M. Adachi, T. Shimomura, M. Komatsu, H. Yakuwa, and A. Miya, A novel mediator???polymer-modified anode for microbial fuel cells, Chemical Communications, vol.41, issue.17, pp.2055-2057, 2008.
DOI : 10.1039/b717773a

J. Babauta, R. Renslow, Z. Lewandowski, and H. Beyenal, Electrochemically active biofilms: facts and fiction. A review, Biofouling, vol.30, issue.8, pp.789-812, 2012.
DOI : 10.1371/journal.pcbi.1002363
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4242416

V. M. Balc~-ao and M. M. Vila, Structural and functional stabilization of protein entities: state-of-the-art, Advanced Drug Delivery Reviews, vol.93, pp.25-41, 2015.
DOI : 10.1016/j.addr.2014.10.005

Z. Bayat, M. Hassanshahian, C. , and S. , Immobilization of microbes for bioremediation of crude oil polluted environments: a mini review, Open Microbiol J, vol.9, pp.48-54, 2015.

J. Bjerketorp, S. Belkin, S. Jansson, and J. K. , Advances in preservation methods: keeping biosensor microorganisms alive and active, Current Opinion in Biotechnology, vol.17, issue.1, pp.43-49, 2006.
DOI : 10.1016/j.copbio.2005.12.005

P. S. Bonanni, D. Massazza, and J. P. Busalmen, Stepping stones in the electron transport from cells to electrodes in Geobacter sulfurreducens biofilms, Physical Chemistry Chemical Physics, vol.46, issue.25, pp.10300-10306, 2013.
DOI : 10.1039/c3cp50411e

D. R. Bond and D. R. Lovley, Electricity Production by Geobacter sulfurreducens Attached to Electrodes, Applied and Environmental Microbiology, vol.69, issue.3, pp.1548-1555, 2003.
DOI : 10.1128/AEM.69.3.1548-1555.2003
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC150094

D. R. Bond, S. M. Strycharz-glaven, L. M. Tender, and C. I. Torres, On Electron Transport through Geobacter Biofilms, ChemSusChem, vol.302, issue.6, pp.1099-1105, 2012.
DOI : 10.1002/cssc.201100748

Z. Borjas, Physiological and operation strategies for optimizing geobacter-based electrochemical systems, 2016.

Z. Borjas, J. M. Ortiz, A. Aldaz, J. Feliu, E. U~-nez et al., Strategies for Reducing the Start-up Operation of Microbial Electrochemical Treatments of Urban Wastewater, Energies, vol.8, issue.12, pp.14064-14077, 2015.
DOI : 10.1002/bit.21821

J. P. Busalmen, A. Esteve-n-u~-nez, A. Bern-a, and J. M. Feliu, C-Type Cytochromes Wire Electricity-Producing Bacteria to Electrodes, Angewandte Chemie International Edition, vol.7, issue.26, pp.4874-4877, 2008.
DOI : 10.1002/anie.200801310

D. F. Call, L. , and B. E. , Lactate Oxidation Coupled to Iron or Electrode Reduction by Geobacter sulfurreducens PCA, Applied and Environmental Microbiology, vol.77, issue.24, pp.8791-8794, 2011.
DOI : 10.1128/AEM.06434-11
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3233085

J. M. Dantas, L. Morgado, M. Aklujkar, M. Bruix, Y. Y. Londer et al., Rational engineering of Geobacter sulfurreducens electron transfer components: a foundation for building improved Geobacter-based bioelectrochemical technologies, Frontiers in Microbiology, vol.24, p.752, 2015.
DOI : 10.1016/j.bios.2009.05.004

C. Depagne, S. Masse, T. Link, C. , and T. , Bacteria survival and growth in multi-layered silica thin films, Journal of Materials Chemistry, vol.402, issue.25, pp.12457-12460, 2012.
DOI : 10.1039/c2jm32186f
URL : https://hal.archives-ouvertes.fr/hal-01475867

D. J. Dickson, M. D. Luterra, E. , and R. L. , Transcriptomic responses of Synechocystis sp. PCC 6803 encapsulated in silica gel, Applied Microbiology and Biotechnology, vol.2007, issue.4, pp.183-196, 2012.
DOI : 10.1007/s00253-012-4307-6

