L. Keller and M. G. Surette, Communication in bacteria: an ecological and evolutionary perspective, Nat. Rev. Microbiol, vol.4, pp.249-258, 2006.

R. D. Monds and G. A. O'toole, Metabolites as intracellular signals for regulation of community level traits, Chemical communication among bacteria, pp.105-129, 2008.

P. D. Straight and R. Kolter, Interspecies chemical communication in bacterial development, Annu. Rev. Microbiol, vol.63, pp.99-118, 2009.

S. Schulz and J. S. Dickschat, Bacterial volatiles: the smell of small organisms, Nat. Prod. Rep, vol.24, pp.814-842, 2007.

M. Dunkel, U. Schmidt, S. Struck, L. Berger, B. Gruening et al., Superscent-a database of flavors and scents, Nucleic Acids Res, vol.37, pp.291-294, 2009.

L. Bos, P. J. Sterk, and M. J. Schultz, Volatile metabolites of pathogens: a systematic review, PLoS Pathog, vol.9, 2013.

D. H. Williams, M. J. Stone, P. R. Hauck, and S. K. Rahman, Why are secondary metabolites (natural products) biosynthesized?, J. Nat. Prod, vol.52, pp.1189-1208, 1989.

M. Kai, M. Haustein, F. Molina, A. Petri, B. Scholz et al., Bacterial volatiles and their action potential, Appl. Microbiol. Biotechnol, vol.81, pp.1001-1012, 2009.

Q. Niu, X. Huang, L. Zhang, J. Xu, D. Yang et al., A Trojan horse mechanism of bacterial pathogenesis against nematodes, Proc. Natl. Acad. Sci. U. S. A, vol.107, pp.16631-16636, 2010.

D. Blom, C. Fabbri, L. Eberl, and L. Weisskopf, Volatile-mediated killing of Arabidopsis thaliana by bacteria is mainly due to hydrogen cyanide, Appl. Environ. Microbiol, vol.77, pp.1000-1008, 2011.

U. Effmert, J. Kalderas, R. Warnke, and B. Piechulla, Volatile mediated interactions between bacteria and fungi in the soil, J. Chem. Ecol, vol.38, pp.665-703, 2012.

Q. Ma, A. Fonseca, W. Liu, A. T. Fields, M. L. Pimsler et al., Proteus mirabilis interkingdom swarming signals attract blow flies, ISME J, vol.6, pp.1356-1366, 2012.

R. D. Heal and A. T. Parsons, Novel intercellular communication system in Escherichia coli that confers antibiotic resistance between physically separated populations, J. Appl. Microbiol, vol.92, pp.1116-1122, 2002.

J. J. Cepl, I. Patkova, A. Blahuskova, F. Cvrckova, and M. A. , Patterning of mutually interacting bacterial bodies: close contacts and airborne signals, BMC Microbiol, vol.10, p.139, 2010.
DOI : 10.1186/1471-2180-10-139

URL : https://doi.org/10.1186/1471-2180-10-139

R. Nijland and J. G. Burgess, Bacterial olfaction, Biotechnol. J, vol.5, pp.974-977, 2010.
DOI : 10.1002/biot.201000174

URL : https://hal.archives-ouvertes.fr/hal-00599454

J. H. Lee and J. Lee, Indole as an intercellular signal in microbial communities, FEMS Microbiol. Rev, vol.34, pp.426-444, 2010.
DOI : 10.1111/j.1574-6976.2009.00204.x

URL : https://academic.oup.com/femsre/article-pdf/34/4/426/18141679/34-4-426.pdf

S. P. Bernier, S. Letoffe, M. Delepierre, and J. M. Ghigo, Biogenic ammonia modifies antibiotic resistance at a distance in physically separated bacteria, Mol. Microbiol, vol.81, pp.705-716, 2011.
DOI : 10.1111/j.1365-2958.2011.07724.x

URL : https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-2958.2011.07724.x

M. Kesarwani, R. Hazan, J. He, Y. A. Que, Y. Apidianakis et al., A quorum sensing regulated small volatile molecule reduces acute virulence and promotes chronic infection phenotypes, PLoS Pathog, vol.7, 2011.
DOI : 10.1371/journal.ppat.1002192

URL : https://hal.archives-ouvertes.fr/pasteur-00722217

K. S. Kim, S. Lee, and C. M. Ryu, Interspecific bacterial sensing through airborne signals modulates locomotion and drug resistance, Nat. Commun, vol.4, p.1809, 2013.
DOI : 10.1038/ncomms2789

URL : https://www.nature.com/articles/ncomms2789.pdf

E. L. Barrett and H. S. Kwan, Bacterial reduction of trimethylamine oxide, Annu. Rev. Microbiol, vol.39, pp.131-149, 1985.
DOI : 10.1146/annurev.micro.39.1.131

S. L. Mccrindle, U. Kappler, and A. G. Mcewan, Microbial dimethylsulfoxide and trimethylamine-N-oxide respiration, Adv. Microb. Physiol, vol.50, pp.147-198, 2005.

