Genetic diversity of indigenous Bradyrhizobium nodulating promiscuous soybean [Glycine max (L) Merr.] varieties in Kenya: Impact of phosphorus and lime fertilization in two contrasting sites

Plant and Soil

Volumn 322, Issue 1, 2009, Pages 151-163

  Wasike, V W ^a,b,c   Lesueur, D ^d   Wachira, F N ^c   Mungai, N W ^c   Mumera, L M ^c   Sanginga, N ^b   Mburu, H N ^b   Mugadi, D ^b   Wango, P ^b   Vanlauwe, B ^b  

^a KENYA AGRICULTURAL RESEARCH INSTITUTE   (Kenya)

^b Tropical Soil Biology and Fertility Inst of the International Centre for Tropical Agri (TSBF CIAT)   (Kenya)

^c EGERTON UNIVERSITY   (Kenya)

^d CIRAD   (France)

Author keywords

Agro ecological zones; Genetic diversity; Polymerase chain reactionrestriction fragment length polymorphism; Promiscuous soybean

Indexed keywords

EID: 84871258311     PISSN: 0032079X     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11104-009-9902-7     Document Type: Article

References (62)

1. Abaidoo RC, Keyser HH, Singleton PW, Borthakur D (2000) Bradyrhizobia 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: 225-234.
2. Abaidoo RC, Keyser HH, Singleton PW, Borthakur D (2002) Comparison of molecular and antibiotic resistance profile method for the population analysis of bradyrhizobia spp (TGx) isolates that nodulate the new TGx soybean cultivars in Africa. J Appl Microbiol 92: 109-117.
3. Abaidoo RC, Keyser HH, Singleton PW, Dashiell KE, Sanginga N (2007) Population size, distribution, and symbiotic characteristics of indigenous Bradyrhizobium spp. that nodulate TGx soybean genotypes in Africa. Appl Soil Ecol 35: 57-67.
4. Andrade DS, Murthy PJ, Giller KE (2002) The diversity of Phaseolus-nodulating rhizobial populations is altered by liming of acid soils planted with Phaseolus vulgaris L. in Brazil. Appl Environ Microbiol 68(8): 4025-4034.
5. Anyango B, Wilson KJ, Beynon JL, Giller KE (1995) Diversity of rhizobia nodulating P. vulgaris L. in two Kenya soils with contrasting pH. Appl Environ Microbiol 61: 4016-4021.
6. Ayanaba A (1977) Toward a better use of inoculants in the humid tropics. In: Ayanaba A, Dart PJ (eds) Biological nitrogen fixation in farming systems of the tropics. Wiley, New York, pp 181-187.
7. Batista JSS, Hungria M, Barcellos FG, Ferreira MC, Mendes IC (2006) Variability in Bradyrhizobium japonicum and B. elkanii seven years after introduction of both the exotic microsymbiont and the soybean host in the Cerrados soil. Microbiol Ecol 53: 270-284.
8. Brockwell J, Pilka A, Halliday RA (1991) Soil pH is a major determinant of the numbers of naturally occurring Rhizobium meliloti, in non cultivated soils of New South Wales. Aust J Exp Agric 31: 211-219.
9. Caldwel BE, Vest GE (1968) Effects of Rhizobium japonicum on soybean. Crop Sci 10: 19-21.
10. Chen W, Qiaoyun H, Xiaojiao X (2004) Distribution and biodiversity of soybean rhizobia in the soils of Shennongjia forest reserve, China. Biol Fert Soil 40(5): 306-312.
11. 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: 3987-3997.
12. FAO UNESCO (1990) FAO UNESCO soil map of the world 1: 5, 000, 000. Vol VI Africa. UNESCO, Paris
13. Fehr WR, Caviness CE, Burmood DT, Penington JS (1971) Stage of development descriptions of soybean Glycine max (L) Merr. Crop Sc 11: 929-931.
14. Felsestein J (1993) Phylogenetic. Inference package version 3. 5c. Department of Genetics University of Washington.
15. Giongo A, Ambrosini A, Vargas LK, Freire JRJ, Bodanese-Zanettini MH, Passaglia LMP (2008) Evaluation of genetic diversity of bradyrhizobia strains nodulating soybean [Glycine max (L.) Merrill] isolated from South Brazilian fields. Appl Soil Ecol 38(3): 261-269.
16. Graham PH, Sadowsky MJ, Keyser HH, Barnet YM, Bradley RS, Cooper JE, De Ley DJ, Jarvis BDW, Roslycky EB, Strijdom BW, Young JPW (1991) Proposed minimum standards for the description of new genera and species of root-and stem-nodulationg bacteria. Int J Syst Bacteriol 41: 582-587.
17. GTZ (1996) Kenya soybean cook book. Ministry of Agriculture and Livestock Development and Marketing, Nairobi.
