Secondary metabolism in Trichoderma – Chemistry meets genomics

Chemotropism Assays for Plant Symbiosis and Mycoparasitism Related Compound Screening in Trichoderma atroviride

Trichoderma atroviride is a mycoparasitic fungus used as biological control agent to protect plants against fungal pathogens. Successful biocontrol is based on the perception of signals derived from both the plant symbiont and the fungal prey. Here, we applied three different chemotropic assays to study the chemosensing capacity of T. atroviride toward compounds known or suspected to play a role in the mycoparasite/plant or host/prey fungal interactions and to cover the complete spectrum of T. atroviride developmental stages. Purified compounds, including nutrients, the fungal secondary metabolite 6-amyl-α-pyrone (6-pentyl-α-pyrone, 6-PP) and the plant oxylipin 13-(s)-HODE, as well as culture supernatants derived from fungal preys, including Rhizoctonia solani, Botrytis cinerea and Fusarium oxysporum, were used to evaluate chemotropic responses of conidial germlings, microcolonies and fully differentiated mycelia. Our results show that germlings respond preferentially to compounds secreted by plant roots and T. atroviride itself than to compounds secreted by prey fungi. With the progression of colony development, host plant cues and self-generated signaling compounds remained the strongest chemoattractants. Nevertheless, mature hyphae responded differentially to certain prey-derived signals. Depending on the fungal prey species, chemotropic responses resulted in either increased or decreased directional colony extension and hyphal density at the colony periphery closest to the test compound source. Together these findings suggest that chemotropic sensing during germling development is focused on plant association and colony network formation, while fungal prey recognition develops later in mature hyphae of fully differentiated mycelium. Furthermore, the morphological alterations of T. atroviride in response to plant host and fungal prey compounds suggest the presence of both positive and negative chemotropism. The presented assays will be useful for screening of candidate compounds, and for evaluating their impact on the developmental spectrum of T. atroviride and other related species alike. Conidial germlings proved particularly useful for simple and rapid compound screening, whereas more elaborate microscopic analysis of microcolonies and fully differentiated mycelia was essential to understand process-specific responses, such as plant symbiosis and biocontrol.

Mycosinthetized Ag, CuO and ZnO nanoparticles from a promising Trichoderma harzianum strain and their antifungal potential against important phytopathogens

Fungal green biosynthesis of nanoparticles (NPs) is a promising eco-friendly method for mass-scale production. In the present study Ag, CuO and ZnO nanoparticles were biogenically synthetized using a cell filtrate of a strain of Trichoderma harzianum as a reducer and stabilizer agent. The structure, morphology and physicochemical properties of the NPs were characterized through transmission electron microscopy, dynamic light scattering, wide angle X-ray scattering and thermogravimetric analysis. Since nanotechnology could offer promising applications in agricultural area, we evaluated the ability of the NPs to reduce the growth of important fungal phytopathogens as Alternaria alternata, Pyricularia oryzae and Sclerotinia sclerotiorum. Silver and CuO NPs reduced significantly the mycelial growth of A. alternata and P. oryzae in a dose dependent manner. This is the first report of a multiple extracellular biosynthesis of NPs from T. harzianum and the first time that CuO and ZnO NPs were obtained from this fungus. In addition, we highlighted the rapid production of NPs, as well as, the potential of Ag and CuO for the control of phytopathogens. On the other hand, the three types of NPs could be easily and sustainably produced on a large scale with the chance of having multiple applications in biotechnological processes.

Influence of Different Light Regimes on the Mycoparasitic Activity and 6-Pentyl-α-pyrone Biosynthesis in Two Strains of Trichoderma atroviride

The ascomycete Trichoderma atroviride is well known for its mycoparasitic lifestyle. Similar to other organisms, light is an important cue for T. atroviride. However, besides triggering of conidiation, little is known on the physiological responses of T. atroviride to light. In this study, we analyzed how cultivation under different light wavelengths and regimes impacted the behavior of two T. atroviride wild-type strains: IMI206040 and P1. While colony extension of both strains was slightly affected by light, massive differences in their photoconidation responses became evident. T. atroviride P1 colonies conidiated under all conditions tested including growth in complete darkness, while IMI206040 required white, blue or green light to trigger asexual reproduction. Interestingly, deletion of the stress-activated MAP kinase-encoding gene tmk3 abolished the ability of strain P1 to conidiate in red and yellow light as well as in darkness. Furthermore, light-dependent differences in the mycoparasitic activity and in the biosynthesis of the secondary metabolite 6-pentyl-α-pyrone (6-PP) became evident. 6-PP production was highest upon dark incubation, while light, especially exposure to white light as light/dark cycles, had an inhibitory effect on its biosynthesis. We conclude that the response of T. atroviride to light is strain-dependent and impacts differentiation, mycoparasitism, and 6-PP production; hence, this should be considered in experiments testing the mycoparasitic activity of these fungi.

Combined Comparative Genomics and Gene Expression Analyses Provide Insights into the Terpene Synthases Inventory in Trichoderma

Trichoderma is a fungal genus comprising species used as biocontrol agents in crop plant protection and with high value for industry. The beneficial effects of these species are supported by the secondary metabolites they produce. Terpenoid compounds are key players in the interaction of Trichoderma spp. with the environment and with their fungal and plant hosts; however, most of the terpene synthase (TS) genes involved in their biosynthesis have yet not been characterized. Here, we combined comparative genomics of TSs of 21 strains belonging to 17 Trichoderma spp., and gene expression studies on TSs using T. gamsii T6085 as a model. An overview of the diversity within the TS-gene family and the regulation of TS genes is provided. We identified 15 groups of TSs, and the presence of clade-specific enzymes revealed a variety of terpenoid chemotypes evolved to cover different ecological demands. We propose that functional differentiation of gene family members is the driver for the high number of TS genes found in the genomes of Trichoderma. Expression studies provide a picture in which different TS genes are regulated in many ways, which is a strong indication of different biological functions.

Targeted Amino Acid Substitutions in a Trichoderma Peptaibol Confer Activity against Fungal Plant Pathogens and Protect Host Tissues from Botrytis cinerea Infection

Fungal species belonging to the Trichoderma genus are commonly used as biocontrol agents against several crop pathogens. Among their secondary metabolites, peptaibols are helical, antimicrobial peptides, which are structurally stable even under extreme pH and temperature conditions. The promise of peptaibols as agrochemicals is, however, hampered by poor water solubility, which inhibits efficient delivery for practical use in crop protection. Using a versatile synthetic strategy, based on green chemistry procedures, we produced water-soluble analogs of the short-length peptaibol trichogin. Although natural trichogin was inactive against the tested fungal plant pathogens (Botrytis cinerea, Bipolaris sorokiniana, Fusarium graminearum, and Penicillium expansum), three analogs completely inhibited fungal growth at low micromolar concentrations. The most effective peptides significantly reduced disease symptoms by B. cinerea on common bean and grapevine leaves and ripe grape berries without visible phytotoxic effects. An in-depth conformational analysis featuring a 3D-structure-activity relationship study indicated that the relative spatial position of cationic residues is crucial for increasing peptide fungicidal activity.

