Skip to content
1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 65, Issue Pt_5

gen. nov., sp. nov., a genome-sequenced gammaproteobacterium isolated from an oilfield Free

Abstract

A yellow-pigmented strain, designated strain 3.5X, was isolated from oil-contaminated saline soil in Gudao, Shandong Province, China, and was characterized taxonomically. The results showed that the isolate was a Gram-stain-negative, aerobic, motile, rod-shaped cell with a polar flagellum. Phylogenetic analysis of 16S rRNA gene sequences revealed the strain belonged to the family in the class and represented an independent taxon separated from other genera. The closest relative of strain 3.5X was DSM 14263 (94 % similarity). The genomic DNA G+C content was 67 mol% by thermal denaturation and 66.3 mol% from genome sequences. The cells mainly consisted of branched fatty acids, with iso-C, iso-C, iso-Cω9 and/or C10-methyl and iso-C as the major fatty acids. The main polar lipids were phosphatidylmonomethylethanolamine, diphosphatidylglycerol and phosphatidylethanolamine. In addition, ubiquinone Q-8 was the major component of the quinone system and the polyamine pattern contained the major compound spermidine plus minor amounts of putrescine and spermine. On the basis of phenotypic, genotypic and phylogenetic distinctiveness, it is proposed that the isolate represents a novel species in a novel genus, namely gen. nov., sp. nov. The type strain is 3.5X ( = NBRC 110685 = KCTC 42351 = CPCC 100614).

  • Published Online:
Funding
This study was supported by the:
  • National Natural Science Foundation of China (Award 30970098 and 51138006)
  • National High Technology Research and Development Program of China (Award 2013AA06A210)
  • National Science and Technology Major Project for Water Pollution Control and Treatment (Award 20122×07301-001)
© 2015 IUMS
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.000158
2015-05-01
2025-04-21
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/65/5/1666.html?itemId=/content/journal/ijsem/10.1099/ijs.0.000158&mimeType=html&fmt=ahah

