N. Araki, K. Kusumi, K. Masamoto, Y. Niwa, and K. Iba, Temperature-sensitive Arabidopsis mutant defective in 1-deoxy-d-xylulose 5-phosphate synthase within the plastid non-mevalonate pathway of isoprenoid biosynthesis, Physiol. Plant, vol.108, pp.19-24, 2000.

Y. Bai, D. B. Müller, G. Srinivas, R. Garrido-oter, E. Potthoff et al., Functional overlap of the Arabidopsis leaf and root microbiota, Nature, vol.528, pp.364-369, 2015.

D. A. Baltrus, H. C. Mccann, and D. S. Guttman, Evolution, genomics and epidemiology of Pseudomonas syringae, Mol. Plant Pathol, vol.18, pp.152-168, 2017.

G. Berg, M. Grube, M. Schloter, and K. Smalla, Unraveling the plant microbiome: Looking back and future perspectives, Front. Microbiol, vol.5, 2014.

D. Bulgarelli, K. Schlaeppi, S. Spaepen, E. V. Van-themaat, and P. Schulze-lefert, Structure and functions of the bacterial microbiota of plants, Annu. Rev. Plant Biol, vol.64, pp.807-838, 2013.

R. C. Burdon, R. R. Junker, D. G. Scofield, and A. L. Parachnowitsch, Bacteria colonising Penstemon digitalis show volatile and tissue-specific responses to a natural concentration range of the floral volatile linalool, Chemoecology, vol.28, pp.11-19, 2018.

J. M. Chaparro, D. V. Badri, and J. M. Vivanco, Rhizosphere microbiome assemblage is affected by plant development, ISME J, vol.8, pp.790-803, 2014.

V. M. Conn, A. R. Walker, and C. M. Franco, Endophytic Actinobacteria induce defense pathways in Arabidopsis thaliana, Mol. Plant-Microbe Interact, vol.21, pp.208-218, 2008.

V. Cordovez, V. J. Carrion, D. W. Etalo, R. Mumm, H. Zhu et al.,

J. M. Raaijmakers, Diversity and functions of volatile organic compounds produced by Streptomyces from a disease-suppressive soil, Front. Microbiol, vol.6, pp.1-13, 2015.

T. E. Cotton, P. Pétriacq, D. D. Cameron, M. Meselmani, . Al et al.,

S. A. Rolfe and J. Ton, Metabolic regulation of the maize rhizobiome by benzoxazinoids, ISME J, vol.13, pp.1647-1658, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02627631

T. Czechowski, M. Stitt, T. Altmann, M. K. Udvardi, and W. Scheible, , 2005.

, Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis, Plant Physiol, vol.139, pp.5-17

J. L. Dangl, D. M. Horvath, and B. J. Staskawicz, Pivoting the plant immune system from dissection to deployment, vol.341, pp.746-751, 2013.

M. P. Dias, M. S. Bastos, V. B. Xavier, E. Cassel, L. V. Astarita et al., Plant growth and resistance promoted by Streptomyces spp. in tomato, Plant Physiol. Biochem, vol.118, pp.479-493, 2017.

F. Escudié, L. Auer, M. Bernard, M. Mariadassou, L. Cauquil et al.,

G. Hernandez-raquet, S. Combes, P. , and G. , FROGS: Find, Rapidly, OTUs with Galaxy Solution, Bioinformatics, vol.34, pp.1287-1294, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02626808

D. W. Fadrosh, B. Ma, P. Gajer, N. Sengamalay, S. Ott et al., An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform, vol.2, p.6, 2014.

J. R. Gaiero, C. A. Mccall, K. A. Thompson, N. J. Day, A. S. Best et al., Inside the root microbiome: Bacterial root endophytes and plant growth promotion, Am. J. Bot, vol.100, pp.1738-1750, 2013.

T. Griebel and J. Zeier, A role for ?-sitosterol to stigmasterol conversion in plantpathogen interactions, Plant J, vol.63, pp.254-268, 2010.

D. S. Guttman, A. C. Mchardy, and P. Schulze-lefert, Microbial genome-enabled insights into plant-microorganism interactions, Nat. Rev. Genet, vol.15, pp.797-813, 2014.

K. Hahlbrock, P. Bednarek, I. Ciolkowski, B. Hamberger, A. Heise et al.,

E. Logemann, T. Nürnberger, E. Schmelzer, and I. E. Somssich, Non-self recognition, transcriptional reprogramming, and secondary metabolite accumulation during plant/pathogen interactions, Proc. Natl. Acad. Sci. U. S. A, vol.100, pp.14569-14576, 2003.

P. R. Hardoim, L. S. Van-overbeek, G. Berg, A. M. Pirttilä, S. Compant et al.,

M. Döring and A. Sessitsch, The Hidden World within Plants: Ecological and Evolutionary Considerations for Defining Functioning of Microbial Endophytes, 2015.

, Mol. Biol. Rev, vol.79, pp.293-320

M. A. Hassani, P. Durán, and S. Hacquard, Microbial interactions in plant holobiont, vol.6, p.58, 2018.

D. Heintz, S. Gallien, V. Compagnon, A. Berna, M. Suzuki et al., Phosphoproteome exploration reveals a reformatting of cellular processes in response to low sterol biosynthetic capacity in Arabidopsis, J. Proteome Res, vol.11, pp.1228-1239, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00670011

L. Hu, C. A. Robert, S. Cadot, X. Zhang, M. Ye et al.,

T. Steinger and M. G. Van-der-heijden, Root exudate metabolites drive plant-soil feedbacks on growth and defense by shaping the rhizosphere microbiota, Nat. Commun, vol.9, p.2738, 2018.

S. Hugly and C. Somerville, A role for membrane lipid polyunsaturation in chloroplast biogenesis at low temperature, Plant Physiol, vol.99, pp.197-202, 1992.

G. Innerebner, C. Knief, and J. A. Vorholt, Protection of Arabidopsis thaliana against leaf-pathogenic Pseudomonas syringae by Sphingomonas strains in a controlled model system, Appl. Environ. Microbiol, vol.77, pp.3202-3210, 2011.

J. D. Jones and J. L. Dangl, The plant immune system, Nature, vol.444, pp.323-329, 2006.

P. Jones, B. J. Garcia, A. Furches, G. A. Tuskan, and D. Jacobson, Plant hostassociated mechanisms for microbial selection, Front. Plant Sci, vol.10, pp.1-14, 2019.

F. Katagiri, R. Thilmony, and S. Y. He, The Arabidopsis thaliana-pseudomonas syringae interaction, Arab. B, vol.1, p.39, 2002.

T. Kuzuyama, Biosynthetic studies on terpenoids produced by Streptomyces, J. Antibiot. (Tokyo), vol.70, pp.811-818, 2017.

S. L. Lebeis, Greater than the sum of their parts: characterizing plant microbiomes at the community-level, Curr. Opin. Plant Biol, vol.24, pp.82-86, 2015.

J. H. Leveau and S. Gerards, Discovery of a bacterial gene cluster for catabolism of the plant hormone indole 3-acetic acid, FEMS Microbiol. Ecol, vol.65, pp.238-250, 2008.

H. K. Lichtenthaler and C. Buschmann, Chlorophylls and carotenoids: measurement and characterization by UV-VIS spectroscopy, Curr. Protoc. Food Anal. Chem, 2001.

C. Liu, X. Zhuang, Z. Yu, Z. Wang, Y. Wang et al., , 2019.

S. Abbasi, N. Safaie, A. Sadeghi, and M. Shamsbakhsh, Streptomyces Strains induce resistance to Fusarium oxysporum f. sp. lycopersici Race 3 in tomato through different molecular mechanisms, Front. Microbiol, vol.10, pp.1-16, 2019.

R. B. Abramovitch, J. C. Anderson, and G. B. Martin, Bacterial elicitation and evasion of plant innate immunity, Nat. Rev. Mol. Cell Biol, vol.7, pp.601-611, 2006.

T. Albrecht and C. T. Argueso, Should I fight or should I grow now? The role of cytokinins in plant growth and immunity and in the growth-defence trade-off, Ann. Bot, vol.119, pp.725-735, 2017.

S. Alström, Induction of disease resistance in common bean susceptible to halo blight bacterial pathogen after seed bacterization with rhizosphere pseudomonads, J. Gen, 1991.

