C. L. Andersen, J. L. Jensen, and T. F. Orntoft, Normalization of Real-Time Quantitative Reverse Transcription-PCR Data: A Model-Based Variance Estimation Approach to Identify Genes Suited for Normalization, Applied to Bladder and Colon Cancer Data Sets, Cancer Research, vol.64, issue.15, pp.5245-5250, 2004.
DOI : 10.1158/0008-5472.CAN-04-0496

J. Auclair, F. Lepine, S. Parent, and R. Villemur, Dissimilatory reduction of nitrate in seawater by a Methylophaga strain containing two highly divergent narG sequences, The ISME Journal, vol.61, issue.10, pp.1302-131347, 2010.
DOI : 10.1139/W06-111
URL : https://hal.archives-ouvertes.fr/pasteur-00819611

J. Auclair, S. Parent, and R. Villemur, Functional Diversity in the Denitrifying Biofilm of the Methanol-Fed Marine Denitrification System at the Montreal Biodome, Microbial Ecology, vol.61, issue.4, pp.726-735, 2012.
DOI : 10.1007/s00248-011-9960-2

R. Boden, Emended description of the genus Methylophaga Janvier et al. 1985, INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, vol.62, issue.Pt 7, pp.1644-1646, 2012.
DOI : 10.1099/ijs.0.033639-0

V. Bonnefoy, J. A. Demoss, V. Bonnefoy, and J. A. Demoss, Identification of functional cis-acting sequences involved in regulation of nark gene-expression in Escherichia coli Nitrate reductases in Escherichia coli, Mol. Microbiol. Antonie Van Leeuwenhoek Int. J. Gen. Mol. Microbiol, vol.6, issue.66, pp.3595-3602, 1007.

L. Chang, L. L. Wei, J. P. Audia, R. A. Morton, and H. E. Schellhorn, Expression of the Escherichia coli NRZ nitrate reductase is highly growth phase dependent and is controlled by RpoS, the alternative vegetative sigma factor, Molecular Microbiology, vol.5, issue.4, pp.756-766, 1999.
DOI : 10.1266/ggs.72.167

F. Chen, Q. Xia, and L. K. Ju, Aerobic Denitrification of Pseudomonas aeruginosa Monitored by Online NAD(P)H Fluorescence, Applied and Environmental Microbiology, vol.69, issue.11, pp.6715-6722, 2003.
DOI : 10.1128/AEM.69.11.6715-6722.2003

Y. Chen, F. Wang, J. Xu, M. A. Mehmood, X. et al., Physiological and evolutionary studies of NAP systems in Shewanella piezotolerans WP3, The ISME Journal, vol.145, issue.5, pp.843-855, 2011.
DOI : 10.1099/ijs.0.64500-0

S. J. Clegg, W. J. Jia, C. , and J. A. , Role of the Escherichia coli nitrate transport protein, NarU, in survival during severe nutrient starvation and slow growth, Microbiology, vol.152, issue.7, pp.2091-2100, 2006.
DOI : 10.1099/mic.0.28688-0

K. M. Colvin, V. D. Gordon, K. Murakami, B. R. Borlee, D. J. Wozniak et al., The Pel Polysaccharide Can Serve a Structural and Protective Role in the Biofilm Matrix of Pseudomonas aeruginosa, PLoS Pathogens, vol.336, issue.10, 2011.
DOI : 10.1371/journal.ppat.1001264.s011

E. Déziel, F. Lépine, S. Milot, J. X. He, M. N. Mindrinos et al., Analysis of Pseudomonas aeruginosa 4-hydroxy-2-alkylquinolines (HAQs) reveals a role for 4-hydroxy-2-heptylquinoline in cell-to-cell communication, Proc. Nat. Acad. Sci. U.S.A. 101, pp.1339-1344, 2004.
DOI : 10.1073/pnas.0307694100

N. V. Doronina, V. A. Ezhov, A. P. Beschastnyi, and A. Iu, Biosynthesis of the bioprotectant ectoin by aerobic methylotrophic bacteria from methanol, Applied Biochemistry and Microbiology, vol.46, issue.2, 2010.
DOI : 10.1134/S0003683810020080

A. Ellis, M. J. Grossmann, J. G. Eady, R. R. Hasnain, and S. S. , Genomic analysis reveals widespread occurrence of new classes of copper nitrite reductases, JBIC Journal of Biological Inorganic Chemistry, vol.553, issue.8, pp.173-176, 2007.
DOI : 10.1007/s00775-007-0282-2