A. Dom-inguez-garay, A. Bern-a, I. Ortiz-bernad, E. U~-nez, and A. , Silica Colloid Formation Enhances Performance of Sediment Microbial Fuel Cells in a Low Conductivity Soil, Environmental Science & Technology, vol.47, issue.4, pp.2117-2122, 2013.
DOI : 10.1021/es303436x

N. M. Eleftheriou, X. Ge, J. Kolesnik, S. B. Falconer, R. J. Harris et al., Entrapment of Living Bacterial Cells in Low-Concentration Silica Materials Preserves Cell Division and Promoter Regulation, Chemistry of Materials, vol.25, issue.23, pp.4798-4805, 2013.
DOI : 10.1021/cm403198z

A. Esteve-n-u~-nez, J. P. Busalmen, A. Bern-a, C. Guti-errez-garr-an, and J. M. Feliu, Opportunities behind the unusual ability of geobacter sulfurreducens for exocellular respiration and electricity production, Energy & Environmental Science, vol.23, issue.6, pp.2066-2069, 2011.
DOI : 10.1039/c1ee01067k

M. Estevez-canales, A. Bern-a, Z. Borjas, E. U~-nez, and A. , Screen-printed electrodes: new tools ª 2017 The Authors, Microbial Biotechnology, 2015.

M. Estevez-canales, A. Kuzume, Z. Borjas, M. F?-ueg, D. Lovley et al., eliminates its capacity for extracellular electron transfer, Environmental Microbiology Reports, vol.112, issue.2, pp.219-226, 2015.
DOI : 10.1111/1758-2229.12230

A. E. Franks, K. P. Nevin, H. Jia, M. Izallalen, T. L. Woodard et al., Novel strategy for three-dimensional real-time imaging of microbial fuel cell communities: monitoring the inhibitory effects of proton accumulation within the anode biofilm, Energy Environ. Sci., vol.189, issue.1, pp.113-119, 2008.
DOI : 10.1039/B816445B

A. A. Homaei, R. Sariri, F. Vianello, and R. Stevanato, Enzyme immobilization: an update, Journal of Chemical Biology, vol.6, issue.7, pp.185-205, 2013.
DOI : 10.1007/s12154-013-0102-9
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3787205

K. P. Katuri, P. Kavanagh, S. Rengaraj, and D. Leech, Geobacter sulfurreducens biofilms developed under different growth conditions on glassy carbon electrodes: insights using cyclic voltammetry, Chemical Communications, vol.53, issue.26, pp.4758-4760, 2010.
DOI : 10.1128/AEM.00027-10

K. Katuri, M. L. Ferrer, M. C. Guti-errez, R. Jim-enez, F. Del-monte et al., Three-dimensional microchanelled electrodes in flow-through configuration for bioanode formation and current generation, Energy & Environmental Science, vol.11, issue.23, pp.4201-4210, 2011.
DOI : 10.1039/c1ee01477c

H. J. Kim, H. S. Park, M. S. Hyun, I. S. Chang, M. Kim et al., A mediator-less microbial fuel cell using a metal reducing bacterium, Shewanella putrefaciens, Enzyme and Microbial Technology, vol.30, issue.2, pp.145-152, 2002.
DOI : 10.1016/S0141-0229(01)00478-1

N. J. Kotloski and J. A. Gralnick, Flavin Electron Shuttles Dominate Extracellular Electron Transfer by Shewanella oneidensis, mBio, vol.4, issue.1, pp.553-565, 2013.
DOI : 10.1128/mBio.00553-12
URL : http://doi.org/10.1128/mbio.00553-12

R. Kr?-amer, Bacterial stimulus perception and signal transduction: Response to osmotic stress, The Chemical Record, vol.17, issue.4, pp.217-229, 2010.
DOI : 10.1002/tcr.201000005

E. Labelle and D. R. Bond, Cyclic voltammetry for the study of microbial electron transfer at electrodes. In Bioelectrochemical Systems: From Extracellular Electron Transfer to Biotechnological Application, pp.137-152, 2009.

