1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 66, Issue 11

sp. nov., isolated from oil-contaminated soils Free

Abstract

A bacterial strain named IB1.1 was isolated in a screening of hydrocarbon-degrading bacteria from oil-contaminated soils on the territory of the Turukhansk District of Krasnoyarsk Krai, East Siberia, Russia. The 16S rRNA gene sequence had 98.7 % identity with respect to the closest phylogenetic relative, F-278,770, and the next most closely related species with 98.6 % similarity was , suggesting that IB1.1 should be classified within the genus . The analysis of housekeeping genes , and showed similarities lower than 90 % in all cases with respect to the closest relatives, confirming its phylogenetic affiliation. The strain showed a polar flagellum. The respiratory quinone was Q9. The major fatty acids were 16 : 1ω7/16 : 1ω6 (summed feature 3), 18 : 1ω7 and 16 : 0. The strain was oxidase- and catalase-positive, but the arginine dihydrolase system was not present. Nitrate reduction, urease and β–galactosidase production, and aesculin hydrolysis were negative. The temperature range for growth was 4–34 °C, and the strain could grow at pH 11. The DNA G+C content was 58.5 mol%. DNA–DNA hybridization results showed values of less than 30 % relatedness with respect to the type strains of the eight most closely related species. Therefore, the dataset of genotypic, phenotypic and chemotaxonomic data support the classification of strain IB1.1 into a novel species of the genus , for which the name sp. nov. is proposed. The type strain is IB1.1 (=VKM B-2935=CECT 9091).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): oil-contaminated soil , Pseudomonas , Russia , taxonomy and Turukhansk District
© 2016 IUMS
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.001406
2016-11-01
2024-04-19
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/66/11/4657.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.001406&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 [View Article]
     [Google Scholar]
  2. Andersen S. M., Johnsen K., Sorensen J., Nielsen P., Jacobsen C. S. 2000; Pseudomonas frederiksbergensis sp. nov., isolated from soil at a coal gasification site. Int J Syst Evol Microbiol 50:1957–1964 [View Article]
     [Google Scholar]
  3. Bolshakova A. V., Kiselyova O. I., Filonov A. S., Frolova O. Yu., Lyubchenko Yu. L., Yaminsky I. V. 2001; Comparative studies of bacteria with an atomic force microscopy operating in different modes. Ultramicroscopy 86:121–128 [View Article][PubMed]
     [Google Scholar]
  4. Bolshakova A. V., Kiselyova O. I., Yaminsky I. V. 2004; Microbial surfaces investigated using atomic force microscopy. Biotechnol Prog 20:1615–1622 [View Article][PubMed]
     [Google Scholar]
  5. Chun J., Goodfellow M. 1995; A phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences. Int J Syst Bacteriol 45:240–245 [View Article][PubMed]
     [Google Scholar]
  6. Clark L. L., Dajcs J. J., McLean C. H., Bartell J. G., Stroman D. W. 2006; Pseudomonas otitidis sp. nov., isolated from patients with otic infections. Int J Syst Evol Microbiol 56:709–714 [View Article][PubMed]
     [Google Scholar]
  7. Collins M. D. 1985; Analysis of isoprenoid quinones. In Methods in Microbiology vol. 18 pp. 329–366 Edited by Gottschalk G. London: Academic Press;
     [Google Scholar]
  8. Collins M. D., Jones D. 1981; Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implications. Microbiol Rev 45:316–354
     [Google Scholar]
  9. Doetsch R. N. 1981; Determinative methods of light microscopy. In Manual of Methods for General Bacteriology pp. 21–33 Edited by Gerdhardt P., Murray R. G. E., Costilow R. N., Nester E. W., Wood W. A., Krieg N. R., Phillips G. B. Washington: American Society for Microbiology;
     [Google Scholar]
