Toward deciphering the molecular dialogue in the rhizomicrobiota: Transcriptomic profiling of Trichoderma in rhizobia interaction

Microbial interactions are of key importance for the emergent properties of microbiota and ecosystems, playing a pivotal role in plant health, growth, and productivity. This study explores the interactions between soil fungi and rhizosphere bacteria, focusing specifically on fungi belonging to the genus Trichoderma and the plant symbiotic bacterium Sinorhizobium meliloti. Our aim is to provide evidence of the impact of different strains of the same bacterial species on the fungus. By analysing the effects of four S. meliloti strains on gene expression of T. velutinum, we revealed the presence of several differentially expressed genes (DEGs) (from 139 to 254 genes) indicating a remodelling of its metabolism and growth. Remarkably, the majority of the DEGs (∼90 %) could not be assigned to function, indicating the presence of a large genetic "unknown space" potentially involved in fungal-bacterial interactions. Moreover, results indicated that transcriptomic profiles of T. velutinum significantly changed with respect to the four S. meliloti strains, suggesting the ability of the fungus to perceive the presence of specific bacterial strains. Our study emphasizes that strain specificity of microbial interactions could play crucial role in shaping microbiota functions, and highlights their potential impact on the success of bioinoculants.

Bioinformatics assisted construction of the link between biosynthetic gene clusters and secondary metabolites in fungi

Fungal secondary metabolites are considered as important resources for drug discovery. Despite various methods being employed to facilitate the discovery of new fungal secondary metabolites, the trend of identifying novel secondary metabolites from fungi is inevitably slowing down. Under laboratory conditions, the majority of biosynthetic gene clusters, which store information for secondary metabolites, remain inactive. Therefore, establishing the link between biosynthetic gene clusters and secondary metabolites would contribute to understanding the genetic logic underlying secondary metabolite biosynthesis and alleviating the current challenges in discovering novel natural products. Bioinformatics methods have garnered significant attention due to their powerful capabilities in data mining and analysis, playing a crucial role in various aspects. Thus, we have summarized successful cases since 2016 in which bioinformatics methods were utilized to establish the link between fungal biosynthetic gene clusters and secondary metabolites, focusing on their biosynthetic gene clusters and associated secondary metabolites, with the goal of aiding the field of natural product discovery.

Isolate and plant host specificity of rhizosphere competence in Trichoderma species

Rhizosphere competence, the ability of a microorganism to colonise and proliferate in the rhizosphere of developing roots, is often studied when mechanisms of individual Trichoderma biocontrol agents are investigated. However, the extent of rhizosphere competence of Trichoderma species and isolates within species has not been widely studied. The rhizosphere competence of 22 Trichoderma isolates from a range of species was assessed using Trichoderma coated sweet corn (Zea mays) seeds grown in non-sterile soil. Results showed that 82 % of the Trichoderma isolates inoculated onto the seeds produced rhizosphere populations significantly greater than the control, indicating rhizosphere competence was widespread within the species that were tested. The least and most rhizosphere-competent isolates belonged to the same species indicating that rhizosphere competence was not species specific. The three least (T. crassum LU555, Trichoderma harzianum LU672, and T. virens LU556) and most (Trichoderma atroviride LU132, T. harzianum LU151, and LU673) rhizosphere-competent isolates were assessed on six plant species (sweet corn, ryegrass, cauliflower, carrot, onion, and white clover). Ryegrass and cauliflower were the most receptive plants to colonisation of the rhizosphere by Trichoderma species, and clover the least. Preferential rhizosphere colonisation was observed between some Trichoderma isolates and the plant species indicating that overall rhizosphere competence was dependent on specific interactions between the Trichoderma isolate and the plant species. However, some isolates were more broadly rhizosphere-competent than others and may have greater potential as plant protection agents. Since only one time point was sampled, future work is required to determine the temporal dynamics of rhizosphere colonisation as well as the spatial colonisation along the length of the root to determine whether different isolates preferentially colonise different regions of the root over different time periods.

Harnessing the Ecological and Genomic Adaptability of the Bacterial Genus Massilia for Environmental and Industrial Applications

The bacterial genus Massilia was first described in 1998, and since then has attracted growing interest due to its ecological plasticity and biotechnological promise. Certain species of the genus Massilia inhabit a variety of ecosystems, from arid deserts to polar glaciers, and exhibit unique adaptations such as resistance to cold and heat. In contaminated environments, some members of Massilia contribute significantly to the detoxification of heavy metals and the degradation of organic pollutants, presenting them as promising agents for bioremediation. In addition, Massilia species improve plant resistance and facilitate pollutant absorption in phytoremediation strategies. New research also highlights their potential as bioindicators of environmental health, given their abundance in anthropogenically influenced ecosystems and airborne microbial communities. In addition to their ecological roles, some Massilia species have potential in biotechnological applications by producing biopolymers and secondary metabolites. Here, we integrate findings across various habitats to present a comprehensive overview of the ecological and biotechnological importance of the genus Massilia. We highlight critical knowledge gaps and propose future research directions to fully harness the potential of this not fully explored bacterial genus to address environmental challenges, including contamination.

Phylogenetic analysis of plant-pathogenic and non-pathogenic Trichoderma isolates on maize from plants, soil, and commercial bio-products

Fungi of the genus Trichoderma are primarily associated with the mycobiome of dead wood but can also be occasionally found in soil and plant rhizospheres. Several Trichoderma spp. are used in crop health management to promote growth and control plant diseases. Although widely considered beneficial to plants, some members have been reported to be pathogenic to maize, causing a disease called Trichoderma ear rot. Since 2018, Trichoderma afroharzianum has caused significant infections of maize cobs in Germany, France, and Italy. This study aimed to investigate the pathogenicity and phylogenetic relationships among different Trichoderma strains from diverse sources and geographical origins. While previous studies primarily identified T. afroharzianum as the main species causing Trichoderma ear rot, this study found that isolates of T. asperellum, T. atroviride, and T. guizhouense may also exhibit pathogenicity on maize cobs. Additionally, Trichoderma strains from commercial biocontrol products displayed unexpected pathogenicity inducing up to 92% disease severity on maize cobs. Most T. afroharzianum strains induced high levels of disease severity, although some isolates of the same species did not cause any disease, indicating a large heterogeneity in pathogenicity within the species. Notably, phylogeny reconstruction based on the tef1-α and rpb2 genes did not result in any discernible clustering between pathogenic and non-pathogenic isolates. A further novel finding is the isolation of pathogenic Trichoderma isolates from agricultural soil, demonstrating that soil can serve as a reservoir for pathogenic species. This study highlights the need for biosecurity assessment and monitoring of Trichoderma strains for agricultural use, considering their beneficial and pathogenic potential.IMPORTANCEIn this study, we explored the ability of different Trichoderma species to infect maize plants. Trichoderma is a group of fungi known for its beneficial role in agriculture, often used as a biological pesticide to control fungal plant diseases. However, some species within this genus can also act as pathogens, causing infections in crops like maize. We found that one species, T. afroharzianum, is particularly aggressive, capable of infecting maize without the plant being wounded first. This makes it a potentially serious threat to crop health. In contrast, other species, such as T. atroviride and T. asperellum, only caused infections when maize plants were injured before. Our research suggests that pathogenic Trichoderma species not only effectively infect plants but can also survive well in soil, making their control difficult. These findings highlight the need for better understanding of how these fungi operate in order to manage the risks they pose to important crops like maize, while still taking advantage of their beneficial uses in agriculture.

Viability of microencapsulated species of Trichoderma as a strategy to optimize use in biological control

The increasing use of chemical fungicides without effective control of phytopathogens has led to the development of resistance in microorganisms. As a promising alternative, products formulated with Trichoderma have emerged for their sustainable and effective potential in integrated disease management. However, the predominant formulations do not offer the necessary protection against abiotic factors. In this study, we investigated Trichoderma species encapsulated in sodium alginate through storage viability experiments and their antagonistic potential. The viability and storage conditions of the capsules were evaluated by plating at 5, 15, 30, 45, 60, and 150 days after production, kept in dry or refrigerated environments. The antagonistic potential was determined by the culture pairing method using the phytopathogen Fusarium sp. The results demonstrated that it was possible to maintain the viability of the conidia, with no differences between storage environments. Additionally, the capsule provided UV protection to the conidia encapsulated species possess antagonistic potential, inhibiting 52.54% of Fusarium sp. growth. Consequently, encapsulation is an alternative formulation method that ensures the viability of Trichoderma conidia and optimizes its use in biological control.