References

  1. An D. S., Im W. T., Yang H. C., Yang D. C., Lee S. T. ( 2005 ). Dyella koreensis sp. nov., a β-glucosidase-producing bacterium. . Int J Syst Evol Microbiol 55, 1625–1628. [View Article] [PubMed]
    [Google Scholar]
  2. Angelim A. L., Costa S. P., Farias B. C., Aquino L. F., Melo V. M. ( 2013 ). An innovative bioremediation strategy using a bacterial consortium entrapped in chitosan beads. . J Environ Manage 127, 10–17. [View Article] [PubMed]
    [Google Scholar]
  3. Busse H. J., Auling G. ( 1988 ). Polyamine pattern as a chemotaxonomic marker within the Proteobacteria . . Syst Appl Microbiol 11, 1–8. [View Article]
    [Google Scholar]
  4. Busse H. J., Kämpfer P., Moore E. R. B., Nuutinen J., Tsitko I. V., Denner E. B. M., Vauterin L., Valens M., Rosselló-Mora R., Salkinoja-Salonen M. S. ( 2002 ). Thermomonas haemolytica gen. nov., sp. nov., a gamma-proteobacterium from kaolin slurry. . Int J Syst Evol Microbiol 52, 473–483.[PubMed]
    [Google Scholar]
  5. Chang H. K., Zylstra G. J. ( 2010 ). Xanthomonads. . In Handbook of Hydrocarbon and Lipid Microbiology, pp. 1805–1811. Edited by Kenneth N. T. . Berlin:: Springer;. [View Article]
    [Google Scholar]
  6. 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]
  7. Dastgheib S. M., Amoozegar M. A., Khajeh K., Shavandi M., Ventosa A. ( 2012 ). Biodegradation of polycyclic aromatic hydrocarbons by a halophilic microbial consortium. . Appl Microbiol Biotechnol 95, 789–798. [View Article] [PubMed]
    [Google Scholar]
  8. Dong X., Cai M. ( 2001 ). Cultivation and physiological characteristics. . In Systematic Determinative Manual of General Bacteria, pp. 364–369. Edited by Dong X., Cai M. . Beijing:: Science Press; (in Chinese).
     [Google Scholar]
  9. Fan X., Yu T., Li Z., Zhang X. H. ( 2014 ). Luteimonas abyssi sp. nov., isolated from deep-sea sediment. . Int J Syst Evol Microbiol 64, 668–674. [View Article] [PubMed]
    [Google Scholar]
  10. Felsenstein J. ( 1981 ). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17, 368–376. [View Article] [PubMed]
    [Google Scholar]
  11. Friedrich M. M., Lipski A. ( 2008 ). Alkanibacter difficilis gen. nov., sp. nov. and Singularimonas variicoloris gen. nov., sp. nov., hexane-degrading bacteria isolated from a hexane-treated biofilter. . Int J Syst Evol Microbiol 58, 2324–2329. [View Article] [PubMed]
    [Google Scholar]
  12. Gillis M., Vandamme P., De Vos P., Swings J., Kersters K. ( 2005 ). Polyphasic taxonomy. . In Bergey’s Manual of Systematic Bacteriology, , 2nd edn., vol. 2, pp. 43–48. Edited by Brenner D. J., Krieg N. R., Staley J. T., Garrity G. M. . Berlin:: Springer;. [View Article]
    [Google Scholar]
  13. Hucker G. J. ( 1921 ). A new modification and application of the Gram stain. . J Bacteriol 6, 395–397.[PubMed]
    [Google Scholar]
  14. Janssen P. H., Schuhmann A., Mörschel E., Rainey F. A. ( 1997 ). Novel anaerobic ultramicrobacteria belonging to the Verrucomicrobiales lineage of bacterial descent isolated by dilution culture from anoxic rice paddy soil. . Appl Environ Microbiol 63, 1382–1388.[PubMed]
    [Google Scholar]
  15. Johansen J. E., Binnerup S. J., Kroer N., Mølbak L. ( 2005 ). Luteibacter rhizovicinus gen. nov., sp. nov., a yellow-pigmented gammaproteobacterium isolated from the rhizosphere of barley (Hordeum vulgare L.). . Int J Syst Evol Microbiol 55, 2285–2291. [View Article] [PubMed]
    [Google Scholar]
  16. Jung H. M., Ten L. N., Kim K. H., An D. S., Im W. T., Lee S. T. ( 2009 ). Dyella ginsengisoli sp. nov., isolated from soil of a ginseng field in South Korea. . Int J Syst Evol Microbiol 59, 460–465. [View Article] [PubMed]
    [Google Scholar]
  17. Kämpfer P., Martin E., Lodders N., Langer S., Schumann P., Jäckel U., Busse H. J. ( 2010 ). Pseudofulvimonas gallinarii gen. nov., sp. nov., a new member of the family Xanthomonadaceae . . Int J Syst Evol Microbiol 60, 1427–1431. [View Article] [PubMed]
    [Google Scholar]
  18. Kimura M. ( 1983 ). The Neutral Theory of Molecular Evolution. Cambridge:: Cambridge University Press;. [View Article]
    [Google Scholar]
  19. Kluge A. G., Farris J. S. ( 1969 ). Quantitative phyletics and the evolution of anurans. . Syst Zool 18, 1–32. [View Article]
    [Google Scholar]
  20. Kumar S., Nei M., Dudley J., Tamura K. ( 2008 ). mega: a biologist-centric software for evolutionary analysis of DNA and protein sequences. . Brief Bioinform 9, 299–306. [View Article] [PubMed]
