S. Alström, Characteristics of Bacteria from Oilseed Rape in Relation to their Biocontrol Activity against Verticillium dahliae, Journal of Phytopathology, vol.149, issue.2, pp.57-64, 2001.
DOI : 10.1046/j.1439-0434.2001.00585.x

D. V. Axenov-gribanov, I. V. Voytsekhovskaya, Y. V. Rebets, B. T. Tokovenko, T. A. Penzina et al., Actinobacteria possessing antimicrobial and antioxidant activities isolated from the pollen of scots pine (Pinus sylvestris) grown on the Baikal shore, Antonie van Leeuwenhoek, vol.43, issue.1, pp.1307-1322, 2016.
DOI : 10.1021/ci025591m

G. C. Baker, J. J. Smith, and D. A. Cowan, Review and reanalysis of domain-specific 16S primers, J Microbiol. Methods, vol.55, 2003.

A. A. Belimov and K. J. Dietz, Effect of associative bacteria on element composition of barley seedlings grown in solution culture at toxic cadmium concentrations, Microbiological Research, vol.155, issue.2, pp.113-121, 2000.
DOI : 10.1016/S0944-5013(00)80046-4

J. Bengtsson-palme, M. Ryberg, M. Hartmann, S. Branco, Z. Wang et al., Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data, Methods in Ecology and Evolution, vol.50, issue.S1, pp.914-919, 2013.
DOI : 10.1007/s13225-011-0121-1

A. J. Bennett, G. D. Bending, D. Chandler, S. Hilton, and P. Mills, Meeting the demand for crop production: the challenge of yield decline in crops grown in short rotations, Biological Reviews, vol.81, issue.1, pp.52-71, 2012.
DOI : 10.1016/S0065-2113(03)81003-9

A. J. Bennett, S. Hilton, G. D. Bending, D. Chandler, and P. Mills, Impact of fresh root material and mature crop residues of oilseed rape (Brassica napus) on microbial communities associated with subsequent oilseed rape, Biology and Fertility of Soils, vol.52, issue.4, pp.1267-1279, 2014.
DOI : 10.1016/B978-0-12-372180-8.50042-1

R. L. Berendsen, C. M. Pieterse, and P. A. Bakker, The rhizosphere microbiome and plant health, Trends in Plant Science, vol.17, issue.8, pp.478-486, 2012.
DOI : 10.1016/j.tplants.2012.04.001

S. B. Bintrim, T. J. Donohue, J. Handelsman, G. P. Roberts, and R. M. Goodman, Molecular phylogeny of Archaea from soil, Proceedings of the National Academy of Sciences, vol.53, issue.2, pp.277-282, 1997.
DOI : 10.1111/j.1574-6968.1988.tb02659.x

S. Burggraf, H. Huber, and K. O. Stetter, Reclassification of the Crenarchaeal Orders and Families in Accordance with 16S rRNA Sequence Data, International Journal of Systematic Bacteriology, vol.47, issue.3, pp.657-660, 1997.
DOI : 10.1099/00207713-47-3-657

J. G. Caporaso, J. Kuczynski, J. Stombaugh, K. Bittinger, F. D. Bushman et al., QIIME allows analysis of high-throughput community sequencing data, Nature Methods, vol.8, issue.5, pp.335-336, 2010.
DOI : 10.1038/nmeth.f.303

C. P. Chanway, R. K. Hynes, N. , and L. M. , Plant growth-promoting rhizobacteria: Effects on growth and nitrogen fixation of lentil (Lens esculenta moench) and pea (Pisum sativum L.), Soil Biology and Biochemistry, vol.21, issue.4, pp.511-517, 1989.
DOI : 10.1016/0038-0717(89)90123-5

J. M. Chaparro, A. M. Sheflin, D. K. Manter, and J. M. Vivanco, Manipulating the soil microbiome to increase soil health and plant fertility, Biology and Fertility of Soils, vol.23, issue.5, pp.489-499, 2012.
DOI : 10.1094/MPMI-23-8-1097