Trichoderma Species from Semiarid Regions and Their Antagonism Against the Microorganisms That Cause Pepper Wilt

Chili wilt is a significant challenge in producing jalapeño peppers, which has led to the implementation of strategies to help counteract or combat the microorganisms responsible for it. One of these strategies is the use of biological control microorganisms, such as Trichoderma, a fungus recognized as a natural enemy of the microorganisms that cause chili wilt. Therefore, this study aimed to isolate and identify Trichoderma species from the soils and roots of different plants, and evaluate their antagonism against Rhizoctonia solani, Phytophthora capsici, and Fusarium sp. Due to the complexity in identifying Trichoderma at the species level, performing a multilocus phylogenetic analysis was necessary, using the ITS, RPB2, and TEF1 regions. The species isolated were T. afroharzianum, T. lentiforme, T. rifaii, T. brevicompactum, T. arundinaceum, and T. longibrachiatum. Subsequently, they were used in three antagonism tests (dual culture, non-volatile organic compounds, and volatile organic compounds) against the phytopathogenic microorganisms. The tests demonstrated that the Trichoderma isolates could inhibit the mycelial growth of all three tested pathogens, obtaining the best results with the strains T. brevicompactum (19RCS), T. lentiforme (63DPS), T. longibrachiatum (71JES), T. rifaii (77JCR), and T. afroharzianum (24RQS, 87CCS, 88CCS and 17RCS). The strain with the best results in all three tests was 17RCS.

d-Galactose-Esterification of a Fungal Polyketide Catalyzed by a Carnitine Acyltransferase Domain

While sugar-containing natural products are commonly biosynthesized via glycosyltranferases using sugar-UDP as the electrophile, nature has evolved alternative strategies of glyco-modification to expand the diversity of natural products. Hydroxyl groups on sugars can serve as nucleophiles in the release of polyketide products from polyketide synthases. Herein, we demonstrate a highly reducing polyketide synthase (HRPKS) from the biocontrol fungus Trichoderma afroharzianum T22, which is terminated with a carnitine acyltransferase (cAT) domain, catalyzes the biosynthesis of a d-galactose esterified polyketide named as trichogalactin. Structure-guided enzymatic assays showed that the sugar nucleophile in the esterification reaction catalyzed by cAT is α-d-galactose-1-phosphate (Gal-1-P) instead of free d-galactose. The released product, trichogalactin phosphate, is subsequently dephosphorylated by a host alkaline phosphatase to complete the biosynthesis of trichogalactin. The cAT domain is highly specific for Gal-1-P and does not accept α-d-glucose-1-phosphate or α-d-mannose-1-phosphate. Our study expands the inventory of natural products from an agriculturally important fungus and demonstrates the potential of mining cAT-containing HRPKSs to discover new glyco-esterified natural products.

Synthesis of zinc oxide nanoparticles using Trichoderma harzianum and its bio-efficacy on Alternaria brassicae

Increasing concerns about chemical fungicides require sustainable alternatives for crop protection. Microbe-mediated synthesis of metal nanoparticles offers a sustainable, eco-friendly and highly effective strategy for plant disease management. This study investigates the mycosynthesis of zinc oxide nanoparticles (ZnO NPs) using the culture filtrate of Trichoderma harzianum and their antifungal activity against Alternaria brassicae. Nanoparticles were synthesized under optimized conditions of cell-free culture filtrate (CFCF) concentration, substrate concentration, pH and temperature. Ultraviolet-visible (UV-Vis) spectroscopy confirmed an absorption peak between 200 and 400 nm, while X-ray diffraction (XRD) confirms the hexagonal crystal structure with an average size of 29 nm. Dynamic light scattering (DLS) and zeta potential analysis revealed a hydrodynamic size of 50.79 nm and a surface charge of -17.49 mV, indicating good stability. Fourier transform infrared (FTIR) spectroscopy analysis identified functional groups (C=O, N-O, and O-H) that are crucial for nanoparticles stabilization. Scanning electron microscopy (SEM) and High-resolution transmission electron microscopy (HR-TEM) analysis revealed spherical, rod-shaped and hexagonal nanoparticles with sizes between 12 and 41 nm. Mycogenic-zinc oxide nanoparticles (M-ZnO NPs) significantly inhibited the mycelial growth of A. brassicae by 91.48% at 200 μg/mL, compared to chemically synthesized ZnO NPs at 200 μg/mL (79.62%) and mancozeb 0.2% (82.96%). SEM-EDX analysis revealed deformations and absorption of M-ZnO NPs in fungal hyphae, while confocal laser scanning microscopy (CLSM) showed increased reactive oxygen species (ROS) formation and impaired membrane integrity in treated fungal cells. Stress enzyme analysis confirmed increased superoxide dismutase (SOD) and catalase (CAT) activity by 44.2 U/mol and 39.6 U/mol at 200 μg/mL M-ZnO NPs. Our studies suggest that the M-ZnO NPs synthesized with T. harzianum culture filtrate have increased antifungal activity even at lower doses and can be used as an alternative to traditional fungicides without affecting environment.

Root microbes can improve plant tolerance to insect damage: A systematic review and meta-analysis

To limit damage from insect herbivores, plants rely on a blend of defensive mechanisms that includes partnerships with beneficial microbes, particularly those inhabiting roots. While ample evidence exists for microbially mediated resistance responses that directly target insects through changing phytotoxin and volatile profiles, we know surprisingly little about the microbial underpinnings of plant tolerance. Tolerance defenses counteract insect damage via shifts in plant physiology that reallocate resources to fuel compensatory growth, improve photosynthetic efficiency, and reduce oxidative stress. Despite being a powerful mitigator of insect damage, tolerance remains an understudied realm of plant defenses. Here, we propose a novel conceptual framework that can be broadly applied across study systems to characterize microbial impacts on expression of tolerance defenses. We conducted a systematic review of studies quantifying the impact of rhizosphere microbial inoculants on plant tolerance to herbivory based on several measures-biomass, oxidative stress mitigation, or photosynthesis. We identified 40 studies, most of which focused on chewing herbivores (n = 31) and plant growth parameters (e.g., biomass). Next, we performed a meta-analysis investigating the impact of microbial inoculants on plant tolerance to herbivory, which was measured via differences in plant biomass, and compared across key microbe, insect, and plant traits. Thirty-five papers comprising 113 observations were included in this meta-analysis, with effect sizes (Hedges' d) ranging from -4.67 (susceptible) to 18.38 (overcompensation). Overall, microbial inoculants significantly reduce the cost of herbivory via plant growth promotion, with overcompensation and compensation comprising 25% of observations of microbial-mediated tolerance. The grand mean effect size 0.99 [0.49; 1.49] indicates that the addition of a microbial inoculant increased plant biomass by ~1 SD under herbivore stress, thus improving tolerance. This effect was influenced most by microbial attributes, including functional guild and total soil community diversity. Overall, results highlight the need for additional investigation of microbially mediated plant tolerance, particularly in sap-feeding insects and across a more comprehensive range of tolerance mechanisms. Such attention would round out our current understanding of anti-herbivore plant defenses, offer insight into the underlying mechanisms that promote resilience to insect stress, and inform the application of microbial biotechnology to support sustainable agricultural practices.

Growth-Promoting Effects of Grass Root-Derived Fungi Cadophora fastigiata, Paraphoma fimeti and Plectosphaerella cucumerina on Spring Barley (Hordeum vulgare) and Italian Ryegrass (Lolium multiflorum)

Many endophytic fungi are approved as plant growth stimulants, and several commercial biostimulants have already been introduced in agricultural practice. However, there are still many species of fungi whose plant growth-promoting properties have been understudied or not studied at all. We examined the growth-promoting effect in spring barley (Hordeum vulgare) and Italian ryegrass (Lolium multiflorum) induced by three endophytic fungi previously obtained from the roots of Festuca/Lolium grasses. Surface-sterilized seeds were inoculated with a spore suspension of Cadophora fastigiata (isolate BSG003), Paraphoma fimeti (BSG010), Plectosphaerella cucumerina (BSG006), and their spore mixture. Before harvesting, the inoculated plants were grown in a greenhouse, with the barley being in multi-cavity trays for 30 days and ryegrass being placed in an original cylindric element system for 63 days. All three newly tested fungi had a positive effect on the growth of the barley and ryegrass plants, with the most pronounced impact observed in their root size. The fungal inoculations increased the dry shoot biomass between 11% and 26% in Italian ryegrass, but no such impact was observed in barley. The highest root increment was observed in barley. Herein, P. cucumerina and C. fastigiata inoculations were superior to other treatments, showing an increase in root dry weight of 50% compared to 20%, respectively. All fungal inoculations significantly promoted root growth in Italian ryegrass, resulting in a 20-30% increase in dry weight compared to non-inoculated plants. Moreover, a strong stimulatory effect of the fungi-emitted VOCs on the root development was observed in plate-in-plate arrays. In the presence of C. fastigiata and P. cucumerina cultures, the number of roots and root hairs in barley seedlings doubled compared to control plants. Thus, in our study, we demonstrated the potential of the grass root-derived endophytes C. fastigiata, P. fimeti, and P. cucumerina as growth promoters for spring barley and Italian ryegrass. These studies can be extended to other major crops and grasses by evaluating different fungal isolates.

