N. Agawin, S. Rabouille, M. Veldhuis, L. Servatius, S. Hol et al., Competition and facilitation between unicellular nitrogen-fixing cyanobacteria and non-nitrogen-fixing phytoplankton species, Limnology and Oceanography, vol.52, issue.5, pp.2233-2248, 2007.
DOI : 10.4319/lo.2007.52.5.2233
URL : http://hdl.handle.net/11245/1.272207

M. Asally, M. Kittisopikul, P. Rue, Y. Du, Z. Hu et al., Localized cell death focuses mechanical forces during 3D patterning in a biofilm, Proceedings of the National Academy of Sciences, vol.51, issue.12, pp.18891-18896, 2012.
DOI : 10.1167/iovs.10-5470

Y. Bai, D. Muller, G. Srinivas, R. Garrido-oter, E. Potthoff et al., Functional overlap of the Arabidopsis leaf and root microbiota, Nature, vol.528, issue.7582, pp.364-369, 2015.
DOI : 10.1371/journal.pgen.1004283

J. Baranyi and M. Tamplin, ComBase: A Common Database on Microbial Responses to Food Environments, Journal of Food Protection, vol.67, issue.9, pp.1967-1971, 2004.
DOI : 10.4315/0362-028X-67.9.1967

D. Berry, E. Mader, T. Lee, D. Woebken, Y. Wang et al., O) incorporation for identifying and sorting active microbial cells, Proceedings of the National Academy of Sciences, vol.59, issue.3, pp.194-203, 2015.
DOI : 10.1351/pac200375060683

D. Berry and S. Widder, Deciphering microbial interactions and detecting keystone species with co-occurrence networks, Frontiers in Microbiology, vol.6, p.219, 2014.
DOI : 10.1046/j.1365-294X.1997.00205.x
URL : http://doi.org/10.3389/fmicb.2014.00219

N. Bodenhausen, M. Bortfeld-miller, M. Ackermann, and J. Vorholt, A Synthetic Community Approach Reveals Plant Genotypes Affecting the Phyllosphere Microbiota, PLoS Genetics, vol.54, issue.4, p.1004283, 2014.
DOI : 10.1371/journal.pgen.1004283.s015

J. Bonachela, M. Raghib, and S. Levin, Dynamic model of flexible phytoplankton nutrient uptake, Proceedings of the National Academy of Sciences, vol.257, issue.1, pp.20633-20638, 2011.
DOI : 10.1016/j.jtbi.2008.10.032

S. Brown, L. Chat, L. Taddei, and F. , Evolution of virulence: triggering host inflammation allows invading pathogens to exclude competitors, Ecology Letters, vol.181, issue.0, pp.44-51, 2008.
DOI : 10.1098/rspb.2002.2209

H. Celiker and J. Gore, Clustering in community structure across replicate ecosystems following a long-term bacterial evolution experiment, Nature Communications, vol.26, p.4643, 2014.
DOI : 10.1038/ncomms5643

O. Cordero, L. Ventouras, E. Delong, and M. Polz, Public good dynamics drive evolution of iron acquisition strategies in natural bacterioplankton populations, Proceedings of the National Academy of Sciences, vol.26, issue.7, pp.20059-20064, 2012.
DOI : 10.1093/molbev/msp077

O. Cordero, H. Wildschutte, B. Kirkup, S. Proehl, L. Ngo et al., Ecological Populations of Bacteria Act as Socially Cohesive Units of Antibiotic Production and Resistance, Science, vol.71, issue.12, pp.1228-1231, 2012.
DOI : 10.1128/AEM.71.12.8531-8536.2005

K. Coyte, J. Schluter, and K. Foster, The ecology of the microbiome: Networks, competition, and stability, Science, vol.113, issue.3, pp.663-666, 2015.
DOI : 10.1128/MMBR.00051-12

L. David, C. Maurice, R. Carmody, D. Gootenberg, J. Button et al., Diet rapidly and reproducibly alters the human gut microbiome, Nature, vol.24, issue.7484, pp.559-563, 2014.
DOI : 10.1111/j.1365-294X.1993.tb00005.x

D. Davies, Understanding biofilm resistance to antibacterial agents, Nature Reviews Drug Discovery, vol.2, issue.2, pp.114-122, 2003.
DOI : 10.1038/nrd1008

