B. Annexe, Composition des solutions d'alginate pour micro-billes -84 mM de Zn 2`( sous forme de Zinc acetate

, -84 mM d'EDDA (acide éthylène diamine diacétique, le chélatant)

, -40 mM de MOPS

, Avoir un pH de 6,7 dans les solutions 1* et 2* est nécessaire car sans ça lorsqu'on mélange avec la solution 0 d'alginate on observer la formation du gel

W. B. Whitman, D. C. Coleman, and W. J. Wiebe, Prokaryotes : The unseen majority, Proceedings of the National Academy of Sciences, vol.95, pp.6578-6583, 1998.

R. Hooke, Micrographia, or, some physiological descriptions of minute bodies made by magnifying glasses with observations and inquiries thereupon. Printers to the Royal Society, 1665.

H. Gest, The discovery of microorganisms by robert hooke and antoni van leeuwenhoek, fellows of the royal society, 2004.

D. J. Newman and G. M. Cragg, Natural products as sources of new drugs over the last 25 years, J. Nat. Prod, vol.70, pp.461-477, 2007.

J. Clardy, M. Fischbach, and C. Currie, The natural history of antibiotics, Current biology : CB, vol.19, pp.437-441, 2009.

S. J. Giovannoni, T. B. Britschgi, C. L. Moyer, and K. G. Field, Genetic diversity in sargasso sea bacterioplankton, Nature, vol.345, pp.60-63, 1990.

T. Kaeberlein, K. Lewis, and S. S. Epstein, Isolating uncultivable microorganisms in pure culture in a simulated natural environment, Science, vol.296, p.1127, 2002.

K. J. Locey and J. T. Lennon, Scaling laws predict global microbial diversity, Proceedings of the National Academy of Sciences, vol.113, pp.5970-5975, 2016.

E. J. Stewart, Growing unculturable bacteria, Journal of Bacteriology, vol.194, pp.4151-4160, 2012.

J. T. Staley and A. Konopka, Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats, Annu. Rev. Microbiol, vol.39, pp.321-346, 1985.

P. Yarza, P. Yilmaz, E. Pruesse, F. O. Glockner, W. Ludwig et al., Uniting the classification of cultured and uncultured bacteria and archaea using 16s rrna gene sequences, Nat Rev Micro, vol.12, pp.635-645, 2014.

C. Rinke, P. Schwientek, A. Sczyrba, N. N. Ivanova, I. J. Anderson et al., Insights into the phylogeny and coding potential of microbial dark matter, Nature, vol.499, pp.431-437, 2013.

P. H. Janssen, P. S. Yates, B. E. Grinton, P. M. Taylor, and M. Sait, Improved culturability of soil bacteria and isolation in pure culture of novel members of the divisions acidobacteria, actinobacteria, proteobacteria, and verrucomicrobia, Applied and Environmental Microbiology, vol.68, pp.2391-2396, 2002.

P. Brookes, The soil microbial biomass : Concept, measurement and applications in soil ecosystem research, Microbes and Environments, vol.16, issue.3, pp.131-140, 2001.

J. Overmann, Principles of Enrichment, Isolation, Cultivation and Preservation of Prokaryotes, pp.80-136, 2006.

J. M. Odom and J. D. Wall, Photoproduction of h(2) from cellulose by an anaerobic bacterial coculture, Applied and Environmental Microbiology, vol.45, pp.1300-1305, 1983.

J. Dworkin and I. M. Shah, Exit from dormancy in microbial organisms, Nat Rev Micro, vol.8, pp.890-896, 2010.

K. E. Davis, S. J. Joseph, and P. H. Janssen, Effects of growth medium, inoculum size, and incubation time on culturability and isolation of soil bacteria, Applied and Environmental Microbiology, vol.71, pp.826-834, 2004.

M. E. Hibbing, C. Fuqua, M. R. Parsek, and S. B. Peterson, Bacterial competition : surviving and thriving in the microbial jungle, Nature reviews. Microbiology, vol.8, pp.15-25, 2010.

V. Torsvik and L. Øvreås, Microbial diversity and function in soil : from genes to ecosystems, Current Opinion in Microbiology, vol.5, pp.240-245, 2002.

G. , Sols et environnement chiffres clés, 2015.

N. Fierer, M. Breitbart, J. Nulton, P. Salamon, C. Lozupone et al., Metagenomic and small-subunit rrna analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil, Applied and Environmental Microbiology, vol.73, pp.7059-7066, 2007.

