Fungal (-like) biocontrol organisms in tomato disease control

Aimé, 2013, The endophytic strain Fusarium oxysporum Fo47: a good candidate for priming the defense responses in tomato roots, Mol. Plant Microbe Interact., 26, 918, 10.1094/MPMI-12-12-0290-R Aime, 2008, Comparative analysis of PR gene expression in tomato inoculated with virulent Fusarium oxysporum f. sp lycopersici and the biocontrol strain F. oxysporum Fo47, Physiol. Mol. Plant Pathol., 73, 9, 10.1016/j.pmpp.2008.10.001 Alabouvette, 2009, Microbiological control of soil-borne phytopathogenic fungi with special emphasis on wilt-inducing Fusarium oxysporum, New Phytol., 184, 529, 10.1111/j.1469-8137.2009.03014.x Alfano, 2007, Systemic modulation of gene expression in tomato by Trichoderma hamatum 382, Phytopathology, 97, 429, 10.1094/PHYTO-97-4-0429 Amiri, 2013, Phenotypic characterization of multifungicide resistance in Botrytis cinerea isolates from strawberry fields in Florida, Plant Dis., 97, 393, 10.1094/PDIS-08-12-0748-RE Amselem, 2011, Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea, PLoS Genet., 7, e1002230, 10.1371/journal.pgen.1002230 Anith, 2011, Compatibility of Piriformospora indica and Trichoderma harzianum as dual inoculants in black pepper (Piper nigrum L), Symbiosis, 55, 11, 10.1007/s13199-011-0143-1 Bae, 2006, Necrosis- and ethylene-inducing peptide from Fusarium oxysporum induces a complex cascade of transcripts associated with signal transduction and cell death in Arabidopsis, Plant Physiol., 141, 1056, 10.1104/pp.106.076869 Bae, 2011, Endophytic Trichoderma isolates from tropical environments delay disease onset and induce resistance against Phytophthora capsici in hot pepper using multiple mechanisms, Mol. Plant Microbe Interact., 24, 336, 10.1094/MPMI-09-10-0221 Baxter, 2010, Signatures of adaptation to obligate biotrophy in the Hyaloperonospora arabidopsidis genome, Science, 330, 1549, 10.1126/science.1195203 Benhamou, 2001, Cytological analysis of defense-related mechanisms induced in pea root tissues in response to colonization by nonpathogenic Fusarium oxysporum Fo47, Phytopathology, 91, 730, 10.1094/PHYTO.2001.91.8.730 Benhamou, 2012, Pythium oligandrum: an example of opportunistic success, Microbiology, 158, 2679, 10.1099/mic.0.061457-0 Benhamou, 1997, Treatment with the mycoparasite Pythium oligandrum triggers induction of defense-related reactions in tomato roots when challenged with Fusarium oxysporum f. sp. radicis-lycopersici, Phytopathology, 87, 108, 10.1094/PHYTO.1997.87.1.108 Benhamou, 1999, Ultrastructural and cytochemical aspects of the interaction between the mycoparasite Pythium oligandrum and soilborne plant pathogens, Phytopathology, 89, 506, 10.1094/PHYTO.1999.89.6.506 Benitez, 2004, Biocontrol mechanisms of Trichoderma strains, Int. Microbiol., 7, 249 Berta, 2005, Suppression of Rhizoctonia root-rot of tomato by Glomus mossae BEG12 and Pseudomonas fluorescens A6RI is associated with their effect on the pathogen growth and on the root morphogenesis, Eur. J. Plant Pathol., 111, 279, 10.1007/s10658-004-4585-7 Blancard, 2012 Bolwerk, 2005, Visualization of interactions between a pathogenic and a beneficial Fusarium strain during biocontrol of tomato foot and root rot, Mol. Plant Microbe Interact., 18, 710, 10.1094/MPMI-18-0710 Bonfante, 2010, Mechanisms underlying beneficial plant–fungus interactions in mycorrhizal symbiosis, Nat. Commun., 1, 48, 10.1038/ncomms1046 Bouizgarne, 2006, A putative role for fusaric acid in biocontrol of the parasitic angiosperm Orobanche ramosa, Mol. Plant Microbe Interact., 19, 550, 10.1094/MPMI-19-0550 Boutrot, 2010, Direct transcriptional control of the Arabidopsis immune receptor FLS2 by the ethylene-dependent transcription factors EIN3 and EIL1, Proc. Natl. Acad. Sci. U.S.A., 107, 14502, 10.1073/pnas.1003347107 Camehl, 2010, Ethylene signalling and ethylene-targeted transcription factors are required to balance beneficial and nonbeneficial traits in the symbiosis between the endophytic fungus Piriformospora indica and Arabidopsis thaliana, New Phytol., 185, 1062, 10.1111/j.1469-8137.2009.03149.x Card, 2009, Targeted selection of antagonistic microorganisms for control of Botrytis cinerea of strawberry in New Zealand, Australas. Plant Pathol., 38, 183, 10.1071/AP08097 Cavagnaro, 2006, Arbuscular mycorrhizas, microbial communities, nutrient availability, and soil aggregates in organic tomato production, Plant Soil, 282, 209, 10.1007/s11104-005-5847-7 Chacon, 2007, Microscopic and transcriptome analyses of early colonization of tomato roots by Trichoderma harzianum, Int. Microbiol., 10, 19 Cheng, 2011, Cloning of a