, Appl. Microbiol, vol.37, pp.495-501

N. Araki, K. Kusumi, K. Masamoto, Y. Niwa, and K. Iba, Temperature-sensitive, 2000.

, Arabidopsis mutant defective in 1-deoxy-d-xylulose 5-phosphate synthase within the plastid non-mevalonate pathway of isoprenoid biosynthesis, Physiol. Plant, vol.108, pp.19-24

C. T. Argueso, F. J. Ferreira, P. Epple, J. P. To, C. E. Hutchison et al., Two-component elements mediate interactions between cytokinin and salicylic acid in plant immunity, PLoS Genet, vol.8, 2012.

T. Asai, G. Tena, J. Plotnikova, M. R. Willmann, W. Chiu et al., MAP kinase signalling cascade in Arabidopsis innate immunity, Nature, vol.415, pp.977-983, 2002.

B. Asselbergh, D. De-vleesschauwer, and M. Höfte, Global switches and finetuning-ABA modulates plant pathogen defense, Mol. Plant-Microbe Interact, vol.21, pp.709-719, 2008.

N. J. Atkinson and P. E. Urwin, The interaction of plant biotic and abiotic stresses: from genes to the field, J. Exp. Bot, vol.63, pp.3523-3543, 2012.

Y. Bai, D. B. Müller, G. Srinivas, R. Garrido-oter, E. Potthoff et al., Functional overlap of the Arabidopsis leaf and root microbiota, Nature, vol.528, pp.364-369, 2015.

A. Bajguz, Metabolism of brassinosteroids in plants, Plant Physiol. Biochem, vol.45, pp.95-107, 2007.

D. A. Baltrus, H. C. Mccann, and D. S. Guttman, Evolution, genomics and epidemiology of Pseudomonas syringae, Mol. Plant Pathol, vol.18, pp.152-168, 2017.

M. Barret, M. Briand, S. Bonneau, A. Préveaux, S. Valière et al.,

P. Simoneau and M. A. Jacquesa, Emergence shapes the structure of the seed microbiota, Appl. Environ. Microbiol, vol.81, pp.1257-1266, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01153480

Y. Bashan, G. Holguin, and L. E. De-bashan, Azospirillum-plant relationships: physiological, molecular, agricultural, and environmental advances (1997-2003), Can. J. Microbiol, vol.50, pp.521-577, 2004.

A. A. Belimov, I. C. Dodd, V. I. Safronova, A. I. Shaposhnikov, T. S. Azarova et al., Rhizobacteria that produce auxins and contain 1-amino-cyclopropane-1-carboxylic acid deaminase decrease amino acid concentrations in the rhizosphere and improve growth and yield of well-watered and waterlimited potato (Solanum tuberosum), Ann. Appl. Biol, vol.167, pp.11-25, 2015.

B. J. Belin, N. Busset, E. Giraud, A. Molinaro, A. Silipo et al., , 2018.

, Hopanoid lipids: From membranes to plant-bacteria interactions, Nat. Rev. Microbiol, vol.16, pp.304-315

C. Bender, D. Palmer, A. Peñaloza-vázquez, V. Rangaswamy, and M. Ullrich, , 1996.

, Biosynthesis of coronatine, a thermoregulated phytotoxin produced by the phytopathogen Pseudomonas syringae, Arch. Microbiol, vol.166, pp.71-75

A. Beneduzi, A. Ambrosini, and L. M. Passaglia, Plant growth-promoting rhizobacteria (PGPR): Their potential as antagonists and biocontrol agents, Genet. Mol. Biol, vol.35, pp.1044-1051, 2012.

G. Berg, Plant-microbe interactions promoting plant growth and health: Perspectives for controlled use of microorganisms in agriculture, Appl. Microbiol. Biotechnol, vol.84, pp.11-18, 2009.

G. Berg, M. Grube, M. Schloter, and K. Smalla, Unraveling the plant microbiome: Looking back and future perspectives, Front. Microbiol, vol.5, 2014.

M. D. Bertness and R. Callaway, Positive interactions in communities, Trends Ecol. Evol, vol.9, pp.191-193, 1994.

V. Bitas, H. Kim, J. W. Bennett, and S. Kang, Sniffing on microbes: diverse roles of microbial volatile organic compounds in plant health, Mol. Plant. Microbe. Interact, vol.26, pp.835-843, 2013.

R. E. Blankenship, Early evolution of photosynthesis, Plant Physiol, vol.154, pp.434-438, 2010.

E. G. Bligh and W. J. Dyer, A rapid method of total lipid extraction and purification, 1959.

, Can. J. Biochem. Physiol, vol.37, pp.911-917

G. V. Bloemberg and B. J. Lugtenberg, Molecular basis of plant growth promotion and biocontrol by rhizobacteria, Curr. Opin. Plant Biol, vol.4, pp.343-350, 2001.

N. Bodenhausen, M. W. Horton, and J. Bergelson, Bacterial communities associated with the leaves and the roots of Arabidopsis thaliana, Terpenoid biomaterials. Plant J, vol.8, pp.656-669, 2008.

T. Boller, F. , and G. , A renaissance of elicitors: perception of microbe-associated molecular patterns and danger signals by pattern-recognition receptors, Annu. Rev. Plant Biol, vol.60, pp.379-406, 2009.

T. Boller and S. Y. He, Innate immunity in plants: an arms race between pattern recognition receptors in plants and effectors in microbial pathogens, Science, vol.324, pp.742-744, 2009.

L. A. Brigham, P. J. Michaels, and H. E. Flores, Cell-specific production and antimicrobial activity of naphthoquinones in roots of Lithospermum erythrorhizon, Plant Physiol, vol.119, pp.417-428, 1999.

E. M. Bucci, Xylella fastidiosa, a new plant pathogen that threatens global farming: Ecology, molecular biology, search for remedies, Biochem. Biophys. Res. Commun, vol.502, pp.173-182, 2018.

F. Buchholz, T. Kosti?, A. Sessitsch, and B. Mitter, The potential of plant microbiota in reducing postharvest food loss, Microb. Biotechnol, vol.11, pp.971-975, 2018.

C. R. Buell, V. Joardar, M. Lindeberg, J. Selengut, I. T. Paulsen et al., The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000, Proc. Natl. Acad. Sci, vol.100, pp.10181-10186, 2003.

D. Bulgarelli, M. Rott, K. Schlaeppi, E. Ver-loren-van-themaat, and N. Ahmadinejad,

F. Assenza, P. Rauf, B. Huettel, R. Reinhardt, and E. Schmelzer, Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota, Nature, vol.488, pp.91-95, 2012.

D. Bulgarelli, K. Schlaeppi, S. Spaepen, E. V. Van-themaat, and P. Schulze-lefert, Structure and functions of the bacterial microbiota of plants, Annu. Rev. Plant Biol, vol.64, pp.807-838, 2013.

D. Bulgarelli, R. Garrido-oter, P. C. Münch, A. Weiman, J. Dröge et al., Structure and function of the bacterial root microbiota in wild and domesticated Barley, Cell Host Microbe, vol.17, pp.392-403, 2015.

A. Y. Burch, P. T. Do, A. Sbodio, T. V. Suslow, and S. E. Lindow, High-level culturability of epiphytic bacteria and frequency of biosurfactant producers on leaves, Appl. Environ. Microbiol, vol.82, pp.5997-6009, 2016.

R. C. Burdon, R. R. Junker, D. G. Scofield, and A. L. Parachnowitsch, Bacteria colonising Penstemon digitalis show volatile and tissue-specific responses to a natural concentration range of the floral volatile linalool, Chemoecology, vol.28, pp.11-19, 2018.

M. Cardinale, S. Ratering, C. Suarez, A. M. Zapata-montoya, and R. Geissler-plaum,

S. Schnell, Paradox of plant growth promotion potential of rhizobacteria and their actual promotion effect on growth of barley (Hordeum vulgare L.) under salt stress, Microbiol. Res, vol.181, pp.22-32, 2015.

C. C. De-carvalho, B. Parreño-marchante, G. Neumann, M. M. Da-fonseca, and H. J. Heipieper, Adaptation of Rhodococcus erythropolis DCL14 to growth on nalkanes, alcohols and terpenes, Appl. Microbiol. Biotechnol, vol.67, pp.383-388, 2005.

E. Cella, S. Angeletti, M. Fogolari, R. Bazzardi, L. De-gara et al., , 2018.

, Two different Xylella fastidiosa strains circulating in Italy: phylogenetic and evolutionary analyses, J. Plant Interact, vol.13, pp.428-432

J. H. Chang, J. M. Urbach, T. F. Law, L. W. Arnold, A. Hu et al.,

F. M. Ausubel and J. L. Dangl, A high-throughput, near-saturating screen for type III effector genes from Pseudomonas syringae, Proc. Natl. Acad. Sci, vol.102, pp.2549-2554, 2005.

