1887

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, Pseudomonas granadensis F-278,770, and the next most closely related species with 98.6 % similarity was Pseudomonas punonensis , suggesting that IB1.1 should be classified within the genus Pseudomonas . The analysis of housekeeping genes rpoB, rpoD and gyrB 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 : 1ω7c/16 : 1ω6c (summed feature 3), 18 : 1ω7c 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 Pseudomonas , for which the name Pseudomonas turukhanskensis sp. nov. is proposed. The type strain is IB1.1 (=VKM B-2935=CECT 9091).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.001406
2016-11-01
2019-10-23
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 Biol215:403–410. [CrossRef]
    [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 Microbiol50:1957–1964. [CrossRef]
    [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. . Ultramicroscopy86:121–128. [CrossRef][PubMed]
    [Google Scholar]
  4. Bolshakova A. V., Kiselyova O. I., Yaminsky I. V..( 2004;). Microbial surfaces investigated using atomic force microscopy. . Biotechnol Prog20:1615–1622. [CrossRef][PubMed]
    [Google Scholar]
  5. Chun J., Goodfellow M..( 1995;). A phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences. . Int J Syst Bacteriol45:240–245. [CrossRef][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 Microbiol56:709–714. [CrossRef][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 Rev45:316–354.
    [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 Bacteriol39:224–229. [CrossRef]
    [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 Microbiol58:1339–1345. [CrossRef]
    [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 Bacteriol44:410–415. [CrossRef][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 Microbiol61:1842–1848. [CrossRef]
    [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 Microbiol62:716–721. [CrossRef][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 Evol16:111–120. [CrossRef]
    [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 Med44:301–307.
    [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 Centre3:76–82. (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 Microbiol60:85–91. [CrossRef]
    [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 Microbiol60:2719–2723. [CrossRef]
    [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 Microbiol63:2410–2417. [CrossRef]
    [Google Scholar]
  21. Mandel M., Mamur J..( 1968;). Use of ultraviolet absorbance temperature profile for determining the guanine plus cytosine content of DNA. . Methods Enzymol12B: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 Probes23:140–147. [CrossRef]
    [Google Scholar]
  23. Mulet M., Lalucat J., García-Valdés E..( 2010;). DNA sequence-based analysis of the Pseudomonas species. . Environ Microbiol12:1513–1530.
    [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. Microbiol35:145–149. [CrossRef]
    [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 Microbiol65:625–632. [CrossRef]
    [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 Microbiol55:1107–1112. [CrossRef][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 Microbiol63:1834–1839.[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 Microbiol65:2110–2117. [CrossRef][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 Microbiol44:181–187. [CrossRef]
    [Google Scholar]
  31. Rogers J. S., Swofford D. L..( 1998;). A fast method for approximating maximum likelihoods of phylogenetic trees from nucleotide sequences. . Syst Biol47:77–89.[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 Microbiol60:294–300. [CrossRef][PubMed]
    [Google Scholar]
  33. Saitou N., Nei M..( 1987;). A neighbour-joining method: a new method for reconstructing phylogenetics trees. . Mol Biol Evol4:406–425.
    [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 Microbiol37:89–94. [CrossRef]
    [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 Bacteriol54:31–36. [CrossRef]
    [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 Evol28:2731–2739. [CrossRef][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 Microbiol156:763–773. [CrossRef][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 Res25:4876–4882. [CrossRef][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 Bacteriol37:463–464. [CrossRef]
    [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 Microbiol51:1315–1322. [CrossRef][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 Microbiol59:2594–2598. [CrossRef][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 Bacteriol48:813–819. [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.001406
Loading
/content/journal/ijsem/10.1099/ijsem.0.001406
Loading

Data & Media loading...

Supplements

Supplementary File 1

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