was the major polyamine observed. Phylogenetic analysis, DNA–DNA hybridization, chemotaxonomic and phenotypic analysis support the conclusion that strain LE124 represents a novel species within the genus for which we propose the name sp. nov. The type strain is LE124 ( = CCM 7976 = DSM 25409).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.045443-0
2013-06-01
2019-12-13
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/63/6/2160.html?itemId=/content/journal/ijsem/10.1099/ijs.0.045443-0&mimeType=html&fmt=ahah

References

  1. Addison S. L. , Foote S. M. , Reid N. M. , Lloyd-Jones G. . ( 2007; ). Novosphingobium nitrogenifigens sp. nov., a polyhydroxyalkanoate-accumulating diazotroph isolated from a New Zealand pulp and paper wastewater. . Int J Syst Evol Microbiol 57:, 2467–2471. [CrossRef] [PubMed]
    [Google Scholar]
  2. Arden-Jones M. P. , McCarthy A. J. , Cross T. . ( 1979; ). Taxonomic and serological studies on Micropolyspora faeni and Micropolyspora strains from soil bearing the specific epithet rectivirgula . . J Gen Microbiol 115:, 343–354.[PubMed] [CrossRef]
    [Google Scholar]
  3. Baek S. H. , Lim J. H. , Jin L. , Lee H. G. , Lee S. T. . ( 2011; ). Novosphingobium sediminicola sp. nov. isolated from freshwater sediment. . Int J Syst Evol Microbiol 61:, 2464–2468. [CrossRef] [PubMed]
    [Google Scholar]
  4. 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]
  5. Balkwill D. L. , Drake G. R. , Reeves R. H. , Fredrickson J. K. , White D. C. , Ringelberg D. B. , Chandler D. P. , Romine M. F. , Kennedy D. W. , Spadoni C. M. . ( 1997; ). Taxonomic study of aromatic-degrading bacteria from deep-terrestrial-subsurface sediments and description of Sphingomonas aromaticivorans sp. nov., Sphingomonas subterranea sp. nov., and Sphingomonas stygia sp. nov.. Int J Syst Bacteriol 47:, 191–201. [CrossRef] [PubMed]
    [Google Scholar]
  6. Basta T. , Buerger S. , Stolz A. . ( 2005; ). Structural and replicative diversity of large plasmids from sphingomonads that degrade polycyclic aromatic compounds and xenobiotics. . Microbiology 151:, 2025–2037. [CrossRef] [PubMed]
    [Google Scholar]
  7. Bligh E. G. , Dyer W. J. . ( 1959; ). A rapid method of total lipid extraction and purification. . Can J Biochem Physiol 37:, 911–917. [CrossRef] [PubMed]
    [Google Scholar]
  8. Busse J. , Auling G. . ( 1988; ). Polyamine patterns as a chemotaxonomic marker within the Proteobacteria. . Syst Appl Microbiol 11:, 1–8. [CrossRef]
    [Google Scholar]
  9. 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]
  10. Christensen W. B. . ( 1946; ). Urea decomposition as a means of differentiating Proteus and paracolon cultures from each other and from Salmonella and Shigella types. . J Bacteriol 52:, 461–466.[PubMed]
    [Google Scholar]
  11. 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]
  12. Collins M. D. , Jones D. . ( 1980; ). Lipids in the classification and identification of coryneform bacteria containing peptidoglycan based on 2, 4-diamino butyric acid (DAB). . J Appl Bacteriol 48:, 459–470. [CrossRef]
    [Google Scholar]
  13. Cowan S. T. , Steel K. J. . ( 1965; ). Manual for the Identification of Medical Bacteria. London:: Cambridge University Press;.
    [Google Scholar]
  14. Dadhwal M. , Singh A. , Prakash O. , Gupta S. K. , Kumari K. , Sharma P. , Jit S. , Verma M. , Holliger C. , Lal R. . ( 2009; ). Proposal of biostimulation for hexachlorocyclohexane (HCH)-decontamination and characterization of culturable bacterial community from high-dose point HCH-contaminated soils. . J Appl Microbiol 106:, 381–392. [CrossRef] [PubMed]
    [Google Scholar]
  15. Felsenstein J. . ( 1981; ). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17:, 368–376. [CrossRef] [PubMed]
    [Google Scholar]
  16. Fujii K. , Satomi M. N. , Morita N. , Motomura T. , Tanaka T. , Kikuchi S. . ( 2003; ). Novosphingobium tardaugens sp. nov., an oestradiol-degrading bacterium isolated from activated sludge of a sewage treatment plant in Tokyo. . Int J Syst Evol Microbiol 53:, 47–52. [CrossRef] [PubMed]
