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Biology and Fertility of Soils

, Volume 52, Issue 5, pp 725–738 | Cite as

Distribution, diversity and population composition of soybean-nodulating bradyrhizobia from different agro-climatic regions in Ethiopia

  • Sanjay K. Jaiswal
  • Semira M. Beyan
  • Felix D. DakoraEmail author
Original Paper

Abstract

The genetic diversity and population composition of bradyrhizobial isolates collected from different parts of north-western and southern Ethiopia were studied. A total of 103 bacterial symbionts were trapped from the soils collected from Ethiopia. Genetic diversity and population composition of the bradyrhizobial isolates were assessed using restriction fragment length polymorphism (RFLP) of 16S–23S rRNA region. The results showed the presence of 30 distinct restriction pattern types in the population. The difference in bradyrhizobial communities between pairs of soil samples were estimated by alpha (H′α), beta (H′β) and gamma (H′γ) diversity. Southern Ethiopia showed the most diverse bradyrhizobial populations based on the many RFLP clusters occupied. The ratio of beta to gamma (H′β/ H′γ) diversity between the bradyrhizobial community compositions was greater in north-western than in the southern region of Ethiopia. The RFLP-based population composition suggested the frequent presence of individuals with admixture of ITS (16S–23S rDNA) region and showed the interlineage transfer of ITS genomic region. Phylogenetic analysis of 16S–23S rRNA sequences revealed the presence of a heterogenous group of Bradyrhizobium in Ethiopian soils. These results have provided new insight into the ecology of Bradyrhizobium nodulating soybean under different environmental conditions in Ethiopia.

Keywords

Bradyrhizobium Restriction fragment length polymorphism ITS sequences PCA Diversity indices STRUCTURE 

Notes

Acknowledgments

This work was supported with grants from the Bill and Melinda Gates Foundation Project on Capacity Building in Legume Sciences in Africa, the South African Department of Science and Technology, the Tshwane University of Technology, the National Research Foundation in Pretoria, and the South African Research Chair in Agrochemurgy and Plant Symbioses. SMB is grateful for a competitive fellowship from the Bill and Melinda Gates Foundation Project on Capacity Building in Legume Sciences in Africa.

