D. Citer-ce,

T. P. Vannecke, N. Bernet, M. K. Winkler, G. Santa-catalina, J. Steyer et al., Influence of process dynamics on the microbial diversity in a nitrifying biofilm reactor: Correlation analysis and simulation study, Biotechnology and Bioengineering, vol.113, issue.9, pp.1962-1974, 2016.
URL : https://hal.archives-ouvertes.fr/hal-02635471

J. H. Andrews and R. F. Harris, R-selection and K-selection and microbial ecology, Adv Microbial Ecol, vol.9, pp.99-147, 1986.

A. C. Anthonisen, R. C. Loehr, T. Prakasam, and E. G. Srinath, Inhibition of nitrification by ammonia and nitrous acid, Journal WPCF, vol.48, issue.5, pp.835-852, 1976.

M. Arnaldos, Y. Amerlinck, U. Rehman, T. Maere, S. Van-hoey et al., From the affinity constant to the half-saturation index: Understanding conventional modeling concepts in novel wastewater treatment processes, Water Res, vol.70, pp.458-470, 2015.

M. Bellucci, I. D. Ofiteru, L. Beneduce, D. W. Graham, I. M. Head et al., A preliminary and qualitative study of resource ratio theory to nitrifying labscale bioreactors, Microb Biotechnol, vol.8, issue.3, pp.590-603, 2015.

N. Bernet, P. Dangcong, J. Delgenès, and R. Moletta, Nitrification at low oxygen concentration in biofilm reactor, J Environ Eng, vol.127, issue.3, pp.266-271, 2001.

N. Bernet, O. Sanchez, D. Cesbron, J. P. Steyer, and J. P. Delgenes, Modeling and control of nitrite accumulation in a nitrifying biofilm reactor, Biochem Eng J, vol.24, issue.2, pp.173-183, 2005.

D. Bougard, Traitement biologique d'effluents azotés avec arrêt de la nitrification au stade nitrite, vol.234, 2004.

D. Bougard, N. Bernet, D. Cheneby, and J. P. Delgenes, Nitrification of a high-strength wastewater in an inverse turbulent bed reactor: Effect of temperature on nitrite accumulation, Process, vol.41, pp.106-113, 2006.
URL : https://hal.archives-ouvertes.fr/hal-02666381

D. Bougard, N. Bernet, P. Dabert, J. P. Delgenes, and J. P. Steyer, Influence of closed loop control on microbial diversity in a nitrification process, Water Sci Technol, vol.53, issue.4-5, pp.85-93, 2006.
URL : https://hal.archives-ouvertes.fr/hal-02665339

F. Braun, J. Hamelin, A. Bonnafous, N. Delgenès, J. Steyer et al., Similar PAH fate in anaerobic digesters inoculated with three microbial communities accumulating either volatile fatty acids or methane, PLoS One, vol.10, issue.4, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01159242

D. Brockmann, A. Caylet, R. Escudié, J. P. Steyer, and N. Bernet, Biofilm model calibration and microbial diversity study using Monte Carlo simulations, Biotechnol Bioeng, vol.110, issue.5, pp.1323-1332, 2013.
URL : https://hal.archives-ouvertes.fr/hal-02647170

D. Brockmann and E. Morgenroth, Comparing global sensitivity analysis for a biofilm model for two-step nitrification using the qualitative screening method of Morris or the quantitative variance-based Fourier Amplitude Sensitivity, Water Sci Technol, vol.56, issue.8, pp.85-94, 2007.

D. Brockmann and E. Morgenroth, Evaluating operating conditions for outcompeting nitrite oxidizers and maintaining partial nitrification in biofilm systems using biofilm modeling and Monte Carlo filtering, Water Res, vol.44, issue.6, pp.1995-2009, 2010.
URL : https://hal.archives-ouvertes.fr/hal-02662591

, Version postprint Comment citer ce document

D. Brockmann, K. H. Rosenwinkel, and E. Morgenroth, Practical identifiability of biokinetic parameters of a model describing two-step nitrification in biofilms, Biotechnol Bioeng, vol.101, issue.3, pp.497-514, 2008.

