Identification of Tomato microRNAs in Late Response to Trichoderma atroviride.

The tomato (Solanum lycopersicum) is an important crop worldwide and is considered a model plant to study stress responses. Small RNAs (sRNAs), 21-24 nucleotides in length, are recognized as a conserved mechanism for regulating gene expression in eukaryotes. Plant endogenous sRNAs, such as microRNA (miRNA), have been involved in disease resistance. High-throughput RNA sequencing was used to analyze the miRNA profile of the aerial part of 30-day-old tomato plants after the application of the fungus Trichoderma atroviride to the seeds at the transcriptional memory state. Compared to control plants, ten differentially expressed (DE) miRNAs were identified in those inoculated with Trichoderma, five upregulated and five downregulated, of which seven were known (miR166a, miR398-3p, miR408, miR5300, miR6024, miR6027-5p, and miR9471b-3p), and three were putatively novel (novel miR257, novel miR275, and novel miR1767). miRNA expression levels were assessed using real-time quantitative PCR analysis. A plant sRNA target analysis of the DE miRNAs predicted 945 potential target genes, most of them being downregulated (84%). The analysis of KEGG metabolic pathways showed that most of the targets harbored functions associated with plant-pathogen interaction, membrane trafficking, and protein kinases. Expression changes of tomato miRNAs caused by Trichoderma are linked to plant defense responses and appear to have long-lasting effects.

SARS-CoV-2 RNA Detection in Wastewater and Its Effective Correlation with Clinical Data during the Outbreak of COVID-19 in Salamanca.

Wastewater treatment plants (WWTPs) are the final stage of the anthropogenic water cycle where a wide range of chemical and biological markers of human activity can be found. In COVID-19 disease contexts, wastewater surveillance has been used to infer community trends based on viral abundance and SARS-CoV-2 RNA variant composition, which has served to anticipate and establish appropriate protocols to prevent potential viral outbreaks. Numerous studies worldwide have provided reliable and robust tools to detect and quantify SARS-CoV-2 RNA in wastewater, although due to the high dilution and degradation rate of the viral RNA in such samples, the detection limit of the pathogen has been a bottleneck for the proposed protocols so far. The current work provides a comprehensive and systematic study of the different parameters that may affect the detection of SARS-CoV-2 RNA in wastewater and hinder its quantification. The results obtained using synthetic viral RNA as a template allow us to consider that 10 genome copies per µL is the minimum RNA concentration that provides reliable and consistent values for the quantification of SARS-CoV-2 RNA. RT-qPCR analysis of wastewater samples collected at the WWTP in Salamanca (western Spain) and at six pumping stations in the city showed that below this threshold, positive results must be confirmed by sequencing to identify the specific viral sequence. This allowed us to find correlations between the SARS-CoV-2 RNA levels found in wastewater and the COVID-19 clinical data reported by health authorities. The close match between environmental and clinical data from the Salamanca case study has been confirmed by similar experimental approaches in four other cities in the same region. The present methodological approach reinforces the usefulness of wastewater-based epidemiology (WBE) studies in the face of future pandemic outbreaks.

Effect of Trichoderma asperellum on Wheat Plants' Biochemical and Molecular Responses, and Yield under Different Water Stress Conditions.

Eight Trichoderma strains were evaluated for their potential to protect wheat seedlings against severe (no irrigation within two weeks) water stress (WS). Considering the plant fresh weight and phenotype, T. asperellum T140, which displays 1-aminocyclopropane-1-carboxylic acid deaminase activity and which is able to produce several phytohormones, was selected. The molecular and biochemical results obtained from 4-week-old wheat seedlings linked T140 application with a downregulation in the WS-response genes, a decrease in antioxidant activities, and a drop in the proline content, as well as low levels of hydrogen peroxide and malondialdehyde in response to severe WS. All of these responses are indicative of T140-primed seedlings having a higher tolerance to drought than those that are left untreated. A greenhouse assay performed under high nitrogen fertilization served to explore the long-term effects of T140 on wheat plants subjected to moderate (halved irrigation) WS. Even though all of the plants showed acclimation to moderate WS regardless of T140 application, there was a positive effect exerted by T. asperellum on the level of tolerance of the wheat plants to this stress. Strain T140 modulated the expression of a plant ABA-dependent WS marker and produced increased plant superoxide dismutase activity, which would explain the positive effect of Trichoderma on increasing crop yields under moderate WS conditions. The results demonstrate the effectiveness of T. asperellum T140 as a biostimulant for wheat plants under WS conditions, making them more tolerant to drought.