Harnessing Trichoderma Mycoparasitism as a Tool in the Management of Soil Dwelling Plant Pathogens

Maintaining and enhancing agricultural productivity for food security while preserving the ecology and environment from the harmful effects of toxicants is the main challenge in modern monoculture farming systems. Microbial biological agents can be a promising substitute for traditional synthetic pesticides to manage plant diseases. Trichoderma spp. are soil-dwelling ascomycete fungi and are common biocontrol agents against diverse phytopathogens. Trichoderma-based biocontrol techniques can regulate and control soil-borne plant diseases through mechanisms such as mycoparasitism, the production of antibiotics and hydrolytic enzymes, rhizo-sphere competence, the effective competition for available resources, induction of plant resistance and facilitation of plant growth. Numerous secondary metabolites produced by Trichoderma spp. are reported to prevent the development of soil-borne plant disease. Thus, Trichoderma spp. may have direct and indirect biological impacts on the targeted plant pathogens. Furthermore, this review discusses the convenient implications and challenges of applying Trichoderma-based strategies in agricultural settings. Overall, the assessment underscores the potential of Trichoderma as a sustainable and effective tool for mitigating soil-borne pathogens, highlighting avenues for future research and applications.

Trichoderma gets by with a little help from Streptomyces: fungal-bacterial symbiosis in plant growth promotion

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Kabir AH, Thapa A, Hasan R, Parvej R. 2024. Local signal from Trichoderma afroharzianum T22 induces host transcriptome and endophytic microbiome leading to growth promotion in sorghum. Journal of Experimental Botany 75, https://doi.org/10.1093/jxb/erae340.

Effects of Two Trichoderma Strains on Apple Replant Disease Suppression and Plant Growth Stimulation

Fusarium oxysporum, the pathogen responsible for apple replant disease (ARD), is seriously threatening the apple industry globally. We investigated the antagonistic properties of Trichoderma strains against F. oxysporum HS2, aiming to find a biological control solution to minimize the dependence on chemical pesticides. Two of the thirty-one Trichoderma strains assessed through plate confrontation assays, L7 (Trichoderma atroviride) and M19 (T. longibrachiatum), markedly inhibited = F. oxysporum, with inhibition rates of 86.02% and 86.72%, respectively. Applying 1 × 106 spores/mL suspensions of these strains notably increased the disease resistance in embryonic mung bean roots. Strains L7 and M19 substantially protected Malus robusta Rehd apple rootstock from ARD; the plant height, stem diameter, leaf number, chlorophyll content, and defense enzyme activity were higher in the treated plants than in the controls in both greenhouse and field trials. The results of fluorescent labeling confirmed the effective colonization of these strains of the root soil, with the number of spores stabilizing over time. At 56 days after inoculation, the M19 and L7 spore counts in various soils confirmed their persistence. These results underscore the biocontrol potential of L7 and M19 against HS2, offering valuable insights into developing sustainable ARD management practices.

Assessment of the potential protective effects of culture filtrate of Trichoderma harzianum to ameliorate the damaged histoarchitecture of brain in epileptic rats

The simultaneous hyperexcitability of the neural network is the most well-known manifestation of epilepsy that causes recurrent seizures. The current study was aimed to examine any potential safety benefits of the culture filtrate of Trichoderma harzianum (ThCF) to ameliorate damaged histoarchitecture of the brain in epileptic rats by assessing seizure intensity scale and behavioral impairments and follow up the spontaneous motor seizures during status epilepticus phases in rats. Twenty-four rats were divided into four groups; control (C), epileptic (EP) valproic acid-treated epileptic (EP-VPA), and epileptic treated with T. harzianum cultured filtrate (ThCF). In addition to a seizure intensity score and behavioral tests, routine H&E and Golgi-Copsch histopathology, were used to examine the cell somas, dendrites, axons, and neural spines. ThCF treatment increased activity and recorded movements during grooming, rearing, and ambulation frequency. Brain tissues of epileptic rats exhibited detached meninges, hypercellularity, mild edema in the cortex and markedly degenerated neurons, degenerated glial cells, and microcyst formation in the hippocampus. Moreover, brains of EP-ThCF were noticed with average blood vessels, and increased dendritogenesis. The current data revealed some of negative effects of epileptogenesis brought on by seizure intensity score and retarded histopathological alterations in the hippocampus. Therefore, the study is forecasting to identify novel active components from the metabolites of T. harzianum with a crucial therapeutic role in various disorders.

Impact of tps1 Deletion and Overexpression on Terpene Metabolites in Trichoderma atroviride

Terpenoids are structurally diverse natural products that have been widely used in the pharmaceutical, food, and cosmetic industries. Research has shown that fungi produce a variety of terpenoids, yet fungal terpene synthases remain not thoroughly explored. In this study, the tps1 gene, a crucial component of the terpene synthetic pathway, was isolated from Trichoderma atroviride HB20111 through genome mining. The function of this gene in the terpene synthetic pathway was investigated by constructing tps1-gene-deletion- and overexpression-engineered strains and evaluating the expression differences in the tps1 gene at the transcript level. HS-SPME-GC-MS analysis revealed significant variations in terpene metabolites among wild-type, tps1-deleted (Δtps1), and tps1-overexpressed (Otps1) strains; for instance, most sesquiterpene volatile organic compounds (VOCs) were notably reduced or absent in the Δtps1 strain, while nerolidol, β-acorenol, and guaiene were particularly produced by the Otps1 strain. However, both the Δtps1 and Otps1 strains produced new terpene metabolites compared to the wild-type, which indicated that the tps1 gene played an important role in terpene synthesis but was not the only gene involved in T. atroviride HB20111. The TPS1 protein encoded by the tps1 gene could function as a sesquiterpene cyclase through biological information and evolutionary tree analysis. Additionally, fungal inhibition assay and wheat growth promotion assay results suggested that the deletion or overexpression of the tps1 gene had a minimal impact on fungal inhibitory activity, plant growth promotion, and development, as well as stress response. This implies that these activities of T. atroviride HB20111 might result from a combination of multiple metabolites rather than being solely dependent on one specific metabolite. This study offers theoretical guidance for future investigations into the mechanism of terpenoid synthesis and serves as a foundation for related studies on terpenoid metabolic pathways in fungi.

Flavonoid synthesis is crucial for Trichoderma asperellum-induced systemic resistance to root-knot nematodes in tomato plants

Trichoderma spp. can enhance plant resistance against a wide range of biotic stressors. However, the fundamental mechanisms by which Trichoderma enhances plant resistance against Meloidogyne incognita, known as root-knot nematodes (RKNs), are still unclear. Here, we identified a strain of Trichoderma asperellum (T141) that could effectively suppress RKN infestation in tomato (Solanum lycopersicum L.). Nematode infestation led to an increase in the concentrations of reactive oxygen species (ROS) and malondialdehyde (MDA) in roots but pre-inoculation with T141 significantly decreased oxidative stress. The reduction in ROS and MDA was accompanied by an increase in the activity of antioxidant enzymes and the accumulation of flavonoids and phenols. Moreover, split root test-based analysis showed that T141 inoculation in local roots before RKN inoculation increased the concentration of phytohormone jasmonate (JA) and the transcripts of JA synthesis and signaling-related genes in distant roots. UPLC-MS/MS-based metabolomics analysis identified 1051 differentially accumulated metabolites (DAMs) across 4 pairwise comparisons in root division test, including 81 flavonoids. Notably, 180 DAMs were found in comparison between RKN and T141-RKN, whereas KEGG annotation and enrichment analysis showed that the secondary metabolic pathways, especially the flavonoid biosynthesis, played a key role in the T141-induced systemic resistance to RKNs. The role of up-regulated flavonoids in RKN mortality was further verified by in vitro experiments with the exogenous treatment of kaempferol, hesperidin and rutin on J2-stage RKNs. Our results revealed a critical mechanism by which T141 induced resistance of tomato plants against the RKNs by systemically promoting secondary metabolism in distant roots.

Bioprospecting the roles of Trichoderma in alleviating plants' drought tolerance: Principles, mechanisms of action, and prospects

Drought-induced stress represents a significant challenge to agricultural production, exerting adverse effects on both plant growth and overall productivity. Therefore, the exploration of innovative long-term approaches for addressing drought stress within agriculture constitutes a crucial objective, given its vital role in enhancing food security. This article explores the potential use of Trichoderma, a well-known genus of plant growth-promoting fungi, to enhance plant tolerance to drought stress. Trichoderma species have shown remarkable potential for enhancing plant growth, inducing systemic resistance, and ameliorating the adverse impacts of drought stress on plants through the modulation of morphological, physiological, biochemical, and molecular characteristics. In conclusion, the exploitation of Trichoderma's potential as a sustainable solution to enhance plant drought tolerance is a promising avenue for addressing the challenges posed by the changing climate. The manifold advantages of Trichoderma in promoting plant growth and alleviating the effects of drought stress underscore their pivotal role in fostering sustainable agricultural practices and enhancing food security.