S. Croes, N. Weyens, J. Janssen, H. Vercampt, J. V. Colpaert et al., ???L. grown on trace element-contaminated and non-contaminated fields: a genotypic and phenotypic comparison, Microbial Biotechnology, vol.33, issue.4, pp.371-384, 2013.
DOI : 10.1016/j.envint.2006.12.005

A. F. Cruz, S. Horii, S. Ochiai, A. Yasuda, and T. Ishii, Isolation and analysis of bacteria associated with spores of Gigaspora margarita, Journal of Applied Microbiology, vol.75, issue.1, 2008.
DOI : 10.1073/pnas.81.5.1470

N. Dashti, F. Zhang, R. Hynes, and D. L. Smith, Plant growth promoting rhizobacteria accelerate nodulation and increase nitrogen fixation activity by field grown soybean [Glycine max (L.) Merr.] under short season conditions, Plant and Soil, vol.200, issue.2, pp.205-213, 1998.
DOI : 10.1023/A:1004358100856

S. B. De-campos, J. W. Youn, R. Farina, S. Jaenicke, S. Junemann et al., Changes in Root Bacterial Communities Associated to Two Different Development Stages of Canola (Brassica napus L. var oleifera) Evaluated through Next-Generation Sequencing Technology, Microbial Ecology, vol.13, issue.3, pp.593-601, 2013.
DOI : 10.1016/S0929-1393(99)00028-1

A. Dereeper, V. Guignon, G. Blanc, S. Audic, S. Buffet et al., , 2008.

. Phylogeny, fr: robust phylogenetic analysis for the non-specialist, Nucleic Acids Res, vol.36, pp.465-469

I. C. Dodd, N. Y. Zinovkina, V. I. Safronova, A. A. Belimov, K. E. Dunfield et al., Rhizobacterial mediation of plant hormone status, Annals of Applied Biology, vol.56, issue.3, pp.361-379, 2003.
DOI : 10.1128/jb.177.20.5762-5766.1995

R. C. Edgar, R. Farina, A. Beneduzi, A. Ambrosini, S. B. De-camposa et al., Search and clustering orders of magnitude faster than BLAST Diversity of plant growth-promoting rhizobacteria communities associated with the stages of canola growth, Bioinformatics Agric. Ecosyst. Environ. Appl. Soil Ecol, vol.26, issue.55, pp.2460-2461, 2010.

J. T. Fletcher and K. L. Lord, A stem rot of tomato caused by Fusarium merismoides, Plant Pathology, vol.83, issue.44, pp.443-445, 1985.
DOI : 10.1111/j.1365-3059.1985.tb01387.x

P. Garbeva, J. A. Van-veen, and J. D. Van-elsas, MICROBIAL DIVERSITY IN SOIL: Selection of Microbial Populations by Plant and Soil Type and Implications for Disease Suppressiveness, Annual Review of Phytopathology, vol.42, issue.1, pp.243-270, 2004.
DOI : 10.1146/annurev.phyto.42.012604.135455

J. J. Germida, S. D. Siciliano, J. R. De-freitas, and A. M. Seib, Diversity of root-associated bacteria associated with field-grown canola (Brassica napus L.) and wheat (Triticum aestivum L.), FEMS Microbiology Ecology, vol.62, issue.1, pp.43-50, 1998.
DOI : 10.1007/978-94-011-0479-1_2

K. Gkarmiri, S. Mahmood, A. Ekblad, S. Alström, N. Högberg et al., ABSTRACT, Applied and Environmental Microbiology, vol.83, issue.22, pp.1938-01917, 2017.
DOI : 10.1128/AEM.01938-17

J. J. Goeman and A. Solari, Multiple hypothesis testing in genomics, Statistics in Medicine, vol.34, issue.1, 1946.
DOI : 10.1198/jasa.2011.tm11181

T. Gomiero, D. Pimentel, and M. G. Paoletti, Environmental Impact of Different Agricultural Management Practices: Conventional vs. Organic Agriculture, Critical Reviews in Plant Sciences, vol.406, issue.6, pp.95-124, 2011.
DOI : 10.1038/35021046

