A hexachlorocyclohexane (HCH)-degrading bacterial strain (RL-3) was isolated from an HCH dump site located in the northern part of India. Resting cell assays and analytical GC studies confirmed the ability of strain RL-3 to degrade HCH isomers. Southern blot hybridization studies revealed the presence of genes, which are involved in the HCH degradation pathway, in this bacterium. The 16S rRNA gene sequence of strain RL-3 showed that it was most closely related to JCM 10874 (97.3 %) and MTCC 7295 (96.4 %). Phylogenetic analysis based on 16S rRNA gene sequences placed strain RL-3 between JCM 10874 and MTCC 7295. The DNA G+C content of strain RL-3 was 62 mol%. The DNA–DNA relatedness values of strain RL-3 with JCM 10874 and CCM 7327 were 8.65 and 7.47 %, respectively. SGL1 was the major sphingolipid and spermidine was the major polyamine in strain RL-3. The major fatty acids in strain RL-3 were C 7 (56.6 %), C (14 %) and C 2-OH (7.4 %). Ubiquinone Q-10 was the major respiratory quinone. Phylogenetic distinctiveness, DNA–DNA relatedness values, biochemical and physiological characterization and unique phenotypic characteristics suggest that strain RL-3 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is RL-3 (=MTCC 8599=CCM 7431).


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  1. 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.[CrossRef] [Google Scholar]
  2. Busse, J. & Auling, G.(1988). Polyamine pattern as a chemotaxonomic marker within the Proteobacteria. Syst Appl Microbiol 11, 1–8.[CrossRef] [Google Scholar]
  3. 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.[CrossRef] [Google Scholar]
  4. Busse, H. J., Kämpfer, P. & Denner, E. B. M.(1999). Chemotaxonomic characterization of Sphingomonas. J Ind Microbiol Biotechnol 23, 242–251.[CrossRef] [Google Scholar]
  5. 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. [Google Scholar]
  6. Collins, M. D., Pirouz, T., Goodfellow, M. & Minnikin, D. E.(1977). Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 100, 221–230.[CrossRef] [Google Scholar]
  7. Collins, C. H., Lyne, P. M. & Grange, J. M.(1989).Microbiological Methods, 6th edn. London: Butterworth.
  8. Dogra, C., Raina, V., Pal, R., Suar, M., Lal, S., Gartemann, K. H., Holliger, C., van der Meer, J. R. & Lal, R.(2004). Organization of lin genes and IS6100 among different strains of hexachlorocyclohexane-degrading Sphingomonas paucimobilis: evidence for horizontal gene transfer. J Bacteriol 186, 2225–2235.[CrossRef] [Google Scholar]
  9. Felsenstein, J.(1993).phylip (phylogeny inference package), version 3.5c. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle, USA.
  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, 770–773.[CrossRef] [Google Scholar]
  11. Gordon, R. E., Barnett, D. A., Handerhan, J. E. & Pang, C. H.-N.(1974).Nocardia coeliaca, Nocardia autotrophica, and the nocardin strain. Int J Syst Bacteriol 24, 54–63.[CrossRef] [Google Scholar]
  12. Jukes, T. H. & Cantor, C. R.(1969). Evolution of protein molecules. In Mammalian Protein Metabolism, vol. 3, pp. 21–132. Edited by H. N. Munro. New York: Academic Press.
  13. 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, 861–865.[CrossRef] [Google Scholar]
  14. 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, 6021–6028.[CrossRef] [Google Scholar]
  15. Kutz, F. W., Wood, P. H. & Bottimore, D. P.(1991). Organochlorine pesticides and polychlorinated biphenyls in human adipose tissue. Rev Environ Contam Toxicol 120, 1–82. [Google Scholar]
  16. 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]
  17. Lal, R., Dogra, C., Malhotra, S., Sharma, P. & Pal, R.(2006). Diversity, distribution and divergence of lin genes in hexachlorocyclohexane-degrading sphingomonads. Trends Biotechnol 24, 121–130.[CrossRef] [Google Scholar]
  18. Maruyama, T., Park, H. D., Ozawa, K., Tanaka, Y., Sumino, T., Hamana, K., Hiraishi, A. & Kato, K.(2006).Sphingosinicella microcystinivorans gen. nov., sp. nov., a microcystin-degrading bacterium. Int J Syst Evol Microbiol 56, 85–89.[CrossRef] [Google Scholar]
  19. McCarthy, A. J. & Cross, T.(1984). A taxonomic study of Thermomonospora and other monosporic actinomycetes. J Gen Microbiol 130, 5–25. [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, 584–586. [Google Scholar]
  21. 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.[CrossRef] [Google Scholar]
  22. 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.[CrossRef] [Google Scholar]
  23. Raina, V., Suar, M., Singh, A., Prakash, O., Dadhwal, M., Gupta, S. K., Dogra, C., Lawlor, K., Lal, S. & other authors(2007). Enhanced biodegradation of hexachlorocyclohexane (HCH) in contaminated soils via inoculation with Sphingobium indicum B90A. Biodegradation 19, 27–40. [Google Scholar]
  24. Sahu, S. K., Patnaik, K. K., Sharmila, M. & Sethunathan, N.(1990). Degradation of alpha-, beta-, and gamma-hexachlorocyclohexane by a soil bacterium under aerobic conditions. Appl Environ Microbiol 56, 3620–3622. [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. [Google Scholar]
  26. Sambrook, J., Fritsch, E. F. & Maniatis, T.(1989).Molecular Cloning: a Laboratory Manual, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
  27. Sharma, P., Raina, V., Kumari, R., Malhotra, S., Dogra, C., Kumari, H., Kohler, H. P. E., Buser, H. R., Holliger, C. & Lal, R.(2006). Haloalkane dehalogenase LinB is responsible for β- and δ-hexachlorocyclohexane transformation in Sphingobium indicum B90A. Appl Environ Microbiol 72, 5720–5727.[CrossRef] [Google Scholar]
  28. 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. [Google Scholar]
  29. 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] [Google Scholar]
  30. Tindall, B. J.(1990a). A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 13, 128–130.[CrossRef] [Google Scholar]
  31. Tindall, B. J.(1990b). Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 66, 199–202.[CrossRef] [Google Scholar]
  32. Tourova, T. P. & Antonov, A. S.(1987). Identification of microorganisms by rapid DNA–DNA hybridization. Methods Microbiol 19, 333–355. [Google Scholar]
  33. Walker, K., Vallero, D. A. & Lewis, R. G.(1999). Factors influencing the distribution of lindane and other hexachlorocyclohexanes in the environment. Environ Sci Technol 33, 4373–4378.[CrossRef] [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. & 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.[CrossRef] [Google Scholar]
  35. Willem, J. K. & Wollent, I.(2005). Inventories of obsolete pesticide stocks in central and Eastern Europe, p. 37–39. In Proceedings of the 7th International HCH and Pesticides Forum, Kiev, Ukraine. Edited by E. Elbestawy, L. Moklyachuk, V. Pidlisnyuk, N. Schulz, T. Stefanovska & J. Vijgen. Holte, Denmark: International HCH and Pesticides Association.
  36. Windholz, M., Budavari, S., Stroumtsos, L. Y. & Fertig, M. N. (editors)(1976).The Merck Index, 9th edn. Rahway, NJ: Merck.
  37. 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.[CrossRef] [Google Scholar]

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Cellular fatty acid profiles of strain RL-3 and related species. [ PDF] 25 KB


Degradation of HCH isomers by strain RL-3 in phosphate buffer. [ PDF] 106 KB


Two dimensional TLC of polar lipids of strain RL-3 . [ PDF] 134 KB

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