1887

Abstract

A Gram-stain-negative, rod-shaped and white-coloured bacterial strain, designated LL03, was isolated from hexachlorocyclohexane-contaminated soil at Spolana Neratovice, Czech Republic, where lindane was formerly produced. Strain LL03 was found to be a degrader of α-, γ- and δ-isomers of hexachlorocyclohexane, although no significant degradation activity was observed for the β-isomer. A neighbour-joining tree based on 16S rRNA gene sequences showed that strain LL03 occupied a distinct phylogenetic position in the cluster, showing the highest similarity with JZ-1 (99.2 %). The DNA G+C content of strain LL03 was 67.0 mol%. DNA–DNA relatedness values of strain LL03 with its close phylogenetic neighbours were below the threshold level of 70 %, supporting its identification as a representative of a novel species of the genus . The predominant respiratory quinone was ubiquinone Q-10. The polar lipid profile of strain LL03 also corresponded to those reported for other species (phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, phosphatidylmonomethylethanolamine and sphingoglycolipid), supporting its identification as a member of the genus . Spermidine was identified as the major polyamine. The predominant fatty acids were 16 : 0, summed feature 3 (16 : 1ω7 and/or 16 : 1ω6), summed feature 8 (18 : 1ω7 and/or 18 : 1ω6) and 14 : 0 2-OH. The polar lipid pattern, the presence of spermidine and ubiquinone Q-10, the predominance of the cellular fatty acids Cω7, C and C 2-OH and the G+C content of the genomic DNA supported the affiliation of the strain to the genus . The results obtained after DNA–DNA hybridization, biochemical and physiological tests clearly distinguished it from closely related species of the genus . Therefore, strain LL03 represents a novel species of the genus for which the name LL03 sp. nov. is proposed; the type strain is LL03 ( = CCM 7981 = DSM 25433).

Funding
This study was supported by the:
  • Department of Biotechnology
  • National Bureau of Agriculturally Important Microorganisms
  • DU/DST-PURSE
  • Government of India
  • Grant Agency of the Czech Republic (Award P202/10/1435 and 203/08/0114)
  • Grant Agency of the Czech Academy of Sciences (Award IAA401630901)
  • European Regional Development Fund (Award CZ.1.05/1.1.00/02.0123 and CZ.1.05/2.1.00/01.0001)
  • Council for Scientific and Industrial Research
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.039834-0
2013-02-01
2021-04-17
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/63/2/673.html?itemId=/content/journal/ijsem/10.1099/ijs.0.039834-0&mimeType=html&fmt=ahah

References

  1. Altschul S. F., Madden T. L., Schäffer A. A., Zhang J., Zhang Z., Miller W., Lipman D. J. ( 1997 ). Gapped blast and psi-blast: a new generation of protein database search programs. . Nucleic Acids Res 25, 33893402. [CrossRef] [PubMed]
    [Google Scholar]
  2. Arden-Jones M. P., McCarthy A. J., Cross T. ( 1979 ). Taxonomic and serologic studies on Micropolyspora faeni and Micropolyspora strains from soil bearing the specific epithet rectivirgula . . J Gen Microbiol 115, 343354. [CrossRef] [PubMed]
    [Google Scholar]
  3. ATSDR ( 2005 ). Toxicological Profile for Hexachlorocyclohexanes. U.S. Department of Health & Human Services. Public Health Service. Agency for Toxic Substances and Disease Registry. August, 2005. http://www.atsdr.cdc.gov/toxprofiles/tp43.html
  4. Bligh E. G., Dyer W. J. ( 1959 ). A rapid method of total lipid extraction and purification. . Can J Biochem Physiol 37, 911917. [CrossRef] [PubMed]
    [Google Scholar]
  5. Brosius J., Palmer M. L., Kennedy P. J., Noller H. F. ( 1978 ). Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli . . Proc Natl Acad Sci U S A 75, 48014805. [CrossRef] [PubMed]
    [Google Scholar]
  6. Busse H.-J., Kämpfer P., Denner E. B. M. ( 1999 ). Chemotaxonomic characterisation of Sphingomonas . . J Ind Microbiol Biotechnol 23, 242251. [CrossRef] [PubMed]
    [Google Scholar]
  7. Christensen W. B. ( 1946 ). Urea decomposition as means of differentiating Proteus and Paracolon cultures from each other and from Salmonella and Shigella . . J Bacteriol 52, 461466.
    [Google Scholar]
  8. 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, 459470. [CrossRef]
    [Google Scholar]
  9. Cowan S. T., Steel K. J. ( 1965 ). Manual for the Identification of Medical Bacteria. London:: Cambridge University Press;.
    [Google Scholar]
  10. 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, 770773. [CrossRef] [PubMed]
    [Google Scholar]
  11. Gordon R. E., Barnett D. A., Handerhan J. E., Pang C. H.-N. ( 1974 ). Nocardia coeliaca, Nocardia autotrophica and Nocardia strain. . Int J Syst Bacteriol 24, 5463. [CrossRef]
    [Google Scholar]
  12. Ito M., Prokop Z., Klvana M., Otsubo Y., Tsuda M., Damborský J., Nagata Y. ( 2007 ). Degradation of β-hexachlorocyclohexane by haloalkane dehalogenase LinB from γ-hexachlorocyclohexane-utilizing bacterium Sphingobium sp. MI1205. . Arch Microbiol 188, 313325. [CrossRef] [PubMed]
    [Google Scholar]
  13. Jukes T. H., Cantor C. R. ( 1969 ). Evolution of protein molecules. . In Mammalian Protein Metabolism, vol. 3, pp. 21132. Edited by Munro H. N. . New York:: Academic Press;.
    [Google Scholar]
  14. Kaur J., Kaur J., Niharika N., Lal R. ( 2012 ). Sphingomonas laterariae LNB2T sp. nov. isolated from hexachlorocyclohexane (HCH) contaminated dumpsite in Lucknow. . Int J Syst Evol Microbiol 62, 28912896.[PubMed] [CrossRef]
    [Google Scholar]
  15. Kumar M., Verma M., Lal R. ( 2008 ). Devosia chinhatensis sp. nov., isolated from a hexachlorocyclohexane (HCH) dump site in India. . Int J Syst Evol Microbiol 58, 861865. [CrossRef] [PubMed]
    [Google Scholar]
  16. Kumari R., Subudhi S., Suar M., Dhingra G., Raina V., Dogra C., Lal S., van der Meer J. R., Holliger C., Lal R. ( 2002 ). Cloning and characterization of lin genes responsible for the degradation of hexachlorocyclohexane isomers by Sphingomonas paucimobilis strain B90. . Appl Environ Microbiol 68, 60216028. [CrossRef] [PubMed]
    [Google Scholar]
  17. Kuykendall L. D., Roy M. A., O’Neil J. J., Devine T. E. ( 1988 ). Fatty acids, antibiotic resistance and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum . . Int J Syst Bacteriol 38, 358361. [CrossRef]
    [Google Scholar]
  18. Lal R., Dadhwal M., Kumari K., Sharma P., Singh A., Kumari H., Jit S., Gupta S. K., Nigam A. & other authors ( 2008 ). Pseudomonas sp. to Sphingobium indicum: a journey of microbial degradation and bioremediation of hexachlorocyclohexane. . Indian J Microbiol 48, 318. [CrossRef]
    [Google Scholar]
  19. Madhubala R. ( 1997 ). Methods in molecular biology. . In Polyamine Protocols, vol. 79, pp. 131136. Edited by Morgan D. . Totowa:: Humana;. [CrossRef]
    [Google Scholar]
  20. 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, 584586.[PubMed]
    [Google Scholar]
  21. Prakash O., Verma M., Sharma P., Kumar M., Kumari K., Singh A., Kumari H., Jit S., Gupta S. K. & other authors ( 2007a ). Polyphasic approach of bacterial classification – an overview of recent advances. . Indian J Microbiol 47, 98108. [CrossRef]
    [Google Scholar]
  22. Prakash O., Kumari K., Lal R. ( 2007b ). Pseudomonas delhiensis sp. nov., from a fly ash dumping site of a thermal power plant. . Int J Syst Evol Microbiol 57, 527531. [CrossRef] [PubMed]
    [Google Scholar]
  23. Saitou N., Nei M. ( 1987 ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4, 406425.[PubMed]
    [Google Scholar]
  24. Smibert R. M., Kreig N. R. ( 1994 ). Phenotypic characterization. . In Methods for General and Molecular Bacteriology, pp. 607654. Edited by Gerhardt P., Murray R. G. E., Wood W. A., Kreig N. R. . Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  25. 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, 14051417.[PubMed]
    [Google Scholar]
  26. 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, 48764882. [CrossRef] [PubMed]
    [Google Scholar]
  27. Tourova T. P., Antonov A. S. ( 1988 ). Identification of microorganisms by rapid DNA-DNA hybridization. . Methods Microbiol 19, 333355. [CrossRef]
    [Google Scholar]
  28. 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, 569570.[PubMed]
    [Google Scholar]
  29. 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, 17761780. [CrossRef] [PubMed]
    [Google Scholar]
  30. 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, 463464. [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.039834-0
Loading
/content/journal/ijsem/10.1099/ijs.0.039834-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited this month 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