1887

Abstract

A Gram-stain-negative, pinkish-red, rod-shaped bacterium designated strain NKM1 was isolated from soil samples contaminated with hexachlorocyclohexane isomers, collected from Ummari village, Lucknow, Uttar Pradesh, India. The strain was characterized by a polyphasic taxonomic approach. 16S rRNA gene sequence analysis showed that strain NKM1 clustered exclusively with members of the genus of the family , phylum The 16S rRNA gene sequence similarity to type strains of the genus ranged from 96.7 to 93.8 %, with the highest sequence similarity found with JC130 (96.7 %). Cells of strain NKM1 were aerobic, non-flagellated and non-motile. Strain NKM1 was catalase- and oxidase-positive but negative for nitrate reduction and hydrolysis of gelatin. The major fatty acids in strain NKM1 were anteiso-C, iso-C, C, Cω9 and summed feature 3 (Cω7 and/or Cω6). The polar lipid profile of strain NKM1 showed the presence of phosphatidylethanolamine and unknown glycolipids as well as aminolipids. Homospermidine was found to be the major polyamine and menaquinone 7 (MK-7) was the major respiratory quinone. The DNA G+C content of strain NKM1 was determined to be 58.6 mol%. Based on phenotypic, chemotaxonomic, physiological and biochemical evidence, it is proposed that isolate NKM1 represents a novel species that belongs to the genus , for which the name sp. nov. is proposed. The type strain is NKM1 ( = DSM 100161 = KCTC 42944 = MCC 2777).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.000840
2016-02-01
2019-10-21
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/66/2/1080.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.000840&mimeType=html&fmt=ahah