S. Goyal, K. Chander, M. C. Mundra, K. K. Kapoor, T. Gräfenhan et al., Influence of inorganic fertilizers and organic amendments on soil organic matter and soil microbial properties under tropical conditions, Biology and Fertility of Soils, vol.29, issue.2, pp.196-200, 1999.
DOI : 10.1007/s003740050544

C. A. Grant, R. Wu, F. Selles, K. N. Harker, G. W. Clayton et al., Crop yield and nitrogen concentration with controlled release urea and split applications of nitrogen as compared to non-coated urea applied at seeding, Field Crops Research, vol.127, pp.170-180, 2012.
DOI : 10.1016/j.fcr.2011.11.002

C. Grant, R. Wu, E. J. Gray, and D. L. Smith, Enhanced-efficiency fertilizers for use on the Canadian Prairies Crop Manage. 7. doi: 10.1094/CM-2008-0730-01 Intracellular and extracellular PGPR: commonalities and distinctions in the plant-bacterium signaling processes, Soil Biol. Biochem, vol.37, pp.395-412, 2005.

X. W. Guo, W. G. Fernando, and M. Entz, Effects of crop rotation and tillage on blackleg disease of canola, Canadian Journal of Plant Pathology, vol.8, issue.1, pp.53-57, 2005.
DOI : 10.1094/PDIS.1998.82.2.247

D. Haas and G. Défago, Biological control of soil-borne pathogens by fluorescent pseudomonads, Nature Reviews Microbiology, vol.94, issue.4, pp.307-319, 1139.
DOI : 10.1094/PHYTO.2004.94.11.1267

C. Hamel, V. Vujanovic, R. Jeannotte, A. Nakano-hylander, and M. St-arnaud, Negative feedback on a perennial crop: Fusarium crown and root rot of asparagus is related to changes in soil microbial community structure, Plant and Soil, vol.85, issue.1, pp.75-87, 2005.
DOI : 10.1007/978-3-0348-8109-8_6

K. N. Harker, G. W. Clayton, R. E. Blackshaw, J. T. O-'donovan, and F. C. Stevenson, ), Canadian Journal of Plant Science, vol.83, issue.2, pp.433-440, 2003.
DOI : 10.4141/P02-073

K. N. Harker, J. T. O-'donovan, E. G. Smith, E. N. Johnson, G. Peng et al., Seed size and seeding rate effects on canola emergence, development, yield and seed weight, Canadian Journal of Plant Science, vol.55, issue.1, pp.1-8, 2015.
DOI : 10.1093/jxb/erh038

K. N. Harker, J. T. O-'donovan, T. K. Turkington, R. E. Blackshaw, N. Z. Lupwayi et al., Canola cultivar mixtures and rotations do not mitigate the negative impacts of continuous canola, Canadian Journal of Plant Science, vol.90, issue.6, pp.1085-1099, 2015.
DOI : 10.4141/CJPS10049

K. N. Harker, J. T. O-'donovan, T. K. Turkington, R. E. Blackshaw, N. Z. Lupwayi et al., High-yield no-till canola production on the Canadian prairies, Canadian Journal of Plant Science, vol.82, issue.2, pp.221-233, 2012.
DOI : 10.4141/P01-149

L. M. Hartwright, P. J. Hunter, W. , and J. A. , A comparison of Olpidium isolates from a range of host plants using internal transcribed spacer sequence analysis and host range studies, Fungal Biology, vol.114, issue.1, pp.26-33, 2010.
DOI : 10.1016/j.mycres.2009.09.008

S. Hilton, A. J. Bennett, G. Keane, G. D. Bending, D. Chandler et al., Impact of Shortened Crop Rotation of Oilseed Rape on Soil and Rhizosphere Microbial Diversity in Relation to Yield Decline, PLoS ONE, vol.28, issue.4, 2013.
DOI : 10.1371/journal.pone.0059859.s002

S. F. Hwang, H. U. Ahmed, B. D. Gossen, H. R. Kutcher, S. A. Brandt et al., Effect of Crop Rotation on the Soil Pathogen Population Dynamics and Canola Seedling Establishment, Plant Pathology Journal, vol.8, issue.3, pp.106-112, 2009.
DOI : 10.3923/ppj.2009.106.112

