Trichoderma as biological control agent: scope and prospects to improve efficacy

Cytochrome P450 CYP736A12 is crucial for Trichoderma asperellum-induced alleviation of phoxim phytotoxicity and reduction of pesticide residue in tomato roots

Trichoderma can enhance the metabolism of organophosphate pesticides in plants, but the mechanism is unclear. Here, we performed high-throughput transcriptome sequencing of roots upon Trichoderma asperellum (TM) inoculation and phoxim (P) application in tomato (Solanum lycopersicum L.). A total of 4059 differentially expressed genes (DEGs) were obtained, including 2110 up-regulated and 1949 down-regulated DEGs in P vs TM+P. COG and KOG analysis indicated that DEGs were mainly enriched in signal transduction mechanisms. We then focused on the pesticide detoxification pathway and screened out cytochrome P450 CYP736A12 as a putative gene for functional analysis. We suppressed the expression of CYP736A12 in tomato plants by virus-induced gene silencing and analyzed tissue-specific phoxim residues, oxidative stress markers, glutathione pool, GST activity and related gene expression. Silencing CYP736A12 significantly increased phoxim residue and induced oxidative stress in tomato plants, by attenuating the TM-induced increased activity of antioxidant and detoxification enzymes, redox homeostasis and transcripts of detoxification genes including CYP724B2, GSH1, GSH2, GR, GPX, GST1, GST2, GST3, and ABC. The study revealed a critical mechanism by which TM promotes the metabolism of phoxim in tomato roots, which can be useful for further understanding the Trichoderma-induced xenobiotic detoxification and improving food safety.

Inhibition of Potato Fusarium Wilt by Bacillus subtilis ZWZ-19 and Trichoderma asperellum PT-29: A Comparative Analysis of Non-Targeted Metabolomics

Potato Fusarium Wilt is a soil-borne fungal disease that can seriously harm potatoes throughout their growth period and occurs at different degrees in major potato-producing areas in China. To reduce the use of chemical agents and improve the effect of biocontrol agents, the inhibitory effects of the fermentation broth of Bacillus subtilis ZWZ-19 (B) and Trichoderma asperellum PT-29 (T) on Fusarium oxysporum were compared under single-culture and co-culture conditions. Furthermore, metabolomic analysis of the fermentation broths was conducted. The results showed that the inhibitory effect of the co-culture fermentation broth with an inoculation ratio of 1:1 (B1T1) was better than that of the separately cultured fermentation broths and had the best control effect in a potted experiment. Using LC-MS analysis, 134 metabolites were determined and classified into different types of amino acids. Furthermore, 10 metabolic pathways had the most significant variations, and 12 were related to amino acid metabolism in the KEGG analysis. A correlation analysis of the 79 differential metabolites generated through the comprehensive comparison between B, T, and B1T1 was conducted, and the results showed that highly abundant amino acids in B1T1 were correlated with amino acids in B, but not in T.

Pest risk assessment of Leucinodes orbonalis for the European Union

Following a request from the European Commission, the EFSA Panel on Plant Health performed a quantitative risk assessment of Leucinodes orbonalis (Lepidoptera: Crambidae), the eggplant fruit and shoot borer, for the EU. The assessment focused on potential pathways for entry, climatic conditions favouring establishment, spread and impact. Options for risk reduction are discussed but effectiveness was not quantified. L. orbonalis is a key pest of eggplant (aubergine/brinjal) in the Indian subcontinent and occurs throughout most of southern Asia with records mostly from India and Bangladesh. The main pathway of entry is fruit of solanaceous plants, primarily exotic varieties of eggplant, Solanum melongena and turkey berry, S. torvum. The trade in both commodities from Asia is small but nevertheless dwarfs the trade in other Solanum fruits from Asia (S. aethiopicum, S. anguivi, S. virginianum, S. aculeatissimum, S. undatum). Other Solanum fruits were therefore not further assessed as potential pathways. The trade in eggplant from Asia consists of special fruit types and caters mostly to niche markets in the EU, while most eggplant consumed in Europe is produced in southern European and northern African countries, where L. orbonalis does not occur. Using expert knowledge elicitation (EKE) and pathway modelling, the Panel estimated that approximately 3-670 infested fruit (90% certainty range, CR) of S. melongena or fruit bunches of S. torvum enter into regions of the EU that are suitable for L. orbonalis establishment each year. Based on CLIMEX modelling, and using two possible thresholds of ecoclimatic index (EI) to indicate uncertainty in establishment potential, climates favouring establishment occur mostly in southern Europe, where, based on human population, approximately 14% of the imported produce is distributed across NUTS2 regions where EI ≥ 30; or 23% of the produce is distributed where EI ≥ 15. Escape of adult moths occurs mostly from consumer waste. By analysing results of different scenarios for the proportion of S. melongena and S. torvum in the trade, and considering uncertainties in the climatic suitability of southern Europe, adult moth emergence in areas suitable for establishment is expected to vary between 84 individuals per year and one individual per 40 years (based on 90% CR in different scenarios). In the baseline scenario, 25% of the solanaceous fruit from Asia is S. torvum, 75% is S. melongena and EI ≥ 30 is required for establishment. After accounting for the chances of mating, host finding and establishment, the probability of a mated female establishing a founder population in the EU is less than 1 in 100,000 to about 1 event per 622 years (90% CR in baseline scenario). The waiting time until the first establishment is then 622 to more than 100,000 years (CR). If such a founder population were established, the moth is estimated to spread at a rate of 0.65-7.0 km per year after a lag phase of 5-92 years. The impact of the insect on the production of eggplant is estimated to be 0.67%-13% (CR) if growers take no specific action against the insect and 0.13%-1.9% if they do take targeted actions. Tomato (S. lycopersicum) and potato (S. tuberosum) are hosts of L. orbonalis, but the insect does not develop to maturity in tomato fruit, and it does not feed on potato tubers under field conditions; hence, damage to potato can only occur due to feeding on shoots. Tomato and potato are not preferred hosts; nevertheless, impact can occur if populations of L. orbonalis are high and preferred hosts are not available. The Panel did not assess this damage due to insufficient information.

Trichoderma application methods differentially affect the tomato growth, rhizomicrobiome, and rhizosphere soil suppressiveness against Fusarium oxysporum

Trichoderma spp. are widely used to enhance crop growth and suppress diverse diseases. However, inconsistent field efficacy remains a major barrier to their use as a reliable alternative to synthetic pesticides. Various strategies have been investigated to enhance the robustness of their application. Here, we evaluated how T. virens application methods (pre-, at-, and post-transplant) affect the growth of two tomato varieties and their rhizosphere fungal and bacterial communities. Although the greatest rhizosphere abundance of T. virens was observed in the post-transplant application, the at-transplant application promoted tomato growth the most, indicating that greater rhizosphere abundance does not necessarily result in better tomato growth. None of the application methods significantly altered the global rhizosphere fungal and bacterial communities of the tested varieties. Changes in specific microbial genera and guilds may underpin the enhanced tomato growth. We also investigated whether the resulting microbiome changes affect the mycelial growth and conidial germination of Fusarium oxysporum f. sp. lycopersici and F. oxysporum f. sp. radicis-lycopersici, soilborne fungal pathogens of tomato, upon exposure to volatile compounds emitted by culturable rhizosphere microbes and metabolites extracted from the rhizosphere soils after Trichoderma treatments. Volatile compounds produced by cultured rhizosphere microbes after the at-transplant application suppressed the mycelial growth of both pathogens better than those after the other treatments. Similarly, water-soluble metabolites extracted from the rhizosphere soil samples after the at-transplant application most effectively suppressed the germination rate of F. oxysporum spores. Overall, our results suggest that the at-transplant application is most advantageous for promoting the growth of the tested tomato varieties and building soil suppressiveness against the tested fusaria. However, further studies are needed before applying this method to support tomato production. We discuss critical future questions.

Thielaviopsis paradoxa and cultivable mycobiota associated with carapace of Rhynchophorus palmarum L. (Coleoptera: Curculionidae) in the state of Alagoas, Brazil

Rhynchophorus palmarum (Coleoptera: Curculionidae) is a significant agricultural pest in palm plantations across tropical America, playing a critical role as a vector of the fungus Thielaviopsis paradoxa, which is the causative agent of stem bleeding disease in coconut palms. This disease has raised concerns due to its rapid spread and subsequent reduction in coconut production in northeastern Brazil. Additionally, this insect can establish mutualistic interactions with various fungi, including saprophytic, phytopathogenic, and entomopathogenic fungi, underscoring the importance of identifying its external mycobiota. The aim of this study was to assess the presence of T. paradoxa in the digestive tract and identify the cultivable mycobiota associated with the carapace of R. palmarum. To achieve this, a mycological study was conducted by culturing the external surface and digestive tract of field-caught adult insects (10 males and 10 females) on potato dextrose agar (PDA) in Maceió, Alagoas, Brazil. Fungal identification was performed by correlating microscopic features with the macroscopic characteristics of the obtained colonies. The results showed that T. paradoxa was detected in 15.0% of carapace isolates but was not found in the insects' intestinal tract. Additionally, nine fungal genera frequently associated with saprophytic or phytopathogenic behaviors were identified on the carapace. Eight of these genera belong to the Ascomycota phylum, while one is classified in the Basidiomycota phylum. The ubiquitous presence of Paecilomyces spp. and the occurrence of Trichosporon spp. in 95% of the assessed insects stand out. Furthermore, other potentially phytopathogenic fungi such as Penicillium spp., Fusarium spp., and Aspergillus spp., as well as fungi with entomopathogenic potential like Paecilomyces spp., Trichoderma spp., Metarhizium spp., and Beauveria bassiana, were detected. These findings enhance the understanding of the complex interactions between R. palmarum and its fungal hosts, providing insights for integrated pest management strategies.

