1887

Abstract

The genetic diversity within 195 rhizobial strains isolated from root nodules of 18 agroforestry species (15 woody and three herbaceous legumes) growing in diverse ecoclimatic zones in southern Ethiopia was investigated by using PCR–RFLP of the ribosomal operon [16S rRNA gene, 23S rRNA gene and the internal transcribed spacer (ITS) region between the 16S rRNA and 23S rRNA genes] and 16S rRNA gene partial sequence (800 and 1350 bp) analyses. All of the isolates and the 28 reference strains could be differentiated by using these methods. The size of the ITS varied among test strains (500–1300 bp), and 58 strains contained double copies. UPGMA dendrograms generated from cluster analyses of the 16S and 23S rRNA gene PCR–RFLP data were in good agreement, and the combined distance matrices delineated 87 genotypes, indicating considerable genetic diversity among the isolates. Furthermore, partial sequence analysis of 67 representative strains revealed 46 16S rRNA gene sequence types, among which 12 were 100 % similar to those of previously described species and 34 were novel sequences with 94–99 % similarity to those of recognized species. The phylogenetic analyses suggested that strains indigenous to Ethiopia belonged to the genera , , , , and . Many of the rhizobia isolated from previously uninvestigated indigenous woody legumes had novel 16S rRNA gene sequences and were phylogenetically diverse. This study clearly shows that the characterization of symbionts of unexplored legumes growing in previously unexplored biogeographical areas will reveal additional diversity.

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2005-07-01
2024-03-28
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References

  1. Al Amin H. M. 1990 Trees and Shrubs of the Sudan Guildford & King's Lynn, UK: Biddles;
    [Google Scholar]
  2. Andronov E. E., Terefework Z., Roumiantseva M. L. 7 other authors 2003; Symbiotic and genetic diversity of Rhizobium galegae isolates collected from the Galega orientalis gene center in the Caucasus. Appl Environ Microbiol 69:1067–1074 [CrossRef]
    [Google Scholar]
  3. Anyango B., Wilson K. J., Beynon J. L., Giller K. E. 1995; Diversity of rhizobia nodulating Phaseolus vulgaris in two Kenyan soils of contrasting pHs. Appl Environ Microbiol 61:4016–4021
    [Google Scholar]
  4. Bala A., Giller K. E. 2001; Symbiotic specificity of tropical tree rhizobia for host legumes. New Phytol 149:495–507
    [Google Scholar]
  5. Bala A., Murphy P., Giller K. E. 2002; Occurrence and genetic diversity of rhizobia nodulating Sesbania sesban in African soils. Soil Biol Biochem 34:1759–1768 [CrossRef]
    [Google Scholar]
  6. Bala A., Murphy P., Giller K. E. 2003; Distribution and diversity of rhizobia nodulating agroforestry legumes in soils from three continents in the tropics. Mol Ecol 12:917–930 [CrossRef]
    [Google Scholar]
  7. Barrera L. L., Trujillo M. E., Goodfellow M., García F. J., Hernández-Lucas I., Dávila G., van Berkum P., Martínez-Romero E. 1997; Biodiversity of bradyrhizobia nodulating Lupinus spp. Int J Syst Bacteriol 47:1086–1091 [CrossRef]
    [Google Scholar]
  8. Beyene D., Kassa S., Ampy F., Asseffa A., Gebremedhin T., van Berkum P. 2004; Ethiopian soils harbor natural populations of rhizobia that form symbioses with common bean ( Phaseolus vulgaris L.). Arch Microbiol 181:129–136 [CrossRef]
    [Google Scholar]
  9. Boom R., Sol C. J. A., Salimans M. M. M., Jansen C. L., Wertheim-van Dillen P. M. E., van der Noordaa J. 1990; Rapid and simple method for purification of nucleic acids. J Clin Microbiol 28:495–503
    [Google Scholar]
  10. Chen W.-M., Lee T.-M., Lan C.-C., Cheng C.-P. 2000; Characterization of halotolerant rhizobia isolated from root nodules of Canavalia rosea from seaside areas. FEMS Microbiol Ecol 34:9–16 [CrossRef]
    [Google Scholar]
  11. de Lajudie P., Willems A., Pot B. 7 other authors 1994; Polyphasic taxonomy of rhizobia: emendation of the genus Sinorhizobium and description of Sinorhizobium meliloti comb. nov., Sinorhizobium saheli sp. nov., and Sinorhizobium teranga sp. nov. Int J Syst Bacteriol 44:715–733 [CrossRef]
    [Google Scholar]
  12. de Lajudie P., Willems A., Nick G. 9 other authors 1998; Characterization of tropical tree rhizobia and description of Mesorhizobium plurifarium sp. nov. Int J Syst Bacteriol 48:369–382 [CrossRef]
    [Google Scholar]
  13. de Lajudie P., Willems A., Nick G. 7 other authors 1999; Agrobacterium bv. 1 strains isolated from nodules of tropical legumes. Syst Appl Microbiol 22:119–132 [CrossRef]
    [Google Scholar]
  14. Doyle J. J. 1994; Phylogeny of the legume family: an approach to understanding the origins of nodulation. Annu Rev Ecol Syst 25:325–349 [CrossRef]
    [Google Scholar]
  15. Eardly B. D., Wang F.-S., van Berkum P. 1996; Corresponding 16S rRNA gene segments in Rhizobiaceae and Aeromonas yield discordant phylogenies. Plant Soil 186:69–74 [CrossRef]
    [Google Scholar]
  16. Gao J., Terefework Z., Chen W., Lindström K. 2001; Genetic diversity of rhizobia isolated from Astragalus adsurgens growing in different geographical regions of China. J Biotechnol 91:155–168 [CrossRef]
    [Google Scholar]
  17. Giller K. E. 2001; Nitrogen Fixation in Tropical Cropping Systems . , 2nd edn. pp 37222–250 Wallingford, UK: CAB International;
  18. Heyndrickx M., Vauterin L., Vandamme P., Kersters K., de Vos P. 1996; Application of combined amplified ribosomal DNA restriction analysis (ARDRA) patterns in bacterial phylogeny and taxonomy. J Microbiol Methods 26:247–259 [CrossRef]
    [Google Scholar]
  19. Hunde A., Thulin M. 1989; Mimosoideae. In Flora of Ethiopia vol 3 pp  71–96 Edited by Hedberg M., Edwards S. Addis Ababa, Ethiopia: The National Herbarium;
    [Google Scholar]
  20. Janeca J., Jenkins M. B., Brackett N. S., Lion L. W., Ghiorse W. C. 2002; Characterization of Sinorhizobium isolate and its extracellular polymer implicated in pollutant transport in soil. Appl Environ Microbiol 68:423–426 [CrossRef]
    [Google Scholar]
  21. Khbaya B., Neyra M., Normand P., Zerhari K., Filali-Maltouf A. 1998; Genetic diversity and phylogeny of rhizobia that nodulate Acacia spp. in Morocco assessed by analysis of rRNA genes. Appl Environ Microbiol 64:4912–4917
    [Google Scholar]
  22. Kumar S., Tamura K., Jakobsen I. B., Nei M. 2001; mega2: molecular evolutionary genetics analysis software. Bioinformatics 17:1244–1245 [CrossRef]
    [Google Scholar]
  23. Lafay B., Burdon J. J. 2001; Small-subunit rRNA genotyping of rhizobia nodulating Australian Acacia spp. Appl Environ Microbiol 67:396–402 [CrossRef]
    [Google Scholar]
  24. Laguerre G., Allard M.-R., Revoy F., Aarger N. 1994; Rapid identification of rhizobia by restriction fragment length polymorphism analysis of PCR-amplified 16S rRNA genes. Appl Environ Microbiol 60:56–63
    [Google Scholar]
  25. Martínez-Romero E., Caballero-Mellado J. 1996; Rhizobium phylogenies and bacterial genetic diversity. Crit Rev Plant Sci 15:113–140 [CrossRef]
    [Google Scholar]
  26. Mbuya L. P., Msanga H. P., Ruffo C. K., Birnie A., Tengnäs Bo. 1994; Useful Trees and Shrubs for Tanzania: Identification, Propagation and Management for Agricultural and Pastoral Communities . Nairobi, Kenya: Regional Soil Conservation Unit (RSCU), Swedish International Development Authority
  27. McInroy S. G., Campbell C. D., Haukka K. E., Odee D. W., Sprent J. I., Wang W.-J., Young J. P. W., Sutherland J. M. 1999; Characterisation of rhizobia from African acacias and other tropical woody legumes using Biolog and partial 16S rRNA sequencing. FEMS Microbiol Lett 170:111–117
    [Google Scholar]
  28. Moreira F. M. S., Haukka K., Young J. P. W. 1998; Biodiversity of rhizobia isolated from a wide range of forest legumes in Brazil. Mol Ecol 7:889–895 [CrossRef]