C. H. Ettema and D. A. Wardle, Spatial soil ecology, Trends in Ecology & Evolution, vol.17, issue.4, pp.177-183, 2002.

M. Hayatsu, K. Tago, and M. Saito, Various players in the nitrogen cycle : Diversity and functions of the microorganisms involved in nitrification and denitrification, Soil Science & Plant Nutrition, vol.54, pp.33-45, 2008.

P. R. Hardoim, L. S. Van-overbeek, G. Berg, A. M. Pirttilä, S. Compant et al., The hidden world within plants : Ecological and evolutionary considerations for defining functioning of microbial endophytes, Microbiology and molecular biology reviews : MMBR, vol.79, pp.293-320, 2015.

E. Barrios, Soil biota, ecosystem services and land productivity, Special Section -Ecosystem Services and Agriculture, vol.64, pp.269-285, 2007.

A. L. Demain, Importance of microbial natural products and the need to revitalize their discovery, Journal of Industrial Microbiology & Biotechnology, vol.41, pp.185-201, 2014.

. Bibliographie,

L. Mottet, Hydrogel composite conducteur pour l'encapsulation de bactéries électroactives, 2015.

K. Gruber, Deep influence of soil microbes, Nature Plants, vol.1, p.15194, 2015.

J. Lagier, P. Hugon, S. Khelaifia, P. Fournier, B. L. Scola et al., The rebirth of culture in microbiology through the example of culturomics to study human gut microbiota, Clinical Microbiology Reviews, vol.28, pp.237-264, 2015.

L. Collins and M. Methods, , pp.60-88, 2004.

C. C. De-la-tour, Mémoire sur la fermentation vineuse, Annales de chimie et de physique, vol.68, pp.206-222, 1838.

L. Pasteur, Mémoire sur la fermentation alcoolique, p.1860

K. Bartscht, H. Cypionka, and J. Overmann, Evaluation of cell activity and of methods for the cultivation of bacteria from a natural lake community, FEMS Microbiology Ecology, vol.28, pp.249-259, 1999.

R. Koch, Zur Untersuchung von pathogenen Organismen (Methods for the study of pathogenic organisms), vol.1, p.1881

W. Hess, Walther and angelina hesse : Early contributors to bacteriology, ASM News, vol.58, p.425, 1992.

R. Koch, Die Atiologie der Tuberkulose (The etiology of tuberculosis), p.1882

R. J. Petri, Eine kleine Modification des Koch'schen Plattenverfahrens (A minor modification of the plating technique of Koch), p.1887

M. Wainwright, Who did invent the petri dish ? the mystery deepens, Microbiology Today, p.13, 1999.

F. C. Vieira and E. Nahas, Comparison of microbial numbers in soils by using various culture media and temperatures, Microbiological Research, vol.160, pp.197-202, 2005.

J. Harper, Semi-solid agar as a selective medium for salmonella, J. Pathol, vol.95, issue.2, pp.550-554, 1968.

G. M. Balestra and I. J. Misaghi, Increasing the efficiency of the plate counting method for estimating bacterial diversity, Journal of Microbiological Methods, vol.30, pp.111-117, 1997.

R. M. Morris, M. S. Rappe, S. A. Connon, K. L. Vergin, W. A. Siebold et al., Sar11 clade dominates ocean surface bacterioplankton communities, Nature, vol.420, pp.806-810, 2002.

M. S. Rappe, S. A. Connon, K. L. Vergin, and S. J. Giovannoni, Cultivation of the ubiquitous sar11 marine bacterioplankton clade, Nature, vol.418, pp.630-633, 2002.

H. G. Schlegel and H. W. Jannasch, Enrichment cultures, Annu. Rev. Microbiol, vol.21, pp.49-70, 1967.

M. Tourna, M. Stieglmeier, A. Spang, M. Könneke, A. Schintlmeister et al., Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil, Proceedings of the National Academy of Sciences, vol.108, pp.8420-8425, 2011.

J. Overmann, Phototrophic consortia : A tight cooperation between non-related eubacteria, Symbiosis : Mechanisms and Model Systems, pp.239-255, 2002.