The Lipoxygenase Lox1 Is Involved in Light- and Injury-Response, Conidiation, and Volatile Organic Compound Biosynthesis in the Mycoparasitic Fungus Trichoderma atroviride

The necrotrophic mycoparasite Trichoderma atroviride is a biological pest control agent frequently applied in agriculture for the protection of plants against fungal phytopathogens. One of the main secondary metabolites produced by this fungus is 6-pentyl-α-pyrone (6-PP). 6-PP is an organic compound with antifungal and plant growth-promoting activities, whose biosynthesis was previously proposed to involve a lipoxygenase (Lox). In this study, we investigated the role of the single lipoxygenase-encoding gene lox1 encoded in the T. atroviride genome by targeted gene deletion. We found that light inhibits 6-PP biosynthesis but lox1 is dispensable for 6-PP production as well as for the ability of T. atroviride to parasitize and antagonize host fungi. However, we found Lox1 to be involved in T. atroviride conidiation in darkness, in injury-response, in the production of several metabolites, including oxylipins and volatile organic compounds, as well as in the induction of systemic resistance against the plant-pathogenic fungus Botrytis cinerea in Arabidopsis thaliana plants. Our findings give novel insights into the roles of a fungal Ile-group lipoxygenase and expand the understanding of a light-dependent role of these enzymes.

Deletion of the Trichoderma virens NRPS, Tex7, induces accumulation of the anti-cancer compound heptelidic acid

The anticancer antibiotic heptelidic acid is a sesquiterpene lactone produced by the beneficial plant fungus Trichoderma virens. This species has been separated into two strains, referred to as P and Q, based on its biosynthesis of secondary metabolites; notably, only P-strains were reported to produce heptelidic acid. While characterizing a Q-strain of T. virens containing a directed mutation in the non-ribosomal peptide synthetase encoding gene Tex7, the appearance of an unknown compound in anomalously large quantities was visualized by TLC. Using a combination of HPLC, LC-MS/MS, and NMR spectroscopy, this compound was identified as heptelidic acid. This discovery alters the strain classification structure of T. virens. Additionally, the Tex7 mutants inhibited growth of maize seedlings, while retaining the ability to induce systemic resistance against the foliar fungal pathogen, Cochliobolus heterostrophus.

Beneficial effects of Trichoderma secondary metabolites on crops

Selected microbial strains used as active ingredients of biopesticides for agricultural management practices (e.g., IPM, Integrated Pest Management) are known for their ability to control phytopathogens, promote plant growth, and/or induce disease resistance. Microbes belonging to the Trichoderma genus are considered as an appropriate example of beneficial microbes and are model organisms to study plant-microbe interactions. Several Trichoderma strains are marketed as biocontrol agents and are known to increase plant growth, stress tolerance, and nutrient availability. These effects have sometimes been related to the production of effector metabolites that beneficial microbes produce during the interaction with plant and other microbes. Secondary metabolites (SMs) comprise different classes of natural compounds with low molecular weight and having numerous biological roles, especially in the interactions among organisms. Metabolomic analysis of the interactions between plants, phytopathogens, and beneficial fungi aided in the identification of several bioactive fungal SMs that positively affect plant metabolism. Some of these compounds showed direct activity against phytopathogens, but also increased disease resistance by triggering the plant defence system, and/or enhanced vegetative growth. A new generation of bioformulations based on microbial metabolites and living consortia responsible for the desired beneficial effects on crops may overcome the difficulties associated with the use of a single living microbial strain.

Whole Genome Sequencing Reveals Major Deletions in the Genome of M7, a Gamma Ray-Induced Mutant of Trichoderma virens That Is Repressed in Conidiation, Secondary Metabolism, and Mycoparasitism

Trichoderma virens is a commercial biofungicide used in agriculture. We have earlier isolated a mutant of T. virens using gamma ray-induced mutagenesis. This mutant, designated as M7, is defective in morphogenesis, secondary metabolism, and mycoparasitism. The mutant does not produce conidia, and the colony is hydrophilic. M7 cannot utilize cellulose and chitin as a sole carbon source and is unable to parasitize the plant pathogens Rhizoctonia solani and Pythium aphanidermatum in confrontation assay. Several volatile (germacrenes, beta-caryophyllene, alloaromadendrene, gamma-muurolene) and non-volatile (viridin, viridiol, gliovirin, heptelidic acid) metabolites are not detected in M7. In transcriptome analysis, many genes related to secondary metabolism, carbohydrate metabolism, hydrophobicity, and transportation, among others, were found to be downregulated in the mutant. Using whole genome sequencing, we identified five deletions in the mutant genome, totaling about 250 kb (encompassing 71 predicted ORFs), which was confirmed by PCR. This study provides novel insight into genetics of morphogenesis, secondary metabolism, and mycoparasitism and eventually could lead to the identification of novel regulators of beneficial traits in plant beneficial fungi Trichoderma spp. We also suggest that this mutant can be developed as a microbial cell factory for the production of secondary metabolites and proteins.

Bioactive Secondary Metabolites from Trichoderma spp. against Phytopathogenic Fungi

Phytopathogenic fungi, causing significant economic and production losses, are becoming a serious threat to global food security. Due to an increase in fungal resistance and the hazardous effects of chemical fungicides to human and environmental health, scientists are now engaged to explore alternate non-chemical and ecofriendly management strategies. The use of biocontrol agents and their secondary metabolites (SMs) is one of the potential approaches used today. Trichoderma spp. are well known biocontrol agents used globally. Many Trichoderma species are the most prominent producers of SMs with antimicrobial activity against phytopathogenic fungi. Detailed information about these secondary metabolites, when grouped together, enhances the understanding of their efficient utilization and further exploration of new bioactive compounds for the management of plant pathogenic fungi. The current literature provides the information about SMs of Trichoderma spp. in a different context. In this review, we summarize and group different antifungal SMs of Trichoderma spp. against phytopathogenic fungi along with a comprehensive overview of some aspects related to their chemistry and biosynthesis. Moreover, a brief overview of the biosynthesis pathway, action mechanism, and different approaches for the analysis of SMs and the factors affecting the regulation of SMs in Trichoderma is also discussed.

Changes in Peptaibol Production of Trichoderma Species during In Vitro Antagonistic Interactions with Fungal Plant Pathogens

Trichoderma species are widely used as biofungicides for the control of fungal plant pathogens. Several studies have been performed to identify the main genes and compounds involved in Trichoderma–plant–microbial pathogen cross-talks. However, there is not much information about the exact mechanism of this profitable interaction. Peptaibols secreted mainly by Trichoderma species are linear, 5–20 amino acid residue long, non-ribosomally synthesized peptides rich in α-amino isobutyric acid, which seem to be effective in Trichoderma–plant pathogenic fungus interactions. In the present study, reversed phase (RP) high-performance liquid chromatography (HPLC) coupled with electrospray ionization (ESI) mass spectrometry (MS) was used to detect peptaibol profiles of Trichoderma strains during interactions with fungal plant pathogens. MS investigations of the crude extracts deriving from in vitro confrontations of Trichoderma asperellum and T. longibrachiatum with different plant pathogenic fungi (Fusarium moniliforme, F. culmorum, F. graminearum, F. oxysporum species complex, Alternaria solani and Rhizoctonia solani) were performed to get a better insight into the role of these non-ribosomal antimicrobial peptides. The results revealed an increase in the total amount of peptaibols produced during the interactions, as well as some differences in the peptaibol profiles between the confrontational and control tests. Detection of the expression level of the peptaibol synthetase tex1 by qRT-PCR showed a significant increase in T. asperellum/R. solani interaction in comparison to the control. In conclusion, the interaction with plant pathogens highly influenced the peptaibol production of the examined Trichoderma strains.

Bivalent Metal-Chelating Properties of Harzianic Acid Produced by Trichoderma pleuroticola Associated to the Gastropod Melarhaphe neritoides

Harzianic acid is a secondary metabolite of Trichoderma, structurally belonging to the dienyltetramic acid subgroup of the tetramic acids. Biological activities of harzianic acid are of great interest for its antimicrobial and plant growth-promoting activities, which might be related to its chelating properties. In the present work harzianic acid, isolated from cultures of a strain of Trichoderma pleuroticola associated to the gastropod Melarhaphe neritoides, was studied as a complexant agent of a number of biologically relevant transition metals (i.e., Zn²⁺, Fe²⁺, Cu²⁺, and Mn²⁺), using UV-VIS, potentiometry, MS and NMR techniques. Our findings show the coordination capacity of harzianic acid toward the above cations through the formation of neutral or charged complexes in a variable ratio depending on the metal and pH conditions.

