Genetic diversity of Acacia seyal Del. rhizobial populations indigenous to senegalese soils in relation to salinity and pH of the sampling sites

Microbial Ecology

Volumn 54, Issue 3, 2007, Pages 553-566

  Diouf, Diegane ^a,b   Samba Mbaye, Ramatoulaye ^b   Lesueur, Didier ^c   Ba, Amadou T ^a   Dreyfus, Bernard ^d   De Lajudie, Philippe ^d   Neyra, Marc ^d  

^a UNIVERSITÉ CHEIKH ANTA DIOP   (Senegal)

^b Centre IRD de Bel Air   (Senegal)

^c WORLD AGROFORESTRY CENTRE ICRAF   (Kenya)

^d CIRAD   (France)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S; RNA 23S;

ACACIA; ARTICLE; CLASSIFICATION; DNA SEQUENCE; GENETIC VARIABILITY; GENETICS; GROWTH, DEVELOPMENT AND AGING; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PH; PHYLOGENY; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; RHIZOBIACEAE; SALINITY; SENEGAL;

ACACIA; HYDROGEN-ION CONCENTRATION; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; RHIZOBIACEAE; RNA, RIBOSOMAL, 16S; RNA, RIBOSOMAL, 23S; SALINITY; SENEGAL; SEQUENCE ANALYSIS, DNA; SOIL MICROBIOLOGY; VARIATION (GENETICS);

ACACIA; ACACIA SEYAL; AGROBACTERIUM; BURKHOLDERIA; MESORHIZOBIUM; RHIZOBIACEAE; RHIZOBIUM; SINORHIZOBIUM;

EID: 35148827630     PISSN: 00953628     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00248-007-9243-0     Document Type: Article

References (60)