B. K. Kim, M. Y. Jung, D. S. Yu, S. J. Park, T. K. Oh et al., Genome Sequence of an Ammonia-Oxidizing Soil Archaeon, "Candidatus Nitrosoarchaeum koreensis" MY1, Journal of Bacteriology, vol.193, issue.19, pp.5539-5540, 1128.
DOI : 10.1128/JB.05717-11

A. Klindworth, E. Pruesse, T. Schweer, J. Peplies, C. Quast et al., Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies, Nucleic Acids Research, vol.3, issue.1, 2013.
DOI : 10.1093/nar/gks808

J. W. Kloepper, D. J. Hume, F. M. Scher, C. Singleton, B. Tipping et al., Plant Growth-Promoting Rhizobacteria on Canola (Rapeseed), Plant Disease, vol.72, issue.1, pp.42-46, 1988.
DOI : 10.1094/PD-72-0042

N. Klykleung, S. Tanasupawat, P. Pittayakhajonwut, M. Ohkuma, and T. Kudo, Amycolatopsis stemonae sp. nov., isolated from a Thai medicinal plant, International Journal of Systematic and Evolutionary Microbiology, vol.151, issue.11, pp.3894-3899, 2015.
DOI : 10.1099/ijs.0.031039-0

U. Kõljalg, R. H. Nilsson, K. Abarenkov, L. Tedersoo, A. F. Taylor et al., Towards a unified paradigm for sequence-based identification of fungi, Molecular Ecology, vol.6, issue.21, pp.5271-5277, 2013.
DOI : 10.1016/j.funeco.2013.03.004

Y. Kudo, S. Shibata, T. Miyaki, T. Aono, and H. Oyaizu, Bioscience, Biotechnology, and Biochemistry, vol.61, issue.5, pp.917-920, 1997.
DOI : 10.1271/bbb.61.917

A. Kumar, A. Prakash, and B. N. Johri, Bacillus as PGPR in Crop Ecosystem, Bacteria in Agrobiology: Crop Ecosystems, pp.37-59, 2011.
DOI : 10.1007/978-3-642-18357-7_2

A. Macrae, D. L. Rimmer, O. , and A. G. , Novel bacterial diversity recovered from the rhizosphere of oilseed rape (Brassica napus) determined by the analysis of 16S ribosomal DNA, Antonie van Leeuwenhoek, vol.78, issue.1, pp.13-21, 2000.
DOI : 10.1023/A:1002745312030

D. K. Manter and J. M. Vivanco, Use of the ITS primers, ITS1F and ITS4, to characterize fungal abundance and diversity in mixed-template samples by qPCR and length heterogeneity analysis, Journal of Microbiological Methods, vol.71, issue.1, pp.7-14, 2007.
DOI : 10.1016/j.mimet.2007.06.016

K. J. Martin, R. , and P. T. , Fungal-specific PCR primers developed for analysis of the ITS region of environmental DNA extracts, BMC Microbiology, vol.5, issue.1, pp.28-38, 2005.
DOI : 10.1186/1471-2180-5-28

Q. Miao, S. Qin, G. K. Bian, B. Yuan, K. Xing et al., Amycolatopsis endophytica sp. nov., a novel endophytic actinomycete isolated from oil-seed plant Jatropha curcas L., Antonie van Leeuwenhoek, vol.56, issue.3, pp.333-339, 2011.
DOI : 10.1099/ijs.0.64149-0

D. Minerdi, M. Moretti, G. Gilardi, C. Barberio, M. L. Gullino et al., Bacterial ectosymbionts and virulence silencing in a Fusarium oxysporum strain, Environmental Microbiology, vol.24, issue.7, pp.1725-1741, 2008.
DOI : 10.1099/mic.0.26112-0

A. L. Misko and J. J. Germida, Taxonomic and functional diversity of pseudomonads isolated from the roots of field-grown canola, FEMS Microbiology Ecology, vol.80, issue.3, pp.399-407, 2002.
DOI : 10.1093/treephys/16.11-12.1031

S. Neupane, B. Andersson, N. Högberg, K. Ihrmark, A. et al., Fungal communities associated with field grown oilseed rape (Brassica napus L.) -their possible role in early crop establishment, Acta Agric. Scand, vol.63, pp.241-252, 2013.

