D. Plouchart, K. Milferstedt, G. Guizard, E. Latrille, and J. Hamelin, Multiplexed chemostat system for quantification of biodiversity and ecosystem functioning in anaerobic digestion, PLoS ONE, vol.13, issue.3, p.193748
URL : https://hal.archives-ouvertes.fr/hal-02623358

D. Plouchart, K. Milferstedt, G. Guizard, E. Latrille, and J. Hamelin, Multiplexed chemostats: a smart way for testing ecological theory, International Symposium on Microbial Ecology, vol.16, issue.16, pp.21-26, 2016.
URL : https://hal.archives-ouvertes.fr/hal-02739627

J. Hamelin, D. Plouchart, G. Guizard, E. Latrille, and K. Milferstedt,

, Replication of experiments in anaerobic digestion: simpler, greater and easier than you had ever hoped, Presented at 15. IWA World Conference on Anaerobic Digestion (AD-15), 2017.

P. S. Adam, G. Borrel, C. Brochier-armanet, and S. Gribaldo, The growing tree of Archaea: new perspectives on their diversity, evolution and ecology, ISME J, vol.11, pp.2407-2425, 2017.
URL : https://hal.archives-ouvertes.fr/pasteur-02445405

M. Akuzawa, T. Hori, S. Haruta, Y. Ueno, M. Ishii et al., Distinctive Responses of Metabolically Active Microbiota to Acidification in a, Thermophilic Anaerobic Digester. Microb. Ecol, vol.61, pp.595-605, 2011.

S. D. Allison and J. B. Martiny, Colloquium paper: resistance, resilience, and redundancy in microbial communities, Proc. Natl. Acad. Sci. 105, 2008.

, , pp.11512-11521

A. Alvarado, L. E. Montanez-hernandez, S. L. Palacio-molina, R. Oropeza-navarro, M. P. Luévanos-escareno et al., Microbial trophic interactions and mcrA gene expression in monitoring of anaerobic digesters, Front. Microbiol, vol.5, pp.1-14, 2014.

T. Amani, M. Nosrati, and T. R. Sreekrishnan, Anaerobic digestion from the viewpoint of microbiological, chemical, and operational aspects -a review, Environ. Rev, vol.18, pp.255-278, 2010.

, Standard methods for the examination of water and wastewater, 21sted, APHA, 2005.

R. Arditi, J. Michalski, and A. H. Hirzel, Rheagogies: Modelling non-trophic effects in food webs, Ecol. Complex, vol.2, pp.249-258, 2005.

M. Badshah, D. M. Lam, J. Liu, and B. Mattiasson, Use of an Automatic Methane Potential Test System for evaluating the biomethane potential of sugarcane bagasse after different treatments, Bioresour. Technol, vol.114, pp.262-269, 2012.

S. C. Bagby and S. W. Chisholm, Response of Prochlorococcus to varying CO2:O2 ratios, ISME J, vol.9, pp.2232-2245, 2015.

A. D. Barnosky, N. Matzke, S. Tomiya, G. O. Wogan, B. Swartz et al., Has the Earth's sixth mass extinction already arrived?, Nature, vol.471, pp.51-57, 2011.

D. J. Batstone, J. Keller, I. Angelidaki, S. V. Kalyuzhnyi, S. G. Pavlostathis et al., The IWA Anaerobic Digestion Model No 1 (ADM1), Water Sci. Technol, vol.45, pp.65-73, 2002.

K. Baumann, M. Dignac, C. Rumpel, G. Bardoux, A. Sarr et al., Soil microbial diversity affects soil organic matter decomposition in a silty grassland soil, Biogeochemistry, vol.114, pp.201-212, 2013.
URL : https://hal.archives-ouvertes.fr/hal-02646838

T. Bell, J. Newman, B. W. Silverman, S. L. Turner, and A. K. Lilley, The contribution of species richness and composition to bacterial services, Nature, vol.436, pp.1157-1160, 2005.

A. Bensmann, R. Hanke-rauschenbach, and K. Sundmacher, Reactor configurations for biogas plants -a model based analysis, Chem. Eng. Sci, vol.104, pp.413-426, 2013.

R. L. Bier, E. S. Bernhardt, C. M. Boot, E. B. Graham, E. K. Hall et al., Linking microbial community structure and microbial processes: An empirical and conceptual overview, FEMS Microbiol. Ecol, vol.91, pp.1-11, 2015.

A. A. Boaro, Y. Kim, A. E. Konopka, S. J. Callister, and B. K. Ahring, Integrated 'omics analysis for studying the microbial community response to a pH perturbation of a cellulose-degrading bioreactor culture, Fems Microbiol. Ecol, vol.8, pp.802-815, 2014.

T. Bouchez, D. Patureau, P. Dabert, S. Juretschko, J. Doré et al., Ecological study of a bioaugmentation failure, Environ. Microbiol, vol.2, pp.179-190, 2000.
URL : https://hal.archives-ouvertes.fr/hal-02695943

D. Branton, D. W. Deamer, A. Marziali, H. Bayley, S. Benner et al., The potential and challenges of nanopore sequencing, Nat. Biotechnol, vol.26, pp.1146-1153, 2008.

F. Braun, J. Hamelin, A. Bonnafous, N. Delgenès, J. P. 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, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01159242

A. Briones and L. Raskin, Diversity and dynamics of microbial communities in engineered environments and their implications for process stability, Curr. Opin. Biotechnol, vol.14, pp.270-276, 2003.

,

M. W. Cadotte and T. Fukami, Dispersal, spatial scale, and species diversity in a hierarchically structured experimental landscape, Ecol. Lett, vol.8, pp.548-557, 2005.