    [Google Scholar]
  29. Nick G., de Lajudie P., Eardly B. D., Suomalainen S., Paulin L., Zhang X., Gillis M., Lindström K. 1999; Sinorhizobium arboris sp. nov. and Sinorhizobium kostiense sp. nov., isolated fromleguminous trees in Sudan and Kenya. Int J Syst Bacteriol 49:1359–1368 [CrossRef]
    [Google Scholar]
  30. Normand P., Cournoyer B., Simonet P., Nazaret S. 1992; Analysis of a ribosomal operon in the actinomycete Frankia . Gene 111:119–124 [CrossRef]
    [Google Scholar]
  31. Odee D. W., Sutherland J. M., Msksyisni E. T., McInroy S. G., Sprent J. I. 1997; Phenotypic characteristics and composition of rhizobia associated with woody legumes growing in diverse Kenyan conditions. Plant Soil 188:65–75 [CrossRef]
    [Google Scholar]
  32. Odee D. W., Haukka K., McInroy S. G., Sprent J. I., Sutherland J. M., Young J. P. W. 2002; Genetic and symbiotic characterization of rhizobia isolated from tree and herbaceous legumes grown in soils from ecologically diverse sites in Kenya. Soil Biol Biochem 34:801–811 [CrossRef]
    [Google Scholar]
  33. Raven P. H., Polhill R. M. 1981; Biography of the Leguminosae. In Advances in Legume Systematics part 1 pp  27–34 Edited by Polhill R. M., Raven P. H. Kew, UK: Royal Botanic Gardens;
    [Google Scholar]
  34. Salmassi T. M., Venkateswaren K., Satomi M., Neolson K. H., Newman D. K., Hering J. G. 2002; Oxidation of arsenite by Agrobacterium albertimagni , AOL15, sp. nov., isolated from Hot Creek, California. Geomicrobiol J 19:53–66 [CrossRef]
    [Google Scholar]
  35. Samba R. T., de Lajudie P., Gillis M., Neyra M., Barreto M. M. S., Dreyfus B. 1999; Diversity of rhizobia nodulating Crotalaria spp. from Senegal. Symbiosis 27:259–268
    [Google Scholar]
  36. Sawada H., Kuykendall L. D., Young J. M. 2003; Changing concepts in the systematics of bacterial nitrogen-fixing legume symbionts. J Gen Appl Microbiol 49:155–179 [CrossRef]
    [Google Scholar]
  37. Somasegaran P., Hoben H. J. 1994 Handbook for Rhizobia: Methods in Legume – Rhizobium Technology New York: Springer;
    [Google Scholar]
  38. Stackebrandt E., Goebel B. M. 1994; Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44:846–849 [CrossRef]
    [Google Scholar]
  39. Sy A., Giraud E., Jourand P. 8 other authors 2001; Methylotrophic M ethylobacterium bacteria nodulate and fix nitrogen in symbiosis with legumes. J Bacteriol 183:214–220 [CrossRef]
    [Google Scholar]
  40. Terefework Z., Nick G., Suomalainen S., Paulin L., Lindström K. 1998; Phylogeny of Rhizobium galegae with respect to other rhizobia and agrobacteria. J Biotechnol 48:349–356
    [Google Scholar]
  41. Terefework Z., Kaijalainen S., Lindström K. 2001; AFLP fingerprinting as a tool to study the genetic diversity of Rhizobium galegae isolated from Galega orientalis and Galega officianlis . J Biotechnol 91:169–180 [CrossRef]
    [Google Scholar]
  42. Thompson J. D., Gibson T. J., Plewniak F., Jeanmougin F., Higgins D. G. 1997; The clustal_x Windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882 [CrossRef]
    [Google Scholar]
  43. Toledo I., Lloret L., Martínez-Romero E. 2003; Sinorhizobium americanus sp. nov., a new Sinorhizobium species nodulating native Acacia spp. in Mexico. Syst Appl Microbiol 26:54–64 [CrossRef]
    [Google Scholar]
  44. van Berkum P., Fuhrmann J. 2000; Evolutionary relationships among the soybean bradyrhizobia reconstructed from 16S rRNA gene and internally transcribed spacer region sequence divergence. Int J Syst Evol Microbiol 50:2165–2172 [CrossRef]
    [Google Scholar]
  45. van Berkum P., Beyene D., Bao G., Campbell T. A., Eardly B. D. 1998; Rhizobium mongolense sp. nov. is one of three rhizobial genotypes identified which nodulate and form nitrogen-fixing symbioses with Medicago ruthenica [(L.) Ledebour]. Int J Syst Bacteriol 48:13–22 [CrossRef]
    [Google Scholar]
