Y. Bashan, G. Holguin, and L. E. De-bashan, Azospirillum-plant relationships: Physiological, molecular, agricultural, and environmental advances, Can. J. Microbiol, vol.521, p.577, 2004.

O. Steenhoudt and J. Vanderleyden, Azospirillum, a free-living nitrogen-fixing bacterium closely associated with grasses: Genetic, biochemical and ecological aspects, FEMS Microbiol. Rev, vol.487, p.506, 2000.

L. Miché, M. L. Bouillant, R. Rohr, G. Sallé, and R. Bally, Physiological and cytological studies on the inhibition of Striga seed germination by the plant growth-promoting bacterium Azospirillum brasilense, Eur. J. Plant Pathol, vol.106, p.351, 2000.

Y. Bashan and L. E. De-bashan, Protection of tomato seedlings against infection by Pseudomonas syringae pv. tomato by using the plant growth-promoting bacterium Azospirillum brasilense, Appl. Environ. Microbiol, p.68, 2002.

M. Yasuda, T. Isawa, S. Shinozaki, K. Minamisawa, and H. Nakashita, Effects of colonization of a bacterial endophyte, Azospirillum sp. B510, on disease resistance in rice, Biosci. Biotechnol. Biochem, p.73, 2009.

S. A. Covarrubias, L. E. De-bashan, M. Moreno, and Y. Bashan, Alginate beads provide a beneficial physical barrier against native microorganisms in wastewater treated with immobilized bacteria and microalgae, Appl. Environ. Microbiol, p.93, 2012.

S. Fibach-paldi, S. Burdman, and Y. Okon, Key physiological properties contributing to rhizosphere adaptation and plant growth promotion abilities of Azospirillum brasilense, FEMS Microbiol. Lett, vol.99, p.108, 2012.

J. Caballero-mellado, L. Lopez-reyes, and R. Bustillos-cristales, Presence of 16S rRNA genes in multiple replicons in Azospirillum brasilense, FEMS Microbiol. Lett, vol.283, p.288, 1999.

C. C. Martin-didonet, L. S. Chubatsu, E. M. Souza, M. Kleina, F. G. Rego et al., Genome structure of the genus Azospirillum, J. Bacteriol, vol.4113, p.4116, 2000.

T. Kaneko, K. Minamisawa, T. Isawa, H. Nakatsukasa, H. Mitsui et al., Complete genomic structure of the cultivated rice endophyte Azospirillum sp. B510, DNA Res, vol.37, p.50, 2010.

F. H. Sant'anna, L. G. Almeida, R. Cecagno, L. A. Reolon, F. M. Siqueira et al., Genomic insights into the versatility of the plant growth-promoting bacterium Azospirillum amazonense, BMC Genomics, vol.12, p.409, 2011.

F. Wisniewski-dyé, K. Borziak, G. Khalsa-moyers, G. Alexandre, L. O. Sukharnikov et al., Azospirillum genomes reveal transition of bacteria from aquatic to terrestrial environments, PLoS Genet, 2011.

P. W. Harrison, R. P. Lower, N. K. Kim, and J. P. Young, Introducing the bacterial 'chromid': not a chromosome, not a plasmid, Trends Microbiol, vol.141, p.148, 2010.

L. Vial, C. Lavire, P. Mavingui, D. Blaha, J. Haurat et al., Phase variation and genomic architecture changes in Azospirillum, J. Bacteriol, vol.5364, p.5373, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00112563

M. Boyer, J. Haurat, S. Samain, B. Segurens, F. Gavory et al., Bacteriophage prevalence in the genus Azospirillum and analysis of the first genome sequence of an Azospirillum brasilense integrative phage, Appl. Environ. Microbiol, vol.861, p.874, 2008.
URL : https://hal.archives-ouvertes.fr/halsde-00259504

J. Garcia-olivares, V. Moreno-medina, I. Rodriguez-luna, A. Mendoza-herrera, and N. Mayek-pérez, Efecto de cepas de Azospirillum brasilense en el crecimiento y rendimiento de grano del maiz, Rev. Fitotec. Mex, vol.305, p.310, 2007.