Bio-synthesis and characterization of silver nanoparticles from Trichoderma species against cassava root rot disease

Cassava root rot disease caused by the fungal pathogens Fusarium solani and Lasiodiplodia theobromae produces severe damages on cassava production. This research was conducted to produce and assess silver nanoparticles (AgNPs) synthesized by Trichoderma harzianum for reducing root rot disease. The results revealed that using the supernatants of T. harzianum on a silver nitrate solution changed it to reddish color at 48 h, indicating the formation of AgNPs. Further characterization was identified using dynamic light scattering (DLS) and scanning electron microscope (SEM). DLS supported that the Z-average size is at 39.79 nm and the mean zeta potential is at - 36.5 mV. SEM revealed the formation of monodispersed spherical shape with a diameter between 60-75 nm. The antibacterial action of AgNPs as an antifungal agent was demonstrated by an observed decrease in the size of the fungal colonies using an increasing concentration of AgNPs until the complete inhibition growth of L. theobromae and F. solani at > 58 µg mL-1 and at ≥ 50 µg mL-1, respectively. At in vitro conditions, the applied AgNPs caused a decrease in the percentage of healthy aerial hyphae of L. theobromae (32.5%) and of F. solani (70.0%) compared to control (100%). The SR-FTIR spectra showed the highest peaks in the first region (3000-2800 cm-1) associated with lipids and fatty acids located at 2962, 2927, and 2854 cm-1 in the AgNPs treated samples. The second region (1700-1450 cm-1) consisting of proteins and peptides revealed the highest peaks at 1658, 1641, and 1548 cm-1 in the AgNPs treated samples. The third region (1300-900 cm-1), which involves nucleic acid, phospholipids, polysaccharides, and carbohydrates, revealed the highest peaks at 1155, 1079, and 1027 cm-1 in the readings from the untreated samples. Finally, the observed root rot severity on cassava roots treated with AgNPs (1.75 ± 0.50) was significantly lower than the control samples (5.00 ± 0.00).

Spectroscopic Investigation of Tomato Seed Germination Stimulated by Trichoderma spp

Seed germination is a complex process that can be negatively affected by numerous stresses. Trichoderma spp. are known as effective biocontrol agents as well as plant growth and germination stimulators. However, understanding of the early interactions between seeds and Trichoderma spp. remains limited. In the present paper, Fourier-transform infrared spectroscopy (FTIR) and Raman spectroscopy were used to reveal the nature of tomato seed germination as stimulated by Trichoderma. A rapid response of tomato seeds to Trichoderma spp. was observed within 48 h on Murashige and Skoog medium (MS) substrate, preceding any physical contact. Raman analysis indicated that both Trichoderma species stimulated phenolic compound synthesis by triggering plant-specific responses in seed radicles. The impact of T. harzianum and T. brevicompactum on two tomato cultivars resulted in alterations to the middle lamella pectin, cellulose, and xyloglucan in the primary cell wall. The Raman spectra indicated increased xylan content in NA with T9 treatment as well as increased hemicelluloses in GZ with T4 treatment. Moreover, T4 treatment resulted in elevated conjugated aldehydes in lignin in GZ, whereas the trend was reversed in NA. Additionally, FTIR analysis revealed significant changes in total protein levels in Trichoderma spp.-treated tomato seed radicles, with simultaneous decreases in pectin and/or xyloglucan. Our results indicate that two complementary spectroscopic methods, FTIR and Raman spectroscopy, can give valuable information on rapid changes in the plant cell wall structure of tomato radicles during germination stimulated by Trichoderma spp.

The regulatory pathway of transcription factor MYB36 from Trichoderma asperellum Tas653 resistant to poplar leaf blight pathogen Alternaria alternata Aal004

In fungi, MYB transcription factors (TFs) mainly regulate growth, development, and resistance to stress. However, as major disease-resistance TFs, they have rarely been studied in biocontrol fungi. In this study, MYB36 of Trichoderma asperellum Tas653 (Ta) was shown to respond strongly to the stress caused by Alternaria alternata Aa1004. Compared with wild-type Ta (Ta-Wt), the inhibition rate of the MYB36 knockout strain (Ta-Kn) on Aa1004 decreased by 11.06%; the superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) activities decreased by 82.15 U/g, 0.19 OD470/min/g, and 1631.2 μmol/min/g, respectively. The MYB36 overexpression strain (Ta-Oe) not only enhanced hyperparasitism on Aa1004, caused its hyphae to swell, deform, or even rupture, but also reduced the incidence rate of poplar leaf blight. MYB36 regulates downstream (TFs, detoxification genes, defense genes, and other antifungal-related genes by binding to the cis-acting elements "ACAT" and "ATCG". Zinc finger TFs, as the main antifungal TFs, account for 90% of the total TFs, and Zn37.5 (23.24-) and Zn83.7 (23.18-fold) showed the greatest expression difference when regulated directly by MYB36. The detoxification genes mainly comprised 11 major major facilitator superfamily (MFS) genes, among which MYB36 directly increased the expression levels of three genes by more than 2-3.44-fold. The defense genes mainly encoded cytochrome P450 (P450) and hydrolases. e.g., P45061.3 (2-10.95-), P45060.2 (2-7.07-), and Hyd44.6 (2-2.30-fold). This study revealed the molecular mechanism of MYB36 regulation of the resistance of T. asperellum to A. alternata and provides theoretical guidance for the biocontrol of poplar leaf blight and the anti-disease mechanism of biocontrol fungi.

Genomic insights into the evolution and adaptation of secondary metabolite gene clusters in fungicolous species Cladobotryum mycophilum ATHUM6906

Mycophilic or fungicolous fungi can be found wherever fungi exist since they are able to colonize other fungi, which occupy a diverse range of habitats. Some fungicolous species cause important diseases on Basidiomycetes, and thus, they are the main reason for the destruction of mushroom cultivations. Nonetheless, despite their ecological significance, their genomic data remain limited. Cladobotryum mycophilum is one of the most aggressive species of the genus, destroying the economically important Agaricus bisporus cultivations. The 40.7 Mb whole genome of the Greek isolate ATHUM6906 is assembled in 16 fragments, including the mitochondrial genome and 2 small circular mitochondrial plasmids, in this study. This genome includes a comprehensive set of 12,282 protein coding, 56 rRNA, and 273 tRNA genes. Transposable elements, CAZymes, and pathogenicity related genes were also examined. The genome of C. mycophilum contained a diverse arsenal of genes involved in secondary metabolism, forming 106 biosynthetic gene clusters, which renders this genome as one of the most BGC abundant among fungicolous species. Comparative analyses were performed for genomes of species of the family Hypocreaceae. Some BGCs identified in C. mycophilum genome exhibited similarities to clusters found in the family Hypocreaceae, suggesting vertical heritage. In contrast, certain BGCs showed a scattered distribution among Hypocreaceae species or were solely found in Cladobotryum genomes. This work provides evidence of extensive BGC losses, horizontal gene transfer events, and formation of novel BGCs during evolution, potentially driven by neutral or even positive selection pressures. These events may increase Cladobotryum fitness under various environmental conditions and potentially during host-fungus interaction.

Mechanisms for plant growth promotion activated by Trichoderma in natural and managed terrestrial ecosystems

Trichoderma spp. are free-living fungi present in virtually all terrestrial ecosystems. These soil fungi can stimulate plant growth and increase plant nutrient acquisition of macro- and micronutrients and water uptake. Generally, plant growth promotion by Trichoderma is a consequence of the activity of potent fungal signaling metabolites diffused in soil with hormone-like activity, including indolic compounds as indole-3-acetic acid (IAA) produced at concentrations ranging from 14 to 234 μg l-1, and volatile organic compounds such as sesquiterpene isoprenoids (C15), 6-pentyl-2H-pyran-2-one (6-PP) and ethylene (ET) produced at levels from 10 to 120 ng over a period of six days, which in turn, might impact plant endogenous signaling mechanisms orchestrated by plant hormones. Plant growth stimulation occurs without the need of physical contact between both organisms and/or during root colonization. When associated with plants Trichoderma may cause significant biochemical changes in plant content of carbohydrates, amino acids, organic acids and lipids, as detected in Arabidopsis thaliana, maize (Zea mays), tomato (Lycopersicon esculentum) and barley (Hordeum vulgare), which may improve the plant health status during the complete life cycle. Trichoderma-induced plant beneficial effects such as mechanisms of defense and growth are likely to be inherited to the next generations. Depending on the environmental conditions perceived by the fungus during its interaction with plants, Trichoderma can reprogram and/or activate molecular mechanisms commonly modulated by IAA, ET and abscisic acid (ABA) to induce an adaptative physiological response to abiotic stress, including drought, salinity, or environmental pollution. This review, provides a state of the art overview focused on the canonical mechanisms of these beneficial fungi involved in plant growth promotion traits under different environmental scenarios and shows new insights on Trichoderma metabolites from different chemical classes that can modulate specific plant growth aspects. Also, we suggest new research directions on Trichoderma spp. and their secondary metabolites with biological activity on plant growth.

Chemistry and biology of marine-derived Trichoderma metabolites

Marine-derived fungi of the genus Trichoderma have been surveyed for pharmaceuticals and agrochemicals since 1993, with various new secondary metabolites being characterized from the strains of marine animal, plant, sediment, and water origin. Chemical structures and biological activities of these metabolites are comprehensively reviewed herein up to the end of 2022 (covering 30 years). More than 70 strains that belong to at least 18 known Trichoderma species have been chemically investigated during this period. As a result, 445 new metabolites, including terpenes, steroids, polyketides, peptides, alkaloids, and others, have been identified, with over a half possessing antimicroalgal, zooplankton-toxic, antibacterial, antifungal, cytotoxic, anti-inflammatory, and other activities. The research is highlighted by the molecular diversity and antimicroalgal potency of terpenes and steroids. In addition, metabolic relevance along with co-culture induction in the production of new compounds is also concluded. Trichoderma strains of marine origin can transform and degrade heterogeneous molecules, but these functions need further exploration.

