Skip to content
1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 63, Issue Pt_6

sp. nov., isolated from a high dose point hexachlorocyclohexane (HCH)-contaminated dumpsite Free

Abstract

A Gram-stain-negative, aerobic, non-motile, non-spore-forming, rod-shaped and light-yellow-pigmented bacterium, designated DS15, was isolated from a soil sample collected from a hexachlorocyclohexane dumpsite in Lucknow, Uttar Pradesh, India. Strain DS15 showed highest 16S rRNA gene sequence similarity to DCY34 (98.7 %) and BL03 (98.0 %). The 16S rRNA gene sequence similarity between strain DS15 and species of genus with validly published names ranged from 92.5 % to 98.7 %. The DNA G+C content of strain DS15 was 67.5 mol%. The chemotaxonomic markers in strain DS15 were consistent with its classification in the genus , i.e. Q-10 as the major ubiquinone and summed feature 8 (Cω7/Cω9), Cω6, summed feature 3 (Cω7/Cω6), C 2-OH, C2-OH, C and Cω8 as the predominant fatty acids. The major polar lipids of strain DS15 were phosphatidylethanolamine (PE), diphosphatidylglycerol (DPG), phosphatidylcholine (PC), phosphatidylglycerol (PG) and sphingoglycolipids (SGL) and spermidine was detected as the major polyamine. Phylogenetic analysis, DNA–DNA hybridization, and chemotaxonomic and phenotypic analysis support the conclusion that strain DS15 represents a novel species within the genus , for which the name is proposed. The type strain is DS15 ( = MTCC 9455 = CCM 7542 = MCC 2023).

  • Published Online:
Funding
This study was supported by the:
  • University of Delhi – Department of Science and Technology (DU/DST)
  • Department of Biotechnology (DBT)
  • Government of India
  • National Bureau of Agriculturally Important Micro-organisms (NBAIM)
  • DBT
  • Council of Scientific and Industrial Research (CSIR), Government of India
© 2013 IUMS
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.040840-0
2013-06-01
2025-12-14

Metrics

Loading full text...

Full text loading...

/deliver/fulltext/ijsem/63/6/2186.html?itemId=/content/journal/ijsem/10.1099/ijs.0.040840-0&mimeType=html&fmt=ahah

