Nicolas Denancé

Fungal mycoparasitism is commonly viewed as a broadly conserved lifestyle relying on the secretion of cell wall-degrading enzymes and specialized metabolites. However, whether Trichoderma deploys a universal antagonistic program or dynamically adapts its molecular arsenal according to prey identity remains largely unknown. Here, we investigated the phenotypic and transcriptomic responses of four highly antagonistic Trichoderma atroviride strains confronted with damping off pathogens from three phylogenetically distinct lineages: the ascomycete Alternaria brassicicola , the basidiomycete Rhizoctonia solani , and the oomycete Globisporangium ultimum . In vitro confrontation assays were performed between the four T. atroviride strains and nine pathogen strains (three strains per species). Despite notable intraspecific variation in pathogen sensitivity, all four T. atroviride strains remained highly effective against all tested pathogens. Comparative RNA-seq analyses during direct confrontation with one representative strain per pathogen species revealed strong prey-dependent transcriptional plasticity. Interactions with the two fungal pathogens elicited a robust induction of classical mycoparasitic machinery, including glycoside hydrolases, secreted peptidases, and effector-like proteins, whereas these responses were markedly attenuated in interaction with G. ultimum . Specialized metabolite biosynthetic genes were broadly induced across all interactions, but with largely distinct gene sets depending on the pathogen, with the strongest divergence observed for confrontation with G. ultimum . Beyond this shared response, each fungal pathogen also triggered a distinct host-specific program. In response to A. brassicicola and R. solani , T. atroviride induced distinct sets of genes associated with cell wall organization, while the response to R. solani specifically involved the activation of peroxisomal functions and aromatic amino acid biosynthesis pathways. Receptors potentially involved in pathogen perception also showed pathogen-dependent expression patterns, with distinct GPCRs (G protein-coupled receptors) overexpressed depending on the pathogen encountered. NLRs (NOD-like receptors) displayed a similar pattern, although overexpression was detected only in response to A. brassicicola and G. ultimum . Together, these results demonstrate that T. atroviride does not rely on a fixed mycoparasitic program but instead dynamically remodels its transcriptome according to prey identity, revealing a high degree of transcriptional plasticity underlying broad-spectrum antagonism.

Trichoderma species are widely used as biological control agents due to their ability to parasitize plant pathogens. However, substantial variability in mycoparasitic performance exists among strains, even within the same species, and the underlying molecular mechanisms remain poorly understood. Here, we performed comparative genomic and transcriptomic analyses of six Trichoderma atroviride strains exhibiting contrasting mycoparasitic performance (weakly or highly parasitic; WP or HP) against Alternaria brassicicola, Rhizoctonia solani, and Globisporangium ultimum.Comparative genomics revealed limited strain-specific differences, mainly restricted to NLR (NOD-like receptor) repertoires, with certain NLR-coding genes absent from WP strain genomes compared to HP strains, while overall genomic variation remained low. In contrast, transcriptomic analyses revealed strong differences in gene expression dynamics between HP and WP strains.Co-expression network analysis identified two modules associated with mycoparasitic performance. The first was specifically induced in response to pathogen contact and was enriched in genes encoding cell wall-degrading enzymes, with stronger expression in HP strains. The second module was more broadly overexpressed in HP strains across all conditions and included genes involved in detoxification and defense-related pathways. In addition, this module encompassed genes involved in specialized metabolite biosynthesis and effector-like protein secretion, with WP and HP strains differentially expressing distinct gene subsets within these categories.Together, these results provide a comprehensive framework for identifying the molecular drivers of mycoparasitic performance in T. atroviride. This study deepens our understanding of the functional diversity within the species and establishes a robust foundation for the future development of molecular markers to predict strain efficiency.