References

  1. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J.. ( 1990;). Basic local alignment search tool. J Mol Biol 215: 403–410 [CrossRef] [PubMed].
    [Google Scholar]
  2. Arden Jones M. P., McCarthy A. J., Cross T.. ( 1979;). Taxonomic and serological 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. Bauer A. W., Kirby W. M. M, Sherris J. C., Turck M.. ( 1966;). Antibiotic susceptibility testing by a standardized single disk method. Am J Clin Pathol 45: 493–496 [PubMed].
    [Google Scholar]
  4. 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]
  5. Bowman J. P., Nichols C. M., Gibson J. A. E. ( 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 [CrossRef] [PubMed].
    [Google Scholar]
  6. Busse J., Auling G.. ( 1988;). Polyamine pattern as a chemotaxonomic marker within the Proteoteobacteria. Syst Appl Microbiol 11: 1–8 [CrossRef].
    [Google Scholar]
  7. Cao H., Nie Y., Zeng X. C., Xu L., He Z., Luo X., Wu R.. ( 2014;). Pontibacter yuliensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 64: 968–972 [CrossRef] [PubMed].
    [Google Scholar]
  8. 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] [PubMed].
    [Google Scholar]
  9. Collins M. D., Shah H. N., Minnikin D. E.. ( 1980;). A note on the separation of natural mixtures of bacterial menaquinones using reverse phase thin-layer chromatography. J Appl Bacteriol 48: 277–282 [CrossRef] [PubMed].
    [Google Scholar]
  10. Consden R., Gordon A. H.. ( 1948;). Effect of salt on partition chromatograms. Nature 162: 180–181 [CrossRef] [PubMed].
    [Google Scholar]
  11. Cowan S. T., Steel K. J.. ( 1965;). Manual for the Identification of Medical Bacteria London: Cambridge University Press;.
    [Google Scholar]
  12. Dai J., Xu M., Peng F., Jiang F., Chen X., Wang Z., Fang C.. ( 2014;). Pontibacter soli sp. nov., isolated from the soil of a Populus rhizosphere in Xinjiang, China. Antonie van Leeuwenhoek 105: 65–72 [CrossRef] [PubMed].
    [Google Scholar]
  13. Dastager S. G., Raziuddin Q. S., Deepa C. K., Li W. J., Pandey A.. ( 2010;). Pontibacter niistensis sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 60: 2867–2870 [CrossRef] [PubMed].
    [Google Scholar]
  14. 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 [CrossRef] [PubMed].
    [Google Scholar]
  15. Farmer J. J. III. ( 1999;). Enterobacteriaceae: introduction and identification. . In Manual of Clinical Microbiology, 7th edn., pp. 448–452. 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.. ( 1981;). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17: 368–376 [CrossRef] [PubMed].
    [Google Scholar]
  17. Felsenstein J.. ( 1985;). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783–791 [CrossRef].
    [Google Scholar]
  18. 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]
  19. 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]
  20. Gunstone F. D., Jacobsberg F. R.. ( 1972;). Fatty acids, part 35: the preparation and properties of a complete series of methyl epoxyoctadecanoates. Chem Phys Lipids 9: 26–34 [CrossRef].
    [Google Scholar]
  21. 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 [CrossRef] [PubMed].
    [Google Scholar]
  22. Joung Y., Kim H., Ahn T. S., Jon K.. ( 2011;). Pontibacter salisaro sp. nov., isolated from a clay tablet solar saltern in Korea. J Microbiol 49: 290–293 [CrossRef] [PubMed].
    [Google Scholar]
  23. Joung Y., Kim H., Lee B.-I.I., Kang H., Jang T. Y., Kwon O. S., Joh K.. ( 2013;). Pontibacter jeungdoensis sp. nov., isolated from a solar saltern in Korea. J Microbiol 51: 531–535 [CrossRef] [PubMed].
    [Google Scholar]
  24. 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; [CrossRef].
    [Google Scholar]
  25. Kang J. Y., Joung Y., Chun J., Kim H., Joh K., Jahng K. Y.. ( 2013;). Pontibacter saemangeumensis sp. nov., isolated from seawater. Int J Syst Evol Microbiol 63: 565–569 [CrossRef] [PubMed].
    [Google Scholar]
  26. Kim O. S., Cho Y. J., Lee K., Yoon S. H., Kim M., Na H., Park S. C., Jeon Y. S., Lee J. H., other authors. ( 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 [CrossRef] [PubMed].
    [Google Scholar]
  27. Kumar R., Dwivedi V., Nayyar N., Verma H., Singh A. K., Rani P., Rao D. L. N, Lal R.. ( 2015;). Parapedobacter indicus sp. nov., isolated from hexachlorocyclohexane-contaminated soil. Int J Syst Evol Microbiol 65: 129–134 [CrossRef] [PubMed].
    [Google Scholar]
  28. Kuykendall L. D., Roy M. A., O'Neill J. J., Devine T. E.. ( 1988;). Fatty acids, antibiotic resistance and deoxyribonucleic acid homology groups of Bradyrhizbium japonicum. Int J Syst Bacteriol 38: 358–361 [CrossRef].
    [Google Scholar]
  29. Lane D. J.. ( 1991;). 16S/23S rRNA sequencing. . In Nucleic Acid Techniques in Bacterial Systematics, pp. 115–175. Edited by Stackebrandt E., Goodfellow M.. Chichester: Wiley;.
    [Google Scholar]
  30. Larkin M. A., Blackshields G., Brown N. P., Chenna R., McGettigan P. A., McWilliam H., Valentin F., Wallace I. M., Wilm A., other authors. ( 2007;). Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947–2948 [CrossRef] [PubMed].