V. Denef, R. Mueller, and J. Banfield, AMD biofilms: using model communities to study microbial evolution and ecological complexity in nature, The ISME Journal, vol.10, issue.5, pp.599-610, 2010.
DOI : 10.1016/j.cbpa.2003.12.003

D. Quemener, E. Bouchez, and T. , A thermodynamic theory of microbial growth, The ISME Journal, vol.683, issue.8, pp.1747-1751, 2014.
DOI : 10.1038/ismej.2014.7
URL : https://hal.archives-ouvertes.fr/hal-00825781

O. Eilam, R. Zarecki, M. Oberhardt, L. Ursell, M. Kupiec et al., Glycan Degradation (GlyDeR) Analysis Predicts Mammalian Gut Microbiota Abundance and Host Diet-Specific Adaptations, mBio, vol.5, issue.4, 2014.
DOI : 10.1128/mBio.01526-14
URL : http://doi.org/10.1128/mbio.01526-14

S. Elias and E. Banin, Multi-species biofilms: living with friendly neighbors, FEMS Microbiology Reviews, vol.36, issue.5, pp.990-1004, 2012.
DOI : 10.1111/j.1574-6976.2012.00325.x

S. Estrela, M. Whiteley, and S. Brown, The demographic determinants of human microbiome health, Trends in Microbiology, vol.23, issue.3, pp.134-141, 2015.
DOI : 10.1016/j.tim.2014.11.005

J. Faith, P. Ahern, V. Ridaura, J. Cheng, and J. Gordon, Identifying Gut Microbe-Host Phenotype Relationships Using Combinatorial Communities in Gnotobiotic Mice, Science Translational Medicine, vol.110, issue.33, pp.220-211, 2014.
DOI : 10.1073/pnas.1312524110

K. Faust, J. Sathirapongsasuti, J. Izard, N. Segata, D. Gevers et al., Microbial Co-occurrence Relationships in the Human Microbiome, PLoS Computational Biology, vol.22, issue.7, p.1002606, 2012.
DOI : 10.1371/journal.pcbi.1002606.s013

F. Fiegna, A. Moreno-letelier, T. Bell, and T. Barraclough, Evolution of species interactions determines microbial community productivity in new environments, The ISME Journal, vol.38, issue.5, pp.1235-1245, 2014.
DOI : 10.1111/ele.12056

H. Flint, S. Duncan, K. Scott, and P. Louis, Interactions and competition within the microbial community of the human colon: links between diet and health, Environmental Microbiology, vol.64, issue.5, pp.1101-1111, 2007.
DOI : 10.1016/j.mimet.2004.06.002

K. Foster and T. Bell, Competition, Not Cooperation, Dominates Interactions among Culturable Microbial Species, Current Biology, vol.22, issue.19, pp.1845-1850, 2012.
DOI : 10.1016/j.cub.2012.08.005
URL : http://doi.org/10.1016/j.cub.2012.08.005

S. Freilich, A. Kreimer, I. Meilijson, U. Gophna, R. Sharan et al., The large-scale organization of the bacterial network of ecological co-occurrence interactions, Nucleic Acids Research, vol.38, issue.12, pp.3857-3868, 2010.
DOI : 10.1093/nar/gkq118

S. Freilich, R. Zarecki, O. Eilam, E. Segal, C. Henry et al., Competitive and cooperative metabolic interactions in bacterial communities, Nature Communications, vol.25, p.589, 2011.
DOI : 10.1038/ncomms1597

Z. Frentz, S. Kuehn, D. Hekstra, and S. Leibler, Microbial population dynamics by digital in-line holographic microscopy, Review of Scientific Instruments, vol.1, issue.8, p.84301, 2010.
DOI : 10.1038/nature02945

J. Friedman and E. Alm, Inferring Correlation Networks from Genomic Survey Data, PLoS Computational Biology, vol.8, issue.9, p.1002687, 2012.
DOI : 10.1371/journal.pcbi.1002687.s010
URL : http://doi.org/10.1371/journal.pcbi.1002687

J. Fuhrman, Microbial community structure and its functional implications, Nature, vol.62, issue.7244, pp.193-199, 2009.
DOI : 10.1038/nature08058

