H. Fones and S. Gurr, The impact of Septoria tritici blotch disease on wheat: an EU perspective, Fungal Genet Biol, vol.79, pp.3-7, 2015.

W. Quaedvlieg, G. Kema, J. Groenewald, G. Verkley, S. Seifbarghi et al., Zymoseptoria gen. nov.: a new genus to accommodate Septoria-like species occurring on graminicolous hosts, Persoonia Mol Phylogeny Evol Fungi, vol.26, p.57, 2011.

F. Suffert, I. Sache, and C. Lannou, Early stages of Septoria tritici blotch epidemics of winter wheat: build-up, overseasoning, and release of primary inoculum, Plant Pathol, vol.60, pp.166-77, 2011.

F. Suffert, G. Delestre, and S. Gélisse, Sexual reproduction in the fungal foliar pathogen Zymoseptoria tritici is driven by antagonistic density-dependence mechanisms, Microb Ecol, vol.77, pp.110-133, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02618787

H. J. Cools and B. A. Fraaije, Are azole fungicides losing ground against Septoria wheat disease? Resistance mechanisms in Mycosphaerella graminicola, Pest Manag Sci, vol.64, pp.681-685, 2008.

L. K. Estep, M. Zala, N. P. Anderson, K. E. Sackett, M. Flowers et al., First report of resistance to QoI fungicides in North American populations of Zymoseptoria tritici, causal agent of Septoria tritici blotch of wheat, Plant Dis, vol.97, p.1511, 2013.

L. K. Estep, S. Torriani, M. Zala, N. P. Anderson, M. D. Flowers et al., Emergence and early evolution of fungicide resistance in north American populations of Zymoseptoria tritici, Plant Pathol, vol.64, pp.961-71, 2015.

L. E. Hayes, K. E. Sackett, N. P. Anderson, M. D. Flowers, and C. C. Mundt, Evidence of selection for fungicide resistance in Zymoseptoria tritici populations on wheat in western Oregon, Plant Dis, vol.100, pp.483-492, 2016.

C. Cowger, M. Hoffer, and C. Mundt, Specific adaptation by Mycosphaerella graminicola to a resistant wheat cultivar, Plant Pathol, vol.49, pp.445-51, 2000.

R. L. Berendsen, G. Vismans, K. Yu, Y. Song, R. Jonge et al., Disease-induced assemblage of a plant-beneficial bacterial consortium, ISME J, vol.12, p.1496, 2018.

H. Toju, K. G. Peay, M. Yamamichi, K. Narisawa, K. Hiruma et al., Core microbiomes for sustainable agroecosystems, Nat Plants, vol.4, pp.247-57, 2018.

I. Cho and M. J. Blaser, The human microbiome: at the interface of health and disease, Nat Rev Genet, vol.13, pp.260-70, 2012.

B. Jakuschkin, V. Fievet, L. Schwaller, T. Fort, C. Robin et al., Deciphering the Pathobiome: intra-and interkingdom interactions involving the pathogen Erysiphe alphitoides, Microb Ecol, vol.72, pp.870-80, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01607740

L. Lebreton, A. Guillerm-erckelboudt, K. Gazengel, J. Linglin, M. Ourry et al., Temporal dynamics of bacterial and fungal communities during the infection of Brassica rapa roots by the protist Plasmodiophora brassicae, PLoS One, vol.14, p.204195, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02094715

M. Vayssier-taussat, A. E. Citti, C. Cosson, J. Jacques, M. Lebrun et al., Shifting the paradigm from pathogens to pathobiome: new concepts in the light of meta-omics, Front Cell Infect Microbiol, vol.4, p.29, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01153583

L. Kerdraon, M. Balesdent, M. Barret, V. Laval, and F. Suffert, Crop residues in wheat-oilseed rape rotation system: a pivotal, shifting platform for microbial meetings, Microb Ecol, vol.77, pp.931-976, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02620072

J. F. Cobo-díaz, R. Baroncelli, L. Floch, G. Picot, and A. , Combined metabarcoding and co-occurrence network analysis to profile the bacterial, fungal and Fusarium communities and their interactions in maize stalks, Front Microbiol, vol.10, p.261, 2019.

A. Hadas, L. Kautsky, M. Goek, and K. E. Erman, Rates of decomposition of plant residues and available nitrogen in soil, related to residue composition through simulation of carbon and nitrogen turnover, Soil Biol Biochem, vol.36, pp.255-66, 2004.

