Alikhani, H., Yakhchali, B., Antoun, H. (2007). Genetic Grouping of Certain Rhizobial Strains Native to Iranian Soils by 16S-23S IGS PCR-RFLP and Plasmid Profile Techniques. , 21(1), 89-100. doi: 10.22092/ijsr.2007.127027
H. A. Alikhani; B. Yakhchali; H. Antoun. "Genetic Grouping of Certain Rhizobial Strains Native to Iranian Soils by 16S-23S IGS PCR-RFLP and Plasmid Profile Techniques". , 21, 1, 2007, 89-100. doi: 10.22092/ijsr.2007.127027
Alikhani, H., Yakhchali, B., Antoun, H. (2007). 'Genetic Grouping of Certain Rhizobial Strains Native to Iranian Soils by 16S-23S IGS PCR-RFLP and Plasmid Profile Techniques', , 21(1), pp. 89-100. doi: 10.22092/ijsr.2007.127027
Alikhani, H., Yakhchali, B., Antoun, H. Genetic Grouping of Certain Rhizobial Strains Native to Iranian Soils by 16S-23S IGS PCR-RFLP and Plasmid Profile Techniques. , 2007; 21(1): 89-100. doi: 10.22092/ijsr.2007.127027

Genetic Grouping of Certain Rhizobial Strains Native to Iranian Soils by 16S-23S IGS PCR-RFLP and Plasmid Profile Techniques