J. M. Chaparro, D. V. Badri, and J. M. Vivanco, Rhizosphere microbiome assemblage is affected by plant development, ISME J, vol.8, pp.790-803, 2014.

S. T. Chisholm, G. Coaker, B. Day, and B. J. Staskawicz, Host-Microbe Interactions: Shaping the Evolution of the Plant Immune Response, Cell, vol.124, pp.803-814, 2006.

J. Choi, S. U. Huh, M. Kojima, H. Sakakibara, K. Paek et al., The cytokinin-activated transcription factor ARR2 promotes plant immunity via TGA3/NPR1-dependent salicylic acid signaling in Arabidopsis, Dev. Cell, vol.19, pp.284-295, 2010.

S. D. Clouse, Brassinosteroid signal transduction: from receptor kinase activation to transcriptional networks regulating plant development, Plant Cell, vol.23, pp.1219-1230, 2011.

A. Collmer, J. L. Badel, A. O. Charkowski, W. Deng, D. E. Fouts et al., Pseudomonas syringae Hrp type III secretion system and effector proteins, Proc. Natl. Acad. Sci, vol.97, pp.8770-8777, 2000.

V. M. Conn, A. R. Walker, and C. M. Franco, Endophytic Actinobacteria induce defense pathways in Arabidopsis thaliana, Mol. Plant-Microbe Interact, vol.21, pp.208-218, 2008.

V. Cordovez, V. J. Carrion, D. W. Etalo, R. Mumm, H. Zhu et al.,

J. M. Raaijmakers, Diversity and functions of volatile organic compounds produced by Streptomyces from a disease-suppressive soil, Front. Microbiol, vol.6, pp.1-13, 2015.

T. E. Cotton, P. Pétriacq, D. D. Cameron, M. Meselmani, . Al et al.,

S. A. Rolfe and J. Ton, Metabolic regulation of the maize rhizobiome by benzoxazinoids, ISME J, vol.13, pp.1647-1658, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02627631

M. M. Cowan, Plant products as antimicrobial agents, Clin. Microbiol. Rev, vol.12, pp.564-582, 1999.

S. Cunnac, M. Lindeberg, and A. Collmer, Pseudomonas syringae type III secretion system effectors: repertoires in search of functions, Curr. Opin. Microbiol, vol.12, pp.53-60, 2009.

D. A. Cuppels, Generation and characterization of Tn5 insertion mutations in Pseudomonas syringae pv. tomato, Appl. Environ. Microbiol, vol.51, pp.323-327, 1986.

T. P. Cushnie and A. J. Lamb, Antimicrobial activity of flavonoids, Int. J, 2005.

, Antimicrob. Agents, vol.26, pp.343-356

T. P. Cushnie and A. J. Lamb, Recent advances in understanding the antibacterial properties of flavonoids, Int. J. Antimicrob. Agents, vol.38, pp.99-107, 2011.

T. Czechowski, M. Stitt, T. Altmann, M. K. Udvardi, and W. Scheible, Genomewide identification and testing of superior reference genes for transcript normalization in Arabidopsis, Plant Physiol, vol.139, pp.5-17, 2005.

J. L. Dangl, D. M. Horvath, and B. J. Staskawicz, Pivoting the plant immune system from dissection to deployment, vol.341, pp.746-751, 2013.

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

S. Guindon, V. Lefort, and M. Lescot, Phylogeny.fr: robust phylogenetic analysis for the non-specialist, Nucleic Acids Res, vol.36, pp.465-469, 2008.
URL : https://hal.archives-ouvertes.fr/lirmm-00324099

L. Deslandes and S. Rivas, Catch me if you can: bacterial effectors and plant targets, Trends Plant Sci, vol.17, pp.644-655, 2012.
URL : https://hal.archives-ouvertes.fr/hal-02646805

Y. Dessaux, C. Grandclément, and D. Faure, Engineering the Rhizosphere, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01443849

, Trends Plant Sci, vol.21, pp.266-278

M. P. Dias, M. S. Bastos, V. B. Xavier, E. Cassel, L. V. Astarita et al., Plant growth and resistance promoted by Streptomyces spp. in tomato, Plant Physiol. Biochem, vol.118, pp.479-493, 2017.

L. Ding, H. Goerls, K. Dornblut, W. Lin, A. Maier et al., , 2015.

A. Bacaryolanes, rare bacterial caryolanes from a mangrove endophyte, J. Nat. Prod, vol.78, pp.2963-2967

S. Dobbelaere, A. Croonenborghs, and A. Thys, Phytostimulatory effect of, 1999.

, Azospirillum brasilense wild type and mutant strains altered in IAA production on wheat, Plant Soil, vol.6, pp.155-164

P. N. Dodds and J. P. Rathjen, Plant immunity: towards an integrated view of plantpathogen interactions, Nat. Rev. Genet, vol.11, pp.539-548, 2010.

R. C. Edgar, MUSCLE: A multiple sequence alignment method with reduced time and space complexity, BMC Bioinformatics, vol.5, pp.1-19, 2004.

J. Edwards, C. Johnson, C. Santos-medellín, E. Lurie, N. K. Podishetty et al.,

J. A. Eisen and V. Sundaresan, Structure, variation, and assembly of the rootassociated microbiomes of rice, Proc. Natl. Acad. Sci, vol.112, pp.911-920, 2015.

F. Escudié, L. Auer, M. Bernard, M. Mariadassou, L. Cauquil et al.,

G. Hernandez-raquet, S. Combes, P. , and G. , FROGS: Find, Rapidly, OTUs with Galaxy Solution, Bioinformatics, vol.34, pp.1287-1294, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02626808

D. W. Fadrosh, B. Ma, P. Gajer, N. Sengamalay, S. Ott et al., An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform, vol.2, p.6, 2014.

C. Fahlgren, A. Hagström, D. Nilsson, and U. L. Zweifel, Annual variations in the diversity, viability, and origin of airborne bacteria, Appl. Environ. Microbiol, vol.76, pp.3015-3025, 2010.

J. Fan, C. Crooks, and C. Lamb, High-throughput quantitative luminescence assay of the growth in planta of Pseudomonas syringae chromosomally tagged with Photorhabdus luminescens luxCDABE, Plant J, vol.53, pp.393-399, 2007.

G. Felix, J. D. Duran, S. Volko, and T. Boller, Plants have a sensitive perception system for the most conserved domain of bacterial flagellin, Plant J, vol.18, pp.265-276, 1999.

O. M. Finkel, G. Castrillo, S. Herrera-paredes, I. Salas-gonzález, and J. L. Dangl, , 2017.

, Understanding and exploiting plant beneficial microbes, Curr. Opin. Plant Biol, vol.38, pp.155-163

H. H. Flor, Current status of the gene-for-gene concept, Annu. Rev. Phytopathol, vol.9, pp.275-296, 1971.

Ú. Flores-pérez, J. Pérez-gil, M. Closa, L. P. Wright, P. Botella-pavía et al., , 2010.

F. Frugier, S. Kosuta, J. D. Murray, M. Crespi, and K. Szczyglowski, Cytokinin: secret agent of symbiosis, Trends Plant Sci, vol.13, pp.115-120, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00856256

M. Fujita, Y. Fujita, Y. Noutoshi, F. Takahashi, Y. Narusaka et al., Crosstalk between abiotic and biotic stress responses: a current view from the points of convergence in the stress signaling networks, Curr. Opin. Plant Biol, vol.9, pp.436-442, 2006.

J. R. Gaiero, C. A. Mccall, K. A. Thompson, N. J. Day, A. S. Best et al., Inside the root microbiome: Bacterial root endophytes and plant growth promotion, 2013.

J. Bot, , vol.100, pp.1738-1750

A. Gargallo-garriga, J. Sardans, M. Pérez-trujillo, A. Guenther, J. Llusià et al.,

J. Terradas, G. Farré-armengol, I. Filella, and T. Parella, , 2016.

L. Del-giudice, D. R. Massardo, P. Pontieri, C. M. Bertea, D. Mombello et al.,

S. M. Tredici, A. Talà, M. Mucciarelli, and V. I. Groudeva, The microbial community of Vetiver root and its involvement into essential oil biogenesis, Environ. Microbiol, vol.10, pp.2824-2841, 2008.

E. Glawischnig, Camalexin, Phytochemistry, vol.68, pp.401-406, 2007.

J. Glazebrook, Contrasting mechanisms of defense against biotrophic and necrotrophic pathogens, Annu. Rev. Phytopathol, vol.43, pp.205-227, 2005.