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.810-832, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00847889

N. Pascault, L. Cécillon, O. Mathieu, C. Hénault, A. Sarr et al., In situ dynamics of microbial communities during decomposition of wheat, rape, and alfalfa residues, Microb Ecol, vol.60, pp.6-28, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00542893

L. Kerdraon, V. Laval, and F. Suffert, Microbiomes and pathogen survival in crop 1057 residues, an ecotone between plant and soil, Phytobiomes J. accepted

B. Nicolardot, L. Bouziri, F. Bastian, and L. Ranjard, A microcosm experiment to evaluate the influence of location and quality of plant residues on residue decomposition and genetic structure of soil microbial communities, Soil Biol Biochem, vol.39, pp.1631-1675, 2007.

F. M. Dugan, S. L. Lupien, M. Hernandez-bello, T. L. Peever, and W. Chen, Fungi resident in chickpea debris and their suppression of growth and reproduction of Didymella rabiei under laboratory conditions, J Phytopathol, vol.153, pp.431-440, 2005.

M. R. Fernandez, The effect of Trichoderma harzianum on fungal pathogens infesting wheat and black oat straw, Soil Biol Biochem, vol.24, pp.1031-1035, 1992.

S. Inch and J. Gilbert, Effect of Trichoderma harzianum on perithecial production of Gibberella zeae on wheat straw, Biocontrol Sci Tech, vol.17, pp.635-681, 2007.

I. Bujold, T. C. Paulitz, and O. Carisse, Effect of Microsphaeropsis sp. on the production of perithecia and ascospores of Gibberella zeae, Plant Dis, vol.85, pp.977-84, 2001.

J. M. Palazzini, B. Groenenboom-de-haas, A. M. Torres, J. Köhl, and S. N. Chulze, Biocontrol and population dynamics of Fusarium spp. on wheat stubble in Argentina, Plant Pathol, vol.62, pp.859-66, 2013.

A. Schöneberg, T. Musa, R. Voegele, and S. Vogelgsang, The potential of antagonistic fungi for control of Fusarium graminearum and Fusarium crookwellense varies depending on the experimental approach, J Appl Microbiol, vol.118, pp.1165-79, 2015.

J. M. Palazzini, N. Yerkovich, E. Alberione, M. Chiotta, and S. N. Chulze, An integrated dual strategy to control Fusarium graminearum sensu stricto by the biocontrol agent Streptomyces sp. RC 87B under field conditions, Plant Gene, vol.9, pp.13-21, 2017.

F. Legrand, A. Picot, J. F. Cobo-díaz, C. W. , L. Floch et al., Challenges facing the biological control strategies for the management of Fusarium head blight of cereals caused by F. graminearum, Biol Control, vol.113, pp.26-38, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01866801

C. Perez, R. Dill-macky, and L. L. Kinkel, Management of soil microbial communities to enhance populations of Fusarium graminearum-antagonists in soil, Plant Soil, vol.302, pp.53-69, 2008.

S. Kildea, V. Ransbotyn, M. R. Khan, B. Fagan, G. Leonard et al., Bacillus megaterium shows potential for the biocontrol of Septoria tritici blotch of wheat, Biol Control, vol.47, pp.37-45, 2008.

E. Levy, Z. Eyal, and C. I. , Suppression of Septoria tritici blotch and leaf rust on wheat seedling leaves by pseudomonads, Plant Pathol, vol.37, pp.551-558, 1988.

A. Perelló, M. R. Simón, A. M. Arambarri, and C. A. Cordo, Greenhouse screening of the saprophytic resident microflora for control of leaf spots of wheat (Triticum aestivum), Phytoparasitica, vol.29, pp.341-51, 2001.

M. C. Stocco, C. I. Mónaco, C. Abramoff, G. Lampugnani, G. Salerno et al., Selection and characterization of Argentine isolates of Trichoderma harzianum for effective biocontrol of Septoria leaf blotch of wheat, World J Microbiol Biotechnol, vol.32, p.49, 2016.

C. A. Cordo, C. I. Monaco, C. I. Segarra, M. R. Simon, A. Y. Mansilla et al., Trichoderma spp. as elicitors of wheat plant defense responses against Septoria tritici, Biocontrol Sci Tech, vol.17, pp.687-98, 2007.

D. Morais, I. Sache, F. Suffert, and V. Laval, Is the onset of septoria tritici blotch epidemics related to the local pool of ascospores?, Plant Pathol, vol.65, pp.250-60, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01584419

A. Newton, C. Gravouil, and J. Fountaine, Managing the ecology of foliar pathogens: ecological tolerance in crops, Ann Appl Biol, vol.157, pp.343-59, 2010.