P. Gomez and A. Buckling, Real-time microbial adaptive diversification in soil, Ecology Letters, vol.66, issue.5, pp.650-655, 2013.
DOI : 10.1111/ele.12093

R. Gonzalez-cabaleiro, J. Lema, J. Rodríguez, and R. Kleerebezem, Linking thermodynamics and kinetics to assess pathway reversibility in anaerobic bioprocesses, Energy & Environmental Science, vol.28, issue.12, pp.3780-3789, 2013.
DOI : 10.1039/c3ee42754d

J. Gore, H. Youk, and A. Van-oudenaarden, Snowdrift game dynamics and facultative cheating in yeast, Nature, vol.33, issue.7244, pp.253-256, 2009.
DOI : 10.1038/nature07921

T. Gro?kopf and O. Soyer, Synthetic microbial communities, Current Opinion in Microbiology, vol.18, pp.72-77, 2014.
DOI : 10.1016/j.mib.2014.02.002

W. Harcombe, W. Riehl, I. Dukovski, B. Granger, A. Betts et al., Metabolic Resource Allocation in Individual Microbes Determines Ecosystem Interactions and Spatial Dynamics, Cell Reports, vol.7, issue.4, pp.1104-1115, 2014.
DOI : 10.1016/j.celrep.2014.03.070

M. Hibbing, C. Fuqua, M. Parsek, and S. Peterson, Bacterial competition: surviving and thriving in the microbial jungle, Nature Reviews Microbiology, vol.44, issue.1, pp.15-25, 2010.
DOI : 10.1038/nrmicro2259

K. Hillesland, S. Lim, J. Flowers, S. Turkarslan, N. Pinel et al., Erosion of functional independence early in the evolution of a microbial mutualism, Proceedings of the National Academy of Sciences, vol.4, issue.3, pp.14822-14827, 2014.
DOI : 10.1038/nmeth1010

A. Janulevicius, M. Van-loosdrecht, and C. Picioreanu, Short-Range Guiding Can Result in the Formation of Circular Aggregates in Myxobacteria Populations, PLOS Computational Biology, vol.89, issue.4, p.1004213, 2015.
DOI : 10.1371/journal.pcbi.1004213.s025

Q. Jin, E. Roden, and J. Giska, Geomicrobial Kinetics: Extrapolating Laboratory Studies to Natural Environments, Geomicrobiology Journal, vol.180, issue.2, pp.173-185, 2013.
DOI : 10.1016/S1093-0191(00)00057-5

D. Johnson, D. Helbling, T. Lee, J. Park, K. Fenner et al., Association of Biodiversity with the Rates of Micropollutant Biotransformations among Full-Scale Wastewater Treatment Plant Communities, Applied and Environmental Microbiology, vol.81, issue.2, pp.666-675, 2015.
DOI : 10.1128/AEM.03286-14

B. Kerr, M. Riley, M. Feldman, and B. Bohannan, Local dispersal promotes biodiversity in a real-life game of rock???paper???scissors, Nature, vol.142, issue.6894, pp.171-174, 2002.
DOI : 10.1046/j.1461-0248.2001.00256.x

H. Kettle, P. Louis, G. Holtrop, S. Duncan, and H. Flint, Modelling the emergent dynamics and major metabolites of the human colonic microbiota, Environmental Microbiology, vol.6, issue.5, pp.1615-1630, 2015.
DOI : 10.1111/1462-2920.12599

T. Kiorboe, K. Tang, H. Grossart, and H. Ploug, Dynamics of Microbial Communities on Marine Snow Aggregates: Colonization, Growth, Detachment, and Grazing Mortality of Attached Bacteria, Applied and Environmental Microbiology, vol.69, issue.6, pp.3036-3047, 2003.
DOI : 10.1128/AEM.69.6.3036-3047.2003

I. Klapper and J. Dockery, Mathematical Description of Microbial Biofilms, SIAM Review, vol.52, issue.2, pp.221-265, 2010.
DOI : 10.1137/080739720

N. Klitgord and D. Segrè, Environments that Induce Synthetic Microbial Ecosystems, PLoS Computational Biology, vol.34, issue.11, p.1001002, 2010.
DOI : 10.1371/journal.pcbi.1001002.s011
URL : http://doi.org/10.1371/journal.pcbi.1001002