J. Glazebrook and F. M. Ausubel, Isolation of phytoalexin-deficient mutants of, 1994.

, Arabidopsis thaliana and characterization of their interactions with bacterial pathogens, Proc. Natl. Acad. Sci. U. S. A, vol.91, pp.8955-8959

B. R. Glick, Plant growth-promoting bacteria: mechanisms and applications, 2012.

, Scientifica (Cairo), vol.2012, pp.1-15

B. R. Glick, Bacteria with ACC deaminase can promote plant growth and help to feed the world, Microbiol. Res, vol.169, pp.30-39, 2014.

O. G. Gorshkova, N. V. Korotaeva, A. M. Ostapchuk, O. V. Voliuvach, and T. V. Gudzenko, Fatty acids composition of Microbacterium genus bacteria -destructors of oil hydrocarbons, Mikrobiol. Zh, vol.78, pp.92-98, 2016.

J. T. Greenberg and N. Yao, The role of regulation of programmed cell death in plant-pathogen interactions, Cell. Microbiol, vol.6, pp.201-211, 2004.

T. Griebel and J. Zeier, A role for ?-sitosterol to stigmasterol conversion in plantpathogen interactions, Plant J, vol.63, pp.254-268, 2010.

M. Guo, F. Tian, Y. Wamboldt, A. , and J. R. , The majority of the type III effector inventory of Pseudomonas syringae pv. tomato DC3000 can suppress plant immunity, Mol. Plant-Microbe Interact, vol.22, pp.1069-1080, 2009.

D. S. Guttman, A. C. Mchardy, and P. Schulze-lefert, Microbial genome-enabled insights into plant-microorganism interactions, Nat. Rev. Genet, vol.15, pp.797-813, 2014.

D. Haas and C. Keel, Regulation of antibiotic production in root-colonizing, 2003.

, Pseudomonas spp. and relevance for biological control of plant disease, Annu. Rev. Phytopathol, vol.41, pp.117-153

S. Hacquard, S. Spaepen, R. Garrido-oter, and P. Schulze-lefert, Interplay between innate immunity and the plant microbiota, Annu. Rev. Phytopathol, vol.55, pp.565-589, 2017.

K. Hahlbrock, P. Bednarek, I. Ciolkowski, B. Hamberger, A. Heise et al.,

E. Logemann, T. Nürnberger, E. Schmelzer, and I. E. Somssich, Non-self recognition, transcriptional reprogramming, and secondary metabolite accumulation during plant/pathogen interactions, Proc. Natl. Acad. Sci. U. S. A, vol.100, pp.14569-14576, 2003.

R. Hammerschmidt, Induced disease resistance: how do induced plants stop pathogens?, Physiol. Mol. Plant Pathol, vol.55, pp.77-84, 1999.

P. R. Hardoim, L. S. Van-overbeek, J. D. Elsas, and . Van, Properties of bacterial endophytes and their proposed role in plant growth, Trends Microbiol, vol.16, pp.463-471, 2008.

P. R. Hardoim, L. S. Van-overbeek, G. Berg, A. M. Pirttilä, S. Compant et al.,

M. Döring and A. Sessitsch, The Hidden World within Plants: Ecological and Evolutionary Considerations for Defining Functioning of Microbial Endophytes. Microbiol, Mol. Biol. Rev, vol.79, pp.293-320, 2015.

M. Hartmann, Plant sterols and the membrane environment, Trends Plant Sci, vol.3, pp.170-175, 1998.

A. Hartmann, M. Rothballer, and M. Schmid, Lorenz Hiltner, a pioneer in rhizosphere microbial ecology and soil bacteriology research, Plant Soil, vol.312, pp.7-14, 2008.

U. A. Hartwig, C. M. Joseph, and D. A. Phillips, Flavonoids released naturally from alfalfa seeds enhance growth rate of Rhizobium meliloti, Plant Physiol, vol.95, pp.797-803, 1991.

M. A. Hassani, P. Durán, and S. Hacquard, Microbial interactions in plant holobiont, vol.6, p.58, 2018.

P. Hauck, R. Thilmony, and S. Y. He, A Pseudomonas syringae type III effector suppresses cell wall-based extracellular defense in susceptible Arabidopsis plants, Proc. Natl. Acad. Sci, vol.100, pp.8577-8582, 2003.

M. G. Van-der-heijden and K. Schlaeppi, Root surface as a frontier for plant microbiome research, Proc. Natl. Acad. Sci, vol.112, pp.2299-2300, 2015.

M. Heil, Induced Systemic Resistance (ISR) against pathogens in the context of induced plant defences, Ann. Bot, vol.89, pp.503-512, 2002.

D. Heintz, S. Gallien, V. Compagnon, A. Berna, M. Suzuki et al., Phosphoproteome exploration reveals a reformatting of cellular processes in response to low sterol biosynthetic capacity in Arabidopsis, J. Proteome Res, vol.11, pp.1228-1239, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00670011

H. J. Heipieper and J. A. De-bont, Adaptation of Pseudomonas putida S12 to ethanol and toluene at the level of fatty acid composition of membranes, Appl. Environ, 1994.

. Microbiol, , vol.60, pp.4440-4444

H. J. Heipieper, R. Diefenbach, and H. Keweloh, Conversion of cis unsaturated fatty acids to trans, a possible mechanism for the protection of phenol-degrading Pseudomonas putida P8 from substrate toxicity, Appl. Environ. Microbiol, vol.58, pp.1847-1852, 1992.

A. Hemmerlin, J. F. Hoeffler, O. Meyer, D. Tritsch, I. A. Kagan et al.,

C. Rohmer, M. Bach, and T. J. , Cross-talk between the cytosolic mevalonate and the plastidial methylerythritol phosphate pathways in tobacco bright yellow-2 cells, J. Biol. Chem, vol.278, pp.26666-26676, 2003.

A. Henry, W. Doucette, J. Norton, S. Jones, J. Chard et al., An axenic plant culture system for optimal growth in long-term studies, J. Environ. Qual, vol.35, p.590, 2006.

S. Herrera-paredes, T. Gao, T. F. Law, O. M. Finkel, T. Mucyn et al., Design of synthetic bacterial communities for predictable plant phenotypes, PLOS Biol, vol.16, p.2003962, 2018.

S. S. Hirano and C. D. Upper, Bacteria in the leaf ecosystem with emphasis on Pseudomonas syringae-a pathogen, ice nucleus, and epiphyte. Microbiol, Mol. Biol. Rev, vol.64, pp.624-653, 2000.

E. Hoffland, C. M. Pieterse, L. Bik, and J. A. Van-pelt, Induced systemic resistance in radish is not associated with accumulation of pathogenesis, 1995.

, Physiol. Mol. Plant Pathol, vol.46, pp.309-320

M. W. Horton, N. Bodenhausen, K. Beilsmith, D. Meng, B. D. Muegge et al.,

M. M. Vetter, B. J. Vilhjálmsson, M. Nordborg, and J. I. Gordon, , 2014.

, Genome-wide association study of Arabidopsis thaliana leaf microbial community, Nat. Commun, vol.5, p.5320

S. Horuz, A. , and Y. , Biological control of watermelon seedling blight caused by Acidovorax citrulli using antagonistic bacteria from the genera Curtobacterium, Microbacterium and Pseudomonas, Plant Prot. Sci, vol.54, pp.138-146, 2018.

L. Hu, C. A. Robert, S. Cadot, X. Zhang, M. Ye et al.,

T. Steinger and M. G. Van-der-heijden, Root exudate metabolites drive plant-soil feedbacks on growth and defense by shaping the rhizosphere microbiota, Nat. Commun, vol.9, p.2738, 2018.

X. Huang and A. Madan, CAP3: A DNA sequence assembly program, Genome Res, vol.9, pp.868-877, 1999.

S. Hugly and C. Somerville, A role for membrane lipid polyunsaturation in chloroplast biogenesis at low temperature, Plant Physiol, vol.99, pp.197-202, 1992.

G. Innerebner, C. Knief, and J. A. Vorholt, Protection of Arabidopsis thaliana against leaf-pathogenic Pseudomonas syringae by Sphingomonas strains in a controlled model system, Appl. Environ. Microbiol, vol.77, pp.3202-3210, 2011.

M. P. Johnson, Photosynthesis. Essays Biochem, vol.60, pp.255-273, 2016.

J. D. Jones and J. L. Dangl, Plant pathogens and integrated defence responses to infection, Nature, vol.411, p.833, 2001.