    [Google Scholar]
  17. 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. [CrossRef] [PubMed]
    [Google Scholar]
  18. Glaeser S. P. , Kämpfer P. , Busse H.-J. , Langer S. , Glaeser J. . ( 2009; ). Novosphingobium acidiphilum sp. nov., an acidophilic salt-sensitive bacterium isolated from the humic acid-rich Lake Grosse Fuchskuhle. . Int J Syst Evol Microbiol 59:, 323–330. [CrossRef] [PubMed]
    [Google Scholar]
  19. Glaeser S. P. , Bolte K. , Martin K. , Busse H.-J. , Grossart H. P. , Kämpfer P. , Glaeser J. . ( 2012; ). Novosphingobium fuchskuhlense sp. nov., isolated from the north-east basin of Lake Grosse Fuchskuhle. . Int J Syst Evol Microbiol 63:, 586–592.[PubMed] [CrossRef]
    [Google Scholar]
  20. Gonzalez J. M. , Saiz-Jimenez C. . ( 2002; ). A fluorimetric method for the estimation of G+C mol% content in microorganisms by thermal denaturation temperature. . Environ Microbiol 4:, 770–773. [CrossRef] [PubMed]
    [Google Scholar]
  21. Gupta S. K. , Lal D. , Lal R. . ( 2009; ). Novosphingobium panipatense sp. nov. and Novosphingobium mathurense sp. nov., from oil-contaminated soil. . Int J Syst Evol Microbiol 59:, 156–161. [CrossRef] [PubMed]
    [Google Scholar]
  22. Jeffries C. D. , Holtman D. F. , Guse D. G. . ( 1957; ). Rapid method for determining the activity of microorganisms on nucleic acids. . J Bacteriol 73:, 590–591.[PubMed]
    [Google Scholar]
  23. Jit S. , Dadhwal M. , Prakash O. , Lal R. . ( 2008; ). Flavobacterium lindanitolerans sp. nov., isolated from hexachlorocyclohexane-contaminated soil. . Int J Syst Evol Microbiol 58:, 1665–1669. [CrossRef] [PubMed]
    [Google Scholar]
  24. Jukes T. H. , Cantor C. R. . ( 1969; ). Evolution of protein molecules. . In Mammalian Protein Metabolism, pp. 21–132. Edited by Munro H. N. . . New York:: Academic Press;.
    [Google Scholar]
  25. Kämpfer P. , Witzenberger R. , Denner E. B. M. , Busse H.-J. , Neef A. . ( 2002; ). Novosphingobium hassiacum sp. nov., a new species isolated from an aerated sewage pond. . Syst Appl Microbiol 25:, 37–45. [CrossRef] [PubMed]
    [Google Scholar]
  26. Kämpfer P. , Young C. C. , Busse H. J. , Lin S. Y. , Rekha P. D. , Arun A. B. , Chen W. M. , Shen F. T. , Wu Y. H. . ( 2011; ). Novosphingobium soli sp. nov., isolated from soil. . Int J Syst Evol Microbiol 61:, 259–263. [CrossRef] [PubMed]
    [Google Scholar]
  27. Kuykendall L. D. , Roy M. A. , O’Neill J. J. , Devine T. E. . ( 1988; ). Fatty acids, antibiotic resistance and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum . . Int J Syst Bacteriol 38:, 358–361. [CrossRef]
    [Google Scholar]
  28. Lal R. , Pandey G. , Sharma P. , Kumari K. , Malhotra S. , Pandey R. , Raina V. , Kohler H. P. E. , Holliger C. et al. ( 2010; ). Biochemistry of microbial degradation of hexachlorocyclohexane and prospects for bioremediation. . Microbiol Mol Biol Rev 74:, 58–80. [CrossRef] [PubMed]
    [Google Scholar]
  29. Lim Y. W. , Moon E. Y. , Chun J. . ( 2007; ). Reclassification of Flavobacterium resinovorum Delaporte and Daste 1956 as Novosphingobium resinovorum comb. nov., with Novosphingobium subarcticum (Nohynek et al. 1996) Takeuchi et al. 2001 as a later heterotypic synonym. . Int J Syst Evol Microbiol 57:, 1906–1908. [CrossRef] [PubMed]
    [Google Scholar]
  30. Liu Z.-P. , Wang B.-J. , Liu Y.-H. , Liu S. J. . ( 2005; ). Novosphingobium taihuense sp. nov., a novel aromatic-compound-degrading bacterium isolated from Taihu Lake, China. . Int J Syst Evol Microbiol 55:, 1229–1232. [CrossRef] [PubMed]
    [Google Scholar]
  31. McCarthy A. J. , Cross T. . ( 1984; ). A taxonomic study of Thermomonospora and other monosporic actinomycetes. . J Gen Microbiol 130:, 5–25.
    [Google Scholar]
  32. Miller L. T. . ( 1982; ). Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. . J Clin Microbiol 16:, 584–586.[PubMed]
    [Google Scholar]
  33. Nigam A. , Jit S. , Lal R. . ( 2010; ). Sphingomonas histidinilytica sp. nov., isolated from a hexachlorocyclohexane dump site. . Int J Syst Evol Microbiol 60:, 1038–1043. [CrossRef] [PubMed]
    [Google Scholar]
