P. Stewart, W. Costerton, and J. , Antibiotic resistance of bacteria in biofilms, The Lancet, vol.358, issue.9276, pp.135-138, 2001.
DOI : 10.1016/S0140-6736(01)05321-1

H. Anwar, T. Van-biesen, M. Dasgupta, K. Lam, and J. Costerton, Interaction of biofilm bacteria with antibiotics in a novel in vitro chemostat system., Antimicrobial Agents and Chemotherapy, vol.33, issue.10, pp.1824-1826, 1989.
DOI : 10.1128/AAC.33.10.1824

D. Evans, D. Allison, M. Brown, and P. Gilbert, biofilms towards ciprofloxacin: effect of specific growth rate, Journal of Antimicrobial Chemotherapy, vol.27, issue.2, pp.177-184, 1991.
DOI : 10.1093/jac/27.2.177

B. Levin and D. Rozen, Non-inherited antibiotic resistance, Nature Reviews Microbiology, vol.41, issue.7, pp.556-562, 2006.
DOI : 10.1038/nrmicro1445

K. Lewis, Persister Cells, Annual Review of Microbiology, vol.64, issue.1, pp.357-372, 2010.
DOI : 10.1146/annurev.micro.112408.134306

O. Gefen and N. Balaban, The importance of being persistent: heterogeneity of bacterial populations under antibiotic stress, FEMS Microbiology Reviews, vol.33, issue.4, pp.704-717, 2009.
DOI : 10.1111/j.1574-6976.2008.00156.x

P. Stewart and M. Franklin, Physiological heterogeneity in biofilms, Nature Reviews Microbiology, vol.167, issue.3, pp.199-210, 2008.
DOI : 10.1038/nrmicro1838

J. Anderl, J. Zahller, F. Roe, and P. Stewart, Role of Nutrient Limitation and Stationary-Phase Existence in Klebsiella pneumoniae Biofilm Resistance to Ampicillin and Ciprofloxacin, Antimicrobial Agents and Chemotherapy, vol.47, issue.4, pp.1251-1256, 2003.
DOI : 10.1128/AAC.47.4.1251-1256.2003

B. Boles and P. Singh, Endogenous oxidative stress produces diversity and adaptability in biofilm communities, Proceedings of the National Academy of Sciences, vol.105, issue.34, pp.12503-12508, 2008.
DOI : 10.1073/pnas.0801499105

B. Boles, M. Thoendel, and P. Singh, Self-generated diversity produces "insurance effects" in biofilm communities, Proceedings of the National Academy of Sciences, vol.101, issue.47, pp.16630-16635, 2004.
DOI : 10.1073/pnas.0407460101

K. Lewis, Persister cells, dormancy and infectious disease, Nature Reviews Microbiology, vol.71, issue.1, pp.48-56, 2007.
DOI : 10.1128/AAC.00684-06

D. Nguyen, A. Joshi-datar, F. Lepine, E. Bauerle, and O. Olakanmi, Active Starvation Responses Mediate Antibiotic Tolerance in Biofilms and Nutrient-Limited Bacteria, Science, vol.334, issue.6058, pp.982-986, 2011.
DOI : 10.1126/science.1211037
URL : https://hal.archives-ouvertes.fr/pasteur-00722468

A. Lenz, K. Williamson, B. Pitts, P. Stewart, and M. Franklin, Localized Gene Expression in Pseudomonas aeruginosa Biofilms, Applied and Environmental Microbiology, vol.74, issue.14, pp.4463-4471, 2008.
DOI : 10.1128/AEM.00710-08

A. Pérez-osorio, K. Williamson, and M. Franklin, Heterogeneous rpoS and rhlR mRNA Levels and 16S rRNA/rDNA (rRNA Gene) Ratios within Pseudomonas aeruginosa Biofilms, Sampled by Laser Capture Microdissection, Journal of Bacteriology, vol.192, issue.12, pp.2991-3000, 2010.
DOI : 10.1128/JB.01598-09

E. Tuomanen, R. Cozens, W. Tosch, O. Zak, and A. Tomasz, The rate of killing of Escherichia coli by beta-lactam antibiotics is strictly proportional to the rate of bacterial growth, J Gen Microbiol, vol.132, pp.1297-1304, 1986.