A. Mendoza-herrera, M. A. Cruz-hernandez, and C. Jacques-hernandez, Bacterias que incrementan la producción agrícola y procedimientos para aislar y producir con ellas un biofertilizante y para aplicarlo sobre cultivos y suelos similares a su origen, Instituto Politechnico Nacional, p.2005008322, 2005.

E. Acosta-cruz, F. Wisniewski-dyé, Z. Rouy, V. Barbe, M. Valdes et al., Insights into the 1.59-Mbp largest plasmid of Azospirillum brasilense CBG497, Arch. Microbiol, vol.725, p.736, 2012.
URL : https://hal.archives-ouvertes.fr/hal-02532814

L. C. Crossman, S. Castillo-ramirez, C. Mcannula, L. Lozano, G. S. Vernikos et al., A common genomic framework for a diverse assembly of plasmids in the symbiotic nitrogen fixing bacteria, PLoS One, vol.3, p.2567, 2008.

A. Elbeltagy, K. Nishioka, T. Sato, H. Suzuki, B. Ye et al., Endophytic colonization and in planta nitrogen fixation by a Herbaspirillum sp isolated from wild rice species, Appl. Environ. Microbiol, vol.5285, p.5293, 2001.

J. Goris, K. T. Konstantinidis, J. A. Klappenbach, T. Coenye, P. Vandamme et al., DNA-DNA hybridization values and their relationship to whole-genome sequence similarities, Int. J. Syst. Evol. Microbiol, vol.57, p.91, 2007.

A. J. Enright, S. Van-dongen, and C. A. Ouzounis, An efficient algorithm for large-scale detection of protein families, Nucleic Acids Res, 2002.

M. Richter, M. Kube, D. A. Bazylinski, T. Lombardot, F. O. Glockner et al., Comparative genome analysis of four magnetotactic bacteria reveals a complex set of group-specific genes implicated in magnetosome biomineralization and function, J. Bacteriol, vol.4899, p.4910, 2007.

T. Lefébure and M. J. Stanhope, Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition, Genome Biol, vol.8, p.71, 2007.

O. Choi, J. Kim, J. G. Kim, Y. Jeong, J. S. Moon et al., Pyrroloquinoline quinone is a plant growth promotion factor produced by Pseudomonas fluorescens B16, Plant Physiol, vol.657, p.668, 2008.

S. Burdman, E. Jurkevitch, M. E. Soria-diaz, A. M. Serrano, and Y. Okon, Extracellular polysaccharide composition of Azospirillum brasilense and its relation with cell aggregation, FEMS Microbiol. Lett, vol.259, p.264, 2000.

I. M. Skvortsov and V. V. Ignatov, Extracellular polysaccharides and polysaccharide-containing biopolymers from Azospirillum species: Properties and the possible role in interaction with plant roots, FEMS Microbiol. Lett, vol.223, p.229, 1998.

A. Lerner, S. Castro-sowinski, A. Valverde, H. Lerner, R. Dror et al., The Azospirillum brasilense Sp7 noeJ and noeL genes are involved in extracellular polysaccharide biosynthesis, Microbiology, vol.4058, p.4068, 2009.

P. Detroch and J. Vanderleyden, Surface properties and motility of Rhizobium and Azospirillum in relation to plant root attachment, Microb. Ecol, vol.149, p.169, 1996.

M. Tomich, P. J. Planet, and D. H. Figurski, The tad locus: Postcards from the widespread colonization island, Nat. Rev. Microbiol, vol.5, p.375, 2007.

D. N. Rodriguez-navarro, M. S. Dardanelli, and J. E. Ruiz-sainz, Attachment of bacteria to the roots of higher plants, FEMS Microbiol. Lett, vol.127, p.136, 2007.

B. Assmus, P. Hutzler, G. Kirchhof, R. Amann, J. R. Lawrence et al., In-situ localization of Azospirillum brasilense in the rhizosphere of wheat with fluorescently labeled, ribosomal-RNA-targeted oligonucleotide probes and scanning confocal laser microscopy, Appl. Environ. Microbiol, p.61, 1995.

