Endophytic strains of Trichoderma increase plants' photosynthetic capability

Interaction of beneficial microorganisms and phenolic compounds in hydroponically cultivated tomato plants

The combined effects of applying extracts derived from plant debris and biostimulant microorganisms have not been thoroughly investigated. Furthermore, the interaction between these components and plants remains poorly understood. Utilizing the commercial cherry tomato (Solanum lycopersicum cv. Unidarkwin) as a study model, we conducted a hydroponic experiment in a controlled growth chamber to assess the impact of foliar application of phenolic compounds extracted from Vitis vinifera leaves, combined with the inoculation of Trichoderma harzianum or Bacillus velezensis via roots. Plant growth, gas exchange and root architecture were measured and mineral nutrients, chlorophylls and phenolic compounds were analysed. The results showed that phenolic compounds produced an increase in root fresh weight, by the enhanced root length. This could be related to the improved transpiration rate, sub-stomatal CO2 concentration, phosphorus and iron concentration in the roots. A positive effect was also found by B. velezensis application in root length development that could be related to the increase in hydraulic conductance. However, T. harzianum inoculation only showed higher root diameter and volume in combination to phenolic application, but with no effect on growth. The absence of caffeic acid and sinapic acid in the Hoagland solution used in the B. velezensis treatments and of chlorogenic acid in all treatments with added microorganisms suggested their metabolization. Therefore, our findings establish that the phenolic exudation could regulate the interaction of microorganism with plants resulting in beneficial physiological changes.

Response of Chinese potato (Colocasia esculenta, Araceae) to abiotic and biotic stress, and the effectiveness of treatment with the fungus Trichoderma harzianum

Climate change intensifies drought, which increases susceptibility to phytopathogens in several crops such as the Chinese potato (Colocasia esculenta). This species is cultivated in tropical areas mainly for the production of corms, which are affected by Fusarium oxysporum dry rot. Phytopathology treated with toxic chemicals, which highlights the biocontroller Trichoderma harzianum, which also helps reduce the effects related to drought in other crops. Therefore, the objective was to characterize the response of C. esculenta to drought and infection by F. oxysporum, and the effectiveness of treatment with T. harzianum. Greenhouse tests were carried out with three factors (F. oxysporum, T. harzianum and drought), each with two levels (presence and absence) (N=48). Plant growth was evaluated for 30 days, in addition to the relative chlorophyll content, maximum efficiency of photosystem II, water content (WC%), incidence and severity. It was obtained that abiotic and biotic stress decreases growth. Drought lowered photosynthetic efficiency, and both stressors reduced chlorophyll in plants not treated with T. harzianum. Stress decreased leaf and corm WC%, but this effect was reduced by the biocontroller. This fungus reduced the incidence of F. oxysporum, and the severity of foliar symptoms for both types of stress. In conclusion, abiotic and biotic stress differentially impacts C. esculenta, and T. harzianum tends to improve growth under stress. However, more studies are required to evaluate its benefit on productivity. This work is one of the first to describe the stress response of this crop, and highlights its importance for future technification plans.

Endophytic seed pretreatment: a strategy for boosting morphophysiological traits in tomato seedlings

This study investigated the effects of fungal (Penicillium chrysogenum, Thielavia basicola, Curvularia hawaiiensis) and bacterial (Sphingomonas aquatilis, Bacillus licheniformis, Exiguobacterium aurantiacum, Micromonospora echinaurantiaca, Kocuria rhizophila) endophytes on the growth and physiological traits of tomato plants (Solanum lycopersicum L.) under greenhouse conditions. Both individual and combined endophyte treatments significantly enhanced key growth parameters, including stem weight, height, and dry weight, with notable synergies observed in fungal-bacterial combinations such as P. chrysogenum + E. aurantiacum and S. aquatilis + M. echinaurantiaca. These combinations also optimised photosynthetic activity, increasing chlorophyll content, carotenoids, and photosystem II efficiency, improving plant vitality. Additionally, these endophytes stimulated a marked increase in carotenoid levels, with fungal-bacterial combinations leading to substantial improvements in antioxidant activity. Furthermore, inoculation with these endophytes promoted higher phenolic and proline content, with distinct combinations showing remarkable effects on carbohydrate accumulation. The findings underscore the synergistic potential of fungal-bacterial endophyte interactions in enhancing plant resilience, offering promising strategies for improving crop productivity and sustainability in agriculture.