P. Liang, H. Wang, X. Xia, X. Huang, Y. Mo et al., Carbon nanotube powders as electrode modifier to enhance the activity of anodic biofilm in microbial fuel cells, Biosensors and Bioelectronics, vol.26, issue.6, pp.3000-3004, 2011.
DOI : 10.1016/j.bios.2010.12.002

Q. Liu, J. Wang, and B. J. Boyd, Peptide-based biosensors, Talanta, vol.136, pp.114-127, 2015.
DOI : 10.1016/j.talanta.2014.12.020
URL : http://arrow.monash.edu.au/hdl/1959.1/1214130

D. R. Lovley, Live wires: direct extracellular electron exchange for bioenergy and the bioremediation of energy-related contamination, Energy & Environmental Science, vol.9, issue.12, pp.4896-4906, 2011.
DOI : 10.1039/c1ee02229f

D. R. Lovley and E. J. Phillips, Novel mode of microbial energy metabolism: organic carbon oxidation coupled to dissimilatory reduction of iron or manganese, 1988.

D. R. Lovley, T. Ueki, T. Zhang, N. S. Malvankar, P. M. Shrestha et al., Geobacter, Adv Microb Physiol, vol.59, pp.1-100, 2011.
DOI : 10.1016/B978-0-12-387661-4.00004-5

H. R. Luckarift, S. R. Sizemore, K. E. Farrington, J. Roy, C. Lau et al., Facile Fabrication of Scalable, Hierarchically Structured Polymer/Carbon Architectures for Bioelectrodes, ACS Applied Materials & Interfaces, vol.4, issue.4, pp.2082-2087, 2012.
DOI : 10.1021/am300048v

L. U. Magnusson, T. Nystr?-om, and A. Farewell, Underproduction of ??70 Mimics a Stringent Response: A PROTEOME APPROACH, Journal of Biological Chemistry, vol.278, issue.2, pp.968-973, 2003.
DOI : 10.1074/jbc.M209881200

E. Marsili, D. B. Baron, I. D. Shikhare, D. Coursolle, J. A. Gralnick et al., Shewanella secretes flavins that mediate extracellular electron transfer, Proceedings of the National Academy of Sciences, vol.74, issue.3, pp.3968-3973, 2008.
DOI : 10.1128/AEM.01387-07
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2268775

E. Marsili, J. Sun, and D. R. Bond, Voltammetry and Growth Physiology of Geobacter sulfurreducens Biofilms as a Function of Growth Stage and Imposed Electrode Potential, Electroanalysis, vol.10, issue.7-8, pp.865-874, 2010.
DOI : 10.1002/elan.200800007

B. A. Meth-e, K. E. Nelson, J. A. Eisen, I. T. Paulsen, W. Nelson et al., Genome of Geobacter sulfurreducens: Metal Reduction in Subsurface Environments, Science, vol.302, issue.5652, pp.1967-1969, 2003.
DOI : 10.1126/science.1088727

N. Nassif, O. Bouvet, N. Rager, M. Roux, C. Coradin et al., Living bacteria in silica gels, Nature Materials, vol.1, issue.1, pp.42-44, 2002.
DOI : 10.1038/nmat709

T. Nguyen, Y. Yu, X. Wang, J. Wang, and H. Song, A 3D mesoporous polysulfone???carbon nanotube anode for enhanced bioelectricity output in microbial fuel cells, Chemical Communications, vol.13, issue.91, pp.10754-10756, 2013.
DOI : 10.1039/c3cc45775c

G. D. Nicodemus and S. J. Bryant, Cell Encapsulation in Biodegradable Hydrogels for Tissue Engineering Applications, Tissue Engineering Part B: Reviews, vol.14, issue.2, pp.149-165, 2008.
DOI : 10.1089/ten.teb.2007.0332

S. B. Nimse, K. Song, M. D. Sonawane, D. R. Sayyed, K. et al., Immobilization Techniques for Microarray: Challenges and Applications, Sensors, vol.14, issue.172, pp.22208-22229, 2014.
DOI : 10.1103/PhysRevE.66.041905
URL : http://doi.org/10.3390/s141222208

Q. Ping, O. Porat, C. G. Dosoretz, and Z. He, Bioelectricity inhibits back diffusion from the anolyte into the desalinated stream in microbial desalination cells, Water Research, vol.88, pp.266-273, 2016.
DOI : 10.1016/j.watres.2015.10.018