J. G. Caporaso, C. L. Lauber, W. A. Walters, D. Berg-lyons, J. Huntley et al., Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms, ISME J, vol.6, pp.1621-1624, 2012.

G. Capson-tojo, E. Trably, M. Rouez, M. Crest, N. Bernet et al., Cardboard proportions and total solids contents as driving factors in dry co-fermentation of food waste, Bioresour. Technol, vol.248, pp.229-237, 2017.
URL : https://hal.archives-ouvertes.fr/hal-02621022

M. Carballa, L. Regueiro, and J. M. Lema, Microbial management of anaerobic digestion: exploiting the microbiome-functionality nexus, Curr. Opin. Biotechnol, vol.33, pp.103-111, 2015.

M. Carballa, M. Smits, C. Etchebehere, N. Boon, and W. Verstraete, Correlations between molecular and operational parameters in continuous lab-scale anaerobic reactors, Appl. Microbiol. Biotechnol, vol.89, pp.303-314, 2011.

B. J. Cardinale, J. E. Duffy, A. Gonzalez, D. U. Hooper, C. Perrings et al., Biodiversity loss and its impact on humanity, Nature, vol.489, pp.326-326, 2012.

B. J. Cardinale, K. L. Matulich, D. U. Hooper, J. E. Byrnes, E. Duffy et al., The functional role of producer diversity in ecosystems, Am. J. Bot, vol.98, pp.572-592, 2011.

T. Caruso, Y. Chan, D. C. Lacap, M. C. Lau, C. P. Mckay et al., Stochastic and deterministic processes interact in the assembly of desert microbial communities on a global scale, ISME J, vol.5, pp.1406-1413, 2011.

A. Chao, Nonparametric Estimation of the, Scandinavian Journal of Statistics. Scand. J. Stat, vol.11, pp.265-270, 1984.

O. Chapleur, A. Bize, T. Serain, L. Mazéas, and T. Bouchez, Co-inoculating ruminal content neither provides active hydrolytic microbes nor improves methanization of 13C-cellulose in batch digesters, FEMS Microbiol. Ecol, vol.87, pp.616-629, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02598975

R. Chouari, S. Guermazi, and A. Sghir, Co-occurence of Crenarchaeota, Thermoplasmata and methanogens in anaerobic sludge digesters, World J. Microbiol. Biotechnol, vol.31, pp.805-812, 2015.

T. P. Curtis, I. M. Head, M. Lunn, S. Woodcock, P. D. Schloss et al., What is the extent of prokaryotic diversity?, Philos. Trans. R. Soc. B Biol. Sci, vol.361, pp.2023-2037, 2006.

K. De-roy, M. Marzorati, A. Negroni, O. Thas, A. Balloi et al., Environmental conditions and community evenness determine the outcome of biological invasion, Nat. Commun, vol.4, pp.1383-1385, 2013.

K. De-roy, M. Marzorati, P. Van-den-abbeele, T. Van-de-wiele, and N. Boon, Synthetic microbial ecosystems: an exciting tool to understand and apply microbial communities, Environ. Microbiol, vol.16, pp.1472-1481, 2014.

J. De-vrieze, S. Gildemyn, R. Vilchez-vargas, R. Jáuregui, D. H. Pieper et al., Inoculum selection is crucial to ensure operational stability in anaerobic digestion, Appl. Microbiol. Biotechnol, vol.99, pp.189-199, 2014.

J. De-vrieze, A. J. Pinto, W. T. Sloan, and U. Z. Ijaz, The active microbial community more accurately reflects the anaerobic digestion process: 16S rRNA (gene) sequencing as a predictive tool, vol.6, 2018.

J. De-vrieze, L. Raport, H. Roume, R. Vilchez-vargas, R. Jáuregui et al., The full-scale anaerobic digestion microbiome is represented by specific marker populations, Water Res, vol.104, pp.101-110, 2016.

J. De-vrieze, W. Verstraete, and N. Boon, Repeated pulse feeding induces functional stability in anaerobic digestion, Microb. Biotechnol, vol.6, pp.414-424, 2013.

J. De-vrieze and W. Verstraete, Perspectives for microbial community composition in anaerobic digestion: from abundance and activity to connectivity, Environ. Microbiol, vol.32, pp.2-43, 2016.

T. De-wiele, P. Den-abbeele, W. Ossieur, S. Possemiers, M. Marzorati et al., The Simulator of the Human Intestinal Microbial Ecosystem (SHIME®), The Impact of Food Bioactives on Health: In Vitro and Ex Vivo Models, 2015.

. Cham, , pp.305-317

J. E. Duffy, C. M. Godwin, and B. J. Cardinale, Biodiversity effects in the wild are common and as strong as key drivers of productivity, Nature, vol.549, pp.261-264, 2017.

A. J. Dumbrell, M. Nelson, T. Helgason, C. Dytham, and A. H. Fitter, Relative roles of niche and neutral processes in structuring a soil microbial community, ISME J, vol.4, pp.337-345, 2010.

E. A. Eloe-fadrosh, N. N. Ivanova, T. Woyke, and N. C. Kyrpides, Metagenomics uncovers gaps in amplicon-based detection of microbial diversity, Nat. Microbiol, vol.1, p.15032, 2016.

A. Escalas, T. Bouvier, M. A. Mouchet, F. Leprieur, C. Bouvier et al., A unifying quantitative framework for exploring the multiple facets of microbial biodiversity across diverse scales, Environ. Microbiol, vol.15, pp.2642-2657, 2013.

