A. Bertron, Understanding interactions between cementitious materials and microorganisms: a key to sustainable and safe concrete structures in various contexts, Mater. Struct, vol.47, pp.1787-1806, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02001745

A. Bertron, M. P. Lavigne, and C. Patapy, Biodeterioration of concrete in agricultural, agro-food and biogas plants: state of the art and challenges, RILEM Tech. Lett, vol.2, pp.83-89, 2017.

C. Voegel, A. Bertron, and B. Erable, Mechanisms of cementitious material deterioration in biogas digester, Sci. Total Environ, vol.571, pp.892-901, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01849702

M. Giroudon, M. P. Lavigne, and C. Patapy, Biodeterioration mechanisms and kinetics of SCM and aluminate based cements and AAM in the liquid phase of an anaerobic digestion, MATEC Web Conf, vol.199, 2003.
URL : https://hal.archives-ouvertes.fr/hal-02002334

C. Magniont, M. Coutand, and A. Bertron, A new test method to assess the bacterial deterioration of cementitious materials, Cem. Concr. Res, vol.41, pp.429-438, 2011.
URL : https://hal.archives-ouvertes.fr/hal-02165383

M. Giroudon, P. Lavigne, M. Patapy, and C. , Biodeterioration mechanisms and durability of SCM and aluminate based cements and AAM in the liquid phase of an anaerobic digestion system, Proc. RILEM 253-MCI Conf. Toulouse: Bertron A, Jonkers H, 2018.

A. Koenig and F. Dehn, Main considerations for the determination and evaluation of the acid resistance of cementitious materials, Mater. Struct, vol.49, pp.1693-1703, 2016.

C. Voegel, A. Bertron, and B. Erable, Chemical treatment with oxalic acid to improve the durability of cement-based materials in acidic environment, Proc. 13th Int. Conf. Durab. Build. Mater. Compon. RILEM Proceedings. Sao Paulo: Marco Quattrone, Vanderley M. John, pp.670-678, 2014.

S. Larreur-cayol, A. Bertron, and G. Escadeillas, Degradation of cement-based materials by various organic acids in agro-industrial waste-waters, Cem. Concr. Res, vol.41, pp.882-892, 2011.
URL : https://hal.archives-ouvertes.fr/hal-02165381

Y. Landon and M. Cherif, Characterization of the Surface Quality of Holes Drilled in CFRP Laminates, Adv. Mater. Res, vol.698, pp.107-116, 2013.
URL : https://hal.archives-ouvertes.fr/hal-02138245

L. Neves, R. Oliveira, and M. M. Alves, Influence of inoculum activity on the bio-methanization of a kitchen waste under different waste/inoculum ratios, Process Biochem, vol.39, pp.2019-2024, 2004.

E. Elbeshbishy, G. Nakhla, and H. Hafez, Biochemical methane potential (BMP) of food waste and primary sludge: Influence of inoculum pre-incubation and inoculum source, Bioresour. Technol, vol.110, pp.18-25, 2012.

C. Voegel, A. Bertron, and B. Erable, Biodeterioration of cementitious materials in biogas digester, Matér. Tech, vol.103, p.202, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01849735

E. Blanchet, E. Desmond, and B. Erable, Comparison of synthetic medium and wastewater used as dilution medium to design scalable microbial anodes: Application to food waste treatment, Bioresour. Technol, vol.185, pp.106-115, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01149751

R. C. Edgar, UPARSE: highly accurate OTU sequences from microbial amplicon reads, Nat. Methods, vol.10, pp.996-998, 2013.

Z. Zhang, S. Schwartz, and L. Wagner, A greedy algorithm for aligning DNA sequences, J. Comput. Biol. J. Comput. Mol. Cell Biol, vol.7, pp.203-214, 2000.

T. H. Tran, A. Govin, and R. Guyonnet, Influence of the intrinsic characteristics of mortars on biofouling by Klebsormidium flaccidum, Int. Biodeterior. Biodegrad, vol.70, pp.31-39, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00680295

S. Manso, M. Á. Calvo-torras, D. Belie, and N. , Evaluation of natural colonisation of cementitious materials: Effect of bioreceptivity and environmental conditions, Sci. Total Environ, pp.444-453, 2015.