P. Buffiere, J. P. Bergeon, and R. Moletta, The inverse turbulent bed: a novel bioreactor for anaerobic treatment, Water Res, vol.34, issue.2, pp.673-677, 2000.

H. Daims, U. Purkhold, L. Bjerrum, A. E. Wilderer, P. A. Wagner et al., Nitrification in sequencing biofilm batch reactors: lessons from molecular approaches, Water Sci Technol, vol.43, issue.3, pp.9-18, 2001.

L. S. Downing and R. Nerenberg, Effect of oxygen gradients on the activity and microbial community structure of a nitrifying, membrane-aerated biofilm, Biotechnol Bioeng, vol.101, issue.6, pp.1193-1204, 2008.

K. Egli, C. Langer, H. Siegrist, A. Zehnder, M. Wagner et al., Community analysis of ammonia and nitrite oxidizers during start-up of nitritation reactors, Appl Environ Microbiol, vol.69, issue.6, pp.3213-3222, 2003.

A. Elawwad, H. Sandner, U. Kappelmeyer, and H. Koeser, Long-term starvation and subsequent recovery of nitrifiers in aerated submerged fixed-bed biofilm reactors, Environ Technol, vol.34, issue.8, pp.945-959, 2013.

J. M. Garrido, W. Van-benthum, M. Van-loosdrecht, and J. J. Heijnen, Influence of dissolved oxygen concentration on nitrite accumulation in a biofilm airlift suspension reactor, Biotechnol Bioeng, vol.53, issue.2, pp.168-178, 1997.

A. Gieseke, L. Bjerrum, M. Wagner, and R. Amann, Structure and activity of multiple nitrifying bacterial populations co-existing in a biofilm, Environ Microbiol, vol.5, issue.5, pp.355-369, 2003.

D. W. Graham, C. W. Knapp, E. S. Van-vleck, K. Bloor, T. B. Lane et al., Experimental demonstration of chaotic instability in biological nitrification, The ISME journal, vol.1, issue.5, pp.385-393, 2007.

X. D. Hao, J. J. Heijnen, and M. Van-loosdrecht, Model-based evaluation of temperature and inflow variations on a partial nitrification-ANAMMOX biofilm process, Water Res, vol.36, issue.19, pp.4839-4849, 2002.

X. D. Hao, J. J. Heijnen, and M. Van-loosdrecht, Sensitivity analysis of a biofilm model describing a one-stage completely autotrophic nitrogen removal (CANON) process, Biotechnol Bioeng, vol.77, issue.3, pp.266-277, 2002.

M. Henze, W. Gujer, T. Mino, and M. Van-loosdrecht, IWA Task Group on Mathematical Modelling for Design and Operation of Biological Wastewater Treatment, IWA Scientific and Technical Report, issue.9, 2000.

, Version postprint Comment citer ce document

A. Hermansson and P. Lindgren, Quantification of ammonia-oxidizing bacteria in arable soil by real-time PCR, Appl Environ Microbiol, vol.67, issue.2, pp.972-976, 2001.

S. Jayamohan, S. Ohgaki, and K. Hanaki, Effect of DO on kinetics of nitrification. Water Supply: the review journal of the international water supply association, vol.6, pp.141-150, 1988.

I. Jubany, J. Lafuente, J. A. Baeza, and J. Carrera, Total and stable washout of nitrite oxidizing bacteria from a nitrifying continuous activated sludge system using automatic control based on Oxygen Uptake Rate measurements, Water Res, vol.43, issue.11, pp.2761-2772, 2009.

G. A. Kowalchuk, J. R. Stephen, D. Boer, W. Prosser, J. I. Embley et al., Analysis of ammonia-oxidizing bacteria of the beta subdivision of the class Proteobacteria in coastal sand dunes by denaturing gradient gel electrophoresis and sequencing of PCR-amplified 16S, 1997.