C. Eskicioglu, F. Monlau, A. Barakat, I. Ferrer, P. Kaparaju et al., Assessment of hydrothermal pretreatment of various lignocellulosic biomass with CO2 catalyst for enhanced methane and hydrogen production, Water Res, vol.120, pp.32-42, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01604979

R. Evans, A. M. Alessi, S. Bird, S. J. Mcqueen-mason, N. C. Bruce et al., Defining the functional traits that drive bacterial decomposer community productivity, ISME J, vol.11, pp.1680-1687, 2017.

P. G. Falkowski, T. Fenchel, and E. F. Delong, The microbial engines that drive Earth's biogeochemical cycles, Science, vol.320, pp.1034-1039, 2008.

K. Faust, G. Lima-mendez, J. S. Lerat, J. F. Sathirapongsasuti, R. Knight et al., Cross-biome comparison of microbial association networks, Front. Microbiol, vol.6, pp.1-13, 2015.

K. Faust and J. Raes, Microbial interactions: from networks to models, Nat. Rev. Microbiol, vol.10, pp.538-550, 2012.

A. Fernández, S. Huang, S. Seston, J. Xing, R. Hickey et al., , 1999.

, Appl. Environ. Microbiol, vol.65, pp.3697-3704

A. S. Fernandez, S. A. Hashsham, S. L. Dollhopf, L. Raskin, O. Glagoleva et al., Flexible community structure correlates with stable community function in methanogenic bioreactor communities perturbed by glucose, Appl. Environ. Microbiol, vol.66, pp.4058-4067, 2000.

I. Fetzer, K. Johst, R. Schäwe, T. Banitz, H. Harms et al., The extent of functional redundancy changes as species' roles shift in different environments, Proc. Natl. Acad. Sci, vol.112, pp.14888-14893, 2015.

S. Freilich, R. Zarecki, O. Eilam, E. S. Segal, C. S. Henry et al., Competitive and cooperative metabolic interactions in bacterial communities, Nat. Commun, vol.2, pp.587-589, 2011.

T. Fukami, Historical Contingency in Community Assembly: Integrating Niches, Species Pools, and Priority Effects, Annu. Rev. Ecol. Evol. Syst, vol.46, pp.1-23, 2015.

N. Gagnon, M. Barret, E. Topp, M. Kalmokoff, D. Massé et al., A novel fingerprint method to assess the diversity of methanogens in microbial systems, FEMS Microbiol. Lett, vol.325, pp.115-122, 2011.

F. Gause, The Struggle for Existence, Yale J. Biol. Med, vol.7, 1934.

G. Gebhardt, R. Hortsch, K. Kaufmann, M. Arnold, and D. Weuster-botz, A new microfluidic concept for parallel operated milliliter-scale stirred tank bioreactors, Biotechnol. Prog, vol.27, pp.684-690, 2011.

E. B. Graham, J. E. Knelman, A. Schindlbacher, S. Siciliano, M. Breulmann et al., Microbes as engines of ecosystem function: When does community structure enhance predictions of ecosystem processes?, Front. Microbiol, vol.7, pp.1-10, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01588095

E. B. Graham, W. R. Wieder, J. W. Leff, S. R. Weintraub, A. R. Townsend et al., Do we need to understand microbial communities to predict ecosystem function? A comparison of statistical models of nitrogen cycling processes, Soil Biol. Biochem, vol.68, pp.279-282, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02632393

B. Haegeman, J. Hamelin, J. Moriarty, P. Neal, J. Dushoff et al., Robust estimation of microbial diversity in theory and in practice, ISME J, vol.7, pp.1092-101, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00859547

B. Haegeman, B. Sen, J. Godon, and J. Hamelin, Only simpson diversity can be estimated accurately from microbial community fingerprints, Microb. Ecol, vol.68, pp.169-72, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01190153

B. Haegeman, D. Vanpeteghem, J. J. Godon, and J. Hamelin, DNA reassociation kinetics and diversity indices: Richness is not rich enough, 2008.
URL : https://hal.archives-ouvertes.fr/hal-02660651

L. H. Hagen, V. Vivekanand, P. B. Pope, V. G. Eijsink, and S. J. Horn, The effect of storage conditions on microbial community composition and biomethane potential in a biogas starter culture, Appl. Microbiol. Biotechnol, pp.5749-5761, 2015.

K. Hagos, J. Zong, D. Li, C. Liu, and X. Lu, Anaerobic co-digestion process for biogas production: progress, challenges and perspectives, Renew. Sustain. Energy Rev, vol.76, pp.1485-1496, 2017.

A. Hanreich, U. Schimpf, M. Zakrzewski, A. Schlüter, D. Benndorf et al., Metagenome and metaproteome analyses of microbial communities in mesophilic biogasproducing anaerobic batch fermentations indicate concerted plant carbohydrate degradation, Syst. Appl. Microbiol, vol.36, pp.330-338, 2013.

L. Hao, A. Bize, D. Conteau, O. Chapleur, S. Courtois et al., New insights into the key microbial phylotypes of anaerobic sludge digesters under different operational conditions, Water Res, vol.102, pp.158-169, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01602845

R. Heyer, F. Kohrs, U. Reichl, and D. Benndorf, Metaproteomics of complex microbial communities in biogas plants, Microb. Biotechnol, vol.8, pp.749-763, 2015.

A. Ho, K. De-roy, O. Thas, J. De-neve, S. Hoefman et al., The more, the merrier: heterotroph richness stimulates methanotrophic activity, ISME J, vol.8, pp.1945-1948, 2014.

A. Holm and E. Vikström, Quorum sensing communication between bacteria and human cells: signals, targets, and functions, Front. Plant Sci, vol.5, pp.1-7, 2014.

L. V. Hooper and J. I. Gordon, Commensal Host-Bacterial Relationships in the Gut, Science, vol.1115, pp.1-7, 2001.

M. C. Horner-devine, M. A. Leibold, V. H. Smith, and B. J. Bohannan, Bacterial diversity patterns along a gradient of primary productivity, Ecol. Lett, vol.6, pp.613-622, 2003.