Antimicrobial secondary metabolites from agriculturally important fungi as next biocontrol agents.

Synthetic chemical pesticides have been used for many years to increase the yield of agricultural crops. However, in the future, this approach is likely to be limited due to negative impacts on human health and the environment. Therefore, studies of the secondary metabolites produced by agriculturally important microorganisms have an important role in improving the quality of the crops entering the human food chain. In this review, we have compiled information about the most important secondary metabolites of fungal species currently used in agriculture pest and disease management.

Synthesis of Trichodermin Derivatives and Their Antimicrobial and Cytotoxic Activities.

Trichothecene mycotoxins are recognized as highly bioactive compounds that can be used in the design of new useful bioactive molecules. In Trichoderma brevicompactum, the first specific step in trichothecene biosynthesis is carried out by a terpene cyclase, trichodiene synthase, that catalyzes the conversion of farnesyl diphosphate to trichodiene and is encoded by the tri5 gene. Overexpression of tri5 resulted in increased levels of trichodermin, a trichothecene-type toxin, which is a valuable tool in preparing new molecules with a trichothecene skeleton. In this work, we developed the hemisynthesis of trichodermin and trichodermol derivatives in order to evaluate their antimicrobial and cytotoxic activities and to study the chemo-modulation of their bioactivity. Some derivatives with a short chain at the C-4 position displayed selective antimicrobial activity against Candida albicans and they showed MIC values similar to those displayed by trichodermin. It is important to highlight the cytotoxic selectivity observed for compounds 9, 13, and 15, which presented average IC50 values of 2 µg/mL and were cytotoxic against tumorigenic cell line MCF-7 (breast carcinoma) and not against Fa2N4 (non-tumoral immortalized human hepatocytes).

Novel aspinolide production by Trichoderma arundinaceum with a potential role in Botrytis cinerea antagonistic activity and plant defence priming.

Harzianum A (HA), a trichothecene produced by Trichoderma arundinaceum, has recently been described to have antagonistic activity against fungal plant pathogens and to induce plant defence genes. In the present work, we have shown that a tri5 gene-disrupted mutant that lacks HA production overproduces two polyketides, aspinolides B and C, which were not detected in the wild-type strain. Furthermore, four new aspinolides (D-G) were characterized. These compounds confirm that a terpene-polyketide cross-pathway exists in T. arundinaceum, and they may be responsible for the antifungal activity and the plant sensitization effect observed with the tri5-disrupted mutant. In addition, the molecular changes involving virulence factors in the phytopathogenic fungus Botrytis cinerea 98 (Bc98) during interaction with T. arundinaceum were investigated. The expression of genes involved in the production of botrydial by Bc98 was relatively repressed by HA, whereas other virulence genes of this pathogen were induced by the presence of T. arundinaceum, for example atrB and pg1 which encode for an ABC transporter and endopolygalacturonase 1 respectively. In addition, the interaction with Bc98 significantly repressed the production of HA by T. arundinaceum, indicating that a bidirectional transcriptional regulation is established between these two antagonistic fungi.

Identifying beneficial qualities of Trichoderma parareesei for plants.

