S. Widder, Challenges in microbial ecology: building predictive understanding of community function and dynamics, The ISME Journal, vol.11, issue.11, pp.2557-2568, 2016.
DOI : 10.1038/ismej.2011.11

URL : https://hal.archives-ouvertes.fr/hal-01512087

D. T. Hughes and V. Sperandio, Inter-kingdom signalling: communication between bacteria and their hosts, Nature Reviews Microbiology, vol.270, issue.2, pp.111-120, 2008.
DOI : 10.1099/00221287-148-4-1119

URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2667375/pdf

K. Vetsigian, R. Jajoo, and R. Kishony, Structure and Evolution of Streptomyces Interaction Networks in Soil and In Silico, PLoS Biology, vol.37, issue.10, p.1001184, 2011.
DOI : 10.1371/journal.pbio.1001184.s008

E. H. Wintermute and P. A. Silver, Dynamics in the mixed microbial concourse, Genes & Development, vol.24, issue.23, pp.2603-2614, 2010.
DOI : 10.1101/gad.1985210

E. A. Shank and R. Kolter, Extracellular signaling and multicellularity in Bacillus subtilis, Current Opinion in Microbiology, vol.14, issue.6, pp.741-747, 2011.
DOI : 10.1016/j.mib.2011.09.016

URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3291330/pdf

M. Ackermann, A functional perspective on phenotypic heterogeneity in microorganisms, Nature Reviews Microbiology, vol.10, issue.8, pp.497-508, 2015.
DOI : 10.1371/journal.ppat.1003987

D. Claessen, D. E. Rozen, O. P. Kuipers, L. Søgaard-andersen, and G. P. Van-wezel, Bacterial solutions to multicellularity: a tale of biofilms, filaments and fruiting bodies, Nature Reviews Microbiology, vol.107, issue.2, pp.115-124, 2014.
DOI : 10.1073/pnas.0911299107

H. Vlamakis, C. Aguilar, R. Losick, and R. Kolter, Control of cell fate by the formation of an architecturally complex bacterial community, Genes & Development, vol.22, issue.7, pp.945-953, 2008.
DOI : 10.1101/gad.1645008

P. D. Straight and R. Kolter, Interspecies Chemical Communication in Bacterial Development, Annual Review of Microbiology, vol.63, issue.1, pp.99-118, 2009.
DOI : 10.1146/annurev.micro.091208.073248

M. Fauvart, V. N. De-groote, and J. Michiels, Role of persister cells in chronic infections: clinical relevance and perspectives on anti-persister therapies, Journal of Medical Microbiology, vol.60, issue.6, pp.699-709, 2011.
DOI : 10.1099/jmm.0.030932-0

S. T. Rutherford and B. L. Bassler, Bacterial quorum sensing: its role in virulence and possibilities for itscontrol. Cold Spring Harb, Perspect. Med, vol.2, pp.12427-012427, 2012.
DOI : 10.1101/cshperspect.a012427

URL : http://perspectivesinmedicine.cshlp.org/content/2/11/a012427.full.pdf

M. Ackermann, Self-destructive cooperation mediated by phenotypic noise, Nature, vol.261, issue.7207, pp.987-990, 2008.
DOI : 10.1038/nature07067

C. Grandclément, Quorum quenching: role in nature and applied developments, FEMS Microbiology Reviews, vol.40, issue.1, pp.86-116, 2016.
DOI : 10.1093/femsre/fuv038

P. Wang, Robust Growth of Escherichia coli, Current Biology, vol.20, issue.12, pp.1099-1103, 2010.
DOI : 10.1016/j.cub.2010.04.045

URL : https://doi.org/10.1016/j.cub.2010.04.045

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

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

URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3329571/pdf

J. S. Chuang, Engineering multicellular traits in synthetic microbial populations, Current Opinion in Chemical Biology, vol.16, issue.3-4, pp.370-378, 2012.
DOI : 10.1016/j.cbpa.2012.04.002

W. Kong, V. Celik, C. Liao, Q. Hua, and T. Lu, Programming the group behaviors of bacterial communities with synthetic cellular communication, Bioresources and Bioprocessing, vol.12, issue.3, p.24, 2014.
DOI : 10.1016/j.ymben.2010.01.002

C. C. Guet, M. B. Elowitz, W. Hsing, and S. Leibler, Combinatorial Synthesis of Genetic Networks, Science, vol.296, issue.5572, pp.1466-1470, 2002.
DOI : 10.1126/science.1067407