M. B. Miller and B. L. Bassler, Quorum sensing in bacteria, Annu. Rev. Microbiol, vol.55, pp.165-199, 2001.

K. H. Nealson and J. W. Hastings, Bacterial bioluminescence : its control and ecological significance, Microbiological Reviews, vol.43, pp.496-518, 1979.

Y. Li and X. Tian, Quorum sensing and bacterial social interactions in biofilms, Sensors, vol.12, pp.2519-2538, 2012.

L. Passador, J. M. Cook, M. J. Gambello, L. Rust, and B. H. Iglewski, Expression of pseudomonas aeruginosa virulence genes requires cell-to-cell communication, Science, vol.260, p.1127, 1993.

M. Dworkin and D. Kaiser, Cell interactions in myxobacterial growth and development, Science, vol.230, p.18, 1985.

P. Albuquerque, A. M. Nicola, E. Nieves, H. C. Paes, P. R. Williamson et al., Quorum sensing-mediated, cell density-dependent regulation of growth and virulence in cryptococcus neoformans, mBio, vol.5, 2014.

J. Q. Boedicker, M. E. Vincent, and R. F. Ismagilov, Microfluidic confinement of single cells of bacteria in small volumes initiates high-density behavior of quorum sensing and growth and reveals its variability, Angewandte Chemie, vol.48, pp.5908-5911, 2009.

L. Hall-stoodley, J. W. Costerton, and P. Stoodley, Bacterial biofilms : from the natural environment to infectious diseases, Nat Rev Micro, vol.2, pp.95-108, 2004.

M. Burmølle, D. Ren, T. Bjarnsholt, and S. J. Sørensen, Interactions in multispecies biofilms : do they actually matter ?, Trend in microbiology, vol.22, pp.84-91, 2014.

O. H. Michiyo, I. Okano, T. Watsuji, T. Kakinuma, U. E. Kenji et al., Establishing the independent culture of a strictly symbiotic bacterium symbiobacterium thermophilum from its supporting bacillus strain, Bioscience, Biotechnology, and Biochemistry, vol.63, pp.1083-1090, 1999.

S. Sieuwerts, F. A. De-bok, J. Hugenholtz, J. E. Van-hylckama, and . Vlieg, Unraveling microbial interactions in food fermentations : from classical to genomics approaches, Applied and Environmental Microbiology, vol.74, pp.4997-5007, 2008.

B. E. Wolfe, J. E. Button, M. Santarelli, and R. J. Dutton, Cheese rind communities provide tractable systems for in situ and in vitro studies of microbial diversity, Cell, vol.158, pp.422-433, 2014.

. Bibliographie,

J. A. Gilbert, D. Van-der-lelie, and I. Zarraonaindia, Microbial terroir for wine grapes, Proceedings of the National Academy of Sciences of the United States of America, vol.111, pp.5-6, 2013.

N. A. Bokulich, J. H. Thorngate, P. M. Richardson, and D. A. Mills, Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate, Proceedings of the National Academy of Sciences of the United States of America, vol.111, pp.139-148, 2013.

C. Heil, J. N. Burton, I. Liachko, A. Friedrich, N. A. Hanson et al., Identification of a novel interspecific hybrid yeast from a metagenomic open fermentation sample using hi-c, 2017.

C. Delbès, L. Ali-mandjee, and M. Montel, Monitoring bacterial communities in raw milk and cheese by culture-dependent and -independent 16s rrna gene-based analyses, Applied and Environmental Microbiology, vol.73, pp.1882-1891, 2007.

T. Großkopf and O. S. Soyer, Synthetic microbial communities, Cell regulation, vol.18, pp.72-77, 2014.

A. Onofrio, J. M. Crawford, E. J. Stewart, K. Witt, E. Gavrish et al., Siderophores from neighboring organisms promote the growth of uncultured bacteria, Chemistry & biology, vol.17, pp.254-264, 2010.

E. Ahmed and S. J. Holmström, Siderophores in environmental research : roles and applications, Microbial Biotechnology, vol.7, pp.196-208, 2014.

J. Park, A. Kerner, M. A. Burns, and X. N. Lin, Microdroplet-enabled highly parallel co-cultivation of microbial communities, PLoS ONE, vol.6, p.17019, 2011.

J. Monod, The growth of bacterial cultures, Annu. Rev. Microbiol, vol.3, pp.371-394, 1949.

K. Foster and T. Bell, Competition, not cooperation, dominates interactions among culturable microbial species, Current biology, vol.22, pp.1845-1850, 2012.