S. J. Ferguson, Denitrification and its control, Antonie van Leeuwenhoek, vol.219, issue.1-3, pp.89-110, 1994.
DOI : 10.1007/BF00871634

A. D. Goddard, J. W. Moir, D. J. Richardson, F. , S. J. Gonzalez et al., Interdependence of two NarK domains in a fused nitrate/nitrite transporter, Molecular Microbiology, vol.61, issue.3, pp.667-681, 2006.
DOI : 10.1111/j.1365-2958.2008.06436.x

S. F. Gothel, M. A. Marahiel, R. P. Gunsalus, and S. J. Park, Peptidyl-prolyl cis-trans isomerases, a superfamily of ubiquitous folding catalysts Aerobic-anaerobic gene regulation in Escherichia coli -control by the ArcAB and Fnr regulons, Cell Mol. Life Sci. Res. Microbiol, vol.5594, issue.145, pp.423-436, 1994.

A. Hartsock and J. P. Shapleigh, Physiological Roles for Two Periplasmic Nitrate Reductases in Rhodobacter sphaeroides 2.4.3 (ATCC 17025), Journal of Bacteriology, vol.193, issue.23, pp.6483-6489, 2011.
DOI : 10.1128/JB.05324-11

F. P. Healey, Slope of the Monod equation as an indicator of advantage in nutrient competition, Microbial Ecology, vol.11, issue.4, pp.281-286, 1980.
DOI : 10.1007/BF02020335

K. Heurlier, M. J. Thomson, N. Aziz, and J. W. Moir, The Nitric Oxide (NO)-Sensing Repressor NsrR of Neisseria meningitidis Has a Compact Regulon of Genes Involved in NO Synthesis and Detoxification, Journal of Bacteriology, vol.190, issue.7, pp.2488-2495, 1128.
DOI : 10.1128/JB.01869-07

T. T. Hoang, R. R. Karkhoff-schweizer, A. J. Kutchma, and H. P. Schweizer, A broad-host-range Flp-FRT recombination system for site-specific excision of chromosomally-located DNA sequences: application for isolation of unmarked Pseudomonas aeruginosa mutants, Gene, vol.212, issue.1, pp.77-86, 1998.
DOI : 10.1016/S0378-1119(98)00130-9

R. Jain and B. I. Kazmierczak, A Conservative Amino Acid Mutation in the Master Regulator FleQ Renders Pseudomonas aeruginosa Aflagellate, PLoS ONE, vol.212, issue.5, 2014.
DOI : 10.1371/journal.pone.0097439.s002

P. A. Jordan, A. J. Thomson, E. T. Ralph, J. R. Guest, and J. Green, FNR is a direct oxygen sensor having a biphasic response curve, FEBS Letters, vol.156, issue.3, pp.349-352, 1997.
DOI : 10.1016/S0014-5793(97)01219-2

N. Labbé, V. Laurin, P. Juteau, S. Parent, and R. Villemur, Microbiological Community Structure of the Biofilm of a Methanol-Fed, Marine Denitrification System, and Identification of the Methanol-Utilizing Microorganisms, Microbial Ecology, vol.61, issue.4, pp.621-630, 2007.
DOI : 10.1007/s00248-006-9168-z

J. Li, S. Kustu, and V. Stewart, In Vitro Interaction of Nitrate-responsive Regulatory Protein NarL with DNA Target Sequences in the fdnG, narG, narK and frdA Operon Control Regions of Escherichia coli K-12, Journal of Molecular Biology, vol.241, issue.2, pp.150-1651485, 1994.
DOI : 10.1006/jmbi.1994.1485

K. J. Livak and T. D. Schmittgen, Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2???????CT Method, Methods, vol.25, issue.4, pp.402-408, 2001.
DOI : 10.1006/meth.2001.1262

C. Martineau, F. Mauffrey, and R. Villemur, Comparative Analysis of Denitrifying Activities of Hyphomicrobium nitrativorans, Hyphomicrobium denitrificans, and Hyphomicrobium zavarzinii, Applied and Environmental Microbiology, vol.81, issue.15, pp.5003-5014, 2015.
DOI : 10.1128/AEM.00848-15
URL : https://hal.archives-ouvertes.fr/pasteur-01352580