J. Rodrigo, K. Boltes, E. Nez, and A. , Microbial-electrochemical bioremediation and detoxification of dibenzothiophene-polluted soil, Chemosphere, vol.101, pp.61-65, 2014.
DOI : 10.1016/j.chemosphere.2013.11.060

J. Rodrigo, U. D?-orfler, R. Schroll, E. U~-nez, and A. , Stimulating soil microorganisms for mineralizing the herbicide isoproturon by means of microbial electroremediating cells, Microbial Biotechnology, vol.40, issue.200, pp.369-380, 2016.
DOI : 10.1111/1751-7915.12351

U. Schr?-oder, F. Harnisch, and L. T. Angenent, Microbial electrochemistry and technology: terminology and classification, Energy Environ. Sci., vol.101, issue.2, pp.513-519, 2015.
DOI : 10.1039/C4EE03359K

G. D. Schrott, M. V. Ordo~-nez, L. Robuschi, and J. P. Busalmen, Physiological stratification in electricity-producing biofilms of Geobacter sulfurreducens, Chem- SusChem, vol.7, pp.598-603, 2014.

K. Scott, Y. , and E. H. , Microbial Electrochemical and Fuel Cells: Fundamentals and Applications, 2015.

D. Segura, R. Mahadevan, K. Ju-arez, and D. R. Lovley, Computational and Experimental Analysis of Redundancy in the Central Metabolism of Geobacter sulfurreducens, PLoS Computational Biology, vol.116, issue.2, p.36, 2008.
DOI : 10.1371/journal.pcbi.0040036.st004

S. Selimovi-c, J. Oh, H. Bae, M. Dokmeci, and A. Khademhosseini, Microscale Strategies for Generating Cell-Encapsulating Hydrogels, Polymers, vol.95, issue.4, p.1554, 2012.
DOI : 10.1039/c0lc00273a

I. Serra, C. D. Serra, S. Rocchietti, D. Ubiali, and M. Terreni, Stabilization of thymidine phosphorylase from Escherichia coli by immobilization and post immobilization techniques, Enzyme and Microbial Technology, vol.49, issue.1, pp.52-58, 2011.
DOI : 10.1016/j.enzmictec.2011.03.011

S. Shaharuddin and I. I. Muhamad, Microencapsulation of alginate-immobilized bagasse with Lactobacillus rhamnosus NRRL 442: Enhancement of survivability and thermotolerance, Carbohydrate Polymers, vol.119, pp.173-181, 2015.
DOI : 10.1016/j.carbpol.2014.11.045

S. R. Sizemore, R. Nichols, R. Tatum, P. Atanassov, G. R. Johnson et al., Immobilization of Whole Cells by Chemical Vapor Deposition of Silica, Methods Mol Biol, vol.1051, pp.301-312, 2013.
DOI : 10.1007/978-1-62703-550-7_20

J. A. Smith, P. Tremblay, P. M. Shrestha, O. L. Snoeyenbos-west, A. E. Franks et al., Going Wireless: Fe(III) Oxide Reduction without Pili by Geobacter sulfurreducens Strain JS-1, Applied and Environmental Microbiology, vol.80, issue.14, pp.4331-4340, 2014.
DOI : 10.1128/AEM.01122-14
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4068678

R. M. Snider, S. M. Strycharz-glaven, S. D. Tsoi, J. S. Erickson, and L. M. Tender, Long-range electron transport in Geobacter sulfurreducens biofilms is redox gradient-driven, Proceedings of the National Academy of Sciences, vol.60, issue.10, pp.15467-15472, 2012.
DOI : 10.1128/AEM.69.3.1548-1555.2003
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3458377

A. M. Speers, R. , and G. , Electron Donors Supporting Growth and Electroactivity of Geobacter sulfurreducens Anode Biofilms, Applied and Environmental Microbiology, vol.78, issue.2, pp.437-444, 2012.
DOI : 10.1128/AEM.06782-11

S. Srikanth, E. Marsili, M. C. Flickinger, and D. R. Bond, Electrochemical characterization ofGeobacter sulfurreducens cells immobilized on graphite paper electrodes, Biotechnology and Bioengineering, vol.78, issue.5, pp.1065-1073, 2008.
DOI : 10.1002/bit.21671

