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Volume 58, Issue 6

sp. nov., isolated from an oil-contaminated site Free

Abstract

A Gram-negative, motile, rod-shaped, non-sporulating, aerobic bacterial strain (Esp-1) was isolated from oil-contaminated soil of Panipat Oil Refinery, India, and its taxonomic position was determined using a polyphasic approach. Strain Esp-1 grew in the presence of 2 % NaCl at 30 °C and was characterized chemotaxonomically by having C as the major fatty acid followed by C cyclo and C 7. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Esp-1 formed a cluster together with DSM 6978 (98.9 % sequence similarity), MTCC 7601 (98.5 %), DSM 14399 (98.5 %), DSM 50332 (98.7 %), ATCC 700690 (98.9 %) and DSM 16612 (97.8 %). DNA–DNA hybridization values of strain Esp-1 with DSM 6978, MTCC 7601, DSM 16612, DSM 50332, ATCC 700690 and DSM 14399 were 32.9, 30.2, 20.6, 23.4, 23.4 and 20.0 %, respectively. Low levels of DNA–DNA hybridization and phenotypic and chemotaxonomic results are sufficient to delineate strain Esp-1 from other closely related species of . Phenotypic and chemotaxonomic data confirm that strain Esp-1 represents a novel species, for which the name sp. nov. is proposed. The type strain of sp. nov. is Esp-1 (=MTCC 8990=CCM 7469).

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Keyword(s): TEM, transmission electron microscope
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2008-06-01
2023-06-05
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References