References

  1. 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. [View Article] [PubMed]
    [Google Scholar]
  2. Bligh E. G., Dyer W. J. ( 1959 ). A rapid method of total lipid extraction and purification. . Can J Biochem Physiol 37, 911–917. [View Article] [PubMed]
    [Google Scholar]
  3. Brosius J., Palmer M. L., Kennedy P. J., Nolther H. F. ( 1978 ). Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli.. . Proc Natl Acad Sci U S A 75, 4801–4805. [View Article]
    [Google Scholar]
  4. Busse J., Auling G. ( 1988 ). Polyamine patterns as a chemotaxonomic marker within the Proteobacteria. . Syst Appl Microbiol 11, 1–8. [View Article]
    [Google Scholar]
  5. Choi J. H., Kim M. S., Jung M. J., Roh S. W., Shin K. S., Bae J. W. ( 2010 ). Sphingopyxis soli sp. nov., isolated from landfill soil. . Int J Syst Evol Microbiol 60, 1682–1686. [View Article] [PubMed]
    [Google Scholar]
  6. 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. [View Article] [PubMed]
    [Google Scholar]
  7. Collins M. D., Jones D. ( 1980 ). Lipids in the classification 316 and identification of coryneform bacteria containing peptidoglycan based on 2, 4-diamino butyric acid (DAB). . J Appl Bacteriol 48, 459–470. [View Article]
    [Google Scholar]
  8. Cowan S. T., Steel K. J. ( 1965 ). Manual for the Identification of Medical Bacteria. London:: Cambridge University Press;.
     [Google Scholar]
  9. Felsenstein J. ( 1981 ). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17, 368–376. [View Article] [PubMed]
    [Google Scholar]
  10. Felsenstein J. ( 1985 ). Confidence limits on phylogenies: an approach using the bootstrap. . Evolution 39, 783–791. [View Article]
    [Google Scholar]
  11. Felsenstein, J. (1993). phylip (phylogeny inference package) version 3.5.1. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle, USA.
  12. Godoy F., Vancanneyt M., Martínez M., Steinbüchel A., Swings J., Rehm B. H. A. ( 2003 ). Sphingopyxis chilensis sp. nov., a chlorophenol-degrading bacterium that accumulates polyhydroxyalkanoate, and transfer of Sphingomonas alaskensis to Sphingopyxis alaskensis comb. nov.. Int J Syst Evol Microbiol 53, 473–477. [View Article] [PubMed]
    [Google Scholar]
  13. 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. [View Article] [PubMed]
    [Google Scholar]
  14. Jukes T., 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]
  15. Kämpfer P., Witzenberger R., Denner E. B. M., Busse H.-J., Neef A. ( 2002 ). Sphingopyxis witflariensis sp. nov., isolated from activated sludge. . Int J Syst Evol Microbiol 52, 2029–2034. [View Article] [PubMed]
    [Google Scholar]
  16. Kim M. K., Im W.-T., Ohta H., Lee M., Lee S.-T. ( 2005 ). Sphingopyxis granuli sp. nov., a β-glucosidase-producing bacteria in the family Sphingomonadaceae in α-4 subclass of the Proteobacteria. . J Microbiol 43, 152–157.[PubMed]
    [Google Scholar]
  17. Kim B. S., Lim Y. W., Chun J. ( 2008 ). Sphingopyxis marina sp. nov. and Sphingopyxis litoris sp. nov., isolated from seawater. . Int J Syst Evol Microbiol 58, 2415–2419. [View Article] [PubMed]
    [Google Scholar]
  18. Kumar M., Verma M., Lal R. ( 2008 ). Devosia chinhatensis sp. nov., isolated from hexachlorocyclohexane (HCH) dump site in India. . Int J Syst Evol Microbiol 58, 861–865. [View Article] [PubMed]
    [Google Scholar]
  19. Kumari K., Sharma P., Tyagi K., Lal R. ( 2011 ). Pseudoxanthomonas indica sp. nov., isolated from a hexachlorocyclohexane dumpsite. . Int J Syst Evol Microbiol 61, 2107–2111. [View Article] [PubMed]
    [Google Scholar]
  20. 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. [View Article]
    [Google Scholar]
  21. Lee J.-S., Shin Y. K., Yoon J.-H., Takeuchi M., Pyun Y.-R., Park Y.-H. ( 2001 ). Sphingomonas aquatilis sp. nov., Sphingomonas koreensis sp. nov., and Sphingomonas taejonensis sp. nov., yellow-pigmented bacteria isolated from natural mineral water. . Int J Syst Evol Microbiol 51, 1491–1498. [View Article] [PubMed]
    [Google Scholar]
  22. Lee H. W., Ten I. L., Jung H. M., Liu Q. M., Im W. T., Lee S. T. ( 2008a ). Sphingopyxis panaciterrae sp. nov., isolated from soil from ginseng field. . J Microbiol Biotechnol 18, 1011–1015.[PubMed]
    [Google Scholar]
  23. Lee M., Ten L. N., Lee H.-W., Oh H. W., Im W.-T., Lee S.-T. ( 2008b ). Sphingopyxis ginsengisoli sp. nov., isolated from soil of a ginseng field in South Korea. . Int J Syst Evol Microbiol 58, 2342–2347. [View Article] [PubMed]
    [Google Scholar]
  24. McCarthy A. J., Cross T. ( 1984 ). A taxonomic study of Thermomonospora and other monosporic actinomycetes. . J Gen Microbiol 130, 5–25. [View Article]
    [Google Scholar]
  25. 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]
  26. Pal R., Bhasin V. K., Lal R. ( 2006 ). Proposal to reclassify [Sphingomonas] xenophaga Stolz et al. 2000 and [Sphingomonas] taejonensis Lee et al. 2001 as Sphingobium xenophagum comb. nov. and Sphingopyxis taejonensis comb. nov., respectively. . Int J Syst Evol Microbiol 56, 667–670. [View Article] [PubMed]
    [Google Scholar]
  27. 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. [View Article] [PubMed]
    [Google Scholar]
  28. 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]
  29. Srinivasan S., Kim M. K., Sathiyaraj G., Veena V., Mahalakshmi M., Kalaiselvi S., Kim Y. J., Yang D. C. ( 2010 ). Sphingopyxis panaciterrulae sp. nov., isolated from soil of a ginseng field. . Int J Syst Evol Microbiol 60, 2358–2363. [View Article] [PubMed]
    [Google Scholar]
  30. 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 analysis. . Int J Syst Evol Microbiol 51, 1405–1417.[PubMed]
    [Google Scholar]
  31. 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. [View Article] [PubMed]
    [Google Scholar]
  32. Tourova T. P., Antonov A. S. ( 1988 ). Identification of microorganisms by rapid DNA-DNA hybridization. . Meth Microbiol 19, 333–355. [View Article]
    [Google Scholar]
  33. Vancanneyt M., Schut F., Snauwaert C., Goris J., Swings J., Gottschal J. C. ( 2001 ). Sphingomonas alaskensis sp. nov., a dominant bacterium from a marine oligotrophic environment. . Int J Syst Evol Microbiol 51, 73–79.[PubMed]
    [Google Scholar]
  34. 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. [View Article]
    [Google Scholar]
  35. Yoon J.-H., Oh T.-K. ( 2005 ). Sphingopyxis flavimaris sp. nov., isolated from sea water of the Yellow Sea in Korea. . Int J Syst Evol Microbiol 55, 369–373. [View Article] [PubMed]
    [Google Scholar]
  36. Yoon J.-H., Lee C.-H., Yeo S.-H., Oh T.-K. ( 2005 ). Sphingopyxis baekryungensis sp. nov., an orange-pigmented bacterium isolated from sea water of the Yellow Sea in Korea. . Int J Syst Evol Microbiol 55, 1223–1227. [View Article] [PubMed]
    [Google Scholar]
  37. Zhang D. C., Liu H. C., Xin Y. H., Zhou Y. G., Schinner F., Margesin R. ( 2010 ). Sphingopyxis bauzanensis sp. nov., a psychrophilic bacterium isolated from soil. . Int J Syst Evol Microbiol 60, 2618–2622. [View Article] [PubMed]
    [Google Scholar]
/content/journal/ijsem/10.1099/ijs.0.040840-0
Loading
Sphingopyxis indica sp. nov., isolated from a high dose point hexachlorocyclohexane (HCH)-contaminated dumpsite
Int J Syst Evol Microbiol 63, 2186 (2013); https://doi.org/10.1099/ijs.0.040840-0
/content/journal/ijsem/10.1099/ijs.0.040840-0
/content/journal/ijsem/10.1099/ijs.0.040840-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

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