novel l-amino acid oxidase from Trichoderma harzianum ETS 323 and bioactivity analysis of overexpressed l-amino acid oxidase, J. Agric. Food Chem., 59, 9142, 10.1021/jf201598z Chowdappa, 2013, Growth stimulation and induction of systemic resistance in tomato against early and late blight by Bacillus subtilis OTPB1 or Trichoderma harzianum OTPB3, Biol. Control, 65, 109, 10.1016/j.biocontrol.2012.11.009 Chugh, 2001, Peptaibols: models for ion channels, Biochem. Soc. Trans., 29, 565, 10.1042/bst0290565 Contreras-Cornejo, 2009, Trichoderma virens, a plant beneficial fungus, enhances biomass production and promotes lateral root growth through an auxin-dependent mechanism in Arabidopsis, Plant Physiol., 149, 1579, 10.1104/pp.108.130369 Cordier, 1998, Cell defense responses associated with localized and systemic resistance to Phytophthora parasitica induced in tomato by an arbuscular mycorrhizal fungus, Mol. Plant Microbe Interact., 11, 1017, 10.1094/MPMI.1998.11.10.1017 De Cremer, 2013, Development of a screening system for ISR-inducing Trichoderma spp. based on ISR-marker genes, IOBC Bull., 89, 219 De Jaeger, 2010, Mycoparasitism of arbuscular mycorrhizal fungi: a pathway for the entry of saprotrophic fungi into roots, FEMS Microbiol. Ecol., 73, 312 de la Noval, 2007, Exogenous systemin has a contrasting effect on disease resistance in mycorrhizal tomato (Solanum lycopersicum). plants infected with necrotrophic or hemibiotrophic pathogens, Mycorrhiza, 17, 449, 10.1007/s00572-007-0122-9 De Meyer, 1998, Induced systemic resistance in Trichoderma harzianum T39 biocontrol of Botrytis cinerea, Eur. J. Plant Pathol., 104, 279, 10.1023/A:1008628806616 Dean, 2012, The Top 10 fungal pathogens in molecular plant pathology, Mol. Plant Pathol., 13, 414, 10.1111/j.1364-3703.2011.00783.x Deshmukh, 2006, The root endophytic fungus Piriformospora indica requires host cell death for proliferation during mutualistic symbiosis with barley, Proc. Natl. Acad. Sci. U.S.A., 103, 18450, 10.1073/pnas.0605697103 Di Pietro, 2001, A MAP kinase of the vascular wilt fungus Fusarium oxysporum is essential for root penetration and pathogenesis, Mol. Microbiol., 369, 1140, 10.1111/j.1365-2958.2001.02307.x Druzhinina, 2011, Trichoderma: the genomics of opportunistic success, Nat. Rev. Microbiol., 9, 749, 10.1038/nrmicro2637 Duijff, 1998, Implication of systemic induced resistance in the suppression of Fusarium wilt of tomato by Pseudomonas fluorescens WCS417r and by nonpathogenic Fusarium oxysporum Fo47, Eur. J. Plant Pathol., 104, 903, 10.1023/A:1008626212305 Durrant, 2004, Systemic acquired resistance, Annu. Rev. Phytopathol., 42, 185, 10.1146/annurev.phyto.42.040803.140421 Duyvesteijn, 2005, Frp1 is a Fusarium oxysporum F-box protein required for pathogenicity on tomato, Mol. Microbiol., 57, 1051, 10.1111/j.1365-2958.2005.04751.x Elad, 1999, The role of Trichoderma harzianum protease in the biocontrol of Botrytis cinerea, Eur. J. Plant Pathol., 105, 177, 10.1023/A:1008753629207 Fakhro, 2010, Impact of Piriformospora indica on tomato growth and on interaction with fungal and viral pathogens, Mycorrhiza, 20, 191, 10.1007/s00572-009-0279-5 Fammartino, 2007, Characterization of a divinyl ether biosynthetic pathway specifically associated with pathogenesis in tobacco, Plant Physiol., 143, 378, 10.1104/pp.106.087304 Fillion, 1999, Direct interaction between the arbuscular mycorrhizal fungus Glomus intraradices and different rhizosphere microorganisms, New Phytol., 141, 525, 10.1046/j.1469-8137.1999.00366.x Fiorilli, 2011, The arbuscular mycorrhizal symbiosis reduces disease severity in tomato plants infected by Botrytis cinerea, J. Plant Pathol., 93, 237 Fiorilli, 2009, Global and cell-type gene expression profiles in tomato plants colonized by an arbuscular mycorrhizal fungus, New Phytol., 184, 975, 10.1111/j.1469-8137.2009.03031.x Foolad, 2008, Genetics, genomics and breeding of late blight and early blight resistance in tomato, Crit. Rev. Plant Sci., 27, 75, 10.1080/07352680802147353 Franken, 2012, The plant strengthening root endophyte Piriformospora indica: potential application and the biology behind, Appl. Microbiol. Biotechnol., 96, 1455, 10.1007/s00253-012-4506-1 Fravel, 2003, Fusarium oxysporum and its biocontrol, New Phytol., 157, 493, 10.1046/j.1469-8137.2003.00700.x Fritz, 2006, Arbuscular mycorrhiza reduces susceptibility of tomato to Alternaria solani, Mycorrhiza, 16, 413, 10.1007/s00572-006-0051-z Fuchs, 1997, Nonpathogenic Fusarium oxysporum strain Fo47 induces resistance to Fusarium wilt in tomato, Plant Dis., 81, 492, 10.1094/PDIS.1997.81.5.492 Gamalero, 2002, Morphogenetic modifications