A. Spoering and K. Lewis, Biofilms and Planktonic Cells of Pseudomonas aeruginosa Have Similar Resistance to Killing by Antimicrobials, Journal of Bacteriology, vol.183, issue.23, pp.6746-6751, 2001.
DOI : 10.1128/JB.183.23.6746-6751.2001

X. Zhao, M. Malik, N. Chan, A. Drlica-wagner, and J. Wang, Lethal Action of Quinolones against a Temperature-Sensitive dnaB Replication Mutant of Escherichia coli, Antimicrobial Agents and Chemotherapy, vol.50, issue.1, pp.362-364, 2006.
DOI : 10.1128/AAC.50.1.362-364.2006

N. Vega, K. Allison, A. Khalil, and J. Collins, Signaling-mediated bacterial persister formation, Nature Chemical Biology, vol.102, issue.5, pp.431-433, 2012.
DOI : 10.1073/pnas.1004333107

K. Poole, Stress responses as determinants of antimicrobial resistance in Gram-negative bacteria, Trends in Microbiology, vol.20, issue.5, pp.227-234, 2012.
DOI : 10.1016/j.tim.2012.02.004

K. Potrykus and M. Cashel, (p)ppGpp: Still Magical?, Annual Review of Microbiology, vol.62, issue.1, pp.35-51, 2008.
DOI : 10.1146/annurev.micro.62.081307.162903

A. Srivatsan and J. Wang, Control of bacterial transcription, translation and replication by (p)ppGpp, Current Opinion in Microbiology, vol.11, issue.2, pp.100-105, 2008.
DOI : 10.1016/j.mib.2008.02.001

H. Xiao, M. Kalman, K. Ikehara, S. Zemel, and G. Glaser, Residual guanosine 39,59-bispyrophosphate synthetic activity of relA null mutants can be eliminated by spoT null mutations, J Biol Chem, vol.266, pp.5980-5990, 1991.

T. Dorr, K. Lewis, and M. Vulic, SOS Response Induces Persistence to Fluoroquinolones in Escherichia coli, PLoS Genetics, vol.178, issue.12, 2009.
DOI : 10.1371/journal.pgen.1000760.t001

T. Dorr, M. Vulic, and K. Lewis, Ciprofloxacin Causes Persister Formation by Inducing the TisB toxin in Escherichia coli, PLoS Biology, vol.183, issue.2, 2010.
DOI : 10.1371/journal.pbio.1000317.s001

D. Fung, E. Chan, M. Chin, and R. Chan, Delineation of a Bacterial Starvation Stress Response Network Which Can Mediate Antibiotic Tolerance Development, Antimicrobial Agents and Chemotherapy, vol.54, issue.3, pp.1082-1093, 2010.
DOI : 10.1128/AAC.01218-09

M. Butala, D. Zgur-bertok, and S. Busby, The bacterial LexA transcriptional repressor, Cellular and Molecular Life Sciences, vol.66, issue.1, pp.82-93, 2009.
DOI : 10.1007/s00018-008-8378-6

H. Bierne, M. Seigneur, S. Ehrlich, and B. Michel, chromosome via SOS induction of the RecF recombination pathway, Molecular Microbiology, vol.26, issue.03, pp.557-567, 1997.
DOI : 10.1046/j.1365-2958.1997.6011973.x

N. Kaldalu, R. Mei, and K. Lewis, Killing by Ampicillin and Ofloxacin Induces Overlapping Changes in Escherichia coli Transcription Profile, Antimicrobial Agents and Chemotherapy, vol.48, issue.3, pp.890-896, 2004.
DOI : 10.1128/AAC.48.3.890-896.2004

L. Van-melderen, Toxin???antitoxin systems: why so many, what for?, Current Opinion in Microbiology, vol.13, issue.6, pp.781-786, 2010.
DOI : 10.1016/j.mib.2010.10.006

K. Pedersen and K. Gerdes, Multiple hok genes on the chromosome of Escherichia coli, Molecular Microbiology, vol.267, issue.5, pp.1090-1102, 1999.
DOI : 10.1146/annurev.ge.07.120173.001411

Y. Yamaguchi, J. Park, and M. Inouye, Toxin-Antitoxin Systems in Bacteria and Archaea, Annual Review of Genetics, vol.45, issue.1, pp.61-79, 2011.
DOI : 10.1146/annurev-genet-110410-132412

K. Gerdes and E. Maisonneuve, Bacterial Persistence and Toxin-Antitoxin Loci, Annual Review of Microbiology, vol.66, issue.1, pp.103-123, 2012.
DOI : 10.1146/annurev-micro-092611-150159

I. Erill, S. Campoy, and J. Barbe, Aeons of distress: an evolutionary perspective on the bacterial SOS response, FEMS Microbiology Reviews, vol.31, issue.6, pp.637-656, 2007.
DOI : 10.1111/j.1574-6976.2007.00082.x

J. Petrosino, R. Galhardo, L. Morales, and S. Rosenberg, Stress-Induced ??-Lactam Antibiotic Resistance Mutation and Sequences of Stationary-Phase Mutations in the Escherichia coli Chromosome, Journal of Bacteriology, vol.191, issue.19, pp.5881-5889, 2009.
DOI : 10.1128/JB.00732-09

