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Abstract

A Gram-staining negative, reddish-pink, non-motile, rod-shaped bacterial strain designated W29, was isolated from a hexachlorocyclohexane-contaminated dumpsite located in the northern part of India at Ummari Village, Lucknow. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain W29 formed a lineage within the genus and exhibited highest sequence similarity to MS7 (98.8 %), followed by AC-74 (97.1 %). The 16S rRNA gene sequence similarity between strain W29 and other species of the genus ranged from 93.3–98.8 %. The DNA–DNA relatedness between strain W29 and MS7 was 47 % and with other related strains was found to be less than 45 %, confirming strain W29 represents a novel species. The DNA G+C content of strain W29 was 46.2 mol%. Strain W29 was oxidase- and catalase-positive. The major fatty acids (>10 %) of strain W29 were iso-C, summed feature 9 (comprising 10-methyl C and/or iso-Cω9) and summed feature 3 (comprising Cω6 and/or Cω7). The respiratory quinone was MK-7. The polar lipid profile consisted of phosphatidylethanolamine, diphosphatidylglycerol, two unidentified aminolipids, an unidentified aminophospholipid, an unidentified phospholipid and unidentified lipids. On the basis of the results obtained from DNA–DNA hybridization, and biochemical and physiological tests in this study, strain W29 represents a novel species of the genus for which the name sp. nov. is proposed. The type strain is W29 (=KCTC 42940=MCC 2876=DSM 100160).

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2016-09-01
2024-03-19
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References

  1. Ahmed I., Yokota A., Fujiwara T. 2007; Chimaereicella boritolerans sp. nov., a boron-tolerant and alkaliphilic bacterium of the family Flavobacteriaceae isolated from soil. Int J Syst Evol Microbiol 57:986–992 [View Article][PubMed]
    [Google Scholar]
  2. Altenburger P., Ka¨mpfer P., Akimov V. N., Lubitz W., Busse H.-J. 1997; Polyamine distribution in actinomycetes with group B peptidoglycan and species of the genera Brevibacterium, Corynebacterium Tsukamurella . Int J Syst Bacteriol 47:270–277 [CrossRef]
    [Google Scholar]
  3. 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 [View Article][PubMed]
    [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 [View Article][PubMed]
    [Google Scholar]
  5. Bernardet J. F., Nakagawa Y., Holmes B. Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes 2002; Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 52:1049–1070 [View Article][PubMed]
    [Google Scholar]
  6. Bowman J. P., Nichols C. M., Gibson J. A. 2003; Algoriphagus ratkowskyi gen. nov., sp. nov., Brumimicrobium glaciale gen. nov., sp. nov., Cryomorpha ignava gen. nov., sp. nov. and Crocinitomix catalasitica gen. nov., sp. nov., novel flavobacteria isolated from various polar habitats. Int J Syst Evol Microbiol 53:1343–1355 [View Article][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[PubMed] [CrossRef]
    [Google Scholar]
  8. Busse J., Auling G. 1988; Polyamine pattern as a chemotaxonomic marker within the Proteobacteria . Syst Appl Microbiol 11:1–8 [CrossRef]
    [Google Scholar]
  9. 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[PubMed]
    [Google Scholar]
  10. 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]
  11. Collins M. D., Pirouz T., Goodfellow M., Minnikin D. E. 1977; Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 100:221–230 [View Article][PubMed]
    [Google Scholar]
  12. Cowan S. T., Steel K. J. 1965 Manual for the Identification of Medical Bacteria London, UK: Cambridge University Press;
    [Google Scholar]
  13. Dadhwal M., Jit S., Kumari H., Lal R. 2009; Sphingobium chinhatense sp. nov., a hexachlorocyclohexane (HCH)-degrading bacterium isolated from an HCH dumpsite. Int J Syst Evol Microbiol 59:3140–3144 [View Article][PubMed]
    [Google Scholar]
  14. Dadhwal M., Singh A., Prakash O., Gupta S. K., Kumari K., Sharma P., Jit S., Verma M., Holliger C. et al. 2009; Proposal of biostimulation for hexachlorocyclohexane (HCH)-decontamination and characterization of cultural bacterial community from high-dose point HCH-contaminated soils. J Appl Microbiol 106:381–392 [CrossRef]
    [Google Scholar]
  15. De Ley J., Cattoir H., Reynaerts A. 1970; The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12:133–142[PubMed] [CrossRef]
    [Google Scholar]