Trichoderma cf. asperellum and plant-based titanium dioxide nanoparticles initiate morphological and biochemical modifications in Hordeum vulgare L. against Bipolaris sorokiniana

BACKGROUND

Spot blotch is a serious foliar disease of barley (Hordeum vulgare L.) plants caused by Bipolaris sorokiniana, which is a hemibiotrophic ascomycete that has a global impact on productivity. Some Trichoderma spp. is a promising candidate as a biocontrol agent as well as a plant growth stimulant. Also, the application of nanomaterials in agriculture limits the use of harmful agrochemicals and helps improve the yield of different crops. The current study was carried out to evaluate the effectiveness of Trichoderma. cf. asperellum and the biosynthesized titanium dioxide nanoparticles (TiO2 NPs) to manage the spot blotch disease of barley caused by B. sorokiniana and to assess the plant's innate defense response.

RESULTS

Aloe vera L. aqueous leaf extract was used to biosynthesize TiO2 NPs by reducing TiCl4 salt into TiO2 NPs and the biosynthesized NPs were detected using SEM and TEM. It was confirmed that the NPs are anatase-crystalline phases and exist in sizes ranging from 10 to 25 nm. The T. cf. asperellum fungus was detected using morphological traits and rDNA ITS analysis. This fungus showed strong antagonistic activity against B. sorokiniana (57.07%). Additionally, T. cf. asperellum cultures that were 5 days old demonstrated the best antagonistic activity against the pathogen in cell-free culture filtrate. Also, B. sorokiniana was unable to grow on PDA supplemented with 25 and 50 mg/L of TiO2 NPs, and the diameter of the inhibitory zone increased with increasing TiO2 NPs concentration. In an in vivo assay, barley plants treated with T. cf. asperellum or TiO2 NPs were used to evaluate their biocontrol efficiency against B. sorokiniana, in which T. cf. asperellum and TiO2 NPs enhanced the growth of the plant without displaying disease symptoms. Furthermore, the physiological and biochemical parameters of barley plants treated with T. cf. asperellum or TiO2 NPs in response to B. sorokiniana treatment were quantitively estimated. Hence, T. cf. asperellum and TiO2 NPs improve the plant's tolerance and reduce the growth inhibitory effect of B. sorokiniana.

CONCLUSION

Subsequently, T. cf. asperellum and TiO2 NPs were able to protect barley plants against B. sorokiniana via enhancement of chlorophyll content, improvement of plant health, and induction of the barley innate defense system. The present work emphasizes the major contribution of T. cf. asperellum and the biosynthesized TiO2 NPs to the management of spot blotch disease in barley plants, and ultimately to the enhancement of barley plant quality and productivity.

6-Pentyl-α-Pyrone from Trichoderma gamsii Exert Antioxidant and Anti-Inflammatory Properties in Lipopolysaccharide-Stimulated Mouse Macrophages

Filamentous fungi produce several beneficial secondary metabolites, including bioactive compounds, food additives, and biofuels. Trichoderma, which is a teleomorphic Hypocrea that falls under the taxonomic groups Ascomycota and Dikarya, is an extensively studied fungal genus. In an ongoing study that seeks to discover bioactive natural products, we investigated potential bioactive metabolites from the methanolic extract of cultured Trichoderma gamsii. Using liquid chromatography-mass spectrometry (LC-MS), one major compound was isolated and structurally identified as 6-pentyl-α-pyrone (6PP) based on nuclear magnetic resonance data and LC-MS analysis. To determine its antioxidant and anti-inflammatory activity, as well as the underlying mechanisms, we treated lipopolysaccharide (LPS)-stimulated Raw264.7 mouse macrophages with 6PP. We found that 6PP suppresses LPS-induced increase in the levels of nitric oxide, a mediator of oxidative stress and inflammation, and restores LPS-mediated depletion of total glutathione by stabilizing nuclear factor erythroid 2-related factor 2 (Nrf2), an antioxidative factor, and elevating heme oxygenase-1 levels. Furthermore, 6PP inhibited LPS-induced production of proinflammatory cytokines, which are, at least in part, regulated by heme oxygenase-1 (HO-1). 6PP suppressed proinflammatory responses by inhibiting the nuclear localization of nuclear factor kappa B (NF-κB), as well as by dephosphorylating the mitogen-activated protein kinases (MAPKs). These results indicate that 6PP can protect macrophages against oxidative stress and LPS-induced excessive inflammatory responses by activating the Nrf2/HO-1 pathway while inhibiting the proinflammatory, NF-κB, and MAPK pathways.

Microbial consortium mediated acceleration of the defense response in potato against Alternaria solani through prodigious inflation in phenylpropanoid derivatives and redox homeostasis

The present study was carried out in a pot experiment to examine the bioefficacy of three biocontrol agents, viz., Trichoderma viride, Bacillus subtilis, and Pseudomonas fluorescens, either alone or in consortium, on plant growth promotion and activation of defense responses in potato against the early blight pathogen Alternaria solani. The results demonstrate significant enhancement in growth parameters in plants bioprimed with the triple-microbe consortium compared to other treatments. In potato, the disease incidence percentage was significantly reduced in plants treated with the triple-microbe consortium compared to untreated control plants challenged with A. solani. Potato tubers treated with the consortium and challenged with pathogen showed significant activation of defense-related enzymes such as peroxidase (PO) at 96 h after pathogen inoculation (hapi) while, both polyphenol oxidase (PPO), and phenylalanine ammonia-lyase (PAL) at 72 hapi, compared to the individual and dual microbial consortia-treated plants. The expression of antioxidant enzymes like superoxide dismutase (SOD) and catalase (CAT) and the accumulation of pathogenesis-related proteins such as chitinase and β-1,3-glucanase were observed to be highest at 72 hapi in the triple microbe consortium as compared to other treatments. HPLC analysis revealed significant induction in polyphenolic compounds in triple-consortium bioprimed plants compared to the control at 72 hapi. Histochemical analysis of hydrogen peroxide (H2O2) clearly showed maximum accumulation of H2O2 in pathogen-inoculated control plants, while the lowest was observed in triple-microbe consortium at 72 hapi. The findings of this study suggest that biopriming with a microbial consortium improved plant growth and triggered defense responses against A. solani through the induction of systemic resistance via modulation of the phenylpropanoid pathway and antioxidative network.

Transboundary milRNAs: Indispensable molecules in the process of Trichoderma breve T069 mycoparasitism of Botrytis cinerea

Despite the increasing number of fungal microRNA-like small RNAs (milRNAs) being identified and reported, profiling of milRNAs in biocontrol fungi and their roles in the mycoparasitism of pathogenic fungi remains limited. Therefore, in this study, we constructed a GFP fluorescence strain to evaluate the critical period of mycoparasitism in the interaction system between T. breve T069 and B. cinerea. The results showed that the early stage of Trichoderma mycoparasitism occurred 12 h after hyphal contact and was characterized by hyphal parallelism, whereas the middle stage lasted 36 h was characterized by wrapping. The late stage of mycoparasitism occurred at 72 h was characterized by the degradation of B. cinerea mycelia. We subsequently identified the sRNAs of T. breve T069 and B. cinerea during the critical period of mycoparasitism using high-throughput sequencing. In ltR1, 45 potential milRNA targets were identified for 243 genes, and 73 milRNAs targeted 733 genes in ltR3. Additionally, to identify potential transboundary miRNAs in T. breve T069, we screened for miRNAs that were exclusively expressed and had precursor structures in the T. breve T069 genome but were absent in the B. cinerea genome. Next, we predicted the target genes of B. cinerea. Our findings showed that 14 potential transboundary milRNAs from T. breve T069 targeted 41 genes in B. cinerea. Notably, cme-MIR164a-p5_1ss17CT can target 15 genes, including Rim15 (BCIN_15g00280), Nop53 (BCIN_12g03770), Skn7 (BCIN_02g08650), and Vel3 (BCIN_03g06410), while ppe-MIR477b-p3_1ss11TC targeted polyketide synthase (BCIN_03g04360, PKS3). The target gene of PC-5p-27397_41 was a non-ribosomal peptide synthetase (BCIN_01g03730, Bcnrps6). PC-3p-0029 (Tri-milR29) targeted chitin synthetase 7. These genes play crucial roles in normal mycelial growth and pathogenicity of B. cinerea. In conclusion, this study highlights the significance of milRNAs in Trichoderma mycoparasitism of B. cinerea. This discovery provides a new strategy for the application of miRNAs in the prevention and treatment of fungal pathogens.

Molecular Identification of Juglans Regia Endophyte LTL-G3, Its Antifungal Potential and Bioactive Substances

Background

Endophyte is one of the potential biocontrol agents for inhibiting plant pathogens. However, the mechanisms and characteristics involved in the inhibition of different phytopathogenic fungi by endophytes, especially walnut endophytes, are still largely unknown.