Lipids, proteins and extracellular metabolites of Trichoderma harzianum modifications caused by 2,4-dichlorophenoxyacetic acid as a plant growth stimulator

Strains of Trichoderma harzianum are well-known producers of bioactive secondary metabolites and have a beneficial effect on plants. However, to the best of our knowledge, the effect of the commonly used pesticides on the activity of this fungus is not yet investigated. Therefore, in the present study, the effect of the herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) on the lipidome and selected extracellular compounds synthesized by T. harzianum IM 0961 was examined. It was observed that the herbicide 2,4-D caused changes in the lipid composition of the mycelium and that the herbicide exhibited lipophilic properties. In addition, the herbicide disturbed the phosphatidylcholine (PC)/phosphatidylethanolamine (PE) ratio and increased membrane permeability. The higher amount of cardiolipin CL 72:7 and the lower amount of CL 72:8 could have been associated with a decreased ratio of 18:2 and 18:1 fatty acids in the herbicide-treated samples. Moreover, in the presence of 2,4-D, an increased lipid peroxidation (twofold), as well as a higher content of oxylipin (9-HODE and 13-HODE) and phosphatidic acid (PA), was noted, confirming that 2,4-D induced lipid peroxidation in the mycelium. The herbicide also exerted its toxic effect on the production of 14-aminoacid peptaibols and two compounds, harzianic acid and t22-azaphilone, exhibiting antibiotic and plant growth-promoting activity. During proteomic analysis, the synthesis of some proteins, such as calcineurin-like phosphoesterase metallophosphatases (MPPs), which modulate the properties of cell walls, was found to be inhibited by the herbicide. These presented findings may be of significant value in understanding the effect of 2,4-D on the activity of T. harzianum.

Using the CODIT model to explain secondary metabolites of xylem in defence systems of temperate trees against decay fungi

BACKGROUND

In trees, secondary metabolites (SMs) are essential for determining the effectiveness of defence systems against fungi and why defences are sometimes breached. Using the CODIT model (Compartmentalization of Damage/Dysfunction in Trees), we explain defence processes at the cellular level. CODIT is a highly compartmented defence system that relies on the signalling, synthesis and transport of defence compounds through a three-dimensional lattice of parenchyma against the spread of decay fungi in xylem.

SCOPE

The model conceptualizes 'walls' that are pre-formed, formed during and formed after wounding events. For sapwood, SMs range in molecular size, which directly affects performance and the response times in which they can be produced. When triggered, high-molecular weight SMs such as suberin and lignin are synthesized slowly (phytoalexins), but can also be in place at the time of wounding (phytoanticipins). In contrast, low-molecular weight phenolic compounds such as flavonoids can be manufactured de novo (phytoalexins) rapidly in response to fungal colonization. De novo production of SMs can be regulated in response to fungal pathogenicity levels. The protective nature of heartwood is partly based on the level of accumulated antimicrobial SMs (phytoanticipins) during the transitionary stage into a normally dead substance. Effectiveness against fungal colonization in heartwood is largely determined by the genetics of the host.

CONCLUSION

Here we review recent advances in our understanding of the role of SMs in trees in the context of CODIT, with emphasis on the relationship between defence, carbohydrate availability and the hydraulic system.We also raise the limitations of the CODIT model and suggest its modification, encompassing other defence theory concepts. We envisage the development of a new defence system that is modular based and incorporates all components (and organs) of the tree from micro- to macro-scales.

Chemical Composition of an Aphid Antifeedant Extract from an Endophytic Fungus, Trichoderma sp. EFI671

Botanical and fungal biopesticides, including endophytes, are in high demand given the current restrictive legislations on the use of chemical pesticides. As part of an ongoing search for new biopesticides, a series of fungal endophytes have been isolated from selected medicinal plants including Lauraceae species. In the current study, an extract from the endophytic fungus Trichoderma sp. EFI 671, isolated from the stem parts of the medicinal plant Laurus sp., was screened for bioactivity against plant pathogens (Fusarium graminearum, Rhizoctonia solani, Sclerotinia sclerotiorum and Botrytis cinerea), insect pests (Spodoptera littoralis, Myzus persicae, Rhopalosiphum padi) and plant parasites (Meloidogyne javanica), with positive results against M. persicae. The chemical study of the neutral fraction of the active hexane extract resulted in the isolation of a triglyceride mixture (m1), eburicol (2), β-sitostenone (3), ergosterol (4) and ergosterol peroxide (5). The free fatty acids present in the acid fraction of the extract and in m1 (oleic, linoleic, palmitic and stearic) showed strong dose-dependent antifeedant effects against M. persicae. Liquid (potato dextrose broth, PDB and Sabouraud Broth, SDB) and solid (corn, sorghum, pearl millet and rice) growth media were tested in order to optimize the yield and bioactivity of the fungal extracts. Pearl millet and corn gave the highest extract yields. All the extracts from these solid media had strong effects against M. persicae, with sorghum being the most active. Corn media increased the methyl linoleate content of the extract, pearl millet media increased the oleic acid and sorghum media increased the oleic and linoleic acids compared to rice. The antifeedant effects of these extracts correlated with their content in methyl linoleate and linoleic acid. The phytotoxic effects of these extracts against ryegrass, Lolium perenne, and lettuce, Lactuca sativa, varied with culture media, with sorghum being non- toxic.

Antibacterial harziane diterpenoids from a fungal symbiont Trichoderma atroviride isolated from Colquhounia coccinea var. mollis

Fungal endophytes from plants are an important source for discovery of novel bioactive natural products. In this study, five undescribed harziane diterpenoids with a 4/7/5/6 tetracyclic scaffold, harzianols F‒J and three known derivatives, were obtained from the liquid fermentation of an endophytic fungus Trichoderma atroviride B7, which was isolated from the healthy flower of a Lamiaceae plant Colquhounia coccinea var. mollis. Their structures were elucidated by comprehensive spectroscopic analyses and X-ray crystallographic diffraction in the case of harzianol F. Harzianol I exhibited significant antibacterial effect against the growth of Staphylococcus aureus (EC₅₀ = 7.7 ± 0.8 μg/mL), Bacillus subtilis (EC₅₀ = 7.7 ± 1.0 μg/mL), and Micrococcus luteus (EC₅₀ = 9.9 ± 1.5 μg/mL). Meanwhile, cytotoxic activity of harzianol I against three cancer cell lines was also observed. A plausible biosynthetic pathway for harziane diterpenoids was proposed.

Secreted metabolite-mediated interactions between rhizosphere bacteria and Trichoderma biocontrol agents

Trichoderma has been used as an alternative to synthetic pesticides to control a variety of phytopathogenic fungi, oomycetes, and nematodes. Although its mechanism of pathogen suppression has been extensively studied, how Trichoderma interacts with non-target microbes is not well understood. Here, we investigated how two Trichoderma biological control agents (BCAs) interact with rhizosphere bacteria isolated from a tomato plant via secreted proteins, metabolites, and volatile compounds (VCs). Culture filtrates (CFs) of T. virens and T. harzianum, containing secreted proteins and metabolites, strongly inhibited (>75% reduction in growth) 39 and 19, respectively, out of 47 bacterial strains tested. Their CFs inhibited the remaining strains at lower degrees. Both metabolites and proteins are involved in inhibiting bacteria, but they seem to antagonize each other in inhibiting some strains. Trichoderma and bacteria suppressed the growth of each other using VCs. The secretion of antibacterial and antifungal molecules by T. virens and T. harzianum was significantly affected by VCs from some bacteria, suggesting that both Trichoderma BCAs and rhizosphere bacteria use VCs to influence each other in multiple ways. In light of these results, we discuss how metabolite-mediated interactions can potentially affect the effectiveness of biocontrol.