Whole genome sequence data of Trichoderma yunnanense strain TM10, a plant growth-promoting fungus and biocontrol agent

Trichoderma yunnanense strain TM10 was isolated from rhizosphere soil of rice plants cultivated under system of rice intensification (SRI) practises in West Java, Indonesia. It exhibits significant potential as a plant growth promoter and biocontrol agent in rice plants. Although this strain has shown promise in promoting plant growth and suppressing phytopathogens under in vitro and in planta conditions, there is still a lack of genomic data to elucidate the molecular mechanisms underlying its plant growth-promoting and biocontrol capabilities. This study reports the whole genome sequence of T. yunnanense strain TM10. The genome of the fungus was sequenced using the MGI DNBSEQ-G400 high-throughput sequencing platform. The assembled genome of T. yunnanense strain TM10 was approximately 36 Mbp in length, comprising 385 contigs with a GC content of 48 % and a sequencing coverage of 43.8×. This genomic data provides a foundation for harnessing the plant growth-promoting and biocontrol potential of this strain. The complete genome sequence has been deposited at the National Center for Biotechnology Information (NCBI) under Bioproject accession number PRJNA1181959, BioSample ID SAMN44575400, and genome accession number JBIYZQ000000000. These data are valuable for further research into the biotechnological potential of this strain and for exploring the molecular mechanisms underlying its plant growth-promoting and biocontrol activities.

Impact of Beneficial Microorganisms Inoculated Cotton Plants on Spodoptera exigua (Lepidoptera: Noctuidae)

This study discusses plant-mediated effects of beneficial soil-borne microorganisms on population growth parameters of Spodoptera exigua (Lepidoptera: Noctuidae), a major cotton pest. In particular, we investigated the impact of these microorganisms on oxidative stress, chlorophyll content, and sugar and protein levels in cotton plants, and how these changes in the plant affect the survival, development, reproduction, and ultimately population growth of the pest. A longer preadult period, lower preadult survival rate, and lower reproduction were obtained for the pest cohort feeding on treated plants, which resulted in lower population parameters, i.e., intrinsic growth rate, finite growth rate, and net reproduction rate. The population projection results showed the same trend as the population parameters. These results can be attributed to the changes caused by microorganisms in the treated plants. There was no oxidative stress in the treated plants. Instead, the chlorophyll content in these plants increased, and the protein-carbohydrate ratio decreased. Additionally, we assessed the effects of plant-insect-microorganisms interaction on total glutathione levels, glutathione S-transferase, and esterase enzyme activities in S. exigua. Overall results indicate that beneficial microorganisms tested enhance the plant's ability to defend against the pest. Additionally, the findings from this study provide valuable insights into the complex interplay among plants, microorganisms, and pests, offering potential strategies for incorporating these interactions into pest management practices.

Endophytic entomopathogenic fungi as biological control agents of insect pests

Entomopathogenic fungi capable of establishing mutualistic endophytic relationships with plants have a tremendous potential as biocontrol agents of insect pests. While fungi have long played an important and highly effective role in pest suppression, the utility of endophytic entomopathogenic fungi in pest management is a relatively new and emerging topic of biocontrol. Here we discuss the relevance of endophytic fungi to plant health in general, synthesize the current knowledge of the effectiveness of endophytic entomopathogenic fungi against diverse insect pests, discuss the indirect plant-mediated effects of endophytic entomopathogenic fungi on arthropods, and describe the diverse benefits of endophytic fungi to plants that are likely to affect herbivores and plant pathogens as well. Lastly, we consider major challenges to incorporating endophytic entomopathogenic fungi in biocontrol, such as their non-target effects and field efficacy, which can be variable and influenced by environmental factors. Continued research on endophyte-insect-plant-environment interactions is critical to advancing our knowledge of these fungi as a sustainable pest management tactic. © 2024 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