Trichoderma parareesei and Trichoderma reesei (teleomorph Hypocrea jecorina) produce cellulases and xylanases of industrial interest. Here, the anamorphic strain T6 (formerly T. reesei) has been identified as T. parareesei, showing biocontrol potential against fungal and oomycete phytopathogens and enhanced hyphal growth in the presence of tomato exudates or plant cell wall polymers in in vitro assays. A Trichoderma microarray was used to examine the transcriptomic changes in T6 at 20 h of interaction with tomato plants. Out of a total 34,138 Trichoderma probe sets deposited on the microarray, 250 showed a significant change of at least 2-fold in expression in the presence of tomato plants, with most of them being downregulated. T. parareesei T6 exerted beneficial effects on tomato plants in terms of seedling lateral root development, and in adult plants it improved defense against Botrytis cinerea and growth promotion under salt stress. Time course expression patterns (0 to 6 days) observed for defense-related genes suggest that T6 was able to prime defense responses in the tomato plants against biotic and abiotic stresses. Such responses undulated, with a maximum upregulation of the jasmonic acid (JA)/ethylene (ET)-related LOX1 and EIN2 genes and the salt tolerance SOS1 gene at 24 h and that of the salicylic acid (SA)-related PR-1 gene at 48 h after T6 inoculation. Our study demonstrates that the T. parareesei T6-tomato interaction is beneficial to both partners.

Relevance of trichothecenes in fungal physiology: disruption of tri5 in Trichoderma arundinaceum.

Trichothecenes are sesquiterpenoid mycotoxins produced mainly by Fusarium species. Harzianum A (HA), a non-phytotoxic trichothecene produced by Trichoderma arundinaceum, has recently been found to have antagonistic activity against fungal plant pathogens and to induce plant genes involved in defense responses. In the present work, we have shown that disruption of the T. arundinaceum tri5 gene, which encodes a terpene synthase, stops the production of HA, alters the expression of other tri genes involved in HA biosynthesis, and alters the expression of hmgR, dpp1, erg9, erg1, and erg7, all genes involved in terpene biosynthetic pathways. An increase in the level of ergosterol biosynthesis was also observed in the tri5 disrupted transformant in comparison with the wild type strain. The loss of HA also resulted in a drastic reduction of the biocontrol activity of the transformants against the phytopathogenic fungi Botrytis cinerea and Rhizoctonia solani. Finally, the effect of tri5 gene disruption on the regulation and balance of intermediates in terpene biosynthetic pathways, as well as the hypothetical physiological role of trichothecenes, both inter- and intracellularly, on regulation and biocontrol, are discussed.

Trichoderma: a multipurpose, plant-beneficial microorganism for eco-sustainable agriculture.

Trichoderma is a cosmopolitan and opportunistic ascomycete fungal genus including species that are of interest to agriculture as direct biological control agents of phytopathogens. Trichoderma utilizes direct antagonism and competition, particularly in the rhizosphere, where it modulates the composition of and interactions with other microorganisms. In its colonization of plants, on the roots or as an endophyte, Trichoderma has evolved the capacity to communicate with the plant and produce numerous multifaceted benefits to its host. The intricacy of this plant-microorganism association has stimulated a marked interest in research on Trichoderma, ranging from its capacity as a plant growth promoter to its ability to prime local and systemic defence responses against biotic and abiotic stresses and to activate transcriptional memory affecting plant responses to future stresses. This Review discusses the ecophysiology and diversity of Trichoderma and the complexity of its relationships in the agroecosystem, highlighting its potential as a direct and indirect biological control agent, biostimulant and biofertilizer, which are useful multipurpose properties for agricultural applications. We also highlight how the present legislative framework might accommodate the demonstrated evidence of Trichoderma proficiency as a plant-beneficial microorganism contributing towards eco-sustainable agriculture.

Trichoderma harzianum Volatile Organic Compounds Regulated by the THCTF1 Transcription Factor Are Involved in Antifungal Activity and Beneficial Plant Responses.

