1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 64, Issue Pt_1

Pontibacter sp. nov., isolated from hexachlorocyclohexane-contaminated soil Free

Abstract

An orange-pigmented bacterial strain, designated LP100, was isolated from hexachlorocyclohexane-contaminated soil (Lucknow, India). A neighbour-joining tree based on 16S rRNA gene sequences showed that strain LP100 occupied a distinct phylogenetic position in the species cluster, showing highest similarity with DM9 (97.4 %). Levels of similarity to strains of other species ranged between 94.0 and 96.8 %. Strain LP100 contained MK-7 as the predominant menaquinone and -homospermidine was the major polyamine in the cell. The major cellular fatty acids of strain LP100 were anteiso-C A, iso-C and iso-C H. The polar lipid profile of strain LP100 showed the presence of phosphatidylethanolamine, an unidentified aminophospholipid, three unknown aminolipids and two unknown polar lipids. The G+C content of strain LP100 was 58.2 mol%. The results of DNA–DNA hybridization, biochemical and physiological tests clearly distinguish the novel strain from closely related species of the genus . Therefore, strain LP100 represents a novel species of the genus for which the name is proposed. The type strain is LP100 ( = CCM8435 = MCC2027).

  • Published Online:
Funding
This study was supported by the:
  • Department of Biotechnology (DBT)
  • National Bureau of Agriculturally Important Micro-organisms (NBAIM, ICAR)
  • DU/DST-PURSE Grant, Government of India
  • Alexander von Humboldt Fellowship
© 2014 IUMS
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.055319-0
2014-01-01
2024-04-24
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/64/1/254.html?itemId=/content/journal/ijsem/10.1099/ijs.0.055319-0&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.[PubMed] [CrossRef]
    [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. [View Article] [PubMed]
    [Google Scholar]
  3. 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]
  4. Bligh E. G., Dyer W. J. ( 1959 ). A rapid method of total lipid extraction and purification. . Can J Biochem Physiol 37, 911–917. [View Article] [PubMed]
    [Google Scholar]
  5. Bowman J. P. ( 2000 ). Description of Cellulophaga algicola sp. nov., isolated from the surfaces of Antarctic algae, and reclassification of Cytophaga uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Cellulophaga uliginosa comb. nov.. Int J Syst Evol Microbiol 50, 1861–1868.[PubMed]
    [Google Scholar]
  6. 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. [View Article] [PubMed]
    [Google Scholar]
  7. Busse J., Auling G. ( 1988 ). Polyamine pattern as a chemotaxonomic marker within the Proteobacteria . . Syst Appl Microbiol 11, 1–8. [View Article]
    [Google Scholar]
  8. 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.[PubMed]
    [Google Scholar]
  9. 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]
  10. Cowan S. T., Steel K. J. ( 1965 ). Manual for the Identification of Medical Bacteria. London:: Cambridge University Press;.
     [Google Scholar]
  11. 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. [View Article] [PubMed]
    [Google Scholar]
  12. Dwivedi V., Niharika N., Lal R. ( 2012 ). Pontibacter lucknowesis sp. nov., isolated from a hexachlorocyclohexane dump site. . Int J Syst Evol Microbiol 63, 309–313. [View Article] [PubMed]
    [Google Scholar]
  13. 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. [View Article] [PubMed]
    [Google Scholar]
  14. 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. [View Article]
    [Google Scholar]
  15. 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. [View Article] [PubMed]
    [Google Scholar]
  16. 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]
  17. 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. [View Article] [PubMed]
    [Google Scholar]
  18. 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. [View Article] [PubMed]
    [Google Scholar]
  19. 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]
  20. 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. [View Article] [PubMed]
    [Google Scholar]
  21. Kuykendall L. D., Roy M. A., O’Neil J. J., Devine T. E. ( 1988 ). Fatty acids, antibiotic resistance and deoxyribonucleic acid homology groups of Bradorhizobium japonicum . . Int J Syst Bacteriol 38, 358–361. [View Article]
    [Google Scholar]
  22. Lal R., Pandey G., Sharma P., Kumari K., Malhotra S., Pandey R., Raina V., Kohler H. P. E., Holliger C. & other authors ( 2010 ). Biochemistry of microbial degradation of hexachlorocyclohexane and prospects for bioremediation. . Microbiol Mol Biol Rev 74, 58–80. [View Article]
    [Google Scholar]
  23. 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]
  24. Maidak B. L., Cole J. R., Lilburn T. G., Parker C. T. Jr, Saxman P. R., Farris R. J., Garrity G. M., Olsen G. J., Schmidt T. M., Tiedje J. M. ( 2001 ). The RDP-II (Ribosomal database project). . Nucleic Acids Res 29, 173–174. [View Article] [PubMed]
    [Google Scholar]
  25. McCarthy A. J., Cross T. ( 1984 ). A taxonomic study of Thermomonospora and other monosporic actinomycetes. . J Gen Microbiol 130, 5–25.
     [Google Scholar]
  26. 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]
  27. 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. [View Article] [PubMed]
    [Google Scholar]
  28. 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. [View Article] [PubMed]
    [Google Scholar]
  29. 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]
  30. Sasser M. ( 1990 ). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. Newark, DE:: MIDI Inc;.
     [Google Scholar]
  31. Singh A. K., Garg N., Sangwan N., Negi V., Kumar R., Vikram S., Lal R. ( 2013 ). Pontibacter ramchanderi sp. nov., isolated from hexachlorocyclohexanecontaminated pond sediment. . Int J Syst Evol Microbiol 63, 2829–2834. [View Article] [PubMed]
    [Google Scholar]
  32. 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]
  33. 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. [View Article] [PubMed]
    [Google Scholar]
  34. 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]
  35. Tourova T. P., Antonov A. S. ( 1988 ). Identification of microorganisms by rapid DNA-DNA hybridization. . Methods Microbiol 19, 333–355. [View Article]
    [Google Scholar]
  36. 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]
  37. 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. [View Article] [PubMed]
    [Google Scholar]
  38. Wang Y., Zhang K., Cai F., Zhang L., Tang Y., Dai J., Fang C. X. ( 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. [View Article] [PubMed]
    [Google Scholar]
  39. 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 systematic. . Int J Syst Evol Microbiol 37, 463–464.
     [Google Scholar]
  40. Xu M., Wang Y., Dai J., Jiang F., Rahman E., Peng F., Fang C. X. ( 2012 ). Pontibacter populi sp. nov., isolated from the soil of a Euphrates poplar (Populus euphratica) forest. . Int J Syst Evol Microbiol 62, 665–670. [View Article] [PubMed]
    [Google Scholar]
  41. Zhang L., Zhang Q. J., Luo X. S., Tang Y. L., Dai J., Li Y. W., Wang Y., Chen G., Fang C. X. ( 2008 ). Pontibacter korlensis sp. nov., isolated from the desert of Xinjiang, China. . Int J Syst Evol Microbiol 58, 1210–1214. [View Article] [PubMed]
    [Google Scholar]
  42. 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. [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.055319-0
Loading
Pontibacter indicus sp. nov., isolated from hexachlorocyclohexane-contaminated soil
Int J Syst Evol Microbiol 64, 254 (2014); https://doi.org/10.1099/ijs.0.055319-0
/content/journal/ijsem/10.1099/ijs.0.055319-0
/content/journal/ijsem/10.1099/ijs.0.055319-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

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