M. Ansaldi, L. Theraulaz, C. Baraquet, G. Panis, and V. Mejean, Aerobic TMAO respiration in Escherichia coli, Mol. Microbiol, vol.66, pp.484-494, 2007.
DOI : 10.1111/j.1365-2958.2007.05936.x

URL : https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-2958.2007.05936.x

J. J. Joffraud, F. Leroi, C. Roy, and J. L. Berdague, Characterisation of volatile compounds produced by bacteria isolated from the spoilage flora of cold-smoked salmon, Int. J. Food Microbiol, vol.66, pp.175-184, 2001.

M. A. Farag, C. M. Ryu, L. W. Sumner, and P. W. Pare, GC-MS SPME profiling of rhizobacterial volatiles reveals prospective inducers of growth promotion and induced systemic resistance in plants, Phytochemistry, vol.67, pp.2262-2268, 2006.

M. Bunge, N. Araghipour, T. Mikoviny, J. Dunkl, R. Schnitzhofer et al., On-line monitoring of microbial volatile metabolites by proton transfer reactionmass spectrometry, Appl. Environ. Microbiol, vol.74, pp.2179-2186, 2008.
DOI : 10.1128/aem.02069-07

URL : https://aem.asm.org/content/aem/74/7/2179.full.pdf

R. M. Thorn, D. M. Reynolds, and J. Greenman, Multivariate analysis of bacterial volatile compound profiles for discrimination between selected species and strains in vitro, J. Microbiol. Methods, vol.84, pp.258-264, 2011.

C. J. Rebouche and H. Seim, Carnitine metabolism and its regulation in microorganisms and mammals, Annu. Rev. Nutr, vol.18, pp.39-61, 1998.
DOI : 10.1146/annurev.nutr.18.1.39

M. Al-waiz, M. Mikov, S. C. Mitchell, and R. L. Smith, The exogenous origin of trimethylamine in the mouse, Metab. Clin. Exp, vol.41, pp.135-136, 1992.

R. A. Koeth, Z. Wang, B. S. Levison, J. A. Buffa, E. Org et al., Intestinal microbiota metabolism of l-carnitine, a nutrient in red meat, promotes atherosclerosis, Nat. Med, vol.19, pp.576-585, 2013.

F. Sargent, B. C. Berks, and T. Palmer, Assembly of membrane-bound respiratory complexes by the Tat protein-transport system, Arch. Microbiol, vol.178, pp.77-84, 2002.

S. P. Lubitz and J. H. Weiner, The Escherichia coli ynfEFGHI operon encodes polypeptides which are paralogues of dimethyl sulfoxide reductase (DmsABC), Arch. Biochem. Biophys, vol.418, pp.205-216, 2003.

R. M. Kappes, B. Kempf, and E. Bremer, Three transport systems for the osmoprotectant glycine betaine operate in Bacillus subtilis: characterization of OpuD, J. Bacteriol, vol.178, pp.5071-5079, 1996.

C. Ziegler, E. Bremer, and R. Kramer, The BCCT family of carriers: from physiology to crystal structure, Mol. Microbiol, vol.78, pp.13-34, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00572623

K. A. Loftin, C. D. Adams, M. T. Meyer, and R. Surampalli, Effects of ionic strength, temperature, and pH on degradation of selected antibiotics, J. Environ. Qual, vol.37, pp.378-386, 2008.

A. Yamaguchi, H. Ohmori, M. Kaneko-ohdera, T. Nomura, and T. Sawai, Delta pH-dependent accumulation of tetracycline in Escherichia coli, Antimicrob. Agents Chemother, vol.35, pp.53-56, 1991.

S. Da-re, L. Quere, B. Ghigo, J. M. Beloin, and C. , Tight modulation of Escherichia coli bacterial biofilm formation through controlled expression of adhesion factors, Appl. Environ. Microbiol, vol.73, pp.3391-3403, 2007.
URL : https://hal.archives-ouvertes.fr/pasteur-00331439

A. Korpi, A. L. Pasanen, and P. Pasanen, Volatile compounds originating from mixed microbial cultures on building materials under various humidity conditions, Appl. Environ. Microbiol, vol.64, pp.2914-2919, 1998.

R. E. Wheatley, The consequences of volatile organic compound mediated bacterial and fungal interactions, Antonie Van Leeuwenhoek, vol.81, pp.357-364, 2002.

D. Martino, P. Fursy, R. Bret, L. Sundararaju, B. Phillips et al., Indole can act as an extracellular signal to regulate biofilm formation of Escherichia coli and other indole-producing bacteria, Can. J. Microbiol, vol.49, pp.443-449, 2003.

J. Domka, J. Lee, and T. K. Wood, YliH (BssR) and YceP (BssS) regulate Escherichia coli K-12 biofilm formation by influencing cell signaling, Appl. Environ. Microbiol, vol.72, pp.2449-2459, 2006.

M. Hu, C. Zhang, Y. Mu, Q. Shen, and Y. Feng, Indole affects biofilm formation in bacteria, Indian J. Microbiol, vol.50, pp.362-368, 2010.