References

  1. Abaidoo RC, Keyser HH, Singleton PW, Borthakur D (2000) Bradyrhizobium spp. (TGx) isolates nodulating the new soybean cultivars in Africa are diverse and distinct from bradyrhizobia that nodulate North American soybeans. Int J Syst Evol Microbiol 50:225–234CrossRefPubMedGoogle Scholar
  2. Abate T, Alene AD, Bergvinson D, Shiferaw B, Silim S, Orr A, Asfaw S (2012) Tropical grain legumes in Africa and south Asia: knowledge and opportunities. International Crops Research Institute for the Semi-Arid Tropics, ICRISATGoogle Scholar
  3. Adhikari D, Kaneto M, Itoh K, Suyama K, Pokharel BB, Gaihre YK (2012) Genetic diversity of soybean-nodulating rhizobia in Nepal in relation to climate and soil properties. Plant Soil 357:131–145CrossRefGoogle Scholar
  4. Appunu C, Angele N, Laguerre G (2008) Genetic diversity of native bradyrhizobia isolated from soybeans (Glycine max L.) in different agricultural-ecological-climatic regions of India. Appl Environ Microbiol 74:5991–5996CrossRefPubMedPubMedCentralGoogle Scholar
  5. Appunu C, Sasirekha N, Prabavathy VR, Nair S (2009) A significant proportion of indigenous rhizobia from India associated with soybean (Glycine max L.) distinctly belong to Bradyrhizobium and Ensifer genera. Biol Fertil Soils 46:57–63CrossRefGoogle Scholar
  6. Aserse AA, Räsänen LA, Aseffa F, Hailemariam A, Lindström K (2012) Phylogenetically diverse groups of Bradyrhizobium isolated from nodules of Crotalaria spp., Indigofera spp., Erythrina brucei and Glycine max growing in Ethiopia. Mol Phylogen Evol 65:595–609CrossRefGoogle Scholar
  7. Bala A, Murphy P, Giller KE (2003) Distribution and diversity of rhizobia nodulating agroforestry legumes in soils from three continents in the tropics. Mol Ecol 12:917–929CrossRefPubMedGoogle Scholar
  8. Broughton W, Dilworth M (1971) Control of leghaemoglobin synthesis in snake beans. Biochem J 125:1075–1080CrossRefPubMedPubMedCentralGoogle Scholar
  9. Caballero-Mellado J, Martinez-Romero E (1999) Soil fertilization limits the genetic diversity of Rhizobium in bean nodules. Symbiosis 26:111–121Google Scholar
  10. Central Statistical Authority (CSA) (2009) Agricultural Sample Survey. 2008/9 Report on Area and Production for Major Crops (Private Peasant Holdings, Main Season). Addis Ababa, Ethiopia, p 45–47Google Scholar
  11. Chen LS, Figueredo A, Pedrosa FO, Hungria M (2000) Genetic characterization of soybean rhizobia in Paraguay. Applied Environ Microbiol 66:5099–5103CrossRefGoogle Scholar
  12. Chen W, Wang E, Wang S, Li Y, Chen X, Li Y (1995) Characteristics of Rhizobium tianshanense sp. nov., a moderately and slowly growing root nodule bacterium isolated from an arid saline environment in Xinjiang, People’s Republic of China. Int J Syst Bacteriol 45:153–159CrossRefPubMedGoogle Scholar
  13. Delmont TO, Francioli D, Jacquesson S, Laoudi S, Mathieu A, Nesme J, Ceccherini MT, Nannipieri P, Simonet P, Vogel TM (2014) Microbial community development and unseen diversity recovery in inoculated sterile soil. Biol Fertil Soils 50:1069–1076CrossRefGoogle Scholar
  14. Didelot X, Maiden MC (2010) Impact of recombination on bacterial evolution. Trends Microbiol 18:315–322CrossRefPubMedPubMedCentralGoogle Scholar
  15. Doignon-Bourcier F, Willems A, Coopman R, Laguerre G, Gillis M, de Lajudie P (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 66:3987–3997CrossRefPubMedPubMedCentralGoogle Scholar
  16. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap Evol: 783–791Google Scholar
  17. Germano MG, Menna P, Mostasso FL, Hungria M (2006) RFLP analysis of the rRNA operon of a Brazilian collection of bradyrhizobial strains from 33 legume species. Int J Syst Evol Microbiol 56:217–229CrossRefPubMedGoogle Scholar
  18. Giongo A, Ambrosini A, Vargas L, Freire J, Bodanese-Zanettini M, Passaglia L (2008) Evaluation of genetic diversity of bradyrhizobia strains nodulating soybean [Glycine max (L.) Merrill] isolated from South Brazilian fields. Appl Soil Ecol 38:261–269CrossRefGoogle Scholar
