A. Wezel, S. Bellon, T. Doré, C. Francis, D. Vallod et al., Agroecology as a science, a movement and a practice, Agron Sustain Dev, vol.29, p.503, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00886499

P. Nannipieri, J. Ascher, M. T. Ceccherini, L. Dl, L. Pietramellar et al., Microbial diversity and soil functions, Eur J Soil Sci, vol.54, p.655, 2003.

A. Miltner, H. H. Richnow, F. D. Kopinke, and M. Kästner, Assimilation of CO2 by soil microorganisms and transformation into soil organic matter, Org Geochem, vol.35, pp.1015-1024, 2004.

M. Gardes and T. D. Bruns, ITS primers with enhanced specificity for basidiomycetes -application to the identification of mycorrhizae and rusts, Mol Ecol, vol.2, p.8180733, 1993.

T. White, T. Bruns, S. B. Lee, and J. Taylor, Amplification and direct sequencing of fungal ribosomal RNA Genes for phylogenetics. PCR Protocols: a guide to methods and applications, pp.315-322, 1990.

L. Raskin, J. M. Stromley, B. E. Rittmann, and D. A. Stahl, Group-specific 16S rRNA hybridization probes to describe natural communities of methanogens, Appl Environ Microbiol, vol.60, 1994.

K. Takai, K. Horikoshi, and K. Takai, Rapid detection and quantification of members of the archaeal community by quantitative PCR using fluorogenic probes rapid detection and quantification of members of the archaeal community by quantitative PCR using fluorogenic probes, Appl Environ Microbiol, vol.66, p.11055964, 2000.

S. Andrews, FastQC: a quality control tool for high throughput sequence data, 2010.

F. Escudié, L. Auer, M. Bernard, M. Mariadassou, L. Cauquil et al., FROGS: Find, Rapidly, OTUs with Galaxy Solution, Bioinformatics, vol.34, p.29228191, 2018.

H. S. Gweon, A. Oliver, J. Taylor, T. Booth, M. Gibbs et al., PIPITS: An automated pipeline for analyses of fungal internal transcribed spacer sequences from the Illumina sequencing platform, Methods Ecol Evol, vol.6, p.27570615, 2015.

T. Magoc and S. L. Salzberg, FLASH: Fast Length Adjustment of Short reads to improve genome assemblies, Bioinformatics, pp.1-8, 2011.

F. Mahé, T. Rognes, C. Quince, C. De-vargas, and M. Dunthorn, Swarm: robust and fast clustering method for amplicon-based studies, PeerJ, vol.2, p.25276506, 2014.

R. C. Edgar, B. J. Haas, J. C. Clemente, C. Quince, and R. Knight, UCHIME improves sensitivity and speed of chimera detection, Bioinformatics, vol.27, p.21700674, 2011.

T. Rognes, T. Flouri, B. Nichols, C. Quince, and F. Mahé, VSEARCH: a versatile open source tool for metagenomics, PeerJ, vol.4, p.27781170, 2016.

C. Quast, E. Pruesse, P. Yilmaz, J. Gerken, T. Schweer et al., The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools, Nucleic Acids Res, vol.41, p.23193283, 2013.

S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, Basic local alignment search tool, J Mol Biol, vol.215, p.2231712, 1990.

T. M. Bowles, V. Acosta-martínez, F. Calderón, and L. E. Jackson, Soil enzyme activities, microbial communities, and carbon and nitrogen availability in organic agroecosystems across an intensively-managed agricultural landscape, Soil Biol. Bioch, vol.58, pp.252-262, 2014.

J. P. Van-leeuwen, I. Djukic, J. Bloem, T. Lehtinen, L. Hemerik et al., Effects of land use on soil microbial biomass, activity and community structure at different soil depths in the Danube floodplain

, European J Soil Biol, vol.79, pp.14-20, 2017.

S. Chen, S. Subler, and C. Edwards, Effects of agricultural biostimulants on soil microbial activity and nitrogen dynamics, Appl Soil Ecol, vol.19, pp.2-3, 2002.

S. Chen, C. A. Edwards, and S. Subler, The influence of two agricultural biostimulants on nitrogen transformations, microbial activity, and plant growth in soil microcosms, Soil Biol Biochem, vol.35, pp.9-19, 2003.

M. Tejada, C. Benítez, I. Gó-mez, and J. Parrado, Use of biostimulants on soil restoration: Effects on soil biochemical properties and microbial community, Appl Soil Ecol, vol.49, pp.11-17, 2011.