The transcription factor THCTF1 from Trichoderma harzianum, previously linked to the production of 6-pentyl-2H-pyran-2-one (6-PP) derivatives and antifungal activity against Fusarium oxysporum, has been related in this study to conidiation, production of an array of volatile organic compounds (VOCs) and expression of methyltransferase genes. VOCs emitted by three T. harzianum strains (wild type T34, transformant ΔD1-38 that is disrupted in the Thctf1 gene encoding the transcription factor THCTF1, and ectopic integration transformant ΔJ3-16) were characterized by Proton Transfer Reaction-Quadrupole interface-Time-Of-Flight-Mass Spectrometry (PTR-Qi-TOF-MS). Thctf1 disruption affected the production of numerous VOCs such as the antifungal volatiles 2-pentyl furan and benzaldehyde which were under-emitted, and acetoine, a plant systemic defense inductor, which was over-emitted. Biological assays show that VOCs regulated by THCTF1 are involved in the T. harzianum antifungal activity against Botrytis cinerea and in the beneficial effects leading to Arabidopsis plant development. The VOC blend from the disruptant ΔD1-38: (i) inhibited Arabidopsis seed germination for at least 26 days and (ii) when applied to Arabidopsis seedlings resulted in increased jasmonic acid- and salicylic acid-dependent defenses.

Plant-beneficial effects of Trichoderma and of its genes.

Trichoderma (teleomorph Hypocrea) is a fungal genus found in many ecosystems. Trichoderma spp. can reduce the severity of plant diseases by inhibiting plant pathogens in the soil through their highly potent antagonistic and mycoparasitic activity. Moreover, as revealed by research in recent decades, some Trichoderma strains can interact directly with roots, increasing plant growth potential, resistance to disease and tolerance to abiotic stresses. This mini-review summarizes the main findings concerning the Trichoderma-plant interaction, the molecular dialogue between the two organisms, and the dramatic changes induced by the beneficial fungus in the plant. Efforts to enhance plant resistance and tolerance to a broad range of stresses by expressing Trichoderma genes in the plant genome are also addressed.

Comparative study of Trichoderma gene expression in interactions with tomato plants using high-density oligonucleotide microarrays.

Trichoderma spp. are widely used as biopesticides and biofertilizers to control diseases and to promote positive physiological responses in plants. In vitro and in vivo assays with Trichoderma harzianum CECT 2413 (T34), Trichoderma virens Gv29-8 (T87) and Trichoderma hamatum IMI 224801 (T7) revealed that these strains affected the growth and development of lateral roots in tomato plants in different ways. The early expression profiles of these Trichoderma strains were studied after 20 h of incubation in the presence of tomato plants, using a high-density oligonucleotide (HDO) microarray, and compared to the profiles in the absence of plants. Out of the total 34 138 Trichoderma probe sets deposited on the microarray, 1077 (3.15 %) showed a significant change of at least 2-fold in expression in the presence of tomato plants. The numbers of probe sets identified in the individual Trichoderma strains were 593 in T. harzianum T34, 336 in T. virens T87 and 94 in T. hamatum T7. Carbohydrate metabolism - the chitin degradation enzymes N-acetylglucosamine-6-phosphate deacetylase, glucosamine-6-phosphate deaminase and chitinase - was the most significantly overrepresented process commonly observed in the three Trichoderma strains in early interactions with tomato plants. Strains T7 and T34, which had similar positive effects on plant development in biological assays, showed a significantly overrepresented hexokinase activity in interaction with tomato. In addition, genes encoding a 40S ribosomal protein and a P23 tumour protein were altered in both these strains.

Overexpression of the trichodiene synthase gene tri5 increases trichodermin production and antimicrobial activity in Trichoderma brevicompactum.

