Skip to main content
SpringerLink
Log in

Solirubrobacter taibaiensis sp. nov., isolated from a stem of Phytolacca acinosa Roxb.

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

Abstract

A white-coloured bacterium, designated strain GTJR-20T, was isolated from a stem of Phytolacca acinosa Roxb. collected from Taibai Mountain in Shaanxi Province, north-west China, and was subjected to a taxonomic study by using a polyphasic approach. The novel isolate was found to grow optimally at 28–30 °C, at pH 7.5–8.0 and in the absence of NaCl. Cells were observed to be Gram-stain positive, strictly aerobic, rod-shaped and non-motile. The predominant respiratory quinone was identified as MK-7(H4) and the major cellular fatty acids were identified as iso-C16:0 (35.8 %), C18:1 ω9c (17.7 %), C17:1 ω6c (11.0 %), C17:1 ω8c (7.8 %) and C18:3 ω6c (6, 9, 12) (7.2 %). The DNA G+C content was determined to be 71.6 mol %. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain GTJR-20T is a member of the genus Solirubrobacter and is closely related to Solirubrobacter phytolaccae GTGR-8T (16S rRNA gene sequence similarity, 98.4 %), Solirubrobacter soli KCTC 12628T (97.8 %), Solirubrobacter pauli KCTC 9974T (97.7 %) and Solirubrobacter ginsenosidimutans KCTC 19420T (97.6 %). No other recognized bacterial species showed more than 94.6 % 16S rRNA gene sequence similarity to the novel isolate. DNA–DNA relatedness values for strain GTJR-20T with respect to its closely related neighbours S. phytolaccae GTGR-8T, S. soli KCTC 12628T, S. pauli KCTC 9974T and S. ginsenosidimutans KCTC 19420T were 48.3 ± 8.6, 21.3 ± 5.2, 36.8 ± 6.2 and 36.0 ± 5.5 %, respectively. Based on the phenotypic, phylogenetic and genotypic data, strain GTJR-20T is considered to represent a novel species of the genus Solirubrobacter, for which the name Solirubrobacter taibaiensis sp. nov. is proposed. The type strain is GTJR-20T (=CCTCC AB 2013308T = KCTC 29222T).

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

  • An DS, Wang L, Kim MS, Bae HM, Lee ST, Im WT (2011) Solirubrobacter ginsenosidimutans sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 61:2606–2609

    Article  CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • Cleenwerck I, Vandemeulebroecke K, Janssens D, Swings J (2002) Re-examination of the genus Acetobacter, with descriptions of Acetobacter cerevisiae sp. nov. and Acetobacter malorum sp. nov. Int J Syst Evol Microbiol 52:1551–1558

    Article  CAS  PubMed  Google Scholar 

  • Doetsch RN (1981) Determinative methods of light microscopy. In: Gerhardt P, Murray RGE, Costilow RN, Nester EW, Wood WA, Krieg NR, Phillips GH (eds) Manual of methods for general bacteriology. American Society for Microbiology, Washington, DC, pp 21–33

    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 (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376

    Article  CAS  PubMed  Google Scholar 

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

    Article  Google Scholar 

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

    Article  Google Scholar 

  • Kim MK, Na JR, Lee TH, Im WT, Soung NK, Yang DC (2007) Solirubrobacter soli sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 57:1453–1455

    Article  PubMed  Google Scholar 

  • Kim BC, Poo H, Lee KH, Kim MN, Kwon OY, Shin KS (2012a) Mucilaginibacter angelicae sp. nov., isolated from the rhizosphere of Angelica polymorpha Maxim. Int J Syst Evol Microbiol 62:55–60

    Article  CAS  PubMed  Google Scholar 

  • Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, Park SC, Jeon YS, Lee JH, Yi H, Won S, Chun J (2012b) 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 

  • 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 

  • 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 

  • Li WJ, Xu P, Schumann P, Zhang YQ, Pukall R, Xu LH, Stackebrandt E, Jiang CL (2007) Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China), and emended description of the genus Georgenia. Int J Syst Evol Microbiol 57:1424–1428

    Article  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 

  • 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 

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

    Google Scholar 

  • Singleton DR, Furlong MA, Peacock AD, White DC, Coleman DC, Whitman WB (2003) Solirubrobacter pauli gen. nov., sp. nov., a mesophilic bacterium within the Rubrobacteridae related to common soil clones. Int J Syst Evol Microbiol 53:485–490

    Article  PubMed  Google Scholar 

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

    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 Central  PubMed  Google Scholar 

  • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882

    Article  CAS  PubMed Central  PubMed  Google Scholar 

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

    Article  Google Scholar 

  • Wei L, Ouyang S, Wang Y, Shen X, Zhang L (2014) Solirubrobacter phytolaccae sp. nov., an endophytic bacterium isolated from roots of Phytolacca acinosa Roxb. Int J Syst Evol Microbiol 64:858–862

    Article  PubMed  Google Scholar 

  • Whitman WB, Shieh J, Sohn S, Caras DS, Premachandran U (1986) Isolation and characterization of 22 mesophilic methanococci. Syst Appl Microbiol 7:235–240

    Article  Google Scholar 

  • Wilson K (1987) Preparation of genomic DNA from bacteria. In: Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K (eds) Current protocols in molecular biology. Greene Publishing and Wiley Interscience, New York, pp 241–245

    Google Scholar 

  • Xie CH, Yokota A (2003) Phylogenetic analysis of Lampropedia hyalina based on the 16S rRNA gene sequence. J Gen Appl Microbiol 49:345–349

    Article  CAS  PubMed  Google Scholar 

  • Xu P, Li WJ, Tang SK, Zhang YQ, Chen GZ, Chen HH, Xu LH, Jiang CL (2005) Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family ‘Oxalobacteraceae’ isolated from China. Int J Syst Evol Microbiol 55:1149–1153

    Article  CAS  PubMed  Google Scholar 

  • Zhang L, Wang Y, Wei L, Wang Y, Shen X, Li S (2013) Taibaiella smilacinae gen. nov., sp. nov., an endophytic member of the family Chitinophagaceae isolated from the stem of Smilacina japonica, and emended description of Flavihumibacter petaseus. Int J Syst Evol Microbiol 63:3769–3776

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

This work was supported by the National High Technology Research and Development Program of China (863 program, Grant 2013AA102802), the National Natural Science Foundation of China (Grant No. 31100001) and the Natural Science Foundation of Shaanxi Province, China (Grant No. 2012JQ3006).

Author information

Authors and Affiliations

  1. State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, People’s Republic of China

    Lei Zhang, Lingfang Zhu, Meiru Si, Changfu Li, Liang Zhao, Yahong Wei & Xihui Shen

Authors
  1. Lei Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Lingfang Zhu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Meiru Si
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Changfu Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Liang Zhao
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Yahong Wei
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Xihui Shen
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Xihui Shen.

Additional information

Lei Zhang and Lingfang Zhu have contributed equally to this work.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 335 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Zhang, L., Zhu, L., Si, M. et al. Solirubrobacter taibaiensis sp. nov., isolated from a stem of Phytolacca acinosa Roxb.. Antonie van Leeuwenhoek 106, 279–285 (2014). https://doi.org/10.1007/s10482-014-0194-4

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10482-014-0194-4

Keywords

Search

Navigation