18. Gunawardena SFBN, Danso SKA, Zapata F (1993) Phosphorus requirement and success of nitrogen in three soybean (Glycine max) genotypes, Bragg, nts 382 and Chippewa. Plant Soil 151: 1-9.
19. Hulton CSJ, Higgins CF, Sharp PM (1991) ERIC sequences: A novel family of repetitive elements in the genomes of Escherichia coli, Salmonella typhimurium and other Enterobacteriaceae. Mol Microbiol 5: 825-834.
20. Hungria M, Campo RJ, Chueire LM, Youssef L, Agustin P, Guttierrez-Mañero FJ, Rubens JC (2006) Genetic diversity of indigenous tropical fast-growing rhizobia isolated from soybean nodules. Plant Soil 288: 343-356 ICRAF laboratory methods for soil and plant analysis, May 1999.
21. Kahindi JHP, Woomer P, George T, de Souza Moreira FM, Karanja NK, Giller KE (1997) Agricultural intensification soil biodiversity and ecosystem function in the tropics: the role of nitrogen fixing bacteria. Appl Soil Ecol 6: 55-76.
22. Kasasa P (1999) Biological nitrogen fixation by promiscuous nodulating soybean (Glycine max [L] Merr) varieties in the communal soils of Zimbabwe. M. Phil Thesis University of Zimbabwe, Harare, pp 118.
23. King LM, Schaal BA (1989) Ribosomal DNA variation and distribution in Rudbeckia missouriensis. Evol l42: 1117-1119.
24. Krasova-Wade T, Ndoye I, Braconnier S, Sarr B, de Lajuide P, Neyra M (2003) Diversity of indigenous bradyrhizobia associated with three cowpea cultivars (Vigna unguiculata L.) (Walp.) grown under limited and favorable water conditions in Senegal (West Africa). Afr J Bacteriol 2 (1): 13-22.
25. Kueneman EA, Root WR, Dashiell KE, Hohenberg J (1984) Breeding soyabean for the tropics capable of nodulating effectively with indigenous Rhizobium spp. Plant Soil 82: 387-396.
26. Laguerre G, Allard M, Revoy R, Amager N (1994) Rapid identification of rhizobia by restriction length polymorphism analysis of PCR amplified 16S rRNA genes. Appl Environ Microbiol 60: 56-63.
27. Lane DJ (1991) 16S-23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, London, pp 115-175.
28. Lanham PG, Brennan RM (1999) Genetic characterization of gooseberry Ribes grossularia subgenus grossularia germplasm using RAPD, ISSR and ALFP markers. Hort Sci Biotech J 74: 361-366.
29. Mpepereki S, Javaheri F, Davis P, Giller KE (2000) Soybean and Sustainable Agriculture: Promiscuous soyabeans in Southern Africa. Field Crop Res 65: 137-149.
30. Mullen DM, Israel DW, Wollum AG (1988) Effects of Bradyrhizobium japonicum and soybean (Glycine max (L) Merr.) on phosphorus nutrition, nodulation and nitrogen fixation. Appl Environ Microbiol 54: 2387-2392.
31. Mulongoy K, Ayanaba A (1986) Dynamics of population sizes of cowpea and soybean rhizobia at three locations in West Africa. Mircen J 2: 301-308.
32. Munns DN, Hohenberg JS, Righetti TL, Lauter DJ (1981) Soil acidity tolerance of symbiotic and nitrogen-fertilized Soybean. Agron J 73: 407-410.
33. Musiyiwa K, Mpepereki S, Giller KE (2005) Physiological diversity of rhizobia nodulating promiscuous soyabean in Zimbabwean soils. Symbiosis 40: 97-107.
34. Nakamura Y, Leppert M, O'Connell P, Wolff R, Holm T, Culver M, Martin C, Fujimoto E, Hoff M, Kumlin E, White R (1987) Variable number tandem repeat (VNTR) markers for human gene mapping. Sci 235: 1616-1622.
35. Navarro E, Simonet P, Normand P, Bardin R (1992) Characterization of natural population of Nitrobacter spp using PCR-RFLP analysis of ribosomal intergenic spacer. Arch Microbiol 157: 107-115.
36. Njuguna SK (1985) Potential of soybeans in fulfilling Kenya's protein and oil requirements. Proc. of American Soybean Association Conference. ILRAD, Kenya.
37. Odee DW, Haukka K, McInroy SG, Sprent JI, Sutherland JM, Young JPW (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: 804-811.
38. Okereke GU, Eaglesham ARJ (1992) Nodulation and Nitrogen fixation by 79 "promiscuous" soybean genotypes in a soil in east Nigeria. Agron Afr V 2: 23-136.
39. Padzemik DL, Vance CP, Sadowsky MJ, Graham PH, Orf JH (1977) A host controlled sero group-specific, infective nodulation system in the Bradyrhizobium-soybean (Glycine max) symbiosis. Mol Plant-Microbe Interactions 10: 994-1001.
