Q. Feng, J. Wu, G. Chen, F. Cui, T. Kim et al., A mechanistic study of the antibacterial effect of silver ions onEscherichia coli andStaphylococcus aureus, Journal of Biomedical Materials Research, vol.3, issue.4, pp.662-670, 2000.
DOI : 10.1002/1097-4636(20001215)52:4<662::AID-JBM10>3.0.CO;2-3

A. Lansdown, Silver I: its antibacterial properties and mechanism of action, Journal of Wound Care, vol.11, issue.4, pp.125-155, 2002.
DOI : 10.12968/jowc.2002.11.4.26389

Y. Matsumura, K. Yoshikata, S. Kunisaki, and T. Tsuchido, Mode of Bactericidal Action of Silver Zeolite and Its Comparison with That of Silver Nitrate, Applied and Environmental Microbiology, vol.69, issue.7, pp.4278-81000184082100082, 2003.
DOI : 10.1128/AEM.69.7.4278-4281.2003

S. Silver, L. Phung, and G. Silver, Silver as biocides in burn and wound dressings and bacterial resistance to silver compounds, Journal of Industrial Microbiology & Biotechnology, vol.20, issue.7, pp.627-661, 2006.
DOI : 10.1007/s10295-006-0139-7

M. Kierans, A. Staines, H. Bennett, and G. Gadd, Silver tolerance and accumulation in yeasts, Biology of Metals, vol.32, issue.2, pp.100-106, 1991.
DOI : 10.1007/BF01135386

A. Lansdown, Silver 2: toxicity in mammals and how its products aid wound repair, Journal of Wound Care, vol.11, issue.5, pp.173-180, 2002.
DOI : 10.12968/jowc.2002.11.5.26398

H. Klasen, Historical review of the use of silver in the treatment of burns. I. Early uses, Burns, vol.26, issue.2, pp.117-147, 2000.
DOI : 10.1016/S0305-4179(99)00108-4

S. Liau, D. Read, W. Pugh, J. Furr, and A. Russell, Interaction of silver nitrate with readily identifiable groups: relationship to the antibacterialaction of silver ions, Letters in Applied Microbiology, vol.25, issue.4, pp.279-83, 1997.
DOI : 10.1046/j.1472-765X.1997.00219.x

O. Gordon, T. Slenters, P. Brunetto, A. Villaruz, D. Sturdevant et al., Silver Coordination Polymers for Prevention of Implant Infection: Thiol Interaction, Impact on Respiratory Chain Enzymes, and Hydroxyl Radical Induction, Antimicrobial Agents and Chemotherapy, vol.54, issue.10, pp.4208-4226, 2010.
DOI : 10.1128/AAC.01830-09

M. Radzig, V. Nadtochenko, O. Koksharova, J. Kiwi, V. Lipasova et al., Antibacterial effects of silver nanoparticles on gram-negative bacteria: Influence on the growth and biofilms formation, mechanisms of action, Colloids and Surfaces B: Biointerfaces, vol.102, pp.300-306, 2013.
DOI : 10.1016/j.colsurfb.2012.07.039

Y. Inoue, M. Hoshino, H. Takahashi, T. Noguchi, T. Murata et al., Bactericidal activity of Ag???zeolite mediated by reactive oxygen species under aerated conditions, Journal of Inorganic Biochemistry, vol.92, issue.1, pp.37-42, 2002.
DOI : 10.1016/S0162-0134(02)00489-0

H. Park, J. Kim, J. Kim, J. Lee, J. Hahn et al., Silver-ion-mediated reactive oxygen species generation affecting bactericidal activity, Water Research, vol.43, issue.4, pp.1027-1059, 2009.
DOI : 10.1016/j.watres.2008.12.002

C. Saulou, F. Jamme, L. Girbal, C. Maranges, I. Fourquaux et al., Synchrotron FTIR microspectroscopy of Escherichia coli at single-cell scale under silver-induced stress conditions, Analytical and Bioanalytical Chemistry, vol.9, issue.8???9, pp.2685-97, 2013.
DOI : 10.1007/s00216-013-6725-4

URL : https://hal.archives-ouvertes.fr/hal-01003324

M. Wu, K. Suryanarayanan, W. Van-ooij, and D. Oerther, Using microbial genomics to evaluate the effectiveness of silver to prevent biofilm formation. Water science and technology: a journal of the International Association on Water Pollution Research, pp.8-9413, 2007.

