C. Stover, Complete genome sequence of Pseudomonas aeruginosa PA01, an opportunistic pathogen, Nature, vol.406, pp.959-964, 2000.

I. Paulsen, Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5, Nature Biotechnology, vol.65, issue.7, pp.873-878, 2005.
DOI : 10.1093/nar/30.11.2478

K. Nelson, Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440, Environmental Microbiology, vol.5, issue.7, pp.799-808, 2002.
DOI : 10.1046/j.1462-2920.2003.00480.x

H. Feil, Comparison of the complete genome sequences of Pseudomonas syringae pv. syringae B728a and pv. tomato DC3000, Proceedings of the National Academy of Sciences, vol.102, issue.31, pp.11064-11069, 2005.
DOI : 10.1073/pnas.0504930102

N. Vodovar, Complete genome sequence of the entomopathogenic and metabolically versatile soil bacterium Pseudomonas entomophila, Nature Biotechnology, vol.172, issue.6, pp.673-679, 2006.
DOI : 10.1038/nbt1212
URL : https://hal.archives-ouvertes.fr/hal-00133119

J. Lalucat, A. Bennasar, R. Bosch, E. Garcia-valdes, and N. Palleroni, Biology of Pseudomonas stutzeri, Microbiology and Molecular Biology Reviews, vol.70, issue.2, pp.510-547, 2006.
DOI : 10.1128/MMBR.00047-05

Y. Qiu, S. Zhou, X. Mo, C. You, and D. Wang, Investigation of dinitrogen fixation bacteria isolated from rice rhizosphere, Chinese Sc BullKexue Tongbao), vol.26, pp.383-384, 1981.

C. You, M. Lin, X. Fang, and W. Song, Attachment of Alcaligenes to rice roots, Soil Biology and Biochemistry, vol.27, issue.4-5, pp.463-466, 1995.
DOI : 10.1016/0038-0717(95)98620-4

H. Vermeiren, The Rice Inoculant Strain Alcaligenes faecalis A15 is a Nitrogen-fixing Pseudomonas stutzeri, Systematic and Applied Microbiology, vol.22, issue.2, pp.215-224, 1999.
DOI : 10.1016/S0723-2020(99)80068-X

K. Hatayama, S. Kawai, H. Shoun, Y. Ueda, and A. Nakamura, Pseudomonas azotifigens sp. nov., a novel nitrogen-fixing bacterium isolated from a compost pile, INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, vol.55, issue.4, pp.1539-1544, 2005.
DOI : 10.1099/ijs.0.63586-0

N. Desnoues, Nitrogen fixation genetics and regulation in a Pseudomonas stutzeri strain associated with rice, Microbiology, vol.149, issue.8, pp.2251-2262, 2003.
DOI : 10.1099/mic.0.26270-0
URL : https://hal.archives-ouvertes.fr/hal-00135698

C. Elmerich and W. Newton, Associative and Endophytic Nitrogen fixing Bacteria and Cyanobacterial Associations?Introduction The Nether- lands), 2007.

A. Krause, Complete genome of the mutualistic, N2-fixing grass endophyte Azoarcus sp. strain BH72, Nature Biotechnology, vol.357, issue.11, pp.1385-1391, 2006.
DOI : 10.1038/nbt1243

H. Rediers, Development and Application of a dapB-Based In Vivo Expression Technology System To Study Colonization of Rice by the Endophytic Nitrogen-Fixing Bacterium Pseudomonas stutzeri A15, Applied and Environmental Microbiology, vol.69, issue.11, pp.6864-6874, 2003.
DOI : 10.1128/AEM.69.11.6864-6874.2003

C. You and F. Zhou, Non-nodular endorhizospheric nitrogen fixation in wetland rice, Canadian Journal of Microbiology, vol.35, issue.3, pp.403-408, 1989.
DOI : 10.1139/m89-062

U. Dobrindt, B. Hochhut, U. Hentschel, and J. Hacker, Genomic islands in pathogenic and environmental microorganisms, Nature Reviews Microbiology, vol.31, issue.5, pp.414-424, 2004.
DOI : 10.1006/plas.1997.1280

J. Young, The genome of Rhizobium leguminosarum has recognizable core and accessory components, Genome Biology, vol.7, issue.4, p.34, 2006.
DOI : 10.1186/gb-2006-7-4-r34

C. Baar, Complete genome sequence and analysis of Wolinella succinogenes, Proceedings of the National Academy of Sciences, vol.100, issue.20, pp.11690-11695, 2003.
DOI : 10.1073/pnas.1932838100

W. Klipp, B. Masepohl, J. Gallon, and W. Newton, Genetics and Regulation of Nitrogen Fixation in Free-Living Bacteria (Kluwer Academic, 2004.