Harnessing root exudates for plant microbiome engineering and stress resistance in plants

A wide range of abiotic and biotic stresses adversely affect plant's growth and production. Under stress, one of the main responses of plants is the modulation of exudates excreted in the rhizosphere, which consequently leads to alterations in the resident microbiota. Thus, the exudates discharged into the rhizospheric environment play a preponderant role in the association and formation of plant-microbe interactions. In this review, we aimed to provide a synthesis of the latest and most pertinent literature on the diverse biochemical and structural compositions of plant root exudates. Also, this work investigates into their multifaceted role in microbial nutrition and intricate signaling processes within the rhizosphere, which includes quorum-sensing molecules. Specifically, it explores the contributions of low molecular weight compounds, such as carbohydrates, phenolics, organic acids, amino acids, and secondary metabolites, as well as the significance of high molecular weight compounds, including proteins and polysaccharides. It also discusses the state-of-the-art omics strategies that unveil the vital role of root exudates in plant-microbiome interactions, including defense against pathogens like nematodes and fungi. We propose multiple challenges and perspectives, including exploiting plant root exudates for host-mediated microbiome engineering. In this discourse, root exudates and their derived interactions with the rhizospheric microbiota should receive greater attention due to their positive influence on plant health and stress mitigation.

Use of Trichoderma in the Production of Forest Seedlings

Forest production has great relevance in the Brazilian economy, characterized by several production sectors, including the production of seedlings. With the focus on maximizing the capacity of survival, development, and adaptation of seedlings, Trichoderma is highlighted as a potentially useful genus of microorganisms for promoting growth and higher product quality. In this sense, this review aims to describe the main mechanisms of fungi action in forest seedlings' production. The different species of the genus Trichoderma have specific mechanisms of action, and the current scenario points to more advances in the number of species. The interaction process mediated by different mechanisms of action begins in the communication with plants, from the colonization process. After the interaction, chemical dialogues allow the plant to develop better because, from colonization, the forest seedlings can maximize height and increase shoot and root development. Fungi promote solubilization and availability of nutrients to seedlings, which show numerous benefits to the development. The use of beneficial microorganisms, such as fungi of the genus Trichoderma, has become a sustainable strategy to enhance seedling development, reducing the use of agrochemicals and industrial fertilizers.

Combined microbe-plant remediation of cadmium in saline-alkali soil assisted by fungal mycelium-derived biochar

Cadmium contamination in saline-alkali soil is becoming a great concern. Combined microbe-plant remediation is an economic way to treat this contamination, but is compromised by its low cadmium-removing capacity. In this study, the novel fungus-derived biochar was prepared to enhance the salt-tolerant bacterium-plant remediation of cadmium-contaminated saline-alkali soil. This biochar was prepared by pre-incubation of living Trichoderma atroviride hyphae with imidazole and further heating at 500 °C for 1 h. The obtained fungus-derived nitrogen-doped biochar (FBioCN) exhibited the high affinity to bacterial cells, leading to efficient colonization of exogenous salt-tolerant bacteria (e.g., Rhizobacter sp. and Sphingomonas sp.) on Amaranthus hypochondriacus roots. During culturing of the plants in the cadmium-contaminated saline-alkali soil, FBioCN drastically remodeled the rhizosphere microbiome, leading to enhance colonization of the exogeneous salt-tolerant bacteria, and increase bacterial diversity. The combination of FBioCN and the exogeneous bacteria further improved the activity of rhizosphere functional enzymes, protected the plants from the multiple stress, and promoted cadmium transport from the soil to the plants. Consequently, FBioCN together with the salt-tolerant bacteria drastically improved cadmium removal from the saline-alkali soil, with the percent of cadmium removal at the rhizosphere region increasing from 35.1% to 95.1%. This study sheds a light on the application of fungus-derived biochar in combined microbe-plant remediation in saline-alkali soil.

Trichoderma virens Big Ras GTPase-1, a molecular switch for transforming a mutualistic fungus to plants in a deleterious microbe

Trichoderma spp. are ascomycete filamentous fungi widely distributed worldwide that establish mutualistic relationships with plants by antagonizing phytopathogens in the rhizosphere and colonizing the plant roots, hence, promoting plant growth and triggering the systemic resistance against phytopathogens. During the first stages of root colonization by Trichoderma, plants recognize the fungus as an invader by inducing the plant defense system, including the production of reactive oxygen species (ROS). Some members of the small Ras GTPases regulate NADPH oxidases and, therefore, ROS production. However, their role in mutualistic microorganisms that colonize plant roots is poorly understood. It has been demonstrated that Trichoderma virens strains lacking TBRG-1, a member of a new family of the Ras GTPases, impair their biocontrol capability and behave like a pathogen on tomato seeds and seedlings. Here, we found that TBRG-1 is essential in T. virens to maintain the mutualistic relationship with plants because a mutant-lacking tbrg-1 gen could not induce plant growth in Arabidopsis and tomatoes. Furthermore, treatment of Arabidopsis seedlings with Δtbrg-1 induced strongly PR-1a, the systemic acquired resistance (SAR) marker gene at early times of the interaction, which correlated with enhanced foliar damage by Botrytis cinerea, resembling the behavior of a biotrophic phytopathogen. Additionally, leaves of plants treated with either T. virens wild-type (wt) or Δtbrg-1 and challenged or not with Botrytis showed ROS production to a different extent, as well as differential expression of cell detoxification-related genes, CAT1, and APX1. Root colonization assays of sid-2 and jar1 mutant lines affected in SAR and induced systemic resistance (ISR) by Δtbrg-1 and the wt strain, suggest an important role of both pathways in the recognition of the fungus and that TBRG-1 plays a pivotal role in root colonization. Furthermore, we found that TBRG-1 is a negative regulator of NoxR expression, which may impact the mutualistic interaction.

Role of plant metabolites in the formation of bacterial communities in the rhizosphere of Tetrastigma hemsleyanum

Tetrastigma hemsleyanum Diels et Gilg, commonly known as Sanyeqing (SYQ), is an important traditional Chinese medicine. The content of bioactive constituents varies in different cultivars of SYQ. In the plant growth related researches, rhizosphere microbiome has gained significant attention. However, the role of bacterial communities in the accumulation of metabolites in plants have not been investigated. Herein, the composition of bacterial communities in the rhizosphere soils and the metabolites profile of different SYQ cultivars' roots were analyzed. It was found that the composition of microbial communities varied in the rhizosphere soils of different SYQ cultivars. The high abundance of Actinomadura, Streptomyces and other bacteria was found to be associated with the metabolites profile of SYQ roots. The findings suggest that the upregulation of rutin and hesperetin may contribute to the high bioactive constituent in SYQ roots. These results provide better understanding of the metabolite accumulation pattern in SYQ, and also provide a solution for enhancing the quality of SYQ by application of suitable microbial consortia.

Trichoderma harzianum Cellulase Gene thph2 Affects Trichoderma Root Colonization and Induces Resistance to Southern Leaf Blight in Maize

Trichoderma, widely distributed all over the world, is commonly found in soil and root ecosystems. It is a group comprising beneficial fungi that improve plant disease resistance and promote plant growth. Studies have shown that Trichoderma cellulases can also improve plant disease resistance. Based on previous studies, we reported that a C6 zinc finger protein (Thc6) regulates two cellulase genes, thph1 and thph2, to induce ISR responses in plants. Therefore, in this study, we focused on the role of thph2 in the colonization of maize roots by T. harzianum and the induction of systemic resistance against southern leaf blight. The results showed that thph2 had a positive regulatory effect on the Trichoderma colonization of maize roots. After the root was treated with Trichoderma, the leaf defense genes AOS, LOX5, HPL, and OPR1 were expressed to resist the attack of Cochliobolus heterostrophus. The pure Thph2 protein also resulted in a similar induction activity of the AOS, LOX5, HPL, and OPR1 expression in maize roots, further demonstrating that thph2 can induce plant defense responses and that signal transduction occurs mainly through the JA signaling pathway.

Counter-attack of biocontrol agents: Environmentally benign Approaches against Root-knot nematodes (Meloidogyne spp.) on Agricultural crops

Root-knot nematodes (Meloidogyne spp.) are obligate sedentary endoparasites, considered severe crop-damaging taxa among all plant-parasitic nematodes globally. Their attacks through parasitic proteins alter the physiology and machinery of the host cells to favour parasitism and reduction in crop yield. Currently, the use of excessive pesticides as a fast remedy to manage this pest is hazardous for both the environment and humans. Keeping this view in mind, there is an urgent need for developing efficient eco-friendly strategies. Bio-control as an eco-friendly is considered the best approach to manage nematodes without disturbing non-target microbes. In bio-control, living agents such as fungi and bacteria are the natural enemies of nematodes and the best substitute for pesticides. Fungi, including nematode-trapping fungi, can sense host signals and produce special trapping devices viz., constricting rings and adhesive knobs/loops, to capture nematodes and kill them. Whereas, endo-parasitic fungi kill nematodes by enzymatic secretions and spore adhesion through their hyphae. Bacteria can also control nematodes by producing antibiotic compounds, competing for nutrients and rhizosphere, production of hydrolytic enzymes viz., chitinases, proteases, lipases, and induction of systemic resistance (ISR) in host plants. Scientists throughout the world are trying to evolve environmentally benign methods that sustain agricultural production and keep nematodes below a threshold level. Whatever methods evolve, in the future the focus should be on important aspects like green approaches for managing nematodes without disturbing human health and the environment.