  10. Ezaki T., Hashimoto Y., Yabuchi E. 1989; Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 39:224–229 [View Article]
     [Google Scholar]
  11. 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 [View Article]
     [Google Scholar]
  12. Hildebrand D. C., Palleroni N. J., Hendson M., Toth J., Johnson J. L. 1994; Pseudomonas flavescens sp. nov., isolated from walnut blight cankers. Int J Syst Bacteriol 44:410–415 [View Article][PubMed]
     [Google Scholar]
  13. Hirota K., Yamahira K., Nakajima K., Nodasaka Y., Okuyama H., Yumoto I. 2011; Pseudomonas toyotomiensis sp. nov., a psychrotolerant facultative alkaliphile that utilizes hydrocarbons. Int J Syst Evol Microbiol 61:1842–1848 [View Article]
     [Google Scholar]
  14. 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]
  15. 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 [View Article]
     [Google Scholar]
  16. King E. O., Ward M. K., Raney D. E. 1954; Two simple media for the demonstration of pyocyanin and fluorescein. J Lab Clin Med 44:301–307
     [Google Scholar]
  17. Korshunova T. Y., Sabirov A. A., Chetverikov S. P., Bakaeva M. D., Loginov O. N. 2012; Mikroorganizmy razlagayushchie neftyanye uglevodorody pri ponizhennoy temperature [Microorganisms decomposing oil hydrocarbons at low temperatures]. Izvestiya Ufimskogo nauchnogo tsentra RAN – Bulletin of the RAS Ufa Scientific Centre 3:76–82 (In Russian)
    [Google Scholar]
  18. Lang E., Burghartz M., Spring S., Swiderski J., Sproeer C. 2010; Pseudomonas benzenivorans sp. nov. and Pseudomonas saponiphila sp. nov., represented by xenobiotics degrading type strains. Curr Microbiol 60:85–91 [View Article]
     [Google Scholar]
  19. Lee D.-H., Moon S.-R., Park Y.-H., Kim J.-H., Kim H., Parales R. E., Kahng H.-Y. 2010; Pseudomonas taeanensis sp. nov., isolated from a crude oil-contaminated seashore. Int J Syst Evol Microbiol 60:2719–2723 [View Article]
     [Google Scholar]
  20. Lin S.-Y., Hameed A., Liu Y.-C., Hsu Y.-H., Lai W.-A., Chen W.-M., Shen F.-T., Young C.-C. 2013; Pseudomonas sagittaria sp. nov., a siderophore-producing bacterium isolated from oil-contaminated soil. Int J Syst Evol Microbiol 63:2410–2417 [View Article]
     [Google Scholar]
  21. Mandel M., Mamur J. 1968; Use of ultraviolet absorbance temperature profile for determining the guanine plus cytosine content of DNA. Methods Enzymol 12B:195–206 [CrossRef]
     [Google Scholar]
  22. Mulet M., Bennasar A., Lalucat J., García-Valdés E. 2009; An rpoD-based PCR procedure for the identification of Pseudomonas species and for their detection in environmental samples. Mol Cell Probes 23:140–147 [View Article]
     [Google Scholar]
  23. Mulet M., Lalucat J., García-Valdés E. 2010; DNA sequence-based analysis of the Pseudomonas species. Environ Microbiol 12:1513–1530
     [Google Scholar]
  24. Mulet M., Gomila M., Lemaitre B., Lalucat J., García-Valdés E. 2012; Taxonomic characterisation of Pseudomonas strain L48 and formal proposal of Pseudomonas entomophila sp. nov. Syst. Appl. Microbiol 35:145–149 [View Article]
     [Google Scholar]
  25. Palleroni N. J. 2005; Genus I. Pseudomonas Migula 1894, 237AL (Nom. Cons., Opin. 5 of the Jud. Comm. 1952, 121). In Bergey’s Manual of Systematic Bacteriology, 2nd edn. vol. 2, part B pp. 323–379 Edited by Boone D. R., Brenner D. J., Castenholz R. W., Garrity G. M., Krieg N. R., Staley J. T. New York: Springer;
     [Google Scholar]
  26. Pascual J., García-López M., Bills G. F., Genilloud O. 2015; Pseudomonas granadensis sp. nov., a new bacterial species isolated from the Tejeda, Almijara and Alhama Natural Park, Granada, Spain. Int J Syst Evol Microbiol 65:625–632 [View Article]
     [Google Scholar]
  27. Peix A., Berge O., Rivas R., Abril A., Velázquez E. 2005; Pseudomonas argentinensis sp. nov., a novel yellow pigment-producing bacterial species, isolated from rhizospheric soil in Cordoba, Argentina. Int J Syst Evol Microbiol 55:1107–1112 [View Article][PubMed]