P. A. Hoskisson and G. Hobbs, Continuous culture -Making a comeback? Microbiology, vol.151, pp.3153-3159, 2005.

S. P. Hubbell, MacArthur and Wilson ' s Radical Theory. Unified Neutral Theory Biodivers, pp.3-29, 2001.

G. E. Hutchinson, The paradox of the pankton, Am. Nat, vol.95, pp.137-145, 1961.

B. Jaillard, A. Rapaport, J. Harmand, A. Brauman, and N. Nunan, Community assembly effects shape the biodiversity-ecosystem functioning relationships, Funct. Ecol, vol.28, pp.1523-1533, 2014.
URL : https://hal.archives-ouvertes.fr/hal-00937779

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

L. Jost, Entropy and diversity, Oikos, vol.113, pp.363-375, 2006.

P. F. Kemp and J. Y. Aller, Bacterial diversity in aquatic and other environments: What 16S rDNA libraries can tell us, FEMS Microbiol. Ecol, vol.47, pp.161-177, 2004.

F. M. Kerckhof, E. N. Courtens, A. Geirnaert, S. Hoefman, A. Ho et al., Optimized cryopreservation of mixed microbial communities for conserved functionality and diversity, PLoS One, vol.9, 2014.

J. E. Knelman and D. R. Nemergut, Changes in community assembly may shift the relationship between biodiversity and ecosystem function, Front. Microbiol, vol.5, pp.1-4, 2014.

K. Koch, T. Lippert, and J. E. Drewes, The role of inoculum's origin on the methane yield of different substrates in biochemical methane potential (BMP) tests, Bioresour. Technol, vol.243, pp.457-463, 2017.

A. Konopka, S. Lindemann, and J. Fredrickson, Dynamics in microbial communities: unraveling mechanisms to identify principles, ISME J, vol.9, pp.1488-1495, 2014.

K. T. Konstantinidis and J. M. Tiedje, Genomic insights that advance the species definition for prokaryotes, Proc. Natl. Acad. Sci, vol.102, pp.2567-2572, 2005.

D. M. Kottmeier, S. D. Rokitta, and B. Rost, Acidification, not carbonation, is the major regulator of carbon fluxes in the coccolithophore Emiliania huxleyi, New Phytol, vol.211, pp.126-137, 2016.

A. Kusterer, C. Krause, K. Kaufmann, M. Arnold, and D. Weuster-botz, Fully automated single-use stirred-tank bioreactors for parallel microbial cultivations, Bioprocess Biosyst. Eng, vol.31, pp.207-215, 2008.

S. Langenheder, M. T. Bulling, M. Solan, and J. I. Prosser, Bacterial Biodiversity-Ecosystem Functioning Relations Are Modified by Environmental Complexity, PLoS One, vol.5, 2010.

S. Langer, D. Schropp, F. R. Bengelsdorf, M. Othman, and M. Kazda, Dynamics of biofilm formation during anaerobic digestion of organic waste, Anaerobe, vol.29, pp.44-51, 2014.

W. Laperrière, B. Barry, M. Torrijos, B. Pechiné, N. Bernet et al., Optimal conditions for flexible methane production in a demandbased operation of biogas plants, Bioresour. Technol, vol.245, pp.698-705, 2017.

M. Leclerc, J. Delgènes, and J. Godon, Diversity of the archaeal community in 44 anaerobic digesters as determined by single strand conformation polymorphism analysis and 16S rDNA sequencing, Environ. Microbiol, vol.6, pp.809-828, 2004.

L. N. Lemos, R. R. Fulthorpe, E. W. Triplett, and L. F. Roesch, Rethinking microbial diversity analysis in the high throughput sequencing era, J. Microbiol. Methods, vol.86, pp.42-51, 2011.

J. T. Lennon, Replication, lies and lesser-known truths regarding experimental design in environmental microbiology, Environ. Microbiol, vol.13, pp.1383-1386, 2011.

Q. Lin, J. De-vrieze, C. Li, J. Li, J. Li et al., Temperature regulates deterministic processes and the succession of microbial interactions in anaerobic digestion process, Water Res, vol.123, pp.134-143, 2017.

K. J. Locey and J. T. Lennon, Scaling laws predict global microbial diversity, Proc. Natl. Acad. Sci, vol.113, pp.5970-5975, 2016.

M. Loreau, Biodiversity and Ecosystem Functioning: Current Knowledge and Future Challenges, Science, vol.294, pp.804-808, 2001.

S. Louca and M. Doebeli, Taxonomic variability and functional stability in microbial communities infected by phages, Environ. Microbiol, vol.2, issue.28, 2017.

C. Lozupone and R. Knight, UniFrac : a new phylogenetic method for comparing microbial communities, Appl. Environ. Microbiol, vol.71, pp.8228-8235, 2005.

C. A. Lozupone, M. Hamady, S. T. Kelley, and R. Knight, Quantitative and qualitative Beta diversity measures lead to different insights into factors that structure microbial communities, Appl. Environ. Microbiol, vol.73, pp.1576-1585, 2007.

X. Lu, S. Rao, Z. Shen, and P. K. Lee, Substrate induced emergence of different active bacterial and archaeal assemblages during biomethane production, Bioresour. Technol, vol.148, pp.517-524, 2013.

H. Luo, H. Zhang, T. Suzuki, S. Hattori, and Y. Kamagata, Differential expression of methanogenesis genes of Methanothermobacter thermoautotrophicus (Formerly Methanobacterium thermoautotrophicum) in pure culture and in cocultures with fatty acid-oxidizing syntrophs, Appl. Environ. Microbiol, vol.68, pp.1173-1179, 2002.