Insights into the molecular mechanism of Trichoderma stimulating plant growth and immunity against phytopathogens

Trichoderma species have received significant interest as beneficial fungi for boosting plant growth and immunity against phytopathogens. By establishing a mutualistic relationship with plants, Trichoderma causes a series of intricate signaling events that eventually promote plant growth and improve disease resistance. The mechanisms contain the indirect or direct involvement of Trichoderma in enhancing plant growth by modulating phytohormones signaling pathways, improving uptake and accumulation of nutrients, and increasing soil bioavailability of nutrients. They contribute to plant resistance by stimulating systemic acquired resistance through salicylic acid, jasmonic acid, and ethylene signaling. A cascade of signal transduction processes initiated by the interaction of Trichoderma and plants regulate the expression of defense-related genes, resulting in the synthesis of defense hormones and pathogenesis-related proteins (PRPs), which collectively improve plant resistance. Additionally, advancements in omics technologies has led to the identification of key pathways, their regulating genes, and molecular interactions in the plant defense and growth promotion responses induced by Trichoderma. Deciphering the molecular mechanism behind Trichoderma's induction of plant defense and immunity is essential for harnessing the full plant beneficial potential of Trichoderma. This review article sheds light on the molecular mechanisms that underlie the positive effects of Trichoderma-induced plant immunity and growth and opens new opportunities for developing environmentally friendly and innovative approaches to improve plant immunity and growth.

In Vitro Assessment of Eight Selected Indigenous Fungal Isolates Tolerance to Various Abiotic Stresses and their Effects on Seed Germination

Fungal bio-control agents (BCA) can minimize use of agro-chemicals while increasing plant productivity and tolerance to biotic-abiotic stressors. Ideally, BCA should tolerate varying environmental conditions they are introduced into, to successfully dominate and protect plants from stressors. However, BCA are living micro-organisms, their survival and efficacy can be impeded by extreme conditions. The current study aimed at evaluating whether indigenous fungal isolates, viz, Aspergillus flavus, A. terreus, Penicillium sp. AL-38 IRH-2012b, Talaromyces minioluteus, T. purpureogenus, T. sayulitensis, Trichoderma ghanense and T. viride can tolerate different levels of salinity, pH, nutrient and temperature. Certain fungal species are pests with potential of destroying many crops; the pathogenic effects of the aforementioned fungal isolates were further assessed on different crops' seeds. The results showed that, although being indigenous, Aspergillus, T. sayulitensis and T. ghanense failed to thrive in high salinity and pH. While Penicillium sp. AL-38 IRH-2012b failed to thrive under reduced nutrient level and all fungal isolates failed to grow at 10-20 °C. Furthermore, it was noted species within the same genus could affect crops in both favorable and unfavorable ways. The study demonstrated that the selected indigenous fungal isolates can tolerate different abiotic conditions and have potential to improve seed germination and seedling growth.

Trichoderma harzianum Peptaibols Stimulate Plant Plasma Membrane H+-ATPase Activity

Because of their ability to promote growth, act as biopesticides, and improve abiotic stress tolerance, Trichoderma spp. have been used for plant seed coating. However, the mechanism for the promotion of plant growth remains unknown. In this study, we investigate the effect of fungal extracts on the plant plasma membrane (PM) H+-ATPase, which is essential for plant growth and often a target of plant-associated microbes. We show that Trichoderma harzianum extract increases H+-ATPase activity, and by fractionation and high-resolution mass spectrometry (MS), we identify the activating components trichorzin PA (tPA) II and tPA VI that belong to the class of peptaibols. Peptaibols are nonribosomal peptides that can integrate into membranes and form indiscriminate ion channels, which causes pesticidal activity. To further investigate peptaibol-mediated H+-ATPase activation, we compare the effect of tPA II and VI to that of the model peptaibol alamethicin (AlaM). We show that AlaM increases H+-ATPase turnover rates in a concentration-dependent manner, with a peak in activity measured at 31.25 μM, above which activity decreases. Using fluorescent probes and light scattering, we find that the AlaM-mediated increase in activity is not correlated to increased membrane fluidity or vesicle integrity, whereas the activity decrease at high AlaM concentrations is likely due to PM overloading of AlaM pores. Overall, our results suggest that the symbiosis of fungi and plants, specifically related to peptaibols, is a concentration-dependent balance, where peptaibols do not act only as biocontrol agents but also as plant growth stimulants.

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.

Structures and Biological Activities of Secondary Metabolites from the Trichoderma genus (Covering 2018-2022)

Trichoderma, a genus with more than 400 species, has a long history of use as an industrial bioreactor, biofertilizer, and biocontrol agent. It is considered a significant source of secondary metabolites (SMs) that possess unique structural features and a wide range of bioactivities. In recent years, numerous secondary metabolites of Trichoderma, including terpenoids, polyketides, peptides, alkaloids, and steroids, have been identified. Most of these SMs displayed antimicrobial, cytotoxic, and antifungal effects. This review focuses on the structural diversity, biological activities, and structure-activity relationships (SARs) of the SMs isolated from Trichoderma covered from 2018 to 2022. This study provides insights into the exploration and utilization of bioactive compounds from Trichoderma species in the agriculture or pharmaceutical industry.

Trichoderma harzianum inoculation promotes sweet sorghum growth in the saline soil by modulating rhizosphere available nutrients and bacterial community

As one of the major abiotic stresses, salinity can affect crop growth and plant productivity worldwide. The inoculation of rhizosphere or endophytic microorganisms can enhance plant tolerance to salt stresses, but the potential mechanism is not clear. In this study, Trichoderma harzianum ST02 was applied on sweet sorghum [Sorghum bicolor (L.) Moench] in a field trial to investigate the effects on microbiome community and physiochemical properties in the rhizosphere soil. Compared with the non-inoculated control, Trichoderma inoculation significantly increased the stem yield, plant height, stem diameter, and total sugar content in stem by 35.52%, 32.68%, 32.09%, and 36.82%, respectively. In addition, Trichoderma inoculation improved the nutrient availability (e.g., N, P, and K) and organic matter in the rhizosphere soil and changed the bacterial community structure and function in both bulk and rhizosphere soil by particularly increasing the relative abundance of Actinobacter and N-cycling genes (nifH, archaeal and bacterial amoA). We proposed that T. harzianum ST02 could promote sweet sorghum growth under saline conditions by regulating available nutrients and the bacterial community in the rhizosphere soil.

Identification of a pathogen causing fruiting body rot of Sanghuangporus vaninii

Sanghuangporus vaninii is a medicinal macrofungus that is increasingly cultivated in China. During cultivation, it was found that the fruiting body of S. vaninii was susceptible to pathogenic fungi, resulting in significant economic losses to the industry. The symptoms of the disease occur in the initial stage of fruiting body development. The isolate YZB-1 was obtained from the junction of the diseased and healthy areas of the fruiting body. In order to verify the pathogenicity of YZB-1, its purified spore suspension was inoculated into the exposed area nearby the developing fruiting body of S. vaninii. After 10 days, the same disease symptoms appeared in the inoculated area. Morphological identification and molecular analysis of rDNA ITS region confirmed that the isolate YZB-1 was identified as Trichoderma virens. The temperature stability assay revealed that the mycelia of YZB-1 grew the fastest at 25 °C, with growth slowing down gradually as the temperature increased or decreased. Dual-culture tests of T. virens and S. vaninii showed that the inhibition rate of T. virens on S. vaninii mycelium was the highest (79.01 ± 2.79%) at 25 °C, and more green spores were produced at the intersection of T. virens and S. vaninii.

Genomic Based Analysis of the Biocontrol Species Trichoderma harzianum: A Model Resource of Structurally Diverse Pharmaceuticals and Biopesticides

Fungi represents a rich repository of taxonomically restricted, yet chemically diverse, secondary metabolites that are synthesised via specific metabolic pathways. An enzyme's specificity and biosynthetic gene clustering are the bottleneck of secondary metabolite evolution. Trichoderma harzianum M10 v1.0 produces many pharmaceutically important molecules; however, their specific biosynthetic pathways remain uncharacterised. Our genomic-based analysis of this species reveals the biosynthetic diversity of its specialised secondary metabolites, where over 50 BGCs were predicted, most of which were listed as polyketide-like compounds associated clusters. Gene annotation of the biosynthetic candidate genes predicted the production of many medically/industrially important compounds including enterobactin, gramicidin, lovastatin, HC-toxin, tyrocidine, equisetin, erythronolide, strobilurin, asperfuranone, cirtinine, protoilludene, germacrene, and epi-isozizaene. Revealing the biogenetic background of these natural molecules is a step forward towards the expansion of their chemical diversification via engineering their biosynthetic genes heterologously, and the identification of their role in the interaction between this fungus and its biotic/abiotic conditions as well as its role as bio-fungicide.