Objectives

The present study aimed to identify the walnut endophytic fungus LTL-G3 from a genetic point of view, assess the strain's antifungal activity, and determine the bioactivities of the substances it produces against plant pathogens.

Materials and Methods

The homologous sequence of strain LTL-G3 was examined, and typical strains of the Trichoderma virens group were used to build NJ phylogenetic trees and analyze the taxonomic position of the strain. The biocontrol agent's antagonistic potential for many plant pathogenic fungi. By using silica gel G chromatography, the active components of the strain were separated and purified. The active components were identified using GC-MS and NMR.

Results

The strain LTL-G3 was identified as Trichoderma virens. Its fermentation and secondary metabolite extracts had a broad spectrum and strong inhibitory effect on the spread of six plant pathogens (Botrytis cinerea, Fusarium graminearum, Gloeosporium fructigenum, Phytophthora capsici, Rhizoctonia solani, and Valsa mali) evaluated, of which, its inhibition rate against Valsa mali reached 76.6% (fermentation extract) and 100% (ethyl acetate and n-butanol extracts). On silica gel G chromatography, bioactive compounds were divided into 6 fractions and 7 sub-fractions. Fr.2-2 was the sub-fraction that showed the greatest inhibitory against V. mali, as an inhibition percentage of 89.36% in 1 mg. mL-1. Fifteen key inhibitory chemicals identified using GC-MS. By examining the NMR data, the chemical make-up of the precipitated white solid was identified. The inhibition rate against V. mali increased by over 95% at a dosage of 1 mg. mL-1, indicating a significant linear association between compound A and that rate.

Conclusions

The strain LTL-G3 can be applied as an efficient biological control agent against V. mali, and its highly inhibitive secondary metabolites provide the mechanism for this action.

Bacterial and Fungal Biocontrol Agents for Plant Disease Protection: Journey from Lab to Field, Current Status, Challenges, and Global Perspectives

Plants are constantly exposed to various phytopathogens such as fungi, Oomycetes, nematodes, bacteria, and viruses. These pathogens can significantly reduce the productivity of important crops worldwide, with annual crop yield losses ranging from 20% to 40% caused by various pathogenic diseases. While the use of chemical pesticides has been effective at controlling multiple diseases in major crops, excessive use of synthetic chemicals has detrimental effects on the environment and human health, which discourages pesticide application in the agriculture sector. As a result, researchers worldwide have shifted their focus towards alternative eco-friendly strategies to prevent plant diseases. Biocontrol of phytopathogens is a less toxic and safer method that reduces the severity of various crop diseases. A variety of biological control agents (BCAs) are available for use, but further research is needed to identify potential microbes and their natural products with a broad-spectrum antagonistic activity to control crop diseases. This review aims to highlight the importance of biocontrol strategies for managing crop diseases. Furthermore, the role of beneficial microbes in controlling plant diseases and the current status of their biocontrol mechanisms will be summarized. The review will also cover the challenges and the need for the future development of biocontrol methods to ensure efficient crop disease management for sustainable agriculture.

New frontiers of soil fungal microbiome and its application for biotechnology in agriculture

The fungi-based technology provided encouraging scenarios in the transition from a conventionally based economic system to the potential security of sources closely associated with the agricultural sphere such as the agriculture. In recent years, the intensification of fungi-based processes has generated significant gains, additionally to the production of materials with significant benefits and strong environmental importance. Furthermore, the growing concern for human health, especially in the agriculture scenario, has fostered the investigation of organisms with high biological and beneficial potential for use in agricultural systems. Accordingly, this study offered a comprehensive review of the diversity of the soil fungal microbiome and its main applications in a biotechnological approach aimed at agriculture and food chain-related areas. Moreover, the spectrum of opportunities and the extensive optimization platform for obtaining fungi compounds and metabolites are discussed. Finally, future perspectives regarding the insurgency of innovations and challenges on the broad rise of visionary solutions applied to the biotechnology context are provided.

Trichoderma as a biological control agent: mechanisms of action, benefits for crops and development of formulations

Currently, the food and economic losses generated by the attack of phytopathogens on the agricultural sector constitute a severe problem. Conventional crop protection techniques based on the application of synthetic pesticides to combat these undesirable microorganisms have also begun to represent an inconvenience since the excessive use of these substances is associated with contamination problems and severe damage to the health of farmers, consumers, and communities surrounding the fields, as well as the generation of resistance by the phytopathogens to be combated. Using biocontrol agents such as Trichoderma to mitigate the attack of phytopathogens represents an alternative to synthetic pesticides, safe for health and the environment. This work explains the mechanisms of action through which Trichoderma exerts biological control, some of the beneficial aspects that it confers to the development of crops through its symbiotic interaction with plants, and the bioremedial effects that it presents in fields contaminated by synthetic pesticides. Also, detail the production of spore-based biopesticides through fermentation processes and formulation development.

Evaluation of Trichoderma spp. on Fusarium oxysporum f. sp. asparagi and Fusarium wilt Control in Asparagus Crop

Among the key diseases affecting the asparagus crop (Asparagus officinalis L.), vascular wilting of asparagus caused by Fusarium oxysporum f. sp. asparagi stands out worldwide. This disease significantly shortens the longevity of the crop and limits economic production. Traditional control measures have been largely ineffective, and chemical control methods are difficult to apply, making biological control approaches, specifically the use of Trichoderma, an economical, effective, and risk-free alternative. This study aimed to identify the main factors that affect the efficacy of biopesticides studied as Biological Control Agents (BCAs) against Fusarium wilt in asparagus and to assess the efficacy of Trichoderma-based biopesticides under greenhouse and semi-field conditions. We evaluated the response of three Trichoderma spp. (T. atroviride, T. asperellum, and T. saturnisporum) to environmental variables, such as temperature and water activity, and their antagonistic capacity against Fusarium oxysporum f. sp. asparagi. All three Trichoderma species inhibited the growth of the pathogen in vitro. A decrease in water activity led to a greater reduction in the growth rate. The efficacy of the three biological control agents decreased with higher temperatures, resulting in minimal inhibition, particularly under conditions of restricted available water in the environment. The effect of the fungal inoculum density was also analyzed at two different temperatures. A direct correlation between the amount of inoculum and the score on the Disease Severity Index (DSI) was observed. A notable reduction in DSI was evident in treatments with high inoculum density (106 conidium/mL) for all three species of Trichoderma tested at both temperatures. In greenhouse and semi-field tests, we observed less disease control than expected, although T. asperellum and T. atroviride showed lower disease severity indices and increased the dry weight of seedlings and crowns, whereas T. saturnisporum resulted in the highest disease rate and lowest dry weight. This work highlights that the efficacy of Trichoderma as BCAs is influenced by various factors, including the quantity of soil inocula, and environmental conditions. The study findings have strong implications for selecting appropriate Trichoderma species for controlling specific pathogens under specific environmental conditions.

Effect of Metarhizium anisopliae (MetA1) on growth enhancement and antioxidative defense mechanism against Rhizoctonia root rot in okra

Rhizoctonia solani is an important necrotrophic pathogenic fungus that causes okra root disease and results in severe yield reduction. Many biocontrol agents are being studied with the intent of improving plant growth and defense systems and reducing crop loss by preventing fungal infections. Recently, a member of the Hypocrealean family, Metarhizium anisopliae, has been reported for insect pathogenicity, endophytism, plant growth promotion, and antifungal potentialities. This research investigated the role of M. anisopliae (MetA1) in growth promotion and root disease suppression in okra. The antagonism against R. solani and the plant growth promotion traits of MetA1 were tested in vitro. The effects of endophytic MetA1 on promoting plant growth and disease suppression were assessed in planta. Dual culture and cell-free culture filtrate assays showed antagonistic activity against R. solani by MetA1. Some plant growth promotion traits, such as phosphate solubilization and catalase activity were also exhibited by MetA1. Seed primed with MetA1 increased the shoot, root, leaves, chlorophyll content, and biomass content compared to control okra plants. The plants challenged with R. solani showed the highest hydrogen peroxide (H2O2) and lipid peroxidation (MDA) contents in the leaves of okra. Whereas MetA1 applied plants showed a reduction of H2O2 and MDA by 5.21 and 14.96%, respectively, under pathogen-inoculated conditions by increasing antioxidant enzyme activities, including catalase (CAT), peroxidase (POD), glutathione S-transferase (GST), and ascorbate peroxidase (APX), by 30.11, 10.19, 5.62, and 5.06%, respectively. Moreover, MetA1 increased soluble sugars, carbohydrates, proline, and secondary metabolites, viz., phenol and flavonoid contents in okra resulting in a better osmotic adjustment of diseases infecting plants. MetA1 reduced disease incidence by 58.33% at 15 DAI compared to the R. solani inoculated plant. The results revealed that MetA1 improved plant growth, elevated the plant defense system, and suppressed root diseases caused by R. solani. Thus, MetA1 was found to be an effective candidate for the biological control program.