J. Parrado, J. Bautista, E. J. Romero, A. M. García-martínez, V. Friaza et al., Production of a carob enzymatic extract: Potential use as a biofertilizer, Bioresour Technol, vol.99, p.17601731, 2008.

S. Kocira, A. Szparaga, and A. Kocira, Modeling biometric traits, yield and nutritional and antioxidant properties of seeds of three soybean cultivars through the application of biostimulant containing seaweed and amino acids, Front Plant Sci, vol.9, p.29636764, 2018.

N. S. Yokoya, W. A. Stirk, J. Van-staden, O. Novak, V. Tureckova et al., Endogenous cytokinins, auxins, and abscisic acid in red algae from Brazil, J Phycol, vol.46, pp.1198-1205, 2010.

P. Maini, The experience of the first biostimulant, based on amino acids and peptides: a short retrospective review on the laboratory researches and the practical results, Fertilitas Agrorum, vol.1, pp.29-43, 2006.

M. Farrell, M. Prendergast-miller, D. L. Jones, P. W. Hill, and L. M. Condron, Soil microbial organic nitrogen uptake is regulated by carbon availability, Soil Biol Biochem, vol.77, pp.261-267, 2014.

C. W. Bingeman, J. E. Varner, and W. P. Martin, The effect of the addition of organic materials on the decomposition of an organic soil, Soil Sci Soc Am J, vol.17, p.34, 1953.

L. Bernard, C. Mougel, P. A. Maron, V. Nowak, J. Lé-vêque et al., Dynamics and identification of soil microbial populations actively assimilating carbon from 13C-labelled wheat residue as estimated by DNA-and RNA-SIP techniques, Environ Microbiol, vol.9, p.17298374, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00294737

N. Pascault, L. Ranjard, A. Kaisermann, D. Bachar, R. Christen et al., Stimulation of different functional groups of bacteria by various plant residues as a driver of soil priming effect, Ecosystems, vol.16, pp.810-822, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00847889

M. Shahbaz, Y. Kuzyakov, M. Sanaullah, F. Heitkamp, V. Zelenev et al., Microbial decomposition of soil organic matter is mediated by quality and quantity of crop residues: mechanisms and thresholds

, Biol Fertil Soils, vol.53, pp.287-301, 2017.

O. Niemenmaa, A. Uusi-rauva, and A. Hatakka, Demethoxylation of [O14CH3]-labelled lignin model compounds by the brown-rot fungi Gloeophyllum trabeum and Poria (Postia) placenta, Biodegradation, vol.19, p.17973193, 2008.

Y. Kuzyakov, Priming effects: Interactions between living and dead organic matter, Soil Biol Biochem, vol.42, pp.1363-1371, 2010.

F. C. Hoyle, D. Murphy, and P. C. Brookes, Microbial response to the addition of glucose in low-fertility soils, pp.571-579, 2008.

E. Blagodatskaya, T. Yuyukina, S. Blagodatsky, and Y. Kuzyakov, Three-source-partitioning of microbial biomass and of CO2 efflux from soil to evaluate mechanisms of priming effects, Soil Biol Biochem, vol.43, pp.778-786, 2011.

J. Rousk, E. Bååth, P. C. Brookes, C. L. Lauber, C. Lozupone et al., Soil bacterial and fungal communities across a pH gradient in an arable soil, The ISME J, vol.4, p.20445636, 2010.

S. J. Kemmitt, D. Wright, K. Goulding, and D. L. Jones, pH regulation of carbon and nitrogen dynamics in two agricultural soils, Soil Biol. Biochem, vol.38, pp.898-911, 2006.

N. Fierer and R. B. Jackson, The diversity and biogeography of soil bacterial communities, Proc Natl Acad Sci, vol.103, p.16407148, 2006.

S. Liu, Y. Zhang, Y. Zong, Z. Hu, S. Wu et al., Response of soil carbon dioxide fluxes, soil organic carbon and microbial biomass carbon to biochar amendment: a meta-analysis, GCB Bioenergy, vol.8, pp.392-406, 2016.

N. Fierer, M. A. Bradford, and R. B. Jackson, Toward an ecological classificatin of soil bacteria, Ecology, vol.88, p.17601128, 2007.

P. Padmanabhan, S. Padmanabhan, C. Derito, A. Gray, D. Gannon et al., Respiration of 13 Clabeled substrates added to soil in the field and subsequent 16S rRNA gene analysis of 13 C-labeled soil DNA, vol.69, pp.1614-1622, 2003.

