Skip to main content
SpringerLink
Log in

Sphingomonas arantia sp. nov., isolated from Hoh Xil basin, China

  • Original Paper
  • Published:
Antonie van Leeuwenhoek Aims and scope Submit manuscript

Abstract

A Gram-negative, rod-shaped, non-motile, non-spore forming, aerobic, orange-pigmented bacterium, designated strain 6PT, was isolated from a soil sample collected from the Hoh Xil basin, China. Strain 6PT grew optimally at 25 °C, pH 7.0–7.5 and NaCl concentration of 0–1 % (w/v). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 6PT belongs to the genus Sphingomonas, with high sequence similarity (97.1 %) to Sphingomonas fennica. The DNA–DNA hybridization homology with S. fennica DSM 13665T was 45.3 %. The DNA G+C content of the novel strain is 65.3 mol%. The isolate contained Q-10 as the only respiratory quinone. The major polar lipids are diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylcholine (PC) and sphingoglycolipid (SGL). C18:1 ω7c and C16:1 ω7c are the major fatty acids. On the basis of the polyphasic evidence presented, strain 6PT represents a novel species of the genus Sphingomonas, for which the name Sphingomonas arantia sp. nov. is proposed. The type strain is 6PT (=CGMCC 1.12702T = JCM 19855T).

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1

Similar content being viewed by others

References

  • Bowman JP (2000) Description of Cellulophaga algicola sp. nov., isolated from the surfaces of Antarctic algae, and reclassification of Cytophaga uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Cellulophaga uliginosa comb. nov. Int J Syst Evol Microbiol 50:1861–1868

    Article  CAS  PubMed  Google Scholar 

  • Buck JD (1982) Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 44:992–993

    CAS  PubMed  PubMed Central  Google Scholar 

  • Busse HJ, Denner EB, Buczolits S, Salkinoja Salonen M, Bennasar A, Kämpfer P (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 

  • Da Costa MS, Albuquerque L, Nobre M, Wait R (2011a) The extraction and Identification of respiratory lipoquinones of prokaryotes and their use in taxonomy. Meth Microbiol 38:197–206

    Article  Google Scholar 

  • Da Costa MS, Albuquerque L, Nobre M, Wait R (2011b) The identification of polar lipids in prokaryotes. Meth Microbiol 38:165–181

    Article  Google Scholar 

  • Ezaki T, Hashimoto Y, Yabuuchi 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

    Article  Google Scholar 

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

    Article  PubMed  Google Scholar 

  • Han L, Wu SJ, Qin CY, Zhu YH, Lu ZQ, Xie B, Lv J (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 

  • Kaur J, Kaur J, Niharika N, Lal R (2012) Sphingomonas laterariae sp. nov., isolated from a hexachlorocyclohexane-contaminated dump site. Int J Syst Evol Microbiol 62:2891–2896

    Article  CAS  PubMed  Google Scholar 

  • Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, Park SC, Jeon YS, Lee JH, Chun J (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 

  • 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 

  • Leifson E (1951) Staining shape and arrangement of bacterial flagella. J Bacteriol 62:377–389

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lin SY, Shen FT, Lai WA, Zhu ZL, Chen WM, Chou JH, Lin ZY, Young CC (2012) Sphingomonas formosensis sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from agricultural soil. Int J Syst Evol Microbiol 62:1581–1586

    Article  CAS  PubMed  Google Scholar 

  • Maruyama T, Park HD, Ozawa K, Tanaka Y, Sumino T, Hamana K, Hiraishi A, Kato K (2006) Sphingosinicella microcystinivorans gen. nov., sp. nov., a microcystin-degrading bacterium. Int J Syst Evol Microbiol 56:85–89

    Article  CAS  PubMed  Google Scholar 

  • 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 

  • Minnikin D, O’donnell A, Goodfellow M, Alderson G, Athalye M, Schaal A, Parlett J (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Meth 2:233–241