  16. Doyle J. J., Doyle J. L. 1987; A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bulletin 19:11–15
    [Google Scholar]
  17. Dwivedi V., Niharika N., Lal R. 2013; Pontibacter lucknowensis sp. nov., isolated from a hexachlorocyclohexane dump site. Int J Syst Evol Microbiol 63:309–313 [View Article][PubMed]
    [Google Scholar]
  18. Eden P. A., Schmidt T. M., Blakemore R. P., Pace N. R. 1991; Phylogenetic analysis of Aquaspirillum magnetotacticum using polymerase chain reaction-amplified 16S rRNA-specific DNA. Int J Syst Bacteriol 41:324–325 [View Article]
    [Google Scholar]
  19. Felsenstein J. 1981; Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376 [CrossRef]
    [Google Scholar]
  20. Felsenstein J. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791 [CrossRef]
    [Google Scholar]
  21. Fitch W. M. 1971; Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416 [CrossRef]
    [Google Scholar]
  22. Garg N., Bala K., Lal R. 2012; Sphingobium lucknowense sp. nov., a hexachlorocyclohexane (HCH)-degrading bacterium isolated from HCH-contaminated soil. Int J Syst Evol Microbiol 62:618–623 [View Article][PubMed]
    [Google Scholar]
  23. 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[PubMed] [CrossRef]
    [Google Scholar]
  24. Gordon R. E., Barnett D. A., Handerran J. E., Pang C. H. N. 1974; Nocardia coeliaca, Nocardia autotrophica and the nocardin strain. Int J Syst Evol Microbiol 24:54–63
    [Google Scholar]
  25. Huß V. A. R., Festl H., Schleifer K. H. 1983; Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 4:184–192 [CrossRef]
    [Google Scholar]
  26. Inan K., Kacagan M., Ozer A., Osman Belduz A., Canakci S, Belduz A. O. 2015; Algoriphagus trabzonensis sp. nov., isolated from freshwater, and emended description ofAlgoriphagus alkaliphilus . Int J Syst Evol Microbiol 65:2234–2240 [View Article][PubMed]
    [Google Scholar]
  27. Jit S., Dadhwal M., Kumari H., Jindal S., Kaur J., Lata P., Niharika N., Lal D., Garg N. et al. 2011; Evaluation of hexachlorocyclohexane contamination from the last lindane production plant operating in India. Environ Sci Pollut Res Int 18:586–597 [View Article][PubMed]
    [Google Scholar]
  28. Kim H., Joung Y., Joh K. 2014; Algoriphagus taeanensis sp. nov., isolated from a tidal flat, and emended description of Algoriphagus hitonicola . Int J Syst Evol Microbiol 64:21–26 [View Article][PubMed]
    [Google Scholar]
  29. Kim O. S., Cho Y. J., Lee K., Yoon S. H., Kim M., Na H., Park S. C., Jeon Y. S., Lee J. H. et al. 2012; Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716–721 [View Article][PubMed]
    [Google Scholar]
  30. 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 [View Article][PubMed]
    [Google Scholar]
  31. 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 38:358–361 [View Article]
    [Google Scholar]
  32. Lal R., Pandey G., Sharma P., Kumari K., Malhotra S., Pandey R., Raina V., Kohler H. P., Holliger C. et al. 2010; Biochemistry of microbial degradation of hexachlorocyclohexane and prospects for bioremediation. Microbiol Mol Biol Rev 74:58–80 [View Article][PubMed]
    [Google Scholar]
  33. Lane D. J. 1991; 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics pp 115–175 Edited by Stackebrandt E., Goodfellow M. New York: Wiley;
    [Google Scholar]
  34. Lee D. H., Kahng H. Y., Lee S. B. 2012; Algoriphagus jejuensis sp. nov., isolated from seawater. Int J Syst Evol Microbiol 62:409–413 [View Article][PubMed]
    [Google Scholar]
  35. Loveland-Curtze J., Miteva V. I., Brenchley J. E. 2011; Evaluation of a new fluorimetric DNA-DNA hybridization method. Can J Microbiol 57:250–255 [View Article][PubMed]
    [Google Scholar]
  36. McCarthy A. J., Cross T. 1984; A taxonomic study of Thermomonospora and other monosporicactinomycetes. J Gen Microbiol 130:5–25
    [Google Scholar]
  37. 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]
  38. Minnikin D. E., O'Donnell A. G., Goodfellow M., Alderson G., Athalye M., Schaal A., Parlett J. H. 1984; An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241 [View Article]
    [Google Scholar]
  39. Nedashkovskaya O. I., Kim S. B., Kwon K. K., Shin D. S., Luo X., Kim S. J., Mikhailov V. V. 2007; Proposal ofAlgoriphagus vanfongensis sp. nov., transfer of members of the genera Hongiella Yi and Chun 2004 emend. Nedashkovskaya et al. 2004 and Chimaereicella Tiago et al. 2006 to the genus Algoriphagus, and emended description of the genus Algoriphagus Bowman et al. 2003 emend. Nedashkovskayaet al. 2004. Int J Syst Evol Microbiol 57:1988–1994 [View Article][PubMed]