P. E. Luton, J. M. Wayne, R. J. Sharp, and P. W. Riley, The mcrA gene as an alternative to 16S rRNA in the phylogenetic analysis of methanogen populations in landfill, Microbiology, vol.148, pp.3521-3530, 2002.

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

G. T. Macfarlane, S. Macfarlane, and G. R. Gibson, Validation of a threestage compound continuous culture system for investigating the effect of retention time on the ecology and metabolism of bacteria in the human colon, Microb. Ecol, vol.35, pp.180-187, 1998.

Y. Maspolim, Y. Zhou, C. Guo, K. Xiao, and W. J. Ng, Determination of the archaeal and bacterial communities in two-phase and single-stage anaerobic systems by 454 pyrosequencing, J. Environ. Sci, vol.36, pp.121-129, 2015.

K. S. Mccann, The diversity-stability debate, Nature, vol.405, pp.228-233, 2000.

J. A. Mcdonald, K. Schroeter, S. Fuentes, I. Heikamp-dejong, C. M. Khursigara et al., Evaluation of microbial community reproducibility, stability and composition in a human distal gut chemostat model, J. Microbiol. Methods, vol.95, pp.167-174, 2013.

P. J. Mcmurdie and S. Holmes, Phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data, PLoS One, vol.8, 2013.

R. Moletta, La méthanisation, 1ère, 2008.

F. Mosbaek, H. Kjeldal, D. G. Mulat, M. Albertsen, A. J. Ward et al., Identification of syntrophic acetate-oxidizing bacteria in anaerobic digesters, ISME J, vol.2, pp.1-14, 2016.

R. Moscoviz, C. Flayac, . Desmond-le, E. Quéméner, E. Trably et al., Revealing extracellular electron transfer mediated parasitism: energetic considerations, Sci. Rep, vol.7, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01602758

J. Mounier, C. Monnet, T. Vallaeys, R. Arditi, A. S. Sarthou et al., Microbial interactions within a cheese microbial community, Appl. Environ. Microbiol, vol.74, pp.172-181, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00556971

M. C. Nelson, H. G. Morrison, J. Benjamino, S. L. Grim, and J. Graf, Analysis, optimization and verification of illumina-generated 16s rRNA gene amplicon surveys, PLoS One, vol.9, 2014.

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.

D. Nemergut, A. Shade, and C. Violle, When, where and how does microbial community composition matter?, Front. Microbiol, vol.5, 2012.

N. Nguyen, T. Warnow, M. Pop, and B. White, A perspective on 16S rRNA operational taxonomic unit clustering using sequence similarity, Biofilms Microbiomes, vol.2, pp.10-13, 2016.

H. B. Nielsen, H. Uellendahl, and B. K. Ahring, Regulation and optimization of the biogas process: propionate as a key parameter, Biomass and Bioenergy, vol.31, pp.820-830, 2007.

J. Oksanen, F. G. Blanchet, M. Friendly, R. Kindt, P. Legendre et al., Vegan: community ecology package, R Packag. version, vol.2, 2015.

M. G. Pereira and S. M. Mudge, Cleaning oiled shores: laboratory experiments testing the potential use of vegetable oil biodiesels, Chemosphere, vol.54, issue.03, pp.665-674, 2004.

A. R. Perrotta, R. Kumaraswamy, J. R. Bastidas-oyanedel, E. J. Alm, and J. Rodríguez, Inoculum composition determines microbial community and function in an anaerobic sequential batch reactor, PLoS One, vol.12, 2017.

L. Philippot, A. Spor, C. Hénault, D. Bru, F. Bizouard et al., Loss in microbial diversity affects nitrogen cycling in soil, ISME J, vol.7, pp.1609-1619, 2013.
URL : https://hal.archives-ouvertes.fr/hal-02651652

M. K. Pholchan, J. Baptista, C. De, R. J. Davenport, and T. P. Curtis, Systematic study of the effect of operating variables on reactor performance and microbial diversity in laboratory-scale activated sludge reactors, Water Res, vol.44, pp.1341-1352, 2010.

M. K. Pholchan, J. C. De-baptista, R. J. Davenport, W. T. Sloan, and T. P. Curtis, Microbial community assembly, theory and rare functions, Front. Microbiol, vol.4, pp.1-9, 2013.

T. Pohlert, PMCMR: Calculate Pairwise Multiple Comparisons of Mean Rank Sums, 2016.

J. I. Prosser, Replicate or lie, Environ. Microbiol, vol.12, pp.1806-1810, 2010.

J. I. Prosser, B. J. Bohannan, T. P. Curtis, R. J. Ellis, M. K. Firestone et al., The role of ecological theory in microbial ecology, Nat. Rev. Microbiol, vol.5, pp.384-92, 2007.

M. Quéméneur, J. Hamelin, E. Latrille, J. P. Steyer, and E. Trably, Functional versus phylogenetic fingerprint analyses for monitoring hydrogen-producing bacterial populations in dark fermentation cultures, Int. J. Hydrogen Energy, vol.36, pp.3870-3879, 2011.

M. Quéméneur, J. Hamelin, E. Latrille, J. P. Steyer, and E. Trably, Development and application of a functional CE-SSCP fingerprinting method based on [Fe-Fe]-hydrogenase genes for monitoring hydrogenproducing Clostridium in mixed cultures, Int. J. Hydrogen Energy, vol.35, pp.13158-13167, 2010.

. R-core-team, R: A language and environment for statistical computing, 2016.