  1. Anzai, Y., Kim, H., Park, J.-Y., Wakabayashi, H. & Oyaizu, H.(2000). Phylogenetic affiliation of the pseudomonads based on 16S rRNA sequence. Int J Syst Evol Microbiol 50, 1563–1589.[CrossRef] [Google Scholar]
  2. Bala, S., Khanna, R., Dadhwal, M., Prabagaran, S. R., Shivaji, S., Cullum, J. & Lal, R.(2004). Reclassification of Amycolatopsis mediterranei DSM 46095 as Amycolatopsis rifamycinica sp. nov. Int J Syst Evol Microbiol 54, 1145–1149.[CrossRef] [Google Scholar]
  3. Bhattacharya, D., Sarma, P. M., Krishnan, S., Mishra, S. & Lal, B.(2003). Evaluation of genetic diversity among Pseudomonas citronellolis strains isolated from oily sludge-contaminated sites. Appl Environ Microbiol 69, 1435–1441.[CrossRef] [Google Scholar]
  4. Collins, C. H., Lyne, P. M. & Grange, J. M.(1989). Microbiological Methods, 6th edn. London: Butterworth.
  5. Elkin, S. & Geddes, D.(2003). Pseudomonal infection in cystic fibrosis: the battle continues. Expert Rev Anti Infect Ther 1, 609–618.[CrossRef] [Google Scholar]
  6. Farmer, J. J., III(1999).Enterobacteriaceae: introduction and identification. In Manual of Clinical Microbiology, 7th edn, pp. 442–458. Edited by P. R. Murray, E. J. Baron, M. A. Pfaller, F. C. Tenover & R. H. Yolken. Washington, DC: American Society for Microbiology.
  7. 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]
  8. Johnsen, K., Andersen, S. & Jacobsen, C. S.(1996). Phenotypic and genotypic characterization of phenanthrene-degrading fluorescent Pseudomonas biovars. Appl Environ Microbiol 62, 3818–3825. [Google Scholar]
  9. Kersters, K., Ludwig, W., Vancanneyt, M., De Vos, P., Gillis, M. & Schleifer, K. H.(1996). Recent changes in the classification of the pseudomonads: an overview. Syst Appl Microbiol 19, 465–477.[CrossRef] [Google Scholar]
  10. Kimura, M.(1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16, 111–120.[CrossRef] [Google Scholar]
  11. Kiyohara, H., Nagao, K. & Yana, K.(1982). Rapid screen for bacteria degrading water-insoluble, solid hydrocarbons on agar plates. Appl Environ Microbiol 43, 454–457. [Google Scholar]
  12. Kiyohara, H., Takizawa, N. & Nagao, K.(1992). Natural distribution of bacteria metabolizing many kinds of polycyclic aromatic hydrocarbons. J Ferment Bioeng 74, 49–51.[CrossRef] [Google Scholar]
  13. Kumar, S., Tamura, K. & Nei, M.(2004).mega3: integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief Bioinform 5, 150–163.[CrossRef] [Google Scholar]
  14. 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]
  15. Kwon, S. W., Kim, J. S., Park, I. C., Yoon, S. H., Park, D. H., Lim, C. K. & Go, S. J.(2003).Pseudomonas koreensis sp. nov., Pseudomonas umsongensis sp. nov. and Pseudomonas jinjuensis sp. nov., novel species from farm soils in Korea. Int J Syst Evol Microbiol 53, 21–27.[CrossRef] [Google Scholar]
  16. Lal, B. & Khanna, S.(1996). Degradation of crude oil by Acinetobacter calcoaceticus and Alcaligenes odorans. J Appl Bacteriol 81, 355–362. [Google Scholar]
  17. Lang, E., Griese, B., Spröer, C., Schumann, P., Steffen, M. & Verbarg, S.(2007). Characterization of ‘Pseudomonas azelaica’ DSM 9128, leading to emended descriptions of Pseudomonas citronellolis Seubert 1960 (Approved Lists 1980) and Pseudomonas nitroreducens Iizuka and Komagata 1964 (Approved Lists 1980), including Pseudomonas multiresinivorans as its later heterotypic synonym. Int J Syst Evol Microbiol 57, 878–882.[CrossRef] [Google Scholar]
  18. Levitski-Heikkila, T. V. & Ullian, M. E.(2005). Peritonitis with multiple rare environmental bacteria in a patient receiving long-term peritoneal dialysis. Am J Kidney Dis 46, e119–e124.[CrossRef] [Google Scholar]
  19. López-Romalde, S., Magariños, B., Ravelo, C., Toranzo, A. E. & Romalde, J. L.(2003). Existence of two O-serotypes in the fish pathogen Pseudomonas anguilliseptica. Vet Microbiol 94, 325–333.[CrossRef] [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. Mishra, S., Lal, B., Jyot, J., Rajan, S. & Khanna, S.(1999). Field study: in situ bioremediation of oily sludge contaminated land using oilzapper. In Proceedings of Hazardous and Industrial Wastes, pp. 177–186. Edited by D Bishop. Pennsylvania, USA: Technomic Publishing Co.
  22. Mishra, S., Jyot, J., Kuhad, R. C. & Lal, B.(2001). In situ bioremediation potential of an oily sludge-degrading bacterial consortium. Curr Microbiol 43, 328–335.[CrossRef] [Google Scholar]