Microbial Consortia for Plant Protection against Diseases: More than the Sum of Its Parts

Biological plant protection presents a promising and exciting alternative to chemical methods for safeguarding plants against the increasing threats posed by plant diseases. This approach revolves around the utilization of biological control agents (BCAs) to suppress the activity of significant plant pathogens. Microbial BCAs have the potential to effectively manage crop disease development by interacting with pathogens or plant hosts, thereby increasing their resistance. However, the current efficacy of biological methods remains unsatisfactory, creating new research opportunities for sustainable plant cultivation management. In this context, microbial consortia, comprising multiple microorganisms with diverse mechanisms of action, hold promise in terms of augmenting the magnitude and stability of the overall antipathogen effect. Despite scientific efforts to identify or construct microbial consortia that can aid in safeguarding vital crops, only a limited number of microbial consortia-based biocontrol formulations are currently available. Therefore, this article aims to present a complex analysis of the microbial consortia-based biocontrol status and explore potential future directions for biological plant protection research with new technological advancements.

Molecular Real-Time PCR Monitoring of Onion Fusarium Basal Rot Chemical Control

Fusarium basal rot disease (FBR) is a destructive threat to onion crops around the globe. It causes seedlings' death, development disruption, and pre- and post-harvest bulb infection and rotting, with a concern for toxin infestation. It is an emerging disease in Israel, with new reports from farms nationwide. Recently, we reported on a full-season pot experiment to protect two leading commercial cultivars against FBR chemically. Here, we present new real-time qPCR molecular tracking of the pathogens inside the host plant and compare the infection levels to a deep analysis of the impacts of this experiment's treatments on plant growth and health indexes. The new findings reveal variations within each treatment's effectiveness regarding sprout development and bulb ripening stages. For instance, in the yellow Orlando cv., high protection was obtained with Azoxystrobin + Tebuconazole (Az-Te) in sprouts against F. oxysporum f. sp. cepae and with Fludioxonil + Sedaxen in mature plants against Fusarium acutatum. Thus, combining these fungicides may protect plants throughout their lifecycle. Also, Prochloraz at low dose was highly efficient in the Orlando cv. Still, to shield red Noam cv. plants from both pathogens, increasing this fungicide concentration towards the season-ending should be preferred. The qPCR tracking showed that all chemical treatments tested could reduce infection from pathogens by 80-90%, even with compounds such as Az-Te that were less effective. This implies that the pesticide was effective but probably phytotoxic to the plants, and thus, lower dosages must be considered. The molecular-based analysis discloses the high infection ability of F. oxysporum f. sp. cepae compared to F. acutatum in both cultivars. It also indicates an antagonism between those species in the Orlando cv. and synergism in the Noam cv. The current work reveals weak and strong points in chemical FBR protection and offers new ways to improve its application. The qPCR-based method enables us to closely monitor the pathogenesis and efficacy of chemical-preventing treatments and optimize crop-protection protocols.

Biochemical and Biotechnological Insights into Fungus-Plant Interactions for Enhanced Sustainable Agricultural and Industrial Processes

The literature is full of studies reporting environmental and health issues related to using traditional pesticides in food production and storage. Fortunately, alternatives have arisen in the last few decades, showing that organic agriculture is possible and economically feasible. And in this scenario, fungi may be helpful. In the natural environment, when associated with plants, these microorganisms offer plant-growth-promoting molecules, facilitate plant nutrient uptake, and antagonize phytopathogens. It is true that fungi can also be phytopathogenic, but even they can benefit agriculture in some way-since pathogenicity is species-specific, these fungi are shown to be useful against weeds (as bioherbicides). Finally, plant-associated yeasts and molds are natural biofactories, and the metabolites they produce while dwelling in leaves, flowers, roots, or the rhizosphere have the potential to be employed in different industrial activities. By addressing all these subjects, this manuscript comprehensively reviews the biotechnological uses of plant-associated fungi and, in addition, aims to sensitize academics, researchers, and investors to new alternatives for healthier and more environmentally friendly production processes.

Pathogenicity of Trichoderma afroharzianum in Cereal Crops

Species of the genus Trichoderma occur ubiquitously in soils, on plant roots and in decaying plant residues. Due to its competitiveness and mycoparasitic potential against other microorganisms, particular strains of Trichoderma spp. are used in agriculture as biocontrol agents against plant pathogens. However, Trichoderma afroharzianum has been recently reported as a pathogen causing ear rot disease on maize in Germany, France and Italy, leading to massive infections on maize cobs. This raised the question, whether and to what extent Trichoderma spp. can infect cereal crops other than maize and cause disease symptoms and yield losses. To address this question, two varieties of wheat, barley and sorghum were grown in the greenhouse and artificially inoculated with T. afroharzianum by both spray and point inoculation at the time of flowering. Disease severity was scored weekly, and thousand-kernel weight and colonization rate were determined after harvest. As early as 14 days after inoculation, the first visual symptoms appeared on wheat and barley as tan or brown discoloration of the base of a floret within the spikelets. After spray inoculation, clear discolorations of the entire ear were seen, while point inoculation only showed symptoms at the injection site and above. No visible symptoms were observed on sorghum millet. The colonization rate on wheat and barley grains was significantly increased compared to the control, while thousand-kernel weights (TKWs) were significantly reduced. No differences in colonization rate and TKW compared to the control were observed in sorghum. This is the first report of Trichoderma afroharzianum infecting wheat and barley, causing disease symptoms and significantly reducing thousand-kernel weights.

Disclosing the native blueberry rhizosphere community in Portugal-an integrated metagenomic and isolation approach

Backgorund

The production of red fruits, such as blueberry, has been threatened by several stressors from severe periods of drought, nutrient scarcity, phytopathogens, and costs with fertilization programs with adverse consequences. Thus, there is an urgent need to increase this crop's resilience whilst promoting sustainable agriculture. Plant growth-promoting microorganisms (PGPMs) constitute not only a solution to tackle water and nutrient deficits in soils, but also as a control against phytopathogens and as green compounds for agricultural practices.

Methods

In this study, a metagenomic approach of the local fungal and bacterial community of the rhizosphere of Vaccinium corymbosum plants was performed. At the same time, both epiphytic and endophytic microorganisms were isolated in order to disclose putative beneficial native organisms.

Results

Results showed a high relative abundance of Archaeorhizomyces and Serendipita genera in the ITS sequencing, and Bradyrhizobium genus in the 16S sequencing. Diversity analysis disclosed that the fungal community presented a higher inter-sample variability than the bacterial community, and beta-diversity analysis further corroborated this result. Trichoderma spp., Bacillus spp., and Mucor moelleri were isolated from the V. corymbosum plants.

Discussion

This work revealed a native microbial community capable of establishing mycorrhizal relationships, and with beneficial physiological traits for blueberry production. It was also possible to isolate several naturally-occurring microorganisms that are known to have plant growth-promoting activity and confer tolerance to hydric stress, a serious climate change threat. Future studies should be performed with these isolates to disclose their efficiency in conferring the needed resilience for this and several crops.

Effect of fertilizer type on antibiotic resistance genes by reshaping the bacterial community and soil properties

Conventional and bio-organic fertilizers play an important role in maintaining soil health and promoting crop growth. However, the effect of organic fertilizers on the prevalence of antibiotic resistance genes (ARGs) in the vegetable cropping system has been largely overlooked. In this study, we investigated the impacts of soil properties and biotic factors on ARG profiles by analyzing ARG and bacterial communities in vegetable copping soils with a long-term history of manure and bio-organic fertilizer application. The ARG abundance in the soil was significantly increased by 116% with manure application compared to synthetic NPK fertilizer application. This finding was corroborated by our meta-analysis that the longer the duration of manure application, the greater the response of increased soil ARG abundance. However, bio-organic fertilizers containing Trichoderma spp. Significantly reduced ARG contamination by 31% compared to manure application. About half of the ARG variation was explained by changes in bacterial abundance and structure, followed by soil properties. The mitigation of ARG by Trichoderma spp. Is achieved by altering the structure of the bacterial community and weakening the close association between bacteria and ARG prevalence. Taken together, these findings shed light on the contribution of bio-organic fertilizers in mitigating ARG contamination in agricultural soils, which can help manage the ecological risk posed by ARG inputs associated with manure application.

Effect of Trichoderma viride on rhizosphere microbial communities and biocontrol of soybean root rot

Biological seed dressing is a cost-effective means to protect plant roots from pathogens. Trichoderma is generally considered as one of the most common biological seed dressings. However, there is still a dearth of information on the effects of Trichoderma on microbial community of rhizosphere soil. High-throughput sequencing was used to analyze the effects of Trichoderma viride and a chemical fungicide on microbial community of soybean rhizosphere soil. The results showed that both T. viride and chemical fungicide could significantly reduce the disease index of soybean (15.11% for Trichoderma and 17.33% for Chemical), while no significant difference was observed between them. Both T. viride and chemical fungicide could affect the structure of rhizosphere microbial community, they increased the β-diversity of microbial community and significantly reduce the relative abundance of Saprotroph-Symbiotroph. Chemical fungicide could reduce the complexity and stability of co-occurrence network. However, T. viride is beneficial for maintaining network stability and increasing network complexity. There were 31 bacterial genera and 21 fungal genera significantly correlated with the disease index. Furthermore, several potential plant pathogenic microorganisms were also positively correlated with disease index, such as Fusarium, Aspergillus, Conocybe, Naganishia, and Monocillium. From this work, T. viride may be used as a substitute for chemical fungicide to control soybean root rot and be more friendly to soil microecology.