H. Du, T. Lo, J. Sitompul, and M. Chang, Systems-level analysis of Escherichia coli response to silver nanoparticles: the roles of anaerobic respiration in microbial resistance. Biochemical and biophysical research communications, pp.657-62, 2012.

A. Gutleb, J. Freitas, A. Murk, S. Verhaegen, E. Ropstad et al., NanoSIMS50-a powerful tool to elucidate cellular localization of halogenated organic compounds. Analytical and bioanalytical chemistry, pp.2693-2701, 2012.

P. Hoppe, S. Cohen, and A. Meibom, NanoSIMS: Technical Aspects and Applications in Cosmochemistry and Biological Geochemistry, Geostandards and Geoanalytical Research, vol.17, issue.Suppl S2, pp.111-54, 2013.
DOI : 10.1111/j.1751-908X.2013.00239.x

URL : http://hdl.handle.net/11858/00-001M-0000-0014-C390-7

C. Mueller, P. Weber, M. Kilburn, C. Hoeschen, M. Kleber et al., Advances in the Analysis of Biogeochemical Interfaces, Adv Agron, vol.121, pp.1-46, 2013.
DOI : 10.1016/B978-0-12-407685-3.00001-3

F. Blattner and . The, The Complete Genome Sequence of Escherichia coli K-12, Science, vol.277, issue.5331, pp.1453-62, 1997.
DOI : 10.1126/science.277.5331.1453

C. Saulou, B. Despax, P. Raynaud, S. Zanna, A. Seyeux et al., Plasma-Mediated Nanosilver-Organosilicon Composite Films Deposited on Stainless Steel: Synthesis, Surface Characterization, and Evaluation of Anti-Adhesive and Anti-Microbial Properties on the Model Yeast Saccharomyces cerevisiae, Plasma Processes and Polymers, vol.83, issue.144, pp.324-362, 2012.
DOI : 10.1002/ppap.201100033

URL : https://hal.archives-ouvertes.fr/hal-01268402

C. Lechene, F. Hillion, G. Mcmahon, D. Benson, A. Kleinfeld et al., High-resolution quantitative imaging of mammalian and bacterial cells using stable isotope mass spectrometry, Journal of Biology, vol.5, issue.6, pp.20-50, 2006.
DOI : 10.1186/jbiol42

R. Team, R: A language and environment for statistical computing. R Foundation for Statistical Computing V, Austria, 2012.

L. Gautier, L. Cope, B. Bolstad, and R. Irizarry, affy--analysis of Affymetrix GeneChip data at the probe level, Bioinformatics, vol.20, issue.3, pp.307-322, 2004.
DOI : 10.1093/bioinformatics/btg405

G. Smyth, R. Limma, . Bioconductor, R. Gentleman, V. Carey et al., linear models for microarray data, Bioinformatics and Computational Biology Solutions using, pp.397-420, 2005.
DOI : 10.1007/0-387-29362-0_23

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.182.2271

R. Irizarry, B. Hobbs, C. F. Beazer-barclay, Y. Antonellis, K. Scherf et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data, Biostatistics, vol.4, issue.2, pp.249-64, 2003.
DOI : 10.1093/biostatistics/4.2.249

G. Smyth, Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Statistical applications in genetics and molecular biology, 2004.
DOI : 10.2202/1544-6115.1027

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.135.8477

Y. Benjamini and Y. Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B, vol.57, pp.289-300, 1995.

A. Alexa and J. Rahnenfuhrer, topGO: Enrichment analysis for Gene Ontology, 2.2.0 Rpv, 2010.

L. Cao, K. Rossouw, D. Robert-granie, C. Besse, and P. , A Sparse PLS for Variable Selection when Integrating Omics Data. Statistical applications in genetics and molecular biology, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00300204