  23. Mohn, W. W., Wilson, A. E., Bicho, P. & Moore, E. R. B.(1999). Physiological and phylogenetic diversity of bacteria growing on resin acids. Syst Appl Microbiol 22, 68–78.[CrossRef] [Google Scholar]
  24. Nei, M. & Kumar, S.(2000).Molecular Evolution and Phylogenetics. New York: Oxford University Press.
  25. O'Mahony, M. M., Dobson, A. D., Barnes, J. D. & Singleton, I.(2006). The use of ozone in the remediation of polycyclic aromatic hydrocarbon contaminated soil. Chemosphere 63, 307–314.[CrossRef] [Google Scholar]
  26. Onaca, C., Kieninger, M., Engesser, K.-H. & Altenbuchner, J.(2007). Degradation of alkyl methyl ketones by Pseudomonas veronii MEK700. J Bacteriol 189, 3759–3767.[CrossRef] [Google Scholar]
  27. Oyaizu, H. & Komagata, K.(1983). Grouping of Pseudomonas species on the basis of cellular fatty acid composition and the quinone system with special reference to the existence of 3-hydroxy fatty acids. J Gen Appl Microbiol 29, 17–40.[CrossRef] [Google Scholar]
  28. 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 Sphingomonaspaucimobilis 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]
  29. Palleroni, N. J.(1984). Genus I. Pseudomonas Migula 1894, 237. In Bergey's Manual of Systematic Bacteriology, vol. 1, pp. 141–199. Edited by N. R. Krieg & J. G. Holt. Baltimore: Williams & Wilkins.
  30. Palleroni, N. J.(1993).Pseudomonas classification. A new case history in the taxonomy of Gram-negative bacteria. Antonie Van Leeuwenhoek 64, 231–251. [Google Scholar]
  31. Palleroni, N. J.(2005). Genus I. Pseudomonas Migula 1894, 237AL. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, The Proteobacteria, Part B The Gammaproteobacteria, pp. 323–379. Edited by D. J. Brenner, N. R. Krieg & J. T. Staley. New York: Springer.
  32. Pearson, W. R. & Lipman, D. J.(1988). Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A 85, 2444–2448.[CrossRef] [Google Scholar]
  33. Prakash, O., Kumari, K. & Lal, R.(2007a).Pseudomonas delhiensis sp. nov., from a fly ash dumping site of a thermal power plant. Int J Syst Evol Microbiol 57, 527–531.[CrossRef] [Google Scholar]
  34. Prakash, O., Verma, M., Sharma, P., Kumar, M., Kumari, K., Singh, A., Kumari, H., Jit, S., Gupta, S. K., Khanna, M. & Lal, R.(2007b). Polyphasic approach of bacterial classification – an overview of recent advances. Indian J Microbiol 47, 98–108.[CrossRef] [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. [Google Scholar]
  36. Sneath, P. H. A., Stevens, M. & Sackin, M. J.(1981). Numerical taxonomy of Pseudomonas based on published record of substrate utilization. Antonie van Leeuwenhoek 47, 423–448.[CrossRef] [Google Scholar]
  37. Stackebrandt, E., Frederiksen, W., Garrity, G. M., Grimont, P. A. D., Kämpfer, P., Maiden, M. C. J., Nesme, X., Rosselló-Mora, R., Swings, J. & other authors(2002). Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52, 1043–1047.[CrossRef] [Google Scholar]
  38. Stanier, R. Y., Palleroni, N. J. & Doudoroff, M.(1966). The aerobic pseudomonads: a taxonomic study. J Gen Microbiol 43, 159–271.[CrossRef] [Google Scholar]
  39. Stolz, A., Busse, H.-J. & Kampfer, P.(2007).Pseudomonas knackmussii sp. nov. Int J Syst Evol Microbiol 57, 572–576.[CrossRef] [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] [Google Scholar]
  41. Tourova, T. P. & Antonov, A. S.(1987). Identification of microorganisms by rapid DNA-DNA hybridization. Methods Microbiol 19, 333–355. [Google Scholar]
  42. Vancanneyt, M., Witt, S., Abraham, W.-R., Kersters, K. & Fredrickson, H. L.(1996). Fatty acid content in whole-cell hydrolysates and phospholipid fractions of pseudomonads: a taxonomic evaluation. Syst Appl Microbiol 19, 528–540.[CrossRef] [Google Scholar]
  43. 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 Evol Microbiol 37, 463–464. [Google Scholar]
  44. Whyte, L. G., Goalen, B., Hawari, J., Labbé, D., Greer, C. W. & Nahir, M.(2001). Bioremediation treatability assessment of hydrocarbon-contaminated soils from Eureka, Nunavut. Cold Regions Sci Technol 32, 121–132.[CrossRef] [Google Scholar]
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Pseudomonas panipatensis sp. nov., isolated from an oil-contaminated site
Int J Syst Evol Microbiol 58, 1339 (2008); https://doi.org/10.1099/ijs.0.65401-0
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vol. , part 6, pp. 1339 - 1345

DNA–DNA relatedness (%) of strain Esp-1 with phylogeetically related strains [PDF](23 KB)

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