Exploration of non-phytopathogenic Aspergillus spp. isolates recovered from soil and compost as potential source of bioactive metabolites for potato Fusarium dry rot control

During storage, infected potato tubers by Fusarium species leads to significant losses. Searching natural-based alternatives to chemical fungicides for the control of tuber dry rot pathogens is becoming essential. Nine Aspergillus spp. (A. niger, A. terreus, A. flavus, and Aspergillus sp.) isolates, recovered from soil and compost samples, were explored and evaluated for their ability to suppress Fusarium sambucinum the main causal agent of potato tuber dry rot disease in Tunisia. All conidial suspensions of Aspergillus spp. tested and their cell-free culture filtrates had significantly inhibited the in vitro pathogen growth by 18.5 to 35.9% and by 9 to 69% compared to control, respectively. A. niger CH12 cell-free filtrate was the most active against F. sambucinum at the three concentration tested (10, 15, and 20% v v-1). Chloroform and ethyl acetate extracts from four Aspergillus spp., tested at 5% v v-1, had limited F. sambucinum mycelial growth by 34-60% and 38-66%, respectively, compared to control, with A. niger CH12 ethyl extract being the most active. Tested on potato tubers inoculated with F. sambucinum, all tested Aspergillus spp. isolates, their cell-free filtrates and organic extracts had significantly decreased the external diameter of dry rot lesion compared to pathogen-inoculated and untreated control tubers. For the rot penetration, all Aspergillus spp. isolates, their organic extracts and only filtrates from A. niger CH12 and MC2 isolates had significantly limited dry rot severity compared to pathogen-inoculated and untreated control. The highest reductions in the external diameter of dry rot lesion (76.6 and 64.1%) and the average rot penetration (77.1 and 65.1%) were achieved using chloroform and ethyl acetate extracts from A. niger CH12, respectively. These results clearly demonstrated the presence of bioactive compounds in Aspergillus spp. that can be extracted and explored as an eco-friendly alternative for the control of the target pathogen.

Establishment of a CRISPR/Cas9-Mediated Efficient Knockout System of Trichoderma hamatum T21 and Pigment Synthesis PKS Gene Knockout

Trichoderma hamatum is a filamentous fungus that serves as a biological control agent for multiple phytopathogens and as an important resource promising for fungicides. However, the lack of adequate knockout technologies has hindered gene function and biocontrol mechanism research of this species. This study obtained a genome assembly of T. hamatum T21, with a 41.4 Mb genome sequence comprising 8170 genes. Based on genomic information, we established a CRISPR/Cas9 system with dual sgRNAs targets and dual screening markers. CRISPR/Cas9 plasmid and donor DNA recombinant plasmid were constructed for disruption of the Thpyr4 and Thpks1 genes. The result indicates the consistency between phenotypic characterization and molecular identification of the knockout strains. The knockout efficiencies of Thpyr4 and Thpks1 were 100% and 89.1%, respectively. Moreover, sequencing revealed fragment deletions between dual sgRNA target sites or GFP gene insertions presented in knockout strains. The situations were caused by different DNA repair mechanisms, nonhomologous end joining (NHEJ), and homologous recombination (HR). Overall, we have successfully constructed an efficient and convenient CRISPR/Cas9 system in T. hamatum for the first time, which has important scientific significance and application value for studies on functional genomics of Trichoderma and other filamentous fungi.

First study on the root endophytic fungus Trichoderma hamatum as an entomopathogen: Development of a fungal bioinsecticide against cotton leafworm (Spodoptera littoralis)

Cotton leaf worm (Spodoptera littoralis) is a pest that produces important losses in horticultural and ornamental crops in greenhouse, being classified as quarantine pest A2 by EPPO. One of the strategies proposed to control agricultural pests in a health and environmentally friendly way is biological control with entomopathogenic fungi. The genus of filamentous fungi Trichoderma includes different species with direct (infection, antibiosis, anti-feeding, etc.) and indirect (systemic activation of plant defenses) insecticidal capacity, however, the species T. hamatum has never been described previously as entomopathogenic. In this work, the entomopathogenic capacity of T. hamatum on S. littoralis L₃ larvae was analyzed by applying spores and fungal filtrates (topically and orally). Infection by spores was compared with the commercial entomopathogenic fungus Beauveria bassiana, obtaining similar results with respect to the production of larval mortality. Oral application of spores reported high mortality and fungal colonization of larvae, however, T. hamatum did not show chitinase activity when grown in the presence of S. littoralis tissues. Therefore, infection of S. littoralis larvae by T. hamatum is through natural openings such as mouth, anus or spiracles. With respect to the application of filtrates, only those obtained from the liquid culture of T. hamatum in contact with S. littoralis tissues reported a significant reduction in larval growth. Metabolomic analysis of the filtrates determined that the filtrate with insecticidal capacity presented the siderophore rhizoferrin in large quantities, which could be responsible for this activity. However, the production of this siderophore had never been previously described in Trichoderma and its insecticidal capacity was unknown. In conclusion, T. hamatum presents entomopathogenic capacity against S. littoralis larvae through the application of spores and filtrates, and both ways could be the basis for the development of efficient bioinsecticides against the pest.

Toward the Analysis of Volatile Organic Compounds from Tomato Plants (Solanum lycopersicum L.) Treated with Trichoderma virens or/and Botrytis cinerea

Gray mold caused by Botrytis cinerea causes significant losses in tomato crops. B. cinerea infection may be halted by volatile organic compounds (VOCs), which may exhibit fungistatic activity or enhance the defense responses of plants against the pathogen. The enhanced VOC generation was observed in tomato (Solanum lycopersicum L.), with the soil-applied biocontrol agent Trichoderma virens (10⁶ spores/1 g soil), which decreased the gray mold disease index in plant leaves at 72 hpi with B. cinerea suspension (1 × 10⁶ spores/mL). The tomato leaves were found to emit 100 VOCs, annotated and putatively annotated, assigned to six classes by the headspace GCxGC TOF-MS method. In Trichoderma-treated plants with a decreased grey mold disease index, the increased emission or appearance of 2-hexenal, (2E,4E)-2,4-hexadienal, 2-hexyn-1-ol, 3,6,6-trimethyl-2-cyclohexen-1-one, 1-octen-3-ol, 1,5-octadien-3-ol, 2-octenal, octanal, 2-penten-1-ol, (Z)-6-nonenal, prenol, and acetophenone, and 2-hydroxyacetophenone, β-phellandrene, β-myrcene, 2-carene, δ-elemene, and isocaryophyllene, and β-ionone, 2-methyltetrahydrofuran, and 2-ethyl-, and 2-pentylfuran, ethyl, butyl, and hexyl acetate were most noticeable. This is the first report of the VOCs that were released by tomato plants treated with Trichoderma, which may be used in practice against B. cinerea, although this requires further analysis, including the complete identification of VOCs and determination of their potential as agents that are capable of the direct and indirect control of pathogens.

Chemical Characterization of Trichoderma spp. Extracts with Antifungal Activity against Cocoa Pathogens

Ecuador is one of the major cocoa producers worldwide, but its productivity has lately been affected by diseases. Endophytic biocontrol agents have been used to minimize pathogenic effects; however, compounds produced by endophytes are minimally understood. This work presents the chemical characterization of the Trichoderma species extracts that proved inhibition against cocoa pathogens. Solid-liquid extraction was performed as a partitioning method using medium with the fungal mycelia of Trichoderma reesei (C2A), Trichoderma sp. (C3A), Trichoderma harzianum (C4A), and Trichoderma spirale (C10) in ethyl acetate individually. The extract of T. spirale (C10) exhibited the growth inhibition (32.97-47.02%) of Moniliophthora perniciosa at 10 µg/mL, while a slight stimulation of Moniliophthora roreri was shown by the extracts of T. reesei (C2A) and T. harzianum (C4A) at higher concentrations. The inhibitory activity could be related to alkaloids, lactones, quinones, flavonoids, triterpenes, and sterols, as indicated by chemical screening and antifungal compounds, such as widdrol, β-caryophyllene, tyrosol, butyl isobutyrate, sorbic acid, palmitic acid, palmitelaidic acid, linoleic acid, and oleic acid, which were identified by gas chromatography-mass spectrometry (GC-MS). The results showed that the extracts, particularly T. spirale (C10), have the potential as biocontrol agents against witches' broom disease; however, further studies are needed to confirm their effectiveness.

Seed biopriming with potential bioagents influences physiological processes and plant defense enzymes to ameliorate sheath blight induced yield loss in rice (Oryza sativa L.)