TBRG-1 a Ras-like protein in Trichoderma virens involved in conidiation, development, secondary metabolism, mycoparasitism, and biocontrol unveils a new family of Ras-GTPases

Ras-GTPases are nucleotide hydrolases involved in key cellular processes. In fungi, Ras-GTPases regulate conidiation, development, virulence, and interactions with other fungi or plants. Trichoderma spp. are filamentous saprophytic fungi, widely distributed along all latitudes, characterized by their rapid growth and metabolic diversity. Many species of this genus interact with other fungi, animals or plants. Furthermore, these fungi are used as biocontrol agents due to their ability to antagonize phytopathogenic fungi and oomycetes, through competence, antibiosis, and parasitism. However, the genetic and molecular regulation of these processes is scarcely described in these fungi. In this work, we investigated the role of the gene tbrg-1 product (GenBank accession number XP_013956100; JGI ID: Tv_70852) of T. virens during its interaction with other fungi and plants. Sequence analyses predicted that TBRG-1 bears the characteristic domains of Ras-GTPases; however, its size (1011 aa) is 3- to 4-times bigger compared with classical GTPases. Interestingly, phylogenetic analyses grouped the TBRG-1 protein with hypothetical proteins of similar sizes, sharing conserved regions; whereas other known Ras-GTPases were perfectly grouped with their respective families. These facts led us to classify TBRG-1 into a new family of Ras-GTPases, the Big Ras-GTPases (BRG). Therefore, the gene was named tbrg-1 (TrichodermaBigRas-GTPase-1). Quantification of conidia and scanning electron microscopy showed that the mutants-lacking tbrg-1 produced less conidia, as well as a delayed conidiophore development compared to the wild-type (wt). Moreover, a deregulation of conidiation-related genes (con-10, con-13, and stuA) was observed in tbrg-1-lacking strains, which indicates that TBRG-1 is necessary for proper conidiophore and conidia development. Furthermore, the lack of tbrg-1 affected positively the antagonistic capability of T. virens against the phytopathogens Rhizoctonia solani, Sclerotium rolfsii, and Fusarium oxysporum, which was consistent with the expression patterns of mycoparasitism-related genes, sp1 and cht1, that code for a protease and for a chitinase, respectively. Furthermore, the antibiosis effect of mycelium-free culture filtrates of Δtbrg-1 against R. solani was considerably enhanced. The expression of secondary metabolism-related genes, particularly gliP, showed an upregulation in Δtbrg-1, which paralleled an increase in gliotoxin production as compared to the wt. These results indicate that TBRG-1 plays a negative role in secondary metabolism and antagonism. Unexpectedly, the biocontrol activity of Δtbrg-1 was ineffective to protect the tomato seeds and seedlings against R. solani. On the contrary, Δtbrg-1 behaved like a plant pathogen, indicating that TBRG-1 is probably implicated in the recognition process for establishing a beneficial relationship with plants.

Phytohormones (Auxin, Gibberellin) and ACC Deaminase In Vitro Synthesized by the Mycoparasitic Trichoderma DEMTkZ3A0 Strain and Changes in the Level of Auxin and Plant Resistance Markers in Wheat Seedlings Inoculated with this Strain Conidia

Both hormonal balance and plant growth may be shaped by microorganisms synthesizing phytohormones, regulating its synthesis in the plant and inducing plant resistance by releasing elicitors from cell walls (CW) by degrading enzymes (CWDE). It was shown that the Trichoderma DEMTkZ3A0 strain, isolated from a healthy rye rhizosphere, colonized the rhizoplane of wheat seedlings and root border cells (RBC) and caused approximately 40% increase of stem weight. The strain inhibited (in over 90%) the growth of polyphagous Fusarium spp. (F. culmorum, F. oxysporum, F. graminearum) phytopathogens through a mechanism of mycoparasitism. Chitinolytic and glucanolytic activity, strongly stimulated by CW of F. culmorum in the DEMTkZ3A0 liquid culture, is most likely responsible for the lysis of hyphae and macroconidia of phytopathogenic Fusarium spp. as well as the release of plant resistance elicitors. In DEMTkZ3A0 inoculated plants, an increase in the activity of the six tested plant resistance markers and a decrease in the concentration of indoleacetic acid (IAA) auxin were noted. IAA and gibberellic acid (GA) but also the 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase (ACCD) enzyme regulating ethylene production by plant were synthesized by DEMTkZ3A0 in the liquid culture. IAA synthesis was dependent on tryptophan and negatively correlated with temperature, whereas GA synthesis was positively correlated with the biomass and temperature.

A Novel Seed-Dressing Formulation Based on an Improved Mutant Strain of Trichoderma virens, and Its Field Evaluation

Using gamma-ray-induced mutagenesis, we have developed a mutant (named G2) of Trichoderma virens that produced two- to three-fold excesses of secondary metabolites, including viridin, viridiol, and some yet-to-be identified compounds. Consequently, this mutant had improved antibiosis against the oomycete test pathogen Pythium aphanidermatum. A transcriptome analysis of the mutant vis-à-vis the wild-type strain showed upregulation of several secondary-metabolism-related genes. In addition, many genes predicted to be involved in mycoparasitism and plant interactions were also upregulated. We used tamarind seeds as a mass multiplication medium in solid-state fermentation and, using talcum powder as a carrier, developed a novel seed dressing formulation. A comparative evaluation of the wild type and the mutant in greenhouse under high disease pressure (using the test pathogen Sclerotium rolfsii) revealed superiority of the mutant over wild type in protecting chickpea (Cicer arietinum) seeds and seedlings from infection. We then undertook extensive field evaluation (replicated micro-plot trials, on-farm demonstration trials, and large-scale trials in farmers' fields) of our mutant-based formulation (named TrichoBARC) for management of collar rot (S. rolfsii) in chickpea and lentil (Lens culinaris) over multiple locations in India. In certain experiments, other available formulations were included for comparison. This formulation consistently, over multiple locations and years, improved seed germination, reduced seedling mortality, and improved plant growth and yield. We also noticed growth promotion, improved pod bearing, and early flowering (7-10 days) in TrichoBARC-treated chickpea and lentil plants under field conditions. In toxicological studies in animal models, this formulation exhibited no toxicity to mammals, birds, or fish.

A comprehensive review on fungal endophytes and its dynamics on Orchidaceae plants: current research, challenges, and future possibilities

In the development of medicinally important Orchidaceae, the extent of fungal endophytes specificity is not presently very clear. Limited study has been available on natural products formed and its role on plant growth, defence mechanism by endophytes, and to characterize the chief treasure of bioactive molecules. Therefore, this review article presents an evaluation of the endophytes associated with Orchidaceae for physiology, metabolism, and genomics which have prominently contributed to the resurgence of novel metabolite research increasing our considerate of multifaceted mechanisms regulatory appearance of biosynthetic gene groups encoding diverse metabolites. Additionally, we presented the comprehensive recent development of bio-strategies for the cultivation of endophytes from Orchidaceae and integration of bioengineered ‘Genomics with metabolism’ approaches with emphases collective omics as powerful approach to discover novel metabolite compounds. The Orchidaceae-fungal endophytes' biodynamics for sustainable development of bioproducts and its applications are supported in large-scale biosynthesis of industrially and pharmaceutical important biomolecules.