, ribosomal DNA fragments. Appl Environ, vol.63, issue.4, pp.1489-1497

S. Lochtman, Proceskeuze en -optimalisatie van het SHARON proces voor slibverwerkingsbedrijf Sluisjesdijk (Process choice and optimisation of the SHARON process for the sludge treatment plant Sluisjesdijk), 1995.

P. Loisel, B. Haegeman, J. Hamelin, J. Harmand, and J. Godon, -10-22. A method for measuring the biological diversity of a sample, 2008.

C. M. Lopez-vazquez, A. Oehmen, C. M. Hooijmans, D. Brdjanovic, H. J. Gijzen et al., Modeling the PAO-GAO competition: Effects of carbon source, pH and temperature, Water Res, vol.43, pp.450-462, 2009.

S. Lücker, M. Wagner, F. Maixner, E. Pelletier, H. Koch et al., A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria, PNAS, vol.107, issue.30, pp.13479-13484, 2010.

S. Meijer, M. Van-loosdrecht, and J. Heijnen, Modelling the start-up of a full-scale biological nitrogen and phosphorus removing WWTP's, Water Res, vol.6, pp.4667-4682, 2002.

R. J. Michelland, S. Dejean, S. Combes, L. Fortun-lamothe, and L. Cauquil, StatFingerprints: a friendly graphical interface program for processing and analysis of microbial fingerprint profiles, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00658772

, Mol Ecol Resour, vol.9, issue.5, pp.1359-1363

M. Mozumder, C. Picioreanu, M. Van-loosdrecht, and E. Volcke, Effect of heterotrophic growth on autotrophic nitrogen removal in a granular sludge reactor, Environ Technol, vol.35, issue.8, pp.1027-1037, 2014.

J. Nash and J. V. Sutcliffe, River flow forecasting through conceptual models part I-A discussion of principles, J Hydrol, vol.10, issue.3, pp.282-290, 1970.

C. Nicolella, M. Van-loosdrecht, and J. J. Heijnen, Wastewater treatment with particulate biofilm reactors, J Biotechnol, vol.80, issue.1, pp.1-33, 2000.

, Version postprint Comment citer ce document

J. M. Norton, J. J. Alzerreca, Y. Suwa, and M. G. Klotz, Diversity of ammonia monooxygenase operon in autotrophic ammonia-oxidizing bacteria, ArchMicrobiol, vol.177, issue.2, pp.139-149, 2002.

Y. Z. Peng and G. Zhu, Biological nitrogen removal with nitrification and denitrification via nitrite pathway, Appl Microbiol Biotechnol, vol.73, issue.1, pp.15-26, 2006.

F. Poly, S. Wertz, E. Brothier, and V. Degrange, First exploration of Nitrobacter diversity in soils by a PCR cloning-sequencing approach targeting functional gene nxrA, FEMS Microbiol Ecol, vol.63, issue.1, pp.132-140, 2008.
URL : https://hal.archives-ouvertes.fr/halsde-00216150

M. L. Ralston and R. I. Jennrich, DUD, A derivative-free algorithm for nonlinear least squares, Technometrics, vol.20, issue.1, pp.7-14, 1978.

I. Ramirez, E. Volcke, R. Rajinikanth, and J. P. Steyer, Modeling microbial diversity in anaerobic digestion through an extended ADM1 model, Water Res, vol.43, issue.11, pp.2787-2800, 2009.
URL : https://hal.archives-ouvertes.fr/hal-02658092

M. Ras, D. Lefebvre, N. Derlon, E. Paul, and E. Girbal-neuhauser, Extracellular polymeric substances diversity of biofilms grown under contrasted environmental conditions, Water Res, vol.45, issue.4, pp.1529-1567, 2011.
URL : https://hal.archives-ouvertes.fr/hal-02647487

P. Reichert, Aquasim -a tool for simulation and data-analysis of aquatic systems, Water Sci Technol, vol.30, issue.2, pp.21-30, 1994.