R. Kwok, Five hard truths for synthetic biology, Nature, vol.463, issue.7279, pp.288-291, 2010.
DOI : 10.1038/463288a

URL : http://www.nature.com/news/2010/100120/pdf/463288a.pdf

L. Potvin-trottier, N. D. Lord, G. Vinnicombe, and J. Paulsson, Synchronous long-term oscillations in a synthetic gene circuit, Nature, vol.5, issue.7626, pp.514-517, 2016.
DOI : 10.1371/journal.pone.0015179

URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5637407/pdf

W. J. Holtz and J. D. Keasling, Engineering Static and Dynamic Control of Synthetic Pathways, Cell, vol.140, issue.1, pp.19-23, 2010.
DOI : 10.1016/j.cell.2009.12.029

URL : https://doi.org/10.1016/j.cell.2009.12.029

A. Milias-argeitis, In silico feedback for in vivo regulation of a gene expression circuit, Nature Biotechnology, vol.5, issue.12, pp.1114-1116, 2011.
DOI : 10.1186/1754-1611-3-15

A. Milias-argeitis, M. Rullan, S. K. Aoki, P. Buchmann, and M. Khammash, Automated optogenetic feedback control for precise and robust regulation of gene expression and cell growth, Nature Communications, vol.405, p.12546, 2016.
DOI : 10.1016/j.jmb.2010.10.038

J. Ruess, F. Parise, A. Milias-argeitis, M. Khammash, and J. Lygeros, Iterative experiment design guides the characterization of a light-inducible gene expression circuit, Proc. Natl Acad. Sci. USA, pp.8148-8153, 2015.
DOI : 10.1371/journal.pcbi.1002010

J. Uhlendorf, Long-term model predictive control of gene expression at the population and single-cell levels, Proc. Natl Acad. Sci. USA, pp.14271-14276, 2012.
DOI : 10.1016/0031-3203(81)90009-1

URL : https://hal.archives-ouvertes.fr/hal-01528440

E. J. Olson, L. A. Hartsough, B. P. Landry, R. Shroff, and J. J. Tabor, Characterizing bacterial gene circuit dynamics with optically programmed gene expression signals, Nature Methods, vol.498, issue.4, pp.449-455, 2014.
DOI : 10.1371/journal.pone.0003647

F. Menolascina, In-Vivo Real-Time Control of Protein Expression from Endogenous and Synthetic Gene Networks, PLoS Computational Biology, vol.5, issue.5, p.1003625, 2014.
DOI : 10.1371/journal.pcbi.1003625.s028

J. Melendez, Real-time optogenetic control of intracellular protein concentration in microbial cell cultures, Integrative Biology, vol.11, issue.3, pp.366-372, 2014.
DOI : 10.1038/nrm2904

J. E. Toettcher, D. Gong, W. A. Lim, and O. D. Weiner, Light-based feedback for controlling intracellular signaling dynamics, Nature Methods, vol.497, issue.10, pp.837-839, 2011.
DOI : 10.1016/B978-0-12-385075-1.00017-2

URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3184382/pdf

S. R. Schmidl, R. U. Sheth, A. Wu, and J. J. Tabor, Two-Component Systems, ACS Synthetic Biology, vol.3, issue.11, pp.820-831, 2014.
DOI : 10.1021/sb500273n

Y. Hirose, T. Shimada, R. Narikawa, M. Katayama, and M. Ikeuchi, Cyanobacteriochrome CcaS is the green light receptor that induces the expression of phycobilisome linker protein, Proc. Natl Acad. Sci. USA 105, pp.9528-9533, 2008.
DOI : 10.1016/0076-6879(88)67004-2

G. Fiore, G. Perrino, M. Di-bernardo, and D. Di-bernardo, Real-Time Control of Gene Expression: A Comparative Analysis of Feedback Control Strategies in Yeast, ACS Synthetic Biology, vol.5, issue.2, pp.154-162, 2016.
DOI : 10.1021/acssynbio.5b00135

C. J. Davidson and M. G. Surette, Individuality in Bacteria, Annual Review of Genetics, vol.42, issue.1, pp.253-268, 2008.
DOI : 10.1146/annurev.genet.42.110807.091601