A. E. Richardson, J. M. Barea, A. M. Mcneill, and C. Prigent-combaret, Acquisition of phosphorus and nitrogen in the rhizosphere and plant growth promotion by microorganisms, Plant Soil, vol.305, p.339, 2009.
URL : https://hal.archives-ouvertes.fr/halsde-00525548

P. De-werra, M. Pechy-tarr, C. Keel, and M. Maurhofer, Role of gluconic acid production in the regulation of biocontrol traits of Pseudomonas fluorescens CHA0, Appl. Environ. Microbiol, vol.4162, p.4174, 2009.

H. Rodriguez, T. Gonzalez, I. Goire, and Y. Bashan, Gluconic acid production and phosphate solubilization by the plant growth-promoting bacterium Azospirillum spp, Naturwissenschaften, vol.552, p.555, 2004.

Y. Bashan and L. E. De-bashan, How the plant growth-promoting bacterium Azospirillum promotes plant growth -A critical assessment, Adv. Agron, vol.77, p.135, 2010.

A. Costacurta, V. Keijers, and J. Vanderleyden, Molecularcloning and sequence analysis of an Azospirillum brasilense indole 3-pyruvate decarboxylase gene, Mol. Gen. Genet, vol.463, p.472, 1994.

O. Ona, J. Van-impe, E. Prinsen, and J. Vanderleyden, Growth and indole 3-acetic acid biosynthesis of Azospirillum brasilense Sp245 is environmentally controlled, FEMS Microbiol. Lett, vol.125, p.132, 2005.

S. Spaepen, W. Versees, D. Gocke, M. Pohl, J. Steyaert et al., Characterization of phenylpyruvate decarboxylase, involved in auxin production of Azospirillum brasilense, J. Bacteriol, vol.7626, p.7633, 2007.

J. Castro-guerrero, A. Romero, J. J. Aguilar, M. L. Xiqui, J. O. Sandoval et al., The hisC1 gene, encoding aromatic amino acid aminotransferase 1 in Azospirillum brasilense Sp7, expressed in wheat, Plant Soil, 2011.

B. E. Baca and C. Elmerich, Associative and endophytic nitrogen-fixing bacteria and cyanobacterial associations, 2003.

R. Carreno-lopez, N. Campos-reales, C. Elmerich, and B. E. Baca, Physiological evidence for differently regulated tryptophan-dependent pathways for indole 3-acetic acid synthesis in Azospirillum brasilense, Mol. Gen. Genet, vol.264, p.530, 2000.

M. D. Mikkelsen, C. H. Hansen, U. Wittstock, and B. A. Halkier, Cytochrome P450 CYP79B2 from Arabidopsis catalyzes the conversion of tryptophan to indole-3-acetaldoxime, a precursor of indole glucosinolates and indole-3-acetic acid, J. Biol. Chem, vol.33712, p.33717, 2000.

J. H. Leveau and S. Gerards, Discovery of a bacterial gene cluster for catabolism of the plant hormone indole 3-acetic acid, FEMS Microbiol. Ecol, vol.238, p.250, 2008.

J. H. Leveau and S. E. Lindow, Utilization of the plant hormone indole 3-acetic acid for growth by Pseudomonas putida strain 1290, Appl. Environ. Microbiol, p.71, 2005.

B. R. Glick, Z. Y. Cheng, J. Czarny, and J. Duan, Promotion of plant growth by ACC deaminaseproducing soil bacteria, Eur. J. Plant Pathol, vol.329, p.339, 2007.

D. Blaha, C. Prigent-combaret, M. S. Mirza, and Y. Moenne-loccoz, Phylogeny of the 1-aminocyclopropane-1-carboxylic acid deaminase-encoding gene acdS in phytobeneficial and pathogenic Proteobacteria and relation with strain biogeography, FEMS Microbiol. Ecol, vol.56, p.470, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00124530

C. Prigent-combaret, D. Blaha, J. F. Pothier, L. Vial, M. A. Poirier et al., Physical organization and phylogenetic analysis of acdR as leucineresponsive regulator of the 1-aminocyclopropane-1-carboxylate deaminase gene acdS in phytobeneficial Azospirillum lipoferum 4B and other Proteobacteria, FEMS Microbiol. Ecol, vol.202, p.219, 2008.
URL : https://hal.archives-ouvertes.fr/hal-02555008

J. C. Neff, E. A. Holland, F. J. Dentener, W. H. Mcdowell, and K. M. Russel, The origin, composition and rated of organic nitrogen deposition: A missing piece of the nitrogen cycle? Biogeochemistry, vol.99, p.136, 2002.