     [Google Scholar]
  28. Ramos E., Ramírez-Bahena M. H., Valverde A., Velázquez E., Zúñiga D., Velezmoro C., Peix A. 2013; Pseudomonas punonensis sp. nov., a novel species isolated from grasses in Puno region (Peru). Int J Syst Evol Microbiol 63:1834–1839 [CrossRef]
     [Google Scholar]
  29. Ramírez-Bahena M. H., Cuesta M. J., Tejedor C., Igual J. M., Fernández-Pascual M., Peix Á. 2015; Pseudomonas endophytica sp. nov., isolated from stem tissue of Solanum tuberosum in Spain. Int J Syst Evol Microbiol 65:2110–2117 [View Article][PubMed]
     [Google Scholar]
  30. Rivas R., García-Fraile P., Mateos P. F., Martínez-Molina E., Velázquez E. 2007; Characterization of xylanolytic bacteria present in the bract phyllosphere of the date palm Phoenix dactylifera. Lett Appl Microbiol 44:181–187 [View Article]
     [Google Scholar]
  31. Rogers J. S., Swofford D. L. 1998; A fast method for approximating maximum likelihoods of phylogenetic trees from nucleotide sequences. Syst Biol 47:77–89 [CrossRef]
     [Google Scholar]
  32. Saha R., Spröer C., Beck B., Bagley S. 2010; Pseudomonas oleovorans subsp. lubricantis subsp. nov., and reclassification of Pseudomonas pseudoalcaligenes ATCC 17440T as later synonym of Pseudomonas oleovorans ATCC 8062 T. Curr Microbiol 60:294–300 [View Article][PubMed]
     [Google Scholar]
  33. Saitou N., Nei M. 1987; A neighbour-joining method: a new method for reconstructing phylogenetics trees. Mol Biol Evol 4:406–425
     [Google Scholar]
  34. Sanchez D., Mulet M., Rodriguez A. C., David Z., Lalucat J., Garcia-Valdes E. 2014; Pseudomonas aestusnigri sp. nov., isolated from crude oil-contaminated intertidal sand samples after the Prestige oil spill. Syst Appl Microbiol 37:89–94 [View Article]
     [Google Scholar]
  35. Sasser M. 1990 Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc;
     [Google Scholar]
  36. Tamaoka J., Katayama-Fujimura Y., Kuraishi H. 1983; Analysis of bacterial menaquinone mixtures by high performance liquid chromatography. J Appl Bacteriol 54:31–36 [View Article]
     [Google Scholar]
  37. 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]
  38. Tayeb L., Ageron E., Grimont F., Grimont P. A. D. 2005; Molecular phylogeny of the genus Pseudomonas based on rpoB sequences and application for the identification of isolates. Res Microbiol 156:763–773 [View Article][PubMed]
     [Google Scholar]
  39. 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]
  40. 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; Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464 [View Article]
     [Google Scholar]
  41. Willems A., Doignon-Bourcier F., Goris J., Coopman R., de Lajudie P., De Vos P., Gillis M. 2001; DNA-DNA hybridization study of Bradyrhizobium strains. Int J Syst Evol Microbiol 51:1315–1322 [View Article][PubMed]
     [Google Scholar]
  42. Xiao Y. P., Hui W., Wang Q., Roh S. W., Shi X. Q., Shi J. H., Quan Z. X. 2009; Pseudomonas caeni sp. nov., a denitrifying bacterium isolated from the sludge of an anaerobic ammonium-oxidizing bioreactor. Int J Syst Evol Microbiol 59:2594–2598 [View Article][PubMed]
     [Google Scholar]
  43. Yamamoto S., Harayama S. 1998; Phylogenetic relationships of Pseudomonas putida strains deduced from the nucleotide sequences of gyrB, rpoD and 16S rRNA genes. Int J Syst Bacteriol 48:813–819 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.001406
Loading
Pseudomonas turukhanskensis sp. nov., isolated from oil-contaminated soils
Int J Syst Evol Microbiol 66, 4657 (2016); https://doi.org/10.1099/ijsem.0.001406
/content/journal/ijsem/10.1099/ijsem.0.001406
/content/journal/ijsem/10.1099/ijsem.0.001406
Loading

Data & Media loading...

Supplements

Supplementary File 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