C. M. Jessup, R. Kassen, S. E. Forde, B. Kerr, A. Buckling et al., Big questions, small worlds : microbial model systems in ecology, Trends in ecology & evolution, vol.19, pp.189-197, 2004.

A. M. Earl, R. Losick, and R. Kolter, Ecology and genomics of bacillus subtilis, Trends in microbiology, vol.16, p.269, 2008.

H. P. Browne, S. C. Forster, B. O. Anonye, N. Kumar, B. A. Neville et al., Culturing of 'unculturable' human microbiota reveals novel taxa and extensive sporulation, Nature, vol.533, p.543, 2016.

M. D. Lynch and J. D. Neufeld, Ecology and exploration of the rare biosphere, Nat Rev Micro, vol.13, pp.217-229, 2015.

M. Keller and K. Zengler, Tapping into microbial diversity, Nat Rev Micro, vol.2, pp.141-150, 2004.

. Bibliographie,

J. T. Lennon, Z. T. Aanderud, B. K. Lehmkuhl, and D. R. Schoolmaster, Mapping the niche space of soil microorganisms using taxonomy and traits, Ecology, vol.93, pp.1867-1879, 2012.

T. Thorsen, R. W. Roberts, F. H. Arnold, and S. R. Quake, Dynamic pattern formation in a vesicle-generating microfluidic device, Phys. Rev. Lett, vol.86, pp.4163-4166, 2001.

P. B. Umbanhowar, V. Prasad, and D. A. Weitz, Monodisperse emulsion generation via drop break off in a coflowing stream, Langmuir, vol.16, pp.347-351, 2000.

F. J. Hol and C. Dekker, Zooming in to see the bigger picture : Microfluidic and nanofabrication tools to study bacteria, Science, vol.346, 2014.

R. Rusconi, M. Garren, and R. Stocker, Microfluidics expanding the frontiers of microbial ecology, Annual review of biophysics, vol.43, pp.65-91, 2014.

A. Grodrian, J. Metze, T. Henkel, K. Martin, M. Roth et al., Segmented flow generation by chip reactors for highly parallelized cell cultivation, Micro and Nano Bioengineering, vol.19, pp.1421-1428, 2004.

J. Clausell-tormos, D. Lieber, J. Baret, A. El-harrak, O. J. Miller et al., Droplet-based microfluidic platforms for the encapsulation and screening of mammalian cells and multicellular organisms, Chemistry & Biology, vol.15, pp.427-437, 2008.
URL : https://hal.archives-ouvertes.fr/hal-02148746

K. Martin, T. Henkel, V. Baier, A. Grodrian, T. Schon et al., Generation of larger numbers of separated microbial populations by cultivation in segmented-flow microdevices, Lab Chip, vol.3, issue.3, pp.202-207, 2003.

A. B. Theberge, F. Courtois, Y. Schaerli, M. Fischlechner, C. Abell et al., Microdroplets in microfluidics : An evolving platform for discoveries in chemistry and biology, Angewandte Chemie International Edition, vol.49, pp.5846-5868, 2010.

T. D. Brock, Microbial growth rates in nature, Bacteriological Reviews, vol.35, pp.39-58, 1971.

D. Nichols, N. Cahoon, E. M. Trakhtenberg, L. Pham, A. Mehta et al., Use of ichip for high-throughput in situ cultivation of "uncultivable" microbial species, Applied and Environmental Microbiology, vol.76, pp.2445-2450, 2010.

L. L. Ling, T. Schneider, A. J. Peoples, A. L. Spoering, I. Engels et al., A new antibiotic kills pathogens without detectable resistance, Nature, vol.517, pp.455-459, 2015.

K. Zengler, G. Toledo, M. Rappé, J. Elkins, E. J. Mathur et al., Cultivating the uncultured, Proceedings of the National Academy of Sciences, vol.99, pp.15681-15686, 2002.

. Bibliographie,

W. Du, L. Li, K. P. Nichols, and R. F. Ismagilov, Slipchip, Lab on a chip, vol.9, pp.2286-2292, 2009.

L. Ma, S. S. Datta, M. A. Karymov, Q. Pan, S. Begolo et al., Individually addressable arrays of replica microbial cultures enabled by splitting slipchips, Integrative biology : quantitative biosciences from nano to macro, vol.6, pp.796-805, 2014.

