The analysis of core and symbiotic genes of rhizobia nodulating Vicia from different continents reveals their common phylogenetic origin and suggests the distribution of Rhizobium leguminosarum strains together with Vicia seeds

Springer Science and Business Media LLC - Tập 191 Số 8 - Trang 659-668 - 2009
Estela R. Álvarez-Martínez1, Ángel Valverde2, Martha-Helena Ramírez-Bahena1, Paula García‐Fraile1, Carmen Tejedor1, Pedro F. Mateos1, Nery Santillana3, Doris Zúñiga3, Álvaro Péix2, Encarna Velázquez1
1Departamento de Microbiología y Genética, Lab. 209, Edificio Departamental de Biología, Universidad de Salamanca, Salamanca, Spain
2Instituto de Recursos Naturales y Agrobiología, IRNASA-CSIC, Salamanca, Spain
3Departamento de Biología, Laboratorio de Ecología Microbiana y Biotecnología Marino Tabusso, Universidad Nacional Agraria La Molina, Lima, Peru

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Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410

Downie JA, Ma QS, Knight CD, Hombrecher G, Johnston AWB (1983) Cloning of the symbiotic region of Rhizobium leguminosarum: the nodulation genes are between the nitrogenase genes and a nifA-like gene. EMBO J 2:947–952

Gaunt MW, Turner SL, Rigottier-Gois L, Lloyd-Macgilp SA, Young JPW (2001) Phylogenies of atpD and recA support the small subunit rRNA-based classification of rhizobia. Int J Syst Evol Microbiol 51:2037–2048

Han TX, Wang ET, Han LL, Chen WF, Sui XH, Chen WX (2008) Molecular diversity and phylogeny of rhizobia associated with wild legumes native to Xinjiang, China. Syst Appl Microbiol 31:287–301

Hou BC, Wang ET, Li Y, Jia RZ, Chen WF, Man CX, Sui XH, Chen WX (2009) Rhizobial resource associated with epidemic legumes in Tibet. Microb Ecol 57:69–81

Iglesias O, Rivas R, García-Fraile P, Abril A, Mateos PF, Martinez-Molina E, Velázquez E (2007) Genetic characterization of fast-growing rhizobia able to nodulate Prosopis alba in North Spain. FEMS Microbiol Lett 277:210–216

Janczarek M, Kalita M, Skorupska AM (2009) New taxonomic markers for identification of Rhizobium leguminosarum and discrimination between closely related species. Arch Microbiol 191:207–219

Jordan DC (1984) Family III. Rhizobiaceae. In: Krieg NR, Holt JG (eds) Bergey’s manual of systematic bacteriology. Williams & Wilkins, Baltimore, pp 234–242

Kan FL, Chen ZY, Wang ET, Tian CF, Sui XH, Chen WX (2007) Characterization of symbiotic and endophytic bacteria isolated from root nodules of herbaceous legumes grown in Qinghai-Tibet plateau and in other zones of China. Arch Microbiol 188:103–115

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

Kuykendall LD (2005) Family I. Rhizobiaceae Conn 1938, 321AL. In: Brenner DJ, Krieg NR, Stanley JT (eds) Bergey’s Manual of Systematic Bacteriology. Vol. 2, part C. Springer, New York, pp 324–361

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

Laguerre G, Nour SM, Macheret V, Sanjuan J, Drouin P, Amarger N (2001) Classification of rhizobia based on nodC and nifH gene analysis reveals a close phylogenetic relationship among Phaseolus vulgaris symbionts. Microbiology 147:981–993

Laguerre G, Louvrier P, Allard MR, Amarger N (2003) Compatibility of rhizobial genotypes within natural populations of Rhizobium leguminosarum biovar viciae for nodulation of host legumes. Appl Environ Microbiol 69:2276–2283

Lei X, Wang ET, Chen WF, Sui XH, Chen WX (2008) Diverse bacteria isolated from root nodules of wild Vicia species grown in temperate region of China. Arch Microbiol. doi: 10.1007/s00203-008-0418-y

Moschetti G, Peluso A, Protopapa A, Anastasio M, Pepe O, Defez R (2005) Use of nodulation pattern, stress tolerance, nodC gene amplification, RAPD-PCR and RFLP-16S rDNA to discriminate genotypes of Rhizobium leguminosarum biovar viciae. Syst Appl Microbiol 28:619–631

Mutch LA, Young JPW (2004) Diversity and specificity of Rhizobium leguminosarum biovar viciae on wild and cultivated legumes. Mol Ecol 13:2435–2444

Perret X, Staehelin C, Broughton WJ (2000) Molecular basis of symbiotic promiscuity. Microbiol Mol Biol Rev 64:180–201

Potokina E, Blattner R, Alexandrova T, Bachmann K (2002) AFLP diversity in the common vetch (Vicia sativa L.) on the world scale. Theor Appl Genet 105:58–67