Y. Rafrafi, E. Trably, J. Hamelin, E. Latrille, I. Meynial-salles et al., Sub-dominant bacteria as keystone species in microbial communities producing bio-hydrogen, Int. J. Hydrogen Energy, vol.38, pp.4975-4985, 2013.
URL : https://hal.archives-ouvertes.fr/hal-02649108

F. Raposo, V. Fernandez-cegri, M. A. De-la-rubia, R. Borja, F. Béline et al., Biochemical methane potential (BMP) of solid organic substrates: evaluation of anaerobic biodegradability using data from an international interlaboratory study, J. Chem. Technol. Biotechnol, vol.86, pp.1088-1098, 2011.
URL : https://hal.archives-ouvertes.fr/hal-02652567

L. Regueiro, P. Veiga, M. Figueroa, J. Alonso-gutierrez, A. J. Stams et al., Relationship between microbial activity and microbial community structure in six full-scale anaerobic digesters, Microbiol. Res, vol.167, pp.581-590, 2012.

M. C. Rillig, J. Antonovics, T. Caruso, A. Lehmann, J. R. Powell et al., Interchange of entire communities: Microbial community coalescence, Trends Ecol. Evol, vol.30, pp.470-476, 2015.

M. C. Rillig, A. Tsang, and J. Roy, Microbial community coalescence for microbiome engineering, Front. Microbiol, vol.7, pp.6-8, 2016.

D. Rivière, V. Desvignes, E. Pelletier, S. Chaussonnerie, S. Guermazi et al., Towards the definition of a core of microorganisms involved in anaerobic digestion of sludge, ISME J, vol.3, pp.700-714, 2009.

F. Roger, S. Bertilsson, S. Langenheder, O. Ahmed, and L. Gamfeldt, Multiple dimensions of bacterial diversity on functioning , stability and multifunctionality, Ecology, vol.97, pp.2716-2728, 2016.

M. Ronaghi, M. Uhlén, and P. Nyrén, A Sequencing Method Based on Real-Time Pyrophosphate, Science, vol.281, pp.363-365, 1998.

S. Roux, F. Enault, G. Le-bronner, and D. Debroas, Comparison of 16S rRNA and protein-coding genes as molecular markers for assessing microbial diversity (Bacteria and Archaea) in ecosystems, FEMS Microbiol. Ecol, vol.78, pp.617-628, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00840983

K. Rummens, L. De-meester, and C. Souffreau, Inoculation history affects community composition in experimental freshwater bacterioplankton communities, Environ. Microbiol, vol.20, pp.1120-1133, 2018.

M. Saleem, I. Fetzer, H. Harms, and A. Chatzinotas, Diversity of protists and bacteria determines predation performance and stability, ISME J, vol.7, pp.1912-1933, 2013.

J. Salles, F. Poly, B. Schmid, and X. Roux, Community niche predicts the functioning of denitrifying bacterial assemblages, Ecology, vol.90, pp.3324-3332, 2009.
URL : https://hal.archives-ouvertes.fr/halsde-00525103

S. D. Salles and J. F. , Functional redundancy and ecosystem function -the soil microbiota as a case study, Biodiversity in Ecosystems -Linking Structure and Function, 2015.

A. M. Saunders, M. Albertsen, J. Vollesen, and P. H. Nielsen, The activated sludge ecosystem contains a core community of abundant organisms, 2015.

, ISME J, vol.10, pp.11-20

D. E. Schindler, J. B. Armstrong, and T. E. Reed, The portfolio concept in ecology and evolution, Front. Ecol. Environ, vol.13, pp.257-263, 2015.

P. D. Schloss and J. Handelsman, Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness, Appl. Environ. Microbiol, vol.71, pp.1501-1506, 2005.

P. D. Schloss, S. L. Westcott, T. Ryabin, J. R. Hall, M. Hartmann et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities, Appl. Environ. Microbiol, vol.75, pp.7537-7541, 2009.

A. Schmideder, T. S. Severin, J. H. Cremer, and D. Weuster-botz, A novel milliliter-scale chemostat system for parallel cultivation of microorganisms in stirred-tank bioreactors, J. Biotechnol, vol.210, pp.19-24, 2015.

A. Shade, Diversity is the question, not the answer, ISME J, vol.4, pp.1-6, 2017.

A. Shade, C. C. Carey, E. Kara, S. Bertilsson, K. D. Mcmahon et al., Can the black box be cracked? The augmentation of microbial ecology by high-resolution, automated sensing technologies, ISME J, vol.3, pp.881-888, 2009.

A. Shade and J. Handelsman, Beyond the Venn diagram: the hunt for a core microbiome, Environ. Microbiol, vol.14, pp.4-12, 2012.

A. Shade, H. Peter, S. D. Allison, D. L. Baho, M. Berga et al., Fundamentals of microbial community resistance and resilience, Front. Microbiol, vol.3, pp.1-19, 2012.

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

O. H. Shapiro, A. Kushmaro, and A. Brenner, Bacteriophage predation regulates microbial abundance and diversity in a full-scale bioreactor treating industrial wastewater, ISME J, vol.4, pp.327-336, 2010.

P. Sierocinski, K. Milferstedt, F. Bayer, T. Großkopf, M. Alston et al., A Single Community Dominates Structure and Function of a Mixture of Multiple Methanogenic Communities, Curr. Biol, vol.27, pp.3390-3395, 2017.
URL : https://hal.archives-ouvertes.fr/hal-02624588

E. Simpson, Measurement of Diversity, 1949.

W. T. Sloan, M. Lunn, S. Woodcock, I. M. Head, S. Nee et al., Quantifying the roles of immigration and chance in shaping prokaryote community structure, Environ. Microbiol, vol.8, pp.732-740, 2006.