L. Ma, J. Kim, R. Hatzenpichler, M. A. Karymov, N. Hubert et al., Gene-targeted microfluidic cultivation validated by isolation of a gut bacterium listed in human microbiome project's most wanted taxa, Proceedings of the National Academy of Sciences of the United States of America, vol.111, pp.9768-9773, 2014.

A. G. Hati, D. C. Bassett, J. M. Ribe, P. Sikorski, D. A. Weitz et al., Versatile, cell and chip friendly method to gel alginate in microfluidic devices, Lab Chip, vol.16, issue.19, pp.3718-3727, 2016.

P. D. Comandon, La chambre à huile, ses avantages pour l'étude des microorganismes vivants, la culture des tissus et la micromanipulation, Annales de l'Institut Pasteur, vol.60, p.113, 1938.

J. Lederberg, A simple method for isolating individual microbes, Journal of Bacteriology, vol.68, pp.258-259, 1954.

S. A. Connon and S. J. Giovannoni, High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates, Applied and Environmental Microbiology, vol.68, pp.3878-3885, 2002.

R. Seemann, M. Brinkmann, T. Pfohl, and S. Herminghaus, Droplet based microfluidics, Reports on Progress in Physics, vol.75, issue.1, p.16601, 2012.

X. Casadevall-i-solvas and A. Demello, Droplet microfluidics : recent developments and future applications, Chem. Commun, vol.47, issue.7, pp.1936-1942, 2011.

M. T. Guo, A. Rotem, J. A. Heyman, and D. A. Weitz, Droplet microfluidics for high-throughput biological assays, Lab Chip, vol.12, issue.12, pp.2146-2155, 2012.

D. L. Chen and R. F. Ismagilov, Microfluidic cartridges preloaded with nanoliter plugs of reagents : an alternative to 96-well plates for screening, Combinatorial chemistry and molecular diversity, vol.10, pp.226-231, 2006.

P. Watnick and R. Kolter, Biofilm, city of microbes, Journal of Bacteriology, vol.182, pp.2675-2679, 2000.

D. Ren, J. S. Madsen, S. J. Sørensen, and M. Burmølle, High prevalence of biofilm synergy among bacterial soil isolates in cocultures indicates bacterial interspecific cooperation, The ISME Journal, vol.9, pp.81-89, 2014.

A. Huebner, M. Srisa-art, D. Holt, C. Abell, F. Hollfelder et al., Quantitative detection of protein expression in single cells using droplet microfluidics, Chem. Commun, issue.12, pp.1218-1220, 2007.

S. L. Anna, N. Bontoux, and H. A. Stone, Formation of dispersions using "flow focusing" in microchannels, Appl. Phys. Lett, vol.82, pp.364-366, 2003.

C. J. Ingham, A. Sprenkels, J. Bomer, D. Molenaar, A. Van-den et al., The micro-petri dish, a million-well growth chip for the culture and high-throughput screening of microorganisms, Proceedings of the National Academy of Sciences of the United States of America, vol.104, pp.18217-18222, 2007.

H. L. Lee, P. Boccazzi, R. J. Ram, and A. J. Sinskey, Microbioreactor arrays with integrated mixers and fluid injectors for high-throughput experimentation with ph and dissolved oxygen control, Lab Chip, vol.6, issue.9, pp.1229-1235, 2006.

L. Baraban, F. Bertholle, M. L. Salverda, N. Bremond, P. Panizza et al., Millifluidic droplet analyser for microbiology, Lab Chip, vol.11, issue.23, pp.4057-4062, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00647595

S. P. Damodaran, S. Eberhard, L. Boitard, J. G. Rodriguez, Y. Wang et al., A millifluidic study of cell-to-cell heterogeneity in growth-rate and cell-division capability in populations of isogenic cells of chlamydomonas reinhardtii, PLOS ONE, vol.10, p.118987, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01236845

D. Cottinet, F. Condamine, N. Bremond, A. D. Griffiths, P. B. Rainey et al., Lineage tracking for probing heritable phenotypes at single-cell resolution, PLoS ONE, vol.11, p.152395, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01400779

L. Jiang, L. Boitard, P. Broyer, A. Chareire, P. Bourne-branchu et al., Digital antimicrobial susceptibility testing using the millidrop technology, European Journal of Clinical Microbiology & Infectious Diseases, vol.35, pp.415-422, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01400797

