Skip to main content

Sphingomonas qilianensis sp. nov., Isolated from Surface Soil in the Permafrost Region of Qilian Mountains, China

Abstract

A Gram-stain-negative, strictly aerobic, non-motile and rod-shaped bacterial strain, designated X1T, was isolated from the permafrost region of Qilian Mountains in northwest of China. Phylogenetic analyses of 16S rRNA gene sequence revealed that strain X1T was a member of the genus Sphingomonas and shared the highest 16S rRNA gene sequence similarity with Sphingomonas oligophenolica JCM 12082T (96.9 %), followed by Sphingomonas glacialis CGMCC 1.8957T (96.7 %) and Sphingomonas alpina DSM 22537T (96.4 %). Strain X1T was able to grow at 15–30 °C, pH 6.0–10.0 and with 0–0.3 % NaCl (w/v). The DNA G+C content of the isolate was 64.8 mol%. Strain X1T-contained Q-10 as the dominant ubiquinone and C18:1 ω7c, C16:1 ω7c, C16:0 and C14:0 2-OH as the dominant fatty acids. The polar lipid profile of strain XIT-contained sphingoglycolipid, phosphatidylglycerol, phosphatidylethanolamine, one unidentified glycolipid and two unidentified phospholipid. Due to the phenotypic and genetic distinctiveness and other characteristic studied in this article, we consider X1T as a novel species of the genus Sphingomonas and propose to name it Sphingomonas qilianensis sp. nov. The type strain is X1T (=CGMCC 1.15349T = KCTC 42862T).

This is a preview of subscription content, access via your institution.

Fig. 1

References

  1. 1.

    Yabuuchi E, Yano I, Oyaizu H et al (1990) Proposals of Sphingomonas paucimobilis gen. nov. and comb. nov., Sphingomonas parapaucimobilis sp. nov., Sphingomonas yanoikuyae sp. nov., Sphingomonas adhaesiva sp. nov., Sphingomonas capsulata comb. nov., and two genospecies of the genus Sphingomonas. Microbiol Immunol 34:99–119

    Article  CAS  PubMed  Google Scholar 

  2. 2.

    Takeuchi M, Kawai F, Shimada Y et al (1993) Taxonomic study of polyethylene glycerol-utilizing bacteria: emended description of the genus Sphingomonas and new descriptions of Sphingomonas macrogoltabidus sp. nov., Sphingomonas sanguis sp. nov. and Sphingomonas terrae sp. nov. Syst Appl Microbiol 16:227–238

    Article  CAS  Google Scholar 

  3. 3.

    Takeuchi M, Hamana K, Hiraishi A (2001) Proposal of the genus Sphingomonas sensu stricto and three new genera, Sphingobium, Novosphingobium and Sphingopyxis, on the basis of phylogenetic and chemotaxonomic analyses. Int J Syst Evol Microbiol 51:1405–1417

    Article  CAS  PubMed  Google Scholar 

  4. 4.

    Yabuuchi E, Kosako Y, Fujiwara N et al (2002) Emendation of the genus Sphingomonas Yabuuchi et al. 1990 and junior objective synonymy of the species of three genera, Sphingobium, Novosphingobium and Sphingopyxis, in conjunction with Blastomonas ursincola. Int J Syst Evol Microbiol 52:1485–1496

    CAS  PubMed  Google Scholar 

  5. 5.

    Busse HJ, Denner EBM, Buczolits S et al (2003) Sphingomonas aurantiaca sp. nov., Sphingomonas aerolata sp. nov. and Sphingomonas faeni sp. nov., air and dustborne and Antarctic, orange-pigmented, psychrotolerant bacteria, and emended description of the genus Sphingomonas. Int J Syst Evol Microbiol 53:1253–1260

    Article  CAS  PubMed  Google Scholar 

  6. 6.

    Huang FQ, Zhang YL, Zhu YH et al (2014) Flavobacterium qiangtangensis sp. nov., isolated from Qiangtang Basin in Qinghai-Tibetan plateau, China. Curr Microbiol 69:234–239

    Article  CAS  PubMed  Google Scholar 

  7. 7.

    Jia L, Feng XM, Zheng Z et al (2015) Polymorphobacter fuscus sp. nov., isolated from permafrost soil, and emended description of the genus Polymorphobacter. Int J Syst Evol Microbiol. doi:10.1099/ijsem.0.000514

    Google Scholar 

  8. 8.

    Jia L, Nogi Y, Yang AC et al (2015) Sphingomonas arantia sp. nov., isolated from Hoh Xil basin, China. Antonie van Leeuwenhoek. doi:10.1007/s10482-015-0586-0

    Google Scholar 

  9. 9.

    Han L, Wu SJ, Qin CY et al (2014) Hymenobacter qilianensis sp. nov., isolated from a subsurface sandstone sediment in the permafrost region of Qilian Mountains, China and emended description of the genus Hymenobacter. Antonie Van Leeuwenhoek 105:971–978

    Article  CAS  PubMed  Google Scholar 

  10. 10.