Genetic dereplication of Trichoderma hypoxylon reveals two novel polycyclic lactones

Previous study demonstrated large scale production of trichochecenes which limited the discovery of novel metabolites in Trichoderma hypoxylon. By genetic deletion of trichothecene synthase encoding gene thtri5, we created the dereplication mutant which eliminated the production of trichothecenes. Through chemical isolation, we characterized a couple of rare new polycyclic lactones tricholactones A and B from the thtri5 deletion strain. The structures of these two compounds were well determined by NMR, HR-ESI-MS and IECD analysis.

Trichoderma atroviride: an isolate from forest environment with secondary metabolites with high antimicrobial potential

This work was focused on the characterization of novel isolate of Trichoderma atroviride O1, found in the forest around the village of Zázrivá (the Northern Slovakia, region Orava). The isolate was identified by sequencing its internal transcribed spacer (ITS) region of rDNA. T. atroviride O1 stimulated the development of lateral roots of model plant Lepidium sativum. Simultaneously, the isolate has proved its high mycoparasitic potential as it displayed the ability to attack colonies of phytopathogenic fungi (Alternaria alternata, Fusarium culmorum, Botrytis cinerea). This isolate produced secondary metabolites, which were isolated and tested for the antimicrobial activity against gram-positive bacteria Staphylococcus epidermidis and Staphylococcus aureus. The growth of these bacteria was suppressed to 10 % and 40 %, respectively. The suppression of the growth of two Candida species was also strong (10 % growth). However, growth parameters of three phytopathogenic fungi (Alternaria alternata, Botrytis cinerea and Fusarium culmorum) were less affected (75 % growth in comparison with the control). Attempts were made to characterize secondary metabolites isolated from T. atroviride O1. Known peptaibols, 20—21 amino acid long, but also shorter peptides, were detected by MALDI-TOF mass spectrometry. Thus, this study demonstrates the plant growth promotion, strong mycoparasitic potential and antimicrobial activity of the isolate T. atroviride O1, which could be in part ascribed to the production of secondary metabolites. This isolate does have a potential in the biocontrol in eco-farming. Further study, particularly, the identification of produced secondary metabolites, is needed.

Effects of ultraviolet irradiation on the in vitro antagonistic potential of Trichoderma spp. against soil-borne fungal pathogens

Development of new effective biocontrol agents is largely based on the antagonistic capacity of candidate agents against targeted pathogens in vitro. Different mechanisms contribute to such capacity, including the activity of cell wall-degrading enzymes, secretion of antimicrobial secondary metabolites, growth vigour and resistance to exogenous and endogenous toxins. In this study, a series of laboratory experiments were designed to improve the antagonistic activities of Trichoderma spp. against two plant fungal pathogens, Sclerotium rolfsii and Rhizoctonia solani. A simple but efficient mutagenesis programme was carried out using ultraviolet light to induce modifications in the genetic structure of two Trichoderma biocontrol agents, T. virens and T. asperellum. The obtained mutants were subjected to a) initial screening for media-permeable antifungal metabolites using the cellophane membrane-based method, and b) selected mutants were subjected to a series of antagonistic tests. Results revealed that the antagonistic potential of selected mutants was significantly improved against the two plant pathogens. Genetic stability test results indicated that the UV-derived mutant Tv3, maintained its elevated performance after 12 rounds of sub-culture. Gene expression analysis for five antagonism-associated genes were examined using real-Time PCR. Results revealed that the gene expression of two genes, chitinase 33, a cell wall degrading enzyme and, polyketide synthase, which is responsible for polyketide biosynthesis, a class of secondary metabolites with antimicrobial roles, were significantly upregulated in one of the mutated T. virens strains. Results of our in vitro antagonistic studies along with our molecular analysis indicate that the UV mutagenesis could be an effective strategy to improve Trichoderma antagonistic potential.

Trichodermatides E and F from fungus Trichoderma applanatum

Two new polyketide derivatives, trichodermatides E (1) and F (2), are unprecedented examples of a polyketide with 6/6/6/6 tetracyclic skeleton, together with five known analogs koninginin B (3), koninginin D (4), 7-O-methylkoninginin D (5), koninginins E and F (6-7), were isolated from the plant endophytic fungus Trichoderma applanatum. The structures of these two compounds were determined by NMR data and HR-ESI-MS analysis. The putative biosynthesis of compounds 1-7 was presented.

An effective method of utilizing vegetable waste in the form of carriers for Trichoderma strains with phytosanitary properties

It has been assumed that compost from savoy cabbage and rapeseed straw is a good substrate for discrimination of the reproduction potential of Trichoderma strains. This hypothesis was verified based on a two-stage incubation experiment. The prepared mixture was fermented in a bio-reactor for 11 weeks. In the second experiment, the mature compost was inoculated with four strains of Trichoderma and a spore concentration of 10⁴ and 10⁶, and then incubated for four weeks. The biomass of autogenic fungi reached a maximum of 12.5 mg∙g^-1 DM in the cooling phase. The variability in temperature during composting significantly affected NH₃ emission. The pH of mature compost from cabbage wastes, as a result of the elevated NH₃ emission reached the alkaline range. The survival of the Trichoderma fungi introduced into the alkali substrate was a result of strain sensitivity to the high pH of the compost and to the initial inoculum density. The adaptation potential of Trichoderma harzianum to the alkali milieu depended on the pH stabilization of the substrate by this fungi, provided the spore inoculum density was 10⁶. The strains of Trichoderma atroviride responded negatively, regardless of the inoculum density, to the alkaline pH of the substrate and to self-induced changes in the compost pH.

Dithiodiketopiperazine derivatives from endophytic fungi Trichoderma harzianum and Epicoccum nigrum

A new epidithiodiketopiperazine (ETP), pretrichodermamide G (1), along with three known (epi)dithiodiketopiparazines (2-4) were isolated from cultures of Trichoderma harzianum and Epicoccum nigrum, endophytic fungi associated with medicinal plants Zingiber officinale and Salix sp., respectively. The structure of the new compound (1) was established on the basis of spectroscopic data, including 1D/2D NMR and HRESIMS. The isolated compounds were investigated for their antifungal, antibacterial and cytotoxic potential against a panel of microorganisms and cell lines. Pretrichodermamide A (2) displayed antimicrobial activity towards the plant pathogenic fungus Ustilago maydis and the human pathogenic bacterium Mycobacterium tuberculosis with MIC values of 1 mg/mL (2 mM) and 25 µg/mL (50 µM), respectively. Meanwhile, epicorazine A (3) exhibited strong to moderate cytotoxicity against L5178Y, Ramos, and Jurkat J16 cell lines with IC₅₀ values ranging from 1.3 to 28 µM. Further mechanistic studies indicated that 3 induces apoptotic cell death.

Co-cultivation of Trichoderma asperellum GDFS1009 and Bacillus amyloliquefaciens 1841 Causes Differential Gene Expression and Improvement in the Wheat Growth and Biocontrol Activity

In an effort to balance the demands of plant growth promoting and biological control agents in a single product, the technology on the co-cultivation of two microbes, Trichoderma asperellum GDFS1009 and Bacillus amyloliquefaciens 1841 has been developed and demonstrated its effectiveness in synergistic interactions and its impact on the plant growth and biocontrol potential. In this study, optimization of T. asperellum and B. amyloliquefaciens growth in a single medium was carried out using response surface methodology (RSM). The optimal medium for enhanced growth was estimated as 2% yeast extract, 2% molasses and 2% corn gluten meal. T. asperellum evolved the complicated molecular mechanisms in the co-culture by the induction of BLR-1/BLR-2, VELVET, and NADPH oxidases genes. In performance with these genes, conserved signaling pathways, such as heterotrimeric G proteins and mitogen-activated protein kinases (MAPKs) had also involved in this molecular orchestration. The co-cultivation induced the expression of T. asperellum genes related to secondary metabolism, mycoparasitism, antioxidants and plant growth. On the other hand, the competition during co-cultivation induced the production of new compounds that are not detected in axenic cultures. In addition, the co-culture significantly enhanced the plant growth and protection against Fusarium graminearum. The present study demonstrated the potential of co-cultivation technology could be a used to grow the T. asperellum GDFS1009 and B. amyloliquefaciens 1841 synergistically to improve the production of mycoparasitism related enzymes, secondary metabolites, and plant growth promoting compounds to significantly enhance the plant growth and protection against plant pathogens.