K. J. Stout and E. J. Davis, Surface topography of cylinder bores-the relationship between manufacture, characterization and function, Wear, vol.95, pp.111-125, 1984.

S. H. Flint, J. D. Brooks, and P. J. Bremer, Properties of the stainless steel substrate, influencing the adhesion of thermo-resistant streptococci, J. Food Eng, vol.43, pp.235-242, 2000.

N. Mitik-dineva, J. Wang, and R. C. Mocanasu, Impact of nano-topography on bacterial attachment, Biotechnol. J, vol.3, pp.536-544, 2008.

E. Shannon, A mathematical theory of communication, Bell Syst. Tech. J, vol.27, pp.379-423, 1948.

E. Simpson, Measurement of diversity, Nature, vol.163, p.688, 1949.

M. C. Nelson, M. Morrison, and Z. Yu, A meta-analysis of the microbial diversity observed in anaerobic digesters, Bioresour. Technol, vol.102, pp.3730-3739, 2011.

S. Lee, H. Kang, and Y. H. Lee, Monitoring bacterial community structure and variability in time scale in full-scale anaerobic digesters, J. Environ. Monit, vol.14, pp.1893-1905, 2012.
DOI : 10.1039/c2em10958a

J. De-vrieze, A. M. Saunders, and Y. He, Ammonia and temperature determine potential clustering in the anaerobic digestion microbiome, Water Res, vol.75, pp.312-323, 2015.

T. Zhang, M. Shao, and L. Ye, 454 Pyrosequencing reveals bacterial diversity of activated sludge from 14 sewage treatment plants, ISME J, vol.6, pp.1137-1147, 2012.

G. R. Warnes, B. Bolker, and L. Bonebakker, gplots: Various R Programming Tools for Plotting Data, 2016.

A. Bize, L. Cardona, D. Quemener, and E. , Shotgun metaproteomic profiling of biomimetic anaerobic digestion processes treating sewage sludge, Proteomics, vol.15, pp.3532-3543, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01536494

W. G. Characklis and K. C. Marchall, Biofilms: a basis for an interdisciplinary approach, Characklis WG, Marshall KC, 1990.

A. K. Epstein, D. Hong, and P. Kim, Biofilm attachment reduction on bioinspired, dynamic, micro-wrinkling surfaces, New J. Phys, vol.15, p.95018, 2013.
DOI : 10.1088/1367-2630/15/9/095018
URL : http://iopscience.iop.org/article/10.1088/1367-2630/15/9/095018/pdf

N. Lu, W. Zhang, and Y. Weng, Fabrication of PDMS surfaces with micro patterns and the effect of pattern sizes on bacteria adhesion, Food Control, vol.68, pp.344-351, 2016.

H. Dang and C. R. Lovell, Microbial Surface Colonization and Biofilm Development in Marine Environments. Microbiol, Mol. Biol. Rev, vol.80, pp.91-138, 2016.

A. Leemann, B. Lothenbach, and C. Hoffmann, Biologically induced concrete deterioration in a wastewater treatment plant assessed by combining microstructural analysis with thermodynamic modeling, Cem. Concr. Res, vol.40, pp.1157-1164, 2010.

D. Giovannacci, C. Leclaire, and M. Horgnies, Algal colonization kinetics on roofing and façade tiles: Influence of physical parameters, Constr. Build. Mater, vol.48, pp.670-676, 2013.

S. Poirier, C. Madigou, and T. Bouchez, Improving anaerobic digestion with support media: Mitigation of ammonia inhibition and effect on microbial communities, Bioresour. Technol, vol.235, pp.229-239, 2017.

S. Montalvo, L. Guerrero, and R. Borja, Application of natural zeolites in anaerobic digestion processes: A review, Appl. Clay Sci, vol.58, pp.125-133, 2012.

J. Andersson and L. Björnsson, Evaluation of straw as a biofilm carrier in the methanogenic stage of two-stage anaerobic digestion of crop residues, Bioresour. Technol, vol.85, pp.51-56, 2002.