T. Kosaka, S. Kato, T. Shimoyama, S. Ishii, T. Abe et al., The genome of Pelotomaculum thermopropionicum reveals niche-associated evolution in anaerobic microbiota, Genome Research, vol.18, issue.3, pp.442-448, 2008.
DOI : 10.1101/gr.7136508

H. Leggett, S. Brown, and S. Reece, War and peace: social interactions in infections, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.2013, issue.1, p.20130365, 2014.
DOI : 10.1093/emph/eot011

A. Little, C. Robinson, S. Peterson, K. Raffa, and J. Handelsman, Rules of Engagement: Interspecies Interactions that Regulate Microbial Communities, Annual Review of Microbiology, vol.62, issue.1, pp.375-401, 2008.
DOI : 10.1146/annurev.micro.030608.101423

R. Mahadevan, J. Edwards, R. Doyle, and F. J. , Dynamic Flux Balance Analysis of Diauxic Growth in Escherichia coli, Biophysical Journal, vol.83, issue.3, pp.1331-1340, 2002.
DOI : 10.1016/S0006-3495(02)73903-9

L. Mcnally, M. Viana, and S. Brown, Cooperative secretions facilitate host range expansion in bacteria, Nature Communications, vol.6, p.4594, 2014.
DOI : 10.1086/519860

M. Mee and H. Wang, Engineering ecosystems and synthetic ecologies, Molecular BioSystems, vol.107, issue.10, pp.2470-2483, 2012.
DOI : 10.1039/c2mb25133g
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3430802

B. Momeni, A. Waite, and W. Shou, Spatial selforganization favors heterotypic cooperation over cheating, Elife, vol.2, p.960, 2013.
DOI : 10.7554/elife.00960
URL : http://doi.org/10.7554/elife.00960

R. Muñoz-tamayo, B. Laroche, E. Walter, J. Dorè, and M. Leclerc, Mathematical modelling of carbohydrate degradation by human colonic microbiota, Journal of Theoretical Biology, vol.266, issue.1, pp.189-201, 2010.
DOI : 10.1016/j.jtbi.2010.05.040

D. Orhon and N. Artan, Modelling of Activated Sludge Systems, 1994.

J. Orth, I. Thiele, and B. Palsson, What is flux balance analysis?, Nature Biotechnology, vol.19, issue.3, pp.245-248, 2010.
DOI : 10.1038/nbt.1614
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3108565

E. Pagaling, F. Strathdee, B. Spears, M. Cates, R. Allen et al., Community history affects the predictability of microbial ecosystem development, The ISME Journal, vol.13, issue.1, pp.19-30, 2014.
DOI : 10.1073/pnas.95.12.6578

J. Passarge, S. Hol, M. Escher, and J. Huisman, COMPETITION FOR NUTRIENTS AND LIGHT: STABLE COEXISTENCE, ALTERNATIVE STABLE STATES, OR COMPETITIVE EXCLUSION?, Ecological Monographs, vol.76, issue.1, pp.57-72, 2006.
DOI : 10.2307/1940605
URL : http://dx.doi.org/10.6084/M9.FIGSHARE.C.3309183

T. Pfeiffer, S. Schuster, and S. Bonhoeffer, Cooperation and Competition in the Evolution of ATP-Producing Pathways, Science, vol.292, issue.5516, pp.504-507, 2001.
DOI : 10.1126/science.1058079

D. Post and E. Palkovacs, Eco-evolutionary feedbacks in community and ecosystem ecology: interactions between the ecological theatre and the evolutionary play, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.182, issue.4111, pp.1629-1640, 2009.
DOI : 10.1126/science.182.4111.449

H. Reichenbach, H. Heunert, and H. Kuczka, Archangium violaceum (Myxobacteriales)?Schwarmentwicklung und Bildung von Protocysten, 1968.