C. S. Stephen, E. V. Labelle, S. L. Brantley, and D. R. Bond, Abundance of the Multiheme c-Type Cytochrome OmcB Increases in Outer Biofilm Layers of Electrode-Grown Geobacter sulfurreducens, PLoS ONE, vol.72, issue.8, p.104336, 2014.
DOI : 10.1371/journal.pone.0104336.s001

S. M. Strycharz, A. P. Malanoski, R. M. Snider, H. Yi, D. R. Lovley et al., Application of cyclic voltammetry to investigate enhanced catalytic current generation by biofilm-modified anodes of Geobacter sulfurreducens strain DL1vs. variant strain KN400, Energy Environ. Sci., vol.60, issue.3, pp.896-913, 2011.
DOI : 10.1039/C0EE00260G

S. Tejedor-sanz, T. Bacchetti-de-gregoris, J. J. Salas, L. Pastor, E. U~-nez et al., Integrating a microbial electrochemical system into a classical wastewater treatment configuration for removing nitrogen from low COD effluents, Environ. Sci.: Water Res. Technol., vol.48, issue.5, pp.884-893, 2016.
DOI : 10.1039/C6EW00100A

J. M. Tront, J. D. Fortner, M. Pl?-otze, J. B. Hughes, and A. M. Puzrin, Microbial fuel cell biosensor for in situ assessment of microbial activity, Biosensors and Bioelectronics, vol.24, issue.4, pp.586-590, 2008.
DOI : 10.1016/j.bios.2008.06.006

M. Vargas, N. S. Malvankar, P. Tremblay, C. Leang, J. A. Smith et al., Aromatic amino acids required for pili conductivity and long-range extracellular electron transport in Geobacter sulfurreducens, MBio, vol.4, pp.105-00113, 2013.

H. Wang and Z. J. And-ren, A comprehensive review of microbial electrochemical systems as a platform technology, Biotechnology Advances, vol.31, issue.8, pp.1796-1807, 2013.
DOI : 10.1016/j.biotechadv.2013.10.001

X. Wang, N. B. Ahmed, G. S. Alvarez, M. V. Tuttolomondo, C. Desimone et al., Sol-gel Encapsulation of Biomolecules and Cells for Medicinal Applications, Current Topics in Medicinal Chemistry, vol.15, issue.3, pp.223-244, 2015.
DOI : 10.2174/1568026614666141229112734
URL : https://hal.archives-ouvertes.fr/hal-01274323

L. Wang, N. Liu, Z. Guo, D. Wu, W. Chen et al., Nitric Acid-Treated Carbon Fibers with Enhanced Hydrophilicity for Candida tropicalis Immobilization in Xylitol Fermentation, Materials, vol.88, issue.3, p.206, 2016.
DOI : 10.1021/am101064s

X. Xie, C. Criddle, C. , and Y. , Design and fabrication of bioelectrodes for microbial bioelectrochemical systems, Energy Environ. Sci., vol.170, issue.12, pp.3418-3441, 2015.
DOI : 10.1039/C5EE01862E

M. D. Yates, J. P. Golden, J. Roy, S. M. Strycharz-glaven, S. Tsoi et al., Thermally activated long range electron transport in living biofilms, Phys. Chem. Chem. Phys., vol.322, issue.48, pp.32564-32570, 2015.
DOI : 10.1039/C5CP05152E

Y. Yu, H. Chen, Y. Yong, D. Kim, and H. Song, Conductive artificial biofilm dramatically enhances bioelectricity production in Shewanella-inoculated microbial fuel cells, Chemical Communications, vol.25, issue.48, pp.12825-12827, 2011.
DOI : 10.1039/c1cc15874k

L. Yu, Y. Yuan, J. Tang, Y. Wang, and S. Zhou, Biochar as an electron shuttle for reductive dechlorination of pentachlorophenol by Geobacter sulfurreducens, Scientific Reports, vol.48, issue.245, p.16221, 2015.
DOI : 10.1021/es403968e

Y. Zhang, R. , and C. O. , Membrane lipid homeostasis in bacteria, Nature Reviews Microbiology, vol.50, issue.3, pp.222-233, 2008.
DOI : 10.1038/nrmicro1839