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Research paper thumbnail of Pythium oligandrum: an example of opportunistic success

Microbiology, 2012

Pythium oligandrum, a non-pathogenic soil-inhabiting oomycete, colonizes the root ecosystem of ma... more Pythium oligandrum, a non-pathogenic soil-inhabiting oomycete, colonizes the root ecosystem of many crop species. Whereas most members in the genus Pythium are plant pathogens, P. oligandrum distinguishes itself from the pathogenic species by its ability to protect plants from biotic stresses in addition to promoting plant growth. The success of P. oligandrum at controlling soilborne pathogens is partly associated with direct antagonism mediated by mycoparasitism and antimicrobial compounds. Interestingly, P. oligandrum has evolved with specific mechanisms to attack its prey even when these belong to closely related species. Of particular relevance is the question of how P. oligandrum distinguishes between self-and non-self cell wall degradation during the mycoparasitic process of pathogenic oomycete species. The ability of P. oligandrum to enter and colonize the root system before rapidly degenerating is one of the most striking features that differentiate it from all other known biocontrol fungal agents. In spite of this atypical behaviour, P. oligandrum sensitizes the plant to defend itself through the production of at least two types of microbe-associated molecular patterns, including oligandrin and cell wall protein fractions, which appear to be closely involved in the early events preceding activation of the jasmonic acid-and ethylene-dependent signalling pathways and subsequent localized and systemic induced resistance. The aim of this review is to highlight the expanding knowledge of the mechanisms by which P. oligandrum provides beneficial effects to plants and to explore the potential use of this oomycete or its metabolites as new disease management strategies.

Research paper thumbnail of Ability of Pythium oligandrum strains to protect Vitis vinifera L., by inducing plant resistance against Phaeomoniella chlamydospora, a pathogen involved in Esca, a grapevine trunk disease

Biological Control, 2016

h i g h l i g h t s P. oligandrum inocula colonized the rhizosphere throughout the experimental p... more h i g h l i g h t s P. oligandrum inocula colonized the rhizosphere throughout the experimental period. Plant root system colonization by P. oligandrum reduced P. chlamydospora necroses. Plant molecular responses differed according to treatments. P. oligandrum enhanced certain gene expression in P. chlamydospora infected plants.

Research paper thumbnail of Combining potential oomycete and bacterial biocontrol agents as a tool to fight tomato Rhizoctonia root rot

Research paper thumbnail of The Biocontrol Root-Oomycete, Pythium Oligandrum, Triggers Grapevine Resistance and Shifts in the Transcriptome of the Trunk Pathogenic Fungus, Phaeomoniella Chlamydospora

International Journal of Molecular Sciences

The worldwide increase in grapevine trunk diseases, mainly esca, represents a major threat for vi... more The worldwide increase in grapevine trunk diseases, mainly esca, represents a major threat for vineyard sustainability. Biocontrol of a pioneer fungus of esca, Phaeomoniella chlamydospora, was investigated here by deciphering the tripartite interaction between this trunk-esca pathogen, grapevine and the biocontrol-oomycete, Pythium oligandrum. When P. oligandrum colonizes grapevine roots, it was observed that the wood necroses caused by P. chlamydospora were significantly reduced. Transcriptomic analyses of plant and fungus responses were performed to determine the molecular events occurring, with the aim to relate P.chlamydospora degradation of wood to gene expression modulation. Following P. oligandrum-root colonization, major transcriptomic changes occurred both, in the grapevine-defense system and in the P. chlamydospore-virulence factors. Grapevine-defense was enhanced in response to P. chlamydospora attacks, with P. oligandrum acting as a plant-systemic resistance inducer, pro...