J. D. Jones and J. L. Dangl, The plant immune system, Nature, vol.444, pp.323-329, 2006.

P. Jones, B. J. Garcia, A. Furches, G. A. Tuskan, and D. Jacobson, Plant hostassociated mechanisms for microbial selection, Front. Plant Sci, vol.10, pp.1-14, 2019.

E. L. Kannenberg and K. Poralla, Hopanoid biosynthesis and function in bacteria, Naturwissenschaften, vol.86, pp.168-176, 1999.

F. Katagiri, R. Thilmony, and S. Y. He, The Arabidopsis thaliana-pseudomonas syringae interaction, Arab. B, vol.1, p.39, 2002.

K. Vessey and J. , Plant growth promoting rhizobacteria as biofertilizers, Plant Soil, vol.255, pp.571-586, 2003.

M. K. Kim, Y. Kim, H. Kim, S. Kim, T. Yi et al., , 2008.

S. N. Curtobacterium-ginsengisoli, isolated from soil of a ginseng field, Int. J. Syst. Evol. Microbiol, vol.58, pp.2393-2397

A. Koornneef and C. M. Pieterse, Cross talk in defense signaling, Plant Physiol, vol.146, pp.839-844, 2008.

D. Kumar, Salicylic acid signaling in disease resistance, Plant Sci, vol.228, pp.127-134, 2014.

B. N. Kunkel and D. M. Brooks, Cross talk between signaling pathways in pathogen defense, Curr. Opin. Plant Biol, vol.5, pp.325-331, 2002.

T. Kuzuyama, Biosynthetic studies on terpenoids produced by Streptomyces, J. Antibiot. (Tokyo), vol.70, pp.811-818, 2017.

T. Kuzuyama and H. Seto, Diversity of the biosynthesis of the isoprene units, Nat. Prod. Rep, vol.20, pp.171-183, 2003.

T. Kuzuyama, J. P. Noel, R. , and S. B. , Structural basis for the promiscuous biosynthetic prenylation of aromatic natural products, Nature, vol.435, pp.983-987, 2005.

E. Lang, B. Griese, C. Sproer, P. Schumann, M. Steffen et al., , 2007.

, DSM 9128, leading to emended descriptions of Pseudomonas citronellolis Seubert 1960 (Approved Lists 1980) and Pseudomonas nitroreducens Iizuka and Komagata 1964 (Approved Lists 1980), includi, Int. J. Syst. Evol

. Microbiol, , vol.57, pp.878-882

B. M. Lange, T. Rujan, W. Martin, and R. Croteau, Isoprenoid biosynthesis: The evolution of two ancient and distinct pathways across genomes, Proc. Natl. Acad. Sci, vol.97, pp.13172-13177, 2002.

S. L. Lebeis, Greater than the sum of their parts: characterizing plant microbiomes at the community-level, Curr. Opin. Plant Biol, vol.24, pp.82-86, 2015.

J. H. Leveau and S. Gerards, Discovery of a bacterial gene cluster for catabolism of the plant hormone indole 3-acetic acid, FEMS Microbiol. Ecol, vol.65, pp.238-250, 2008.

L. A. Lewis, K. Polanski, M. De-torres-zabala, S. Jayaraman, L. Bowden et al.,

C. A. Penfold, D. J. Jenkins, C. Hill, and L. Baxter, Transcriptional dynamics driving MAMP-triggered immunity and pathogen effector-mediated immunosuppression in Arabidopsis leaves following infection with Pseudomonas syringae pv tomato DC3000, Plant Cell, vol.27, pp.3038-3064, 2015.

H. K. Lichtenthaler and C. Buschmann, Chlorophylls and carotenoids: measurement and characterization by UV-VIS spectroscopy, Curr. Protoc. Food Anal. Chem, 2001.

S. E. Lindow and M. T. Brandl, Microbiology of the phyllosphere, Appl. Environ, 2003.

. Microbiol, , vol.69, pp.1875-1883

C. Liu, X. Zhuang, Z. Yu, Z. Wang, Y. Wang et al., , 2019.

, Community structures and antifungal activity of root-associated endophytic actinobacteria of healthy and diseased soybean, vol.7, p.243

X. Liu, Y. Sun, C. J. Kørner, X. Du, M. E. Vollmer et al., , 2015.

, Bacterial leaf infiltration Assay for fine characterization of plant defense responses using the Arabidopsis thaliana-Pseudomonas syringae pathosystem, J. Vis. Exp

C. S. Loo, N. S. Lam, D. Yu, X. Su, and F. Lu, Artemisinin and its derivatives in treating protozoan infections beyond malaria, Pharmacol. Res, vol.117, pp.192-217, 2017.

L. C. Van-loon, P. A. Bakker, C. M. Pieterse, L. C. Loon, . Van et al.,

C. M. Pieterse, Systemic resistance induced by rhizosphere bacteria, Annu. Rev. Phytopathol, vol.36, pp.453-483, 1998.

L. C. Van-loon, Induced resistance in plants and the role of pathogenesis-related proteins, Eur. J. Plant Pathol, vol.103, pp.753-765, 1997.

B. Lugtenberg and F. Kamilova, Plant-Growth-Promoting Rhizobacteria, Annu. Rev. Microbiol, vol.63, pp.541-556, 2009.

D. S. Lundberg, S. L. Lebeis, S. H. Paredes, S. Yourstone, J. Gehring et al.,

J. Tremblay, A. Engelbrektson, V. Kunin, T. G. Rio, and . Del, Defining the core Arabidopsis thaliana root microbiome, Nature, vol.488, pp.86-90, 2012.

A. M. Maldonado, P. Doerner, R. A. Dixon, C. J. Lamb, C. et al., , 2002.

, putative lipid transfer protein involved in systemic resistance signalling in Arabidopsis, Nature, vol.419, pp.399-403

J. M. Mcdowell and J. L. Dangl, Signal transduction in the plant immune response, vol.0004, pp.79-82, 2000.

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.

M. Melotto, W. Underwood, J. Koczan, K. Nomura, and S. Y. He, Plant stomata function in innate immunity against bacterial invasion, Cell, vol.126, pp.969-980, 2006.

J. Memelink, Regulation of gene expression by jasmonate hormones, 2009.

, Phytochemistry, vol.70, pp.1560-1570

R. Mendes, P. Garbeva, and J. M. Raaijmakers, The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms, FEMS Microbiol. Rev, vol.37, pp.634-663, 2013.

M. Mergeay, D. Nies, H. G. Schlegel, J. Gerits, P. Charles et al., , 1985.

, Alcaligenes eutrophus CH34 is a facultative chemolithotroph with plasmid-bound resistance to heavy metals, J. Bacteriol, vol.162, pp.328-334

R. Mittler, Abiotic stress, the field environment and stress combination, Trends Plant Sci, vol.11, pp.15-19, 2006.

W. R. Morrison and L. M. Smith, Preparation of fatty acid methyl esters and dimethylacetals from lipids with boron fluoride-methanol, J. Lipid Res, vol.5, pp.600-608, 1964.

D. B. Müller, C. Vogel, Y. Bai, and J. A. Vorholt, The plant microbiota: systemslevel insights and perspectives, Annu. Rev. Genet, vol.50, pp.211-234, 2016.

E. Nambara and A. Marion-poll, Abscisic acid biosynthesis and catabolism, Annu. Rev. Plant Biol, vol.56, pp.165-185, 2005.
URL : https://hal.archives-ouvertes.fr/hal-02683495

C. Nawrath and J. Métraux, Salicylic acid induction-deficient mutants of Arabidopsis express PR-2 and PR-5 and accumulate high levels of camalexin after pathogen inoculation, Plant Cell, vol.11, pp.1393-1404, 1999.

J. T. Newitt, S. M. Prudence, M. I. Hutchings, and S. F. Worsley, Biocontrol of cereal crop diseases using Streptomycetes, vol.8, p.78, 2019.

K. Nomura, M. Melotto, and S. He, Suppression of host defense in compatible plant-Pseudomonas syringae interactions, Curr. Opin. Plant Biol, vol.8, pp.361-368, 2005.

T. Nürnberger and V. Lipka, Non-host resistance in plants: new insights into an old phenomenon, Mol. Plant Pathol, vol.6, pp.335-345, 2005.

O. S. Olanrewaju and O. O. Babalola, Streptomyces: implications and interactions in plant growth promotion, Appl. Microbiol. Biotechnol, vol.103, pp.1179-1188, 2019.

O. S. Olanrewaju, B. R. Glick, and O. O. Babalola, Mechanisms of action of plant growth promoting bacteria, World J. Microbiol. Biotechnol, vol.33, 0197.