  19. Girvan MS, Bullimore J, Pretty JN, Osborn AM, Ball AS (2003) Soil type is the primary determinant of the composition of the total and active bacterial communities in arable soils. Appl Environ Microbiol 69:1800–1809CrossRefPubMedPubMedCentralGoogle Scholar
  20. Hall T (2004) BioEdit version 7.0. 0 Distributed by the author, website: www mbio ncsu edu/BioEdit/bioedit htmlGoogle Scholar
  21. Handley BA, Hedges AJ, Beringer JE (1998) Importance of host plants for detecting the population diversity of Rhizobium leguminosarum biovar viciae in soil. Soil Biol Biochem 30:241–9CrossRefGoogle Scholar
  22. Hubisz MJ, Falush D, Stephens M, Pritchard JK (2009) Inferring weak population structure with the assistance of sample group information. Mol Ecol Resour 9:1322–1332CrossRefPubMedPubMedCentralGoogle Scholar
  23. Hungria M, de O Chueire LgM, Coca RG, Megias M (2001) Preliminary characterization of fast growing rhizobial strains isolated from soyabean nodules in Brazil Soil Biol Biochem 33:1349–1361Google Scholar
  24. Jordan D (1982) Notes: 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 32:136–139CrossRefGoogle Scholar
  25. Keyser HH, Bohlool BB, Hu T, Weber DF (1982) Fast-growing rhizobia isolated from root nodules of soybean. Science 215:1631–1632CrossRefPubMedGoogle Scholar
  26. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120CrossRefPubMedGoogle Scholar
  27. Kuykendall L, Saxena B, Devine T, Udell S (1992) Genetic diversity in Bradyrhizobium japonicum Jordan 1982 and a proposal for Bradyrhizobium elkanii sp. nov Canad. J Microbiol 38:501–505Google Scholar
  28. Laguerre G, Mavingui P, Allard MR, Charnay MP, Louvrier P, Mazurier SI, Rigottier-Gois L, Amarger N (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 62:2029–2036PubMedPubMedCentralGoogle Scholar
  29. Liu Y, Guan D, Jiang X, Ma M, Li L, Cao F, Chen H, Shen D, Li J (2015) Proteins involved in nodulation competitiveness of two Bradyrhizobium diazoefficiens strains induced by soybean root exudates. Biol Fertil Soils 51:251–260CrossRefGoogle Scholar
  30. 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 58:200–214CrossRefPubMedGoogle Scholar
  31. Menna P, Barcellos FG, Hungria M (2009) Phylogeny and taxonomy of a diverse collection of Bradyrhizobium strains based on multilocus sequence analysis of the 16S rRNA gene ITS region and glnII, recA, atpD and dnaK genes. Int J Syst Evol Microbiol 59:2934–2950CrossRefPubMedGoogle Scholar
  32. Nei M, Li W-H (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Nat Acad Sci 76:5269–5273CrossRefPubMedPubMedCentralGoogle Scholar
  33. Neves MCP, Rumjanek NG (1997) Diversity and adaptability of soybean and cowpea rhizobia in tropical soils. Soil Biol Biochem 29:889–895CrossRefGoogle Scholar
  34. Paffetti D, Daguin F, Fancelli S, Gnocchi S, Lippi F, Scotti C, Bazzicalupo M (1998) Influence of plant genotype on the selection of nodulating Sinorhizobium meliloti strains by Madicago sativa. Antonie van Leeuwenhoek 73:3–8Google Scholar
  35. Palmer K, Young J (2000) Higher diversity of Rhizobium leguminosarum biovar viciae populations in arable soils than in grass soils. Appl Environ Microbiol 66:2445–2450CrossRefPubMedPubMedCentralGoogle Scholar
  36. Peng GX, Tan ZY, Wang ET, Reinhold-Hurek B, Chen WF, Chen WX (2002) Identification of isolates from soybean nodules in Xinjiang Region as Sinorhizobium xinjiangense and genetic differentiation of S. xinjiangense from Sinorhizobium fredii. Int J Syst Evol Microbiol 52:457–462CrossRefPubMedGoogle Scholar
  37. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959PubMedPubMedCentralGoogle Scholar
  38. Risal CP, Yokoyama T, Ohkama-Ohtsu N, Djedidi S, Sekimoto H (2010) Genetic diversity of native soybean bradyrhizobia from different topographical regions along the southern slopes of the Himalayan Mountains in Nepal. Syst Appl Microbiol 33:416–425CrossRefPubMedGoogle Scholar
  39. Rohlf FJ (2009) NTSYS-pc Numerical Taxonomy System Version 2Google Scholar