Ramírez-Bahena MH, García-Fraile P, Peix A, Valverde A, Rivas R, Igual JM, Mateos PF, Martínez-Molina E, Velázquez E (2008) Revision of the taxonomic status of the species Rhizobium leguminosarum (Frank 1879) Frank 1889, R. phaseoli Dangeard 1926AL and R. trifolii Dangeard 1926AL. R. trifolii is a later synonym of R. leguminosarum. Reclassification of the strain Rhizobium leguminosarum DSM 30132T (=NCIMB 11478T) into the new species Rhizobium pisi sp. nov. Int J Syst Evol Microbiol 58:2484–2490

Rivas R, Peix A, Mateos PF, Trujillo ME, Martínez-Molina E, Velázquez E (2006) Biodiversity of populations of phosphate solubilizing rhizobia that nodulate chickpea in different Spanish soils. Plant Soil 287:23–33

Rivas R, García-Fraile P, Mateos PF, Martínez-Molina E, Velázquez E (2007a) Characterization of xylanolytic bacteria present in the bract phyllosphere of the date palm Phoenix dactylifera. Lett Appl Microbiol 44:181–187

Rivas R, Laranjo M, Velázquez E, Mateos PF, Oliveira S, Martínez-Molina E (2007b) Strains of Mesorhizobium amorphae and M. tianshanense carrying symbiotic genes of common chickpea endosymbiotic species constitute a novel biovar (ciceri) able to nodulate Cicer arietinum. Lett Appl Microbiol 44:412–418

Roche P, Maillet F, Plazanet C, Debellé F, Ferro M, Truchet G, Promé JC, Dénarié J (1996) The common nodABC genes of Rhizobium meliloti are host-range determinants. Proc Natl Acad Sci USA 93:15305–15310

Saitou N, Nei M (1987) A neighbour-joining method: a new method for reconstructing phylogenetics trees. Mol Biol Evol 4:406–425

Santillana N, Ramírez-Bahena MH, García-Fraile P, Velázquez E, Zúñiga D (2008) Phylogenetic diversity based on rrs, atpD, recA genes and 16S–23S intergenic sequence analyses of rhizobial strains isolated from Vicia faba and Pisum sativum in Peru. Arch Microbiol 189:239–247

Sarita S, Sharma PK, Priefer UB, Prell J (2005) Direct amplification of rhizobial nodC sequences from soil total DNA and comparison to nodC diversity of root nodule isolates. FEMS Microbiol Ecol 54:1–11

Segovia L, Young JPW, Martínez-Romero E (1993) Reclassification of American Rhizobium leguminosarum biovar phaseoli type I strains as Rhizobium etli sp. nov. Int J Syst Bacteriol 43:374–377

Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599

Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The clustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl Acid Res 25:4876–4882

Tian CF, Wang ET, Han TX, Sui XH, Chen WX (2007) Genetic diversity of rhizobia associated with Vicia faba in three ecological regions of China. Arch Microbiol 188:273–282

Tian CF, Wang ET, Wu LJ, Han TX, Chen WF, Gu CT, Gu JG, Chen WX (2008) Rhizobium fabae sp. nov., a bacterium that nodulates Vicia faba. Int J Syst Evol Microbiol 58:2871–2875

Valverde A, Igual JM, Peix A, Cervantes E, Velázquez E (2006) Rhizobium lusitanum sp. nov. a bacterium that nodulates Phaseolus vulgaris. Int J Syst Evol Microbiol 56:2631–2637

van Berkum P, Beyene D, Temprano-Vera F, Keyser HH (1995) Variability among Rhizobium strains originating from nodules of Vicia faba. Appl Environ Microbiol 61:2649–2653

Velázquez E, Peix A, Zurdo-Piñeiro JL, Palomo JL, Mateos PF, Rivas R, Muñoz-Adelantado E, Toro N, García-Benavides P, Martínez-Molina E (2005) The coexistence of symbiosis and pathogenicity-determining genes in Rhizobium rhizogenes strains enables them to induce nodules and tumors or hairy roots in plants. Mol Plant Microbe Interact 18:1325–1332

Ventorino V, Chiurazzi M, Aponte M, Pepe O, Moschetti G (2007) Genetic diversity of a natural population of Rhizobium leguminosarum bv. viciae nodulating plants of Vicia faba in the Vesuvian area. Curr Microbiol 55:512–517

Vincent JM (1970) The cultivation, isolation and maintenance of rhizobia. In: Vincent JM (ed) A manual for the practical study of root-nodule. Blackwell Scientific Publications, Oxford., pp 1–13

Young JPW, Crossman LC, Johnston AWB, Thomson NR, Ghazoui ZF, Hull KH, Wexler M, Curson AR, Todd JD, Poole PS, Mauchline TH, East AK, Quail MA, Churcher C, Arrowsmith C, Cherevach I, Chillingworth T, Clarke K, Cronin A, Davis P, Fraser A, Hance Z, Hauser H, Jagels K, Moule S, Mungall K, Norbertczak H, Rabbinowitsch E, Sanders M, Simmonds M, Whitehead S, Parkhill J (2006) The genome of Rhizobium leguminosarum has recognizable core and accessory components. Genome Biol 7:R34