Our research objectives

  • Understanding and optimizing the operation of microbial ecosystems in waste treatment and valorisation bioprocesses.
  • Setting the basic principles for the ecological engineering of microbial bioprocesses to maximize services and foster innovation.

Our subjects

  • Methanization of waste:
    • Hydrolysis of lignocellulosic matter
    • Anaerobic digestion stability and resistance to inhibition
    • Biogeochemical dynamics of micropollutants
    • Viruses of microorganisms and anaerobic digestion
  • Towards advanced waste biorefineries:
    • Mixed culture fermentation for the production of added value compounds from waste (Bioethanol)
    • Microbial electrosynthesis (BIORARE). BIORARE project website

Our approaches

  • Developing new concepts and models to integrate ecological information into an engineering framework :
    • Microbial growth and thermodynamics
    • Individual Based modelling and emergence of microbial structures according to process configuration parameters

Advanced methodologies

To diagnose and optimize the functioning of bioprocesses from labscale to full‑scale.

In the centre, Environmental Bioprocesses Research Laboratory building. Opening in 2015. © Irstea


Environmental Bioprocesses Research Laboratory (500 m2) including an experimental hall and laboratories. Opening in 2015. (© Irstea)

Environmental Bioprocesses Research Laboratory (500 m2) including an experimental hall and laboratories. Opening in 2015. (© Irstea)

Our Team




Ariane Bize

Research scientist

Molecular microbial ecology

Théodore Bouchez

Research scientist

Group leader, Microbial biotechnologies

Olivier Chapleur

Research scientist

Molecular microbial ecology

Christian Duquennoi

Research scientist

Process physics

Laurent Mazéas

Research scientist


Chrystelle Bureau



Céline Madigou

Engineering Assistant

Microbial biotechnologies

Nelly Badalato

PhD student

Colonization and degradation of lignocellulosic waste

Carolina Hoyos-Hernandez

PhD student


Grégory Marandat

PhD student

Metatranscriptomic for bioprocesses operating analysis

Simon Poirier

PhD student

Ecological engineering to promote the development of emerging functions associated to anaerobic bioprocesses

Arnaud Bridier

Research scientist


Elie Desmond

Research scientist


The team

© Irstea

C. Madigou, L. Mazéas, A. Bize, C. Bureau, C. Duquennoi, N. Badalato, A. Bridier, C. Hoyos-Hernandez, E. Desmond, T. Bouchez, O. Chapleur, G. Marandat, Simon Poirier, Liping Hao

Our publications


Chapleur O., et al., Co-inoculating ruminal content neither provides active hydrolytic microbes nor improves methanization of 13C-cellulose in batch digesters. FEMS Microbiology Ecology, 2014. 87(3): p. 616-629

Desmond-Le Quéméner, E. & Bouchez, T., A thermodynamic theory of microbial growth. The ISME Journal, 2014.

Driss-Limam, R.,  et al., Members of the uncultured bacterial candidate division WWE1 are implicated in anaerobic digestion of cellulose. MicrobiologyOpen, 2014. 3(2): p.157-167.

Lü, F., et al., Metaproteomics of cellulose methanisation under thermophilic conditions reveals a surprisingly high proteolytic activity. The ISME Journal, 2014. 8: p. 88-102.

Hoyos-Hernandez, C., et al., Elucidation of the thermophilic phenol biodegradation pathway via benzoate during the anaerobic digestion of municipal solid waste. Chemosphere, 2014. 97: p. 115-119.

Bridier, A., & Briandet, R. Contribution of confocal laser scanning microscopy in deciphering biofilm tridimensional structure and reactivity. Microbial biofilms: Methods and Protocols, Methods in Molecular Biology, 2014. 1147: p. 255-266.

Bridier, A., et al., Biofilm-associated persistence of foodborne pathogens (review). Food Microbiology (2014), in press

Bridier, A., et al., A model-based approach to detect interspecific interactions during biofilm development. Biofouling (2014), in press.


Chapleur, O., et al., SIMSISH technique does not alter the apparent isotopic composition of bacterial cells. Plos One, 2013.

Limam, I., et al., Evaluation of biodegradability of phenol and bisphenol A during mesophilic and thermophilic municipal solid waste anaerobic digestion using 13C-labeled contaminants. Chemosphere, 2013. 90(2): p. 512-520.

Ait Baddi, G., et al., Municipal Solid Waste Stabilization Efficiency Using Fluorescence Excitation–Emission Spectroscopy. Environmental Engineering Science, 2013. 30(5): p. 232-240.

Bridier, A., et al., Biofilms 5 International Conference: meeting report. Research in Microbiology, 2013. 164(5): p. 490-496.

Bridier, A., Des édifices à l'architecture très organisée. Biofutur, 2013. 341: p. 29-33

Bouchez, T., Des biofilms pour dépolluer. Biofutur, 2013. 341: p. 40-43.

Mendes, M.J.A., et al., Quantification of diffusion of phenolic compounds in virgin GCL and in GCL after contact with a synthetic leachate. Geotextiles and Geomembranes, 2013. 38: p. 16-25.

Jaubert, C., et al., Genomics and genetics of Sulfolobus islandicus LAL14/1, a model hyperthermophilic archaeon. Open Biology, 2013. 3(4): 130010.