V. H. Smith, Microbial diversity-productivity relationships in aquatic ecosystems, FEMS Microbiol. Ecol, vol.62, pp.181-186, 2007.

L. Solli, O. E. Havelsrud, S. J. Horn, and A. G. Rike, A metagenomic study of the microbial communities in four parallel biogas reactors, Biotechnol. Biofuels, vol.14, 2014.

E. Stackebrandt, W. Frederiksen, G. M. Garrity, P. A. Grimont, P. Kampfer et al., Report of the ad hoc comittee for the re-evaluation of the species definition in bacteriology, Int. J. Syst. Evol. Microbiol, vol.52, pp.1043-1047, 2002.

J. C. Stegen, X. Lin, A. E. Konopka, and J. K. Fredrickson, Stochastic and deterministic assembly processes in subsurface microbial communities, 2012.

, ISME J, vol.6, pp.1653-1664

L. M. Steinberg and J. M. Regan, Response of lab-scale methanogenic reactors inoculated from different sources to organic loading rate shocks, Bioresour. Technol, vol.102, pp.8790-8798, 2011.

B. Steinhaus, M. L. Garcia, A. Q. Shen, and L. T. Angenent, A portable anaerobic microbioreactor reveals optimum growth conditions for the methanogen Methanosaeta concilii, Appl. Environ. Microbiol, vol.73, pp.1653-1658, 2007.

H. Su, L. Liu, S. Wang, Q. Wang, Y. Jiang et al., Semicontinuous anaerobic digestion for biogas production: influence of ammonium acetate supplement and structure of the microbial community, Biotechnol. Biofuels, vol.8, pp.1-11, 2015.

L. Sun, T. Liu, B. Müller, and A. Schnürer, The microbial community structure in industrial biogas plants influences the degradation rate of straw and cellulose in batch tests, Biotechnol. Biofuels, vol.1, issue.20, 2016.

L. Sun, P. B. Pope, V. G. Eijsink, and A. Schnürer, Characterization of microbial community structure during continuous anaerobic digestion of straw and cow manure, Microb. Biotechnol, vol.8, pp.815-827, 2015.

C. Sundberg, W. A. Al-soud, M. Larsson, E. Alm, S. S. Yekta et al., 454 pyrosequencing analyses of bacterial and archaeal richness in 21 full-scale biogas digesters, Fems Microbiol. Ecol, vol.85, pp.612-626, 2013.

E. Szabó, R. Liébana, M. Hermansson, O. Modin, F. Persson et al., Microbial population dynamics and ecosystem functions of anoxic/aerobic granular sludge in sequencing batch reactors operated at different organic loading rates, Front. Microbiol, vol.8, pp.1-14, 2017.

V. P. Tale, J. S. Maki, C. Struble, and D. H. Zitomer, Methanogen community structure-activity relationship and bioaugmentation of overloaded anaerobic digesters, Water Res, vol.45, pp.5249-56, 2011.

V. Tardy, O. Mathieu, J. Lévêque, S. Terrat, A. Chabbi et al., Stability of soil microbial structure and activity depends on microbial diversity, Environ. Microbiol. Rep, vol.6, pp.173-183, 2014.
URL : https://hal.archives-ouvertes.fr/hal-00974712

M. Tikhonov, Community-level cohesion without cooperation, vol.5, pp.1-15, 2016.

D. Tilman and J. A. Downing, Biodiversity and stability in grasslands, Nature, vol.367, pp.363-365, 1994.

V. Torsvik and L. Ovreas, Microbial diversity and function in soil: from genes to ecosystems, Curr. Opin. Microbiol, vol.5, pp.324-331, 2002.

B. P. Tracy, S. W. Jones, A. G. Fast, D. C. Indurthi, and E. T. Papoutsakis, Clostridia: the importance of their exceptional substrate and metabolite diversity for biofuel and biorefinery applications, Curr. Opin. Biotechnol, vol.23, pp.364-381, 2012.

L. Treu, P. G. Kougias, S. Campanaro, I. Bassani, and I. Angelidaki, Deeper insight into the structure of the anaerobic digestion microbial community; the biogas microbiome database is expanded with 157 new genomes, Bioresour. Technol, vol.216, pp.260-266, 2016.

A. Valentin-vargas, G. Toro-labrador, and A. A. Massol-deya, Bacterial community dynamics in full-scale activated sludge bioreactors: operational and ecological factors driving community assembly and performance, PLoS One, vol.7, 2012.

. Van-der, C. J. Gast, D. Ager, and A. K. Lilley, Temporal scaling of bacterial taxa is influenced by both stochastic and deterministic ecological factors, Environ. Microbiol, vol.10, pp.1411-1418, 2008.

I. Vanwonterghem, P. N. Evans, D. H. Parks, P. D. Jensen, B. J. Woodcroft et al., Methylotrophic methanogenesis discovered in the novel archaeal phylum, Nat. Microbiol, pp.1-9, 2016.

,

I. Vanwonterghem, P. D. Jensen, P. G. Dennis, P. Hugenholtz, K. Rabaey et al., Deterministic processes guide long-term synchronised population dynamics in replicate anaerobic digesters, 2014.

, ISME J, vol.8, 2015.

I. Vanwonterghem, P. D. Jensen, D. P. Ho, D. J. Batstone, and G. W. Tyson, Linking microbial community structure, interactions and function in anaerobic digesters using new molecular techniques, Curr. Opin. Biotechnol, vol.27, pp.55-64, 2014.

I. Vanwonterghem, P. D. Jensen, K. Rabaey, and G. W. Tyson, Temperature and solids retention time control microbial population dynamics and volatile fatty acid production in replicated anaerobic digesters, Sci. Rep, vol.5, 2015.