J. L. Burns and A. L. Smith, Chloramphenicol accumulation by Haemophilus influenzae, Antimicrob. Agents Chemother, vol.31, pp.686-690, 1987.

H. W. Taber, J. P. Mueller, P. F. Miller, and A. S. Arrow, Bacterial uptake of aminoglycoside antibiotics, Microbiol. Rev, vol.51, pp.439-457, 1987.

B. S. Speer, N. B. Shoemaker, and A. A. Salyers, Bacterial resistance to tetracycline: mechanisms, transfer, and clinical significance, Clin. Microbiol. Rev, vol.5, pp.387-399, 1992.

H. Nikaido, Transport across the bacterial outer membrane, J. Bioenerget. Biomembr, vol.25, pp.581-589, 1993.

H. Minakami, J. W. Kitzler, and I. Fridovich, Effects of pH, glucose, and chelating agents on lethality of paraquat to Escherichia coli, J. Bacteriol, vol.172, pp.691-695, 1990.

R. B. Gennis, V. Stewart, R. Curtiss, . Iii, A. Böck et al., Chapter 17. Respiration, EcoSal-Escherichia coli and Salmonella. Cellular and molecular biology, 2005.

C. Bordi, L. Theraulaz, V. Mejean, and C. Jourlin-castelli, Anticipating an alkaline stress through the Tor phosphorelay system in Escherichia coli, Mol. Microbiol, vol.48, pp.211-223, 2003.

B. A. Seibel and P. J. Walsh, Trimethylamine oxide accumulation in marine animals: relationship to acylglycerol storage, J. Exp. Biol, vol.205, pp.297-306, 2002.

S. P. Bernier and M. G. Surette, Concentration-dependent activity of antibiotics in natural environments, Front. Microbiol, vol.4, issue.20, 2013.

E. B. Goh, G. Yim, W. Tsui, J. Mcclure, M. G. Surette et al., Transcriptional modulation of bacterial gene expression by subinhibitory concentrations of antibiotics, Proc. Natl. Acad. Sci. U. S. A, vol.99, pp.17025-17030, 2002.

L. R. Hoffman, D. Argenio, D. A. Maccoss, M. J. Zhang, Z. Jones et al., Aminoglycoside antibiotics induce bacterial biofilm formation, Nature, vol.436, pp.1171-1175, 2005.

I. Gusarov, K. Shatalin, M. Starodubtseva, and E. Nudler, Endogenous nitric oxide protects bacteria against a wide spectrum of antibiotics, Science, vol.325, pp.1380-1384, 2009.

H. H. Lee, M. N. Molla, C. R. Cantor, and J. J. Collins, Bacterial charity work leads to population-wide resistance, Nature, vol.467, pp.82-85, 2010.

K. Shatalin, E. Shatalina, A. Mironov, and E. Nudler, H2S: a universal defense against antibiotics in bacteria, Science, vol.334, pp.986-990, 2011.

A. Nostro, L. Cellini, D. Giulio, M. , D. 'arrigo et al., Effect of alkaline pH on staphylococcal biofilm formation, APMIS, vol.120, pp.733-742, 2012.

S. Piccirillo, M. G. White, J. C. Murphy, D. J. Law, and S. M. Honigberg, The Rim101p/PacC pathway and alkaline pH regulate pattern formation in yeast colonies, Genetics, vol.184, pp.707-716, 2010.

S. Vylkova, A. J. Carman, H. A. Danhof, J. R. Collette, H. Zhou et al., The fungal pathogen Candida albicans autoinduces hyphal morphogenesis by raising extracellular pH, vol.2, pp.55-66, 2011.

P. E. Sudbery, Growth of Candida albicans hyphae, Nat. Rev. Microbiol, vol.9, pp.737-748, 2011.

T. Baba, T. Ara, M. Hasegawa, Y. Takai, Y. Okumura et al., Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection, 2006.

, Mol. Syst. Biol, vol.2, p.8

M. K. Chaveroche, J. M. Ghigo, and C. Enfert, A rapid method for efficient gene replacement in the filamentous fungus Aspergillus nidulans, Nucleic Acids Res, vol.28, 2000.

K. A. Datsenko and B. L. Wanner, One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products, Proc. Natl. Acad. Sci. U. S. A, vol.97, pp.6640-6645, 2000.

P. 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, pp.9-14, 1995.

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

M. S. Guyer, R. R. Reed, J. A. Steitz, and K. B. Low, Identification of a sexfactor-affinity site in E. coli as gamma delta, Cold Spring Harb. Symp. Quant. Biol, vol.45, pp.135-140, 1981.

J. M. Ghigo, Natural conjugative plasmids induce bacterial biofilm development, Nature, vol.412, pp.442-445, 2001.

S. Herbert, A. K. Ziebandt, K. Ohlsen, T. Schafer, M. Hecker et al., Repair of global regulators in Staphylococcus aureus 8325 and comparative analysis with other clinical isolates, Infect. Immun, vol.78, pp.2877-2889, 2010.

P. R. Burkholder and N. H. Giles, Induced biochemical mutations in Bacillus subtilis, Am. J. Bot, vol.34, pp.345-348, 1947.

. Létoffé,