S. S. Pandey, S. Singh, H. Pandey, M. Srivastava, T. Ray et al.,

K. Shanker, C. S. Babu, and S. Banerjee, Endophytes of Withania somnifera modulate in planta content and the site of withanolide biosynthesis, Sci. Rep, vol.8, 2018.

S. Lee, K. Y. Oh, and D. Y. Lee, Bacillus aryabhattai SRB02 tolerates oxidative and nitrosative stress and promotes the growth of soybean by modulating the production of phytohormones, PLoS One, vol.12, 2017.

A. Passera, S. Compant, P. Casati, M. G. Maturo, G. Battelli et al.,

D. Salerno, M. Brasca, and S. L. Toffolatti, Not just a pathogen? Description of a plant-beneficial Pseudomonas syringae strain, Front. Microbiol, vol.10, 1409.

K. F. Pedley and G. B. Martin, Role of mitogen-activated protein kinases in plant immunity, Curr. Opin. Plant Biol, vol.8, pp.541-547, 2005.

R. Van-peer and B. Schippers, Lipopolysaccharides of plant-growth promoting, 1992.

, Pseudomonas sp. strain WCS417r induce resistance in carnation to Fusarium wilt

, Netherlands J. Plant Pathol, vol.98, pp.129-139

J. Peñuelas, G. Farré-armengol, J. Llusia, A. Gargallo-garriga, L. Rico et al.,

J. Terradas and I. Filella, Removal of floral microbiota reduces floral terpene emissions, p.6727, 2015.

J. Pérez-gil and M. Rodríguez-concepción, Metabolic plasticity for isoprenoid biosynthesis in bacteria, Biochem. J, vol.452, pp.19-25, 2013.

T. Petnicki-ocwieja, D. J. Schneider, V. C. Tam, S. T. Chancey, L. Shan et al.,

L. M. Schechter, M. D. Janes, C. R. Buell, and X. Tang, Genomewide identification of proteins secreted by the Hrp type III protein secretion system of Pseudomonas syringae pv. tomato DC3000, Proc. Natl. Acad. Sci, vol.99, pp.7652-7657, 2002.

M. W. Pfaffl, A new mathematical model for relative quantification in real-time RT-PCR, Nucleic Acids Res, vol.29, 2001.

S. Pfeilmeier, I. M. Saur, .. Rathjen, J. P. Zipfel, C. Malone et al., High levels of cyclic-di-GMP in plant-associated Pseudomonas correlate with evasion of plant immunity, 2016.

, Mol. Plant Pathol, vol.17, pp.521-531

D. A. Phillips and S. M. Tsai, Flavonoids as plant signals to rhizosphere microbes, 1992.

, Mycorrhiza, vol.1, pp.55-58

M. Phillips, P. León, A. Boronat, and M. Rodríguez-concepción, The plastidial MEP pathway: unified nomenclature and resources, Trends Plant Sci, vol.13, pp.619-623, 2008.

A. Piasecka, P. Kachlicki, M. ;. Stobiecki, S. C. Van-wees, J. A. Van-pelt et al., Analytical methods for detection of plant metabolomes changes in response to biotic and abiotic stresses, 379. Pieterse, vol.20, 2019.

P. J. Weisbeek and L. C. Van-loon, A novel signaling pathway controlling induced systemic resistance in Arabidopsis, Plant Cell, vol.10, pp.1571-1580, 1998.

C. M. Pieterse, S. C. Van-wees, E. Hoffland, J. A. Van-pelt, and L. C. Van-loon, , 1996.

, Systemic resistance in Arabidopsis induced by biocontrol bacteria is independent of salicylic acid accumulation and pathogenesis-related gene expression, Plant Cell, vol.8, p.1225

C. M. Pieterse, J. A. Van-pelt, J. Ton, S. Parchmann, M. J. Mueller et al.,

J. Métraux and L. C. Van-loon, Rhizobacteria-mediated induced systemic resistance (ISR) in Arabidopsis requires sensitivity to jasmonate and ethylene but is not accompanied by an increase in their production, Physiol. Mol. Plant Pathol, vol.57, pp.123-134, 2000.

C. M. Pieterse, A. Leon-reyes, S. Van-der-ent, and S. C. Van-wees, , 2009.

, Networking by small-molecule hormones in plant immunity, Nat. Chem. Biol, vol.5, pp.308-316

C. M. Pieterse, D. Van-der-does, C. Zamioudis, A. Leon-reyes, and S. C. Van-wees, Hormonal modulation of plant immunity, Annu. Rev. Cell Dev. Biol, vol.28, pp.489-521, 2012.

C. M. Pieterse, C. Zamioudis, R. L. Berendsen, D. M. Weller, and S. C. Van-wees,

P. A. Bakker, Induced systemic resistance by beneficial microbes, Annu. Rev. Phytopathol, vol.52, pp.347-375, 2014.

A. Porras-alfaro and P. Bayman, Hidden fungi, emergent properties: endophytes and microbiomes, Annu. Rev. Phytopathol, vol.49, pp.291-315, 2011.

E. Pruesse, J. Peplies, and F. O. Glöckner, SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes, Bioinformatics, vol.28, pp.1823-1829, 2012.

P. Pulido, C. Perello, and M. Rodriguez-concepcion, New insights into plant isoprenoid metabolism, Mol. Plant, vol.5, pp.964-967, 2012.

P. Van-rhijn and J. Vanderleyden, The Rhizobium-plant symbiosis, Microbiol. Rev, vol.59, pp.124-142, 1995.

M. Rodríguez-concepción and A. Boronat, Isoprenoid Biosynthesis in Prokaryotic Organisms, Isoprenoid Synthesis in Plants and Microorganisms, pp.1-16, 2012.

M. Rodríguez-concepción and A. Boronat, Breaking new ground in the regulation of the early steps of plant isoprenoid biosynthesis, Curr. Opin. Plant Biol, vol.25, pp.17-22, 2015.

P. A. Rodriguez, M. Rothballer, S. P. Chowdhury, T. Nussbaumer, C. Gutjahr et al.,

P. Braun, Systems biology of plant-microbiome interactions, Mol. Plant, vol.12, pp.804-821, 2019.

M. Rohmer, The discovery of a mevalonate-independent pathway for isoprenoid biosynthesis in bacteria, algae and higher plants, Nat. Prod. Rep, vol.16, pp.565-574, 1999.

M. Rohmer, Diversity in isoprene unit biosynthesis: The methylerythritol phosphate pathway in bacteria and plastids, Pure Appl. Chem, vol.79, pp.739-751, 2007.

E. Rosenberg and I. Zilber-rosenberg, The hologenome concept of evolution after 10 years, vol.6, p.78, 2018.

E. Rosenberg, O. Koren, L. Reshef, R. Efrony, and I. Zilber-rosenberg, The role of microorganisms in coral health, disease and evolution, Nat. Rev. Microbiol, vol.5, pp.355-362, 2007.

M. Roux, B. Schwessinger, C. Albrecht, D. Chinchilla, A. Jones et al., The Arabidopsis leucine-rich repeat receptorlike kinases BAK1/SERK3 and BKK1/SERK4 are required for innate immunity to hemibiotrophic and biotrophic pathogens, Plant Cell, vol.23, pp.2440-2455, 2011.

R. L. Rubin, K. J. Van-groenigen, and B. A. Hungate, Plant growth promoting rhizobacteria are more effective under drought: a meta-analysis, Plant Soil, vol.416, pp.309-323, 2017.

F. Ryffel, E. J. Helfrich, P. Kiefer, L. Peyriga, J. Portais et al., Metabolic footprint of epiphytic bacteria on Arabidopsis thaliana leaves, ISME J, vol.10, pp.632-643, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01886376

J. P. Sáenz, D. Grosser, A. S. Bradley, T. J. Lagny, O. Lavrynenko et al.,

K. Simons, Hopanoids as functional analogues of cholesterol in bacterial membranes, 2015.

, Proc. Natl. Acad. Sci, vol.112, pp.11971-11976

M. Saleem, A. D. Law, and L. A. Moe, Nicotiana roots recruit rare rhizosphere taxa as major root-inhabiting microbes, Microb. Ecol, vol.71, pp.469-472, 2016.

M. V. Salomon, R. Purpora, R. Bottini, and P. Piccoli, Rhizosphere associated bacteria trigger accumulation of terpenes in leaves of Vitis vinifera L. cv. Malbec that protect cells against reactive oxygen species, Plant Physiol. Biochem, vol.106, pp.295-304, 2016.