    Article  CAS  Google Scholar 

  • 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 

  • 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 

  • Takeuchi M, Hiraishi A (2001) Taxonomic significance of 2-hydroxy fatty acid profiles of the species in the genus Sphingomonas and related taxa. IFO Res Commun 20:72–82

    Google Scholar 

  • 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 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tan X, Zhang RG, Meng TY, Liang HZ, Lv J (2014) Taibaiella chishuiensis sp. nov., isolated from fresh water. Int J Syst Evol Microbiol 64:1795–1801

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tian M, Zhang RG, Han L, Zhao XM, Lv J (2015) Dyadobacter sediminis sp. nov., isolated from a subterranean sediment sample. Int J Syst Evol Microbiol 65:827–832

    Article  CAS  PubMed  Google Scholar 

  • Wayne LG, Brenner DJ, Colwell RR, Grimont P, Kandler O, Krichevsky MI, Moore LH, Moore W, Murray R et al (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464

    Article  Google Scholar 

  • White DC, Sutton SD, Ringelberg DB (1996) The genus Sphingomonas: physiology and ecology. Curr Opin Biotechnol 7:301–306

    Article  CAS  PubMed  Google Scholar 

  • Wittich RM, Busse HJ, Kämpfer P, Macedo AJ, Tiirola M, Wieser M, Abraham WR (2007) Sphingomonas fennica sp. nov. and Sphingomonas haloaromaticamans sp. nov., outliers of the genus Sphingomonas. Int J Syst Evol Microbiol 57:1740–1746

    Article  CAS  PubMed  Google Scholar 

  • Yabuuchi E, Yano I, Oyaizu H, Hashimoto Y, Ezaki T, Yamamoto H (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 

  • Yim MS, Yau YC, Matlow A, So JS, Zou J, Flemming CA, Schraft H, Leung KT (2010) A novel selective growth medium-PCR assay to isolate and detect Sphingomonas in environmental samples. J Microbiol Meth 82:19–27

    Article  CAS  Google Scholar 

  • Zhang RG, Tan X, Zhao XM, Deng J, Lv J (2014) Moheibacter sediminis gen. nov., sp. nov., a member of the family Flavobacteriaeace isolated from sediment, and emended descriptions of Empedobacterbrevis, Wautersiella falsenii and Weeksella virosa. Int J Syst Evol Microbiol 64:1481–1487

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

This research is financed by the National Special Research Fund (Gas Hydrate Resource Exploration and Production Testing Project, Grant No.: GZHL20110308, GZHL20110323). We thank supporters of our lab and also the identification service of the China General Microbiological Culture Collection Center (CGMCC) for their help. Specially, we thank Prof. Bernhard Schink for the help of the guidance about naming the new strain.

Author information

Authors and Affiliations

  1. College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People’s Republic of China

    Li Jia, Zhong Zheng, Xiaomin Feng, Aichen Yang, Yali Zhang, Lu Han & Jie Lv

  2. Research and Development Center for Marine Biosciences, Japan Agency for Marine-EarthScience and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan

    Yuichi Nogi

  3. College of Resources and Environmental Science, East China Normal University, Shanghai, 200241, People’s Republic of China

    Lu Han

  4. Oil and Gas Survey, China Geological Survey, Beijing, 100029, People’s Republic of China

    Zhenquan Lu

Authors
  1. Li Jia
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Zhong Zheng
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Xiaomin Feng
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yuichi Nogi
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Aichen Yang
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Yali Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Lu Han
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Zhenquan Lu
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Jie Lv
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jie Lv.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (PDF 409 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Jia, L., Zheng, Z., Feng, X. et al. Sphingomonas arantia sp. nov., isolated from Hoh Xil basin, China. Antonie van Leeuwenhoek 108, 1341–1347 (2015). https://doi.org/10.1007/s10482-015-0586-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10482-015-0586-0

Keywords

Search

Navigation