Trichoderma brevicompactum produces trichodermin, a simple trichothecene-type toxin that shares the first steps of the sesquiterpene biosynthetic pathway with other phytotoxic trichothecenes from Fusarium spp. Trichodiene synthase catalyses the conversion of farnesyl pyrophosphate to trichodiene and it is encoded by the tri5 gene that was cloned and analysed functionally by homologous overexpression in T. brevicompactum. tri5 expression was up-regulated in media with glucose, H(2)O(2) or glycerol. tri5 repression was observed in cultures supplemented with the antioxidants ferulic acid and tyrosol. Acetone extracts of tri5-overexpressing transformants displayed higher antifungal activity than those from the wild-type. Chromatographic and spectroscopic analyses revealed that tri5 overexpression led to an increased production of trichodermin and tyrosol. Agar diffusion assays with these two purified metabolites from the tri5-overexpressing transformant T. brevicompactum Tb41tri5 showed that only trichodermin had antifungal activity against Saccharomyces cerevisiae, Kluyveromyces marxianus, Candida albicans, Candida glabrata, Candida tropicalis and Aspergillus fumigatus, in most cases such activity being higher than that observed for amphotericin B and hygromycin. Our results point to the significant role of tri5 in the production of trichodermin and in the antifungal activity of T. brevicompactum.

Genetic analyses place most Spanish isolates of Beauveria bassiana in a molecular group with word-wide distribution.

BACKGROUND: The entomopathogenic anamorphic fungus Beauveria bassiana is currently used as a biocontrol agent (BCA) of insects. Fifty-seven Beauveria bassiana isolates -53 from Spain- were characterized, integrating group I intron insertion patterns at the 3'-end of the nuclear large subunit ribosomal gene (LSU rDNA) and elongation factor 1-alpha (EF1-α) phylogenetic information, in order to assess the genetic structure and diversity of this Spanish collection of B. bassiana. RESULTS: Group I intron genotype analysis was based on the four highly conserved insertion sites of the LSU (Ec2653, Ec2449, Ec2066, Ec1921). Of the 16 possible combinations/genotypes, only four were detected, two of which were predominant, containing 44 and 9 members out of 57 isolates, respectively. Interestingly, the members of the latter two genotypes showed unique differences in their growth temperatures. In follow, EF1-α phylogeny served to classify most of the strains in the B. bassiana s.s. (sensu stricto) group and separate them into 5 molecular subgroups, all of which contained a group I intron belonging to the IC1 subtype at the Ec1921 position. A number of parameters such as thermal growth or origin (host, geographic location and climatic conditions) were also examined but in general no association could be found. CONCLUSION: Most Spanish B. bassiana isolates (77.2%) are grouped into a major phylogenetic subgroup with word-wide distribution. However, high phylogenetic diversity was also detected among Spanish isolates from close geographic zones with low climatic variation. In general, no correlation was observed between the molecular distribution and geographic origin or climatic characteristics where the Spanish B. bassiana isolates were sampled.

Phytohormone Production Profiles in Trichoderma Species and Their Relationship to Wheat Plant Responses to Water Stress.

The production of eight phytohormones by Trichoderma species is described, as well as the 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase (ACCD) activity, which diverts the ethylene biosynthetic pathway in plants. The use of the Trichoderma strains T. virens T49, T. longibrachiatum T68, T. spirale T75 and T. harzianum T115 served to demonstrate the diverse production of the phytohormones gibberellins (GA) GA1 and GA4, abscisic acid (ABA), salicylic acid (SA), auxin (indole-3-acetic acid: IAA) and the cytokinins (CK) dihydrozeatin (DHZ), isopenteniladenine (iP) and trans-zeatin (tZ) in this genus. Such production is dependent on strain and/or culture medium. These four strains showed different degrees of wheat root colonization. Fresh and dry weights, conductance, H2O2 content and antioxidant activities such as superoxide dismutase, peroxidase and catalase were analyzed, under optimal irrigation and water stress conditions, on 30-days-old wheat plants treated with four-day-old Trichoderma cultures, obtained from potato dextrose broth (PDB) and PDB-tryptophan (Trp). The application of Trichoderma PDB cultures to wheat plants could be linked to the plants' ability to adapt the antioxidant machinery and to tolerate water stress. Plants treated with PDB cultures of T49 and T115 had the significantly highest weights under water stress. Compared to controls, treatments with strains T68 and T75, with constrained GA1 and GA4 production, resulted in smaller plants regardless of fungal growth medium and irrigation regime.

