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Volumn 28, Issue 8, 2005, Pages 702-716

Molecular systematics of rhizobia based on maximum likelihood and Bayesian phylogenies inferred from rrs, atpD, recA and nifH sequences, and their use in the classification of Sesbania microsymbionts from Venezuelan wetlands

Author keywords

Bayesian phylogenetics; Maximum likelihood; Mesorhizobium plurifarium; Molecular systematics; Nitrogen fixation; Plasmids; Recombination; Rhizobium huautlense; Sesbania

Indexed keywords

RECA PROTEIN;

EID: 25144442706     PISSN: 07232020     EISSN: 16180984     Source Type: Journal    
DOI: 10.1016/j.syapm.2005.05.007     Document Type: Article
Times cited : (155)

References (57)
  • 1
    • 0028161131 scopus 로고
    • Nitrogen cycling in a Venezuelan tropical seasonally flooded forest: Soil nitrogen mineralization and nitrification
    • E. Barrios, and R. Herrera Nitrogen cycling in a Venezuelan tropical seasonally flooded forest: soil nitrogen mineralization and nitrification J. Trop. Ecol. 10 1994 399 416
    • (1994) J. Trop. Ecol. , vol.10 , pp. 399-416
    • Barrios, E.1    Herrera, R.2
  • 4
    • 0000250265 scopus 로고
    • Measures of the amount of ecological association between species
    • L.R. Dice Measures of the amount of ecological association between species J. Ecol. 26 1945 297 302
    • (1945) J. Ecol. , vol.26 , pp. 297-302
    • Dice, L.R.1
  • 5
    • 0033831427 scopus 로고    scopus 로고
    • Genotypic characterization of Bradyrhizobium strains nodulating small Senegalese legumes by 16S-23S rRNA intergenic gene spacers and amplified fragment length polymorphism fingerprint analyses
    • F. Doignon-Bourcier, A. Willems, R. Coopman, G. Laguerre, M. Gillis, and P. de Lajudie 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 2000 3987 3997
    • (2000) Appl. Environ. Microbiol. , vol.66 , pp. 3987-3997
    • Doignon-Bourcier, F.1    Willems, A.2    Coopman, R.3    Laguerre, G.4    Gillis, M.5    De Lajudie, P.6
  • 6
    • 0023836564 scopus 로고
    • Characterization of Azorhizobium caulinodans gen. nov., sp. nov., a stem-nodulationg nitroogen-fixing bacterium isolated from Sesbania rostrata
    • B. Dreyfus, J.L. Garcia, and M. Gillis Characterization of Azorhizobium caulinodans gen. nov., sp. nov., a stem-nodulationg nitroogen-fixing bacterium isolated from Sesbania rostrata Int. J. Syst. Bacteriol. 38 1988 89 98
    • (1988) Int. J. Syst. Bacteriol. , vol.38 , pp. 89-98
    • Dreyfus, B.1    Garcia, J.L.2    Gillis, M.3
  • 7
    • 0018162579 scopus 로고
    • A rapid method for the identification of plasmid desoxyribonucleic acid in bacteria
    • T. Eckhardt A rapid method for the identification of plasmid desoxyribonucleic acid in bacteria Plasmid 1 1978 584 588
    • (1978) Plasmid , vol.1 , pp. 584-588
    • Eckhardt, T.1
  • 9
    • 0000461280 scopus 로고
    • Confidence limits on phylogenies: An approach using the bootstrap
    • J. Felsenstein Confidence limits on phylogenies: An approach using the bootstrap Evolution 39 1985 783 791
    • (1985) Evolution , vol.39 , pp. 783-791
    • Felsenstein, J.1
  • 12
    • 0242578620 scopus 로고    scopus 로고
    • A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
    • S. Guindon, and O. Gascuel A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood Syst. Biol. 52 2003 696 704
    • (2003) Syst. Biol. , vol.52 , pp. 696-704
    • Guindon, S.1    Gascuel, O.2