E. Kussell, Bacterial Persistence: A Model of Survival in Changing Environments, Genetics, vol.169, issue.4, pp.1807-1814, 2005.
DOI : 10.1534/genetics.104.035352

C. Walsh, Antibiotics: Actions, Origins, Resistance, 2003.
DOI : 10.1128/9781555817886

R. I. Aminov, The role of antibiotics and antibiotic resistance in nature, Environmental Microbiology, vol.53, issue.Suppl. 9A, pp.2970-2988, 2009.
DOI : 10.1128/jb.170.3.1319-1324.1988

J. B. Deris, The Innate Growth Bistability and Fitness Landscapes of Antibiotic-Resistant Bacteria, Science, vol.36, issue.3, pp.1237435-1237435, 2013.
DOI : 10.1021/jm00055a008

B. Novák and J. J. Tyson, Design principles of biochemical oscillators, Nature Reviews Molecular Cell Biology, vol.39, issue.12, pp.981-991, 2008.
DOI : 10.1111/j.1749-6632.1979.tb29471.x

T. Danino, O. Mondragón-palomino, L. Tsimring, and J. Hasty, A synchronized quorum of genetic clocks, Nature, vol.44, issue.7279, pp.326-330, 2010.
DOI : 10.1038/msb4100032

J. Stricker, A fast, robust and tunable synthetic gene oscillator, Nature, vol.2, issue.7221, pp.516-519, 2008.
DOI : 10.1038/msb4100032

S. H. Strogatz and I. Stewart, Coupled Oscillators and Biological Synchronization, Scientific American, vol.269, issue.6, pp.102-109, 1993.
DOI : 10.1038/scientificamerican1293-102

T. Tschirhart, Electronic control of gene expression and cell behaviour in Escherichia coli through redox signalling, Nature Communications, vol.504, p.14030, 2017.
DOI : 10.1073/pnas.120163297

M. Rullan, Optogenetic single-cell control of transcription achieves Mrna tunability and reduced variability. Preprint at https://doi.org/10, p.142893, 1101.
DOI : 10.1101/142893

C. Zechner, M. Unger, S. Pelet, M. Peter, and H. Koeppl, Scalable inference of heterogeneous reaction kinetics from pooled single-cell recordings, Nature Methods, vol.92, issue.2, pp.197-202, 2014.
DOI : 10.1109/78.978383

L. Keller and M. G. Surette, Communication in bacteria: an ecological and evolutionary perspective, Nature Reviews Microbiology, vol.184, issue.4, pp.249-258, 2006.
DOI : 10.4049/jimmunol.169.5.2636

F. Jacob, The Possible and the Actual (Pantheon Books, 1982.

A. D. Edelstein, Advanced methods of microscope control using ??Manager software, Journal of Biological Methods, vol.1, issue.2, p.10, 2014.
DOI : 10.14440/jbm.2014.36

URL : https://doi.org/10.14440/jbm.2014.36

A. C. Hindmarsh, SUNDIALS, ACM Transactions on Mathematical Software, vol.31, issue.3, pp.363-396, 2005.
DOI : 10.1145/1089014.1089020

J. N. Stirman, M. M. Crane, S. J. Husson, A. Gottschalk, and H. Lu, A multispectral optical illumination system with precise spatiotemporal control for the manipulation of optogenetic reagents, Nature Protocols, vol.77, issue.2, pp.207-220, 2012.
DOI : 10.1073/pnas.0409009101

M. A. Model and J. K. Burkhardt, A standard for calibration and shading correction of a fluorescence microscope, Cytometry, vol.26, issue.4, pp.309-316, 2001.
DOI : 10.1177/26.4.77868

E. A. Davidson, A. S. Basu, and T. S. Bayer, Programming Microbes Using Pulse Width Modulation of Optical Signals, Journal of Molecular Biology, vol.425, issue.22, pp.4161-4166, 2013.
DOI : 10.1016/j.jmb.2013.07.036

URL : https://doi.org/10.1016/j.jmb.2013.07.036

A. Estévez-torres, A. Yamada, and L. Wang, An inexpensive and durable epoxy mould for PDMS. Chips and Tips, 2009.

T. Bergmiller, Biased partitioning of the multidrug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity, Science, vol.356, issue.6335, pp.311-315, 2017.
DOI : 10.15252/msb.20145949

T. Baba, Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection, Molecular Systems Biology, vol.170, p.8, 2006.
DOI : 10.1353/pbm.1973.0061