Skip to main content
SpringerLink
Log in

Rhizobium rhizosphaerae sp. nov., a novel species isolated from rice rhizosphere

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

Abstract

Two novel, Gram-negative, motile, rod-shaped, aerobic bacterial strains, MH17T and RD15, were isolated from the sterilized root and rhizosphere soil of rice, respectively. Phylogenetic analysis based on 16S rRNA gene sequences showed that the similarity between strains MH17T and RD15 was 100%. The isolates exhibit high sequence similarities to Rhizobium oryzae CGMCC 1.7048T (98.7%) and Rhizobium petrolearium SL-1T (97.0% and 97.1%), which supports that they belong to a novel species in the genus Rhizobium. Strains MH17T and RD15 exhibited growth at 15–45 °C, pH 5.0–11.0, 0–2.0% sodium chloride (w/v). Sequence analysis of housekeeping genes gyrB, recA, atpD, ropB, gltA showed that these two novel strains had less than 94% similarity with the known species, indicating the distinct position of MH17T and RD15 in the genus Rhizobium. The major cellular fatty acids were identified as summed feature 8 (C18:1 ω7c and/or C18:1 ω6c). Type strain MH17T had 87.5% DNA–DNA relatedness with RD15 by using the initial renaturation rate method. Based on draft genome sequences, strain MH17T showed 30.1% DNA–DNA hybridization values to R. oryzae CGMCC 1.7048T, the closely related strain, which supported that MH17T represents a novel species in the genus Rhizobium. Average nucleotide identity (ANI) between strains MH17T and RD15 were 97.8%, and strain MH17T showed 82.2% ANI value with R. oryzae CGMCC 1.7048T. The DNA G+C content was 60.4 mol% (Tm). Based on physiological, biochemical characteristic, genotypic data, strains MH17T and RD15 are concluded to represent a new species within the genus Rhizobium, for which the name Rhizobium rhizosphaerae sp. nov. is proposed. The type strain is MH17T (=ACCC 19963T = KCTC 52414T).

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
Fig. 2

Similar content being viewed by others

References

  • De Ley J (1970) Reexamination of the association between melting point, buoyant density, and chemical base composition of deoxyribonucleic acid. J Bacteriol 101:738–754

    PubMed  PubMed Central  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 

  • Frank B (1889) Ueber die Pilzsymbiose der Leguminosen. Ber DtschBot Ges 7:332–346 (in German)

    Google Scholar 

  • Gu T, Sun LN, Zhang J, Sui XH, Li SP (2014) Rhizobium flavum sp. nov., a triazophos-degrading bacterium isolated from soil under the long-term application of triazophos. Int J Syst Evol Microbiol 64:2017–2022

    Article  CAS  PubMed  Google Scholar 

  • Jordan DC (1984) Genus I. Rhizobium Frank 1889, 338AL. In: Krieg NR, Holt JG (eds) Bergey’s manual of systematic bacteriology, vol 1. Williams & Wilkins, Baltimore, pp 235–242

    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 (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 

  • Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1–6

    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 115–175

    Google Scholar 

  • Lin SY, Hung MH, Hameed A, Liu YC, Hsu YH, Wen CZ, Arun AB, Busse HJ, Glaeser SP, Kämpfer P, Young CC (2015) Rhizobium capsici sp. nov., isolated from root tumor of a green bell pepper (Capsicum annuum var. grossum) plant. Antonie Van Leeuwenhoek 107:773–784

    Article  CAS  PubMed  Google Scholar 

  • Marmur J, Doty P (1962) Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. J Mol Biol 5:109–118

    Article  CAS  PubMed  Google Scholar 

  • Martens M, Delaere M, Coopman R, De Vos P, Gillis M, Willems A (2007) Multilocus sequence analysis of Ensifer and related taxa. Int J Syst Evol Microbiol 57:489–503

    Article  CAS  PubMed  Google Scholar 

  • Martens M, Dawyndt P, Coopman R, Gillis M, De Vos P, Willems A (2008) Advantages of multilocus sequence analysis for taxonomic studies: a case study using 10 housekeeping genes in the genus Ensifer (including former Sinorhizobium). Int J Syst Evol Microbiol 58:200–214