M. Vellend, Conceptual Synthesis in Community Ecology, Q. Rev. Biol, vol.85, pp.183-206, 2010.

P. A. Venail, R. C. Maclean, T. Bouvier, M. A. Brockhurst, M. E. Hochberg et al., Diversity and productivity peak at intermediate dispersal rate in evolving metacommunities, Nature, vol.452, pp.210-214, 2008.

K. Venkiteshwaran, B. Bocher, J. Maki, and D. Zitomer, Relating anaerobic digestion microbial community and process function, 2015.

, Microbiol. Insights, vol.8, pp.37-44

K. Venkiteshwaran, K. Milferstedt, J. Hamelin, M. Fujimoto, M. Johnson et al., Correlating methane production to microbiota in anaerobic digesters fed synthetic wastewater, Water Res, vol.110, pp.161-169, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01608544

K. Venkiteshwaran, K. Milferstedt, J. Hamelin, and D. H. Zitomer, Anaerobic digester bioaugmentation influences quasi steady state performance and microbial community, Water Res, vol.104, pp.128-136, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01608636

W. Verstraete, L. Wittebolle, K. Heylen, B. Vanparys, P. De-vos et al., Microbial resource management: the road to go for environmental biotechnology, Eng. Life Sci, vol.7, pp.117-126, 2007.

C. Violle, Z. Pu, and L. Jiang, Experimental demonstration of the importance of competition under disturbance, Proc. Natl. Acad. Sci, vol.107, pp.12925-12929, 2010.

C. Vogelsang, K. Gollembiewski, and K. Østgaard, Effect of preservation techniques on the regeneration of gel entrapped nitrifying sludge, Water Res, vol.33, pp.200-200, 1999.

D. C. Vuono, J. Benecke, J. Henkel, W. C. Navidi, T. Y. Cath et al., Disturbance and temporal partitioning of the activated sludge metacommunity, ISME J, pp.1-11, 2014.

S. Wang, B. Haegeman, and M. Loreau, Dispersal and metapopulation stability, PeerJ, vol.3, 2015.
URL : https://hal.archives-ouvertes.fr/hal-02331231

Y. Wang and P. Y. Qian, Conservative fragments in bacterial 16S rRNA genes and primer design for 16S ribosomal DNA amplicons in metagenomic studies, PLoS One, vol.4, 2009.

S. Weiss, W. Van-treuren, C. Lozupone, K. Faust, J. Friedman et al., Correlation detection strategies in microbial data sets vary widely in sensitivity and precision, ISME J, vol.10, pp.1-13, 2016.

J. J. Werner, D. Knights, M. L. Garcia, N. B. Scalfone, S. Smith et al., Bacterial community structures are unique and resilient in full-scale bioenergy systems, Proc. Natl. Acad. Sci. U. S. A, vol.108, pp.4158-4163, 2011.

J. J. Werner, O. Koren, P. Hugenholtz, T. Z. Desantis, W. A. Walters et al., Impact of training sets on classification of high-throughput bacterial 16S rRNA gene surveys, 2012.

H. M. Wexler, Bacteroides: The good, the bad, and the nitty-gritty, Clin. Microbiol. Rev, vol.20, pp.593-621, 2007.

W. B. Whitman, D. C. Coleman, and W. J. Wiebe, Prokaryotes: The unseen majority, Proc. Natl. Acad. Sci, vol.95, pp.6578-6583, 1998.

S. Widder, R. J. Allen, T. Pfeiffer, T. P. Curtis, C. Wiuf et al., Challenges in microbial ecology: building predictive understanding of community function and dynamics, ISME J. 1-12, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01512087

C. R. Woese and G. E. Fox, Phylogenetic structure of the prokaryotic domain: The primary kingdoms, Proc. Natl. Acad. Sci, vol.74, pp.5088-5090, 1977.

G. M. Wolfaardt, J. R. Lawrence, R. D. Robarts, S. J. Caldwell, and D. E. Caldwell, Multicellular organization in a degradative biofilm community, Appl. Environ. Microbiol, vol.60, pp.434-446, 1994.

L. Wu, Y. Yang, S. Chen, M. Zhao, Z. Zhu et al., Long-term successional dynamics of microbial association networks in anaerobic digestion processes, Water Res, vol.104, pp.1-10, 2016.

S. Yachi and M. Loreau, Biodiversity and ecosystem productivity in a fluctuating environment: the insurance hypothesis, Proc. Natl. Acad. Sci. 96, pp.1463-1468, 1999.

Y. Yu, C. Lee, J. Kim, and S. Hwang, Group-specific primer and probe sets to detect methanogenic communities using quantitative real-time polymerase chain reaction, Biotechnol. Bioeng, vol.89, pp.670-679, 2005.

J. Zhang, Q. Gao, Q. Zhang, T. Wang, H. Yue et al., Bacteriophage-prokaryote dynamics and interaction within anaerobic digestion processes across time and space, vol.5, 2017.

J. Zhou, W. Liu, Y. Deng, Y. Jiang, and K. Xue, Stochastic assembly leads to alternative communities with distinct functions in a bioreactor microbial community, MBio, vol.4, pp.1-8, 2013.

Z. Berner, A. Fuentes, S. Dostal, A. Payne, A. N. Vazquez-gutierrez et al., Novel Polyfermentor intestinal model (PolyFermS) for controlled ecological studies: validation and effect of pH, PLoS One, vol.8, 2013.

E. Zumstein, R. Moletta, and J. J. Godon, Examination of two years of community dynamics in an anaerobic bioreactor using fluorescence polymerase chain reaction (PCR) single-strand conformation polymorphism analysis, Environ. Microbiol, vol.2, pp.69-78, 2000.
URL : https://hal.archives-ouvertes.fr/hal-02698307