E. Latypova, S. Yang, Y. S. Wang, T. Wang, T. A. Chavkin et al., Genetics of the glutamate-mediated methylamine utilization pathway in the facultative methylotrophic beta-proteobacterium Methyloversatilis universalis FAM5, Mol. Microbiol, vol.426, p.439, 2009.

E. L. Hendrickson, D. A. Beck, T. Wang, M. E. Lidstrom, M. Hackett et al., Expressed genome of Methylobacillus flagellatus as defined through comprehensive proteomics and new insights into methylotrophy, J. Bacteriol, vol.4859, p.4867, 2010.

A. Lapidus, A. Clum, K. Labutti, M. G. Kaluzhnaya, S. Lim et al., Genomes of three methylotrophs from a single niche reveal the genetic and metabolic divergence of the methylophilaceae, J. Bacteriol, vol.3757, p.3764, 2011.

Y. Chen, J. Scanlan, L. Song, A. Crombie, M. T. Rahman et al., {gamma}-Glutamylmethylamide is an essential intermediate in the metabolism of methylamine by Methylocella silvestris, Appl. Environ. Microbiol, vol.4530, p.4537, 2010.

G. Fuchs, M. Boll, and J. Heider, Microbial degradation of aromatic compounds -from one strategy to four, Nat. Rev. Microbiol, vol.9, p.816, 2011.

J. Nogales, R. Macchi, F. Franchi, D. Barzaghi, C. Fernandez et al., Characterization of the last step of the aerobic phenylacetic acid degradation pathway, Microbiology, vol.357, p.365, 2007.

C. S. Harwood, N. N. Nichols, M. K. Kim, J. L. Ditty, and R. E. Parales, Identification of the pcaRKF gene cluster from Pseudomonas putida: involvement in chemotaxis, biodegradation, and transport of 4-hydroxybenzoate, J. Bacteriol, vol.6479, p.6488, 1994.

J. N. Hamlin, R. A. Bloodworth, and S. T. Cardona, Regulation of phenylacetic acid degradation genes of Burkholderia cenocepacia K56-2, BMC Microbiol, vol.9, p.222, 2009.

J. M. Luengo, J. L. Garcia, and E. R. Olivera, The phenylacetyl-CoA catabolon: a complex catabolic unit with broad biotechnological applications, Mol. Microbiol, pp.39-1434, 2001.

L. Leoni, N. Orsi, V. De-lorenzo, and P. Visca, Functional analysis of PvdS, an iron starvation sigma factor of Pseudomonas aeruginosa, J. Bacteriol, p.182, 2000.

M. A. Molina, P. Godoy, M. I. Ramos-gonzalez, N. Munoz, J. L. Ramos et al., Role of iron and the TonB system in colonization of corn seeds and roots by Pseudomonas putida KT2440, Environ. Microbiol, vol.7, p.449, 2005.

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

R. Santos, D. Herouart, S. Sigaud, D. Touati, and A. Puppo, Oxidative burst in alfalfa-Sinorhizobium meliloti symbiotic interaction, Mol. Plant-Microbe Interac, vol.86, p.89, 2001.

M. C. Vargas, S. Encarnacion, A. Davalos, A. Reyes-perez, Y. Mora et al., Only one catalase, katG, is detectable in Rhizobium etli, and is encoded along with the regulator OxyR on a plasmid replicon, Microbiology, p.149, 2003.

S. Schwarz, R. D. Hood, and J. D. Mougous, What is type VI secretion doing in all those bugs?, Trends Microbiol, vol.531, p.537, 2010.