  • 13
    • 0031889348 scopus 로고    scopus 로고
    • Three phylogenetic groups of nodA and nifH genes in Sinorhizobium and Mesorhizobium isolates from leguminous trees growing in Africa and Latin America
    • K. Haukka, K. Lindström, and J.P.W. Young Three phylogenetic groups of nodA and nifH genes in Sinorhizobium and Mesorhizobium isolates from leguminous trees growing in Africa and Latin America Appl. Environ. Microbiol. 64 1998 419 426
    • (1998) Appl. Environ. Microbiol. , vol.64 , pp. 419-426
    • Haukka, K.1    Lindström, K.2    Young, J.P.W.3
  • 14
    • 0035861456 scopus 로고    scopus 로고
    • Bayesian inference of phylogeny and its impact on evolutionary biology
    • J.P. Huelsenbeck, F. Ronquist, R. Nielsen, and J.P. Bollback Bayesian inference of phylogeny and its impact on evolutionary biology Science 294 2001 2310 2314
    • (2001) Science , vol.294 , pp. 2310-2314
    • Huelsenbeck, J.P.1    Ronquist, F.2    Nielsen, R.3    Bollback, J.P.4
  • 15
    • 0001677031 scopus 로고
    • Quantitative analysis of the symbiotic N2-fixation, non-structural carbohydrates and chlorophyll content in sixteen native legume species collected in different savanna sites
    • M.L. Izaguirre-Mayoral, O. Carballo, M. Sicardi de Mallorca, and T. Oropeza Quantitative analysis of the symbiotic N2-fixation, non-structural carbohydrates and chlorophyll content in sixteen native legume species collected in different savanna sites Symbiosis 12 1992 293 312
    • (1992) Symbiosis , vol.12 , pp. 293-312
    • Izaguirre-Mayoral, M.L.1    Carballo, O.2    Sicardi De Mallorca, M.3    Oropeza, T.4
  • 17
    • 4143136662 scopus 로고    scopus 로고
    • Ecological significance of microdiversity: Identical 16S rRNA gene sequences can be found in bacteria with highly divergent genomes and ecophysiologies
    • E. Jaspers, and J. Overmann Ecological significance of microdiversity: identical 16S rRNA gene sequences can be found in bacteria with highly divergent genomes and ecophysiologies Appl. Environ. Microbiol. 70 2004 4831 4839
    • (2004) Appl. Environ. Microbiol. , vol.70 , pp. 4831-4839
    • Jaspers, E.1    Overmann, J.2
  • 18
    • 0242411912 scopus 로고    scopus 로고
    • Nodulation and dinitrogen fixation of legume trees in a tropical freshwater swamp forest in French Guiana
    • P. Koponen, P. Nygren, A.M. Domenach, C. Le Roux, E. Saur, and J.C. Roggy Nodulation and dinitrogen fixation of legume trees in a tropical freshwater swamp forest in French Guiana J. Trop. Ecol. 19 2003 655 666
    • (2003) J. Trop. Ecol. , vol.19 , pp. 655-666
    • Koponen, P.1    Nygren, P.2    Domenach, A.M.3    Le Roux, C.4    Saur, E.5    Roggy, J.C.6
  • 19
    • 0035052315 scopus 로고    scopus 로고
    • Classification of rhizobia based on nodC and nifH gene analysis reveals a close phylogenetic relationship among Phaseolus vulgaris symbionts
    • G. Laguerre, S.M. Nour, V. Macheret, J. Sanjuan, P. Drouin, and N. Amarger Classification of rhizobia based on nodC and nifH gene analysis reveals a close phylogenetic relationship among Phaseolus vulgaris symbionts Microbiology 147 2001 981 993
    • (2001) Microbiology , vol.147 , pp. 981-993
    • Laguerre, G.1    Nour, S.M.2    MacHeret, V.3    Sanjuan, J.4    Drouin, P.5    Amarger, N.6
  • 20
    • 0030763226 scopus 로고    scopus 로고