Trichoderma species are widely used as biological control agents due to their ability to parasitize plant pathogens. However, substantial variability in mycoparasitic performance exists among strains, even within the same species, and the underlying molecular mechanisms remain poorly understood. Here, we performed comparative genomic and transcriptomic analyses of six Trichoderma atroviride strains exhibiting contrasting mycoparasitic performance (weakly or highly parasitic; WP or HP) against Alternaria brassicicola , Rhizoctonia solani , and Globisporangium ultimum . Comparative genomics revealed limited strain-specific differences, mainly restricted to NLR (NOD-like receptor) repertoires, with certain NLR-coding genes absent from WP strain genomes compared to HP strains, while overall genomic variation remained low. In contrast, transcriptomic analyses revealed strong differences in gene expression dynamics between HP and WP strains. Co-expression network analysis identified two modules associated with mycoparasitic performance. The first was specifically induced in response to pathogen contact and was enriched in genes encoding cell wall-degrading enzymes, with stronger expression in HP strains. The second module was more broadly overexpressed in HP strains across all conditions and included genes involved in detoxification and defense-related pathways. In addition, this module encompassed genes involved in specialized metabolite biosynthesis and effector-like protein secretion, with WP and HP strains differentially expressing distinct gene subsets within these categories. Together, these results provide a comprehensive framework for identifying the molecular drivers of mycoparasitic performance in T. atroviride . This study deepens our understanding of the functional diversity within the species and establishes a robust foundation for the future development of molecular markers to predict strain efficiency.

Trichoderma is a genus of beneficial fungi widely used in agriculture disease suppression, plant growth promotion, and soil health improvement. Although some studies have shown that Trichoderma spp. can be seed‐borne, albeit at low frequency, no specific study has so far focused on the diversity of Trichoderma isolates capable of adapting to this particular environment. Over 2 years of routine seed health analyses, we isolated 107 Trichoderma strains associated with seeds from 32 cultivated plant species, and we investigated the diversity of this specific library using multi‐locus analysis. These isolates are distributed among 18 different species, but Trichoderma atroviride is by far the most frequent. R epresentative strains of each species all have the ability to parasitise damping‐off agents, although the intensity of parasitism can vary greatly from one strain to another and depending on the targeted plant pathogens. For two isolates of T. atroviride , we showed that these fungi can be transmitted from fruit to seed and limit the transmission of the plant pathogen Alternaria brassicicola . Furthermore, these strains stimulated seedling growth and provided protection against Globisporangium ultimum . Together, these findings support the benefits of focusing on certain selected seed‐borne Trichoderma which seem particularly well suited to improving seed health.

Xylella fastidiosa (Xf) is a phytopathogenic bacterium with a repertoire of self-replicating genetic elements, including plasmids, pathogenicity islands, and prophages. These elements provide potential avenues for horizontal gene transfer both within and between species and have the ability to confer new virulence traits, including the ability to colonize new host plants. However, they can also serve as a ‘footprint’ to type plasmid-bearing strains. Genome sequencing of several strains of Xf subsp. fastidiosa sequence type (ST) 1 from Mallorca Island, Spain, revealed the presence of a 38 kb plasmid (pXFAS_5235). In this study, we developed a PCR-based typing approach using primers targeting the traC gene to determine the presence of pXFAS_5235 plasmid or other plasmids carrying this gene in a world-wide collection of 65 strains X. fastidiosa from different subspecies and STs or in 226 plant samples naturally infected by the bacterium obtained from the different outbreaks of Xf in Spain. The traC gene was amplified only in the plant samples obtained from Mallorca Island infected by Xf subsp. fastidiosa ST1 and from all Spanish strains belonging to this ST. Maximum-likelihood phylogenetic tree of traC revealed a close relatedness among Spanish and Californian strains carrying similar plasmids. Our results confirm previous studies, which suggested that a single introduction event of Xf subsp. fastidiosa ST1 occurred in the Balearic Islands. Further studies on the presence and role of plasmids in Xf strains belonging to the same or different subspecies and STs can provide important information in studies of epidemiology, ecology, and evolution of this plant pathogen.