The expansion of fungal organisms in environmental biotechnology

Fungal organisms hold vital roles in ecosystem processes. Despite their intricate entanglement with most life on earth and their powerful metabolic capacities, they remain under-represented in environmental biotechnology. The interest in applying fungal biotechnologies to different environments is growing, as light is shed on their versatile potential. A diversity of fungi can be harnessed to promote crop yield, remediate pollutants from terrestrial and aquatic environments, and mitigate climate change impacts. Current technological advancements, such as the increase in high-accuracy 'omics pipelines, provide improvement. However, it is emphasized that there are many knowledge gaps regarding applying fungal biotechnology at scale where other organisms are inherently present. Hence, there is a dire need to increase funding that enables in-depth studies on fungal processes, such as degradation capacities, metabolite production, and cross-kingdom interactions, that promote climate-smart biotechnologies.

Fungus-derived opine enhances plant photosynthesis

INTRODUCTION

Plant-fungal interactions stimulate endophytic fungi to produce a plethora of metabolites that enhance plant growth and improve stress resistance. Opines, naturally occurring compounds formed through the condensation of amino acids with α-keto acids or sugars, have diverse biological functions and are mainly present in bacteria. Interestingly, investigations have revealed the presence of opine synthases (OSases) in fungal species as well, and their functions are yet to be studied.

OBJECTIVES

The objective of this study is to investigate the occurrence of OSases in fungal species, identify their products, and characterize the potential biological activity of the metabolites.

METHODS

We identified a putative class of OSases in fungi through sequence similarity network (SSN) analysis. The function of these enzymes was elucidated using methods including protein heterologous expression, in vitro biochemical characterization, in vivo gene knock-out, as well as product isolation and identification. Additionally, we conducted plant activity testing on the secondary metabolites through foliar spraying and performed transcriptomic analysis to uncover their functions.

RESULTS

A quarter of the PF18631 family members, which contain the C-terminal helical bundle domain of cucumopine synthase, are derived from endophytic fungi. Some of these enzymes catalyze the synthesis of tryptopine A (1-acetyl-3-carboxy-β-carboline) by condensing L-tryptophan and methylglyoxal. The tryptopine A can act as a growth regulator, promoting plant growth and transcriptionally reprogramming photosynthesis-related pathways, while enhancing the rate of plant photosynthesis by 25 %.

CONCLUSION

The findings of this study suggest that tryptopine A plays a crucial role as a signaling molecule in the establishment and maintenance of mutualistic associations between endophytic fungi and host plants, thereby enhancing our comprehension of fungal-plant symbiosis.

Characterization and quantification of peptaibol produced by novel Trichoderma spp: Harnessing their potential to mitigate moisture stress through enhanced biochemical and physiological responses in black pepper (Piper nigrum L.)

Trichoderma spp. is primarily applied to manage biotic stresses in plants. Still, they also can mitigate abiotic stresses by the stimulation of antioxidative protective mechanisms and enhanced synthesis of secondary metabolites. The study optimized the conditions to enhance peptaibol production by novel Trichoderma spp, characterized and quantified peptaibol- alamethicin using HPLC and LC MS-MS. The present study investigated these isolates efficacy in enhancing growth and the associated physio-biochemical changes in black pepper plants under moisture stress. Under in vitro conditions, out of 51 isolates studied, six isolates viz., T. asperellum (IISR NAIMCC 0049), T. erinaceum (IISR APT1), T. harzianum (IISR APT2), T. harzianum (IISR KL3), T. lixii (IISR KA15) and T. asperellum (IISR TN3) showed tolerance to low moisture levels (5, 10 and 20%) and higher temperatures (35 and 40 °C). In vivo evaluation on black pepper plants maintained under four different moisture levels (Field capacity [FC]; 75%, 50%, and 25%) showed that the plants inoculated with Trichoderma accumulated greater quantities of secondary metabolites viz., proline, phenols, MDA and soluble proteins at low moisture levels (50% and 25% FC). In the present study, plants inoculated with T. asperellum and T. harzianum showed significantly increased growth compared to uninoculated plants. The shortlisted Trichoderma isolates exhibited differences in peptaibol production and indicated that the peptide might be the key factor for their efficiency as biocontrol agents. The present study also demonstrated that Trichoderma isolates T. harzianum and T. asperellum (IISR APT2 & NAIMCC 0049) enhanced the drought-tolerant capabilities of black pepper by improving plant growth and secondary metabolite production.