L. Boitard, D. Cottinet, N. Bremond, J. Baudry, and J. Bibette, Growing microbes in millifluidic droplets, Eng. Life Sci, vol.15, pp.318-326, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01230000

L. Boitard, D. Cottinet, C. Kleinschmitt, N. Bremond, J. Baudry et al., Monitoring single-cell bioenergetics via the coarsening of emulsion droplets, Proceedings of the National Academy of Sciences of the United States of America, vol.109, pp.7181-7186, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00760719

P. Tabeling, Introduction à la microfluidique, 2015.

T. M. Squires and S. R. Quake, Microfluidics : Fluid physics at the nanoliter scale, Rev. Mod. Phys, vol.77, pp.977-1026, 2005.

G. M. Whitesides, The origins and the future of microfluidics, Nature, vol.442, pp.368-373, 2006.

N. Nguyen, S. A. Shaegh, N. Kashaninejad, and D. Phan, Design, fabrication and characterization of drug delivery systems based on lab-on-a-chip technology, Lab-on-a-Chip technology, vol.65, pp.1403-1419, 2013.

A. W. Martinez, S. T. Phillips, M. J. Butte, and G. M. Whitesides, Patterned paper as a platform for inexpensive, low volume, portable bioassays, Angewandte Chemie, vol.46, pp.1318-1320, 2007.

E. W. Young and D. J. Beebe, Fundamentals of microfluidic cell culture in controlled microenvironments, Chemical Society reviews, vol.39, pp.1036-1048, 2010.

K. V. Voelkerding, S. A. Dames, and J. D. Durtschi, Next-generation sequencing : From basic research to diagnostics, Clin. Chem, vol.55, p.641, 2009.

V. Sanchez-freire, A. D. Ebert, T. Kalisky, S. R. Quake, and J. C. Wu, Microfluidic single-cell real-time pcr for comparative analysis of gene expression patterns, Nat. Protocols, vol.7, pp.829-838, 2012.

J. Baret, Y. Beck, I. Billas-massobrio, D. Moras, and A. D. Griffiths, Quantitative cell-based reporter gene assays using droplet-based microfluidics, Chemistry & Biology, vol.17, pp.528-536, 2010.
URL : https://hal.archives-ouvertes.fr/hal-02148764

W. S. Broecker, P. E. , and T. , Gas exchange rates between air and sea1, Tellus, vol.26, pp.21-35, 1974.

J. Baret, V. Taly, M. Ryckelynck, C. A. Merten, and A. D. Griffiths, Gouttes et émulsions, Med Sci, vol.25, pp.627-632, 2009.

J. L. Hodges and L. L. Cam, The poisson approximation to the poisson binomial distribution, The Annals of Mathematical Statistics, vol.31, issue.3, pp.737-740, 1960.

C. S. Thakur, M. E. Brown, J. N. Sama, M. E. Jackson, and T. K. Dayie, Growth of wildtype and mutant e. coli strains in minimal media for optimal production of nucleic acids for preparing labeled nucleotides, Applied Microbiology and Biotechnology, vol.88, pp.771-779, 2010.

G. Sezonov, D. Joseleau-petit, and R. D'ari, Escherichia coli physiology in luria-bertani broth, Journal of Bacteriology, vol.189, pp.8746-8749, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00184125

R. González-pinzón, R. Haggerty, and D. D. Myrold, Measuring aerobic respiration in stream ecosystems using the resazurin-resorufin system, J. Geophys. Res, vol.117, issue.G3, 2012.

L. Ranjard and A. Richaume, Quantitative and qualitative microscale distribution of bacteria in soil, Research in Microbiology, vol.152, pp.707-716, 2001.

V. Lindahl and L. R. Bakken, Evaluation of methods for extraction of bacteria from soil, FEMS Microbiology Ecology, vol.16, pp.135-142, 1995.

S. Courtois, P. Frostegård, G. Göransson, P. Depret, P. Jeannin et al., Quantification of bacterial subgroups in soil : comparison of dna extracted directly from soil or from cells previously released by density gradient centrifugation, Environmental Microbiology, vol.3, issue.7, pp.431-439, 2001.

K. E. Williamson, J. Kan, S. W. Polson, and S. J. Williamson, Optimizing the indirect extraction of prokaryotic dna from soils, vol.43, pp.736-748, 2011.