L. Cao, K. Gonzalez, I. Dejean, and S. , integrOmics: an R package to unravel relationships between two omics datasets, Bioinformatics, vol.25, issue.21, pp.2855-2861, 2009.
DOI : 10.1093/bioinformatics/btp515

I. Gonzalez, L. Cao, K. Davis, M. Dejean, and S. , Visualising associations between paired ???omics??? data sets, BioData Mining, vol.43, issue.3, p.19, 2013.
DOI : 10.1002/cem.1180010105

URL : https://hal.archives-ouvertes.fr/hal-00943410

P. Shannon, A. Markiel, O. Ozier, N. Baliga, J. Wang et al., Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks, Genome Research, vol.13, issue.11, pp.2498-504, 2003.
DOI : 10.1101/gr.1239303

T. Eybe, T. Bohn, J. Audinot, T. Udelhoven, H. Cauchie et al., Uptake visualization of deltamethrin by NanoSIMS and acute toxicity to the water flea Daphnia magna, Chemosphere, vol.76, issue.1, pp.134-174, 2009.
DOI : 10.1016/j.chemosphere.2009.02.005

Z. Movasaghi, S. Rehman, and I. Rehman, Fourier Transform Infrared (FTIR) Spectroscopy of Biological Tissues, Applied Spectroscopy Reviews, vol.52, issue.2, pp.134-79, 2008.
DOI : 10.1002/jrs.1107

R. Heath and C. Rock, Roles of the FabA and FabZ beta-hydroxyacyl-acyl carrier protein dehydratases in Escherichia coli fatty acid biosynthesis. The Journal of biological chemistry, pp.27795-801, 1996.

K. Magnuson, S. Jackowski, C. Rock, J. Cronan, and . Jr, Regulation of fatty acid biosynthesis in Escherichia coli. Microbiological reviews, PMID, vol.57, issue.3, pp.522-564, 1993.

A. Georgantzopoulou, Y. Balachandran, P. Rosenkranz, M. Dusinska, A. Lankoff et al., Ag nanoparticles: size- and surface-dependent effects on model aquatic organisms and uptake evaluation with NanoSIMS, Nanotoxicology, vol.401, issue.7, pp.1168-78, 2013.
DOI : 10.1021/es101484s

J. Audinot, A. Georgantzopoulou, J. Piret, A. Gutleb, D. Dowsett et al., Identification and localization of nanoparticles in tissues by mass spectrometry, Surface and Interface Analysis, vol.260, issue.1, pp.230-233, 2013.
DOI : 10.1002/sia.5099

A. Ivask, A. Elbadawy, C. Kaweeteerawat, D. Boren, H. Fischer et al., Toxicity Mechanisms in Escherichia coli Vary for Silver Nanoparticles and Differ from Ionic Silver, ACS Nano, vol.8, issue.1, pp.374-86, 2014.
DOI : 10.1021/nn4044047

B. Moen, A. Janbu, S. Langsrud, O. Langsrud, J. Hobman et al., to adverse conditions determined by microarrays and FT-IR spectroscopy, Canadian Journal of Microbiology, vol.55, issue.6, pp.714-742, 2009.
DOI : 10.1139/W09-016

B. Loffeld and H. Keweloh, cis/trans isomerization of unsaturated fatty acids as possible control mechanism of membrane fluidity inPseudomonas putida P8, Bf02522976 WOS:A1996VD35200003. PMID, pp.811-816, 1996.
DOI : 10.1007/BF02522976

H. Heipieper, F. Meinhardt, and A. Segura, The cis-trans isomerase of unsaturated fatty acids in Pseudomonas and Vibrio: biochemistry, molecular biology and physiological function of a unique stress adaptive mechanism. FEMS microbiology letters, pp.1-7, 2003.