C. Lauber, M. Hamady, R. Knigh, and N. Fierer, Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale, Appl Environ Microbiol, vol.75, p.19502440, 2009.

Y. Zhang, H. Shen, X. He, B. W. Thomas, N. Z. Lupway et al., Fertilization shapes bacterial community structure by alteration of soil pH. Front Microbiol, 2017.

J. Rousk, P. C. Brookes, and E. Bååth, Contrasting soil pH effects on fungal and bacterial growth suggest functional redundancy in carbon mineralization, Appl Environ Microbiol, vol.75, p.19151179, 2009.

J. H. Warcup, The ecology of soil fungi, Trans Br Myco. Soc, vol.34, issue.51, pp.80065-80067, 1951.

T. Yamanaka, The effect of pH on the growth of saprotrophic and ectomycorrhizal ammonia fungi in vitro, Mycologia, vol.95, p.21148967, 2003.

H. Chen, N. V. Mothapo, and W. Shi, Soil moisture and pH control relative contributions of fungi and bacteria to N 2 O production, Micro Ecol, vol.69, pp.180-191, 2015.

A. Rayner and L. Boddy, Fungal decomposition of wood. Its biology and ecology, 1988.

D. J. Yelle, J. Ralph, F. Lu, and K. E. Hammel, Evidence for cleavage of lignin by a brown rot basidiomycete, vol.10, p.18363712, 2008.

M. Kö-nneke, A. E. Bernhard, J. R. De-la-torre, C. B. Walker, J. B. Waterbury et al., Isolation of an autotrophic ammonia-oxidizing marine archaeon, Nature, vol.437, p.16177789, 2005.

D. A. Stahl and J. R. De-la-torre, Physiology and Diversity of Ammonia-Oxidizing Archaea, Annu Rev Microbiol, vol.66, p.22994489, 2012.

H. W. Hu, L. M. Zhang, Y. Dai, H. J. Di, and J. Z. He, pH-dependent distribution of soil ammonia oxidizers across a large geographical scale as revealed by high-throughput pyrosequencing, J Soils Sediments, vol.13, pp.1439-1449, 2013.

D. L. Moorhead and R. L. Sinsabaugh, Simulated patterns of litter-decay predict patterns of extracellular enzyme activities, Appl Soil Ecol, vol.14, pp.43-51, 2000.

S. Fontaine, A. Mariotte, and L. Abbadie, The priming effect of organic matter: a question of microbial competition?, Soil Biol Biochem, vol.35, pp.123-131, 2003.

X. Wang, C. E. Sharp, G. M. Jones, S. E. Grasby, A. L. Brady et al., Stable-Isotope Probing identifies uncultured Planctomycetes as primary degraders of a complex heteropolysaccharide in soil, Appl Environ Microbiol, vol.81, p.25934620, 2015.

A. H. Kjøller and S. Struwe, Enzymes in the environment: activity, ecology and applications, pp.267-284, 2002.

C. A. Hanson, S. D. Allison, M. A. Bradford, M. D. Wallenstein, and K. K. Treseder, Fungal taxa target different carbon sources in forest soil, Ecosystems, vol.11, pp.1157-1167, 2008.

C. Monard, F. Binet, and P. Vandenkoornhuyse, Short-term response of soil bacteria to carbon enrichment in different soil microsites, Appl Environ Microbiol, vol.74, p.18621864, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00335197

M. Mcbride, W. Liu, X. Lu, Y. Zhu, and W. Zhang, The family Cytophagaceae, The Prokaryotes, pp.577-593, 2014.

R. Garcia, . Mü-ller-r.-the, and . Phaselicystidaceae, The Prokaryotes, pp.239-245, 2014.

N. Fierer, J. Ladau, J. C. Clemente, J. W. Leff, O. M. Owen et al., Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States, Sci, vol.342, p.24179225, 2013.

Y. Ogawa, S. Hayashi, D. Yousuke, and Y. Y. Ramicandelaber, a new genus of the Kickxellales, pp.193-199, 2001.

H. Zhang, X. Wu, G. Li, and P. Qin, Interactions between arbuscular mycorrhizal fungi and phosphate-solubilizing fungus (Mortierella sp.) and their effects on Kostelelzkya virginica growth and enzyme activities of rhizosphere and bulk soils at different salinities, pp.543-554, 2011.