U. F. Sammer and K. Reiher, Curtobacterium flaccumfaciens pv. flaccumfaciens on Soybean in Germany -A threat for farming, J. Phytopathol, vol.160, pp.314-316, 2012.

R. Santhanam, K. Groten, D. G. Meldau, and I. T. Baldwin, Analysis of plantbacteria interactions in their native habitat: bacterial communities associated with wild tobacco are independent of endogenous jasmonic acid levels and developmental stages, PLoS One, vol.9, p.94710, 2014.

A. Santner, L. I. Calderon-villalobos, E. , and M. , Plant hormones are versatile chemical regulators of plant growth, Nat. Chem. Biol, vol.5, pp.301-307, 2009.

S. Schäfer, S. Krolzik, G. A. Romanov, and T. Schmülling, Cytokinin-regulated transcripts in tobacco cell culture, Plant Growth Regul, vol.32, pp.307-313, 2000.

D. Scheel, Resistance response physiology and signal transduction, Curr. Opin. Plant Biol, vol.1, pp.305-310, 1998.

K. Schlaeppi and D. Bulgarelli, The plant microbiome at work, Mol. Plant-Microbe Interact, vol.28, pp.212-217, 2015.

K. Schlaeppi, N. Dombrowski, R. G. Oter, E. Ver-loren-van-themaat, and . Schulze-lefert,

P. , Quantitative divergence of the bacterial root microbiota in Arabidopsis thaliana relatives, Proc. Natl. Acad. Sci, vol.111, pp.585-592, 2014.

J. C. Schneider, H. Suzanne, and C. R. Somerville, Chilling-sensitive mutants of Arabidopsis, Plant Mol. Biol. Report, vol.13, pp.11-17, 1995.

L. Schütz, A. Gattinger, M. Meier, A. Müller, T. Boller et al., Improving crop yield and nutrient use efficiency via biofertilization-a global metaanalysis, Front. Plant Sci, vol.8, p.2204, 2018.

W. Seubert, Degradation of isoprenoid compounds by micro-organisms. I. Isolation and characterization of an isoprenoid-degrading bacterium, Pseudomonas citronellolis n. sp, J. Bacteriol, vol.79, pp.426-434, 1960.

W. Shan, Y. Zhou, H. Liu, Y. , and X. , Endophytic Actinomycetes from tea plants (Camellia sinensis): isolation, abundance, antimicrobial, and plant-growth-promoting activities, Biomed Res. Int, pp.1-12, 2018.

A. Silipo, G. Vitiello, D. Gully, L. Sturiale, C. Chaintreuil et al., Covalently linked hopanoid-lipid A improves outermembrane resistance of a Bradyrhizobium symbiont of legumes, Nat. Commun, vol.5, p.5106, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02632287

J. Simon, J. R. Marchesi, C. Mougel, and M. Selosse, Host-microbiota interactions: from holobiont theory to analysis, vol.7, p.5, 2019.
URL : https://hal.archives-ouvertes.fr/hal-01980500

B. Singh and R. A. Sharma, Plant terpenes: defense responses, phylogenetic analysis, regulation and clinical applications, 3 Biotech, vol.5, pp.129-151, 2015.

P. Soares-castro, P. Montenegro-silva, H. J. Heipieper, and P. M. Santos, , 2017.

, Functional characterization of a 28-kilobase catabolic island from Pseudomonas sp. strain M1 involved in biotransformation of ?-myrcene and related plant-derived volatiles, Appl. Environ. Microbiol, vol.83, pp.1-19

A. Soltani, K. Khavazi, H. Asadi-rahmani, M. Omidvari, and P. Abaszadeh-dahaji,

H. Mirhoseyni, Plant growth promoting characteristics in some Flavobacterium spp. isolated from soils of Iran, J. Agric. Sci, vol.2, 2010.

S. Spaepen, J. Vanderleyden, and R. Remans, Indole-3-acetic acid in microbial and microorganism-plant signaling, FEMS Microbiol. Rev, vol.31, pp.425-448, 2007.

S. Spaepen, J. Vanderleyden, and Y. Okon, Plant growth-promoting actions of, 2009.

. Rhizobacteria, Advances in Botanical Research, pp.283-320

E. Stackebrandt, E. Brambilla, and K. Richert, Gene sequence phylogenies of the family Microbacteriaceae, Curr. Microbiol, vol.55, pp.42-46, 2007.

B. J. Staskawicz, M. B. Mudgett, J. L. Dangl, and J. E. Galan, Common and Contrasting Themes of Plant and Animal Diseases, Science, vol.292, pp.2285-2289, 2001.

A. Sturz and J. Nowak, Endophytic communities of rhizobacteria and the strategies required to create yield enhancing associations with crops, Appl. Soil Ecol, vol.15, pp.183-190, 2000.

Z. R. Suárez-moreno, D. M. Vinchira-villarraga, D. I. Vergara-morales, and L. Castellanos,

F. A. Ramos, C. Guarnaccia, G. Degrassi, V. Venturi, and N. Moreno-sarmiento, , 2019.

, Plant-growth promotion and biocontrol properties of three Streptomyces spp. isolates to control bacterial rice bathogens, Front. Microbiol, vol.10, pp.1-17

K. Suzuki and K. Komagata, Taxonomic significance of cellular fatty acid composition in some coryneform bacteria, Int. J. Syst. Bacteriol, vol.33, pp.188-200, 1983.

M. Suzuki, Y. Kamide, N. Nagata, H. Seki, K. Ohyama et al.,

T. Kato and S. Tabata, Loss of function of 3-hydroxy-3-methylglutaryl coenzyme A reductase 1 (HMG1) in Arabidopsis leads to dwarfing, early senescence and male sterility, and reduced sterol levels, Plant J, vol.37, pp.750-761, 2004.

M. Suzuki, S. Nakagawa, Y. Kamide, K. Kobayashi, K. Ohyama et al.,

R. Kiuchi, K. Saito, T. Muranaka, and N. Nagata, Complete blockage of the mevalonate pathway results in male gametophyte lethality, J. Exp. Bot, vol.60, pp.2055-2064, 2009.

N. Suzuki, R. M. Rivero, V. Shulaev, E. Blumwald, and R. Mittler, Abiotic and biotic stress combinations, New Phytol, vol.203, pp.32-43, 2014.

F. Tardieu and R. Tuberosa, Dissection and modelling of abiotic stress tolerance in plants, Curr. Opin. Plant Biol, vol.13, pp.206-212, 2010.
URL : https://hal.archives-ouvertes.fr/hal-02663693

R. Thilmony, W. Underwood, and S. Y. He, Genome-wide transcriptional analysis of the Arabidopsis thaliana interaction with the plant pathogen Pseudomonas syringae pv. tomato DC3000 and the human pathogen Escherichia coli O157:H7, Plant J, vol.46, pp.34-53, 2006.

B. P. Thomma, I. A. Penninckx, W. F. Broekaert, and B. P. Cammue, The complexity of disease signaling in Arabidopsis, Curr. Opin. Immunol, vol.13, pp.63-68, 2001.

B. P. Thomma, I. Nelissen, K. Eggermont, and W. F. Broekaert, Deficiency in phytoalexin production causes enhanced susceptibility of Arabidopsis thaliana to the fungus Alternaria brassicicola, Plant J, vol.19, pp.163-171, 1999.

H. V. Thulasiram, H. K. Erickson, and C. D. Poulter, Chimeras of two isoprenoid synthases catalyze all four coupling reactions in isoprenoid biosynthesis, Science, vol.316, pp.73-76, 2007.

J. Ton, J. A. Van-pelt, L. C. Van-loon, and C. M. Pieterse, Differential effectiveness of salicylate-dependent and jasmonate/ethylene-dependent induced resistance in Arabidopsis, Mol. Plant-Microbe Interact, vol.15, pp.27-34, 2002.

J. Ton, V. Flors, and B. Mauch-mani, The multifaceted role of ABA in disease resistance, Trends Plant Sci, vol.14, pp.310-317, 2009.

C. S. Trinh, H. Lee, W. J. Lee, S. J. Lee, N. Chung et al., Evaluation of the plant growth-promoting activity of Pseudomonas nitroreducens in Arabidopsis thaliana and Lactuca sativa, Plant Cell Rep, vol.37, pp.873-885, 2018.

S. Truyens, N. Weyens, A. Cuypers, and J. Vangronsveld, Changes in the population of seed bacteria of transgenerationally Cd-exposed Arabidopsis thaliana, Plant Biol, vol.15, pp.971-981, 2013.