Disease management with the use of conventional pesticides has emerged as a major threat to the environment and human health. Moreover, the increasing cost of pesticides and their use in staple crops such as rice is not economically sustainable. The present study utilized a combination of two commercial powder formulations of biocontrol agents, Trichoderma harzianum (Th38) and Pseudomonas fluorescens (Pf28) to induce resistance against sheath blight disease via seed biopriming in basmati rice variety Vasumati and compared the performance with systemic fungicide carbendazim. Sheath blight infection significantly increased the levels of stress indicators such as proline (0.8 to 4.25 folds), hydrogen peroxide (0.89 to 1.61 folds), and lipid peroxidation (2.4 to 2.6 folds) in the infected tissues as compared to the healthy control. On the contrary, biopriming with biocontrol formulation (BCF) significantly reduced the level of stress markers, and substantially enhanced the levels of defense enzymes such as peroxidase (1.04 to 1.18 folds), phenylalanine ammonia lyase (1.02 to 1.17 folds), lipoxygenase (1.2 to 1.6 folds), and total phenolics (74% to 83%) as compared to the infected control. Besides, improved photosynthesis (48% to 59%) and nitrate reductase activity (21% to 42%) showed a positive effect on yield and biomass, which compensated disease induced losses in bio-primed plants. Conversely, the comparative analysis of the efficacy levels of BCF with carbendazim revealed BCF as a potential and eco-friendly alternative for reducing disease impact and maintaining higher yield in rice under sheath blight infection.

Trichoderma after crossing kingdoms: infections in human populations

Trichoderma is a saprophytic fungus that is used worldwide as a biocontrol and biofertilizer agent. Although considered nonpathogenic until recently, reports of human infections produced by members of the Trichoderma genus are increasing. Numerous sources of infection were proposed based upon patient data and phylogenetic analysis, including air, agriculture, and healthcare facilities, but the deficit of knowledge concerning Trichoderma infections makes patient treatment difficult. These issues are compounded by isolates that present profiles which exhibit high minimum inhibitory concentration values to available antifungal drugs. The aim of this review is to present the global distribution and sources of infections that affect both immunocompetent and immunocompromised hosts, clinical features, therapeutic strategies that are used to treat patients, as well as highlighting treatments with the best responses. In addition, the antifungal susceptibility profiles of Trichoderma isolates that have emerged in recent decades were examined and which antifungal drugs need to be further evaluated as potential candidates to treat Trichoderma infections are also indicated.

Characterization of the microbiota dynamics associated with Moniliophthora roreri, causal agent of cocoa frosty pod rot disease, reveals new viral species

Introduction

Theobroma cacao, the cocoa tree, is a target for pathogens, such as fungi from the genera Phytophthora, Moniliophthora, Colletotrichum, Ceratocystis, among others. Some cacao pathogens are restricted to specific regions of the world, such as the Cacao swollen shoot virus (CSSV) in West African countries, while others are expanding geographically, such as Moniliophthora roreri in the Americas. M. roreri is one of the most threatening cacao pathogens since it directly attacks the cacao pods driving a significant reduction in production, and therefore economic losses. Despite its importance, the knowledge about the microenvironment of this pathogen and the cocoa pods is still poorly characterized.

Methods

Herein we performed RNA sequencing of spores in differential stages of culture in a medium supplemented with cacao pod extract and mycelium collected of the susceptible variety ICT 7121 naturally infected by the pathogen to evaluate the diversity and transcriptional activity of microorganisms associated with the in vitro sporulation of M. roreri.

Results

Our data revealed a great variety of fungi and bacteria associated with M. roreri, with an exceptional diversity of individuals from the genus Trichoderma sp. Interestingly, the dynamics of microorganisms from different kingdoms varied proportionally, suggesting they are somehow affected by M. roreri culture time. We also identified three sequences similar to viral genomes from the Narnaviridae family, posteriorly confirmed by phylogenetic analysis as members of the genus Narnavirus. Screening of M. roreri public datasets indicated the virus sequences circulating in samples from Ecuador, suggesting a wide spread of these elements. Of note, we did not identify traces of the viral sequences in the M. roreri genome or DNA sequencing, restricting the possibility of these sequences representing endogenized elements.

Discussion

To the best of our knowledge, this is the first report of viruses infecting the fungus of the genus Moniliophthora and only the third description of viruses that are able to parasite elements from the Marasmiaceae family.

Trichoderma Species: Our Best Fungal Allies in the Biocontrol of Plant Diseases-A Review

Biocontrol agents (BCA) have been an important tool in agriculture to prevent crop losses due to plant pathogens infections and to increase plant food production globally, diminishing the necessity for chemical pesticides and fertilizers and offering a more sustainable and environmentally friendly option. Fungi from the genus Trichoderma are among the most used and studied microorganisms as BCA due to the variety of biocontrol traits, such as parasitism, antibiosis, secondary metabolites (SM) production, and plant defense system induction. Several Trichoderma species are well-known mycoparasites. However, some of those species can antagonize other organisms such as nematodes and plant pests, making this fungus a very versatile BCA. Trichoderma has been used in agriculture as part of innovative bioformulations, either just Trichoderma species or in combination with other plant-beneficial microbes, such as plant growth-promoting bacteria (PGPB). Here, we review the most recent literature regarding the biocontrol studies about six of the most used Trichoderma species, T. atroviride, T. harzianum, T. asperellum, T. virens, T. longibrachiatum, and T. viride, highlighting their biocontrol traits and the use of these fungal genera in Trichoderma-based formulations to control or prevent plant diseases, and their importance as a substitute for chemical pesticides and fertilizers.

Defense response of strawberry plants against Botrytis cinerea influenced by coriander extract and essential oil

Essential oils and extracts are investigated in sustainable plant protection area lately. Alternative antifungal substances are especially relevant for major economic-relevance pathogens, like Botrytis cinerea (causal agent of strawberry grey mold), control. However, the reaction of plants to alternative protection with plant-origin products is currently unknown. Induced stress in plants causes changes in antioxidant and photosynthetic systems. The aim of the research was to determine the defense response of strawberry plants under application of coriander seed products. In the first step of the research, we determined coriander seed (Coriandrum sativum), black seed (Nigella sativa) and peppermint leaf (Menta × piperita) products' antifungal activity against B. cinerea in vitro. Secondly, we continued evaluation of antifungal activity under controlled environment on strawberry plants of the most effective coriander seed products. Additionally, we evaluated the antioxidant and photosynthetic parameters in strawberries, to examine the response of plants. Antifungal activity on strawberries was determined based on grey mold incidence and severity after application of coriander products. Impact on photosynthetic system was examined measuring photosynthetic rate, transpiration rate, stomatal conductance, and intercellular to ambient CO₂ concentration. Strawberry leaves were collected at the end of the experiment to analyze the antioxidant response. The highest antifungal activity both in vitro and on strawberries had coriander seed essential oil, which decreased grey mold severity. Coriander extract increased the photosynthetic capacity and antioxidant response of strawberry plants, however had negative effect on suppression of grey mold. In most cases, the essential oil activated antioxidant response of strawberry plants lower than extract. Our study results provide no direct impact of increased photosynthetic capacity values and antifungal effect after treatment with natural oils. The highest concentrations of coriander essential oil and extract potentially demonstrated a phytotoxic effect.

Metabolomic profiling and its association with the bio-efficacy of Aspergillus niger strain against Fusarium wilt of guava

Bio-control agents are the best alternative to chemicals for the successful management of plant diseases. The fungus Aspergillus niger is known to produce diverse metabolites with antifungal activity, attracting researchers to exploit it as a bio-control agent for plant disease control. In the present study, 11 A. niger strains were isolated and screened for their antagonism against the guava wilt pathogen under in vitro and in planta conditions. Strains were identified morphologically and molecularly by sequencing the internal transcribed spacer (ITS), β-tubulin, and calmodulin genes. The strains were evaluated through dual culture, volatile, and non-volatile methods under an in vitro study. AN-11, AN-6, and AN-2 inhibited the test pathogen Fusarium oxysporum f. sp. psidii (FOP) at 67.16%, 64.01%, and 60.48%, respectively. An in planta study was conducted under greenhouse conditions with 6 months old air-layered guava plants (var. Allahabad Safeda) by pre- and post-inoculation of FOP. The AN-11 strain was found to be effective under both pre- and post-inoculation trials. Furthermore, gas chromatography-mass spectrometry (GC-MS) analysis was carried out to characterize the volatile compounds of the most potential strain, A. niger. The hexane soluble fraction showed the appearance of characteristic peaks of hexadecenoic acid methyl ester (4.41%), 10-octadecanoic acid methyl ester (3.79%), dodecane (3.21%), undecane (3.19%), gibepyrone A (0.15%), 3-methylundecane (0.36%), and citroflex A (0.38%). The ethyl acetate fraction of the bio-control fungi revealed the occurrence of major antifungal compounds, such as acetic acid ethyl ester (17.32%), benzopyron-4-ol (12.17%), 1,2,6-hexanetriol (7.16%), 2-propenoic acid ethanediyl ester (2.95%), 1-(3-ethyloxiranyl)-ethenone (0.98%), 6-acetyl-8-methoxy dimethyl chromene (0.96%), 4-hexyl-2,5-dihydro dioxo furan acetic acid (0.19%), and octadecanoic acid (1.11%). Furthermore, bio-control abilities could be due to hyper-parasitism, the production of secondary metabolites, and competition for sites and nutrients. Indeed, the results will enrich the existing knowledge of metabolomic information and support perspectives on the bio-control mechanism of A. niger.