C. S. Bernard, Y. R. Brunet, E. Gueguen, and E. Cascales, Nooks and crannies in type VI secretion regulation, J. Bacteriol, vol.3850, p.3860, 2010.
URL : https://hal.archives-ouvertes.fr/hal-02001273

D. L. Macintyre, S. T. Miyata, M. Kitaoka, and S. Pukatzki, The Vibrio cholerae type VI secretion system displays antimicrobial properties, Proc. Natl. Acad. Sci, p.107, 2010.

S. Van-puyvelde, L. Cloots, K. Engelen, F. Das, K. Marchal et al., Transcriptome Analysis of the Rhizosphere Bacterium Azospirillum brasilense Reveals an Extensive Auxin Response, Microb. Ecol, vol.723, p.728, 2011.

H. Kellner, P. Luis, B. Zimdars, B. Kiesel, and F. Buscot, Diversity of bacterial laccase-like multicopper oxidase genes in forest and grassland Cambisol soil samples, Soil Biol. Biochem, vol.638, p.648, 2008.

A. Givaudan, A. Effosse, D. Faure, P. Potier, M. L. Bouillant et al., Polyphenol Oxidase in Azospirillum lipoferum Isolated from Rice Rhizosphere Evidence for Laccase Activity in Nonmotile Strains of Azospirillum lipoferum, FEMS Microbiol. Lett, vol.205, p.210, 1993.

D. Faure, M. L. Bouillant, and R. Bally, Isolation of Azospirillum lipoferum 4T Tn5 Mutants Affected in Melanization and Laccase Activity, Appl. Environ. Microbiol, vol.3413, p.3415, 1994.

G. Alexandre, R. Bally, B. L. Taylor, and I. B. Zhulin, Loss of cytochrome c oxidase activity and acquisition of resistance to quinone analogs in a laccase-positive variant of Azospirillum lipoferum, J. Bacteriol, vol.6730, p.6738, 1999.

P. Sharma, R. Goel, and N. Capalash, Bacterial lacases. World J. Microbiol. Biotechnol, vol.823, p.832, 2007.

J. F. Pothier, C. Prigent-combaret, J. Haurat, Y. Moenne-loccoz, and F. Wisniewski-dyé, Duplication of plasmid-borne nitrite reductase gene nirK in the wheat-associated plant growth-promoting rhizobacterium Azospirillum brasilense Sp245, Mol. Plant-Microbe Interact, vol.21, p.842, 2008.
URL : https://hal.archives-ouvertes.fr/halsde-00344099

A. S. Lang and J. T. Beatty, Importance of widespread gene transfer agent genes in alphaproteobacteria, Trends Microbiol, vol.54, p.62, 2007.

T. B. Stanton, S. B. Humphrey, D. O. Bayles, and R. L. Zuerner, Identification of a divided genome for VSH 1, the prophage-like gene transfer agent of Brachyspira hyodysenteriae, J. Bacteriol, p.191, 2009.

R. Barrangou, C. Fremaux, H. Deveau, M. Richards, P. Boyaval et al., CRISPR provides acquired resistance against viruses in prokaryotes, Science, p.315, 2007.

, CRISPI: a CRISPR Interactive database, p.23, 2012.

S. Kurtz, A. Phillippy, A. L. Delcher, M. Smoot, M. Shumway et al., Versatile and open software for comparing large genomes, Genome Biol, vol.5, p.12, 2004.

. Homepage-of-microscope, , p.23, 2012.

D. Vallenet, S. Engelen, D. Mornico, S. Cruveiller, L. Fleury et al., MicroScope: A platform for microbial genome annotation and comparative genomics, p.21, 2009.

R. C. Edgar, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res, p.32, 2004.

M. Gouy, S. Guindon, and O. Gascuel, SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building, Mol. Biol. Evol, vol.221, p.224, 2010.
URL : https://hal.archives-ouvertes.fr/lirmm-00511794

S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, Basic local alignment search tool, J. Mol. Biol, vol.403, p.410, 1990.

Z. Zhang, J. Li, X. Q. Zhao, J. Wang, G. K. Wong et al., KaKs_Calculator: calculating Ka and Ks through model selection and model averaging, Genom. Proteom. Bioinf, 2006.