A. Hartmann, M. Schmid, D. Van-tuinen, and G. Berg, Plant-driven selection of microbes, Plant Soil, vol.321, pp.235-57, 2009.

T. Pusztahelyi, I. J. Holb, and I. Pócsi, Secondary metabolites in fungus-plant interactions, Front Plant Sci, vol.6, p.573, 2015.

S. D. Allison and J. Martiny, Resistance, resilience, and redundancy in microbial communities, Proc Natl Acad Sci, vol.105, pp.11512-11521, 2008.

N. P. Shetty, R. Mehrabi, H. Lütken, A. Haldrup, G. H. Kema et al., Role of hydrogen peroxide during the interaction between the hemibiotrophic fungal pathogen Septoria tritici and wheat, New Phytol, vol.174, pp.637-684, 2007.

H. Thordal-christensen, Z. Zhang, Y. Wei, and D. B. Collinge, Subcellular localization of H 2 O 2 in plants. H 2 O 2 accumulation in papillae and hypersensitive response during the barley-powdery mildew interaction, Plant J, vol.11, pp.1187-94, 1997.

M. Trujillo, K. Kogel, and R. Hückelhoven, Superoxide and hydrogen peroxide play different roles in the nonhost interaction of barley and wheat with inappropriate formae speciales of Blumeria graminis, Mol Plant-Microbe Interact, vol.17, pp.304-316, 2004.

E. S. Orton and J. K. Brown, Reduction of growth and reproduction of the biotrophic fungus Blumeria graminis in the presence of a necrotrophic pathogen, Front Plant Sci, vol.7, p.742, 2016.

M. Grudzinska-sterno, J. Yuen, J. Stenlid, and A. Djurle, Fungal communities in organically grown winter wheat affected by plant organ and development stage, Eur J Plant Pathol, vol.146, pp.401-418, 2016.

A. E. Perelló, M. V. Moreno, C. Mónaco, M. R. Simón, and C. Cordo, Biological control of Septoria tritici blotch on wheat by Trichoderma spp. under field conditions in Argentina, BioControl, vol.54, pp.113-135, 2009.

E. B. Nelson, Microbial dynamics and interactions in the spermosphere, Annu Rev Phytopathol, vol.42, pp.271-309, 2004.

M. Saleem, N. Meckes, Z. H. Pervaiz, and M. B. Traw, Microbial interactions in the phyllosphere increase plant performance under herbivore biotic stress, Front Microbiol, vol.8, p.41, 2017.

J. M. Whipps, Microbial interactions and biocontrol in the rhizosphere, J Exp Bot, vol.52, pp.487-511, 2001.

H. Haugaard, L. Jørgensen, H. Lyngkjaer, M. Smedegaard-petersen, V. et al., Control of Blumeria graminis f. sp. hordei by treatment with mycelial extracts from cultured fungi, Plant Pathol, vol.50, pp.552-60, 2001.

G. Weber, S. Gülec, and J. Kranz, Interactions between Erysiphe graminis and Septoria nodorum on wheat, Plant Pathol, vol.43, pp.158-63, 1994.

D. Bello, G. Monaco, C. Simon, and M. , Biological control of seedling blight of wheat caused by Fusarium graminearum with beneficial rhizosphere microorganisms, World J Microbiol Biotechnol, vol.18, pp.627-663, 2002.

D. T. Wicklow and S. M. Poling, Antimicrobial activity of pyrrocidines from Acremonium zeae against endophytes and pathogens of maize, Phytopathology, vol.99, pp.109-124, 2009.

F. Dewey, Y. L. Wong, R. Seery, T. Hollins, and S. Gurr, Bacteria associated with Stagonospora (Septoria) nodorum increase pathogenicity of the fungus, New Phytol, vol.144, pp.489-97, 1999.

R. Poudel, A. Jumpponen, D. Schlatter, T. Paulitz, B. M. Gardener et al., Microbiome networks: a systems framework for identifying candidate microbial assemblages for disease management, Phytopathology, vol.106, pp.1083-96, 2016.

L. Luongo, M. Galli, L. Corazza, E. Meekes, L. D. Haas et al., Potential of fungal antagonists for biocontrol of Fusarium spp. in wheat and maize through competition in crop debris, Biocontrol Sci Tech, vol.15, pp.229-271, 2005.

U. Ritpitakphong, L. Falquet, A. Vimoltust, A. Berger, J. Métraux et al., The microbiome of the leaf surface of Arabidopsis protects against a fungal pathogen, New Phytol, vol.210, pp.1033-1076, 2016.