P. Reichert, R. Von-schulthess, and D. Wild, The use of AQUASIM for estimating parameters of activated sludge models, Water Sci Technol, vol.31, issue.2, pp.135-147, 1995.

M. L. Rosenzweig, Species diversity in space and time, vol.436, 1995.

A. Schramm, D. De-beer, M. Wagner, and R. Amann, Identification and activities in situ of Nitrosospira and Nitrospira spp. as dominant populations in a nitrifying fluidized bed reactor, 1998.

, Appl Environ Microbiol, vol.64, issue.9, pp.3480-3485

S. Siripong and B. E. Rittmann, Diversity study of nitrifying bacteria in full-scale municipal wastewater treatment plants, Water Res, vol.41, issue.5, pp.1110-1120, 2007.

S. F. Stoddard, B. J. Smith, R. Hein, B. Roller, and T. M. Schmidt, rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development, Nucleic Acids Res, vol.43, issue.D1, pp.593-598, 2015.

O. Turk and D. Mavinic, Preliminary assessment of a shortcut in nitrogen removal from wastewater, Can J Civ Eng, vol.13, issue.6, pp.600-605, 1986.

T. Vannecke, N. Bernet, J. P. Steyer, and E. Volcke, Modelling ammonium-oxidizing population shifts in a biofilm reactor, Water Sci Technol, vol.69, issue.1, pp.208-224, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02045929

T. Vannecke and E. Volcke, Modelling microbial competition in nitrifying biofilm reactors, Biotechnol Bioeng, vol.112, issue.12, pp.2550-2561, 2015.

, Version postprint Comment citer ce document

T. Vannecke, G. Wells, N. Hubaux, E. Morgenroth, and E. Volcke, Considering microbial and aggregate heterogeneity in biofilm reactor models: How far do we need to go?, Water Sci Technol, vol.72, issue.10, pp.1692-1699, 2015.

W. Verstraete and S. Philips, Nitrification-denitrification processes and technologies in new contexts, Environ Pollut, vol.102, issue.1, pp.717-726, 1998.

E. Volcke, C. Picioreanu, D. Baets, B. Van-loosdrecht, and M. , The granule size distribution in an anammox-based granular sludge reactor affects the conversion-Implications for modeling, Biotechnol Bioeng, vol.109, pp.1629-1636, 2012.

S. Wertz, F. Poly, L. Roux, X. Degrange, and V. , Development and application of a PCR-denaturing gradient gel electrophoresis tool to study the diversity of Nitrobacter-like nxrA sequences in soil, FEMS Microbiol Ecol, vol.63, issue.2, pp.261-271, 2008.

U. Wiesmann, Biological nitrogen removal from wastewater, Advances in Biochemical Engineering/Biotechnology, pp.113-154, 1994.

M. K. Winkler, J. P. Bassin, R. Kleerebezem, D. Y. Sorokin, and M. C. Van-loosdrecht, Unravelling the reasons for disproportion in the ratio of AOB and NOB in aerobic granular sludge, Appl Microbiol Biotechnol, vol.94, issue.6, pp.1657-1666, 2012.

M. K. Winkler, R. Kleerebezem, L. De-bruin, and P. Verheijen,

M. Loosdrecht, Microbial diversity differences within aerobic granular sludge and activated sludge flocs, Appl Microbiol Biotechnol, vol.97, issue.16, pp.7447-7458, 2013.

L. Wittebolle, H. Vervaeren, W. Verstraete, and N. Boon, Quantifying community dynamics of nitrifiers in functionally stable reactors, Appl Environ Microbiol, vol.74, issue.1, pp.286-293, 2008.

H. Xu, C. Wang, Z. Liang, L. He, and W. Wu, The structure and component characteristics of partial nitrification biofilms under autotrophic and heterotrophic conditions, Appl Microbiol Biotechnol, vol.99, issue.8, pp.3673-83, 2015.

Z. Yuan and L. L. Blackall, Sludge population optimisation: a new dimension for the control of biological wastewater treatment systems, Water Res, vol.36, issue.2, pp.482-90, 2002.