Antonie van Leeuwenhoek

, Volume 99, Issue 4, pp 845–854 | Cite as

Rhizobium sphaerophysae sp. nov., a novel species isolated from root nodules of Sphaerophysa salsula in China

  • Lin Xu
  • Jian Feng Shi
  • Peng Zhao
  • Wei Min Chen
  • Wei Qin
  • Ming Tang
  • Ge Hong Wei
Original Paper

Abstract

Four gram-negative, aerobic, motile, non-spore, forming rods with a wide pH and temperature range for growth (pH 7.0–11.0, optimum pH 8.0; 20–45°C, optimum 28°C) strains were isolated from root nodules of Sphaerophysa salsula and characterized by means of a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the four strains formed a new lineage related to the genus Rhizobium and the sequence similarities between the isolate and the most related type strain Rhizobium giardinii was 96.5%. These strains also formed a distinctive group from the reference strains for defined Rhizobium species based on housekeeping gene sequences (atpD and recA), BOX-PCR fingerprinting, phenotypic features and symbiotic properties. The representative strain CCNWGS0238T has DNA-DNA relatedness of less than 33.4% with the most closely related species R. giardinii. It is therefore proposed as a new species, Rhizobium sphaerophysae sp. nov., with isolate CCNWGS0238T (=ACCC17498T = HAMBI3074T) as the type strain.

Keywords

Sphaerophysa salsula Rhizobia Taxonomy 

Supplementary material

10482_2011_9559_MOESM1_ESM.ppt (68 kb)
Supplementary material 1 (PPT 67 kb)
10482_2011_9559_MOESM2_ESM.ppt (83 kb)
Supplementary material 2 (PPT 83 kb)

References

  1. Barcellos FG, Menna P, Batista JSS, Hungria M (2007) Evidence of horizontal transfer of symbiotic genes from a Bradyrhizobium japonicum inoculant strain to indigenous Sinorhizobium (Ensifer) fredii and Bradyrhizobium elkanii in a Brazilian savannah soil. Appl Environ Microbiol 73:2635–2643PubMedCrossRefGoogle Scholar
  2. Berge O, Lodhi A, Brandelet G, Santaella C, Roncato MA, Christen R, HeulinT AchouakW (2009) Rhizobium alamii sp. nov., an exopolysaccharide-producing species isolated from legume and non-legume rhizospheres. Int J Syst Evol Microbiol 59:367–372PubMedCrossRefGoogle Scholar
  3. Broothaerts W, Mitchell HJ, Weir B, Kaines S, Smith LMA, Yang W, Mayer JE, Roa-Rodríguez C, Jefferson RA (2005) Gene transfer to plants by diverse species of bacteria. Nature 433:629–633PubMedCrossRefGoogle Scholar
  4. De Ley J, Cattoir H, Reynaerts A (1970) The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12:133–142PubMedCrossRefGoogle Scholar
  5. Dong XZ, Cai MY (2001) Determinative manual for routine bacteriology. Scientific Press, BeijingGoogle Scholar
  6. Elliott GN, Chen WM, Bontemps C, Chou JH, Young JPW, Sprent JI, James EK (2007) Nodulation of Cyclopia spp. (Leguminosae, Papilionoideae) by Burkholderia tuberum. Ann. Bot. 100:1403–1411PubMedCrossRefGoogle Scholar
  7. Galtier N, Gouy M, Gautier C (1996) SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny. Comput Appl Biosci 12:543–548PubMedGoogle Scholar
  8. Gao JL, Sun JG, Li Y, Wang ET, Chen WX (1994) Numerical taxonomy and DNA relatedness of tropical rhizobia isolated from Hainan province, China. Int J Syst Bacteriol 44:151–158CrossRefGoogle Scholar
  9. Gaunt MW, Turner SL, Rigottier-Gois L, Lloyd-Macgilp SA, Young JPW (2001) Phylogenies of atpD and recA support the small subunit rRNA-based classification of rhizobia. Int J Syst Evol Microbiol 51:2037–2048PubMedGoogle Scholar
  10. Gogarten JP, Townsend JP (2005) Horizontal gene transfer, genome innovation and evolution. Nat Rev Microbiol 3:679–687PubMedCrossRefGoogle Scholar
  11. Graham PH, Sadowsky MJ, Keyser HH, Barnet YM, Bradley RS, Cooper JE, De Ley DJ, DW JarvisB, Roslycky EB (1991) Proposed minimal standards for the description of new genera and species of root- and stem-nodulating bacteria. Int J Syst Bacteriol 41:582–587CrossRefGoogle Scholar
  12. Gu CT, Wang ET, Tian CF, Han TX, Chen WF, Sui XH, Chen WX (2008) Rhizobium miluonense sp. nov., a symbiotic bacterium isolated from Lespedeza root nodules. Int J Syst Evol Microbiol 58:1364–1368PubMedCrossRefGoogle Scholar
  13. Han TX, Wang ET, Wu LJ, Chen WF, Gu JG, Gu CT, Tian CF, Chen WX (2008) Rhizobium multihospitium sp. nov., isolated from multiple legume species native of Xinjiang, China. Int J Syst Evol Microbiol 58:1693–1699PubMedCrossRefGoogle Scholar
  14. Hou BC, Wang ET, Li Y, Jr-Jia RZ, Chen WF, Gao Y, Dong RJ, Chen WX (2009) Rhizobium tibeticum sp. nov., a symbiotic bacterium isolated from Trigonella archiducis-nicolai (irj.) Vassilcz. Int J Syst Evol Microbiol 59:3051–3057PubMedCrossRefGoogle Scholar
  15. Jordan DC (1984) Family III. Rhizobiaceae Conn 1938, 321 AL. Bergey’s Manual Syst Bacteriol 1:234–235Google Scholar
  16. Kaschuk G, Hungria M, Andrade DS, Campo RJ (2006) Genetic diversity of rhizobia associated with common bean (Phaseolus vulgaris L.) grown under no-tillage and conventional systems in Southern Brazil. Appl Soil Ecol 32:210–220CrossRefGoogle Scholar
  17. Kwon SW, Park JY, Kim JS, Kang JW, Cho YH, Lim CK, Parker MA, Lee GB (2005) Phylogenetic analysis of the genera Bradyrhizobium, Mesorhizobium, Rhizobium and Sinorhizobium on the basis of 16S rRNA gene and internally transcribed spacer region sequences. Int J Syst Evol Microbiol 55:263–270PubMedCrossRefGoogle Scholar
  18. Laguerre G, Nour SM, Macheret V, Sanjuan J, Drouin P, Amarger N (2001) Classification of rhizobia based on nodC and nifH gene analysis reveals a close phylogenetic relationship among Phaseolus vulgaris symbionts. Microbiology 147:981–993PubMedGoogle Scholar