D. M. Weller, J. M. Raaijmakers, B. Gardener, and L. S. Thomashow, Microbial populations responsible for specific soil suppressiveness to plant pathogens, Annu Rev Phytopathol, vol.40, pp.309-357, 2002.

D. Schlatter, L. Kinkel, L. Thomashow, D. Weller, and T. Paulitz, Disease suppressive soils: new insights from the soil microbiome, Phytopathology, vol.107, pp.1284-97, 2017.

G. Berg, D. Rybakova, M. Grube, and M. Köberl, The plant microbiome explored: implications for experimental botany, J Exp Bot, vol.67, pp.995-1002, 2015.

J. G. Ellis, Can plant microbiome studies lead to effective biocontrol of plant diseases? Mol Plant-Microbe Interact, vol.30, pp.190-193, 2017.

R. L. Berendsen, C. M. Pieterse, and P. A. Bakker, The rhizosphere microbiome and plant health, Trends Plant Sci, vol.17, pp.478-86, 2012.

F. Suffert, I. Sache, and C. Lannou, Assessment of quantitative traits of aggressiveness in Mycosphaerella graminicola on adult wheat plants, Plant Pathol, vol.62, pp.1330-1371, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01004711

C. Waalwijk, O. Mendes, E. C. Verstappen, M. A. De-waard, and G. H. Kema, Isolation and characterization of the mating-type idiomorphs from the wheat septoria leaf blotch fungus Mycosphaerella graminicola, Fungal Genet Biol, vol.35, pp.277-86, 2002.

M. Buée, M. Reich, C. Murat, E. Morin, R. H. Nilsson et al., 454 pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity: research, New Phytol, vol.184, pp.449-56, 2009.

J. G. Caporaso, C. L. Lauber, W. A. Walters, D. Berg-lyons, C. A. Lozupone et al., Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample, Proc Natl Acad Sci, vol.108, pp.4516-4538, 2011.

M. Martin, Cutadapt removes adapter sequences from high-throughput sequencing reads, EMBnet Journal, vol.17, pp.10-12, 2011.

B. J. Callahan, P. J. Mcmurdie, M. J. Rosen, A. W. Han, A. Johnson et al., DADA2: high-resolution sample inference from Illumina amplicon data, Nat Methods, vol.13, pp.581-584, 2016.

B. Callahan, DADA2 pipeline tutorial (1.8), 2019.

J. R. Cole, Q. Wang, E. Cardenas, J. Fish, B. Chai et al., The Ribosomal Database Project: improved alignments and new tools for rRNA analysis, Nucleic Acids Res, vol.37, pp.141-146, 2009.

K. Abarenkov, R. H. Nilsson, K. Larsson, I. J. Alexander, U. Eberhardt et al., The UNITE database for molecular identification of fungi -recent updates and future perspectives, New Phytol, vol.186, pp.281-286, 2010.

P. J. Mcmurdie and S. Holmes, phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data, PLoS One, vol.8, p.61217, 2013.

E. Paradis and K. Schliep, Ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R, Bioinformatics, vol.35, pp.526-534, 2019.
URL : https://hal.archives-ouvertes.fr/ird-01920132

J. Oksanen, F. G. Blanchet, M. Friendly, R. Kindt, P. Legendre et al., , 2019.

N. Segata, J. Izard, L. Waldron, D. Gevers, L. Miropolsky et al., Metagenomic biomarker discovery and explanation, Genome Biol, vol.12, p.60, 2011.

Z. D. Kurtz, C. L. Müller, E. R. Miraldi, D. R. Littman, M. J. Blaser et al., Sparse and compositionally robust inference of microbial ecological networks, PLoS Comput Biol, vol.11, p.1004226, 2015.

L. Tipton, C. L. Müller, Z. D. Kurtz, L. Huang, E. Kleerup et al., Fungi stabilize connectivity in the lung and skin microbial ecosystems. Microbiome, vol.6, p.12, 2018.

D. Berry and S. Widder, Deciphering microbial interactions and detecting keystone species with co-occurrence networks, Front Microbiol, vol.5, 2014.

G. Csardi and T. Nepusz, The igraph software package for complex network research, 2019.

P. Shannon, A. Markiel, O. Ozier, N. S. Baliga, J. T. Wang et al., Cytoscape: a software environment for integrated models of biomolecular interaction networks, Genome Res, vol.13, pp.2498-504, 2003.

, Publisher's Note

, Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations