Novosphingobium barchaimii sp. nov., isolated from hexachlorocyclohexane-contaminated soil

International Journal of Systematic and Evolutionary Microbiology

Volumn 63, Issue PART2, 2013, Pages 667-672

  Niharika, Neha ^a   Moskalikova, Hana ^b   Kaur, Jasvinder ^a   Sedlackova, Miroslava ^c   Hampl, Ales ^b,c   Damborsky, Jiri ^b,c   Prokop, Zbynek ^c   Lal, Rup ^a  

^a UNIVERSITY OF DELHI   (India)

^b ST ANNE S UNIVERSITY HOSPITAL   (Czech Republic)

^c MASARYK UNIVERSITY   (Czech Republic)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; CARDIOLIPIN; FATTY ACID; GLYCOSPHINGOLIPID; HEXACHLOROCYCLOHEXANE; LINDANE; PHOSPHATIDYLCHOLINE; PHOSPHATIDYLETHANOLAMINE; PHOSPHATIDYLGLYCEROL; PHOSPHATIDYLMETHYLETHANOLAMINE; RNA 16S; UBIQUINONE; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL STRAIN; BACTERIUM ISOLATION; CLASSIFICATION; CZECH REPUBLIC; DNA DNA HYBRIDIZATION; GENE SEQUENCE; GENUS; NEW SPECIES; NONHUMAN; NOVOSPHINGOBIUM BARCHAIMII; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; RNA GENE; SEQUENCE HOMOLOGY; SOIL POLLUTION;

BACTERIAL TYPING TECHNIQUES; BASE COMPOSITION; CZECH REPUBLIC; DNA, BACTERIAL; FATTY ACIDS; LINDANE; MOLECULAR SEQUENCE DATA; NUCLEIC ACID HYBRIDIZATION; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SOIL MICROBIOLOGY; SOIL POLLUTANTS; SPERMIDINE; SPHINGOMONADACEAE; UBIQUINONE;

EID: 84874027630     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.039826-0     Document Type: Article

References (28)

1. Altschul, S. F., Madden, T. L., Schaffer, 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, 3389-3402.
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, 343-354.
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.
4. Bligh, E. G. & Dyer, W. J. (1959). A rapid method of total lipid extraction and purification. Can J Biochem Physiol 37, 911-917.
5. Busse, H.-J. & Auling, G. (1988). Polyamine patterns as a chemotaxonomic marker within the Proteobacteria. Syst Appl Microbiol 11, 1-8.
6. Busse, H.-J., Kampfer, P. & Denner, E. B. M. (1999). Chemotaxonomic characterisation of Sphingomonas. J Ind Microbiol Biotechnol 23, 242-251.
7. Christensen, W. B. (1946). Urea decomposition as a means of differentiating Proteus and para colon cultures from each other and from Salmonella and Shigella types. J Bacteriol 52, 461-466.
8. 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.
9. 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.
10. Cowan, S. T. & Steel, K. J. (1965). Manual for the Identification of Medical Bacteria. London: Cambridge University Press.
11. 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.
12. 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, 54-63.
13. 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.
14. Ito, M., Prokop, Z., Klvana, M., Otsubo, Y., Tsuda, M., Damborsk ́ J. & Nagata Y. (2007). Degradation of beta-hexachlorocyclohexane by haloalkane dehalogenase LinB from gamma-hexachlorocyclohexaneutilizing bacterium Sphingobium sp. MI1205. Arch Microbiol 188, 313-325.
15. Jukes, T. & Cantor, C. R. (1969). Evolution of Protein Molecules in Mammalian Protein Metabolism, pp. 21-132. Edited by H. N. Munro. New York: Academic Press.
16. Kampfer, 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.
17. 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 Evol Bacteriol 38, 358-361.
18. 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.
19. 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.
20. Prakash, O., Verma, M., Sharma, P., Kumar, M., Kumari, K., Singh, A., Kumari, H., Jit, S., Gupta, S. K. & other authors (2007). Polyphasic approach of bacterial classification an overview of recent advances. Indian J Microbiol 47, 98-108.
21. Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406-425.
22. Smibert, R. M. & Krieg, N. R. (1994). Phenotypic characterization. In Methods for General and Molecular Bacteriology, pp. 607-654. Edited by P. Gerhardt, R. G. E. Murray, W. A. Wood & N. R. Krieg. Washington, DC: American Society for Microbiology.
23. 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.
24. 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.
25. 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.
26. Tourova, T. P. & Antonov, A. S. (1988). Identification of microorganisms by rapid DNA-DNA hybridization. Meth Microbiol 19, 333-355.
27. 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.
28. 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.