S. Neupane, L. A. Goodwin, N. Hogberg, N. C. Kyrpides, S. Alstrom et al., Non-contiguous finished genome sequence of plant-growth promoting Serratia proteamaculans S4, Standards in Genomic Sciences, vol.25, issue.3, pp.441-449, 2013.
DOI : 10.1093/bioinformatics/btp393

T. Oberholster, S. Vikram, D. Cowan, and A. Valverde, Key microbial taxa in the rhizosphere of sorghum and sunflower grown in crop rotation, Science of The Total Environment, vol.624, pp.530-539, 2018.
DOI : 10.1016/j.scitotenv.2017.12.170

C. Pliego, F. Kamilova, and B. Lugtenberg, Plant Growth-Promoting Bacteria: Fundamentals and Exploitation, Bacteria in Agrobiology: Crop Ecosystems, pp.295-343, 2011.
DOI : 10.1007/978-3-642-18357-7_11

F. Poly, L. J. Monrozier, and R. Bally, Improvement in the RFLP procedure for studying the diversity of nifH genes in communities of nitrogen fixers in soil, Research in Microbiology, vol.152, issue.1, pp.95-103, 2001.
DOI : 10.1016/S0923-2508(00)01172-4

V. S. Pylro, L. F. Roesch, D. K. Morais, I. M. Clark, P. R. Hirsch et al., Data analysis for 16S microbial profiling from different benchtop sequencing platforms, Journal of Microbiological Methods, vol.107, pp.30-37, 2014.
DOI : 10.1016/j.mimet.2014.08.018

V. S. Pylro, L. F. Roesch, J. M. Ortega, D. Amaral, A. M. Totola et al., Brazilian Microbiome Project: Revealing the Unexplored Microbial Diversity???Challenges and Prospects, Microbial Ecology, vol.12, issue.7, pp.237-241, 2014.
DOI : 10.1111/j.1462-2920.2010.02201.x

F. Raiesi, Soil properties and N application effects on microbial activities in two winter wheat cropping systems, Biology and Fertility of Soils, vol.40, issue.2, pp.88-92, 2004.
DOI : 10.1007/s00374-004-0741-7

A. Saito, T. Ooya, D. Miyatsuchi, H. Fuchigami, K. Terakado et al., sp. CsO-2, FEMS Microbiology Letters, vol.293, issue.1, pp.79-84, 2009.
DOI : 10.1111/j.1574-6968.2009.01507.x

T. Sasaya and H. Koganezawa, Molecular analysis and virus transmission tests place Olpidium virulentus, a vector of Mirafiori lettuce big-vein virus and tobacco stunt virus, as a distinct species rather than a strain of Olpidium brassicae, Journal of General Plant Pathology, vol.102, issue.1, pp.20-25, 2006.
DOI : 10.1016/B978-0-12-372180-8.50042-1

L. A. Sauder, M. Albertsen, K. Engel, J. Schwarz, P. H. Nielsen et al., Cultivation and characterization of Candidatus Nitrosocosmicus exaquare, an ammonia-oxidizing archaeon from a municipal wastewater treatment system, The ISME Journal, vol.2, issue.5, pp.1142-1157, 2017.
DOI : 10.1111/j.1365-2672.2009.04283.x

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, Applied and Environmental Microbiology, vol.75, issue.23, pp.7537-7541, 1128.
DOI : 10.1128/AEM.01541-09

H. M. Simon, J. A. Dodsworth, and R. M. Goodman, Crenarchaeota colonize terrestrial plant roots, Environ. Microbiol, vol.2, 2000.