    • Nod factors from Sinorhizobium saheli and S. teranga bv. sesbaniae are both arabinosylated and fucosylated, a structural feature specific to Sesbania rostrata symbionts
    • J. Lorquin, G. Lortet, M. Ferro, N. Mear, B. Dreyfus, J.C. Prome, and C. Boivin Nod factors from Sinorhizobium saheli and S. teranga bv. sesbaniae are both arabinosylated and fucosylated, a structural feature specific to Sesbania rostrata symbionts Mol. Plant-Microbe Interact. 10 1997 879 890
    • (1997) Mol. Plant-Microbe Interact. , vol.10 , pp. 879-890
    • Lorquin, J.1    Lortet, G.2    Ferro, M.3    Mear, N.4    Dreyfus, B.5    Prome, J.C.6    Boivin, C.7
  • 23
    • 0035400648 scopus 로고    scopus 로고
    • Gene trees and species trees are not the same Trends
    • R. Nichols Gene trees and species trees are not the same Trends Ecol. Evol. 16 2001 358 364
    • (2001) Ecol. Evol. , vol.16 , pp. 358-364
    • Nichols, R.1
  • 25
    • 9644301241 scopus 로고    scopus 로고
    • Model selection and model averaging in phylogenetics: Advantages of akaike information criterion and bayesian approaches over likelihood ratio tests
    • D. Posada, and T.R. Buckley Model selection and model averaging in phylogenetics: advantages of akaike information criterion and bayesian approaches over likelihood ratio tests Syst. Biol. 53 2004 793 808
    • (2004) Syst. Biol. , vol.53 , pp. 793-808
    • Posada, D.1    Buckley, T.R.2
  • 26
    • 0031773680 scopus 로고    scopus 로고
    • MODELTEST: Testing the model of DNA substitution
    • D. Posada, and K.A. Crandall MODELTEST: testing the model of DNA substitution Bioinformatics 14 1998 817 818
    • (1998) Bioinformatics , vol.14 , pp. 817-818
    • Posada, D.1    Crandall, K.A.2
  • 27
    • 0035923699 scopus 로고    scopus 로고
    • Evaluation of methods for detecting recombination from DNA sequences: Computer simulations
    • D. Posada, and K.A. Crandall Evaluation of methods for detecting recombination from DNA sequences: Computer simulations Proc. Natl. Acad. Sci. USA 98 2001 13757 13762
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 13757-13762
    • Posada, D.1    Crandall, K.A.2
  • 28
    • 0035989122 scopus 로고    scopus 로고
    • Contrasting nifD and ribosomal gene relationships among Mesorhizobium from Lotus oroboides in northern Mexico
    • J. Qian, and M.A. Parker Contrasting nifD and ribosomal gene relationships among Mesorhizobium from Lotus oroboides in northern Mexico Syst. Appl. Microbiol. 25 2002 68 73
    • (2002) Syst. Appl. Microbiol. , vol.25 , pp. 68-73
    • Qian, J.1    Parker, M.A.2
  • 29
    • 25144472557 scopus 로고    scopus 로고
    • Molecular typing of environmental isolates
    • A.M. Osborn BIOS Scientific Publisher Oxford, UK
    • J.L.W. Rademaker, H.J.M. Aarts, and P. Vinuesa Molecular typing of environmental isolates A.M. Osborn Molecular Microbial Ecology 2005 BIOS Scientific Publisher Oxford, UK 1 20 pp. 97-134
    • (2005) Molecular Microbial Ecology , pp. 1-20
    • Rademaker, J.L.W.1    Aarts, H.J.M.2    Vinuesa, P.3
  • 31
    • 0023375195 scopus 로고
    • The neighbor-joining method: A new method for reconstructing phylogenetic trees
    • N. Saitou, and M. Nei The neighbor-joining method: A new method for reconstructing phylogenetic trees Mol. Biol. Evol. 4 1987 406 425
    • (1987) Mol. Biol. Evol. , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 32
    • 0028793170 scopus 로고
    • Identification of breakpoints in intergenotypic recombinants of HIV type 1 by Bootscanning