  40. Saeki Y (2011) Characterization of soybean-nodulating rhizobial communities and diversity. INTECH Open Access PublisherGoogle Scholar
  41. Saitou N, Nei M (1987) The neighbour-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425PubMedGoogle Scholar
  42. Shiro S et al (2013) Genetic diversity and geographical distribution of indigenous soybean-nodulating bradyrhizobia in the United States. Appl Environ Microbiol 79:3610–3618CrossRefPubMedPubMedCentralGoogle Scholar
  43. Shurtleff W, Aoyagi A (2009) History of soybeans and soyfoods in Africa (1857–2009): extensively annotated bibliography and sourcebook. Soyinfo CenterGoogle Scholar
  44. Singh G (2010) The soybean: botany, production and uses. CABIGoogle Scholar
  45. Somasegaran P, Hoben HJ (1994) Counting rhizobia by a plant infection method. Eds Handbook for Rhizobia. Springer-Verlag New York, Inc, pp 58–64Google Scholar
  46. Stępkowski T, Moulin L, Krzyżańska A, McInnes A, Law IJ, Howieson J (2005) European origin of Bradyrhizobium populations infecting lupins and serradella in soils of Western Australia and South Africa. Appl Environ Microbiol 71:7041–7052Google Scholar
  47. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729CrossRefPubMedPubMedCentralGoogle Scholar
  48. Tang J, Bromfield E, Rodrigue N, Cloutier S, Tambong J (2012) Microevolution of symbiotic Bradyrhizobium populations associated with soybeans in east North America. Ecol Evol 2:2943–2961CrossRefPubMedPubMedCentralGoogle Scholar
  49. Tan ZY, Xu XD, Wang ET, Gao JL, Martinez-Romero E, Chen WX (1997) Phylogenetic and genetic relationships of Mesorhizobium tianshanense and related rhizobia. Int J Syst Bacteriol 47:874–879CrossRefPubMedGoogle Scholar
  50. Thies J, Holmes E, Vachot A (2001) Application of molecular techniques to studies in Rhizobium ecology: a review. Animal Prod Sci 41:299–319CrossRefGoogle Scholar
  51. Vincent JM (1970) A manual for the practical study of the root-nodule bacteria . IBP Handbook No. 15, Burgess and Son (Abingdon) Ltd. Britain.Google Scholar
  52. Vinuesa P, Rojas-Jiménez K, Contreras-Moreira B, Mahna SK, Prasad BN, Moe H, Selvaraju SB, Thierfelder H, Werner D (2008) 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 74:6987–6996CrossRefPubMedPubMedCentralGoogle Scholar
  53. Whittaker RH (1972) Evolution and measurement of species diversity Taxon:213–251Google 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 26:203–210CrossRefPubMedGoogle Scholar
  55. Wolde-meskel E, Terefework Z, Lindström K, Frostegård Å (2004) Rhizobia nodulating African Acacia spp. and Sesbania sesban trees in southern Ethiopian soils are metabolically and genomically diverse. Soil Biol Biochem 36:2013–2025CrossRefGoogle Scholar
  56. Xu L, Ge C, Cui Z, Li J, Fan H (1995) Bradyrhizobium liaoningense sp. nov., isolated from the root nodules of soybeans. Int J Syst Bacteriol 45:706–711CrossRefPubMedGoogle Scholar
  57. Yang JK, Zhang WT, Yuan TY, Zhou JC (2006) Genotypic characteristics of the rrn operon and genome of indigenous soybean bradyrhizobia in cropping zones of China. Canad J Microbiol 52:968–976CrossRefGoogle Scholar
  58. Yao ZY, Kan FL, Wang ET, Wei GH, Chen WX (2002) Characterization of rhizobia that nodulate legume species of the genus Lespedeza and description of Bradyrhizobium yuanmingense sp. nov. Int J Syst Evol Microbiol 52:2219–2230PubMedGoogle Scholar
  59. Zhang YM, Li Y, Chen WF, Wang ET, Tian CF, Li QQ, Zhang YZ, Sui XH, Chen WX (2011) Biodiversity and biogeography of rhizobia associated with soybean plants grown in the North China Plain. Appl Environ Microbiol 77:6331–6342CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  • Sanjay K. Jaiswal
    • 1
  • Semira M. Beyan
    • 2
  • Felix D. Dakora
    • 1
    Email author
  1. 1.Department of ChemistryTshwane University of TechnologyPretoriaSouth Africa
  2. 2.Department of Crop SciencesTshwane University of TechnologyPretoriaSouth Africa

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