A. C. Allan and R. Fluhr, Two distinct sources of elicited reactive oxygen species in tobacco epidermal cells, Plant Cell, vol.9, pp.1559-1572, 1997.

C. Amadou, G. Pascal, S. Mangenot, M. Glew, C. Bontemps et al., Genome sequence of the beta-rhizobium Cupriavidus taiwanensis and comparative genomics of rhizobia, Genome Res, vol.18, pp.1472-1483, 2008.

J. E. Barrick and R. E. Lenski, Genome dynamics during experimental evolution, Nat. Rev. Genet, vol.14, pp.827-839, 2013.

J. E. Barrick, D. S. Yu, S. H. Yoon, H. Jeong, T. K. Oh et al., Genome evolution and adaptation in a long-term experiment with Escherichia coli, Nature, vol.461, pp.1243-1274, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00435992

A. Bensadoun and D. Weinstein, Assay of protein in presence of interfering materials, Anal. Biochem, vol.70, pp.241-250, 1976.

R. L. Berendsen, C. M. Pieterse, and P. Bakker, The rhizosphere microbiome and plant health, Trends Plant Sci, vol.17, pp.478-486, 2012.

C. A. Boucher, P. A. Barberis, A. P. Trigalet, and D. A. Demery, Transposon mutagenesis of Pseudomonas solanacearum-Isolation of TN5-induced avirulent mutants, J. Gen. Microbiol, vol.131, pp.2449-2457, 1985.
URL : https://hal.archives-ouvertes.fr/hal-02728459

A. Buckling, R. C. Maclean, M. A. Brockhurst, C. , and N. , The Beagle in a bottle, Nature, vol.457, pp.824-829, 2009.

D. Bulgarelli, M. Rott, K. Schlaeppi, E. V. Van-themaat, N. Ahmadinejad et al., Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota, Nature, vol.488, pp.91-95, 2012.

C. Capela, S. Guan, and C. Masson-boivin, Diversity and Evolution of Nitrogen-Fixing Legume Symbionts. F. de Bruijn, 2013.

W. M. Chen, L. Moulin, C. Bontemps, P. Vandamme, G. Bena et al., Legume symbiotic nitrogen fixation by beta-proteobacteria is widespread in nature, J. Bacteriol, vol.185, pp.7266-7272, 2003.

L. Deslandes, F. Pileur, L. Liaubet, S. Camut, C. Can et al., Genetic characterization of RRS1, a recessive locus in Arabidopsis thaliana that confers resistance to the bacterial soilborne pathogen Ralstonia solanacearum, Mol. Plant-Microbe Interact, vol.11, pp.659-667, 1998.
URL : https://hal.archives-ouvertes.fr/hal-02689557

R. Dixon and D. Kahn, Genetic regulation of biological nitrogen fixation, Nat. Rev. Microbiol, vol.2, pp.621-631, 2004.
URL : https://hal.archives-ouvertes.fr/hal-01213169

G. N. Elliott, J. H. Chou, W. M. Chen, G. V. Bloemberg, C. Bontemps et al., Burkholderia spp. are the most competitive symbionts of Mimosa, particularly under N-limited conditions, Environ. Microbiol, vol.11, pp.762-778, 2009.
URL : https://hal.archives-ouvertes.fr/hal-01655717

G. Felix, J. D. Duran, S. Volko, and T. Boller, Plants have a sensitive perception system for the most conserved domain of bacterial flagellin, Plant J, vol.18, pp.265-276, 1999.

D. X. Feng, C. Tasset, M. Hanemian, X. Barlet, J. Hu et al., Biological control of bacterial wilt in Arabidopsis thaliana involves abscissic acid signalling, New Phytol, vol.194, pp.1035-1045, 2012.
URL : https://hal.archives-ouvertes.fr/hal-02650167

H. Fones and G. M. Preston, Reactive oxygen and oxidative stress tolerance in plant pathogenic Pseudomonas, FEMS (Fed. Eur. Microbiol. Soc.) Microbiol. Lett, vol.327, pp.1-8, 2012.

F. Galibert, T. M. Finan, S. R. Long, A. Puhler, P. Abola et al., The composite genome of the legume symbiont Sinorhizobium meliloti, vol.293, pp.668-672, 2001.
URL : https://hal.archives-ouvertes.fr/hal-01213732

H. S. Gehlot, N. Tak, M. Kaushik, S. Mitra, W. M. Chen et al., An invasive Mimosa in India does not adopt the symbiont of its native relatives, Ann. Bot, vol.112, pp.179-96, 2013.