Boulanger, A., et al., Effect of inoculum to substrate ratio (I/S) on municipal solid waste anaerobic degradation kinetics and potential. Waste Management, 2012. 32(12): p. 2258-2265.

Pons, C., et al., Extraction of oxidation compounds and biofilm growth of pre oxidized polyethelene. Matériaux et Techniques, 2012. 100(3): p. 211-220.

Pons, C., et al., The role of oxidation compounds in biofilm growth on polyethylene geomembrane barriers used in landfill. Journal of Applied Polymer Science, 2012. 124(SUPPL. 1): p. E251-257.

Tronquart, N.H., et al., Fish fins as non-lethal surrogates for muscle tissues in freshwater food web studies using stable isotopes. Rapid Communications in Mass Spectrometry, 2012. 26(14): p. 1603-1608.


Paumier, S., et al., Quantification of volatile organic compounds diffusion for virgin geosynthetic clay liners and for a GCL after contact with a synthetic leachate. Journal of Geotechnical and Geoenvironmental Engineering, 2011. 137(11): p. 1039-1046.

Ahari, M., et al., Quantification of the adsorption of phenolic compounds on the geotextile and bentonite components of four geosynthetic clay liners. Geosynthetics International, 2011. 18(5): p. 322-331.

Pina, M., et al., The Archeoviruses. FEMS Microbiology Reviews, 2011. 35(6): p. 1035-1054.


Limam, R.D., et al., Detection of WWE2-related Lentisphaerae by 16S rRNA gene sequencing and fluorescence in situ hybridization in landfill leachate. Canadian Journal of Microbiology, 2010. 56(10): p. 846-852.

Fechner, L.C., et al., Combined eukaryotic and bacterial community fingerprinting of natural freshwater biofilms using automated ribosomal intergenic spacer analysis. FEMS Microbiology Ecology, 2010. 74(3): p. 542-553.

Limam, I., et al., Simultaneous determination of phenol, methylphenols, chlorophenols and bisphenol-A by headspace solid-phase microextraction-gas chromatography-mass spectrometry in water samples and industrial effluents. International Journal of Environmental Analytical Chemistry, 2010. 90(3-6): p. 230-244.

Bize, A. et al., Les Archéovirus. Virologie, 2010. 14(2): p. 101-117.

Bize, A., et al., Les Virus D'archées : De La Morphologie Aux Nanotechnologies. Biofutur, 2010.  309: p. 39-43.


Tallec, G., et al., Impact of nitrate-enhanced leachate recirculation on gaseous releases from a landfill bioreactor cell. Waste Management, 2009. 29(7): p. 2078-2084.

Mazeas, L., et al., Simultaneous analysis of microbial identity and function using NanoSIMS: Application to anaerobic degradation of methanol. Geochimica et Cosmochimica Acta, 2009. 73(13): p. A853-A853.

Qu, X., et al., Anaerobic biodegradation of cellulosic material: Batch experiments and modelling based on isotopic data and focusing on aceticlastic and non-aceticlastic methanogenesis. Waste Management, 2009. 29(6): p. 1828-1837.

Qu, X., et al., Combined monitoring of changes in delta 13CH4 and archaeal community structure during mesophilic methanization of municipal solid waste. FEMS Microbiology Ecology, 2009. 68(2): p. 236-245.

Li, T., et al., Insights into networks of functional microbes catalysing methanization of cellulose under mesophilic conditions. Environmental Microbiology, 2009. 11(4): p. 889-904.

Vavilin, V.A., et al., Similar evolution in delta 13CH4 and model-predicted relative rate of aceticlastic methanogenesis during mesophilic methanization of municipal solid wastes. Water Science and Technology, 2009. 60(12): p. 3173-3179.

Bouchez, T., et al., Successful bacterial incorporation into activated sludge flocs using alginate. Bioresource Technology, 2009. 100(2): p. 1031-1032


Qu, X., et al., Effect of waste composition on anaerobic methanization of municipal solid waste. China Environmental Science, 2008. 28(8): p. 730-735.

Vavilin, V.A., et al., Methanosarcina as the dominant aceticlastic methanogens during mesophilic anaerobic digestion of putrescible waste. Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology, 2008. 94(4): p. 593-605.

Ganesan, A., et al., Cloacibacillus evryensis gen. nov., sp nov., a novel asaccharolytic, mesophilic, amino-acid-degrading bacterium within the phylum 'Synergistetes', isolated from an anaerobic sludge digester. International Journal of Systematic and Evolutionary Microbiology, 2008. 58: p. 2003-2012.

Guermazi, S., et al., Discovery and characterization of a new bacterial candidate division by an anaerobic sludge digester metagenomic approach. Environmental Microbiology, 2008. 10(8): p. 2111-2123.

Mazéas, L., et al., Elucidation of nitrate reduction pathways in anaerobic bioreactors using a stable isotope approach. Rapid Communications in Mass Spectrometry, 2008. 22(11): p. 1746-1750.

Li, T., et al., Simultaneous analysis of microbial identity and function using NanoSIMS. Environmental Microbiology, 2008. 10(3): p. 580-588.

Behar, F., et al., Elaboration of a new compositional kinetic schema for oil cracking. Organic Geochemistry, 2008. 39(6): p. 764-782.

Gholamifard, S., et al., Modelling anaerobic bioreactor landfills in methanogenic phase: Long term and short term behaviors. Water Research, 2008. 42(20):  p. 5061-5071.