1. Allen, ON, Allen, EK (1981) The Leguminosae: A Source Book of Characteristics, Uses and Nodulation. The University of Wisconsin Press, Madison
2. Altschul, SF, Madden, TL, Schäffer, AA, Zhang, J, Zhang, Z, Miller, W, Lipman, DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402
3. Ba, S, Willems, A, de Lajudie, P, Roche, P, Jeder, H, Quatrini, P, Neyra, M, Ferro, M, Prome, JC, Gillis, M, Boivin-Masson, C, Lorquin, J (2002) Symbiotic and taxonomic diversity of rhizobia isolated from Acacia tortilis subsp. raddiana in Africa. Syst Appl Microbiol 25: 130-145
4. Bala, A, Giller, KE (2001) Symbiotic specificity of tropical tree rhizobia for host legumes. New Phytol 149: 495-507
5. Bordeleau, LM, Prévost, D (1994) Nodulation and nitrogen fixation in extreme environments. Plant Soil 161: 115-125
6. Ben Romdhane, S, Nasr, H, Samba-Mbaye, R, Neyra, M, Ghorbal, MH (2005) Diversity of Acacia tortilis rhizobia revealed by PCR/RFLP on crushed root nodules in Tunisia. Ann Microbiol 55: 249-258
7. Ben Romdhane, S, Nasr, H, Samba-Mbaye, R, Neyra, M, Ghorbal, MH, de Lajudie, P (2006) Genetic diversity of Acacia tortilis ssp. raddiana rhizobia in Tunisia assessed by 16S and 16S-23S rDNA genes analysis. J Appl Microbiol 100: 436-445
8. Carter, JM, Gardner, WK, Gibson, AH (1994) Improved growth and yield of faba bean (Vicia faba cv. Fiord) by inoculation with strains of Rhizobium leguminosarum biovar viceae in acid soils in South-west Victoria. Aust J Agric Res 45: 613-623
9. de Lajudie, P, Willems, A, Nick, G, Moreau, F, Molouba, F, Hoste, B, Torck, U, Neyra, M, Collins, MD, Lindstorm, K, Dreyfus, B, Gillis, M (1998) Characterization of tropical tree rhizobia and description of Mesorhizobium plurifarium sp. nov. Int J Syst Bacteriol 48: 369-382
10. de Lajudie, P, Willems, A, Nick, G, Mohamed, SH, Torck, U, Coopman, R, Filali-Maltouf, A, Kersters, K, Dreyfus, B, Lindström, K, Gillis, M (1999) Agrobacterium bv.1 strains isolated from nodules of tropical legumes. Syst Appl Microbiol 22: 119-132
11. Diouf, D, Duponnois, R, Ba, AT, Neyra, M, Lesueur, D (2005) Symbiosis of Acacia auriculiformis and A. mangium with mycorrhizal fungi and Bradyrhizobium sp. improves salt tolerance in greenhouse conditions. Funct Plant Biol 32: 1143-1152
12. Diouf, D, Forestier, S, Neyra, M, Lesueur, D (2003) Optimization of inoculation of Leucaena leucocephala and Acacia mangium with rhizobium under greenhouse conditions. Ann For Sci 60: 1-6
13. Dolédec, S, Chessel, D (1987) Rythmes saisonniers et composantes stationnelles en milieu aquatique I-Description d'un plan d'observations complet par projection de variables. Acta Oecol 8: 403-426
14. Dommergues, YR (1995) Nitrogen fixation by trees in relation to soil nitrogen economy. Fert Res 42: 215-230
15. Don, RH, Cox, PT, Wainwright, BJ, Baker, K, Mattick, JS (1991) Touchdown PCR to circumvent spurious priming during gene amplification. Nucleic Acids Res 19: 4008
16. Doran, JC, Turnbull, JW (1997) Australian Trees and Shrubs: Species for Land Rehabilitation and Farm Planting in the Tropics. ACIAR Monograph No. 24. ACIAR, Canberra
17. Dreyfus, BL, Dommergues, YR (1981) Nodulation of Acacia species by fast and slow growing tropical strains of Rhizobium. Appl Environ Microbiol 41: 97-99
18. Felsenstein, J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783-791
19. Gibson, AH (1980) Methods for legumes in glasshouses and controlled environment cabinets. In: Bergersen, FJ (Ed.) Methods for Evaluating Biological Nitrogen Fixation. Wiley-Interscience, Chichester, pp 139-184
20. Giri, B, Kapoor, R, Mukerji, KG (2003) Influence of arbuscular mycorrhizal fungi and salinity on growth, biomass, and mineral nutrition of Acacia auriculiformis. Biol Fertil Soils 38: 170-175
21. Hall, JB (1994) Acacia seyal-multipurpose tree of the Sahara desert. NFTA 94-07. FACT Net. Winrock International, Little Rock
22. 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
23. Kimura, M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16: 111-120
24. Krasova-Wade, T, Ndoye, I, Braconnier, S, Sarr, B, de Lajudie, P, Neyra, M (2003) Diversity of indigeneous bradyrhizobia associated with three cowpea cultivars (Vigna unguiculata (L.) Walp.) grown under limited and favorable water conditions in Senegal (West Africa). Afr J Biotechnol 2: 13-22
25. Kwon, SW, Park, JY, Kim, JS, Kang, JW, Cho, YH, Lim, CK, Parker, MA, Lee, GB (2005) Phylogenetic analysis of the genera Bradyrhizobium, Mesorhizobium, Rhizobium and Sinorhizobium on the basis of 16S rRNA gene and internally transcribed spacer region sequences. Int J Syst Evol Microbiol 55: 263-270
26. Laguerre, G, Allard, MR, Revoy, F, Amarger, N (1994) Rapid identification of rhizobia by restriction fragment length polymorphism analysis of PCR-amplified 16S rRNA genes. Appl Environ Microbiol 60: 56-63
27. Mahler, RA, Bezdicek, DF (1978) Diversity of Rhizobium leguminosarum in the Palouse of eastern Washington. Appl Environ Microbiol 36: 780-782
28. Menna, P, Hungria, M, Barcellos, FG, Bangel, EV, Hess, PN, Martinez-Romero, E (2006) Molecular phylogeny based on the 16S rRNA gene of elite rhizobial strains used in Brazilian commercial inoculants. Syst Appl Microbiol 29: 315-332