    Wang YX, Huang FQ, Nogi Y et al (2015) Youhaiella tibetensis gen. nov., sp. nov., isolated from subsurface sediment. Int J Syst Evol Microbiol 65:2048–2055

    Article  CAS  PubMed  Google Scholar 

  11. 11.

    Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, Chichester, pp 125–175

    Google Scholar 

  12. 12.

    Kim OS, Cho YJ, Lee K 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

    Article  CAS  PubMed  Google Scholar 

  13. 13.

    Altschul SF, Gish W, Miller W et al (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    Article  CAS  PubMed  Google Scholar 

  14. 14.

    Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680

    PubMed Central  Article  CAS  PubMed  Google Scholar 

  15. 15.

    Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98

    CAS  Google Scholar 

  16. 16.

    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

    Article  CAS  PubMed  Google Scholar 

  17. 17.

    Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    CAS  PubMed  Google Scholar 

  18. 18.

    Kishino H, Hasegawa M (1989) Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. J Mol Evol 29:170–179

    Article  CAS  PubMed  Google Scholar 

  19. 19.

    Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 20:406–416

    Article  Google Scholar 

  20. 20.

    Tamura K, Peterson D, Peterson N et al (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739

    PubMed Central  Article  CAS  PubMed  Google Scholar 

  21. 21.

    Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791

    Article  Google Scholar 

  22. 22.

    Murray R, Doetsch RN, Robinow CF (1994) Determinative and cytological light microscopy. In: Gerhardt P (ed) Methods for general and molecular bacteriology. ASM Press, Washington, BC, pp 21–41

    Google Scholar 

  23. 23.

    Bernardet JF (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

    CAS  PubMed  Google Scholar 

  24. 24.

    Smibert RM, Krieg NR (1994) Phenotypic characterization. In: Gerhard P, Murra RGE, Wood WA, Krieg N (eds) Methods for general and molecular bacteriology. American Society for Microbiology, Washington, DC, pp 607–654

    Google Scholar 

  25. 25.

    Barrow GI, Feltham RKA (1993) Cowan and steel’s manual for the identification of medical bacteria. Cambridge University Press, Cambridge

    Book  Google Scholar 

  26. 26.

    Mesbah M, Premachandran U, Whitman WB (1989) Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39:159–167

    Article  CAS  Google Scholar 

  27. 27.

    Minnikin DE, O’Donnell AG, Goodfellow M et al (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Meth 2:233–241

    Article  CAS  Google Scholar 

  28. 28.

    Da Costa MS, Albuquerque L, Nobre M et al (2011) The extraction and identification of respiratory lipoquinones of prokaryotes and their use in taxonomy. Method Microbiol 38:197–206

    Article  Google Scholar 

  29. 29.

    Busse J, Auling G (1988) Polyamine pattern as a chemotaxonomic marker within the Proteobacteria. Syst Appl Microbiol 11:1–8

    Article  CAS  Google Scholar 

  30. 30.

    Nigam A, Jit S, Lal R (2010) Sphingomonas histidinilytica sp. nov., isolated from a hexachlorocyclohexane dump site. Int J Syst Evol Microbiol 60:1038–1043

    Article  CAS  PubMed  Google Scholar 

  31. 31.

    Da Costa MS, Albuquerque L, Nobre M et al (2011) The identification of polar lipids in prokaryotes. Method Microbiol 38:165–181

    Article  Google Scholar 

  32. 32.

    Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101

  33. 33.

    Ohta H, Hattori R, Ushiba Y et al (2004) Sphingomonas oligophenolica sp. nov., a halo- and organo-sensitive oligotrophic bacterium from paddy soil that degrades phenolic acids at low concentrations. Int J Syst Evol Microbiol 54:2185–2190

    Article  CAS  PubMed  Google Scholar 

  34. 34.

    Zhang DC, Busse HJ, Liu HC et al (2011) Sphingomonas glacialis sp. nov., a psychrophilic bacterium isolated from alpine glacier cryoconite. Int J Syst Evol Microbiol 61:587–591

    Article  CAS  PubMed  Google Scholar 

  35. 35.

    Margesin R, Zhang DC, Busse HJ (2012) Sphingomonas alpina sp. nov., a psychrophilic bacterium isolated from alpine soil. Int J Syst Evol Microbiol 62:1558–1563

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Affiliations

Authors

Corresponding author

Correspondence to Jie Lv.

Additional information

The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain X1T is KT000387.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (PDF 858 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Piao, AL., Feng, XM., Nogi, Y. et al. Sphingomonas qilianensis sp. nov., Isolated from Surface Soil in the Permafrost Region of Qilian Mountains, China. Curr Microbiol 72, 363–369 (2016). https://doi.org/10.1007/s00284-015-0957-9

Download citation

Keywords

  • Sphingomonas
  • Qilian Mountain
  • Permafrost Region
  • China General Microbiological Culture Collection Center
  • Unidentified Phospholipid