First insights into diversity and potential metabolic pathways of bacterial and fungal communities in the rhizosphere of Argemonemexicana L. (Papaveraceae) from the water-level-fluctuation zone of Wudongde Reservoir of the upper Yangtze river, China

The water-level fluctuation zone (WLFZ) of Wudongde reservoir of the upper Yangtze river is a completely new aquatic-terrestrial transitional zone, and its plant degenerate issue is attracting global concerns. Uncovering the unknown rhizosphere microbiome of dominant plants of this zone is helpful in understanding the plant-microbe interactions and their growth under the largely varying environment. Here, a first exploration of the rhizosphere bacterial and fungal communities of wilted (JB) and unwilted (JA) Argemonemexicana L. individuals from the WLFZ of Wudongde reservoir was carried out using high-throughput sequencing and MetaCyc metabolic pathway analyses. The results showed that rhizosphere of wilted A.mexicana L individuals exhibited a higher microbial richness and diversity than the unwilted ones, irrespective of the bacterial and fungal communities. It was noted that 837 common bacterial amplicon sequence variants (ASV) and 92 common fungal ASV were presented in both JA and JB with 3108 bacteria and 212 fungi unique to JA, and 3569 bacteria and 693 fungi unique to JB. Linear discriminant analysis effect Size (LEfSe) analyses indicated that the taxa that had the most contribution to observed differences between both JA and JB was Proteobacteria, Actinobacteria and Ascomycota for JA, and Bacteroidetes, Firmicutes, Verrucomicrobia, Basidiomycota and Ascomycota for JB. Organic compound conversion pathway (degradation/reduction/oxidation) was consistently highly represented in the rhizosphere microbiomes of both JA and JB. Overall, this study provides insights into the rhizosphere microbiome composition, diversity and metabolic pathways of both wilted and unwilted A.mexicana L. individuals in the WLFZ of Wudongde reservoir, and the results give valuable clues for manipulating microbes to support plant growth in such a recently-formed WLFZ under a dry-hot valley environment.

Aspergillus nomiae and fumigatus Ameliorating the Hypoxic Stress Induced by Waterlogging through Ethylene Metabolism in Zea mays L

Transient and prolonged waterlogging stress (WS) stimulates ethylene (ET) generation in plants, but their reprogramming is critical in determining the plants' fate under WS, which can be combated by the application of symbiotically associated beneficial microbes that induce resistance to WS. The present research was rationalized to explore the potential of the newly isolated 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase-producing fungal endophytic consortium of Aspergillus nomiae (MA1) and Aspergillus fumigatus (MA4) on maize growth promotion under WS. MA1 and MA4 were isolated from the seeds of Moringa oleifera L., which ably produced a sufficient amount of IAA, proline, phenols, and flavonoids. MA1 and MA4 proficiently colonized the root zone of maize (Zea mays L.). The symbiotic association of MA1 and MA4 promoted the growth response of maize compared with the non-inoculated plants under WS stress. Moreover, MA1- and MA4-inoculated maize plants enhanced the production of total soluble protein, sugar, lipids, phenolics, and flavonoids, with a reduction in proline content and H2O2 production. MA1- and MA4-inoculated maize plants showed an increase in the DPPH activity and antioxidant enzyme activities of CAT and POD, along with an increased level of hormonal content (GA3 and IAA) and decreased ABA and ACC contents. Optimal stomatal activity in leaf tissue and adventitious root formation at the root/stem junction was increased in MA1- and MA4-inoculated maize plants, with reduced lysigenous aerenchyma formation, ratio of cortex-to-stele, water-filled cells, and cell gaps within roots; increased tight and round cells; and intact cortical cells without damage. MA1 and MA4 induced a reduction in deformed mesophyll cells, and deteriorated epidermal and vascular bundle cells, as well as swollen metaxylem, phloem, pith, and cortical area, in maize plants under WS compared with control. Moreover, the transcript abundance of ethylene-responsive gene ZmEREB180, responsible for the induction of the WS tolerance in maize, showed optimally reduced expression sufficient for induction in WS tolerance, in MA1- and MA4-inoculated maize plants under WS compared with the non-inoculated control. The existing research supported the use of MA1 and MA4 isolates for establishing the bipartite mutualistic symbiosis in maize to assuage the adverse effects of WS by optimizing ethylene production.

Light-Induced Changes in Secondary Metabolite Production of Trichoderma atroviride

Many studies aim at maximizing fungal secondary metabolite production but the influence of light during cultivation has often been neglected. Here, we combined an untargeted isotope-assisted liquid chromatography-high-resolution mass spectrometry-based metabolomics approach with standardized cultivation of Trichoderma atroviride under three defined light regimes (darkness (PD), reduced light (RL) exposure, and 12/12 h light/dark cycle (LD)) to systematically determine the effect of light on secondary metabolite production. Comparative analyses revealed a similar metabolite profile upon cultivation in PD and RL, whereas LD treatment had an inhibiting effect on both the number and abundance of metabolites. Additionally, the spatial distribution of the detected metabolites for PD and RL was analyzed. From the more than 500 detected metabolites, only 25 were exclusively produced upon fungal growth in darkness and 85 were significantly more abundant in darkness. The majority were detected under both cultivation conditions and annotation revealed a cluster of substances whose production followed the pattern observed for the well-known T. atroviride metabolite 6-pentyl-alpha-pyrone. We conclude that cultivation of T. atroviride under RL can be used to maximize secondary metabolite production.

Assessing the Biosynthetic Inventory of the Biocontrol Fungus Trichoderma afroharzianum T22

Natural products biosynthesized from biocontrol fungi in the rhizosphere can have both beneficial and deleterious effects on plants. Herein, we performed a comprehensive analysis of natural product biosynthetic gene clusters (BGCs) from the widely used biocontrol fungus Trichoderma afroharzianum T22 (ThT22). This fungus encodes at least 64 BGCs, yet only seven compounds and four BGCs were previously characterized or mined. We correlated 21 BGCs of ThT22 with known primary and secondary metabolites through homologous BGC comparison and characterized one unknown BGC involved in the biosynthesis of eujavanicol A using heterologous expression. In addition, we performed untargeted transcriptomics and metabolic analysis to demonstrate the activation of silent ThT22 BGCs via the "one strain many compound" (OSMAC) approach. Collectively, our analysis showcases the biosynthetic capacity of ThT22 and paves the way for fully exploring the roles of natural products of ThT22.

Learning from Seed Microbes: Trichoderma Coating Intervenes in Rhizosphere Microbiome Assembly

Seed-associated microbiomes can impact the later colonization of a plant rhizosphere microbiome. However, there remains little insight into the underlying mechanisms concerning how alterations in the composition of the seed microbiome may intervene in the assembly of a rhizosphere microbiome. In this study, the fungus Trichoderma guizhouense NJAU4742 was introduced to both maize and watermelon seed microbiomes by seed coating. Application was found to significantly promote seed germination and improve plant growth and rhizosphere soil quality. The activities of acid phosphatase, cellulase, peroxidase, sucrase, and α-glucosidase increased significantly in two crops. The introduction of Trichoderma guizhouense NJAU4742 also led to a decrease in the occurrence of disease. Coating with T. guizhouense NJAU4742 did not alter the alpha diversities of the bacterial and fungal communities but formed a key network module that contained both Trichoderma and Mortierella. This key network module comprised of these potentially beneficial microorganisms was positively linked with the belowground biomass and activities of rhizosphere soil enzymes but negatively correlated with disease incidence. Overall, this study provides insights into plant growth promotion and plant health maintenance via seed coating in order to influence the rhizosphere microbiome. IMPORTANCE Seed-associated microbiomes can impact the rhizosphere microbiome assembly and function display. However, there remains little insight into the underlying mechanisms concerning how alterations in the composition of the seed microbiome with the beneficial microbes may intervene in the assembly of a rhizosphere microbiome. Here, we introduced T. guizhouense NJAU4742 to the seed microbiome by seed coating. This introduction led to a decrease in the occurrence of disease and an increase in plant growth; furthermore, it formed a key network module that contained both Trichoderma and Mortierella. Our study provides insights into plant growth promotion and plant health maintenance via seed coating in order to influence the rhizosphere microbiome.

A Simple Formula of the Endophytic Trichoderma viride, a Case Study for the Management of Rhizoctonia solani on the Common Bean

The utilization of beneficial endophytic microorganisms presents a promising and innovative strategy for attaining environmental sustainability and fostering development. The majority of microbial bioagents are unsuitable for preparation in a suitable granular formula, and few are prepared in complicated formulas. In this work, Trichoderma viride was simply prepared in a marketable granular formula to manage Rhizoctonia solani and improve common bean growth. The GC-MS analysis showed several antimicrobial compounds in the fungal filtrate. T. viride was able to suppress the phytopathogenic R. solani in the laboratory. The formula had up to 6 months of shelf-life viability. Under greenhouse conditions, the formula improved plant resistance against R. solani. Moreover, the vegetative plant growth and physiological performance (peroxidase, polyphenol, total phenols, phenylalanine ammonia-lyase, and photosynthetic pigments) of the common bean showed obvious promotion. The formula reduced the disease incidence by 82.68% and increased the yield by 69.28%. This work may be considered a step in the right direction for producing simple bioactive products on a large scale. Moreover, the study's findings suggest that this method can be considered a novel approach to enhancing plant growth and protection, in addition to reducing costs, improving handling and application, and maintaining fungal viability for enhancing plant growth and protecting against fungal infections.