S. Srinivasiah, J. Bhavsar, K. Thapar, M. Liles, T. Schoenfeld et al., Phages across the biosphere : contrasts of viruses in soil and aquatic environments, vol.159, pp.349-357, 2008.

K. E. Williamson, M. Radosevich, and K. E. Wommack, Abundance and diversity of viruses in six delaware soils, Applied and Environmental Microbiology, vol.71, pp.3119-3125, 2005.

. Bibliographie,

D. G. Altman and J. M. Bland, Standard deviations and standard errors, BMJ : British Medical Journal, vol.331, pp.903-903, 2005.

S. Frostegård, V. Courtois, S. Ramisse, D. Clerc, F. L. Bernillon et al., Quantification of bias related to the extraction of dna directly from soils, Applied and Environmental Microbiology, vol.65, pp.5409-5420, 1999.

S. Claassen, E. Toit, M. Kaba, C. Moodley, H. J. Zar et al., A comparison of the efficiency of five different commercial dna extraction kits for extraction of dna from faecal samples, Journal of Microbiological Methods, vol.94, pp.103-110, 2013.

K. Smith, M. A. Diggle, and S. C. Clarke, Comparison of commercial dna extraction kits for extraction of bacterial genomic dna from whole-blood samples, Journal of Clinical Microbiology, vol.41, pp.2440-2443, 2003.

W. Horrigue, S. Dequiedt, N. Prévost-bouré, C. Jolivet, N. P. Saby et al., Predictive model of soil molecular microbial biomass, Ecological Indicators, vol.64, pp.203-211, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01844377

M. Schirmer, U. Z. Ijaz, R. D'amore, N. Hall, W. T. Sloan et al., Insight into biases and sequencing errors for amplicon sequencing with the illumina miseq platform, Nucleic Acids Research, vol.43, pp.37-37, 2014.

W. Chen, C. K. Zhang, Y. Cheng, S. Zhang, and H. Zhao, A comparison of methods for clustering 16s rrna sequences into otus, PLOS ONE, vol.8, p.70837, 2013.

T. Z. Desantis, P. Hugenholtz, N. Larsen, M. Rojas, E. L. Brodie et al., Greengenes, a chimera-checked 16s rrna gene database and workbench compatible with arb, Applied and Environmental Microbiology, vol.72, pp.5069-5072, 2006.

J. B. Hughes, J. J. Hellmann, T. H. Ricketts, and B. J. Bohannan, Counting the uncountable : Statistical approaches to estimating microbial diversity, Applied and Environmental Microbiology, vol.67, pp.4399-4406, 2001.

P. H. Janssen, Identifying the dominant soil bacterial taxa in libraries of 16s rrna and 16s rrna genes, Applied and Environmental Microbiology, vol.72, pp.1719-1728, 2006.

L. Rolland, E. Santanach-carreras, T. Delmas, J. Bibette, and N. Bremond, Physicochemical properties of aqueous core hydrogel capsules, Soft Matter, vol.10, issue.48, pp.9668-9674, 2014.

H. Domejean, M. De-la-motte-saint-pierre, A. Funfak, N. Atrux-tallau, K. Alessandri et al., Controlled production of sub-millimeter liquid core hydrogel capsules for parallelized 3d cell culture, Lab Chip, vol.17, issue.1, pp.110-119, 2017.

J. Noel, L. Mottet, N. Bremond, P. Poulin, C. Combellas et al., Multiscale electrochemistry of hydrogels embedding conductive nanotubes, Chem. Sci, vol.6, issue.7, pp.3900-3905, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01191551

D. Doméjean and H. , Formation of hydrogel aqueous-core capsules via the fragmentation of a compound complex fluid jet, 2014.

V. Torsvik, J. Goksøyr, and F. L. Daae, High diversity in dna of soil bacteria, Applied and Environmental Microbiology, vol.56, pp.782-787, 1990.

C. Jiang, L. Dong, J. Zhao, X. Hu, C. Shen et al., High throughput single-cell cultivation on microfluidic streak plates, Applied and Environmental Microbiology, 2016.

S. Reischke, J. Rousk, and E. Bååth, The effects of glucose loading rates on bacterial and fungal growth in soil, Soil Biology and Biochemistry, vol.70, pp.88-95, 2014.