K. Tsuda, M. Sato, J. Glazebrook, J. D. Cohen, and F. Katagiri, Interplay between MAMP-triggered and SA-mediated defense responses, Plant J, vol.53, pp.763-775, 2008.

S. Uknes, B. Mauch-mani, M. Moyer, S. Potter, S. Williams et al.,

A. Slusarenko, E. Ward, and J. Ryals, Acquired resistance in Arabidopsis, Plant Cell, vol.4, pp.645-656, 1992.

M. Umehara, A. Hanada, S. Yoshida, K. Akiyama, T. Arite et al.,

H. Magome, Y. Kamiya, K. Shirasu, and K. Yoneyama, Inhibition of shoot branching by new terpenoid plant hormones, Nature, vol.455, pp.195-200, 2008.

S. Uroz, P. E. Courty, and P. Oger, Plant symbionts are engineers of the plantassociated microbiome, Trends Plant Sci, pp.1-12, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02334474

J. Vacheron, G. Desbrosses, M. Bouffaud, B. Touraine, Y. Moënne-loccoz et al., Plant growthpromoting rhizobacteria and root system functioning, Front. Plant Sci, vol.4, pp.1-19, 2013.
URL : https://hal.archives-ouvertes.fr/hal-02522224

J. N. Valitova, A. G. Sulkarnayeva, and F. V. Minibayeva, Plant sterols: diversity, biosynthesis, and physiological functions, Biochem, vol.81, pp.819-834, 2016.

P. Vandenkoornhuyse, A. Quaiser, M. Duhamel, A. Le-van, and A. Dufresne, , 2015.

, The importance of the microbiome of the plant holobiont, New Phytol, vol.206, pp.1196-1206

N. Vannier, C. Mony, A. Bittebiere, S. Michon-coudouel, and M. Biget,

P. Vandenkoornhuyse, A microorganisms' journey between plant generations, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01793435

, Microbiome 6, p.79

B. W. Verhagen, J. Glazebrook, T. Zhu, H. Chang, L. C. Van-loon et al.,

C. M. , The transcriptome of rhizobacteria-induced systemic resistance in Arabidopsis, 2004.

, Mol. Plant. Microbe. Interact, vol.17, pp.895-908

C. Vogel, G. Innerebner, J. Zingg, J. Guder, and J. A. Vorholt, Forward genetic in planta screen for identification of plant-protective traits of Sphingomonas sp. strain Fr1 against Pseudomonas syringae DC3000, Appl. Environ. Microbiol, vol.78, pp.5529-5535, 2012.

C. Vogel, N. Bodenhausen, W. Gruissem, and J. A. Vorholt, The Arabidopsis leaf transcriptome reveals distinct but also overlapping responses to colonization by phyllosphere commensals and pathogen infection with impact on plant health, New Phytol, vol.212, pp.192-207, 2016.

M. J. Voges, Y. Bai, P. Schulze-lefert, and E. S. Sattely, Plant-derived coumarins shape the composition of an Arabidopsis synthetic root microbiome, Proc. Natl, 2019.

. Acad and . Sci, , vol.116, pp.12558-12565

J. A. Vorholt, Microbial life in the phyllosphere, Nat. Rev. Microbiol, vol.10, pp.828-840, 2012.

J. A. Vorholt, C. Vogel, C. I. Carlström, and D. B. Müller, Establishing causality: opportunities of synthetic communities for plant microbiome research, Cell Host Microbe, vol.22, pp.142-155, 2017.

K. Wang, L. Kang, A. Anand, G. Lazarovits, and K. S. Mysore, Monitoring in planta bacterial infection at both cellular and whole-plant levels using the green fluorescent protein variant GFPuv, New Phytol, vol.174, pp.212-223, 2007.

K. Wang, M. Senthil-kumar, C. Ryu, L. Kang, and K. S. Mysore, Phytosterols Play a Key Role in Plant Innate Immunity against Bacterial Pathogens by Regulating Nutrient Efflux into the Apoplast, Plant Physiol, vol.158, pp.1789-1802, 2012.

K. Wang, M. Senthil-kumar, C. Ryu, L. Kang, and K. S. Mysore, Phytosterols play a key role in plant innate immunity against bacterial pathogens by regulating nutrient efflux into the apoplast, Plant Physiol, vol.158, pp.1789-1802, 2012.

W. Wang, B. Vinocur, and A. Altman, Plant responses to drought, salinity and extreme temperatures: towards genetic engineering for stress tolerance, Planta, vol.218, pp.1-14, 2003.

S. C. Van-wees, M. Luijendijk, I. Smoorenburg, L. C. Van-loon, and C. M. Pieterse, , 1999.

, Rhizobacteria-mediated induced systemic resistance (ISR) in

S. C. Van-wees, E. A. De-swart, J. A. Van-pelt, L. C. Van-loon, and C. M. Pieterse, Enhancement of induced disease resistance by simultaneous activation of salicylateand jasmonate-dependent defense pathways in Arabidopsis thaliana, Proc. Natl. Acad. Sci, vol.97, pp.8711-8716, 2000.

H. Wei, S. Chakravarthy, J. Mathieu, T. C. Helmann, P. Stodghill et al., Pseudomonas syringae pv. tomato DC3000 Type III Secretion Effector Polymutants Reveal an Interplay between HopAD1 and AvrPtoB, Cell Host Microbe, vol.17, pp.752-762, 2015.
URL : https://hal.archives-ouvertes.fr/hal-02657966

M. C. Whalen, R. W. Innes, A. F. Bent, and B. J. Staskawicz, Identification of Pseudomonas syringae pathogens of Arabidopsis and a bacterial locus determining avirulence on both Arabidopsis and soybean, Plant Cell, vol.3, p.49, 1991.

W. B. Whitman, D. C. Coleman, and W. J. Wiebe, Prokaryotes: The unseen majority, vol.95, p.6, 1998.

J. Wollam, A. , and A. , Sterol regulation of metabolism, homeostasis, and development, Annu. Rev. Biochem, vol.80, pp.885-916, 2011.

L. P. Wright, J. M. Rohwer, A. Ghirardo, A. Hammerbacher, and M. Ortiz-alcaide,

B. Raguschke, J. Schnitzler, J. Gershenzon, and M. A. Phillips, Deoxyxylulose 5-phosphate synthase Ccontrols flux through the methylerythritol 4-phosphate pathway in Arabidopsis, Plant Physiol, vol.165, pp.1488-1504, 2014.

T. Xiang, N. Zong, Y. Zou, Y. Wu, J. Zhang et al., Pseudomonas syringae effector AvrPto blocks innate immunity by targeting receptor kinases, Curr. Biol, vol.18, pp.74-80, 2008.

X. Xin, B. Kvitko, and S. Y. He, Pseudomonas syringae: what it takes to be a pathogen, Nat. Rev. Microbiol, vol.16, pp.316-328, 2018.

S. Yamaguchi, Gibberellin metabolism and its regulation, Annu. Rev. Plant Biol, vol.59, pp.225-251, 2008.

Z. F. Yan, P. Lin, K. H. Won, J. E. Yang, C. T. Li et al.,

S. Microbacterium-hibisci and . Nov, isolated from rhizosphere of mugunghwa (hibiscus syriacus L.), Int. J. Syst. Evol. Microbiol, vol.67, pp.3564-3569

J. Yang, J. W. Kloepper, and C. Ryu, Rhizosphere bacteria help plants tolerate abiotic stress. Trends in Plant Sciences, Trends Plant Sci, vol.14, pp.1-4, 2008.

K. Yazaki, G. Arimura, and T. Ohnishi, Hidden' terpenoids in plants: their biosynthesis, localization and ecological roles, Plant Cell Physiol, vol.58, pp.1615-1621, 2017.

A. Zahid, R. Jaber, F. Laggoun, A. Lehner, I. Remy-jouet et al.,

J. Leprince, M. L. Follet-gueye, and M. Vicré-gibouin, Holaphyllamine, a steroid, is able to induce defense responses in Arabidopsis thaliana and increases resistance against bacterial infection, Planta, vol.246, pp.1109-1124, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01837955

C. Zamioudis and C. M. Pieterse, Modulation of host immunity by beneficial microbes, Mol. Plant-Microbe Interact, vol.25, pp.139-150, 2012.

Z. Zhu, Y. Li, Y. Li, M. Xiao, M. Han et al., Microbacterium suaedae sp. nov., isolated from Suaeda aralocaspica, Int. J. Syst. Evol. Microbiol, vol.69, pp.411-416, 2019.