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f Genetic diversity and symbiotic effectiveness of Bradyrhizobium strains nodulating selected annual grain legumes growing in Ethiopia

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  • Authors: Tulu Degefu1​ ,  Endalkachew Wolde-meskel2​ , Frank Rasche3​
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    • 1​ 1​School of Applied Natural Sciences, Applied Biology Program, Adama Science and Technology University, P.O. Box 1888, Adama, Ethiopia 2​ 2​International Livestock Research Institute, P.O. Box 5689, Addis Ababa, Ethiopia 3​ 3​Institute of Agricultural Sciences in the Tropics (Hans-Ruthenberg-Institute), University of Hohenheim, 70593 Stuttgart, Germany
  • *Correspondence: Tulu Degefu [email protected]
  • First Published Online: 16 November 2017, International Journal of Systematic and Evolutionary Microbiology 68: 449-460, doi: 10.1099/ijsem.0.002486
  • Subject: Evolution, Phylogeny and Biodiversity
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Genetic diversity and symbiotic effectiveness of Bradyrhizobium strains nodulating selected annual grain legumes growing in Ethiopia, Page 1 of 1

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  • Vigna unguiculata, Vigna radiata and Arachis hypogaea growing in Ethiopia are nodulated by a genetically diverse group of Bradyrhizobium strains. To determine the genetic identity and symbiotic effectiveness of these bacteria, a collection of 36 test strains originating from the root nodules of the three hosts was investigated using multilocus sequence analyses (MLSA) of core genes including 16S rRNA, recA, glnII, gyrB, atpD and dnaK. Sequence analysis of nodA and nifH genes along with tests for symbiotic effectiveness using δN analysis were also carried out. The phylogenetic trees derived from the MLSA grouped most test strains into four well-supported distinct positions designated as genospecies I–IV. The maximum likelihood (ML) tree that was constructed based on the nodA gene sequences separated the entire test strains into two lineages, where the majority of the test strains were clustered on one of a well-supported large branch that comprise Bradyrhizobium species from the tropics. This clearly suggested the monophyletic origin of the nodA genes within the bradyrhizobia of tropical origin. The δN-based symbiotic effectiveness test of seven selected strains revealed that strains GN100 (δ N=0.73) and GN102 (δ N=0.79) were highly effective nitrogen fixers when inoculated to cowpea, thus can be considered as inoculants in cowpea production. It was concluded that Ethiopian soils are a hotspot for rhizobial diversity. This calls for further research to unravel as yet unknown bradyrhizobia nodulating legume host species growing in the country. In this respect, prospective research should also address the mechanisms of symbiotic specificity that could lead to high nitrogen fixation in target legumes.

  • Two supplementary figures are available with the online version of this article.

© 2018 IUMS | Published by the Microbiology Society

  • 1. Duke J. Handbook of Legumes of World Economic Importance New York: Plenum Press; 2012
    [Google Scholar]
  • 2. Singh BB, Ajeigbe HA, Tarawali SA, Fernandez-Rivera S, Abubakar M. Improving the production and utilization of cowpea as food and fodder. Field Crops Res 2003; 84: 169– 177 [CrossRef]
    [Google Scholar]
  • 3. Steele WM. Cowpea (Vigna unguiculata (L.) Walp.). In Grain Legume Crops 1985; pp. 520– 583
    [Google Scholar]