T. Reichenbach, M. Mobilia, and E. Frey, Mobility promotes and jeopardizes biodiversity in rock???paper???scissors games, Nature, vol.22, issue.7157, pp.1046-1049, 2007.
DOI : 10.1038/nature06095

T. Reichenbach, M. Mobilia, and E. Frey, Self-organization of mobile populations in cyclic competition, Journal of Theoretical Biology, vol.254, issue.2, pp.368-383, 2008.
DOI : 10.1016/j.jtbi.2008.05.014

M. Riley and J. Wertz, Bacteriocins: Evolution, Ecology, and Application, Annual Review of Microbiology, vol.56, issue.1, pp.117-137, 2002.
DOI : 10.1146/annurev.micro.56.012302.161024

A. Saunders, M. Albertsen, J. Vollertsen, and P. Nielsen, The activated sludge ecosystem contains a core community of abundant organisms, The ISME Journal, vol.9, issue.1, pp.11-20, 2016.
DOI : 10.1038/ismej.2011.188

C. Schilling, S. Schuster, B. Palsson, and R. Heinrich, Metabolic Pathway Analysis: Basic Concepts and Scientific Applications in the Post-genomic Era, Biotechnology Progress, vol.15, issue.3, pp.296-303, 1999.
DOI : 10.1021/bp990048k

J. Shong, M. Diaz, and C. Collins, Towards synthetic microbial consortia for bioprocessing, Current Opinion in Biotechnology, vol.23, issue.5, pp.798-802, 2012.
DOI : 10.1016/j.copbio.2012.02.001

J. Sieber, M. Mcinerney, and R. Gunsalus, Genomic Insights into Syntrophy: The Paradigm for Anaerobic Metabolic Cooperation, Annual Review of Microbiology, vol.66, issue.1, pp.429-452, 2012.
DOI : 10.1146/annurev-micro-090110-102844

S. Stolyar, . Van-dien-steve, K. Hillesland, N. Pinel, T. Lie et al., Metabolic modeling of a mutualistic microbial community, Molecular Systems Biology, vol.185, p.92, 2007.
DOI : 10.1038/msb4100131

B. Szczesny, M. Mobilia, and A. Rucklidge, Characterization of spiraling patterns in spatial rock-paper-scissors games, Physical Review E, vol.90, issue.3, p.32704, 2014.
DOI : 10.1103/PhysRevE.90.032704

F. Teles, R. Teles, N. Uzel, X. Song, G. Torresyap et al., Early microbial succession in redeveloping dental biofilms in periodontal health and disease, Journal of Periodontal Research, vol.155, issue.suppl 11, pp.95-104, 2012.
DOI : 10.1111/j.1600-0765.2011.01409.x

J. Van-gestel, F. Weissing, O. Kuipers, and A. Kovacs, Density of founder cells affects spatial pattern formation and cooperation in Bacillus subtilis biofilms, The ISME Journal, vol.74, issue.10, pp.2069-2079, 2014.
DOI : 10.1038/ismej.2014.52

R. Vannette and T. Fukami, Historical contingency in species interactions: towards niche-based predictions, Ecology Letters, vol.8, issue.3252-3260, pp.115-124, 2014.
DOI : 10.1111/ele.12204

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

J. Vorholt, Microbial life in the phyllosphere, Nature Reviews Microbiology, vol.15, issue.12, pp.828-840, 2012.
DOI : 10.1038/nrmicro2910

S. West, A. Griffin, A. Gardner, and S. Diggle, Social evolution theory for microorganisms, Nature Reviews Microbiology, vol.14, issue.8, pp.597-607, 2006.
DOI : 10.1038/nrmicro1461

S. Widder, K. Besemer, G. Singer, C. S. Bertuzzo, E. Quince et al., Fluvial network organization imprints on microbial co-occurrence networks, Proceedings of the National Academy of Sciences, vol.57, issue.4, pp.12799-12804, 2014.
DOI : 10.1128/mBio.00169-10
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4156742

B. Wolfe and R. Dutton, Fermented Foods as Experimentally Tractable Microbial Ecosystems, Cell, vol.161, issue.1, pp.49-55, 2015.
DOI : 10.1016/j.cell.2015.02.034
URL : http://dx.doi.org/10.1016/j.cell.2015.02.034

S. Woodcock, C. Van-der-gast, T. Bell, M. Lunn, T. Curtis et al., Neutral assembly of bacterial communities, FEMS Microbiology Ecology, vol.62, issue.2, pp.171-180, 2007.
DOI : 10.1111/j.1574-6941.2007.00379.x

J. Zhou, L. Wu, Y. Deng, X. Zhi, Y. Jiang et al., Reproducibility and quantitation of amplicon sequencing-based detection, The ISME Journal, vol.62, issue.8, pp.1303-1313, 2011.
DOI : 10.1073/pnas.0709016105