New seed coating containing Trichoderma viride with anti-pathogenic properties

Background

To ensure food security in the face of climate change and the growing world population, multi-pronged measures should be taken. One promising approach uses plant growth-promoting fungi (PGPF), such as Trichoderma, to reduce the usage of agrochemicals and increase plant yield, stress tolerance, and nutritional value. However, large-scale applications of PGPF have been hampered by several constraints, and, consequently, usage on a large scale is still limited. Seed coating, a process that consists of covering seeds with low quantities of exogenous materials, is gaining attention as an efficient and feasible delivery system for PGPF.

Methods

We have designed a new seed coating composed of chitin, methylcellulose, and Trichoderma viride spores and assessed its effect on canola (Brassica napus L.) growth and development. For this purpose, we analyzed the antifungal activity of T. viride against common canola pathogenic fungi (Botrytis cinerea, Fusarium culmorum, and Colletotrichum sp.). Moreover, the effect of seed coating on germination ratio and seedling growth was evaluated. To verify the effect of seed coating on plant metabolism, we determined superoxide dismutase (SOD) activity and expression of the stress-related RSH (RelA/SpoT homologs).

Results

Our results showed that the T. viride strains used for seed coating significantly restricted the growth of all three pathogens, especially F. culmorum, for which the growth was inhibited by over 40%. Additionally, the new seed coating did not negatively affect the ability of the seeds to complete germination, increased seedling growth, and did not induce the plant stress response. To summarize, we have successfully developed a cost-effective and environmentally responsible seed coating, which will also be easy to exploit on an industrial scale.

Endophytic Trichoderma species from rubber trees native to the Brazilian Amazon, including four new species

Fungi belonging to the genus Trichoderma have been widely recognized as efficient controllers of plant diseases. Although the majority of isolates currently deployed, thus far, have been isolated from soil, endophytic Trichoderma spp. is considered to be a promising option for application in biocontrol. In this study, 30 endophytic Trichoderma isolates-obtained from the leaves, stems, and roots of wild Hevea spp. in the Brazilian Amazon-were analyzed using specific DNA barcodes: sequences of internal transcribed spacers 1 and 2 of rDNA (ITS region), genes encoding translation elongation factor 1-α (TEF1-α), and the second largest subunit of RNA polymerase II (RPB2). The genealogical concordance phylogenetic species recognition (GCPSR) concept was used for species delimitation. A phylogenetic analysis showed the occurrence of Trichoderma species, such as T. erinaceum, T. ovalisporum, T. koningiopsis, T. sparsum, T. lentiforme, T. virens, and T. spirale. Molecular and morphological features resulted in the discovery of four new species, such as T. acreanum sp. nov., T. ararianum sp. nov., T. heveae sp. nov., and T. brasiliensis sp. nov. The BI and ML analyses shared a similar topology, providing high support to the final trees. The phylograms show three distinct subclades, namely, T. acreanum and T. ararianum being paraphyletic with T. koningiopsis; T. heveae with T. subviride; and T. brasiliensis with T. brevicompactum. This study adds to our knowledge of the diversity of endophytic Trichoderma species in Neotropical forests and reveals new potential biocontrol agents for the management of plant diseases.

Trichoderma asperellum empowers tomato plants and suppresses Fusarium oxysporum through priming responses

Plant-associated microbes play crucial roles in plant health and promote growth under stress. Tomato (Solanum lycopersicum) is one of the strategic crops grown throughout Egypt and is a widely grown vegetable worldwide. However, plant disease severely affects tomato production. The post-harvest disease (Fusarium wilt disease) affects food security globally, especially in the tomato fields. Thus, an alternative effective and economical biological treatment to the disease was recently established using Trichoderma asperellum. However, the role of rhizosphere microbiota in the resistance of tomato plants against soil-borne Fusarium wilt disease (FWD) remains unclear. In the current study, a dual culture assay of T. asperellum against various phytopathogens (e.g., Fusarium oxysporum, F. solani, Alternaria alternata, Rhizoctonia solani, and F. graminerarum) was performed in vitro. Interestingly, T. asperellum exhibited the highest mycelial inhibition rate (53.24%) against F. oxysporum. In addition, 30% free cell filtrate of T. asperellum inhibited F. oxysporum by 59.39%. Various underlying mechanisms were studied to explore the antifungal activity against F. oxysporum, such as chitinase activity, analysis of bioactive compounds by gas chromatography–mass spectrometry (GC–MS), and assessment of fungal secondary metabolites against F. oxysporum mycotoxins in tomato fruits. Additionally, the plant growth-promoting traits of T. asperellum were studied (e.g., IAA production, Phosphate solubilization), and the impact on tomato seeds germination. Scanning electron microscopy, plant root sections, and confocal microscopy were used to show the mobility of the fungal endophyte activity to promote tomato root growth compared with untreated tomato root. T. asperellum enhanced the growth of tomato seeds and controlled the wilt disease caused by the phytopathogen F. oxysporum by enhancing the number of leaves as well as shoot and root length (cm) and fresh and dry weights (g). Furthermore, Trichoderma extract protects tomato fruits from post-harvest infection by F. oxysporum. Taking together, T. asperellum represents a safe and effective controlling agent against Fusarium infection of tomato plants.

Autochthonous strains of Trichoderma isolated from tannery solid waste improve phytoextraction potential of heavy metals by sunflower

This research work was aimed at isolating and demonstrating the significant potential of autochthonous fungi for phytoextraction of hazardous metals in metal polluted soil using Helianthus annuus. Four multi-metal resistant strains of Trichoderma were selected from a total of 21 strains isolated from tannery polluted soil and tannery solid waste. Autochthonous Trichoderma strains were used singly and in the form of consortium (TC). Sunflower was grown in pots for 90 days having eight different amendments of tannery polluted soil with and without Trichoderma inoculation. Growth and biochemical attributes of the plants were observed along with metal content extract by different plant parts. The results revealed that TC enhanced shoot length, shoot dry weight, and metal uptake as compared to single specie inoculation. Similarly, BCF (72.8-118.23%) and TF were significantly pronounced in shoots of H. annuus grown with TC at 40% amended soil. The biochemical analysis of the plants showed that Trichoderma strains boosted the enzymatic (catalase, peroxidase, and superoxide dismutase) antioxidants in the plants. The use of indigenous fungi with metal accumulating plants like sunflower can help to alleviate metal contamination from industrial sites and can make the soil cultivable for energy crops.

Crop microbiome: their role and advances in molecular and omic techniques for the sustenance of agriculture

This review is an effort to provide in-depth knowledge of microbe's interaction and its role in crop microbiome using combination of advanced molecular and OMICS technology to translate this information for the sustenance of agriculture. Increasing population, climate change and exhaustive agricultural practices either influenced nutrient inputs of soil or generating biological and physico-chemical deterioration of the soils and affecting the agricultural productivity and agro-ecosystems. Alarming concerns toward food security and crop production claim for renewed attention in microbe-based farming practices. Microbes are omnipresent (soil, water, and air) and their close association with plants would help to accomplish sustainable agriculture goals. In the last few decades, the search for beneficial microbes in crop production, soil fertilization, disease management, and plant growth promotion is the thirst for eco-friendly agriculture. The crop microbiome opens new paths to utilize beneficial microbes and manage pathogenic microbes through integrated advanced biotechnology. The crop microbiome helps plants acquire nutrients, growth, resilience against phytopathogens, and tolerance to abiotic stresses, such as heat, drought, and salinity. Despite the emergent functionality of the crop microbiome as a complicated constituent of the plant fitness, our understanding of how the functionality of microbiome influenced by numerous factors including genotype of host, climatic conditions, mobilization of minerals, soil composition, nutrient availability, interaction between nexus of microbes, and interactions with other external microbiomes is partially understood. However, the structure, composition, dynamics, and functional contribution of such cultured and uncultured crop microbiome are least explored. The advanced biotechnological approaches are efficient tools for acquiring the information required to investigate the microbiome and extract data to develop high yield producing and resistant variety crops. This knowledge fills the fundamental gap between the theoretical concepts and the operational use of these advanced tools in crop microbiome studies. Here, we review (1) structure and composition of crop microbiome, (2) microbiome-mediated role associated with crops fitness, (3) Molecular and -omics techniques for exploration of crop microbiome, and (4) current approaches and future prospectives of crop microbiome and its exploitation for sustainable agriculture. Recent -omic approaches are influential tool for mapping, monitoring, modeling, and management of crops microbiome. Identification of crop microbiome, using system biology and rhizho-engineering, can help to develop future bioformulations for disease management, reclamation of stressed agro-ecosystems, and improved productivity of crops. Nano-system approaches combined with triggering molecules of crop microbiome can help in designing of nano-biofertilizers and nano-biopesticides. This combination has numerous merits over the traditional bioinoculants. They stimulate various defense mechanisms in plants facing stress conditions; provide bioavailability of nutrients in the soil, helps mitigate stress conditions; and enhance chances of crops establishment.