. Hyphomicrobium-nitrativorans-sp, isolated from the biofilm of a methanol-fed denitrification system treating seawater at the Montreal Biodome, Int. J. Syst. Evol. Microbiol, vol.63

J. W. Moir, N. J. Wood, R. Munch, K. Hiller, A. Grote et al., Nitrate and nitrite transport in bacteria Virtual footprint and PRODORIC: an integrative framework for regulon prediction in prokaryotes Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper -Excel-based tool using pair-wise correlations, Cell Mol. Life Sci. Bioinformatics Biotechnol. Lett, vol.58, issue.26, pp.215-224, 2001.

L. Philippot and O. Hojberg, Dissimilatory nitrate reductases in bacteria, Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression, vol.1446, issue.1-2, pp.1-23, 1999.
DOI : 10.1016/S0167-4781(99)00072-X

L. C. Potter, P. Millington, L. Griffiths, G. H. Thomas, C. et al., Competition between Escherichia coli strains expressing either a periplasmic or a membrane-bound nitrate reductase: does Nap confer a selective advantage during nitrate-limited growth?, Biochemical Journal, vol.344, issue.1, pp.77-84, 1999.
DOI : 10.1042/0264-6021:3440077

J. Sambrook, P. Maccallum, R. , and D. , Molecular Cloning: A Laboratory Manual, 2001.

K. Schreiber, R. Krieger, B. Benkert, M. Eschbach, H. Arai et al., The Anaerobic Regulatory Network Required for Pseudomonas aeruginosa Nitrate Respiration, Journal of Bacteriology, vol.189, issue.11, pp.4310-4314, 2007.
DOI : 10.1128/JB.00240-07

N. Silver, S. Best, J. Jiang, and S. L. Thein, Selection of housekeeping genes for gene expression studies in human reticulocytes using real-time PCR, BMC Molecular Biology, vol.7, issue.1, pp.33-43, 2006.
DOI : 10.1186/1471-2199-7-33

C. D. Sohaskey, W. , and L. G. , Role of narK2X and narGHJI in Hypoxic Upregulation of Nitrate Reduction by Mycobacterium tuberculosis, Journal of Bacteriology, vol.185, issue.24, pp.7247-7256, 2003.
DOI : 10.1128/JB.185.24.7247-7256.2003

S. Spiro, Nitric oxide metabolism: physiology and regulatory mechanisms, Nitrogen Cycling in Bacteria, pp.179-196, 2011.

A. M. Stern, B. B. Liu, L. R. Bakken, J. P. Shapleigh, and J. Zhu, A Novel Protein Protects Bacterial Iron-Dependent Metabolism from Nitric Oxide, Journal of Bacteriology, vol.195, issue.20, pp.4702-4708, 2013.
DOI : 10.1128/JB.00836-13

S. Tarazona, F. Garcia-alcalde, J. Dopazo, A. Ferrer, and A. Conesa, Differential expression in RNA-seq: A matter of depth, Genome Research, vol.21, issue.12, pp.2213-2223, 2011.
DOI : 10.1101/gr.124321.111

M. Thongdee, L. A. Gallagher, M. Schell, T. Dharakul, S. Songsivilai et al., Targeted mutagenesis of Burkholderia thailandensis and Burkholdetia pseudomallei through natural transformation of PCR fragments, 2008.

J. Vandesompele, K. De-preter, F. Pattyn, B. Poppe, N. Van-roy et al., Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes, Genome Biol, vol.3, pp.1-11, 2002.

C. Villeneuve, C. Martineau, F. Mauffrey, and R. Villemur, Methylophaga nitratireducenticrescens sp. nov. and Methylophaga frappieri sp. nov., isolated from the biofilm of the methanol-fed denitrification system treating the seawater at the Montreal Biodome, INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, vol.63, issue.Pt 6, pp.2216-2222, 2013.
DOI : 10.1099/ijs.0.044545-0
URL : https://hal.archives-ouvertes.fr/pasteur-01133130

W. Wang, A. R. Richardson, W. Martens-habbena, D. A. Stahl, F. C. Fang et al., Identification of a Repressor of a Truncated Denitrification Pathway in Moraxella catarrhalis, Journal of Bacteriology, vol.190, issue.23, pp.7762-7772, 1128.
DOI : 10.1128/JB.01032-08