M. Jacobson, Physical and genetic map of the major nif gene cluster from Azotobacter vinelandii., Journal of Bacteriology, vol.171, issue.2, pp.1017-1027, 1989.
DOI : 10.1128/jb.171.2.1017-1027.1989

W. Arnold, A. Rump, W. Klipp, U. Priefer, and A. Puhler, Nucleotide sequence of a 24,206-base-pair DNA fragment carrying the entire nitrogen fixation gene cluster of Klebsiella pneumoniae, Journal of Molecular Biology, vol.203, issue.3, pp.715-738, 1988.
DOI : 10.1016/0022-2836(88)90205-7

I. Martínez-argudo, R. Little, N. Shearer, P. Johnson, and R. Dixon, The NifL-NifA System: a Multidomain Transcriptional Regulatory Complex That Integrates Environmental Signals, Journal of Bacteriology, vol.186, issue.3, pp.601-610, 2004.
DOI : 10.1128/JB.186.3.601-610.2004

Z. Xie, Interaction between NifL and NifA in the nitrogen-fixing Pseudomonas stutzeri A1501, Microbiology, vol.152, issue.12, pp.3535-3542, 2006.
DOI : 10.1099/mic.0.29171-0

H. Jeong and Y. Jouanneau, Enhanced Nitrogenase Activity in Strains of Rhodobacter capsulatus That Overexpress the rnf Genes, Journal of Bacteriology, vol.182, issue.5, pp.1208-1214, 2000.
DOI : 10.1128/JB.182.5.1208-1214.2000

B. Lugtenberg and L. Dekkers, What makes Pseudomonas bacteria rhizosphere competent?, Environmental Microbiology, vol.196, issue.1, pp.9-13, 1999.
DOI : 10.1146/annurev.phyto.25.1.339

J. Neilands, Siderophores: Structure and Function of Microbial Iron Transport Compounds, Journal of Biological Chemistry, vol.270, issue.45, pp.26723-26726, 1995.
DOI : 10.1074/jbc.270.45.26723

J. Jimenez, B. Minambres, J. Garcia, and E. Diaz, Genomic analysis of the aromatic catabolic pathways from Pseudomonas putida KT2440, Environmental Microbiology, vol.143, issue.12, pp.824-841, 2002.
DOI : 10.1093/nar/28.21.4317

J. Xi, Hyperproduction of polyesters consisting of medium-chain-length hydroxyalkanoate monomers by strain Pseudomonas stutzeri 1317, Antonie van Leeuwenhoek, vol.78, issue.1, pp.43-49, 2000.
DOI : 10.1023/A:1002714102347

A. Pohlmann, Genome sequence of the bioplastic-producing ???Knallgas??? bacterium Ralstonia eutropha H16, Nature Biotechnology, vol.3, issue.10, pp.1257-1262, 2006.
DOI : 10.1186/1471-2105-5-198

W. Zumft, Cell biology and molecular basis of denitrification, Microbiol Mol Biol Rev, vol.61, pp.533-616, 1997.

H. Rediers, J. Vanderleyden, D. Mot, and R. , Nitrate respiration in Pseudomonas stutzeri A15 and its involvement in rice and wheat root colonization, Microbiological Research, vol.164, issue.4, 2007.
DOI : 10.1016/j.micres.2007.03.003

J. Wood, Osmosensing by Bacteria, Science's STKE, vol.2006, issue.357, pp.230-262, 1999.
DOI : 10.1126/stke.3572006pe43

S. Vuilleumier and M. Pagni, The elusive roles of bacterial glutathione S-transferases: New lessons from genomes, Appl Microbiol Biotechnol, vol.58, pp.138-146, 2002.

J. Sikorski, N. Teschner, and W. Wackernagel, Highly Different Levels of Natural Transformation Are Associated with Genomic Subgroups within a Local Population of Pseudomonas stutzeri from Soil, Applied and Environmental Microbiology, vol.68, issue.2, pp.865-873, 2002.
DOI : 10.1128/AEM.68.2.865-873.2002

C. Chitnis and D. Ohman, Genetic analysis of the alginate biosynthetic gene cluster of Pseudomonas aeruginosa shows evidence of an operonic structure, Molecular Microbiology, vol.266, issue.3, pp.583-593, 1993.
DOI : 10.1016/0378-1119(89)90136-4

B. Glick, Modulation of plant ethylene levels by the bacterial enzyme ACC deaminase, FEMS Microbiology Letters, vol.251, issue.1, pp.1-7, 2005.
DOI : 10.1016/j.femsle.2005.07.030

M. Ginard, J. Lalucat, B. Tummler, and U. Romling, Genome Organization of Pseudomonas stutzeri and Resulting Taxonomic and Evolutionary Considerations, International Journal of Systematic Bacteriology, vol.47, issue.1, pp.132-143, 1997.
DOI : 10.1099/00207713-47-1-132

M. Matilla, Genomic analysis reveals the major driving forces of bacterial life in the rhizosphere, Genome Biology, vol.8, issue.9, p.179, 2007.
DOI : 10.1186/gb-2007-8-9-r179

R. Fani, R. Gallo, and P. Lio, Molecular Evolution of Nitrogen Fixation: The Evolutionary History of the nifD, nifK, nifE, and nifN Genes, Journal of Molecular Evolution, vol.51, issue.1, pp.1-11, 2000.
DOI : 10.1007/s002390010061

J. Raymond, J. Siefert, C. Staples, and R. Blankenship, The Natural History of Nitrogen Fixation, Molecular Biology and Evolution, vol.21, issue.3, pp.541-554, 2004.
DOI : 10.1093/molbev/msh047

K. Kechris, J. Lin, P. Bickel, and A. Glazer, Quantitative exploration of the occurrence of lateral gene transfer by using nitrogen fixation genes as a case study, Proceedings of the National Academy of Sciences, vol.103, issue.25, pp.9584-9589, 2006.
DOI : 10.1073/pnas.0603534103

Q. Jin, Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157, Nucleic Acids Research, vol.30, issue.20, pp.4432-4441, 2002.
DOI : 10.1093/nar/gkf566