    • M.O. Salminen, J.K. Carr, D.S. Burke, and F.E. McCutcham Identification of breakpoints in intergenotypic recombinants of HIV type 1 by Bootscanning AIDS Res. Hum. Retroviruses 11 1995 1423 1425
    • (1995) AIDS Res. Hum. Retroviruses , vol.11 , pp. 1423-1425
    • Salminen, M.O.1    Carr, J.K.2    Burke, D.S.3    McCutcham, F.E.4
  • 33
    • 0141590419 scopus 로고    scopus 로고
    • Changing concepts in the systematics of bacterial nitrogen-fixing legume symbionts
    • H. Sawada, L.D. Kuykendall, and J.M. Young Changing concepts in the systematics of bacterial nitrogen-fixing legume symbionts J. Gen. Appl. Microbiol. 49 2003 155 179
    • (2003) J. Gen. Appl. Microbiol. , vol.49 , pp. 155-179
    • Sawada, H.1    Kuykendall, L.D.2    Young, J.M.3
  • 34
    • 0024356449 scopus 로고    scopus 로고
    • Statistical tests for detecting gene conversion
    • S. Sawyer Statistical tests for detecting gene conversion Mol. Biol. Evol. 6 1998 526 538
    • (1998) Mol. Biol. Evol. , vol.6 , pp. 526-538
    • Sawyer, S.1
  • 35
    • 0033793521 scopus 로고    scopus 로고
    • Consequences of recombination on traditional phylogenetic analysis
    • M.H. Schierup, and J. Hein Consequences of recombination on traditional phylogenetic analysis Genetics 156 2000 879 891
    • (2000) Genetics , vol.156 , pp. 879-891
    • Schierup, M.H.1    Hein, J.2
  • 36
    • 0032766857 scopus 로고    scopus 로고
    • Multiple comparisons of log-likelihoods with applications to phylogenetic inference
    • H. Shimodaira, and M. Hasegawa Multiple comparisons of log-likelihoods with applications to phylogenetic inference Mol. Biol. Evol. 16 1999 1114 1116
    • (1999) Mol. Biol. Evol. , vol.16 , pp. 1114-1116
    • Shimodaira, H.1    Hasegawa, M.2
  • 38
    • 0037058983 scopus 로고    scopus 로고
    • Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics
    • Y. Suzuki, G.V. Glazko, and M. Nei Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics Proc. Natl. Acad. Sci. USA 99 2002 16138 16143
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 16138-16143
    • Suzuki, Y.1    Glazko, G.V.2    Nei, M.3
  • 40
    • 0035433191 scopus 로고    scopus 로고
    • Specific detection of Bradyrhizobium and Rhizobium srains colonizing rice (Oryza sativa) roots by 16S-23S ribosomal DNA intergenic spacer- targeted PCR
    • Z. Tan, T. Hurek, P. Vinuesa, P. Muller, J.K. Ladha, and B. Reinhold-Hurek Specific detection of Bradyrhizobium and Rhizobium srains colonizing rice (Oryza sativa) roots by 16S-23S ribosomal DNA intergenic spacer- targeted PCR Appl. Environ. Microbiol. 67 2001 3655 3664
    • (2001) Appl. Environ. Microbiol. , vol.67 , pp. 3655-3664
    • Tan, Z.1    Hurek, T.2    Vinuesa, P.3    Muller, P.4    Ladha, J.K.5    Reinhold-Hurek, B.6
  • 43
    • 16844373395 scopus 로고    scopus 로고
    • Bradyrhizobium canariense sp. nov., an acid-tolerant endosymbiont that nodulates endemic genistoid legumes (Papilionoideae:Genisteae) growing in the Canary Islands, along with B. japonicum bv. genistearum, Bradyrhizobium genospecies α and Bradyrhizobium genospecies β
    • P. Vinuesa, M. León-Barrios, C. Silva, A. Willems, A. Jarabo-Lorenzo, R. Pérez-Galdona, D. Werner, and E. Martínez- Romero Bradyrhizobium canariense sp. nov., an acid-tolerant endosymbiont that nodulates endemic genistoid legumes (Papilionoideae:Genisteae) growing in the Canary Islands, along with B. japonicum bv. genistearum, Bradyrhizobium genospecies α and Bradyrhizobium genospecies β Int. J. Syst. Evol. Microbiol. 55 2005 569 575