  • 4. Sharma SN, Prasad R, Singh S. The role of mungbean residues and Sesbania aculeata green manure in the nitrogen economy of rice-wheat cropping system. Plant Soil 1995; 172: 123– 129 [CrossRef]
    [Google Scholar]
  • 5. Zhang WT, Yang JK, Yuan TY, Zhou JC. Genetic diversity and phylogeny of indigenous rhizobia from cowpea [Vigna unguiculata (L.) Walp.]. Biol Fertil Soils 2007; 44: 201– 210 [CrossRef]
    [Google Scholar]
  • 6. Giller KE. Nitrogen Fixation in Tropical Cropping Systems London: Cabi; 2001; [Crossref]
    [Google Scholar]
  • 7. Ahenkora K, Adu-Dapaah HK, Asafo-Adjei B, Asafu-Agyei JN, Adjei J et al. Protein productivity and economic feasibility of dual-purpose cowpea. HortScience 1998; 33: 1160– 1162
    [Google Scholar]
  • 8. Hallensleben M, Polreich S, Heller J, Maass BL. 2009; Assessment of the importance and utilization of cowpea (Vigna unguiculata L. Walp.) as leafy vegetable in small-scale farm households in Tanzania-East Africa. https://cgspace.cgiar.org/handle/10568/56192
  • 9. Senaratne R, Liyanage NDL, Soper RJ. Nitrogen fixation of and N transfer from cowpea, mungbean and groundnut when intercropped with maize. Fertilizer Research 1995; 40: 41– 48 [CrossRef]
    [Google Scholar]
  • 10. Dakora FD. Commonality of root nodulation signals and nitrogen assimilation in tropical grain legumes belonging to the tribe Phaseoleae. Functional Plant Biology 2000; 27: 885– 892 [CrossRef]
    [Google Scholar]
  • 11. Dakora FD, Keya SO. Contribution of legume nitrogen fixation to sustainable agriculture in Sub-Saharan Africa. Soil Biol Biochem 1997; 29: 809– 817 [CrossRef]
    [Google Scholar]
  • 12. Graham PH, Vance CP. Legumes: importance and constraints to greater use. Plant Physiol 2003; 131: 872– 877 [CrossRef] [PubMed]
    [Google Scholar]
  • 13. Toomsan B, Mcdonagh JF, Limpinuntana V, Giller KE. Nitrogen fixation by groundnut and soyabean and residual nitrogen benefits to rice in farmers' fields in Northeast Thailand. Plant Soil 1995; 175: 45– 56 [CrossRef]
    [Google Scholar]
  • 14. Dakora FD, Aboyinga RA, Mahama Y, Apaseku J. Assessment of N2 fixation in groundnut (Arachis hypogaea L.) and cowpea (Vigna unguiculata L. Walp) and their relative N contribution to a succeeding maize crop in Northern Ghana. J Appl Microbiol Biotechnol 1987; 3: 389– 399 [CrossRef]
    [Google Scholar]
  • 15. Atasie VN, Akinhanmi TF, Ojiodu CC. Proximate analysis and physico-chemical properties of groundnut (Arachis hypogaea L.). Pakistan J Nutr 2009; 8: 194– 197 [CrossRef]
    [Google Scholar]
  • 16. Mamiro PS, Mbwaga AM, Mamiro DP, Mwanri AW, Mwanri AW et al. Nutritional quality and utilization of local and improved cowpea varieties in some regions in Tanzania. Afric J Food, Agric Nutr Dev 2011; 11: 4490– 4506 [CrossRef]
    [Google Scholar]
  • 17. Bhatty N, Gilani AH, Nagra SA. Nutritional value of mung bean (Vigna radiata) as effected by cooking and supplementation. Arch Latinoam Nutr 2000; 50: 374– 379 [PubMed]
    [Google Scholar]
  • 18. de Lajudie P, Laurent-Fulele E, Willems A, Torck U, Coopman R et al. Allorhizobium undicola gen. nov., sp. nov., nitrogen-fixing bacteria that efficiently nodulate Neptunia natans in Senegal. Int J Syst Bacteriol 1998; 48: 1277– 1290 [CrossRef] [PubMed]
    [Google Scholar]
  • 19. Dreyfus B, Garcia JL, Gillis M. Characterization of Azorhizobium caulinodans gen. nov., sp. nov., a stem-nodulating nitrogen-fixing bacterium isolated from Sesbania rostrata. Int J Syst Bacteriol 1988; 38: 89– 98 [CrossRef]
    [Google Scholar]
  • 20. Jordan DC. Family III. Rhizobiaceae. In Bergey’s Manual of Systematic Bacteriologyvol. 1 Baltimore: Williams and Wilkins Co.,; 1984; pp. 234– 242
    [Google Scholar]
  • 21. Jarvis BDW, van Berkum P, Chen WX, Nour SM, Fernandez MP et al. Transfer of Rhizobium loti, Rhizobium huakuii, Rhizobium ciceri, Rhizobium mediterraneum, and Rhizobium tianshanense to Mesorhizobium gen. nov. Int J Syst Bacteriol 1997; 47: 895– 898 [CrossRef]
    [Google Scholar]
  • 22. de Lajudie P, Willems A, Pot B, Dewettinck D, Maestrojuan G et al. 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 1994; 44: 715– 733 [CrossRef]
    [Google Scholar]
  • 23. Jordan DC. Transfer of Rhizobium japonicum Buchanan 1980 to Bradyrhizobium gen. nov., a genus of slow-growing, root nodule bacteria from leguminous plants. Int J Syst Bacteriol 1982; 32: 136– 139 [CrossRef]
    [Google Scholar]
  • 24. Giller KE, Franke AC, Abaidoo R, Baijukya F, Bala A et al. N2Africa: putting nitrogen fixation to work for smallholder farmers in Africa. In Vanlauwe B, van Asten PJA, Blomme G. (editors) Agro-ecological Intensification of Agricultural Systems in the African Highlands London: Routledge; 2013; pp. 156– 174
    [Google Scholar]
  • 25. Wolde-Meskel E, Terefework Z, Frostegård A, Lindström K. Genetic diversity and phylogeny of rhizobia isolated from agroforestry legume species in southern Ethiopia. Int J Syst Evol Microbiol 2005; 55: 1439– 1452 [CrossRef] [PubMed]
    [Google Scholar]
  • 26. Degefu T, Wolde-Meskel E, Liu B, Cleenwerck I, Willems A et al. Mesorhizobium shonense sp. nov., Mesorhizobium hawassense sp. nov. and Mesorhizobium abyssinicae sp. nov., isolated from root nodules of different agroforestry legume trees. Int J Syst Evol Microbiol 2013; 63: 1746– 1753 [CrossRef] [PubMed]
    [Google Scholar]
  • 27. Beyene D, Kassa S, Ampy F, Asseffa A, Gebremedhin T et al. Ethiopian soils harbor natural populations of rhizobia that form symbioses with common bean (Phaseolus vulgaris L.). Arch Microbiol 2004; 181: 129– 136 [CrossRef] [PubMed]
    [Google Scholar]
  • 28. Tena W, Wolde-Meskel E, Degefu T, Walley F. Genetic and phenotypic diversity of rhizobia nodulating chickpea (Cicer arietinum L.) in soils from southern and central Ethiopia. Can J Microbiol 2017; 63: 690– 707 [CrossRef] [PubMed]
    [Google Scholar]
  • 29. Tena W, Wolde-Meskel E, Degefu T, Walley F. Lentil (Lens culinaris Medik.) nodulates with genotypically and phenotypically diverse rhizobia in Ethiopian soils. Syst Appl Microbiol 2017; 40: 22– 33 [CrossRef] [PubMed]
    [Google Scholar]
  • 30. Lie TA, Göktan D, Engin M, Pijnenborg J, Anlarsal E et al. Co-evolution of the legume-Rhizobium association. In Plant and Soil Interfaces and Interactions Dordrecht, Netherland: Martinus Nijhoff Publishers; 1987; pp. 171– 181 [Crossref]
    [Google Scholar]
  • 31. Somasegaran P, Hoben HJ. Collecting nodules and isolating rhizobia. In Handbook for Rhizobia Heidelberg, Germany: Springer; 1994; pp. 7– 23 [Crossref]
    [Google Scholar]
  • 32. Boom R, Sol CJ, Salimans MM, Jansen CL, Wertheim-van Dillen PM et al. Rapid and simple method for purification of nucleic acids. J Clin Microbiol 1990; 28: 495– 503 [PubMed]
    [Google Scholar]
  • 33. Terefework Z, Kaijalainen S, Lindström K. AFLP fingerprinting as a tool to study the genetic diversity of Rhizobium galegae isolated from Galega orientalis and Galega officinalis. J Biotechnol 2001; 91: 169– 180 [CrossRef] [PubMed]
    [Google Scholar]
  • 34. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173: 697– 703 [CrossRef] [PubMed]
    [Google Scholar]
  • 35. Gaunt MW, Turner SL, Rigottier-Gois L, Lloyd-Macgilp SA, Young JP. Phylogenies of atpD and recA support the small subunit rRNA-based classification of rhizobia. Int J Syst Evol Microbiol 2001; 51: 2037– 2048 [CrossRef] [PubMed]
    [Google Scholar]
  • 36. Vinuesa P, León-Barrios M, Silva C, Willems A, Jarabo-Lorenzo A et al. Bradyrhizobium canariense sp. nov., an acid-tolerant endosymbiont that nodulates endemic genistoid legumes (Papilionoideae: Genisteae) from the Canary Islands, along with Bradyrhizobium japonicum bv. genistearum, Bradyrhizobium genospecies alpha and Bradyrhizobium genospecies beta. Int J Syst Evol Microbiol 2005; 55: 569– 575 [CrossRef] [PubMed]
    [Google Scholar]
  • 37. Martens M, Dawyndt P, Coopman R, Gillis M, de Vos P et al. 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 2008; 58: 200– 214 [CrossRef] [PubMed]
    [Google Scholar]
  • 38. Stepkowski T, Czaplińska M, Miedzinska K, Moulin L. The variable part of the dnaK gene as an alternative marker for phylogenetic studies of rhizobia and related alpha Proteobacteria. Syst Appl Microbiol 2003; 26: 483– 494 [CrossRef] [PubMed]
    [Google Scholar]
  • 39. Stepkowski T, Moulin L, Krzyzańska A, Mcinnes A, Law IJ et al. European origin of Bradyrhizobium populations infecting lupins and serradella in soils of Western Australia and South Africa. Appl Environ Microbiol 2005; 71: 7041– 7052 [CrossRef] [PubMed]
    [Google Scholar]
  • 40. Rivas R, Velázquez E, Willems A, Vizcaíno N, Subba-Rao NS et al. A new species of Devosia that forms a unique nitrogen-fixing root-nodule symbiosis with the aquatic legume Neptunia natans (L.f.) druce. Appl Environ Microbiol 2002; 68: 5217– 5222 [CrossRef] [PubMed]
    [Google Scholar]
  • 41. List of prokaryotic names with standing in nomenclature. www.bacterio.net/
  • 42. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22: 4673– 4680 [CrossRef] [PubMed]
    [Google Scholar]
  • 43. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013; 30: 2725– 2729 [CrossRef] [PubMed]
    [Google Scholar]
  • 44. Villesen P. FaBox: an online toolbox for fasta sequences. Mol Ecol Notes 2007; 7: 965– 968 [CrossRef]
    [Google Scholar]
  • 45. Somasegaran P, Hoben H. Methods in Legume-Rhizobium Technology; NIFTAL Project Heidelberg, Germany: Springer-Verlag; 1994
    [Google Scholar]
  • 46. Chen WF, Guan SH, Zhao CT, Yan XR, Man CX et al. Different Mesorhizobium species associated with Caragana carry similar symbiotic genes and have common host ranges. FEMS Microbiol Lett 2008; 283: 203– 209 [CrossRef] [PubMed]
    [Google Scholar]
  • 47. Maâtallah J, Berraho EB, Sanjuan J, Lluch C. Phenotypic characterization of rhizobia isolated from chickpea (Cicer arietinum) growing in Moroccan soils. Agronomie 2002; 22: 321– 329 [CrossRef]
    [Google Scholar]
  • 48. Wolde-Meskel E, Terefework Z, Lindström K, Frostegård A. Metabolic and genomic diversity of rhizobia isolated from field standing native and exotic woody legumes in southern Ethiopia. Syst Appl Microbiol 2004; 27: 603– 611 [CrossRef] [PubMed]
    [Google Scholar]
  • 49. Aserse AA, Räsänen LA, Aseffa F, Hailemariam A, Lindström K. Phylogenetically diverse groups of Bradyrhizobium isolated from nodules of Crotalaria spp., Indigofera spp., Erythrina brucei and Glycine max growing in Ethiopia. Mol Phylogenet Evol 2012; 65: 595– 609 [CrossRef] [PubMed]
    [Google Scholar]
  • 50. van Berkum P, Terefework Z, Paulin L, Suomalainen S, Lindström K et al. Discordant phylogenies within the rrn loci of Rhizobia. J Bacteriol 2003; 185: 2988– 2998 [CrossRef] [PubMed]
    [Google Scholar]
  • 51. Barrera LL, Trujillo ME, Goodfellow M, García FJ, Hernández-Lucas I et al. Biodiversity of bradyrhizobia nodulating Lupinus spp. Int J Syst Bacteriol 1997; 47: 1086– 1091 [CrossRef] [PubMed]
    [Google Scholar]
  • 52. Willems A, Munive A, de Lajudie P, Gillis M. In most Bradyrhizobium groups sequence comparison of 16S-23S rDNA internal transcribed spacer regions corroborates DNA-DNA hybridizations. Syst Appl Microbiol 2003; 26: 203– 210 [CrossRef] [PubMed]
    [Google Scholar]
  • 53. van Berkum P, Fuhrmann JJ. Evolutionary relationships among the soybean bradyrhizobia reconstructed from 16S rRNA gene and internally transcribed spacer region sequence divergence. Int J Syst Evol Microbiol 2000; 50: 2165– 2172 [CrossRef] [PubMed]
    [Google Scholar]
  • 54. Martens M, Delaere M, Coopman R, de Vos P, Gillis M et al. Multilocus sequence analysis of Ensifer and related taxa. Int J Syst Evol Microbiol 2007; 57: 489– 503 [CrossRef] [PubMed]
    [Google Scholar]
  • 55. Kaneko T, Nakamura Y, Sato S, Minamisawa K, Uchiumi T et al. Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110. DNA Res 2002; 9: 189– 197 [CrossRef] [PubMed]
    [Google Scholar]
  • 56. Nichols R. Gene trees and species trees are not the same. Trends Ecol Evol 2001; 16: 358– 364 [CrossRef] [PubMed]
    [Google Scholar]
  • 57. Rosenberg NA. The probability of topological concordance of gene trees and species trees. Theor Popul Biol 2002; 61: 225– 247 [CrossRef] [PubMed]
    [Google Scholar]
  • 58. Degefu T, Wolde-Meskel E, Woliy K, Frostegård Å. Phylogenetically diverse groups of Bradyrhizobium isolated from nodules of tree and annual legume species growing in Ethiopia. Syst Appl Microbiol 2017; 40: 205– 214 [CrossRef] [PubMed]
    [Google Scholar]
  • 59. Rivas R, Martens M, de Lajudie P, Willems A. Multilocus sequence analysis of the genus Bradyrhizobium. Syst Appl Microbiol 2009; 32: 101– 110 [CrossRef] [PubMed]
    [Google Scholar]
  • 60. Vinuesa P, Rojas-Jiménez K, Contreras-Moreira B, Mahna SK, Prasad BN et al. Multilocus sequence analysis for assessment of the biogeography and evolutionary genetics of four Bradyrhizobium species that nodulate soybeans on the asiatic continent. Appl Environ Microbiol 2008; 74: 6987– 6996 [CrossRef] [PubMed]
    [Google Scholar]
  • 61. Nzoué A, Miché L, Klonowska A, Laguerre G, de Lajudie P et al. Multilocus sequence analysis of bradyrhizobia isolated from Aeschynomene species in Senegal. Syst Appl Microbiol 2009; 32: 400– 412 [CrossRef] [PubMed]
    [Google Scholar]
  • 62. Degefu T, Wolde-Meskel E, Frostegård A. Multilocus sequence analyses reveal several unnamed Mesorhizobium genospecies nodulating Acacia species and Sesbania sesban trees in Southern regions of Ethiopia. Syst Appl Microbiol 2011; 34: 216– 226 [CrossRef] [PubMed]
    [Google Scholar]
  • 63. Degefu T, Wolde-Meskel E, Frostegård A. Phylogenetic multilocus sequence analysis identifies seven novel Ensifer genospecies isolated from a less-well-explored biogeographical region in East Africa. Int J Syst Evol Microbiol 2012; 62: 2286– 2295 [CrossRef] [PubMed]
    [Google Scholar]
  • 64. Degefu T, Wolde-Meskel E, Frostegård Å. Phylogenetic diversity of Rhizobium strains nodulating diverse legume species growing in Ethiopia. Syst Appl Microbiol 2013; 36: 272– 280 [CrossRef] [PubMed]
    [Google Scholar]
  • 65. Yokoyama T, Tomooka N, Okabayashi M, Kaga A, Boonkerd N et al. Variation in the nod gene RFLPs, nucleotide sequences of 16S rRNA genes, Nod factors, and nodulation abilities of Bradyrhizobium strains isolated from Thai Vigna plants. Can J Microbiol 2006; 52: 31– 46 [CrossRef] [PubMed]
    [Google Scholar]
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