Trichoderma and the Plant Heritable Priming Responses.

There is no doubt that Trichoderma is an inhabitant of the rhizosphere that plays an important role in how plants interact with the environment. Beyond the production of cell wall degrading enzymes and metabolites, Trichoderma spp. can protect plants by inducing faster and stronger immune responses, a mechanism known as priming, which involves enhanced accumulation of dormant cellular proteins that function in intracellular signal amplification. One example of these proteins is the mitogen-activated protein kinases (MAPK) that are triggered by the rise of cytosolic calcium levels and cellular redox changes following a stressful challenge. Transcription factors such as WRKYs, MYBs, and MYCs, play important roles in priming as they act as regulatory nodes in the transcriptional network of systemic defence after stress recognition. In terms of long-lasting priming, Trichoderma spp. may be involved in plants epigenetic regulation through histone modifications and replacements, DNA (hypo)methylation, and RNA-directed DNA methylation (RdDM). Inheritance of these epigenetic marks for enhanced resistance and growth promotion, without compromising the level of resistance of the plant's offspring to abiotic or biotic stresses, seems to be an interesting path to be fully explored.

Why Is the Correct Selection of Trichoderma Strains Important? The Case of Wheat Endophytic Strains of T. harzianum and T. simmonsii.

The search for endophytic fungi in the roots of healthy wheat plants from a non-irrigation field trial allowed us to select 4 out of a total of 54 cultivable isolates belonging to the genus Trichoderma, identified as T. harzianum T136 and T139, T. simmonsii T137, and T. afroharzianum T138. In vitro assays against the phytopathogenic fungus Fusarium graminearum showed that the T. harzianum strains had the highest biocontrol potential and that T136 exhibited the highest cellulase and chitinase activities. Production patterns of eight phytohormones varied among the Trichoderma strains. All four, when applied alone or in combination, colonized roots of other wheat cultivars and promoted seed germination, tillering, and plant growth under optimal irrigation conditions in the greenhouse. Apart from T136, the endophytic Trichoderma strains showed plant protection capacity against drought as they activated the antioxidant enzyme machinery of the wheat plants. However, T. simmonsii T137 gave the best plant size and spike weight performance in water-stressed plants at the end of the crop. This trait correlated with significantly increased production of indole acetic acid and abscisic acid and increased 1-aminocyclopropane-1-carboxylic acid deaminase activity by T137. This study shows the potential of Trichoderma endophytes and that their success in agricultural systems requires careful selection of suitable strains.

Microbiological Evaluation of the Disinfecting Potential of UV-C and UV-C Plus Ozone Generating Robots.

This study examined the microbicidal activity of ultraviolet (UV)-C185-256-nm irradiance (robot 1) and ozone generated at UV-C185-nm by low-pressure mercury vapor lamps (robot 2) adapted to mobile robotic devices for surface decontamination, which was achieved in less than 1 h. Depending on their wall structure and outer envelopes, many microorganisms display different levels of resistance to decontaminating agents. Thus, the need for novel disinfection approaches is further exacerbated by the increased prevalence of multidrug-resistant bacteria, as well as the potential of novel microorganisms, with the ability to cause disease outbreaks. To set up a rapid and effective approach for microorganisms propagation prevention, we focused on the effects of UV-C and ozone on a distinct microorganism survival ratio. A set of microorganisms, including Escherichia coli, Micrococcus luteus, Saccharomyces cerevisiae, Trichoderma harzianum, and Bacillus subtilis, were used to evaluate the disinfection power of UV-C and UV-C plus ozone generating robots. UV-C disinfection can be suited to ad hoc tasks, is easy to operate, requires low maintenance, does not have the need for the storage of dangerous chemicals, and does not produce by-products that may affect human health and the environment. The robotic cumulative irradiation technology developed (fluence accumulated values of 2.28 and 3.62 mJ cm-2, for robot 1 and 2, respectively), together with the production of ozone (with a maximum peak of 0.43 ppm) capable of reaching UV-C shaded surfaces, and analyzed in the current study, despite being designed for the need to reduce the risk of epidemic outbreaks in real-life scenarios, represents a versatile tool that could be employed for air and surface disinfection within many circumstances that are faced daily.