K. E. Gibson, H. Kobayashi, and G. C. Walker, Molecular determinants of a symbiotic chronic infection, Annu. Rev. Genet, vol.42, pp.413-441, 2008.

S. H. Guan, C. Gris, S. Cruveiller, C. Pouzet, L. Tasse et al., Experimental evolution of nodule intracellular infection in legume symbionts, ISME J, vol.7, pp.1367-1377, 2013.
URL : https://hal.archives-ouvertes.fr/hal-02646600

P. Gyaneshwar, A. M. Hirsch, L. Moulin, W. M. Chen, G. N. Elliott et al., Legume-nodulating betaproteobacteria: Diversity, host range, and future prospects, vol.24, pp.1276-1288, 2011.
URL : https://hal.archives-ouvertes.fr/hal-01655720

A. Hirsch, M. Lum, and J. Downie, What makes the rhizobia-legume symbiosis so special?, Plant Physiol, vol.127, pp.1484-1492, 2001.

S. Ivanov, E. Fedorova, and T. Bisseling, Intracellular plant microbe associations: Secretory pathways and the formation of perimicrobial compartments, Curr. Opin. Plant Biol, vol.13, pp.372-377, 2010.

J. D. Jones and J. L. Dangl, The plant immune system, Nature, vol.444, pp.323-329, 2006.

K. M. Jones, H. Kobayashi, B. W. Davies, M. E. Taga, and G. C. Walker, How rhizobial symbionts invade plants: The Sinorhizobium-Medicago model, Nat. Rev. Microbiol, vol.5, pp.619-633, 2007.

E. Kiers, R. Rousseau, S. West, and R. Denison, Host sanctions and the legume-rhizobium mutualism, Nature, vol.425, pp.78-81, 2003.

C. Lamb and R. A. Dixon, The oxidative burst in plant disease resistance, Annu. Rev. Plant Physiol. Plant Mol. Biol, vol.48, pp.251-275, 1997.

L. Gac, M. Cooper, T. F. Cruveiller, S. Edigue, C. M. Schneider et al., Evolutionary history and genetic parallelism affect correlated responses to evolution, Mol. Ecol, vol.22, pp.3292-3303, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00961479

R. E. Lenski and M. Travisano, Dynamics of adaptation and diversification-A 10,000 generation experiment with bacterial populations, Proc. Natl. Acad. Sci. U.S.A, vol.91, pp.6808-6814, 1994.

D. S. Lundberg, S. L. Lebeis, S. H. Paredes, S. Yourstone, J. Gehring et al., Defining the core Arabidopsis thaliana root microbiome, Nature, vol.488, pp.86-90, 2012.

M. Marchetti, D. Capela, M. Glew, S. Cruveiller, B. Chane-woon-ming et al., Experimental evolution of a plant pathogen into a legume symbiont, PLoS Biol, vol.8, p.1000280, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00595766

M. Marchetti, O. Catrice, J. Batut, and C. Masson-boivin, Cupriavidus taiwanensis bacteroids in Mimosa pudica indeterminate nodules are not terminally differentiated, Appl. Environ. Microbiol, vol.77, pp.2161-2164, 2011.
URL : https://hal.archives-ouvertes.fr/hal-02644027

C. Masson-boivin, E. Giraud, X. Perret, and J. Batut, Establishing nitrogen-fixing symbiosis with legumes: How many rhizobium recipes?, Trends Microbiol, vol.17, pp.458-466, 2009.

A. Mithofer, Suppression of plant defence in rhizobia-legume symbiosis, Trends Plant Sci, vol.7, pp.440-444, 2002.

S. Moreau, M. Verdenaud, T. Ott, S. Letort, F. De-billy et al., Transcription reprogramming during root nodule development in Medicago truncatula, PLoS One, vol.6, p.16463, 2011.
URL : https://hal.archives-ouvertes.fr/hal-02647172

L. Moulin, A. Munive, B. Dreyfus, and C. Boivin-masson, Nodulation of legumes by members of the beta-subclass of Proteobacteria, Nature, vol.411, pp.948-950, 2001.

V. Oke and S. R. Long, Bacteroid formation in the Rhizobium-Legume symbiosis, Curr. Opin. Microbiol, vol.2, pp.641-646, 1999.