induced by Pseudomonas fluorescens A6RI and Glomus mosseae BEG12 in the root system of tomato differ according to plant growth conditions, New Phytol., 155, 293, 10.1046/j.1469-8137.2002.00460.x Gao, 2004, Expression patterns of defense-related genes in different types of arbuscular mycorrhizal development in wild-type and mycorrhiza-defective mutant tomato, Mol. Plant Microbe Interact., 17, 1103, 10.1094/MPMI.2004.17.10.1103 Gianinazzi, 2010, Agroecology: the key role of arbuscular mycorrhizas in ecosystem services, Mycorrhiza, 20, 519, 10.1007/s00572-010-0333-3 Gianinazzi-Pearson, 2009 Giovannetti, 2002 Glare, 2012, Have biopesticides come of age?, Trends Biotechnol., 30, 250, 10.1016/j.tibtech.2012.01.003 Glazebrook, 2005, Contrasting mechanisms of defense against biotrophic and necrotrophic pathogens, Annu. Rev. Phytopathol., 43, 205, 10.1146/annurev.phyto.43.040204.135923 Gomez-Gomez, 1999, A single locus determines sensitivity to bacterial flagellin in Arabidopsis thaliana, Plant J., 18, 277, 10.1046/j.1365-313X.1999.00451.x Gravel, 2007, Growth stimulation and fruit yield improvement of greenhouse tomato plants by inoculation with Pseudomonas putida or Trichoderma atroviride: possible role of indole acetic acid IAA, Soil Biol. Biochem., 39, 1968, 10.1016/j.soilbio.2007.02.015 Green, 1999, Suppression of the biocontrol agent Trichoderma harzianum by mycelium of the arbuscular mycorrhizal fungus Glomus intraradices in root-free soil, Appl. Environ. Microbiol., 65, 1428, 10.1128/AEM.65.4.1428-1434.1999 Gruber, 2012, Self versus non-self: fungal cell wall degradation in Trichoderma, Microbiology, 158, 26, 10.1099/mic.0.052613-0 Haas, 2009, Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans, Nature, 461, 393, 10.1038/nature08358 Hage-Ahmed, K., Moyses, A., Voglgruber, A., Hadacek, F., and Steinkellner, S., 2013. Alterations in root exudation of intercropped tomato mediated by the arbuscular mycorrhizal fungus Glomus mosseae and the soilborne pathogen Fusarium oxysporum f.sp. lycopersici. Journal of Phytopathology doi: 10.1111/jph.12130. Harman, 2004, Interactions between Trichoderma harzianum strain T22 and maize inbred line Mo17 and effects of these interactions on diseases caused by Pythium ultimum and Colletotrichum graminicola, Phytopathology, 94, 147, 10.1094/PHYTO.2004.94.2.147 Harrier, 2004, The potential role of arbuscular mycorrhizal (AM) fungi in the bioprotection of plants against soil-borne pathogens in organic and/or other sustainable farming systems, Pest Manag. Sci., 60, 149, 10.1002/ps.820 Harrison, 2005, Signaling in the arbuscular mycorrhizal symbiosis, Annu. Rev. Microbiol., 59, 19, 10.1146/annurev.micro.58.030603.123749 Hase, 2008, Involvement of jasmonic acid signalling in bacterial wilt disease resistance induced by biocontrol agent Pythium oligandrum in tomato, Plant. Pathol., 57, 870, 10.1111/j.1365-3059.2008.01858.x Hause, 2009, The role of jasmonates in mutualistic symbioses between plants and soil-born microorganisms, Phytochemistry, 70, 1589, 10.1016/j.phytochem.2009.07.003 Hermosa, 2012, Plant-beneficial effects of Trichoderma and of its genes, Microbiology, 158, 17, 10.1099/mic.0.052274-0 Herrera-Medina, 2007, Abscisic acid determines arbuscule development and functionality in the tomato arbuscular mycorrhiza, New Phytol., 175, 554, 10.1111/j.1469-8137.2007.02107.x Herrera-Medina, 2008, The jasmonic acid signalling pathway restricts the development of the arbuscular mycorrhizal association in tomato, J. Plant Growth Regul., 27, 221, 10.1007/s00344-008-9049-4 Hodge, 2000, Microbial ecology of the arbuscular mycorrhiza, FEMS Microbiol. Ecol., 32, 91, 10.1111/j.1574-6941.2000.tb00702.x Howell, 2000, Induction of terpenoid synthesis in cotton roots and control of Rhizoctonia solani by seed treatment with Trichoderma virens, Phytopathology, 90, 248, 10.1094/PHYTO.2000.90.3.248 Horner, 2012, The oomycete Pythium oligandrum expresses putative effectors during mycoparasitism of Phytophthora infestans and is amenable to transformation, Fungal Biol., 116, 24, 10.1016/j.funbio.2011.09.004 Ito, 2004, Tomatine and lycotetraose, hydrolysis products of alpha-tomatine by Fusarium oxysporum tomatinase, suppress induced defense responses in tomato cells, FEBS Lett., 571, 31, 10.1016/j.febslet.2004.06.053 Jacobs, 2011, Broad-spectrum suppression of innate immunity is required for colonization of Arabidopsis roots by the fungus Piriformospora indica, Plant Physiol., 156, 726, 10.1104/pp.111.176446 Javot, 2007, Phosphate in the arbuscular mycorrhizal symbiosis: transport properties and regulatory roles, Plant, Cell Environ., 30, 310, 10.1111/j.1365-3040.2006.01617.x Jones, 2004, Plant and mycorrhizal regulation of rhizodeposition, New Phytol., 163, 459, 10.1111/j.1469-8137.2004.01130.x Jones, 2006, The plant immune system, Nature, 444, 323, 10.1038/nature05286 Jung, 2012, Mycorrhiza-induced resistance and priming of plant defenses, J. Chem. Ecol., 38, 651, 10.1007/s10886-012-0134-6 Kamper, 2006, Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis, Nature, 444, 97, 10.1038/nature05248 Kapat, 1998, Effect of two isolates of Trichoderma harzianum on the activity of hydrolytic enzymes produced by Botrytis cinerea, Physiol. Mol. Plant Pathol., 52, 127, 10.1006/pmpp.1997.0140 Kavroulakis, 2007, Role of ethylene in the protection of tomato plants against soil-borne fungal pathogens conferred by an endophytic Fusarium solani strain, J. Exp. Bot., 58, 3853, 10.1093/jxb/erm230 Kawahara, 2012, Simultaneous RNA-Seq analysis of a mixed transcriptome of rice and blast fungus interaction, PLoS ONE, 7, e49423, 10.1371/journal.pone.0049423 Kishimoto, 2010, Perception of the chitin oligosaccharides contributes to disease resistance to blast fungus Magnaporthe oryzae in rice, Plant J., 64, 343, 10.1111/j.1365-313X.2010.04328.x Kloppholz, 2011, A secreted fungal effector of Glomus intraradices promotes symbiotic biotrophy, Curr. Biol., 21, 1204, 10.1016/j.cub.2011.06.044 Koltai, 2010, A tomato strigolactone-impaired mutant displays aberrant shoot morphology and plant interactions, J. Exp. Bot., 61, 1739, 10.1093/jxb/erq041 Kretschmer, 2009, Fungicide-driven evolution and molecular basis of multidrug resistance in field populations of the grey mould fungus Botrytis cinerea, PLoS Pathog., 5, e1000696, 10.1371/journal.ppat.1000696 Kubicek, 2011, Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma, Genome Biol., 12, 10.1186/gb-2011-12-4-r40 Kubota, 2005, Co-occurrence of Arum- and Paris-type morphologies of arbuscular mycorrhizae in cucumber and tomato, Mycorrhiza, 15, 73, 10.1007/s00572-004-0299-0 Kyndt, 2012, Transcriptional reprogramming by root knot and migratory nematode infection in rice, New Phytol., 196, 887, 10.1111/j.1469-8137.2012.04311.x Lahrmann, 2012, Opprimo ergo sum-evasion and suppression in the root endophytic fungus Piriformospora indica, Mol. Plant Microbe Interact., 25, 727, 10.1094/MPMI-11-11-0291 Larkin, 1999, Mechanisms of action and dose-response relationships governing biological control of Fusarium wilt oftomato by nonpathogenic Fusarium spp, Phytopathology, 89, 1152, 10.1094/PHYTO.1999.89.12.1152 Larkin, 2002, Effects of varying environmental conditions on biological control of Fusarium wilt of tomato by nonpathogenic Fusarium spp, Phytopathology, 92, 1160, 10.1094/PHYTO.2002.92.11.1160 Larroque, 2012, The unique architecture and function of cellulose-interacting proteins in oomycetes revealed by genomic and structural analyses, BMC Genomics, 13, 605, 10.1186/1471-2164-13-605 Le Floch, 2005, Characterisation of the early events in atypical tomato root colonisation by a biocontrol agent, Pythium oligandrum, Plant Physiol. Biochem., 43, 1, 10.1016/j.plaphy.2004.10.005 Le Floch, 2003, Enhancement of development and induction of resistance in tomato plants by the antagonist, Pythium oligandrum, Agronomie, 23, 455, 10.1051/agro:2003018 Le Floch, 2009, Combining the oomycete Pythium oligandrum with two other antagonistic fungi: root relationships and tomato grey mold biocontrol, Biol. Control, 50, 288, 10.1016/j.biocontrol.2009.04.013 Lerat, 2003, Variable carbon-sink strength of different Glomus mosseae strains colonizing barley roots, Can. J. Bot., 81, 886, 10.1139/b03-070 Leroch, 2011, Fungicide resistance phenotypes of Botrytis cinerea isolates from commercial vineyards in south west Germany, J. Phytopathol., 159, 63, 10.1111/j.1439-0434.2010.01719.x Leroux, 2007, Chemical control of Botrytis and its resistance to chemical fungicides, 195 Lévesque, 2010, Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire, Genome Biol., 11, 10.1186/gb-2010-11-7-r73 L’Haridon, 2011, Isolation of differentially expressed genes during interactions between tomato cells and a protective or a non-protective strain of Fusarium oxysporum, Physiol. Mol. Plant Pathol., 76, 9, 10.1016/j.pmpp.2011.07.001 Lioussanne, 2008, Mycorrhizal colonization with Glomus intraradices and development stage of transformed tomato roots significantly modify the chemotactic response of zoospores of the pathogen Phytophthora nicotianae, Soil Biol. Biochem., 40, 2217, 10.1016/j.soilbio.2008.04.013 Lioussanne, 2009, Role of the modification in root exudation induced by arbuscular mycorrhizal colonization on the intraradical growth of Phytophthora nicotianae in tomato, Mycorrhiza, 19, 443, 10.1007/s00572-009-0257-y Liu, 2009, Study on the anthraquinones separated from the cultivation of Trichoderma harzianum strain Th-R16 and their biological activity, J. Agric. Food Chem., 57, 7288, 10.1021/jf901405c Logi, 1998, Cellular events involved in survival of individual arbuscular mycorrhizal symbionts growing in the absence of the host, Appl. Environ. Microbiol., 64, 3473, 10.1128/AEM.64.9.3473-3479.1998 Lopez-Raez, 2010, Hormonal and transcriptional profiles highlight common and differential host responses to arbuscular mycorrhizal fungi and the regulation of the oxylipin pathway, J. Exp. Bot., 61, 2589, 10.1093/jxb/erq089 Ma, 2010, Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium, Nature, 464, 367, 10.1038/nature08850 Maillet, 2011, Fungal lipochitooligosaccharide symbiotic signals in arbuscular mycorrhiza, Nature, 469, 58-U1501, 10.1038/nature09622 Malmierca, 2012, Involvement of Trichoderma trichothecenes in the biocontrol activity and induction of plant defense-related genes, Appl. Environ. Microbiol., 78, 4856, 10.1128/AEM.00385-12 Marschner, 2003, Changes in bacterial community structure induced by mycorrhizal colonisation in split-root maize, Plant Soil, 251, 279, 10.1023/A:1023034825871 Martin, 2008, The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis, Nature, 452, 88-U87, 10.1038/nature06556 Martin, 2010, Perigord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis, Nature, 464, 1033, 10.1038/nature08867 Masunaka, 2009, Visualization of Ralstonia solanacearum cells during biocontrol of bacterial wilt disease in tomato with Pythium oligandrum, J. Gen. Plant Pathol., 75, 281, 10.1007/s10327-009-0173-1 Masunaka, 2010, Distribution and expression of elicitin-like protein genes of the biocontrol agent Pythium oligandrum, J. Phytopathol., 158, 417, 10.1111/j.1439-0434.2009.01641.x Mathys, 2012, Genome-wide characterization of ISR induced in Arabidopsis thaliana by Trichoderma hamatum T382 against Botrytis cinerea infection, Front. Plant Sci., 3, 108, 10.3389/fpls.2012.00108 McAllister, 1994, Interactions between Trichoderma koningii, Fusarium solani and Glomus mosseae-effects on plant growth, arbuscular mycorrhizas and the saprophyte inoculants, Soil Biol. Biochem., 26, 1363, 10.1016/0038-0717(94)90218-6 McArthur, 1992, Resistance responses of potato to vesicular–arbuscular mycorrhizal fungi under varying abiotic phosphorus levels, Plant Physiol., 100, 341, 10.1104/pp.100.1.341 Mersmann, 2010, Ethylene signaling regulates accumulation of the FLS2 receptor and is required for the oxidative burst contributing to plant immunity, Plant Physiol., 154, 391, 10.1104/pp.110.154567 Miersch, 2008, Hydroxylated jasmonates are commonly occurring metabolites of jasmonic acid and contribute to a partial switch-off in jasmonate signaling, New Phytol., 177, 114, 10.1111/j.1469-8137.2007.02252.x Millet, 2010, Innate immune responses activated in Arabidopsis roots by microbe-associated molecular patterns, Plant Cell, 22, 973, 10.1105/tpc.109.069658 Miya, 2007, CERK1, a LysM receptor kinase, is essential for chitin elicitor signaling in Arabidopsis, Proc. Natl. Acad. Sci. U.S.A., 104, 19613, 10.1073/pnas.0705147104 Molitor, 2011, Barley leaf transcriptome and metabolite analysis reveals new aspects of compatibility and Piriformospora indica-mediated systemic induced resistance to powdery mildew, Mol. Plant Microbe Interact., 24, 1427, 10.1094/MPMI-06-11-0177 Monte, 2001, Understanding Trichoderma: between biotechnology and microbial ecology, Int. Microbiol., 4, 1 Moran-Diez, 2009, The ThPG1 endopolygalacturonase is required for the Trichoderma harzianum-plant beneficial interaction, Mol. Plant Microbe Interact., 22, 1021, 10.1094/MPMI-22-8-1021 Mukherjee, 2012, Trichoderma–plant–pathogen interactions: advances in genetics of biological control, Ind. J. Microbiol., 52, 522, 10.1007/s12088-012-0308-5 Mutawila, 2011, Grapevine cultivar variation to pruning wound protection by Trichoderma species against trunk pathogens, Phytopathol. Mediterr., 50, S264 Nahalkova, 2008, Tomato root colonization by fluorescent-tagged pathogenic and protective strains of Fusarium oxysporum in hydroponic culture differs from root colonization in soil, FEMS Microbiol. Lett., 286, 152, 10.1111/j.1574-6968.2008.01241.x Nonomura, 2010, Polymorphic change of appressoria by the tomato powdery mildew Oidium neolycopersici on host tomato leaves reflects multiple unsuccessful penetration attempts, Fungal Biol., 114, 917, 10.1016/j.funbio.2010.08.008 Oldroyd, 2013, Speak friend, and enter: signaling systems that promote beneficial symbiotic associations in plants, Nat. Rev. Microbiol., 11, 252, 10.1038/nrmicro2990 Olivain, 2006, Colonization of tomato root by pathogenic and nonpathogenic Fusarium oxysporum strains inoculated together and separately into the soil, Appl. Environ. Microbiol., 72, 1523, 10.1128/AEM.72.2.1523-1531.2006 Olivain, 2003, Colonization of flax roots and early physiological responses of flax cells inoculated with pathogenic and nonpathogenic strains of Fusarium oxysporum, Appl. Environ. Microbiol., 69, 5453, 10.1128/AEM.69.9.5453-5462.2003 Panina, 2007, Biocontrol and plant pathogenic Fusarium oxysporum-induced changes in phenolic compounds in tomato leaves and roots, J. Phytopathol., 155, 475, 10.1111/j.1439-0434.2007.01260.x Parniske, 2008, Arbuscular mycorrhiza: the mother of plant root endosymbioses, Nat. Rev. Microbiol., 6, 763, 10.1038/nrmicro1987 Paszkowski, 2006, Maize mutants affected at distinct stages of the arbuscular mycorrhizal symbiosis, Plant J., 47, 165, 10.1111/j.1365-313X.2006.02785.x Perazzolli, 2012, Downy mildew resistance induced by Trichoderma harzianum T39 in susceptible grapevines partially mimics transcriptional changes of resistant genotypes, BMC Genomics, 13, 660, 10.1186/1471-2164-13-660 Peskan-Berghofer, 2004, Association of Piriformospora indica with Arabidopsis thaliana roots represents a novel system to study beneficial plant-microbe interactions and involves early plant protein modifications in the endoplasmic reticulum and at the plasma membrane, Physiol. Plant., 122, 465, 10.1111/j.1399-3054.2004.00424.x Picard, 2000, Cytological effects of cellulases in the parasitism of Phytophthora parasitica by Pythium oligandrum, Appl. Environ. Microbiol., 66, 4305, 10.1128/AEM.66.10.4305-4314.2000 Pieterse, 2009, Networking by small-molecule hormones in plant immunity, Nat. Chem. Biol., 5, 308, 10.1038/nchembio.164 Pieterse, 1996, Systemic resistance in Arabidopsis induced by biocontrol bacteria is independent of salicylic acid accumulation and pathogenesis-related gene expression, Plant Cell, 8, 1225, 10.1105/tpc.8.8.1225 Pieterse, 1998, A novel signaling pathway controling induced systemic resistance in Arabidopsis, Plant Cell, 10, 1571, 10.1105/tpc.10.9.1571 Pinior, 1999, Plants colonized by AM fungi regulate further root colonization by AM fungi through altered root exudation, Can. J. Bot., 77, 891 Pozo, 2007, Unraveling mycorrhiza-induced resistance, Curr. Opin. Plant Biol., 10, 393, 10.1016/j.pbi.2007.05.004 Pozo, 2002, Localized versus systemic effect of arbuscular mycorrhizal fungi on defence responses to Phytophthora infection in tomato plants, J. Exp. Bot., 53, 525, 10.1093/jexbot/53.368.525 Pozo, 2010, Impact of arbuscular mycorrhizal symbiosis on plant response to biotic stress: the role of plant defence mechanisms, 193 Qiang, 2012, Piriformospora indica-a mutualistic basidiomycete with an exceptionally large plant host range, Mol. Plant Pathol., 13, 508, 10.1111/j.1364-3703.2011.00764.x Recorbet, 2013, Protein actors sustaining arbuscular mycorrhizal symbiosis: underground artists break the silence, New Phytol., 199, 26, 10.1111/nph.12287 Recorbet, 1998, Differential accumulation of beta-1,3-glucanase and chitinase isoforms in tomato roots in response to colonization by either pathogenic or non-pathogenic strains of Fusarium oxysporum, Microbiol. Res., 153, 257, 10.1016/S0944-5013(98)80009-8 Reino, 2008, Secondary metabolites from species of the biocontrol agent Trichoderma, Phytochem. Rev., 7, 89, 10.1007/s11101-006-9032-2 Rey, 1998, Interactions between tomato (Lycopersicon esculentum) root tissues and the mycoparasite Pythium oligandrum, Physiol. Mol. Plant Pathol., 53, 105, 10.1006/pmpp.1998.0159 Ron, 2004, The receptor for the fungal elicitor ethylene-inducing xylanase is a member of a resistance-like gene family in tomato, Plant Cell, 16, 1604, 10.1105/tpc.022475 Rotblat, 2002, Identification of an essential component of the elicitation active site of the EIX protein elicitor, Plant J., 32, 1049, 10.1046/j.1365-313X.2002.01490.x Salvioli, 2013, Systems biology and “omics” tools: a cooperation for next-generation mycorrhizal studies, Plant Sci., 203, 107, 10.1016/j.plantsci.2013.01.001 Sarma, 2011, Application of inorganic carrier-based formulations of fluorescent pseudomonads and Piriformospora indica on tomato plants and evaluation of their efficacy, J. Appl. Microbiol., 111, 456, 10.1111/j.1365-2672.2011.05062.x Schäfer, 2007, Root cell death and systemic effects of Piriformospora indica: a study on mutualism, FEMS Microbiol. Lett., 275, 1, 10.1111/j.1574-6968.2007.00848.x Schäfer, 2009, Manipulation of plant innate immunity and gibberellin as factor of compatibility in the mutualistic association of barley roots with Piriformospora indica, Plant J., 59, 461, 10.1111/j.1365-313X.2009.03887.x Scheffknecht, 2006, Root exudates of mycorrhizal tomato plants exhibit a different effect on microconidia germination of Fusarium oxysporum f. sp lycopersici than root exudates from non-mycorrhizal tomato plants, Mycorrhiza, 16, 365, 10.1007/s00572-006-0048-7 Schirmbock, 1994, Parallel formation and synergism of hydrolytic enzymes and peptaibol antibiotics, molecular mechanisms involved in the antagonistic action of Trichoderma harzianum against Phytopathogenic fungi, Appl. Environ. Microbiol., 60, 4364, 10.1128/AEM.60.12.4364-4370.1994 Seifi, 2013, Concurrent overactivation of the cytosolic glutamine synthetase and the GABA shunt in the ABA-deficient sitiens mutant of tomato leads to resistance against Botrytis cinerea, New Phytol., 199, 490, 10.1111/nph.12283 Sharma, 2008, Detection and identification of bacteria intimately associated with fungi of the order Sebacinales, Cell. Microbiol., 10, 2235, 10.1111/j.1462-5822.2008.01202.x Sherameti, 2008, The root colonizing endophyte Pirifomospora indica confers drought tolerance in Arabidopsis by stimulating the expression of drought stress–related genes in leaves, Mol. Plant Microbe Interact., 21, 799, 10.1094/MPMI-21-6-0799 Shoresh, 2010, Induced systemic resistance and plant responses to fungal biocontrol agents, Annu. Rev. Phytopathol., 48, 21, 10.1146/annurev-phyto-073009-114450 Smith, 2011, What is the significance of the arbuscular mycorrhizal colonisation of many economically important crop plants?, Plant Soil, 348, 63, 10.1007/s11104-011-0865-0 Smith, 2011, Roles of arbuscular mycorrhizas in plant phosphorus nutrition: interactions between pathways of phosphorus uptake in arbuscular mycorrhizal roots have important implications for understanding and manipulating plant phosphorus acquisition, Plant Physiol., 156, 1050, 10.1104/pp.111.174581 Sood, 2003, Chemotactic response of plant-growth-promoting bacteria towards roots of vesicular–arbuscular mycorrhizal tomato plants, FEMS Microbiol. Ecol., 45, 219, 10.1016/S0168-6496(03)00155-7 Stein, 2008, Systemic resistance in Arabidopsis conferred by the mycorrhizal fungus Piriformospora indica requires jasmonic acid signaling and the cytoplasmic function of NPR1, Plant Cell Physiol., 49, 1747, 10.1093/pcp/pcn147 Steinkellner, 2007, Flavonoids and strigolactones in root exudates as signals in symbiotic and pathogenic plant–fungus interactions, Molecules, 12, 1290, 10.3390/12071290 Takahashi, 2006, Beta-cyanoalanine synthase as a molecular marker for induced resistance by fungal glycoprotein elicitor and commercial plant activators, Phytopathology, 96, 908, 10.1094/PHYTO-96-0908 Takenaka, 2006, Novel elicitin-like proteins isolated from the cell wall of the biocontrol agent Pythium oligandrum induce defence-related genes in sugar beet, Mol. Plant Pathol., 7, 325, 10.1111/j.1364-3703.2006.00340.x Takenaka, 2003, Induction of defense reactions in sugar beet and wheat by treatment with cell wall protein fractions from the mycoparasite Pythium oligandrum, Phytopathology, 93, 1228, 10.1094/PHYTO.2003.93.10.1228 Takenaka, 2009, Foliar spray of a cell wall protein fraction from the biocontrol agent Pythium oligandrum induces defence-related genes and increases resistance against Cercospora leaf spot in sugar beet, J. Gen. Plant Pathol., 75, 340, 10.1007/s10327-009-0186-9 Takenaka, 2011, Implications of oligomeric forms of POD-1 and POD-2 proteins isolated from cell walls of the biocontrol agent Pythium oligandrum in relation to their ability to induce defense reactions in tomato, J. Plant Physiol., 168, 1972, 10.1016/j.jplph.2011.05.011 Tamietti, 1993, Physiological-response of tomato plants grown in Fusarium suppressive soil, J. Phytopathol., 138, 66, 10.1111/j.1439-0434.1993.tb01361.x Tanaka, 2012, Fungal endophytes of grasses, Curr. Opin. Plant Biol., 15, 462, 10.1016/j.pbi.2012.03.007 Tawaraya, 1996, Effect of onion (Allium cepa) root exudates on the hyphal growth of Gigaspora margarita, Mycorrhiza, 6, 57, 10.1007/s005720050106 Tejeda-Sartorius, 2008, Jasmonic acid influences mycorrhizal colonization in tomato plants by modifying the expression of genes involved in carbohydrate partitioning, Physiol. Plant., 133, 339, 10.1111/j.1399-3054.2008.01081.x 2012, The tomato genome sequence provides insights into fleshy fruit evolution, Nature, 485, 635, 10.1038/nature11119 Tian, 2010, Regulation of the nitrogen transfer pathway in the arbuscular mycorrhizal symbiosis: gene characterization