C. Hartig, N. Loffhagen, and H. Harms, Formation of trans Fatty Acids Is Not Involved in Growth-Linked Membrane Adaptation of Pseudomonas putida, Applied and Environmental Microbiology, vol.71, issue.4, pp.1915-1937, 2005.
DOI : 10.1128/AEM.71.4.1915-1922.2005

D. Pasqua, R. Hoskins, N. Betts, G. Mauriello, and G. , Changes in Membrane Fatty Acids Composition of Microbial Cells Induced by Addiction of Thymol, Carvacrol, Limonene, Cinnamaldehyde, and Eugenol in the Growing Media, Journal of Agricultural and Food Chemistry, vol.54, issue.7, pp.2745-2754, 2006.
DOI : 10.1021/jf052722l

F. Patrignani, L. Lucci, N. Belletti, F. Gardini, A. Guerzoni et al., Effects of sub-lethal concentrations of hexanal and 2-(E)-hexenal on membrane fatty acid composition and volatile compounds of Listeria monocytogenes, Staphylococcus aureus, Salmonella enteritidis and Escherichia coli, International Journal of Food Microbiology, vol.123, issue.1-2, pp.1-8, 2008.
DOI : 10.1016/j.ijfoodmicro.2007.09.009

L. Lee, J. Barrett, and R. Poole, Genome-Wide Transcriptional Response of Chemostat-Cultured Escherichia coli to Zinc, Journal of Bacteriology, vol.187, issue.3, pp.1124-1158, 2005.
DOI : 10.1128/JB.187.3.1124-1134.2005

N. Ishii, K. Nakahigashi, T. Baba, M. Robert, T. Soga et al., Multiple High-Throughput Analyses Monitor the Response of E. coli to Perturbations, Science, vol.316, issue.5824, pp.593-600, 2007.
DOI : 10.1126/science.1132067

J. Flatley, J. Barrett, S. Pullan, M. Hughes, J. Green et al., Transcriptional Responses of Escherichia coli to S-Nitrosoglutathione under Defined Chemostat Conditions Reveal Major Changes in Methionine Biosynthesis, Journal of Biological Chemistry, vol.280, issue.11, pp.10065-72, 2005.
DOI : 10.1074/jbc.M410393200

J. Partridge, C. Scott, Y. Tang, R. Poole, and J. Green, Escherichia coli Transcriptome Dynamics during the Transition from Anaerobic to Aerobic Conditions, Journal of Biological Chemistry, vol.281, issue.38, pp.27806-27821, 2006.
DOI : 10.1074/jbc.M603450200

S. Magnet, L. Dubost, M. A. Arthur, M. Gutmann, and L. , Identification of the L,D-Transpeptidases for Peptidoglycan Cross-Linking in Escherichia coli, Journal of Bacteriology, vol.190, issue.13, pp.4782-4787, 2008.
DOI : 10.1128/JB.00025-08

S. Mclean, L. Bowman, G. Sanguinetti, R. Read, and R. Poole, K12 Elicits Expression of Oxidative Stress Responses and Protein Nitration and Nitrosylation, Journal of Biological Chemistry, vol.285, issue.27, pp.20724-20755, 2010.
DOI : 10.1074/jbc.M109.085506

S. Jozefczuk, S. Klie, G. Catchpole, J. Szymanski, A. Cuadros-inostroza et al., Metabolomic and transcriptomic stress response of Escherichia coli, Molecular Systems Biology, vol.180, 2010.
DOI : 10.1128/JB.183.15.4562-4570.2001

URL : http://doi.org/10.1038/msb.2010.18

C. Kershaw, N. Brown, C. Constantinidou, M. Patel, and J. Hobman, The expression profile of Escherichia coli K-12 in response to minimal, optimal and excess copper concentrations, Microbiology, vol.151, issue.4, pp.1187-98000228509100017, 2005.
DOI : 10.1099/mic.0.27650-0

K. Helbig, C. Grosse, and D. Nies, Cadmium Toxicity in Glutathione Mutants of Escherichia coli, Journal of Bacteriology, vol.190, issue.15, pp.5439-54, 2008.
DOI : 10.1128/JB.00272-08

J. Fantino, B. Py, M. Fontecave, and F. Barras, A genetic analysis of the response of Escherichia coli to cobalt stress, Environmental Microbiology, vol.61, issue.10, pp.2846-57, 2010.
DOI : 10.1111/j.1462-2920.2010.02265.x

URL : https://hal.archives-ouvertes.fr/hal-01145017