    • (2005) Int. J. Syst. Evol. Microbiol. , vol.55 , pp. 569-575
    • Vinuesa, P.1    León-Barrios, M.2    Silva, C.3    Willems, A.4    Jarabo-Lorenzo, A.5    Pérez-Galdona, R.6    Werner, D.7    Martínez-Romero, E.8
  • 44
    • 0031746448 scopus 로고    scopus 로고
    • Genotypic characterization of Bradyrhizobium strains nodulating endemic woody legumes of the Canary Islands by PCR-restriction fragment length polymorphism analysis of genes encoding 16S rRNA (16S rDNA) and 16S-23S rDNA intergenic spacers, repetitive extragenic palindromic PCR genomic fingerprinting and partial 16S rDNA sequencing
    • P. Vinuesa, J.L.W. Rademaker, F.J. de Bruijn, and D. Werner Genotypic characterization of Bradyrhizobium strains nodulating endemic woody legumes of the Canary Islands by PCR-restriction fragment length polymorphism analysis of genes encoding 16S rRNA (16S rDNA) and 16S-23S rDNA intergenic spacers, repetitive extragenic palindromic PCR genomic fingerprinting and partial 16S rDNA sequencing Appl. Environ. Microbiol. 64 1998 2096 2104
    • (1998) Appl. Environ. Microbiol. , vol.64 , pp. 2096-2104
    • Vinuesa, P.1    Rademaker, J.L.W.2    De Bruijn, F.J.3    Werner, D.4
  • 45
    • 9944241194 scopus 로고    scopus 로고
    • Species delineation and biogeography of symbiotic bacteria associated with cultivated and wild legumes
    • D. Werner Springer Berlin
    • P. Vinuesa, and C. Silva Species delineation and biogeography of symbiotic bacteria associated with cultivated and wild legumes D. Werner Biological Resources and Migration 2004 Springer Berlin 143 161
    • (2004) Biological Resources and Migration , pp. 143-161
    • Vinuesa, P.1    Silva, C.2
  • 46
    • 9944222667 scopus 로고    scopus 로고
    • Population genetics and phylogenetic inference in bacterial molecular systematics: The roles of migration and recombination in Bradyrhizobium species cohesion and delineation
    • P. Vinuesa, C. Silva, D. Werner, and E. Martínez-Romero Population genetics and phylogenetic inference in bacterial molecular systematics: the roles of migration and recombination in Bradyrhizobium species cohesion and delineation Mol. Phylogenet. Evol. 34 2005 29 54
    • (2005) Mol. Phylogenet. Evol. , vol.34 , pp. 29-54
    • Vinuesa, P.1    Silva, C.2    Werner, D.3    Martínez-Romero, E.4
  • 48
    • 0033813533 scopus 로고    scopus 로고
    • Sesbania herbacea-Rhizobium huautlense nodulation in flooded soils and comparative characterization of S. herbacea-nodulating rhizobia in different environments
    • E.T. Wang, and E. Martinez-Romero Sesbania herbacea-Rhizobium huautlense nodulation in flooded soils and comparative characterization of S. herbacea-nodulating rhizobia in different environments Microb. Ecol. 40 2000 25 32
    • (2000) Microb. Ecol. , vol.40 , pp. 25-32
    • Wang, E.T.1    Martinez-Romero, E.2
  • 49
    • 0031853141 scopus 로고    scopus 로고
    • Rhizobium huautlense sp. nov., a symbiont of Sesbania herbacea that has a close phylogenetic relationship with Rhizobium galegae
    • E.T. Wang, P. van Berkum, D. Beyene, X.H. Sui, O. Dorado, W.X. Chen, and E. Martinez-Romero Rhizobium huautlense sp. nov., a symbiont of Sesbania herbacea that has a close phylogenetic relationship with Rhizobium galegae Int. J. Syst. Bacteriol. 48 1998 687 699