Seed priming with Metarhizium anisopliae (MetA1) improves physiology, growth and yield of wheat

Microorganisms offer a sustainable way to increase crop production and promote eco-friendly farming. The endophytic fungus Metarhizium anisopliae is known for its multiple roles in plant ecosystems, including plant protection, symbiosis, and abiotic stress mitigation. In this study, we evaluated the potential of seed priming with M. anisopliae isolate MetA1 (MA) to enhance germination, photosynthetic efficiency, growth, and yield of two wheat varieties, BARI Gom 26 (BG26) and BARI Gom 33 (BG33) under field conditions. The study demonstrated that MA seed priming significantly improved wheat germination (by 13% and 26.04%) of BG26 and BG33, respectively. Overall, photosynthetic performance, indicated by increased leaf angle, leaf thickness, relative chlorophyll content, and linear electron flow (LEF), quantum yield of Photo System II (Phi2) was increased in MA primed wheat plants, while reducing non-photochemical quenching like NPQt, PhiNO, PhiNPQ of both varieties. These enhancements were attributed to increased shoot biomass (by 215.64% for BG26 and 280.38% for BG33), root biomass (by 141.79% for BG26 and 207.4% for BG33), effective tiller percentage (by 9.17% for BG26 and 5.7% for BG33), spike length (by 25.05% for BG26 and 25.42% for BG33), grain yield parameters such as filled grain percentage (by 23.8% for BG26 and 12.5% for BG33), and grain weight per plant (by 168.62% for BG26 and 119.62% for BG33). The findings of the research demonstrated the potential of M. anisopliae for field use in an agricultural setting, providing a sustainable means of increasing food production.

The Belowground-Aboveground Interactions of Zucchini: The Effects of Trichoderma afroharzianum Strain T22 on the Population and Behavior of the Aphid Aphis gossypii Glover and Its Endoparasitoid Aphidius colemani Viereck

Fungi belonging to the genus Trichoderma have received high consideration in agriculture due to their beneficial effects on crops from their plant promotion effects and protection from disease. A role of Trichoderma fungi in triggering plant defense mechanisms against insect pests, either directly or by natural enemy attraction, has been proposed, even if the results in different studies are controversial. In this present study, using zucchini plants as a model species, we investigated the effects of Trichoderma afroharzianum strain T22 plant inoculation on the cotton aphid Aphis gossypii and its endoparasitoid Aphidius colemani. Our results showed that the inoculation with T. afroharzianum T22 promotes A. gossypii population growth and makes zucchini more attractive to the aphid. The higher abundance of aphids on Trichoderma-inoculated zucchini was compensated for by a higher presence of the mummies of Aphidius colemani. In this present study, we recorded a higher zucchini biomass, thereby confirming that Trichoderma can act as a plant growth inducer.

Integrated Benefits to Agriculture with Trichoderma and Other Endophytic or Root-Associated Microbes

The use of endophytic microbes is increasing in commercial agriculture. This review will begin with a strain selection. Most strains will not function well, so only a few provide adequate performance. It will also describe the endophyte-plant relationship and the fungi and bacteria involved. Their abilities to alleviate biotic (diseases and pests) and abiotic stresses (drought, salt, and flooding) to remediate pollution and increase photosynthetic capabilities will be described. Their mechanisms of action will be elucidated. These frequently result in increased plant yields. Finally, methods and practices for formulation and commercial use will be described.

Can Trichoderma harzianum be used to enhance the yield and nutrient uptake of Lactuca sativa cv "Lollo Rosso" in floating systems?

An experiment was performed to evaluate the effect of Trichoderma harzianum MVT801 combined with different ratios of nutrient solution (NR) (25%, 50%, and 100%) on the growth and physiological traits of Lactuca sativa "Lollo Rosso" plants cultivated in floating systems. Inoculation of lettuce plants with T. harzianum MVT801 (T1) in a floating system improves biometric properties, photosynthetic parameters, and nutrient uptake compared with uninoculated treatment (T0). The results clearly showed that in T1, despite a 50% reduction in the ratio of nutrient solution, no significant difference was observed in the growth and photosynthesis characteristics and nutrient uptake in L. sativa "Lollo Rosso" leaves compared with a complete nutrient solution treatment (100%), which is one of the notable results of this study. In this regard, the highest yield was observed in T1NR50 (inoculated with fungi and 50% of the nutrient solution) and T1NR100 (inoculated with fungi and complete nutrient solution) treatments. Also, the highest concentrations of phosphorus and potassium in "Lollo Rosso" leaves were observed in T1NR50 and T1NR100 treatments. Accordingly, the use of T. harzianum in floating lettuce cultivation could be recommended to increase crop productivity and reduce the use of chemical fertilizers.

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.

Two diversities meet in the rhizosphere: root specialized metabolites and microbiome

Plants serve as rich repositories of diverse chemical compounds collectively referred to as specialized metabolites. These compounds are of importance for adaptive processes, including interactions with various microbes both beneficial and harmful. Considering microbes as bioreactors, the chemical diversity undergoes dynamic changes when root-derived specialized metabolites (RSMs) and microbes encounter each other in the rhizosphere. Recent advancements in sequencing techniques and molecular biology tools have not only accelerated the elucidation of biosynthetic pathways of RSMs but also unveiled the significance of RSMs in plant-microbe interactions. In this review, we provide a comprehensive description of the effects of RSMs on microbe assembly in the rhizosphere and the influence of corresponding microbial changes on plant health, incorporating the most up-to-date information available. Additionally, we highlight open questions that remain for a deeper understanding of and harnessing the potential of RSM-microbe interactions to enhance plant adaptation to the environment. Finally, we propose a pipeline for investigating the intricate associations between root exometabolites and the rhizomicrobiome.

Trichoderma guizhouense NJAU4742 augments morphophysiological responses, nutrient availability and photosynthetic efficacy of ornamental Ilex verticillata

Winterberry holly (Ilex verticillata [L.] A. Gray), a deciduous shrub producing glossy bright red berries, is a valuable ornamental and medicinal plant with good market prospects. However, the growth and development of I. verticillata are significantly affected by various stresses, and environmentally hazardous agrochemicals are often used to mitigate them. Trichoderma spp., ubiquitous soil-borne eco-friendly plant growth-promoting fungi, are potent biostimulants and biofertilizers and viable alternatives to agrochemicals for healthy and sustainable agriculture. In this study, the temporal efficacy of different dosages of the filamentous fungus Trichoderma guizhouense NJAU4742 in promoting morphophysiological responses of I. verticillata and the physicochemical properties and enzymatic activities of the substrate were investigated. Different concentrations of the strain T. guizhouense NJAU4742 spore suspension (C [0%], T1 [5%, v/m], T2 [10%, v/m] and T3 [15%, v/m]) were injected in the substrate contained in a pot in which 1-year-old I. verticillata was planted for temporal treatment (15, 45 and 75 days) under open-air conditions. The beneficial effects of T2 and/or T3 treatment for a long duration (75 days) were evident on the different root, aerial and photosynthetic traits; total contents of nitrogen (N), phosphorus (P) and potassium (K) in different tissues and the physicochemical properties of the substrate and its enzymatic activities (urease and invertase). Overall, the study revealed the potency of strain T. guizhouense NJAU4742 as a sustainable solution to improve the growth and development and ornamental value of I. verticillata.

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.

Eleven new species of Trichoderma (Hypocreaceae, Hypocreales) from China

Trichoderma spp. are globally distributed and are considered significant fungal resources. This study presents the discovery of 11 new species of Trichoderma: T. caeruleum, T. gongcheniae, T. graminicola, T. graminis, T. hongkuii, T. parapeberdyi, T. neoguizhouense, T. neohongkuii, T. parahamatum, T. parahongkuii, and T. shaanxiensis. All of these new species were isolated from soils, except for T. caeruleum, T. graminicola, T. graminis, and T. neohongkuii, which were found as endophytes in Poaceae plants. The phylogenetic position of these novel species was determined by analysing the concatenated sequences of the second largest nuclear RNA polymerase subunit encoding gene (rpb2) and the translation elongation factor 1-alpha encoding gene (tef1). The results of the phylogenetic analysis revealed that each new species formed a distinct lineage: T. gongcheniae, T. graminicola, T. graminis, T. neoguizhouense, T. parapeberdyi, and T. shaanxiensis belong to the Harzianum Clade, T. hongkuii, T. parahongkuii, and T. neohongkuii are new members of the Koningii Clade, T. parahamatum belongs to the Hamatum Clade, and T. caeruleum does not fall within any of the named clades. The study also provided a detailed description of the morphology and cultural characteristics of the newly discovered Trichoderma species. The discovery contributes to the advancement of knowledge about Trichoderma species resources in China.

Physiological and photochemical profiling of soybean plant using biological and chemical methods of treatment against biotic stress management

Phyto-pathogenic fungal species is a leading biotic stress factor to agri-food production and ecosystem of globe. Chemical (Systemic fungicides) and biological treatment (micro-organism) are globally accepted methods that are being used against biotic stress (disease) management. Plant Growth-Promoting Microbes are being used as an alternative to ease chemical dependency as their overdoses have generated injurious effects on plants and environment. Therefore, present study performs to evaluate the photochemical and physiological profiling of plants exposed to chemical and biological treatment in biotic stress (disease) environment. Two concentrations of each chemical treatment i.e. Topsin-M 70 (Dimethyl 4,4'-o-phenylene bis 3-thioallaphanate, MF1 = 3 g kg-1 and MF2 = 6 g kg-1 seeds) and biological treatment i.e. Trichoderma harzianum strain Th-6 (MT1 = 106 spores mL-1and MT2 = 107 spores mL-1) were used in this experiment. Macrophomina phaseolina (MP) were used as biotic stress factor causing root rot disease in soybean plants. Morpho-physiological assessments and light harvesting efficiency of photosystem II were conducted after 52 days of treatment. Maximum quantum yield (Fv/Fm), number and size of active reaction center (Fv/Fo), photochemical quenching (qP), efficiency of photosystem II (ΦPSII), electron transport rate (ETR), chlorophyll content index (CCI), relative water content (RWC) and stomatal conductance (SC) were increased in MT2 and MF1 treatments as compared to stress plants (MP). Biological (MT2) and chemical (MF1) treatment lessen the production of stress markers showing -48.0 to -54.3% decline in malondialdehyde (MDA) and -42.0 to -53.7% in hydrogen peroxide (H2O2) as compared to stress plant (MP). Biological treatment in both concentration (MF1 & MF2) while chemical treatment at low dose effectively mitigates biotic stress and eases the magnitude of disease. Increasing doses of chemical treatment persuaded deleterious effects on the physiology and light harvesting efficiency of stressed plant suggesting the role of biological treatment (T. harzianum) against biotic stress management in future of crop protection.

Trichoderma atroviride Enhances Impatiens walleriana Hook. f Growth and Flowering in Different Growing Media

Trichoderma spp. are widely reported to regulate plant growth by improving nutrient uptake, photosynthesis, and abiotic stress tolerance. However, their possible application for bedding plants is little explored, especially when comparing different growing media. Considering that coconut coir dust is finding broader application in the ornamental plants sector as a peat substitute, this work was aimed to test the combination of Trichoderma atroviride AT10 and coconut coir dust on Impatiens walleriana plants. Four treatments were tested as a mix of: (i) two growing media (70:30), peat:perlite or coconut coir dust:perlite; and (ii) the absence or presence of a T. atroviride treatment. At the end of the production cycle, the biomass and ornamental parameters, leaf pigments, nutrient content of the plant tissues, and Trichoderma abundance were assessed. The results revealed that T. atroviride can readily colonize coir, and the same positive effects of inoculum were found in plants grown on both substrates. The biostimulant effect of T. atroviride was observed as an increase in the aboveground biomass, number and weight of flowers, pigments and nutrient concentration, thereby improving the commercial quality of I. walleriana. Thus, T. atroviride has shown its potential in making bedding plant cultivation more sustainable and improving the yield and aesthetic parameters of plants grown on peat and coconut coir dust substrates.