Research paper thumbnail of Correction for Compant et al., “Draft Genome Sequence of the Root-Colonizing Fungus Trichoderma harzianum B97”

Research paper thumbnail of Draft Genome Sequence of the Root-Colonizing FungusTrichoderma harzianumB97

Genome Announcements

ABSTRACTTrichoderma harzianumis one of the most beneficial microorganisms applied on diverse crop... more ABSTRACTTrichoderma harzianumis one of the most beneficial microorganisms applied on diverse crops against biotic and abiotic stresses and acts also as a plant growth-promoting fungus. Here, we report the genome ofT. harzianumB97, originating from a French agricultural soil and used as a biofertilizer that can tolerate abiotic stresses.

Research paper thumbnail of Draft Genome Sequence of Biocontrol AgentPythium oligandrumStrain Po37, an Oomycota

Genome Announcements, 2016

The oomycotaPythium oligandrumPo37 is used as a biocontrol agent of plant diseases. Here, we pres... more The oomycotaPythium oligandrumPo37 is used as a biocontrol agent of plant diseases. Here, we present the first draft of theP. oligandrumPo37 genome sequence, which comprises 725 scaffolds with a total length of 35.9 Mb and 11,695 predicted protein-coding genes.

Research paper thumbnail of Lutte biologique contre un champignon pathogène impliqué dans l’esca de la vigne, par utilisation de l’oomycète Pythium oligandrum

Http Www Theses Fr, Oct 24, 2013

Biocontrol research based on the use of microorganisms is expanding very rapidly. However, the us... more Biocontrol research based on the use of microorganisms is expanding very rapidly. However, the use of such bioncontrol agents is still too inconsistent to effectively protect plants in field applications. This phenomenon is often attributed to the non-persistence of biocontrol agents in the rhizosphere or on the plants. In order to reduce the risk of this happening, one solution consists in using microorganisms that are isolated from the plants needing protection. In this thesis, an oomycete called Pythium oligandrum, which colonizes the rhizosphere of many plants, including grapevine, was assessed for the control of esca, a grapevine trunk disease for which no control method is currently available. P. oligandrum strains have been isolated from the rhizosphere of vines cultivated in 3 winegrowing regions (12 grapevines) of Bordeaux with different types of soil: stony-sandy, silty and stony. Analyses of fungal and bacterial communities using a molecular fingerprinting method (Single Strand Conformation Polymorphism) showed that, unlike bacteria, the fungal species varied according to the sampling region. Roots of all the vines sampled were colonized by echinulated-oospore Pythium spp., with P. oligandrum strains predominating. Phylogenetic analyses based on the genes encoding the cytochrome oxidase I and one tubulin allowed these strains to be clustered into three groups. The sequencing of the elicitin-like genes, whose proteins are key components in inducing systemic resistance in plants, showed that each strain held at least one gene encoding for each of the two kinds of P. oligandrum elicitors (i.e. oligandrin and Cell Wall Proteins). Sequencing and molecular fingerprinting analyses showed thus that the type of soil and the rhizosphere microbiota did not shape the population structure of P. oligandrum. However, other factors such as the different kinds of rootstock and weeding management can also have an influence on the root colonization by P. oligandrum. The relationship between P. oligandrum and grapevine was studied using a transcriptomic approach (microarray Vitis vinifera, 29 549 genes). The results highlighted the modifications induced by young vines in response to P. oligandrum root colonization, in the genetic expression of several genes belonging to different metabolic pathways. Two aspects, that are usually opposed, were observed: P. oligandrum was perceived by the plant either (i) as a pathogen because certain defence reactions were triggered (e.g. calcium signalling, resistance genes, abscissic acid metabolism) or as (ii) a symbiotic microorganism since several transcriptional changes were similar to those reported in symbiotic interactions (e.g. induction of subtilase genes). An assay aimed at protecting grapevine against a pathogenic fungus involved in esca, and known to be responsible for wood necrosis, i.e. Phaeomoniella chlamydospora, was carried out. The root colonization by P. oligandrum was associated with a reduction in the length of necroses. In line with this result, transcriptomic analyses by microarrays and RT-qPCR showed overexpression of several genes, particularly those of the ethylene pathway. Some of these induced genes could be thus used as resistance markers, but this needs to be validated in further experiments.

Research paper thumbnail of Pythium oligandrum: an example of opportunistic success

Microbiology, 2012

Pythium oligandrum, a non-pathogenic soil-inhabiting oomycete, colonizes the root ecosystem of ma... more Pythium oligandrum, a non-pathogenic soil-inhabiting oomycete, colonizes the root ecosystem of many crop species. Whereas most members in the genus Pythium are plant pathogens, P. oligandrum distinguishes itself from the pathogenic species by its ability to protect plants from biotic stresses in addition to promoting plant growth. The success of P. oligandrum at controlling soilborne pathogens is partly associated with direct antagonism mediated by mycoparasitism and antimicrobial compounds. Interestingly, P. oligandrum has evolved with specific mechanisms to attack its prey even when these belong to closely related species. Of particular relevance is the question of how P. oligandrum distinguishes between self-and non-self cell wall degradation during the mycoparasitic process of pathogenic oomycete species. The ability of P. oligandrum to enter and colonize the root system before rapidly degenerating is one of the most striking features that differentiate it from all other known biocontrol fungal agents. In spite of this atypical behaviour, P. oligandrum sensitizes the plant to defend itself through the production of at least two types of microbe-associated molecular patterns, including oligandrin and cell wall protein fractions, which appear to be closely involved in the early events preceding activation of the jasmonic acid-and ethylene-dependent signalling pathways and subsequent localized and systemic induced resistance. The aim of this review is to highlight the expanding knowledge of the mechanisms by which P. oligandrum provides beneficial effects to plants and to explore the potential use of this oomycete or its metabolites as new disease management strategies.

Research paper thumbnail of Ability of Pythium oligandrum strains to protect Vitis vinifera L., by inducing plant resistance against Phaeomoniella chlamydospora, a pathogen involved in Esca, a grapevine trunk disease

Biological Control, 2016

h i g h l i g h t s P. oligandrum inocula colonized the rhizosphere throughout the experimental p... more h i g h l i g h t s P. oligandrum inocula colonized the rhizosphere throughout the experimental period. Plant root system colonization by P. oligandrum reduced P. chlamydospora necroses. Plant molecular responses differed according to treatments. P. oligandrum enhanced certain gene expression in P. chlamydospora infected plants.

Research paper thumbnail of Combining potential oomycete and bacterial biocontrol agents as a tool to fight tomato Rhizoctonia root rot

Research paper thumbnail of The Biocontrol Root-Oomycete, Pythium Oligandrum, Triggers Grapevine Resistance and Shifts in the Transcriptome of the Trunk Pathogenic Fungus, Phaeomoniella Chlamydospora

International Journal of Molecular Sciences

The worldwide increase in grapevine trunk diseases, mainly esca, represents a major threat for vi... more The worldwide increase in grapevine trunk diseases, mainly esca, represents a major threat for vineyard sustainability. Biocontrol of a pioneer fungus of esca, Phaeomoniella chlamydospora, was investigated here by deciphering the tripartite interaction between this trunk-esca pathogen, grapevine and the biocontrol-oomycete, Pythium oligandrum. When P. oligandrum colonizes grapevine roots, it was observed that the wood necroses caused by P. chlamydospora were significantly reduced. Transcriptomic analyses of plant and fungus responses were performed to determine the molecular events occurring, with the aim to relate P.chlamydospora degradation of wood to gene expression modulation. Following P. oligandrum-root colonization, major transcriptomic changes occurred both, in the grapevine-defense system and in the P. chlamydospore-virulence factors. Grapevine-defense was enhanced in response to P. chlamydospora attacks, with P. oligandrum acting as a plant-systemic resistance inducer, pro...

Research paper thumbnail of Correction for Compant et al., “Draft Genome Sequence of the Root-Colonizing Fungus Trichoderma harzianum B97”

Research paper thumbnail of Draft Genome Sequence of the Root-Colonizing FungusTrichoderma harzianumB97

Genome Announcements

ABSTRACTTrichoderma harzianumis one of the most beneficial microorganisms applied on diverse crop... more ABSTRACTTrichoderma harzianumis one of the most beneficial microorganisms applied on diverse crops against biotic and abiotic stresses and acts also as a plant growth-promoting fungus. Here, we report the genome ofT. harzianumB97, originating from a French agricultural soil and used as a biofertilizer that can tolerate abiotic stresses.

Research paper thumbnail of Draft Genome Sequence of Biocontrol AgentPythium oligandrumStrain Po37, an Oomycota

Genome Announcements, 2016

The oomycotaPythium oligandrumPo37 is used as a biocontrol agent of plant diseases. Here, we pres... more The oomycotaPythium oligandrumPo37 is used as a biocontrol agent of plant diseases. Here, we present the first draft of theP. oligandrumPo37 genome sequence, which comprises 725 scaffolds with a total length of 35.9 Mb and 11,695 predicted protein-coding genes.

Research paper thumbnail of Lutte biologique contre un champignon pathogène impliqué dans l’esca de la vigne, par utilisation de l’oomycète Pythium oligandrum

Http Www Theses Fr, Oct 24, 2013

Biocontrol research based on the use of microorganisms is expanding very rapidly. However, the us... more Biocontrol research based on the use of microorganisms is expanding very rapidly. However, the use of such bioncontrol agents is still too inconsistent to effectively protect plants in field applications. This phenomenon is often attributed to the non-persistence of biocontrol agents in the rhizosphere or on the plants. In order to reduce the risk of this happening, one solution consists in using microorganisms that are isolated from the plants needing protection. In this thesis, an oomycete called Pythium oligandrum, which colonizes the rhizosphere of many plants, including grapevine, was assessed for the control of esca, a grapevine trunk disease for which no control method is currently available. P. oligandrum strains have been isolated from the rhizosphere of vines cultivated in 3 winegrowing regions (12 grapevines) of Bordeaux with different types of soil: stony-sandy, silty and stony. Analyses of fungal and bacterial communities using a molecular fingerprinting method (Single Strand Conformation Polymorphism) showed that, unlike bacteria, the fungal species varied according to the sampling region. Roots of all the vines sampled were colonized by echinulated-oospore Pythium spp., with P. oligandrum strains predominating. Phylogenetic analyses based on the genes encoding the cytochrome oxidase I and one tubulin allowed these strains to be clustered into three groups. The sequencing of the elicitin-like genes, whose proteins are key components in inducing systemic resistance in plants, showed that each strain held at least one gene encoding for each of the two kinds of P. oligandrum elicitors (i.e. oligandrin and Cell Wall Proteins). Sequencing and molecular fingerprinting analyses showed thus that the type of soil and the rhizosphere microbiota did not shape the population structure of P. oligandrum. However, other factors such as the different kinds of rootstock and weeding management can also have an influence on the root colonization by P. oligandrum. The relationship between P. oligandrum and grapevine was studied using a transcriptomic approach (microarray Vitis vinifera, 29 549 genes). The results highlighted the modifications induced by young vines in response to P. oligandrum root colonization, in the genetic expression of several genes belonging to different metabolic pathways. Two aspects, that are usually opposed, were observed: P. oligandrum was perceived by the plant either (i) as a pathogen because certain defence reactions were triggered (e.g. calcium signalling, resistance genes, abscissic acid metabolism) or as (ii) a symbiotic microorganism since several transcriptional changes were similar to those reported in symbiotic interactions (e.g. induction of subtilase genes). An assay aimed at protecting grapevine against a pathogenic fungus involved in esca, and known to be responsible for wood necrosis, i.e. Phaeomoniella chlamydospora, was carried out. The root colonization by P. oligandrum was associated with a reduction in the length of necroses. In line with this result, transcriptomic analyses by microarrays and RT-qPCR showed overexpression of several genes, particularly those of the ethylene pathway. Some of these induced genes could be thus used as resistance markers, but this needs to be validated in further experiments.