40. Ponsonnet C, Nesme X (1994) Identification of agrobacterium strains by PCR-RFLP analysis of pTi and chromosomal regions. Arch Microbiol 161: 300-309.
41. Pueppke SG, Broughton WJ (1999) Rhizobium sp strain NGR 234 and R. freidii USDA 257 share exceptionally broad nested host ranges. Mol Plant-Microbe Interactions 10: 994-1001.
42. Rouvier C, Prin Y, Reddel P, Normand P, Simonet P (1996) Genetic diversity among Frankia strains nodulating members of the family Casuarinaceae in Australia revealed by PCR and restriction fragment length polymorphism analysis with crushed root nodules. Appl Environ Microbiol 62: 979-985.
43. Sanginga N, Abaidoo RC, Dashiel K, Carsky RJ, Okogun AJ (1996) Persistence and effectiveness of rhizobia nodulating promiscuous soybean in moist savanna zones of Nigeria. Appl Soil Ecol 3: 215-224.
44. Sanginga N, Thottappilly G, Dashiel K (2000) Effectiveness of rhizobia nodulating recent promiscuous soybean selections in the moist savanna of Nigeria. Soil Biol Biochem 32: 127-133.
45. Sarr A, Neyra M, Abdeljalil M, Houeibib O, Ndoye I, Oihabi A, Lesueur D (2005) Rhizobial populations in soils from natural Acacia senegal and Acacia nilotica forests in Mauritania and the Senegal River Valley. Microbiol Ecol 50: 152-162.
46. Saitou RR, Nei M (1987) A neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 44: 406-425.
47. Sikora S, Redzepovic S (2003) Genotypic characterization of indigenous soybean rhizobia by PCR-RFLP of 16S rDNA, rep-PCR and RAPD analysis. Food Tech Biotech 41 (1): 61-67.
48. Sinclair TR, Valdez V (2002) Physiological traits for crop yield improvement in low N and P environments. Plant Soil 245: 1-15.
49. Somasegaran P, Hoben HJ (1994) Handbook for rhizobia: Methods in legume-Rhizobium Technology. Springer-Verlag, New York.
50. Stern MJ, Ferro-Luzzi Amess G, Smith NH, Robinson EC, Higgins CF (1984) Repetitive extragenic palindromic sequences: A major component of the bacterial genome. Cell 37: 1015-1026.
51. Thiao M, Neyra M, Isidore E, Sylla S, Lesueur D (2004) Diversity and effectiveness of rhizobium from Gliricidia sepium native to Reunion Island, Kenya and New Caledonia. World J Microbiol Biotech 20: 703-709.
52. Thies JE, Singleton PW, Bohlool BB (1991a) Influence of the size of indigenous rhizobial populations on the establish-ment and symbiotic performance of introduced rhizobia on field-grown legumes. Appl Environ Microbiol 57: 19-28.
53. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acid Res 25: 4876-4882.
54. TSBF (2003) The Comminutor Newsletter of the TSBF Institute of CIAT, Vol 7 No. 1 pp 15-16.
55. Turk D, Keyser HH, Singleton PW (1993) Response of tree legume to rhizobial inoculation in relation to the population density of indigenous rhizobia. Soil Biol Biochem 25: 75-81.
56. Vinuesa P, Rademaker JLW, de Brujin FJ, Werner D (1998) Genotypic characterization of Bradyrhizobium strains nodulating endemic woody legumes of the Canary Islands by PCR-Restriction Length Polymorphism analysis of genes encoding 16S rDNA and 16S-23S rDNA Intergenic Spacers, Repetitive Extragenic Palindromic PCR genomic fingerprinting, and partial 16S r RNA sequencing. Appl Environ Microbiol 64: 2096-2104.
57. Virdi JS, Sachdeva P (2005) Genetic diversity of pathogenic microorganisms: Basic in sights, public health implications and the Indian initiatives. Current Sci 89(1): 113-123.
58. Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Fritjers A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: A new concept for DNA fingerprinting. Nucleic Acid Res 23: 4407-4414.
59. Wei TZ, Yang JK, Yuan TY, Zhou JC (2007) Genetic diversity and phylogeny of indigenous rhizobia from cowpea [Vigna unguiculata (L) Walp]. Biol Fert Soils 44: 201-210.
60. Williams GK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acid Res 18: 6531-6535.
61. Xu LM, Ge C, Cui Z, Li J, Fan H (1995) Bradyrhizobium liaoningense sp nov., isolated from root nodules of soybeans. Int J Syst Bacteriol 45: 706-711.
62. Zahran HH (1999) Rhizobium-legume symbiosis and nitrogen fixation under severe conditions and in an arid climate. Microbiol Mol Rev 63: 968-989.