29. Mhamdi, R, Laguerre, G, Aouani, ME, Mars, M, Amarger, N (2002) Different species and symbiotic genotypes of field rhizobia can nodulate Phaseolus vulgaris in Tunisian soils. FEMS Microbiol Ecol 41: 77-84
30. Mhamdi, R, Mrabet, M, Laguerre, G, Tiwari, R, Aouani, ME (2005) Colonization of Phaseolus vulgaris nodules by Agrobacterium-like strains. Can J Microbiol 51: 105-111
31. Mohammed, SH, Smouni, A, Neyra, M, Kharchaf, D, Filali-Maltouf, A (2000) Phenotypic characteristics of root-nodulating bacteria isolated from Acacia spp. grown in Libya. Plant Soil 224: 171-183
32. Moreira, FMS, Gillis, M, Pot, B, Kersters, K, Franco, AA (1993) Characterization of rhizobia isolated from different divergence groups of tropical Leguminosae by comparative polyacrylamide gel electrophoresis of their total proteins. Syst Appl Microbiol 16: 135-146
33. Mpepereki, S, Makonese, F, Wollum, AG (1997) Physiological characterization of indigenous rhizobia nodulating Vigna unguiculata in Zimbabwean soils. Symbiosis 22: 275-292
34. 15N isotope dilution technique. Plant Soil 172: 175-180
35. Normand, P, Cournoyer, B, Nazaret, S, Simonet, P (1992) Analysis of a ribosomal RNA operon in the actinomycete Frankia. Gene 111: 119-124
36. Normand, P, Ponsonnet, C, Nesme, X, Neyra, M, Simonet, P (1996) ITS analysis of prokariotes. In: Akkermans, ADL, van Elsas, JD, et De Bruijn, FJ (Eds.) Molecular Microbial Ecology Manual. Kluwer, Dordrecht
37. Odee, DW, Sutherland, JM, Makatiani, ET, McInroy, SG, Sprent, JI (1997) Phenotypic characteristics and composition of rhizobia associated with woody legumes growing in diverse Kenya conditions. Plant Soil 188: 65-75
38. Perriere, G, Gouy, M (1996) www-query: an on-line retrieval system for biological sequence banks. Biochimie 78: 364-369
39. Ponsonnet, C, Nesme, X (1994) Identification of Agrobacterium strains by PCR-RFLP analysis of pTi and chromosomal regions. Arch Microbiol 16: 300-309
40. Rouvier, C, Prin, Y, Reddell, 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
41. Saitou, N, Nei, M (1987) The neighbor-joining method: a new method for constructing phylogenetic trees. Mol Biol Evol 4: 406-425
42. Sarr, A, Neyra, M, Ould-Houeibib, MA, Ndoye, I, Oihabi, A, Lesueur, D (2005) Characterization of native rhizobial populations present in soils from natural forests of Acacia senegal and Acacia nilotica in Trarza and Gorgol regions from Mauritania and the Senegal River Valley. Microb Ecol 50: 152-162
43. Segovia, L, Pinero, D, Palacios, R, Martinez-Romero, E (1991) Genetic structure of a soil population of nonsymbiotic Rhizobium leguminosarum. Appl Environ Microbiol 57: 426-433
44. Singleton, PW, El-Swaifi, SA, Bohlool, BB (1982) Effect of salinity on Rhizobium growth and survival. Appl Environ Microbiol 44: 884-890
45. Sullivan, JT, Bertrand, DE, Van Berkum, P, Ronson, CW (1996) Four unnamed species of nonsymbiotic rhizobia isolated from the rhizosphere of Lotus corniculatus. Appl Environ Microbiol 62: 2818-2825
46. Sutherland, JM, Odee, DW, Muluvi, GM, Mcinroy, SG, Patel, A (2000) Single and multi-strain rhizobial inoculation of African acacias in nursery conditions. Soil Biol Biochem 32: 323-333
47. Sy, A, Giraud, E, Jourand, P, Garcia, N, Willems, A, de Lajudie, P, Prin, Y, Neyra, M, Gillis, M, Boivin-Masson, C, Dreyfus, B (2001) Methylotrophic Methylobacterium bacteria nodulate and fix nitrogen in symbiosis with legumes. J Bacteriol 183: 214-220
48. 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 20: 703-709
49. Thioulouse, J, Chessel, D, Dolédec, S, Olivier, JM (1997) ADE-4: a multivariate analysis and graphical display software. Stat Comput 7: 75-83
50. Thompson, JD, Gibson, TJ, Plewniak, F, Jeanmougin, F, Higgins, DG (1997) The CLUSTAL X windows interface: flexible strategies multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25: 4876-4882
51. Van Berkum, P, Fuhrmann, JJ (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
52. Vincent, JM (1970) A Manual for the Practical Study of Root-Nodule Bacteria. International Biological Programme. Handbook no. 15. Blackwell, Oxford
53. Von Maydel, LHJ (1983) Trees and Shrubs of the Sahel, their Characteristics and Uses. GTZ, Verlag Josef Margraf, Eschborn
54. Willems, A, Coopman, R, Gillis, M (2001) Comparison of sequence analysis of 16S-23S rDNA spacer regions, AFLP analysis and DNA-DNA hybridizations in Bradyrhizobium. Int J Syst Evol Microbiol 51: 623-632
55. Zakhia, F, de Lajudie, P (2001) Taxonomy of rhizobia. Agronomie 21: 569-576
56. Zakhia, F, Jeder, H, Willems, A, Gillis, M, Dreyfus, B, de Lajudie, P (2006) Diverse bacteria associated with root nodules of spontaneous legumes in tunisia and first report for nifH-like gene within the genera Microbacterium and Starkeya. Microb Ecol 51: 375-393
57. Zahran, HH (1999) Rhizobium-legume symbiosis and nitrogen fixation under severe conditions and in arid climate. Microb Mol Biol Rev 63: 968-989
58. Zeng, N (2003) Drought in the Sahel. Science 302: 999-1000
59. Zerhari, K, Aurag, J, Khbaya, B, Kharchaf, D, Filali-Maltouf, A (2000) Phenotypic characteristics of rhizobia isolates nodulating Acacia species in the arid and Saharan regions of Morocco. Lett Appl Microbiol 30: 351-357
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