  34. Niharika N. , Moskalikova H. , Kaur J. , Sedlackova M. , Hampl A. , Damborsky J. , Prokop Z. , Lal R. . ( 2012; ). Novosphingobium barchaimii sp. nov., isolated from a hexachlorocyclohexane (HCH) contaminated soil. . Int J Syst Evol Microbiol 63:, 667–672. [CrossRef] [PubMed]
    [Google Scholar]
  35. Nishimura Y. , Ino T. , Iizuka H. . ( 1988; ). Acinetobacter radioresistens sp. nov. isolated from cotton and soil. . Int J Syst Bacteriol 38:, 209–211. [CrossRef]
    [Google Scholar]
  36. Prakash O. , Verma M. , Sharma P. , Kumar M. , Kumari K. , Singh A. , Kumari H. , Jit S. , Gupta S. K. et al. ( 2007; ). Polyphasic approach of bacterial classification – An overview of recent advances. . Indian J Microbiol 47:, 98–108. [CrossRef] [PubMed]
    [Google Scholar]
  37. 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]
  38. Sharma P. , Verma M. , Bala K. , Nigam A. , Lal R. . ( 2010; ). Sphingopyxis ummariensis sp. nov., isolated from a hexachlorocyclohexane dump site. . Int J Syst Evol Microbiol 60:, 780–784. [CrossRef] [PubMed]
    [Google Scholar]
  39. 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]
  40. 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]
  41. Sohn J. H. , Kwon K.-K. , Kang J.-H. , Jung H.-B. , Kim S.-J. . ( 2004; ). Novosphingobium pentaromativorans sp. nov., a high-molecular-mass polycyclic aromatic hydrocarbon-degrading bacterium isolated from estuarine sediment. . Int J Syst Evol Microbiol 54:, 1483–1487. [CrossRef] [PubMed]
    [Google Scholar]
  42. Stanier R. Y. , Palleroni N. J. , Doudoroff M. . ( 1966; ). The aerobic pseudomonads: a taxonomic study. . J Gen Microbiol 43:, 159–271.[PubMed] [CrossRef]
    [Google Scholar]
  43. Suzuki S. , Hiraishi A. . ( 2007; ). Novosphingobium naphthalenivorans sp. nov., a naphthalene-degrading bacterium isolated from polychlorinated-dioxin-contaminated environments. . J Gen Appl Microbiol 53:, 221–228. [CrossRef] [PubMed]
    [Google Scholar]
  44. Takeuchi M. , Sakane T. , Yanagi M. , Yamasato K. , Hamana K. , Yokota A. . ( 1995; ). Taxonomic study of bacteria isolated from plants: proposal of Sphingomonas rosa sp. nov., Sphingomonas pruni sp. nov., Sphingomonas asaccharolytica sp. nov., and Sphingomonas mali sp. nov.. Int J Syst Bacteriol 45:, 334–341. [CrossRef] [PubMed]
    [Google Scholar]
  45. 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]
  46. 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]
  47. Tiirola M. A. , Busse H.-J. , Kämpfer P. , Männistö M. K. . ( 2005; ). Novosphingobium lentum sp. nov., a psychrotolerant bacterium from a polychlorophenol bioremediation process. . Int J Syst Evol Microbiol 55:, 583–588. [CrossRef] [PubMed]
    [Google Scholar]
  48. Tourova T. P. , Antonov A. S. . ( 1987; ). Identification of microorganisms by rapid DNA-DNA hybridization. . Meth Microbiol 19:, 333–355. [CrossRef]
    [Google Scholar]
  49. Van de Peer Y. , De Wachter R. . ( 1994; ). TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. . Comput Appl Biosci 10:, 569–570.[PubMed]
    [Google Scholar]
  50. Vanbroekhoven K. , Ryngaert A. , Bastiaens L. , Wattiau P. , Vancanneyt M. , Swings J. , De Mot R. , Springael D. . ( 2004; ). Streptomycin as a selective agent to facilitate recovery and isolation of introduced and indigenous Sphingomonas from environmental samples. . Environ Microbiol 6:, 1123–1136. [CrossRef] [PubMed]
    [Google Scholar]
  51. 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; ). 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]
  52. 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]
  53. Yuan J. , Lai Q. , Zheng T. , Shao Z. . ( 2009; ). Novosphingobium indicum sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from a deep-sea environment. . Int J Syst Evol Microbiol 59:, 2084–2088. [CrossRef] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.045443-0
Loading
/content/journal/ijsem/10.1099/ijs.0.045443-0
Loading

Data & Media loading...

Supplements

Supplementary material 

PDF

Most Cited This Month

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