M. K. Sliwinski and R. M. Goodman, Comparison of Crenarchaeal Consortia Inhabiting the Rhizosphere of Diverse Terrestrial Plants with Those in Bulk Soil in Native Environments, Applied and Environmental Microbiology, vol.70, issue.3, 2004.
DOI : 10.1128/AEM.70.3.1821-1826.2004

K. Smalla, G. Wieland, A. Buchner, A. Zock, J. Parzy et al., Bulk and Rhizosphere Soil Bacterial Communities Studied by Denaturing Gradient Gel Electrophoresis: Plant-Dependent Enrichment and Seasonal Shifts Revealed, Applied and Environmental Microbiology, vol.67, issue.10, pp.4742-47514742, 2001.
DOI : 10.1128/AEM.67.10.4742-4751.2001

A. Tkacz, J. Cheema, G. Chandra, A. Grant, and P. S. Poole, Stability and succession of the rhizosphere microbiota depends upon plant type and soil composition, The ISME Journal, vol.60, issue.11, 2015.
DOI : 10.1128/AEM.06881-11

T. Ueda, Y. Suga, and T. Matsuguchi, Molecular phylogenetic analysis of a soil microbial community in a soybean field, European Journal of Soil Science, vol.51, issue.3, pp.415-421, 1995.
DOI : 10.1038/345063a0

T. Van-der-lee, H. Zhang, A. Van-diepeningen, and C. Waalwijk, species complex and chemotypes: a review, Food Additives & Contaminants: Part A, vol.65, issue.4, pp.453-460, 1080.
DOI : 10.1007/s10658-010-9588-y

P. Vandenkoornhuyse, A. Quaiser, M. Duhamel, L. Van, A. Dufresne et al., The importance of the microbiome of the plant holobiont, New Phytologist, vol.32, issue.4, pp.1196-1206, 2015.
DOI : 10.1111/j.1574-6976.2008.00123.x
URL : https://hal.archives-ouvertes.fr/hal-01115639

V. Vujanovic, C. Hamel, É. Yergeau, and M. St-arnaud, Biodiversity and Biogeography of Fusarium Species from Northeastern North American Asparagus Fields Based on Microbiological and Molecular Approaches, Microbial Ecology, vol.48, issue.2, pp.242-255, 2006.
DOI : 10.17660/ActaHortic.1990.271.49

E. Weber and H. Bleiholder, Explanations of the BBCH decimal codes for the growth stages of maize, rape, faba beans, sunflowers and peas -with illustrations, Gesunde Pflanzen, vol.42, pp.308-321, 1990.

D. M. Weller, J. M. Raaijmakers, B. B. Gardener, and L. S. Thomashow, Annual Review of Phytopathology, vol.40, issue.1, pp.309-348, 2002.
DOI : 10.1146/annurev.phyto.40.030402.110010

A. Wolf, A. Fritze, M. Hagemann, and G. Berg, Stenotrophomonas rhizophila sp. nov., a novel plant-associated bacterium with antifungal properties, Int. J. Syst. Evol. Microbiol, vol.52, pp.1937-1944, 2002.

K. Xing, W. Liu, Y. J. Zhang, G. K. Bian, W. D. Zhang et al., Amycolatopsis jiangsuensis sp. nov., a novel endophytic actinomycete isolated from a coastal plant in Jiangsu, China, Antonie van Leeuwenhoek, vol.62, issue.2, pp.433-439, 2013.
DOI : 10.1099/ijs.0.029256-0

J. Yang, J. W. Kloepper, and C. M. Ryu, Rhizosphere bacteria help plants tolerate abiotic stress, Trends in Plant Science, vol.14, issue.1, 2009.
DOI : 10.1016/j.tplants.2008.10.004

É. Yergeau, K. Labour, C. Hamel, V. Vujanovic, A. Nakano-hylander et al., Patterns of Fusarium community structure and abundance in relation to spatial, abiotic and biotic factors in soil, FEMS Microbiology Ecology, vol.105, issue.1, pp.34-42, 2006.
DOI : 10.1094/PD-79-0177

C. Yuan, C. Mou, W. Wu, and Y. Guo, Effect of different fertilization treatments on indole-3-acetic acid producing bacteria in soil, Journal of Soils and Sediments, vol.22, issue.supplement, pp.322-329, 2011.
DOI : 10.1093/aob/mci083