Distribution and Evolution of Nonribosomal Peptide Synthetase Gene Clusters in the Ceratocystidaceae

In filamentous fungi, genes in secondary metabolite biosynthetic pathways are generally clustered. In the case of those pathways involved in nonribosomal peptide production, a nonribosomal peptide synthetase (NRPS) gene is commonly found as a main element of the cluster. Large multifunctional enzymes are encoded by members of this gene family that produce a broad spectrum of bioactive compounds. In this research, we applied genome-based identification of nonribosomal peptide biosynthetic gene clusters in the family Ceratocystidaceae. For this purpose, we used the whole genome sequences of species from the genera Ceratocystis,Davidsoniella,Thielaviopsis, Endoconidiophora,Bretziella, Huntiella, and Ambrosiella. To identify and characterize the clusters, different bioinformatics and phylogenetic approaches, as well as PCR-based methods were used. In all genomes studied, two highly conserved NRPS genes (one monomodular and one multimodular) were identified and their potential products were predicted to be siderophores. Expression analysis of two Huntiella species (H. moniliformis and H. omanensis) confirmed the accuracy of the annotations and proved that the genes in both clusters are expressed. Furthermore, a phylogenetic analysis showed that both NRPS genes of the Ceratocystidaceae formed distinct and well supported clades in their respective phylograms, where they grouped with other known NRPSs involved in siderophore production. Overall, these findings improve our understanding of the diversity and evolution of NRPS biosynthetic pathways in the family Ceratocystidaceae.

Symbiotic Root-Endophytic Soil Microbes Improve Crop Productivity and Provide Environmental Benefits

Plants should not be regarded as entities unto themselves, but as the visible part of plant-microbe complexes which are best understood as "holobiomes." Some microorganisms when given the opportunity to inhabit plant roots become root symbionts. Such root colonization by symbiotic microbes can raise crop yields by promoting the growth of both shoots and roots, by enhancing uptake, fixation, and/or more efficient use of nutrients, by improving plants' resistance to pests, diseases, and abiotic stresses that include drought, salt, and other environmental conditions, and by enhancing plants' capacity for photosynthesis. We refer plant-microbe associations with these capabilities that have been purposefully established as enhanced plant holobiomes (EPHs). Here, we consider four groups of phylogenetically distinct and distant symbiotic endophytes: (1) Rhizobiaceae bacteria; (2) plant-obligate arbuscular mycorrhizal fungi (AMF); (3) selected endophytic strains of fungi in the genus Trichoderma; and (4) fungi in the Sebicales order, specifically Piriformospora indica. Although these exhibit quite different "lifestyles" when inhabiting plants, all induce beneficial systemic changes in plants' gene expression that are surprisingly similar. For example, all induce gene expression that produces proteins which detoxify reactive oxygen species (ROS). ROS are increased by environmental stresses on plants or by overexcitation of photosynthetic pigments. Gene overexpression results in a cellular environment where ROS levels are controlled and made more compatible with plants' metabolic processes. EPHs also frequently exhibit increased rates of photosynthesis that contribute to greater plant growth and other capabilities. Soil organic matter (SOM) is augmented when plant root growth is increased and roots remain in the soil. The combination of enhanced photosynthesis, increasing sequestration of CO2 from the air, and elevation of SOM removes C from the atmosphere and stores it in the soil. Reductions in global greenhouse gas levels can be accelerated by incentives for carbon farming and carbon cap-and-trade programs that reward such climate-friendly agriculture. The development and spread of EPHs as part of such initiatives has potential both to enhance farm productivity and incomes and to decelerate global warming.

Plant defense against fungal pathogens by antagonistic fungi with Trichoderma in focus

Fungal diseases cause considerable damage to the economically important crops worldwide thus posing continuous threat to global food security. Management of these diseases is normally done via utilization of chemicals that have severe negative impact upon human health and surrounding ecosystems. Finding eco-friendly alternatives has led the researchers to focus towards biological control of fungal diseases through biocontrol agents such as antagonistic fungi (AF) and other microorganisms. AF include various genera of fungi that cure the fungal diseases on plants effectively. Furthermore, they play a regulatory role in various plant physiological pathways and interactions. AF are highly host specific having negligible effects on non-target organisms and have fast mass production capability. However, understanding the mechanisms of the effects of AF on plant diseases is a prerequisite for their effective utilization as biocontrol agent. Trichoderma is one of the most important fungal genera known for its antagonistic activity against disease causing fungal pathogens. Therefore, in this review, we have focused upon Trichoderma-mediated fungal diseases management via illustrating its taxonomy, important strains, biodiversity and mode of action. Furthermore, we have assessed the criteria to be followed for selection of AF and the factors influencing their efficiency. Finally, we evaluated the advantages and limitations of Trichoderma as AF. We conclude that effective AF utilization against fungal pathogens can serve as a safe strategy for our Planet.

Bacillus subtilis PTA-271 Counteracts Botryosphaeria Dieback in Grapevine, Triggering Immune Responses and Detoxification of Fungal Phytotoxins

Plant pathogens have evolved various strategies to enter hosts and cause diseases. Particularly Neofusicoccum parvum, a member of Botryosphaeria dieback consortium, can secrete the phytotoxins (-)-terremutin and (R)-mellein during grapevine colonization. The contribution of phytotoxins to Botryosphaeria dieback symptoms still remains unknown. Moreover, there are currently no efficient control strategies of this disease, and agro-environmental concerns have raised increasing interest in biocontrol strategies to limit disease spread in vineyards, especially by using some promising beneficial bacteria. Here, we first examined in planta the biocontrol capacity of Bacillus subtilis PTA-271 against N. parvum Np-Bt67 strain producing both (-)-terremutin and (R)-mellein. We then focused on the direct effects of PTA-271 on pathogen growth and the fate of pure phytotoxins, and explored the capacity of PTA-271 to induce or prime grapevine immunity upon pathogen infection or phytotoxin exposure. Results provided evidence that PTA-271 significantly protects grapevine cuttings against N. parvum and significantly primes the expression of PR2 (encoding a β-1,3-glucanase) and NCED2 (9-cis-epoxycarotenoid dioxygenase involved in abscisic acid biosynthesis) genes upon pathogen challenge. Using in vitro plantlets, we also showed that PTA-271 triggers the expression of salicylic acid- and jasmonic acid-responsive genes, including GST1 (encoding a glutathione-S-transferase) involved in detoxification process. However, in PTA-271-pretreated plantlets, exogenous (-)-terremutin strongly lowered the expression of most of upregulated genes, except GST1. Data also indicated that PTA-271 can detoxify both (-)-terremutin and (R)-mellein and antagonize N. parvum under in vitro conditions. Our findings highlight (-)-terremutin and (R)-mellein as key aggressive molecules produced by N. parvum that may weaken grapevine immunity to promote Botryosphaeria dieback symptoms. However, PTA-271 can efficiently attenuate Botryosphaeria dieback by enhancing some host immune responses and detoxifying both phytotoxins produced by N. parvum.