Cultivars Resistance Assay for Maize Late Wilt Disease

Magnaporthiopsis maydis late wilt disease (LWD) in corn is considered to be the most severe in Israel and Egypt and poses a significant threat in other countries. Research efforts extending over a period of five decades led to the development of chemical, biological, agrotechnical, physical (solar disinfection) and other means for controlling late wilt disease. Today, some applications can reduce damage even in severe cases. However, cultivating disease-resistant maize varieties is the primary means for reducing the disease's impact. The current work uses a rapid (six days) laboratory seedling pathogenicity test and a full-season open encloser semi-field conditioned pots assay (101 days) to classify maize varieties according to their LWD resistance. To better evaluate differences between the cultivars, a real-time based molecular assay was applied to track the pathogen's presence in the plants' tissues, and visible light aerial imaging was used in parallel. The findings show that in cases of extreme sensitivity or tolerance (for example, in the highly susceptible Megaton cultivar (cv.) or the resistant Hatai cv.), a similarity in the results exists between the different methods. Thus, a reliable estimate of the varieties' sensitivity can be obtained in a seed assay without the need for a test carried out throughout an entire growing season. At the same time, in most situations of partial or reduced LWD sensitivity/resistance, there is no match between the various tests, and only the entire growing season can provide the most reliable results. Tracking the amount of M. maydis DNA in the plants' bodies is a precise, sensitive scientific tool of great importance for studying the development of the disease and the factors affecting it. Yet, no complete overlap exists between the fungal DNA amount and symptom severity. Such a correlation exists in high sensitivity or resistance cases but not in intermediate situations. Still, the valuation of the pathogen's establishment in asymptomatic corn hybrids can indicate the degree of LWD immunity and the chance of susceptibility development.

Current and future trends in the biocontrol of postharvest diseases

Postharvest diseases of fruits and vegetables cause significant economic losses to producers and marketing firms. Many of these diseases are caused by necrotrophic fungal pathogens that require wounded or injured tissues to establish an infection. Biocontrol of postharvest diseases is an evolving science that has moved from the traditional paradigm of one organism controlling another organism to viewing biocontrol as a system involving the biocontrol agent, the pathogen, the host, the physical environment, and most recently the resident microflora. Thus, the paradigm has shifted from one of simplicity to complexity. The present review provides an overview of how the field of postharvest biocontrol has evolved over the past 40 years, a brief review of the biology of necrotrophic pathogens, the discovery of BCAs, their commercialization, and mechanisms of action. Most importantly, current research on the use of marker-assisted-selection, the fruit microbiome and its relationship to the pathobiome, and the use of double-stranded RNA as a biocontrol strategy is discussed. These latter subjects represent evolving trends in postharvest biocontrol research and suggestions for future research are presented.

Diversity of Trichoderma species associated with soil in the Zoige alpine wetland of Southwest China

The ecology of soil fungi is poorly understood, and recent comprehensive reports on Trichoderma are unavailable for any region, including the Zoige alpine wetland ecological region in China. One hundred soil samples were collected from different soil types and soil layers in Zoige alpine wetland ecological regions. Using the traditional suspension plating method, 80 Trichoderma strains were chosen to analyze species diversity. After a preliminary classification of morphological characteristics and the genes glyceraldehyde-3-phosphate dehydrogenase (gpd), 57 representative strains were selected and eventually identified as seven species via phylogenetic analyses of multilocus sequences based on the genes transcription elongation factor 1 alpha (tef1), encoding RNA polymerase II subunit B (rpb2) and ATP citrate lyase (acl1). Among them, T. harzianum was the dominant species isolated from five soil layers and four soil types, and had the highest isolation frequency (23%) in this zone, while T. polysporum and T. pyramidale were rare species, with isolation frequencies of less than 1%. Our detailed morphological observation and molecular phylogenetic analyses support the recognition of Trichoderma zoigense was described for the first time as a new species, while T. atrobrunneum as a new record for China was found. Our results will be used as a reference for a greater understanding of soil microbial resources, ecological rehabilitation and reconstructions in the Zoige alpine wetland.

The hidden power of secondary metabolites in plant-fungi interactions and sustainable phytoremediation

The global environment is dominated by various small exotic substances, known as secondary metabolites, produced by plants and microorganisms. Plants and fungi are particularly plentiful sources of these molecules, whose physiological functions, in many cases, remain a mystery. Fungal secondary metabolites (SM) are a diverse group of substances that exhibit a wide range of chemical properties and generally fall into one of four main family groups: Terpenoids, polyketides, non-ribosomal peptides, or a combination of the latter two. They are incredibly varied in their functions and are often related to the increased fitness of the respective fungus in its environment, often competing with other microbes or interacting with plant species. Several of these metabolites have essential roles in the biological control of plant diseases by various beneficial microorganisms used for crop protection and biofertilization worldwide. Besides direct toxic effects against phytopathogens, natural metabolites can promote root and shoot development and/or disease resistance by activating host systemic defenses. The ability of these microorganisms to synthesize and store biologically active metabolites that are a potent source of novel natural compounds beneficial for agriculture is becoming a top priority for SM fungi research. In this review, we will discuss fungal-plant secondary metabolites with antifungal properties and the role of signaling molecules in induced and acquired systemic resistance activities. Additionally, fungal secondary metabolites mimic plant promotion molecules such as auxins, gibberellins, and abscisic acid, which modulate plant growth under biotic stress. Moreover, we will present a new trend regarding phytoremediation applications using fungal secondary metabolites to achieve sustainable food production and microbial diversity in an eco-friendly environment.

Mycovirus-encoded suppressors of RNA silencing: Possible allies or enemies in the use of RNAi to control fungal disease in crops

Plants, fungi, and many other eukaryotes have evolved an RNA interference (RNAi) mechanism that is key for regulating gene expression and the control of pathogens. RNAi inhibits gene expression, in a sequence-specific manner, by recognizing and deploying cognate double-stranded RNA (dsRNA) either from endogenous sources (e.g. pre-micro RNAs) or exogenous origin (e.g. viruses, dsRNA, or small interfering RNAs, siRNAs). Recent studies have demonstrated that fungal pathogens can transfer siRNAs into plant cells to suppress host immunity and aid infection, in a mechanism termed cross-kingdom RNAi. New technologies, based on RNAi are being developed for crop protection against insect pests, viruses, and more recently against fungal pathogens. One example, is host-induced gene silencing (HIGS), which is a mechanism whereby transgenic plants are modified to produce siRNAs or dsRNAs targeting key transcripts of plants, or their pathogens or pests. An alternative gene regulation strategy that also co-opts the silencing machinery is spray-induced gene silencing (SIGS), in which dsRNAs or single-stranded RNAs (ssRNAs) are applied to target genes within a pathogen or pest. Fungi also use their RNA silencing machinery against mycoviruses (fungal viruses) and mycoviruses can deploy virus-encoded suppressors of RNAi (myco-VSRs) as a counter-defence. We propose that myco-VSRs may impact new dsRNA-based management methods, resulting in unintended outcomes, including suppression of management by HIGS or SIGS. Despite a large diversity of mycoviruses being discovered using high throughput sequencing, their biology is poorly understood. In particular, the prevalence of mycoviruses and the cellular effect of their encoded VSRs are under-appreciated when considering the deployment of HIGS and SIGS strategies. This review focuses on mycoviruses, their VSR activities in fungi, and the implications for control of pathogenic fungi using RNAi.

Determination of Reactive Oxygen or Nitrogen Species and Novel Volatile Organic Compounds in the Defense Responses of Tomato Plants against Botrytis cinerea Induced by Trichoderma virens TRS 106

In the present study, Trichoderma virens TRS 106 decreased grey mould disease caused by Botrytis cinerea in tomato plants (S. lycopersicum L.) by enhancing their defense responses. Generally, plants belonging to the ‘Remiz’ variety, which were infected more effectively by B. cinerea than ‘Perkoz’ plants, generated more reactive molecules such as superoxide (O₂⁻) and peroxynitrite (ONOO⁻), and less hydrogen peroxide (H₂O₂), S-nitrosothiols (SNO), and green leaf volatiles (GLV). Among the new findings, histochemical analyses revealed that B. cinerea infection caused nitric oxide (NO) accumulation in chloroplasts, which was not detected in plants treated with TRS 106, while treatment of plants with TRS 106 caused systemic spreading of H₂O₂ and NO accumulation in apoplast and nuclei. SPME-GCxGC TOF-MS analysis revealed 24 volatile organic compounds (VOC) released by tomato plants treated with TRS 106. Some of the hexanol derivatives, e.g., 4-ethyl-2-hexynal and 1,5-hexadien-3-ol, and salicylic acid derivatives, e.g., 4-hepten-2-yl and isoamyl salicylates, are considered in the protection of tomato plants against B. cinerea for the first time. The results are valuable for further studies aiming to further determine the location and function of NO in plants treated with Trichoderma and check the contribution of detected VOC in plant protection against B. cinerea.

Ten decadal advances in fungal biology leading towards human well-being

Fungi are an understudied resource possessing huge potential for developing products that can greatly improve human well-being. In the current paper, we highlight some important discoveries and developments in applied mycology and interdisciplinary Life Science research. These examples concern recently introduced drugs for the treatment of infections and neurological diseases; application of -OMICS techniques and genetic tools in medical mycology and the regulation of mycotoxin production; as well as some highlights of mushroom cultivaton in Asia. Examples for new diagnostic tools in medical mycology and the exploitation of new candidates for therapeutic drugs, are also given. In addition, two entries illustrating the latest developments in the use of fungi for biodegradation and fungal biomaterial production are provided. Some other areas where there have been and/or will be significant developments are also included. It is our hope that this paper will help realise the importance of fungi as a potential industrial resource and see the next two decades bring forward many new fungal and fungus-derived products.