Food security is threatened by harmful pests whose impact may strongly differ among crops, agricultural practices and world regions. International movement of seed can be a pathway for pest dissemination into new geographic areas. The most damaging pests are regulated in some countries and/or regions of the world. Scientific evidence is crucial in taking such decisions. Seed testing is key in preventing movement of pests by seeds. It should target pests which have been selected based on defined scientific criteria. The International Seed Testing Association (ISTA) Reference Pest List summarizes scientific knowledge on the possible dissemination of pests through seeds in non‐vegetable plant species. Released as an evolving, free online tool, it currently contains 255 seed‐borne or seed‐contaminating pests in 11 plant species, including 126 host–pest combinations where seed is a pathway of spread (v7.0, Feb. 2021; https://www.seedtest.org/en/pest‐list‐tool‐_content‐‐‐1‐‐3477.html). The ISTA Reference Pest List should become a valuable source for risk assessors and policy makers.

Of American origin, a wide diversity of Xylella fastidiosa strains belonging to different subspecies have been reported in Europe since 2013 and its discovery in Italian olive groves. Strains from the subspecies multiplex (ST6 and ST7) were first identified in France in 2015 in urban and natural areas. To trace back the most probable scenario of introduction in France, the molecular evolution rate of this subspecies was estimated at 3.2165 × 10 ^-7 substitutions per site per year, based on heterochronous genome sequences collected worldwide. This rate allowed the dating of the divergence between French and American strains in 1987 for ST6 and in 1971 for ST7. The development of a new VNTR-13 scheme allowed tracing the spread of the bacterium in France, hypothesizing an American origin. Our results suggest that both sequence types were initially introduced and spread in Provence-Alpes-Côte d’Azur (PACA); then they were introduced in Corsica in two waves from the PACA bridgehead populations.

Significance: Plant cells are surrounded by an extracellular matrix known as the cell wall. We have analyzed the contribution of theArabidopsiscell wall to disease resistance to pathogens with different parasitic styles. Here, we demonstrate that plant cell walls are determinants of immune responses since modification of their composition in a set ofArabidopsiscell wall mutants has an impact on their disease resistance and fitness phenotypes. In these genotypes, we identified specific correlations between the amounts of specific wall carbohydrate epitopes and disease resistance/fitness phenotypes through mathematical analyses. These data support the relevant and specific function of plant cell wall composition in plant immune responses and provide the basis for using wall traits in crop breeding programs.

Plant cell walls are complex structures subject to dynamic remodeling in response to developmental and environmental cues, and play essential functions in disease resistance responses. We tested the specific contribution of plant cell walls to immunity by determining the susceptibility of a set of Arabidopsis cell wall mutants ( cwm ) to pathogens with different parasitic styles: a vascular bacterium, a necrotrophic fungus and a biotrophic oomycete. Remarkably, most cwm mutants tested (31/38; 81.6%) showed alterations in their resistance responses to at least one of these pathogens, in comparison to wild-type plants, illustrating the relevance of wall composition in determining disease resistance phenotypes. We found that the enhanced resistance of cwm plants to the necrotrophic and vascular pathogens negatively impacted on cwm fitness traits, like biomass and seed yield. Enhanced resistance of cwm plants is not only mediated by canonical immune pathways, like those modulated by phytohormones or Microbe-Associated Molecular Patterns, which are not de-regulated in all cwm tested. Pectin-enriched wall fractions isolated from cwm plants triggered immune responses in other plants, suggesting that wall-mediated defensive pathways might contribute to cwm resistance. Cell walls of cwm plants show a high diversity of composition alterations as revealed by glycome profiling that detect specific wall carbohydrate moieties. Mathematical analysis of glycome profiling data identified correlations between the amounts of specific wall carbohydrate moieties and disease resistance phenotypes of cwm plants. These data support the relevant and specific function of plant wall composition in plant immune response modulation and in balancing disease resistance/development trade-offs.