1887

Abstract

A Gram-staining-negative, non-motile, cream-coloured and rod-shaped bacterium, designated strain LNB2, was isolated from a hexachlorocyclohexane-contaminated dump site in the village of Ummari, in northern India. The taxonomic position of the novel strain was investigated by using a polyphasic approach. In a phylogenetic analysis based on 16S rRNA gene sequences, strain LNB2 appeared to be most closely related to A175 (98.0 % sequence similarity) and UM2 (97.3 %). In DNA–DNA hybridizations, the levels of DNA–DNA relatedness between the novel strain and A175 and UM2 were found to be low (8.6 % and 5.6 %, respectively). The genomic DNA G+C content of strain LNB2 was 61.0 mol%. The novel strain’s predominant fatty acids were summed feature 8 (Cω7 and/or Cω6), C, summed feature 3 (Cω7 and/or Cω6), C 2-OH, Cω6 and 11-methyl Cω7. The major ubiquinone was Q-10, the predominant polyamine was homospermidine, and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, sphingoglycolipid, phosphatidylethanolamine and phosphatidyldimethylethanolamine. Based on the phylogenetic, biochemical and chemotaxonomic evidence and the results of the DNA–DNA hybridizations, strain LNB2 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is LNB2 ( = MTCC 10873 = CCM 7880 = DSM 25432).