G. E. Oldroyd and J. M. Downie, Coordinating nodule morphogenesis with rhizobial infection in legumes, Annu. Rev. Plant Biol, vol.59, pp.519-546, 2008.

R. Oono, C. G. Anderson, and R. F. Denison, Failure to fix nitrogen by non-reproductive symbiotic rhizobia triggers host sanctions that reduce fitness of their reproductive clonemates, Proc. Royal Soc. B Biol. Sci, vol.278, pp.2698-2703, 2011.

J. P. Ramsay, J. T. Sullivan, N. Jambari, C. A. Ortori, S. Heeb et al., A LuxRI-family regulatory system controls excision and transfer of the Mesorhizobium loti strain R7A symbiosis island by activating expression of two conserved hypothetical genes, Mol. Microbiol, vol.73, pp.1141-1155, 2009.

P. Remigi, M. Anisimova, A. Guidot, S. Genin, and N. Peeters, Functional diversification of the GALA type III effector family contributes to Ralstonia solanacearum adaptation on different plant hosts, New Phytol, vol.192, pp.976-987, 2011.
URL : https://hal.archives-ouvertes.fr/hal-02651823

J. N. Rodriguez-lopez, D. J. Lowe, J. Hernandez-ruiz, A. N. Hiner, F. Garcia-canovas et al., Mechanism of reaction of hydrogen peroxide with horseradish peroxidase: Identification of intermediates in the catalytic cycle, J. Am. Chem. Soc, vol.123, pp.11838-11847, 2001.

M. Rogel, I. Hernández-lucas, L. Kuykendall, D. Balkwill, and E. Martinez-romero, Nitrogen-fixing nodules with Ensifer adhaerens harboring Rhizobium tropici symbiotic plasmids, Appl. Environ. Microbiol, vol.67, pp.3264-3268, 2001.

K. Saeki, Rhizobial measures to evade host defense strategies and endogenous threats to persistent symbiotic nitrogen fixation: A focus on two legume-rhizobium model systems, Cell. Mol. Life Sci, vol.68, pp.1327-1339, 2011.

J. I. Sprent, Nodulation in Legumes, Royal Botanic Gardens, 2001.

J. I. Sprent, Evolving ideas of legume evolution and diversity: A taxonomic perspective on the occurrence of nodulation, New Phytol, vol.174, pp.11-25, 2007.

J. Sullivan, R. , and C. , Evolution of rhizobia by acquisition of a 500-kb symbiosis island that integrates into a phe-tRNA gene, Proc, 1998.

, Natl. Acad. Sci. U.S.A, vol.95, pp.5145-5149

A. Sy, E. Giraud, P. Jourand, N. Garcia, A. Willems et al., Methylotrophic Methylobacterium bacteria nodulate and fix nitrogen in symbiosis with legumes, J. Bacteriol, vol.183, pp.214-220, 2001.

J. J. Terpolilli, G. A. Hood, and P. S. Poole, What determines the efficiency of N 2 -fixing rhizobium-legume symbioses?, Adv. Microb. Physiol, vol.60, pp.325-389, 2012.

C. F. Tian, Y. J. Zhou, Y. M. Zhang, Q. Q. Li, Y. Z. Zhang et al., Comparative genomics of rhizobia nodulating soybean suggests extensive recruitment of lineage-specific genes in adaptations, Proc. Natl. Acad. Sci. U.S.A, vol.109, pp.8629-8634, 2012.

A. C. Timmers, E. Soupene, M. C. Auriac, F. De-billy, J. Vasse et al., Saprophytic intracellular rhizobia in alfalfa nodules, Mol. Plant-Microbe Interact, vol.13, pp.1204-1213, 2000.

M. Udvardi and P. S. Poole, Transport and metabolism in legumerhizobia symbioses, Annu. Rev. Plant Biol, vol.64, pp.781-805, 2013.

M. Virta, S. Lineri, P. Kankaapaa, M. Karp, K. Peltonen et al., Determination of complement-mediated killing of bacteria by viability staining and bioluminescence, Appl. Environ. Microbiol, vol.64, pp.515-519, 1998.

C. Zamioudis and C. M. Pieterse, Modulation of host immunity by beneficial microbes, Mol. Plant-Microbe Interact, vol.25, pp.139-150, 2012.