F. Taddei, I. Matic, and M. Radman, cAMP-dependent SOS induction and mutagenesis in resting bacterial populations., Proceedings of the National Academy of Sciences, vol.92, issue.25, pp.11736-11740, 1995.
DOI : 10.1073/pnas.92.25.11736

G. Agarwal, A. Kapil, S. Kabra, B. Das, and S. Dwivedi, Characterization of Pseudomonas aeruginosa isolated from chronically infected children with cystic fibrosis in India, BMC Microbiology, vol.5, issue.1, p.43, 2005.
DOI : 10.1186/1471-2180-5-43

S. Thomas, A. Ray, M. Hodson, and T. Pitt, Increased sputum amino acid concentrations and auxotrophy of Pseudomonas aeruginosa in severe cystic fibrosis lung disease, Thorax, vol.55, issue.9, pp.795-797, 2000.
DOI : 10.1136/thorax.55.9.795

S. Bodini, L. Nunziangeli, and F. Santori, Influence of Amino Acids on Low-Density Escherichia coli Responses to Nutrient Downshifts, Journal of Bacteriology, vol.189, issue.8, pp.3099-3105, 2007.
DOI : 10.1128/JB.01753-06

C. Beloin, J. Valle, P. Latour-lambert, P. Faure, and M. Kzreminski, Global impact of mature biofilm lifestyle on Escherichia coli K-12 gene expression, Molecular Microbiology, vol.93, issue.3, pp.659-674, 2004.
DOI : 10.1046/j.1365-2958.2003.03865.x

H. Girgis, K. Harris, and S. Tavazoie, Large mutational target size for rapid emergence of bacterial persistence, Proceedings of the National Academy of Sciences, vol.109, issue.31, pp.12740-12745, 2012.
DOI : 10.1073/pnas.1205124109

S. Hansen, K. Lewis, and M. Vulic, Role of Global Regulators and Nucleotide Metabolism in Antibiotic Tolerance in Escherichia coli, Antimicrobial Agents and Chemotherapy, vol.52, issue.8, pp.2718-2726, 2008.
DOI : 10.1128/AAC.00144-08

Z. Baharoglu and D. Mazel, Vibrio cholerae Triggers SOS and Mutagenesis in Response to a Wide Range of Antibiotics: a Route towards Multiresistance, Antimicrobial Agents and Chemotherapy, vol.55, issue.5, pp.2438-2441, 2011.
DOI : 10.1128/AAC.01549-10
URL : https://hal.archives-ouvertes.fr/pasteur-01423615

J. Blázquez, J. Gómez-gómez, A. Oliver, C. Juan, and V. Kapur, PBP3 inhibition elicits adaptive responses in Pseudomonas aeruginosa, Molecular Microbiology, vol.5, issue.1, pp.84-99, 2006.
DOI : 10.1128/JB.186.23.8066-8073.2004

E. Maiques, C. Ubeda, S. Campoy, N. Salvador, and I. Lasa, ??-Lactam Antibiotics Induce the SOS Response and Horizontal Transfer of Virulence Factors in Staphylococcus aureus, Journal of Bacteriology, vol.188, issue.7, pp.2726-2729, 2006.
DOI : 10.1128/JB.188.7.2726-2729.2006

Z. Baharoglu, D. Bikard, and D. Mazel, Conjugative DNA Transfer Induces the Bacterial SOS Response and Promotes Antibiotic Resistance Development through Integron Activation, PLoS Genetics, vol.310, issue.Pt 9, 2010.
DOI : 10.1371/journal.pgen.1001165.s006

J. Beaber, B. Hochhut, and M. Waldor, SOS response promotes horizontal dissemination of antibiotic resistance genes, Nature, vol.427, issue.6969, pp.72-74, 2004.
DOI : 10.1038/nature02241

E. Guerin, G. Cambray, N. Sanchez-alberola, S. Campoy, and I. Erill, The SOS Response Controls Integron Recombination, Science, vol.324, issue.5930, p.1034, 2009.
DOI : 10.1126/science.1172914
URL : https://hal.archives-ouvertes.fr/hal-00409031

J. Courcelle, A. Khodursky, B. Peter, P. Brown, and P. Hanawalt, Comparative gene expression profiles following UV exposure in wild-type and SOS-deficient Escherichia coli, Genetics, vol.158, pp.41-64, 2001.