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2012-12-01
2019-10-18
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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:, 3389–3402. [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:, 343–354. [CrossRef] [PubMed]
    [Google Scholar]
  3. Bala S. , Khanna R. , Dadhwal M. , Prabagaran S. R. , Shivaji S. , Cullum J. , Lal R. . ( 2004; ). Reclassification of Amycolatopsis mediterranei DSM 46095 as Amycolatopsis rifmaycinica sp. nov.. Int Syst Evol Microbiol 54:, 1145–1149. [CrossRef]
    [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. , Fredrickson J. K. , Romine M. F. . ( 2006; ). Sphingomonas & related genera. . In The Prokaryotes a Handbook on the Biology of Bacteria, vol. 7, pp. 605–629. Edited by Dworkin M. , Falkow S. . . New York:: Springer;.
    [Google Scholar]
  6. 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]
  7. 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:, 4801–4805. [CrossRef] [PubMed]
    [Google Scholar]
  8. 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]
  9. Busse H.-J. , Denner E. B. , Buczolits S. , Salkinoja-Salonen M. , Bennasar A. , Kämpfer P. . ( 2003; ). Sphingomonas aurantiaca sp. nov., Sphingomonas aerolata sp. nov. and Sphingomonas faeni sp. nov., air- and dustborne and Antarctic, orange-pigmented, psychrotolerant bacteria, and emended description of the genus Sphingomonas . . Int J Syst Evol Microbiol 53:, 1253–1260. [CrossRef] [PubMed]
    [Google Scholar]
  10. Christensen W. B. . ( 1946; ). Urea decomposition as means of differentiating Proteus and paracolon cultures from each other and from Salmonella and Shigella types. . J Bacteriol 52:, 461–466.
    [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. Cowan S. T. , Steel K. J. . ( 1965; ). Manual for the Identification of Medical Bacteria. London:: Cambridge University Press;.
    [Google Scholar]
  13. 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]
  14. Euzéby, J. P. (2011). List of Prokaryotic names with Standing in Nomenclature. http://www.bacterio.cict.fr
  15. Farmer J. J. III . ( 1999; ). Enterobacteriaceae: introduction and identification. . In Manual of Clinical Microbiology, , 7th edn., pp. 442–458. Edited by Murray P. R. , Baron E. J. , Pfaller M. A. , Tenover F. C. , Yolken R. H. . . Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  16. Felsenstein, J. (1993). phylip (phylogeny inference package) version 3.5.1. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle, USA.
  17. 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]
  18. 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]
  19. Gupta S. K. , Kumari R. , Prakash O. , Lal R. . ( 2008; ). Pseudomonas panipatensis sp. nov., isolated from an oil-contaminated site. . Int J Syst Evol Microbiol 58:, 1339–1345. [CrossRef] [PubMed]
    [Google Scholar]
  20. Jukes T. H. , Cantor C. R. . ( 1969; ). Evolution of protein molecules. . In Mammalian Protein Metabolism, vol. 3, pp. 21–132. Edited by Munro H. N. . . New York:: Academic Press;.
    [Google Scholar]
  21. Kaur J. , Verma M. , Lal R. . ( 2011; ). Rhizobium rosettiformans sp. nov., isolated from a hexachlorocyclohexane dump site, and reclassification of Blastobacter aggregatus Hirsch and Muller 1986 as Rhizobium aggregatum comb. nov.. Int J Syst Evol Microbiol 61:, 1218–1225. [CrossRef] [PubMed]
    [Google Scholar]
  22. Kawahara K. , Kuraishi H. , Zähringer U. . ( 1999; ). Chemical structure and function of glycosphingolipids of Sphingomonas spp and their distribution among members of the α-4 subclass of Proteobacteria . . J Ind Microbiol Biotechnol 23:, 408–413. [CrossRef] [PubMed]
    [Google Scholar]
  23. 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] [PubMed]
    [Google Scholar]
  24. 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] [PubMed]
    [Google Scholar]
  25. Kumari H. , Gupta S. K. , Jindal S. , Katoch P. , Lal R. . ( 2009; ). Sphingobium lactosutens sp. nov., isolated from a hexachlorocyclohexane dump site and Sphingobium abikonense sp. nov., isolated from oil-contaminated soil. . Int J Syst Evol Microbiol 59:, 2291–2296. [CrossRef] [PubMed]
    [Google Scholar]
  26. Kuykendall L. D. , Roy M. A. , O’Neill J. J. , Devine T. E. . ( 1988; ). Fatty acids, antibiotics resistance and deoxyribonucleic acid homology groups of Bradorhizobium japonicum . . Int J Syst Bacteriol 38:, 358–361. [CrossRef]
    [Google Scholar]
  27. Madhubala R. . ( 1998; ). Thin layer chromatographic methods for assaying polyamines. . Methods Mol Biol. 79:, 131–136. [CrossRef]
    [Google Scholar]
  28. McCarthy A. J. , Cross T. . ( 1984; ). A taxonomic study of Thermomonospora and other monosporic actinomycetes. . Microbiology 130:, 5–25.[CrossRef]
    [Google Scholar]
  29. Mechichi T. , Fardeau M.-L. , Labat M. , Garcia J.-L. , Verhe F. , Patel B. K. C. . ( 2000; ). Clostridium peptivorans sp. nov., a peptide fermenting bacterium from an olive mill wastewater treatment digester. . Int Syst Evol Microbiol 50:, 1259–1264. [CrossRef]
    [Google Scholar]
  30. 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]
  31. 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]
  32. Prakash O. , Kumari K. , Lal R. . ( 2007; ). Pseudomonas delhiensis sp. nov., from a fly ash dumping site of a thermal power plant. . Int J Syst Evol Microbiol 57:, 527–531. [CrossRef] [PubMed]
    [Google Scholar]
  33. Raetz C. R. H. , Reynolds C. M. , Trent M. S. , Bishop R. E. . ( 2007; ). Lipid A modification systems in gram-negative bacteria. . Annu Rev Biochem 76:, 295–329. [CrossRef] [PubMed]
    [Google Scholar]
  34. 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]
  35. 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]
  36. Smibert R. M. , Kreig 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]
  37. Stackebrandt E. , Goebel B. M. . ( 1994; ). Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. . Int J Syst Bacteriol 44:, 846–849. [CrossRef]
    [Google Scholar]
  38. Takeuchi M. , Sawada H. , Oyaizu H. , Yokota A. . ( 1994; ). Phylogenetic evidence for Sphingomonas and Rhizomonas as nonphotosynthetic members of the alpha-4 subclass of the Proteobacteria . . Int J Syst Bacteriol 44:, 308–314. [CrossRef] [PubMed]
    [Google Scholar]
  39. 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]
  40. 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]
  41. 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]
  42. 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]
  43. 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]
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