پژوهش های خاک
Volume 21, Issue 1, May 2007, Pages 89-100    PDF (588.2 K)
Document Type: Research Paper
DOI: 10.22092/ijsr.2007.127027
Authors
H. A. Alikhani* 1; B. Yakhchali2; H. Antoun3
1Assistant Professor,Department of Soil Science, Faculty of Soil and Water Science Engineering, University of Tehran, Karadje, Iran
2Assistant Professor, National Institute for Genetic Engineeing and Biotechnology, Tehran, Iran
3Professor, Agriculture Faculty Instructor of Laval university, Canada
Abstract
Among prokaryotes, there are some soil bacteria called Rhizobia that are very important owing to their N2 fixation ability in legumes. The sequence between two 16S and 23S fragments of rDNA genes complex is called 16S-23S rDNA IGS. It differs by size and nucleotide order, therefore, it is very useful for grouping of rhizobial strains. In this research 16S-23S IGS PCR-RFLP and Plasmid Profile (modified Eckhardt method) grouped 52 superior strains which were found as plant growth promoting Rhizobacteria (PGPR). For cluster analysis, phylip version 3.6a3 software was used. The results show that the16S-23S IGS fragments of different rhizobial strains are very diversified in terms of size (600-1486 bp), and the number of IGS fragment differs from 1 to 3 copies. Based on 16S-23S IGS PCR-RFLP method, all 52 rhizobial strains were located in 46 groups, of which 11 groups had 70% similarity. By this method all strains (77%) except 12 strains (Bj53, Bj54; Rlv27, Rlv28; Rlv23, Rlv24; Rlp16, Rlp17; Sm10, Sm11, Sm12, and Sm13) were separated into different groups. Therefore, the mentioned method is very reliable and practical, besides being simple and having few laboratory requirements (in comparison with other molecular methods). In this research, The grouping based on Plasmid Profile of different rhizobial strains agrees with the results of IGS-RFLP to some extent, for example: Bj53, Bj54; Rlv23, Rlv24 also Rlp16, Rlp17 and Sm11, Sm12, Sm13 in both methods were completely similar and were located in separate cluster groups. 
Keywords
Rhizobial Strains; 16S-23S IGS PCR-RFLP; Plasmid Profile; Genetic grouping
References
  1. Bourcier, F. D., A. Willems, R. Coopman, G. Laguerre, M. Gillis ,and P. Lajudie. (2000). Genotypic characterization of Bradyrhizobium strains nodulating small Senegalese legumes by 16S–23S rRNA intergenic gene spacers and amplified fragment length polymorphism fingerprint analyses. Appl. Environ. Microbiol. 66: 3987-3997.
  2. Chen, W. P., and T. T. Kuo. (1993). A simple and rapid method for the preparation of gram negative bacterial genomic DNA. Nucl. Acids Res. 21: 2260.
  3. Condon, C., and C. L. Squires. (1995). Control of rRNA transcription in Escherichia coli. Microbiol. Rev. 59: 623-645.
  4. de Oliveria,V. M.,H. L. C. Coutinho, B. W. S. Sobral,C. T. Guimares, J. D. Van Elsas, and G. P. Manfio. (1999). Discrimination of Rhizobium tropici and leguminosarum strains by PCR specific amplification of 16S-23S rDNA spacer region fragments and denaturing gradient gel electrophoresis. Lett. Appl. Microbiol. 28:137-141.
  5. Eckhardt, T. (1978). A rapid method for the identification of plasmid desoxyribonucleic acid in bacteria. Plasmid. 1:584-588.
  6. Guo, X. W., X. X. Zhang, and F. Di Li. (1999). Characterization of Astragalus sinicus Rhizobia by restriction fragment length polymorphism analysis of chromosomal and nodulation genes regions. Current Microbiol.39: 358-364.
  7. Gurtler, V. and Stanisich, V.A.(1996). New approaches to typing and identification of bacteria using the 16S-23S rDNA spacer. Microbiology 142,3-16.
  8. Jensen, M. A., J. A. Webster, and N. Straus.(1993). Rapid identification of bacteria on the basis of polymerase chain reaction-amplified ribosomal DNA spacer polymorphisms. Appl. Environ. Microbiol. 59: 945-952.
  9. Kostman, J.R. Edind, T.D., Lipuma, J.J. and Stull, T.L.(1992).Molecular epidemiology of Pseudomonas Cepacia determined by polymerase chain reaction ribotyping. J.Clin Microbiol. 30,2084_2087.
  10. Laguerre, G., M. R. Allard, F. Rovey, and N. Amarger. (1994). Rapid identification of rhizobia by restriction fragment length polymorphism analysis of PCR-amplified 16S rRNA genes. Appl. Environ. Microbial. 60: 56-63.
  11. Laguerre, G., P. Mavingui, M. R. Allard, M. P. Charnay, P. Louvrier, S. I. Mazurier, L. Rigottier-Gois, and N. Amarger. (1996). Typing of rhizobia by PCR DNA fingerprinting and PCR- restriction fragment length polymorphism analysis of chromosomal and symbiotic gene regions: application to Rhizobium leguminosarum and its different biovars. Appl. Environ. Microbiol. 62: 2029-2036.
  12. Laguerre, G., S. I. Mazurier, and N. Amarger. (1992). Plasmid profiles and restriction fragment length polymorphism of Rhizobium leguminosarum Viciae in field populations. FEMS Microbiol. Ecol. 101: 17-26.
  13. Martinez, J. G., S. G. Acinas, A. I. Anton, and F. R. Valera. (1999). Use of the 16S-23S ribosomal gene spacer region in studies of prokaryotic diversity. J. Microbiol. Methods. 36:55-64.
  14. Martinez –Romero, E. and Caballero – Mellado(1996)Rhizobium phylogenies and bacterial genetic diversity. Crit: Rev.Plant Sci. 15:113-140.
  15. Normand, P., C. Ponsonnet, X. Nesme, M. Neyra, and P. Simonet. (1996). ITS analysis of prokaryotes. In Molecular Microbial Ecology Manual ed.Akkermans,A.D.L., van Elsas, J.D. and De Bruijn, F.J.Dordrecht, The Netherlands: Kluwer Academic.
  16. Nour, S. M.,J. C. Cleyet-Marel, D. Beck, A. Effosse, and M. P. Fernandez.(1994a.) Genotypic and phenotypic diversity of Rhizobium isolated from chickpea (Cicer arietinum).Can. J. Microbiol. 40:345-354.
  17. Nour, S. M., M. P. Fernandez, P. Normand, and J. C. Cleyet-Marel. (1994b). Rhisobium ciceri nov., consisting of strains that nodulate chickpeas (Cicer arietinum L.). Int. J. Syst. Bacteriol. 44: 511-522.
  18. Perret, X., and W. J. Broughton. (1998). Rapid identification of Rhizobium strains by targeted PCR fingerprinting. Plant.Soil. 204: 21-34.
  19. Pisabarro, A.,A.Correia and J.Martin (1998). Characterization of the rrnB operon of the plant pathogen Rhodococcus Fascians and targetrd integrations of exogenous genes at rrn loci. Appl.Environ. Microbiol. 64:1276-1282.
  20. Quatrini, P., G. Scaglione, M. Caradonna and A. M. Puglia. (2002).Bradyrhizobium nodulating the Mediterranean shrub spanish broom(Spartium junceum L.). J. Appl. Microbiol. 92: 13-21.
  21. Rainey, F.A., Ward-Rainey, N.L., Janssen, P.H., Hippe, H.and Stackebrandt, E.(1996).Clostridium paradoxum DSM 7308 T Contains multiple 16S rRNA genes with heterogenous intervening sequences. Microbiol. 142:2087 -2095.
  22. Rigottier-Gois, L., S. L. Turner, J. P. W. Young, and N. Amarger.(1998). Distribution of repC plasmid-replication sequences among plasmids and isolates of Rhizobium leguminosarum  bv. viciae from field populations. Microbiol. 144:771-780.
  23. Roth , A.,M.Fischer,M.E.Hamid, michalke , W.ludwing and H.mauch.(1998). Differentiation of phylogenetically related slowly growing mycobacteria based on 16S-23S rRNA gene internal transcribed spacer sequences. J.clin. microbiol.36:139-147.
  24. Somasegaran, P., and H. J. Hoben. (1994). Handbook for Rhizobia Methods in Legume-Rhizobium Technology.P.267-278. Springer-Verlag, New York.
  25. Tan, Z., T. Hurek, P. Vinuesa, P. Muller, J. K. Ladha, and B. R. Hurek.(2001). Specific detection of Bradyrhizobium and Rhizobium strains colonizing rice (Oryza sativa) roots by 16S-23S ribosomal DNA intergenic spacer-targeted PCR. Appl. Environ. Microbiol.67: 3655-3664.
  26. Wernegreen, J. J., E. E. Harding, and M. A. Riley. 1997. Rhizobium gone native: unexpected plasmid stability of indigenous Rhizobium leguminosarum. Proc Natl Acad Sci USA. 94:5483-5488.

 

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