Comparative Transcriptomics Suggests Early Modifications by Vintec® in Grapevine Trunk of Hormonal Signaling and Secondary Metabolism Biosynthesis in Response to Phaeomoniella chlamydospora and Phaeoacremonium minimum

Given their well-known antifungal abilities, species of the genus Trichoderma are of significant interest in modern agriculture. Recent studies have shown that Trichoderma species can induce plant resistance against different phytopathogens. To further extend this line of investigation, we investigate herein the transcriptomic response of grapevine trunk to Vintec^®, which is a Trichoderma atroviride SC1-based commercial formulation for biological control of grapevine trunk diseases and which reduces wood colonization. The aim of the study is to understand whether the biocontrol agent Vintec^® modifies the trunk response to Phaeoacremonium minimum and Phaeomoniella chlamydospora, which are two esca-associated fungal pathogens. An analysis of transcriptional regulation identifies clusters of co-regulated genes whose transcriptomic reprogramming in response to infection depends on the absence or presence of Vintec^®. On one hand, the results show that Vintec^® differentially modulates the expression of putative genes involved in hormonal signaling, especially those involved in auxin signaling. On the other hand, most significant gene expression modifications occur among secondary-metabolism-related genes, especially regarding phenylpropanoid metabolism and stilbene biosynthesis. Taken together, these results suggest that the biocontrol agent Vintec^® induces wood responses that counteract disease development.

Biopriming for induction of disease resistance against pathogens in rice

Rice is attacked by an armada of pathogens. Present review provides a critical evaluation of the potential of different biotic agents used to protect rice yield drop from pathogenicity and an account of unexplored areas, which might be taken into consideration to manage rice diseases. Rice (Oryza sativa L.), is the most important staple food of Asian countries. Rice production is significantly limited by a diversity of pathogens, leading to yield loss and deficit in current rice supply. Application of agrochemicals of diverse types has been considered as the only option to control pathogens and enhance rice production, thereby causing environmental concerns and making the pathogens resistant to the active ingredients. Increase in population and resistance of pathogen towards agrochemicals put pressure on the agronomists to search for safe, novel, eco-friendly alternative ways to manage rice pathogens. Inducing resistance in rice by using different biotic/abiotic agents provides an environmental friendly alternative way to effectively manage bacterial, fungal, and viral rice pathogens. In recent years, a number of protocols have been developed for inducing pathogen resistance by bio-priming of rice. However, a comprehensive evaluation of the potential of different biotic agents to protect rice crop loss from pathogens is hitherto lacking due to which the research on induction of defense against pathogens in rice is discontinuous. This review deals with the detailed analysis of the bacterial and fungal agents used to induce defense against rice pathogens, their mode of application, mechanism (physiological, biochemical, and molecular) of defense induction, and effect of defense induction on the yield of rice. It also provides an account of gaps in the research and the unexplored areas, which might be taken into consideration to effectively manage rice pathogens.

Effects of Trichoderma harzianum Strain T22 on the Arthropod Community Associated with Tomato Plants and on the Crop Performance in an Experimental Field

Fungi belonging to the genus Trichoderma have received much attention in recent years due to their beneficial effects on crop health and their use as pest control agents. Trichoderma activates direct plant defenses against phytophagous arthropods and reinforces indirect plant defense through the attraction of predators. Although the plant defenses against insect herbivores were demonstrated in laboratory experiments, little attention has been paid to the use of Trichoderma spp. in open field conditions. In the present study, we investigated the effects of the inoculation of the commercial Trichoderma harzianum strain T22 on the arthropod community associated with tomato plants and on the crop performance in an experimental field located in South Italy. Our results showed that inoculation with T. harzianum could alter the arthropod community and reduce the abundance of specific pests under field conditions with respect to the sampling period. The present study also confirmed the beneficial effect of T. harzianum against plant pathogens and on tomato fruit. The complex tomato-arthropod-microorganism interactions that occurred in the field are discussed to enrich our current information on the possibilities of using Trichoderma as a green alternative agent in agriculture.

Trichoderma: The Current Status of Its Application in Agriculture for the Biocontrol of Fungal Phytopathogens and Stimulation of Plant Growth

Rhizosphere filamentous fungi of the genus Trichoderma, a dominant component of various soil ecosystem mycobiomes, are characterized by the ability to colonize plant roots. Detailed knowledge of the properties of Trichoderma, including metabolic activity and the type of interaction with plants and other microorganisms, can ensure its effective use in agriculture. The growing interest in the application of Trichoderma results from their direct and indirect biocontrol potential against a wide range of soil phytopathogens. They act through various complex mechanisms, such as mycoparasitism, the degradation of pathogen cell walls, competition for nutrients and space, and induction of plant resistance. With the constant exposure of plants to a variety of pathogens, especially filamentous fungi, and the increased resistance of pathogens to chemical pesticides, the main challenge is to develop biological protection alternatives. Among non-pathogenic microorganisms, Trichoderma seems to be the best candidate for use in green technologies due to its wide biofertilization and biostimulatory potential. Most of the species from the genus Trichoderma belong to the plant growth-promoting fungi that produce phytohormones and the 1-aminocyclopropane-1-carboxylate (ACC) deaminase enzyme. In the present review, the current status of Trichoderma is gathered, which is especially relevant in plant growth stimulation and the biocontrol of fungal phytopathogens.

Effects of Trichoderma asperellum 6S-2 on Apple Tree Growth and Replanted Soil Microbial Environment

Trichoderma asperellum strain 6S-2 with biocontrol effects and potential growth-promoting properties was made into a fungal fertilizer for the prevention of apple replant disease (ARD). 6S-2 fertilizer not only promoted the growth of Malus hupehensis Rehd seedlings in greenhouse and pot experiments, but also increased the branch elongation growth of young apple trees. The soil microbial community structure changed significantly after the application of 6S-2 fertilizer: the relative abundance of Trichoderma increased significantly, the relative abundance of Fusarium (especially the gene copy numbers of four Fusarium species) and Cryptococcus decreased, and the relative abundance of Bacillus and Streptomyces increased. The bacteria/fungi and soil enzyme activities increased significantly after the application of 6S-2 fertilizer. The relative contents of alkenes, ethyl ethers, and citrullines increased in root exudates of M. hupehensis Rehd treated with 6S-2 fertilizer and were positively correlated with the abundance of Trichoderma. The relative contents of aldehydes, nitriles, and naphthalenes decreased, and they were positively correlated with the relative abundance of Fusarium. In addition, levels of ammonium nitrogen (NH₄-N), nitrate nitrogen (NO₃-N), available phosphorus (AP), available potassium (AK), organic matter (SOM), and pH in rhizosphere soil were also significantly related to changes in the microbial community structure. In summary, the application of 6S-2 fertilizer was effective in alleviating some aspects of ARD by promoting plant growth and optimizing the soil microbial community structure.

Changes in microbial community and enzyme activity in soil under continuous pepper cropping in response to Trichoderma hamatum MHT1134 application

To clarify the control effects of Trichoderma hamatum strain MHT1134 on Fusarium wilt in continuous pepper cropping fields and its regulatory effects on soil microecology, the physical and chemical properties, enzyme activities, community structures of soil samples from five field types were analysed. Samples were taken from fields that had been continuously planted for 1, 5, 9 years, and applied the strain MHT1134 for 1 and 2 years. The MHT1134 control effects on pepper wilt after application 1 year and 2 years were 63.03% and 70.21%, respectively. 4 kinds of physical and chemical indexes and 6 kinds of enzyme activities in soil were increased. With the continuous cropping years increased, the microbial abundance and diversity decreasing significantly. The relative abundances of Fusarium, Gibberella increased along with the planting years, but decreased after the MHT11134 application. However, the relative abundances of Trichoderma and Chaetomium significantly increased. Additionally, as the cropping years increased, the soil abundance of Actinobacteria gradually decreased, but it significantly increased from 17.56 to 22.44% after the MHT1134 application. Thus, strain MHT1134 effectively improved the microbial community structure of the soil, and it also positively affected soil quality. A continuous application may improve the control effect.

Biorefineries as the base for accomplishing the sustainable development goals (SDGs) and the transition to bioeconomy: Technical aspects, challenges and perspectives

Sustainable development goals (SDGs) are guidelines to improve the socio-economic and environmental worldwide situation caused by excessive fossil fuel use. These goals must be accomplished before 2030 by implementing a national sustainable development framework in all UN country members. Instead, biorefineries are the seed towards a more sustainable world since biomass upgrading into a series of value-added products and energy vectors can reduce current issues related to waste generation and climate change. Besides, biorefineries are the first step on the way to implement a bioeconomy. This review paper aims to elucidate the existing relation between biorefineries, bioeconomy, and the SDGs through a comprehensive analysis of the technical requirements, challenges, and perspectives of biomass upgrading processes. In this way, this review paper includes a discussion about the biorefinery, bioeconomy, sustainable development, and sustainability concepts. Moreover, this paper elucidates how the implementation of biorefineries is linked to the SDGs accomplishment.