    • (1998) Int. J. Syst. Bacteriol. , vol.48 , pp. 687-699
    • Wang, E.T.1    Van Berkum, P.2    Beyene, D.3    Sui, X.H.4    Dorado, O.5    Chen, W.X.6    Martinez-Romero, E.7
  • 50
    • 0033709697 scopus 로고    scopus 로고
    • Comparative sequence analyses reveal frequent occurrence of short segments containing an abnormally high number of non-random base variations in bacterial rRNA genes
    • Y. Wang, and Z. Zhang Comparative sequence analyses reveal frequent occurrence of short segments containing an abnormally high number of non-random base variations in bacterial rRNA genes Microbiology 146 2000 2845 2854
    • (2000) Microbiology , vol.146 , pp. 2845-2854
    • Wang, Y.1    Zhang, Z.2
  • 51
    • 8144229491 scopus 로고    scopus 로고
    • Unexpectedly diverse Mesorhizobium strains and Rhizobium leguminosarum nodulate native legume genera of New Zealand, while introduced legume weeds are nodulated by Bradyrhizobium species
    • B.S. Weir, S.J. Turner, W.B. Silvester, D.C. Park, and J.M. Young Unexpectedly diverse Mesorhizobium strains and Rhizobium leguminosarum nodulate native legume genera of New Zealand, while introduced legume weeds are nodulated by Bradyrhizobium species Appl. Environ. Microbiol. 70 2004 5980 5987
    • (2004) Appl. Environ. Microbiol. , vol.70 , pp. 5980-5987
    • Weir, B.S.1    Turner, S.J.2    Silvester, W.B.3    Park, D.C.4    Young, J.M.5
  • 53
    • 0034848170 scopus 로고    scopus 로고
    • DAMBE: Software package for data analysis in molecular biology and evolution
    • X. Xia, and Z. Xie DAMBE: Software package for data analysis in molecular biology and evolution J. Hered. 92 2001 371 373
    • (2001) J. Hered. , vol.92 , pp. 371-373
    • Xia, X.1    Xie, Z.2
  • 54
    • 0030451420 scopus 로고    scopus 로고
    • Among-site rate variation and its impact on phylogenetic analyses
    • Z. Yang Among-site rate variation and its impact on phylogenetic analyses Trends Ecol. Evol. 11 1996 367 372
    • (1996) Trends Ecol. Evol. , vol.11 , pp. 367-372
    • Yang, Z.1
  • 55
    • 0035151030 scopus 로고    scopus 로고
    • A revision of Rhizobium Frank 1889, with an emended description of the genus, and the inclusion of all species of Agrobacterium Conn 1942 and Allorhizobium undicola de Lajudie et al. 1998 as new combinations: Rhizobium radiobacter, R. rhizogenes, R. rubi, R. undicola and R. vitis
    • J.M. Young, L.D. Kuykendall, E. Martinez-Romero, A. Kerr, and H. Sawada A revision of Rhizobium Frank 1889, with an emended description of the genus, and the inclusion of all species of Agrobacterium Conn 1942 and Allorhizobium undicola de Lajudie et al. 1998 as new combinations: Rhizobium radiobacter, R. rhizogenes, R. rubi, R. undicola and R. vitis Int. J. Syst. Evol. Microbiol. 51 2001 89 103
    • (2001) Int. J. Syst. Evol. Microbiol. , vol.51 , pp. 89-103
    • Young, J.M.1    Kuykendall, L.D.2    Martinez-Romero, E.3    Kerr, A.4    Sawada, H.5
  • 56
    • 4444380607 scopus 로고    scopus 로고
    • Diversity of 16S rDNA sequences of Rhizobium spp. implications for species determinations
    • J.M. Young, D.C. Park, and B.S. Weir Diversity of 16S rDNA sequences of Rhizobium spp. implications for species determinations FEMS Microbiol. Lett. 238 2004 125 131
    • (2004) FEMS Microbiol. Lett. , vol.238 , pp. 125-131
    • Young, J.M.1    Park, D.C.2    Weir, B.S.3


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