  46. van Berkum P., Terefework Z., Paulin L., Suomalainen S., Lindström K, Eardly D. 2003; Discordant phylogenies within the rrn loci of rhizobia. J Bacteriol 185:2988–2998 [CrossRef]
    [Google Scholar]
  47. Velázquez E., Igual J. M., Willems A. 9 other authors 2001; Mesorhizobium chacoense sp. nov., a novel species that nodulates Prosopis alba in the Chaco Arido region (Argentina). Int J Syst Evol Microbiol 51:1011–1021 [CrossRef]
    [Google Scholar]
  48. Wang S. Y., Chen W. X. 1996; Numerical taxonomy and DNA relatedness of rhizobia isolated from Astagalus spp. In Diversity and Taxonomy of Rhizobia pp  79–84 Edited by Li F. D., Lie T. A., Chen W. X., Zhou J. C. Beijing: China Agricultural Scientech Press;
    [Google Scholar]
  49. Wang E. T., Martínez-Romero E. 2000; Sesbania herbacea - Rhizobium huautlense nodulation in flooded soils and comparative characterization of S. herbacea -nodulating rhizobia in different environments. Microbial Ecol 41:25–32
    [Google Scholar]
  50. Wang E. T., Martínez-Romero J., Martínez-Romero E. 1999; Genetic diversity of rhizobia from Leucaena leucocephala nodules in Mexican soils. Mol Ecol 8:711–724 [CrossRef]
    [Google Scholar]
  51. Wang E. T., Kan F. L., Tan Z. Y., Toledo I., Chen W. X., Martínez-Romero E. 2003; Diverse Mesorhizobium plurifarium populations native to Mexican soils. Arch Microbiol 180:444–454 [CrossRef]
    [Google Scholar]
  52. Weisburg W. G., Barns S. M., Pelletier D. A., Lane D. J. 1991; 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703
    [Google Scholar]
  53. Willems A., Doignon-Bourcier F., Gillis M., de Lajudie P. 2001; Evaluation of AFLP for the grouping of Bradyrhizobium strains. Genet Sel Evol 33 (Suppl. 1:S365–S377
    [Google Scholar]
  54. Willems A., Munive A., de Lajudie P., Gillis M. 2003; In most Bradyrhizobium groups sequence comparison of 16S-23S rDNA internal transcribed spacer regions corroborates DNA-DNA hybridizations. Syst Appl Microbiol 26:203–210 [CrossRef]
    [Google Scholar]
  55. Wolde-meskel E., Berg T., Peters N. K., Frostegård Å. 2004a; Nodulation status of native woody legumes, and phenotypic characteristics of associated rhizobia in soils of southern Ethiopia. Biol Fertil Soils 40:55–66 [CrossRef]
    [Google Scholar]
  56. Wolde-meskel E., Terefework Z., Lindström K., Frostegård Å. 2004b; Metabolic and genomic diversity of rhizobia isolated from field standing native and exotic woody legumes in southern Ethiopia. Syst Appl Microbiol 27:603–611 [CrossRef]
    [Google Scholar]
  57. Wolde-meskel E., Terefework Z., Lindström K., Frostegård Å. 2004c; Rhizobia nodulating African Acacia spp. and Sesbania sesban trees in southern Ethiopian soils are metabolically and genomically diverse. Soil Biol Biochem 36:2013–2025 [CrossRef]
    [Google Scholar]
  58. Young J. P. W., Haukka K. E. 1996; Diversity and phylogeny of rhizobia. New Phytol 133:87–94 [CrossRef]
    [Google Scholar]
  59. Young J. M., Kuykendall L. D., Martínez-Romero E., Kerr A., Sawada H. 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 51:89–103
    [Google Scholar]
  60. Zhang X., Harper R., Karsisto M., Lindström K. 1991; Diversity of Rhizobium bacteria isolated from the root nodules of leguminous trees. Int J Syst Bacteriol 41:104–113 [CrossRef]
    [Google Scholar]
  61. Zhang X.-X., Guo X.-W., Terefework Z., Paulin L., Cao Y.-Z., Hu F.-R., Lindström K., Li F.-D. 1999a; Genetic diversity among rhizobial isolates from field-grown Astragalus sinicus of Southern China. Syst Appl Microbiol 22:312–320 [CrossRef]
    [Google Scholar]
  62. Zhang X., Nick G., Kaijalainen S., Terefework Z., Paulin L., Tighe S. W., Graham P. H., Lindstrom K. 1999b; Phylogeny and diversity of Bradyrhizobium strains isolated from the root nodules of peanut ( Arachis hypogaea ) in Sichuan, China. Syst Appl Microbiol 22:378–386 [CrossRef]
    [Google Scholar]
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