and the coordination of expression with nitrogen flux, Plant Physiol., 153, 1175, 10.1104/pp.110.156430 Trillas, 2009, Interactions between nonpathogenic fungi and plants, Plant Innate Immun., 51, 321 Tucci, 2011, The beneficial effect of Trichoderma spp. on tomato is modulated by the plant genotype, Mol. Plant Pathol., 12, 341, 10.1111/j.1364-3703.2010.00674.x Vadassery, 2008, The role of auxins and cytokinins in the mutualistic interaction between Arabidopsis and Piriformospora indica, Mol. Plant Microbe Interact., 21, 1371, 10.1094/MPMI-21-10-1371 Vadassery, 2009, Monodehydroascorbate reductase 2 and dehydroascorbate reductase 5 are crucial for a mutualistic interaction between Piriformospora indica and Arabidopsis, J. Plant Physiol., 166, 1263, 10.1016/j.jplph.2008.12.016 Verma, 1998, Piriformospora indica, gen. et sp. nov., a new root-colonizing fungus, Mycologia, 90, 896, 10.2307/3761331 Vicedo, 2009, Hexanoic acid-induced resistance against Botrytis cinerea in tomato plants, Mol. Plant Microbe Interact., 22, 1455, 10.1094/MPMI-22-11-1455 Vierheilig, 2004, Further root colonization by arbuscular mycorrhizal fungi in already mycorrhizal plants is suppressed after a critical level of root colonization, J. Plant Physiol., 161, 339, 10.1078/0176-1617-01097 Vierheilig, 2003, Systemic inhibition of arbuscular mycorrhiza development by root exudates of cucumber plants colonized by Glomus mosseae, Mycorrhiza, 13, 167, 10.1007/s00572-002-0219-0 Vierheilig, 2002, Signalling in arbuscular mycorrhiza: facts and hypotheses, Adv. Exp. Med. Biol., 505, 23, 10.1007/978-1-4757-5235-9_3 Vierheilig, 2008, The biocontrol effect of mycorrhization on soilborne fungal pathogens and the autoregulation of the AM symbiosis: one mechanism, two effects?, 307 Vinale, 2009, Factors affecting the production of Trichoderma harzianum secondary metabolites during the interaction with different plant pathogens, Lett. Appl. Microbiol., 48, 705 Vinale, 2008, A novel role for Trichoderma secondary metabolites in the interactions with plants, Physiol. Mol. Plant Pathol., 72, 80, 10.1016/j.pmpp.2008.05.005 Vlot, 2009, Salicylic acid, a multifaceted hormone to combat disease, Annu. Rev. Phytopathol., 47, 177, 10.1146/annurev.phyto.050908.135202 Vogel, 2010, SlCCD7 controls strigolactone biosynthesis, shoot branching and mycorrhiza-induced apocarotenoid formation in tomato, Plant J., 61, 300, 10.1111/j.1365-313X.2009.04056.x Vos, 2012, Arbuscular mycorrhizal fungi reduce root-knot nematode penetration through altered root exudation of their host, Plant Soil, 354, 335, 10.1007/s11104-011-1070-x Vos, 2012, Mycorrhiza-induced resistance in banana acts on nematode host location andpenetration, Soil Biol. Biochem., 47, 60, 10.1016/j.soilbio.2011.12.027 Waller, 2008, Systemic and local modulation of plant responses by Piriformospora indica and related Sebacinales species, J. Plant Physiol., 165, 60, 10.1016/j.jplph.2007.05.017 Wamberg, 2003, The mycorrhizal fungus (Glomus intraradices) affects microbial activity in the rhizosphere of pea plants (Pisum sativum), Soil Biol. Biochem., 35, 1349, 10.1016/S0038-0717(03)00214-1 Wasternack, 2007, Jasmonates: an update on biosynthesis, signal transduction and action in plant stress response, growth and development, Ann. Bot., 100, 681, 10.1093/aob/mcm079 Williamson, 2007, Botrytis cinerea: the cause of grey mould disease, Mol. Plant Pathol., 8, 561, 10.1111/j.1364-3703.2007.00417.x Whipps, 2004, Prospects and limitations for mycorrhizas in biocontrol of root pathogens, Can. J. Bot., 82, 1198, 10.1139/b04-082 Woo, 2007, Exploiting the interactions between fungal antagonists, pathogens and the plant for biocontro, 107 Yang, 2013, Induced systemic resistance (ISR) signaling pathways involved in the Trichoderma hamatum – Tomato – Botrytis cinerea tripartite system, IOBC Bull., 89, 263 Yedidia, 1999, Induction of defense responses in cucumber plants (Cucumis sativus L.) by the biocontrol agent Trichoderma harzianum, Appl. Environ. Microbiol., 65, 1061, 10.1128/AEM.65.3.1061-1070.1999 Zamioudis, 2012, Modulation of host immunity by beneficial microbes, Mol. Plant Microbe Interact., 25, 139, 10.1094/MPMI-06-11-0179 Zimand, 1996, Effect of Trichoderma harzianum on Botrytis cinerea pathogenicity, Phytopathology, 86, 1255, 10.1094/Phyto-86-1255 Zipfel, 2004, Bacterial disease resistance in Arabidopsis through flagellin perception, Nature, 428, 764, 10.1038/nature02485 Zuccaro, 2011, Endophytic life strategies decoded by genome and transcriptome analyses of the mutualistic root symbiont Piriformospora indica, PLoS Pathog., 7, e1002290, 10.1371/journal.ppat.1002290