    [Google Scholar]
  31. McCarthy A. J., Cross T.. ( 1984;). A taxonomic study of Thermomonospora and other monosporic actinomycetes. J Gen Microbiol 130: 5–25.
    [Google Scholar]
  32. 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]
  33. Nedashkovskaya O. I., Kim S. B., Suzuki M., Shevchenko L. S., Lee M. S., Lee K. H., Park M. S., Frolova G. M., Oh H. W., other authors. ( 2005;). Pontibacter actiniarum gen. nov., sp. nov., a novel member of the phylum ‘Bacteroidetes’, and proposal of Reichenbachiella gen. nov. as a replacement for the illegitimate prokaryotic generic name Reichenbachia Nedashkovskaya et al. 2003. Int J Syst Evol Microbiol 55: 2583–2588 [CrossRef] [PubMed].
    [Google Scholar]
  34. Raichand R., Kaur I., Singh N. K., Mayilraj S.. ( 2011;). Pontibacter rhizosphera sp. nov., isolated from rhizosphere soil of an Indian medicinal plant Nerium indicum. Antonie van Leeuwenhoek 100: 129–135 [CrossRef] [PubMed].
    [Google Scholar]
  35. 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]
  36. 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 [CrossRef] [PubMed].
    [Google Scholar]
  37. 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 [CrossRef] [PubMed].
    [Google Scholar]
  38. Singh A. K., Garg N., Lal R.. ( 2015;). Pontibacter chinhatensis sp. nov., isolated from pond sediment containing discarded hexachlorocyclohexane isomer waste. Int J Syst Evol Microbiol 65: 2248–2254 [CrossRef] [PubMed].
    [Google Scholar]
  39. Srinivasan S., Lee J. J., Lee S. S., Kim M. K.. ( 2014;). Pontibacter humi sp. nov., isolated from mountain soil. Curr Microbiol 69: 263–269 [CrossRef] [PubMed].
    [Google Scholar]
  40. Subhash Y., Tushar L., Sasikala Ch., Ramana Ch. V.. ( 2013;). Erythrobacter odishensis sp. nov. and Pontibacter odishensis sp. nov. isolated from dry soil of a solar saltern. Int J Syst Evol Microbiol 63: 4524–4532 [CrossRef] [PubMed].
    [Google Scholar]
  41. Subhash Y., Sasikala Ch., Ramana Ch. V.. ( 2014;). Pontibacter ruber sp. nov. and Pontibacter deserti sp. nov., isolated from the desert. Int J Syst Evol Microbiol 64: 1006–1011 [CrossRef] [PubMed].
    [Google Scholar]
  42. Suresh K., Mayilraj S., Chakrabarti T.. ( 2006;). Effluviibacter roseus gen. nov., sp. nov., isolated from muddy water, belonging to the family ‘Flexibacteraceae’. Int J Syst Evol Microbiol 56: 1703–1707 [CrossRef] [PubMed].
    [Google Scholar]
  43. Tamura K., Stecher G., Peterson D., Filipski A., Kumar S.. ( 2013;). mega6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30: 2725–2729 [CrossRef] [PubMed].
    [Google Scholar]
  44. Vanbroekhoven K., Ryngaert A., Bastiaens L., Wattiau P., Vancanneyt M., Swings J., De Mot R., Springael D.. ( 2004;). Streptomycin as a selective agent to facilitate recovery and isolation of introduced and indigenous Sphingomonas from environmental samples. Environ Microbiol 6: 1123–1136 [CrossRef] [PubMed].
    [Google Scholar]
  45. 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]
  46. Verma H., Rani P., Singh A. K., Kumar R., Dwivedi V., Negi V., Lal R.. ( 2015;). Sphingopyxis flava sp. nov., isolated from a hexachlorocyclohexane (HCH)-contaminated soil. Int J Syst Evol Microbiol 65: 3720–3726 [CrossRef].
    [Google Scholar]
  47. Wang Y., Zhang K., Cai F., Zhang L., Tang Y., Dai J., Fang C.. ( 2010;). Pontibacter xinjiangensis sp. nov., in the phylum ‘Bacteroidetes’, and reclassification of [Effluviibacter] roseus as Pontibacter roseus comb. nov. Int J Syst Evol Microbiol 60: 99–103 [CrossRef] [PubMed].
    [Google Scholar]
  48. Xu M., Wang Y., Dai J., Jiang F., Rahman E., Peng F., Fang C.. ( 2012;). Pontibacter populi sp. nov., isolated from the soil of a Euphrates poplar (Populus euphratica) forest. Int J Syst Evol Microbiol 62: 665–670 [CrossRef] [PubMed].
    [Google Scholar]
  49. Xu L., Zeng X. C., Nie Y., Luo X., Zhou E., Zhou L., Pan Y., Li W.. ( 2014;). Pontibacter diazotrophicus sp. nov., a novel nitrogen-fixing bacterium of the family Cytophagaceae. PLoS One 9: e92294 [CrossRef] [PubMed].
    [Google Scholar]
  50. Zhang L., Zhang Q., Luo X., Tang Y., Dai J., Li Y., Wang Y., Chen G., Fang C.. ( 2008;). Pontibacter korlensis sp. nov., isolated from the desert of Xinjiang, China. Int J Syst Evol Microbiol 58: 1210–1214 [CrossRef] [PubMed].
    [Google Scholar]
  51. Zhang L., Zhu L., Wei L., Li C., Wang Y., Shen X.. ( 2013;). Pontibacter toksunensis sp. nov., isolated from soil, and emended descriptions of Pontibacter roseus and Pontibacter akesuensis. Int J Syst Evol Microbiol 63: 4462–4468 [CrossRef] [PubMed].
    [Google Scholar]
  52. Zhou Y., Wang X., Liu H., Zhang K. Y., Zhang Y. Q., Lai R., Li W. J.. ( 2007;). Pontibacter akesuensis sp. nov., isolated from a desert soil in China. Int J Syst Evol Microbiol 57: 321–325 [CrossRef] [PubMed].
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.000840
Loading
/content/journal/ijsem/10.1099/ijsem.0.000840
Loading

Data & Media loading...

Supplements

Supplementary Data



PDF

Most Cited This Month

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