F. R. Bengelsdorf, C. Gabris, and L. Michel, Syntrophic microbial communities on straw as biofilm carrier increase the methane yield of a biowaste-digesting biogas reactor

, Bioeng, vol.2, pp.264-276, 2015.

,

M. Biodégradations, Les bactéries pour les technologies de l'environnement-Jean Pelmont, 2018.

Y. Rafrafi, N. Durban, and A. Bertron, Use of a continuous-flow bioreactor to evaluate nitrate reduction rate of Halomonas desiderata in cementitious environment relevant to nuclear waste deep repository, Biochem. Eng. J, vol.125, pp.161-170, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01845542

J. Herisson, E. D. Van-hullebusch, and M. Moletta-denat, Toward an accelerated biodeterioration test to understand the behavior of Portland and calcium aluminate cementitious materials in sewer networks, Int. Biodeterior. Biodegrad, vol.84, pp.236-243, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00877540

A. Buvignier, M. Peyre-lavigne, and C. Patapy, Understanding the resistance of calcium aluminate cements in sewer environments: role of soluble aluminium on the SOB activity and role of the biofilm in the degradation, Proc. 14th Int. Conf. Durab. Build. Mater. Compon. Ghent, 2017.

G. Cailleau, M. Mota, and S. Bindschedler, Detection of active oxalate-carbonate pathway ecosystems in the Amazon Basin: Global implications of a natural potential C sink, CATENA, vol.116, pp.132-141, 2014.

G. Martin, M. Guggiari, and D. Bravo, Fungi, bacteria and soil pH: the oxalate-carbonate pathway as a model for metabolic interaction, Environ. Microbiol, vol.14, pp.2960-2970, 2012.

V. Hervé, T. Junier, and S. Bindschedler, Diversity and ecology of oxalotrophic bacteria, World J. Microbiol. Biotechnol, vol.32, p.28, 2016.

C. R. Tracy and M. S. Pearle, Update on the medical management of stone disease, Curr. Opin. Urol, vol.19, 0200.

S. Chutipongtanate, S. Chaiyarit, and V. Thongboonkerd, Citrate, not phosphate, can dissolve calcium oxalate monohydrate crystals and detach these crystals from renal tubular cells, Eur. J. Pharmacol, vol.689, pp.219-225, 2012.

M. Salta, J. A. Wharton, and Y. Blache, Marine biofilms on artificial surfaces: structure and dynamics, Environ. Microbiol, vol.15, pp.2879-2893
URL : https://hal.archives-ouvertes.fr/hal-01364131

C. Pepe-ranney and E. K. Hall, The effect of carbon subsidies on marine planktonic niche partitioning and recruitment during biofilm assembly. Front. Microbiol, vol.6, 2015.

S. Celikkol-aydin, C. C. Gaylarde, and T. Lee, 16S rRNA gene profiling of planktonic and biofilm microbial populations in the Gulf of Guinea using Illumina NGS, Mar. Environ. Res, vol.122, pp.105-112, 2016.

A. Bertron, J. Duchesne, and G. Escadeillas, Accelerated tests of hardened cement pastes alteration by organic acids: analysis of the pH effect, Cem. Concr. Res, vol.35, pp.155-166, 2005.
URL : https://hal.archives-ouvertes.fr/hal-02161240

R. E. Beddoe, Modelling acid attack on concrete: Part II. A computer model, Cem. Concr. Res, vol.88, pp.20-35, 2016.

T. C. Zhang and P. L. Bishop, Structure, Activity and Composition of Biofilms. Water Sci. Technol, vol.29, pp.335-344, 1994.

A. Rochex, A. Massé, and R. Escudié, Influence of abrasion on biofilm detachment: evidence for stratification of the biofilm, J. Ind. Microbiol. Biotechnol, vol.36, pp.467-470, 2009.

N. Derlon, A. Massé, and R. Escudié, Stratification in the cohesion of biofilms grown under various environmental conditions, Water Res, vol.42, pp.2102-2110, 2008.