    [Google Scholar]
  21. Larkin M. A., Blackshields G., Brown N. P., Chenna R., McGettigan P. A., McWilliam H., Valentin F., Wallace I. M., Wilm A. et al. ( 2007 ). clustal w and clustal_x version 2.0. . Bioinformatics 23, 2947–2948. [View Article] [PubMed]
    [Google Scholar]
  22. Le Borgne S., Paniagua D., Vazquez-Duhalt R. ( 2008 ). Biodegradation of organic pollutants by halophilic bacteria and archaea. . J Mol Microbiol Biotechnol 15, 74–92. [View Article] [PubMed]
    [Google Scholar]
  23. Marmur J., Doty P. ( 1962 ). Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. . J Mol Biol 5, 109–118. [View Article] [PubMed]
    [Google Scholar]
  24. Mergaert J., Cnockaert M. C., Swings J. ( 2002 ). Fulvimonas soli gen. nov., sp. nov., a γ-proteobacterium isolated from soil after enrichment on acetylated starch plastic. . Int J Syst Evol Microbiol 52, 1285–1289. [View Article] [PubMed]
    [Google Scholar]
  25. Minnikin D. E., O’Donnell A. G., Goodfellow M., Alderson G., Athalye M., Schaal A., Parlett J. H. ( 1984 ). An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. . J Microbiol Methods 2, 233–241. [View Article]
    [Google Scholar]
  26. Nalin R., Simonet P., Vogel T. M., Normand P. ( 1999 ). Rhodanobacter lindaniclasticus gen. nov., sp. nov., a lindane-degrading bacterium. . Int J Syst Bacteriol 49, 19–23. [View Article] [PubMed]
    [Google Scholar]
  27. Saddler G. S., Bradbury J. F. ( 2005 ). Order III. Xanthomonadales . . In Bergey’s Manual of Systematic Bacteriology, , 2nd edn., vol. 2, pp. 63–122. Edited by Brenner D. J., Kreig N. R., Staley J. T., Garrity G. M. . New York:: Springer;. [View Article]
    [Google Scholar]
  28. 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]
  29. Sasser, M. (1990). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. Newark, DE: MIDI Inc.
  30. Stolz A., Busse H. J., Kämpfer P. ( 2007 ). Pseudomonas knackmussii sp. nov.. Int J Syst Evol Microbiol 57, 572–576. [View Article] [PubMed]
    [Google Scholar]
  31. Widdel F., Pfennig N. ( 1981 ). Studies on dissimilatory sulfate-reducing bacteria that decompose fatty acids. I. Isolation of new sulfate-reducing bacteria enriched with acetate from saline environments. Description of Desulfobacter postgatei gen. nov., sp. nov.. Arch Microbiol 129, 395–400. [View Article] [PubMed]
    [Google Scholar]
  32. Wilson K. ( 1987 ). Preparation of genomic DNA from bacteria. . In Current Protocols in Molecular Biology , pp. 2.4.1–2.4.2. Edited by Ausubel F. M., Brent R., Kingston R. E., Moore D. D., Seidman J. G., Smith J. A., Struhl K. . New York:: Wiley;.
     [Google Scholar]
  33. Woo S. G., Srinivasan S., Kim M. K., Lee M. ( 2012 ). Rhodanobacter caeni sp. nov., isolated from sludge from a sewage disposal plant. . Int J Syst Evol Microbiol 62, 2815–2821. [View Article] [PubMed]
    [Google Scholar]
  34. Xie C. H., Yokota A. ( 2005 ). Dyella japonica gen. nov., sp. nov., a γ-proteobacterium isolated from soil. . Int J Syst Evol Microbiol 55, 753–756. [View Article] [PubMed]
    [Google Scholar]
  35. Zhang J., Xie Q., Liu Z., Goodfellow M. ( 2007 ). Lechevalieria fradiae sp. nov., a novel actinomycete isolated from soil in China. . Int J Syst Evol Microbiol 57, 832–836. [View Article] [PubMed]
    [Google Scholar]
  36. Zhang J. Y., Liu X. Y., Liu S. J. ( 2011 ). Frateuria terrea sp. nov., isolated from forest soil, and emended description of the genus Frateuria . . Int J Syst Evol Microbiol 61, 443–447. [View Article] [PubMed]
    [Google Scholar]
  37. Zhao B., Wang H., Mao X., Li R. ( 2009 ). Biodegradation of phenanthrene by a halophilic bacterial consortium under aerobic conditions. . Curr Microbiol 58, 205–210. [View Article] [PubMed]
    [Google Scholar]
  38. Zhao B., Wang H., Li R., Mao X. ( 2010 ). Thalassospira xianhensis sp. nov., a polycyclic aromatic hydrocarbon-degrading marine bacterium. . Int J Syst Evol Microbiol 60, 1125–1129. [View Article] [PubMed]
    [Google Scholar]
/content/journal/ijsem/10.1099/ijs.0.000158
Loading
Oleiagrimonas soli gen. nov., sp. nov., a genome-sequenced gammaproteobacterium isolated from an oilfield
Int J Syst Evol Microbiol 65, 1666 (2015); https://doi.org/10.1099/ijs.0.000158
/content/journal/ijsem/10.1099/ijs.0.000158
/content/journal/ijsem/10.1099/ijs.0.000158
Loading

Data & Media loading...

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