TvDim1 of Trichoderma virens is involved in redox-processes and confers resistance to oxidative stresses.

The evolutionarily conserved Dim1 proteins belong to the TRX fold superfamily. An EST showing high identity values with genes coding for Dim1 proteins was selected from an EST library collection of Trichoderma virens T59. Here, we report the cloning, characterization, and functional analysis of a T. virens T59 TvDim1 gene. The TvDim1 gene, with a sequence size of 614 bp, was PCR-amplified and found to contain three introns. The TvDim1 gene was present as a single copy in the T. virens genome and was also present in another five Trichoderma strains investigated. Increased levels of expression and redox-activity were detected when the fungus was grown in the presence of H(2)O(2). The overexpression and silencing of TvDim1 in T. harzianum T34 gave rise to transformants, with higher and lower growth, redox-activity, and quantities of biomass, respectively, than the wild-type strain after culture under oxidative stress.

Differential Response of Tomato Plants to the Application of Three Trichoderma Species When Evaluating the Control of Pseudomonas syringae Populations.

Trichoderma species are well known biocontrol agents that are able to induce responses in the host plants against an array of abiotic and biotic stresses. Here, we investigate, when applied to tomato seeds, the potential of Trichoderma strains belonging to three different species, T. parareesei T6, T. asperellum T25, and T. harzianum T34, to control the fully pathogenic strain Pseudomonas syringae pv. tomato (Pst) DC3000, able to produce the coronatine (COR) toxin, and the COR-deficient strain Pst DC3118 in tomato plants, and the molecular mechanisms by which the plant can modulate its systemic defense. Four-week old tomato plants, seed-inoculated, or not, with a Trichoderma strain, were infected, or not, with a Pst strain, and the changes in the expression of nine marker genes representative of salicylic acid (SA) (ICS1 and PAL5) and jasmonic acid (JA) (TomLoxC) biosynthesis, SA- (PR1b1), JA- (PINII and MYC2) and JA/Ethylene (ET)-dependent (ERF-A2) defense pathways, as well as the abscisic acid (ABA)-responsive gene AREB2 and the respiratory burst oxidase gene LERBOH1, were analyzed at 72 hours post-inoculation (hpi) with the bacteria. The significant increase obtained for bacterial population sizes in the leaves, disease index, and the upregulation of tomato genes related to SA, JA, ET and ABA in plants inoculated with Pst DC3000 compared with those obtained with Pst DC3118, confirmed the COR role as a virulence factor, and showed that both Pst and COR synergistically activate the JA- and SA-signaling defense responses, at least at 72 hpi. The three Trichoderma strains tested reduced the DC3118 levels to different extents and were able to control disease symptoms at the same rate. However, a minor protection (9.4%) against DC3000 was only achieved with T. asperellum T25. The gene deregulation detected in Trichoderma-treated plus Pst-inoculated tomato plants illustrates the complex system of a phytohormone-mediated signaling network that is affected by the pathogen and Trichoderma applications but also by their interaction. The expression changes for all nine genes analyzed, excepting LERBOH1, as well as the bacterial populations in the leaves were significantly affected by the interaction. Our results show that Trichoderma spp. are not adequate to control the disease caused by fully pathogenic Pst strains in tomato plants.