    Article  CAS  PubMed  Google Scholar 

  • Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M (2012) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 14:1–14

    Google Scholar 

  • Rzhetsky A, Nei M (1992) A simple method for estimating and testing minimum evolution trees. Mol Biol Evol 9(5):945–967

    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, DE

    Google Scholar 

  • Sheu S, Huang H, Young C, Chen W (2015) Rhizobium alvei sp. nov., isolated from a freshwater river. Int J Syst Evol Microbiol 65:472–478

    Article  CAS  PubMed  Google Scholar 

  • Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTALW: 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 

  • Tighe SW, de Lajudie P, Dipietro K, Lindström K, Nick G, Jarvis BD (2000) Analysis of cellular fatty acids and phenotypic relationships of Agrobacterium, Bradyrhizobium, Mesorhizobium, Rhizobium and Sinorhizobium species using the Sherlock microbial identification system. Int J Syst Evol Microbiol 50:787–801

    Article  CAS  PubMed  Google Scholar 

  • Turdahon M, Osman G, Hamdun M, Yusuf K, Abdurehim Z, Abaydulla G, Abdukerim M, Fang C, Rahman E (2013) Rhizobium tarimense sp. nov., isolated from soil in the ancient Khiyik River. Int J Syst Evol Microbiol 63:2424–2429

    Article  CAS  PubMed  Google Scholar 

  • Vincent JM (1970) The cultivation, isolation and maintenance of rhizobia. In: Vincent JM (ed) A manual for the practical study of the root-nodule bacteria. Blackwell Scientific, Oxford, pp 1–13

    Google Scholar 

  • Young JM, Kuykendall LD, Martínez-Romero E, Kerr A, Sawada H et al (2001) A revision of Rhizobium Frank 1889, with an emended description of the genus, and the inclusion of all species of Agrobacterium Conn 1942 and Allorhizobium undicola de Lajudie, 1998 as new combinations: Rhizobium radiobacter, R. rhizogenes, R. rubi, R. undicola and R. vitis. Int J Syst Evol Microbiol 51:89–103

    Article  CAS  PubMed  Google Scholar 

  • Zhang X, Sun L, Ma X, Sui XH, Jiang R (2011) Rhizobium pseudoryzae sp. nov., isolated from the rhizosphere of rice. Int J Syst Evol Microbiol 61:2425–2429

    Article  CAS  PubMed  Google Scholar 

  • Zhang X, Tang X, Ali Sheirdil R, Sun L, Ma X (2014) Rhizobium rhizoryzae sp. nov., isolated from rice roots. Int J Syst Evol Microbiol 64:1373–1377

    Article  CAS  PubMed  Google Scholar 

  • Zhang X, Gao J, Cao Y, Sheirdil R, Wang X, Zhang L (2015) Isolation and proposal novel rice promoting endophytic bacteria, Rhizobium oryzicola sp. nov. Int J Syst Evol Microbiol 65:2931–2936

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

This work was supported by the Grants from the Chinese Ministry of Science and Technology (2013AA102802) and National Natural Science Foundation of China (316700005; 41271273).

Author information

Authors and Affiliations

  1. Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People’s Republic of China

    Juan-Juan Zhao, Jun Zhang, Rui-Jie Zhang, Cai-Wen Zhang & Xiao-Xia Zhang

  2. School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, People’s Republic of China

    Hua-Qun Yin

Authors
  1. Juan-Juan Zhao
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jun Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Rui-Jie Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Cai-Wen Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Hua-Qun Yin
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Xiao-Xia Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Xiao-Xia Zhang.

Additional information

The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA, gyrB, recA, atpD, ropB, gltA gene sequences of strain MH17T are KX129902, KX434874, KX434876, KY321909, KY321911, KY321915, respectively.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Zhao, JJ., Zhang, J., Zhang, RJ. et al. Rhizobium rhizosphaerae sp. nov., a novel species isolated from rice rhizosphere. Antonie van Leeuwenhoek 110, 651–656 (2017). https://doi.org/10.1007/s10482-017-0831-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10482-017-0831-9

Keywords

Search

Navigation