Trichoderma atroviride from Predator to Prey: Role of the Mitogen-Activated Protein Kinase Tmk3 in Fungal Chemical Defense against Fungivory by Drosophila melanogaster Larvae

Fungi, like other organisms, have natural predators, including fungivorous nematodes and arthropods that use them as an important food source. Thus, they require mechanisms to detect and respond to injury. Trichoderma atroviride responds to mycelial injury by rapidly regenerating its hyphae and developing asexual reproduction structures. Whether this injury response is associated with attack by fungivorous insects is unknown. Therefore, determining the possible conservation of a defense mechanism to predation in T. atroviride and plants and elucidating the mechanisms involved in the establishment of this response is of major interest. Here, we describe the chemical response of T. atroviride to mechanical injury and fungivory and the role of a MAPK pathway in the regulation of this response.

The response to injury represents an important strategy for animals and plants to survive mechanical damage and predation. Plants respond to injury by activating a defense response that includes the production of an important variety of compounds that help them withstand predator attack and recover from mechanical injury (MI). Similarly, the filamentous fungus Trichoderma atroviride responds to MI by strongly modifying its transcriptional profile and producing asexual reproduction structures (conidia). Here, we analyzed whether the response to MI in T. atroviride is related to a possible predator defense mechanism from a metabolic perspective. We found that the production of specific groups of secondary metabolites increases in response to MI but is reduced after fungivory by Drosophila melanogaster larvae. We further show that fungivory results in repression of the expression of genes putatively involved in the regulation of secondary metabolite production in T. atroviride. Activation of secondary metabolite production appears to depend on the mitogen-activated protein kinase (MAPK) Tmk3. Interestingly, D. melanogaster larvae preferred to feed on a tmk3 gene replacement mutant rather than on the wild-type strain. Consumption of the mutant strain, however, resulted in increased larval mortality.

IMPORTANCE Fungi, like other organisms, have natural predators, including fungivorous nematodes and arthropods that use them as an important food source. Thus, they require mechanisms to detect and respond to injury. Trichoderma atroviride responds to mycelial injury by rapidly regenerating its hyphae and developing asexual reproduction structures. Whether this injury response is associated with attack by fungivorous insects is unknown. Therefore, determining the possible conservation of a defense mechanism to predation in T. atroviride and plants and elucidating the mechanisms involved in the establishment of this response is of major interest. Here, we describe the chemical response of T. atroviride to mechanical injury and fungivory and the role of a MAPK pathway in the regulation of this response.

STE20/PAKA Protein Kinase Gene Releases an Autoinhibitory Domain through Pre-mRNA Alternative Splicing in the Dermatophyte Trichophyton rubrum

Signaling pathways are highly diverse in filamentous fungi, allowing the cells to receive and process ambient information. Interaction of components from different pathways results in signaling networks. The mitogen-activated protein kinase (MAPK) pathway is dependent on phosphorylation that is accomplished by kinase proteins. Thus, the STE/PAK protein kinase family plays essential roles in MAPK signal transduction, regulating several cellular functions. The STE/PAK protein displays an autoinhibitory (Cdc42/Rac interactive binding-CRIB) domain on its N-terminal portion, which interacts with the C-terminal catalytic kinase domain. Based on current knowledge, for the STE/PAK kinase to be activated, molecular signals (e.g., interaction with the activated form of Rac1 and Cdc42 proteins) or proteolytic cleavage by caspase 3 is necessary. Both mechanisms release the kinase domain from the CRIB interaction. Here, we hypothesize a novel molecular mechanism for the activation of STE20/PAKA kinase in Trichophyton rubrum based on an alternative pre-mRNA splicing process. Our data suggest that, because of the retention of intron 1 of this gene, it is theoretically possible that the translation of STE20/PAKA kinase will be free of its autoinhibitory CRIB domain. These findings indicate a rapid response system to environmental changes. Furthermore, STE20/PAKA may be a potential T. rubrum virulence factor and an interesting target for new drugs against dermatophytes.

Safety of the fungal workhorses of industrial biotechnology: update on the mycotoxin and secondary metabolite potential of Aspergillus niger, Aspergillus oryzae, and Trichoderma reesei

This review presents an update on the current knowledge of the secondary metabolite potential of the major fungal species used in industrial biotechnology, i.e., Aspergillus niger, Aspergillus oryzae, and Trichoderma reesei. These species have a long history of safe use for enzyme production. Like most microorganisms that exist in a challenging environment in nature, these fungi can produce a large variety and number of secondary metabolites. Many of these compounds present several properties that make them attractive for different industrial and medical applications. A description of all known secondary metabolites produced by these species is presented here. Mycotoxins are a very limited group of secondary metabolites that can be produced by fungi and that pose health hazards in humans and other vertebrates when ingested in small amounts. Some mycotoxins are species-specific. Here, we present scientific basis for (1) the definition of mycotoxins including an update on their toxicity and (2) the clarity on misclassification of species and their mycotoxin potential reported in literature, e.g., A. oryzae has been wrongly reported as an aflatoxin producer, due to misclassification of Aspergillus flavus strains. It is therefore of paramount importance to accurately describe the mycotoxins that can potentially be produced by a fungal species that is to be used as a production organism and to ensure that production strains are not capable of producing mycotoxins during enzyme production. This review is intended as a reference paper for authorities, companies, and researchers dealing with secondary metabolite assessment, risk evaluation for food or feed enzyme production, or considerations on the use of these species as production hosts.

Volatile Compound-Mediated Recognition and Inhibition Between Trichoderma Biocontrol Agents and Fusarium oxysporum

Certain Trichoderma strains protect plants from diverse pathogens using multiple mechanisms. We report a novel mechanism that may potentially play an important role in Trichoderma-based biocontrol. Trichoderma virens and T. viride significantly increased the amount/activity of secreted antifungal metabolites in response to volatile compounds (VCs) produced by 13 strains of Fusarium oxysporum, a soilborne fungus that infects diverse plants. This response suggests that both Trichoderma spp. recognize the presence of F. oxysporum by sensing pathogen VCs and prepare for attacking pathogens. However, T. asperellum did not respond to any, while T. harzianum responded to VCs from only a few strains. Gene expression analysis via qPCR showed up-regulation of several biocontrol-associated genes in T. virens in response to F. oxysporum VCs. Analysis of VCs from seven F. oxysporum strains tentatively identified a total of 28 compounds, including six that were produced by all of them. All four Trichoderma species produced VCs that inhibited F. oxysporum growth. Analysis of VCs produced by T. virens and T. harzianum revealed the production of compounds that had been reported to display antifungal activity. F. oxysporum also recognizes Trichoderma spp. by sensing their VCs and releases VCs that inhibit Trichoderma, suggesting that both types of VC-mediated interaction are common among fungi.

Constitutive hyperproduction of sorbicillinoids in Trichoderma reesei ZC121

BACKGROUND

In addition to its outstanding cellulase production ability, Trichoderma reesei produces a wide variety of valuable secondary metabolites, the production of which has not received much attention to date. Among them, sorbicillinoids, a large group of hexaketide secondary metabolites derived from polyketides, are drawing a growing interest from researchers because they exhibit a variety of important biological functions, including anticancer, antioxidant, antiviral, and antimicrobial properties. The development of fungi strains with constitutive, hyperproduction of sorbicillinoids is thus desired for future industry application but is not well-studied. Moreover, although T. reesei has been demonstrated to produce sorbicillinoids with the corresponding gene cluster and biosynthesis pathway proposed, the underlying molecular mechanism governing sorbicillinoid biosynthesis remains unknown.