    [Google Scholar]
  40. Oh K. H., Kang S. J., Lee S. Y., Park S., Oh T. K., Yoon J. H. 2012; Algoriphagus namhaensis sp. nov., isolated from seawater. Int J Syst Evol Microbiol 62:575–579 [View Article][PubMed]
    [Google Scholar]
  41. Park S., Kim S., Jung Y. T., Yoon J. H. 2016; Algoriphagus confluentis sp. nov., isolated from the junction between the ocean and a freshwater lake. Int J Syst Evol Microbiol 66:118–124 [View Article][PubMed]
    [Google Scholar]
  42. 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]
  43. 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 [View Article][PubMed]
    [Google Scholar]
  44. Singh A. K., Garg N., Sangwan N., Negi V., Kumar R., Vikram S., Lal R. 2013; Pontibacter ramchanderi sp. nov., isolated from hexachlorocyclohexane-contaminated pond sediment. Int J Syst Evol Microbiol 63:2829–2834 [View Article][PubMed]
    [Google Scholar]
  45. Singh A. K., Garg N., Lata P., Kumar R., Negi V., Vikram S., Lal R. 2014; Pontibacter indicus sp. nov., isolated from hexachlorocyclohexane-contaminated soil. Int J Syst Evol Microbiol 64:254–259 [View Article][PubMed]
    [Google Scholar]
  46. 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]
  47. 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]
  48. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. 2011; MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739 [View Article][PubMed]
    [Google Scholar]
  49. 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]
  50. Tiago I., Mendes V., Pires C., Morais P. V., Veríssimo A. 2006; Chimaereicella alkaliphila gen. nov., sp. nov., a Gram-negative alkaliphilic bacterium isolated from a nonsaline alkaline groundwater. Syst Appl Microbiol 29:100–108 [View Article][PubMed]
    [Google Scholar]
  51. Tindall B. J. 1990a; A comparative study of the lipid composition ofHalobacterium saccharovorum from various sources. Syst Appl Microbiol 13:128–130 [CrossRef]
    [Google Scholar]
  52. Tindall B. J. 1990b; Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 66:199–202 [View Article]
    [Google Scholar]
  53. Tindall B. J., Sikorski J., Smibert R. M., Krieg N. R. 2007; Phenotypic characterization and the principles of comparative systematics. In Methods for General and Molecular Microbiology, 3 edn. pp. 330–393 Edited by Reddy C. A., Beveridge T. J., Breznak J. A., Marzluf G., Schmidt T. M., Snyder L. R. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  54. Tittsler R. P., Sandholzer L. A. 1936; The use of semi-solid agar for the detection of bacterial motility. J Bacteriol 31:575–580[PubMed]
    [Google Scholar]
  55. Van Trappen S., Vandecandelaere I., Mergaert J., Swings J. 2004; Algoriphagus antarcticus sp. nov., a novel psychrophile from microbial mats in Antarctic lakes. Int J Syst Evol Microbiol 54:1969–1973 [View Article][PubMed]
    [Google Scholar]
  56. Vandamme P., Pot B., Gillis M., de Vos P., Kersters K., Swings J. 1996; Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev 60:407–438[PubMed]
    [Google Scholar]
  57. 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 Evol Microbiol 37:463–464 [CrossRef]
    [Google Scholar]
  58. Yang C., Li Y., Guo Q., Lai Q., Zheng T., Tian Y. 2013; Algoriphagus zhangzhouensis sp. nov., isolated from mangrove sediment. Int J Syst Evol Microbiol 63:1621–1626 [View Article][PubMed]
    [Google Scholar]
  59. Yoon J.-H., Kang S.-J., Jung S.-Y., Lee C.-H., Oh T. K. 2005a; Algoriphagus yeomjeoni sp. nov., isolated from a marine solar saltern of the Yellow Sea, Korea. Int J Syst Evol 55:865–870 [View Article]
    [Google Scholar]
  60. Yoon J.-H., Kang S.-J., Oh T. K. 2005b; Algoriphagus locisalis sp. nov., isolated from a marine solar saltern. Int J Syst Evol Microbiol 55:1635–1639 [CrossRef]
    [Google Scholar]
  61. Yoon J. H., Lee M. H., Kang S. J., Oh T. K. 2006; Algoriphagus terrigena sp. nov., isolated from soil. Int J Syst Evol Microbiol 56:777–780 [View Article][PubMed]
    [Google Scholar]
  62. Young C. C., Lin S. Y., Arun A. B., Shen F. T., Chen W. M., Rekha P. D., Langer S., Busse H. J., Wu Y. H. et al. 2009; Algoriphagus olei sp. nov., isolated from oil-contaminated soil. Int J Syst Evol Microbiol 59:2909–2915 [View Article][PubMed]
    [Google Scholar]
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