  19. Lin DX, Chen WF, Wang FQ, Hu D, Wang ET, Sui XH, Chen WX (2009) Rhizobium mesosinicum sp. nov., isolated from root nodules of three different legumes. Int J Syst Evol Microbiol 59:1919–1923PubMedCrossRefGoogle Scholar
  20. Lu YL, Chen WF, Han LL, Wang ET, Chen WX (2009) Rhizobium alkalisoli sp. nov., isolated from Caragana intermedia growing in saline-alkaline soils in the north of China. Int J Syst Evol Microbiol 59:3006–3011CrossRefGoogle Scholar
  21. Marmur J (1961) A procedure for the isolation of DNA from microorganisms. J Mol Biol 3:208–218CrossRefGoogle Scholar
  22. Marmur J, Doty P (1962) Determination of the base composition of 171 deoxyribonucleic acid from its thermal denaturation temperature. J Mol Biol 5:109–118PubMedCrossRefGoogle Scholar
  23. Menna P, Pereira AA, Bangel EV, Hungria M (2009) Rep-PCR of tropical rhizobia for strain fingerprinting, biodiversity appraisal and as a taxonomic and phylogenetic tool. Symbiosis 48:120–130CrossRefGoogle Scholar
  24. Nandasena KG, O’Hara GW, Tiwari R, Howieson P, John G (2006) Rapid in situ evolution of nodulating strains for biserrula pelecinus L. through lateral transfer of a symbiosis island from the original mesorhizobial inoculant. Appl Environ Microbiol 72:7365–7367PubMedCrossRefGoogle Scholar
  25. Peng GX, Yuan QH, Li HX, Zhang W, Tan ZY (2008) Rhizobium oryzae sp. nov., isolated from the wild rice Oryza alta. Int J Syst Evol Microbiol 58:2158–2163PubMedCrossRefGoogle Scholar
  26. Ren DW, Chen WF, Sui XH, Wang ET, Chen WX (2010a) Rhizobium vignae sp. nov., a symbiotic bacterium isolated from multiple legume species grown in China. Int J Syst Evol Microbiol. doi:10.1099/ijs.0.023143-0 Google Scholar
  27. Ren DW, Wang ET, Chen WF, Sui XH, Zhang XX, Liu HC, Chen WX (2010b) Rhizobium herbae sp. nov. and Rhizobium giardinii-related bacteria, minor microsymbionts of various wild legumes in China. Int J Syst Evol Microbiol. doi:10.1099/ijs.0.024943-0 Google Scholar
  28. Sneath PHA, Sokal RB (1973) Numerical taxonomy. The principles and practice of numerical classification. W. H. Freeman and Co, San FranciscoGoogle Scholar
  29. Terefework Z, Kaijalainen S, Lindström K (2001) AFLP fingerprinting as a tool to study the genetic diversity of Rhizobium galegae. J Biotechnol 91:169–180PubMedCrossRefGoogle Scholar
  30. Tian CF, Young JPW, Wang ET, Tamimi SM, Chen WX (2010) Population mixing of Rhizobium leguminosarum bv. viciae nodulating Vicia faba: the role of recombination and lateral gene transfer. FEMS Microbiol Ecol 73:563–576PubMedGoogle Scholar
  31. Turner SL, Young JPW (2000) The glutamine synthetases of rhizobia: phylogenetics and evolutionary implications. Mol Biol Evol 17:309–319PubMedGoogle Scholar
  32. Xu L, Xu JJ, Liu QL, Xie RM, Wei GH (2009) Genetic diversity in rhizobia isolated from Sphaerophysa salsula in several regions of northwestern China. Biodiversity Science 17:69–75Google Scholar
  33. Young JM, Kuykendall LD, Martinez-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 et al. 1998 as new combinations: Rhizobium radiobacter, R. rhizogenes, R. rubi, R. undicola and R. vitis. Int J Syst Evol Microbiol 51:89–103PubMedGoogle Scholar
  34. Zhang GX, Ren SZ, Xu MY, Zeng GQ, Luo HD, Chen JL, Tan ZY, Sun GP (2010a) Rhizobium borbori sp. nov., an aniline-degrading bacterium isolated from activated sludge. Int J Syst Evol Microbiol. doi:10.1099/ijs.0.022228-0 Google Scholar
  35. Zhang RJ, Hou BC, Wang ET, Li YJ, Zhang XX, Chen WX (2010b) Rhizobium tubonense sp. nov., a symbiotic bacterium isolated from root nodules of Oxytropis glabra grown in Tibet, China. Int J Syst Evol Microbiol. doi:10.1099/ijs.0.020156-0 Google Scholar

Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  • Lin Xu
    • 1
    • 2
  • Jian Feng Shi
    • 2
  • Peng Zhao
    • 1
  • Wei Min Chen
    • 1
  • Wei Qin
    • 1
  • Ming Tang
    • 1
  • Ge Hong Wei
    • 1
  1. 1.College of Life Sciences, Shaanxi Key Laboratory of Molecular Biology for AgricultureNorthwest A & F UniversityYangling ShaanxiChina
  2. 2.Department of Life Science and EngineeringHexi UniversityZhangye GansuChina

Personalised recommendations