RESULTS

Recombinant T. reesei ZC121 was constructed from strain RUT-C30 by the insertion of the gene 12121-knockout cassette at the telomere of T. reesei chromosome IV in consideration of the off-target mutagenesis encountered during the unsuccessful deletion of gene 121121. Strain ZC121, when grown on cellulose, showed a sharp reduction of cellulase production, but yet a remarkable enhancement of sorbicillinoids production as compared to strain RUT-C30. The hyperproduction of sorbicillinoids is a constitutive process, independent of culture conditions such as carbon source, light, pH, and temperature. To the best of our knowledge, strain ZC121 displays record sorbicillinoid production levels when grown on both glucose and cellulose. Sorbicillinol and bisvertinolone are the two major sorbicillinoid compounds produced. ZC121 displayed a different morphology and markedly reduced sporulation compared to RUT-C30 but had a similar growth rate and biomass. Transcriptome analysis showed that most genes involved in cellulase production were downregulated significantly in ZC121 grown on cellulose, whereas remarkably all genes in the sorbicillinoid gene cluster were upregulated on both cellulose and glucose.

CONCLUSION

A constitutive sorbicillinoid-hyperproduction strain T. reesei ZC121 was obtained by off-target mutagenesis, displaying an overwhelming shift from cellulase production to sorbicillinoid production on cellulose, leading to a record for sorbicillinoid production. For the first time, T. reesei degraded cellulose to produce platform chemical compounds other than protein in high yield. We propose that the off-target mutagenesis occurring at the telomere region might cause chromosome remodeling and subsequently alter the cell structure and the global gene expression pattern of strain ZC121, as shown by phenotype profiling and comparative transcriptome analysis of ZC121. Overall, T. reesei ZC121 holds great promise for the industrial production of sorbicillinoids and serves as a good model to explore the regulation mechanism of sorbicillinoids' biosynthesis.

Functional analysis of polyketide synthase genes in the biocontrol fungus Clonostachys rosea

Clonostachys rosea is a mycoparasitic fungus used for biological control of plant diseases. Its genome contains 31 genes putatively encoding for polyketide synthases (PKSs), 75% of which are arranged in biosynthetic gene clusters. Gene expression analysis during C. rosea interactions with the fungal plant pathogens Botrytis cinerea and Fusarium graminearum showed common and species-specific induction of PKS genes. Our data showed a culture media dependent correlation between PKS gene expression and degree of antagonism in C. rosea. The pks22 and pks29 genes were highly induced during fungal-fungal interactions but not during pigmentation, and gene deletion studies revealed that PKS29 was required for full antagonism against B. cinerea, and for biocontrol of fusarium foot rot on barley. Metabolite analysis revealed that Δpks29 strains has a 50% reduced production (P = 0.001) of an unknown polyketide with molecular formula C₁₅H₂₈O₃, while Δpks22 strains lost the ability to produce four previously unknown polyketides named Clonorosein A-D. Clonorosein A and B were purified, their structures determined, and showed strong antifungal activity against B. cinerea and F. graminearum. These results show that PKS22 is required for production of antifungal polyketide Clonorosein A-D, and demonstrate the role of PKS29 in antagonism and biocontrol of fungal plant diseases.

Genomic characterization of Trichoderma atrobrunneum (T. harzianum species complex) ITEM 908: insight into the genetic endowment of a multi-target biocontrol strain

BACKGROUND

So far, biocontrol agent selection has been performed mainly by time consuming in vitro confrontation tests followed by extensive trials in greenhouse and field. An alternative approach is offered by application of high-throughput techniques, which allow extensive screening and comparison among strains for desired genetic traits. In the genus Trichoderma, the past assignments of particular features or strains to one species need to be reconsidered according to the recent taxonomic revisions. Here we present the genome of a biocontrol strain formerly known as Trichoderma harzianum ITEM 908, which exhibits both growth promoting capabilities and antagonism against different fungal pathogens, including Fusarium graminearum, Rhizoctonia solani, and the root-knot nematode Meloidogyne incognita. By genomic analysis of ITEM 908 we investigated the occurrence and the relevance of genes associated to biocontrol and stress tolerance, providing a basis for future investigation aiming to unravel the complex relationships between genomic endowment and exhibited activities of this strain.

RESULTS

The MLST analysis of ITS-TEF1 concatenated datasets reclassified ITEM 908 as T. atrobrunneum, a species recently described within the T. harzianum species complex and phylogenetically close to T. afroharzianum and T. guizhouense. Genomic analysis revealed the presence of a broad range of genes encoding for carbohydrate active enzymes (CAZYmes), proteins involved in secondary metabolites production, peptaboils, epidithiodioxopiperazines and siderophores potentially involved in parasitism, saprophytic degradation as well as in biocontrol and antagonistic activities. This abundance is comparable to other Trichoderma spp. in the T. harzianum species complex, but broader than in other biocontrol species and in the species T. reesei, known for its industrial application in cellulase production. Comparative analysis also demonstrated similar genomic organization of major secondary metabolites clusters, as in other Trichoderma species.

CONCLUSIONS

Reported data provide a contribution to a deeper understanding of the mode of action and identification of activity-specific genetic markers useful for selection and improvement of biocontrol strains. This work will also enlarge the availability of genomic data to perform comparative studies with the aim to correlate phenotypic differences with genetic diversity of Trichoderma species.

Genome-wide analysis of cytochrome P450s of Trichoderma spp.: annotation and evolutionary relationships

Background

Cytochrome P450s form an important group of enzymes involved in xenobiotics degradation and metabolism, both primary and secondary. These enzymes are also useful in industry as biotechnological tools for bioconversion and a few are reported to be involved in pathogenicity. Trichoderma spp. are widely used in industry and agriculture and are known for their biosynthetic potential of a large number of secondary metabolites. For realising the full biosynthetic potential of an organism, it is important to do a genome-wide annotation and cataloguing of these enzymes.

Results

Here, we have studied the genomes of seven species (T. asperellum, T. atroviride, T. citrinoviride, T. longibrachiatum, T. reesei , T. harzianum and T. virens) and identified a total of 477 cytochrome P450s. We present here the classification, evolution and structure as well as predicted function of these proteins. This study would pave the way for functional characterization of these groups of enzymes and will also help in realization of their full economic potential.

Conclusion

Our CYPome annotation and evolutionary studies of the seven Trichoderma species now provides opportunities for exploration of research-driven strategies to select Trichoderma species for various applications especially in relation to secondary metabolism and degradation of environmental pollutants.

Antifungal potential of crude extracts of Trichoderma spp

Abstract Antibiosis is the mechanism by which certain microorganisms respond to the presence of others, secreting compounds or metabolites capable of inhibiting or impeding their development. The crude extract of Trichoderma contains a mixture of secondary compounds, which may show antibiotic effect, and has been used for the prospect of this fungus for biological control and other industrial purposes. Faced with the increasing demand of agriculture for ecologically compatible alternatives for the management of diseases, this work aimed to investigate the spectrum of action of Non-Volatile Metabolites (NVMs) of Trichoderma isolates against different plant pathogenic fungi. The antagonistic potential of NVMs was evaluated through the incorporation method of the filtered liquid extract in PDA medium. The assays showed that all the NVMs produced inhibited the fungus Sclerotinia sclerotiorum similarly. On the other hand, strains CEN1245 and CEN1274, both belonging to the species Trichoderma brevicompactum, showed broad spectrum against Sclerotium rolfsii, Colletotrichum gloesporioides, Verticillium dahliae, Fusarium oxysporum and Cylindrocladium sp. The present study describes isolates producing non-volatile metabolites with broad spectrum of antifungal action, as well as pathogen-specific. The Trichoderma spp. NVMs obtained from different soil samples cultivated with vegetables, cassava and maize were efficient in inhibiting plant pathogenic fungi belonging to other patossystems, such as forest or fruit, which could increase their potential application in biological control of plant diseases. In addition, these antagonistic fungi should be studied in greater depth for the identification of bioactive molecules of industrial interest or in commercial formulations of products for biological control of plant pathogens.