A. Fernandez-de-henestrosa, T. Ogi, S. Aoyagi, D. Chafin, and J. Hayes, Identification of additional genes belonging to the LexA regulon in Escherichia coli, Molecular Microbiology, vol.180, issue.6, pp.1560-1572, 2000.
DOI : 10.1046/j.1365-2958.2000.01826.x

K. Allison, M. Brynildsen, and J. Collins, Metabolite-enabled eradication of bacterial persisters by aminoglycosides, Nature, vol.31, issue.7346, pp.216-220, 2011.
DOI : 10.1038/nature10069

T. Lu and J. Collins, Engineered bacteriophage targeting gene networks as adjuvants for antibiotic therapy, Proceedings of the National Academy of Sciences, vol.106, issue.12, pp.4629-4634, 2009.
DOI : 10.1073/pnas.0800442106

J. Sexton, T. Wigle, Q. He, M. Hughes, and G. Smith, Novel Inhibitors of E. coli RecA ATPase Activity, Current Chemical Genomics, vol.4, pp.34-42, 2010.
DOI : 10.2174/1875397301004010034

T. Wigle, J. Sexton, A. Gromova, M. Hadimani, and M. Hughes, Inhibitors of RecA Activity Discovered by High-Throughput Screening: Cell-Permeable Small Molecules Attenuate the SOS Response in Escherichia coli, Journal of Biomolecular Screening, vol.14, issue.9, pp.1092-1101, 2009.
DOI : 10.1177/1087057109342126

G. Bertani, Lysogeny at Mid-Twentieth Century: P1, P2, and Other Experimental Systems, Journal of Bacteriology, vol.186, issue.3, pp.595-600, 2004.
DOI : 10.1128/JB.186.3.595-600.2004

O. Toole, G. Kolter, and R. , Initiation of biofilm formation in Pseudomonas fluorescens WCS365 proceeds via multiple, convergent signalling pathways: a genetic analysis, Molecular Microbiology, vol.28, issue.3, pp.449-461, 1998.
DOI : 10.1016/S0168-6496(96)00078-5

A. Roux, C. Beloin, and J. Ghigo, Combined Inactivation and Expression Strategy To Study Gene Function under Physiological Conditions: Application to Identification of New Escherichia coli Adhesins, Journal of Bacteriology, vol.187, issue.3, pp.1001-1013, 2005.
DOI : 10.1128/JB.187.3.1001-1013.2005

G. Ramage, V. Walle, K. Wickes, B. Lopez-ribot, and J. , Standardized Method for In Vitro Antifungal Susceptibility Testing of Candida albicans Biofilms, Antimicrobial Agents and Chemotherapy, vol.45, issue.9, pp.2475-2479, 2001.
DOI : 10.1128/AAC.45.9.2475-2479.2001

D. Hacek, D. Dressel, and L. Peterson, Highly reproducible bactericidal activity test results by using a modified National Committee for Clinical Laboratory Standards broth macrodilution technique, J Clin Microbiol, vol.37, pp.1881-1884, 1999.

S. Chiang and E. Rubin, Construction of a mariner-based transposon for epitope-tagging and genomic targeting, Gene, vol.296, issue.1-2, pp.179-185, 2002.
DOI : 10.1016/S0378-1119(02)00856-9

S. Da-re and J. Ghigo, A CsgD-Independent Pathway for Cellulose Production and Biofilm Formation in Escherichia coli, Journal of Bacteriology, vol.188, issue.8, pp.3073-3087, 2006.
DOI : 10.1128/JB.188.8.3073-3087.2006

T. Baba, A. T. Hasegawa, M. Takai, Y. Okumura, and Y. , Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection, Molecular Systems Biology, vol.170, p.8, 2006.
DOI : 10.1038/msb4100050

M. Chaveroche, J. Ghigo, and C. Enfert, A rapid method for efficient gene replacement in the filamentous fungus Aspergillus nidulans, Nucleic Acids Research, vol.28, issue.22, p.97, 2000.
DOI : 10.1093/nar/28.22.e97

P. Cherepanov and W. Wackernagel, Gene disruption in Escherichia coli: TcR and KmR cassettes with the option of Flp-catalyzed excision of the antibiotic-resistance determinant, Gene, vol.158, issue.1, pp.9-14, 1995.
DOI : 10.1016/0378-1119(95)00193-A

J. Miller, A short course in bacterial genetics: a laboratory manual and handbook for Escherichia coli and related bacteria. Cold Spring Harbor, 1992.

S. Da-re, L. Quere, B. Ghigo, J. Beloin, and C. , Tight Modulation of Escherichia coli Bacterial Biofilm Formation through Controlled Expression of Adhesion Factors, Applied and Environmental Microbiology, vol.73, issue.10, pp.3391-3403, 2007.
DOI : 10.1128/AEM.02625-06
URL : https://hal.archives-ouvertes.fr/pasteur-00331439