Biological roles of soil microbial consortium on promoting safe crop production in heavy metal(loid) contaminated soil: A systematic review

Heavy metal(loid) (HM) pollution of agricultural soils is a growing global environmental concern that affects planetary health. Numerous studies have shown that soil microbial consortia can inhibit the accumulation of HMs in crops. However, our current understanding of the effects and mechanisms of inhibition is fragmented. In this review, we summarise extant studies and knowledge to provide a comprehensive view of HM toxicity on crop growth and development at the biological, cellular and the molecular levels. In a meta-analysis, we find that microbial consortia can improve crop resistance and reduce HM uptake, which in turn promotes healthy crop growth, demonstrating that microbial consortia are more effective than single microorganisms. We then review three main mechanisms by which microbial consortia reduce the toxicity of HMs to crops and inhibit HMs accumulation in crops: 1) reducing the bioavailability of HMs in soil (e.g. biosorption, bioaccumulation and biotransformation); 2) improving crop resistance to HMs (e.g. facilitating the absorption of nutrients); and 3) synergistic effects between microorganisms. Finally, we discuss the prospects of microbial consortium applications in simultaneous crop safety production and soil remediation, indicating that they play a key role in sustainable agricultural development, and conclude by identifying research challenges and future directions for the microbial consortium to promote safe crop production.

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.

Metabolic insights into how multifunctional microbial consortium enhances atrazine removal and phosphorus uptake at low temperature

Agricultural soils in the black soil region of northeast China often face negative stress due to low temperatures, pesticide contamination, and inadequate nutrient supply. In this study, a new cold-tolerant strain of Peribacillus simplex C1 (C1) was selectively isolated from atrazine contaminated soil. The artificially constructed microbial consortium (CPD) [C1, phosphorus-solubilizing bacterium Enterobacter sp. P1, and atrazine-degrading bacterium Acinetobacter lwoffii DNS32] demonstrated the most effective performance in enhancing atrazine degradation and phosphorus-solubilizing capacity when the initial inoculation ratio of 5:1:2 at 15 °C. CPD enhanced energy-related metabolic pathways and increased choline production to regulate bacterial adaptation to temperature decrease. Additionally, the strains could selectively utilize carbon sources (low molecular weight organic acids) or nitrogen sources (some metabolites of atrazine) provided by each other to enhance growth. Furthermore, strain C1 enhanced membrane fluidity through increased expression of the unsaturated fatty acids. Pot experiments demonstrated that CPD assisted soybean seedlings in resisting dual stresses of low temperature and atrazine contamination by inducing the expression of genes related to photosynthesis, membrane permeability, phosphorus response, and cold tolerance.

Endophytic fungi: an overview on biotechnological and agronomic potential

Abstract Endophytic fungi colonize the inter- and/or intracellular regions of healthy plant tissues and have a close symbiotic relationship with their hosts. These microorganisms produce antibiotics, enzymes, and other bioactive compounds that enable them to survive in competitive habitats with other microorganisms. In addition, secondary metabolites confer protection to their host plant against other bacterial and fungal pathogens and/or can promote plant growth. Endophytic fungi are viewed as a promising source of bioactive natural products, which can be optimized through changes in growing conditions. The exploration of novel bioactive molecules produced by these microorganisms has been attracting attention from researchers. The chemical and functional diversity of natural products from endophytic fungi exhibits a broad spectrum of applications in medicine, agriculture, industry and the environment. Fungal endophytes can also enhance the photoprotective effects and photochemical efficiency in the host plants. Modern omic approaches have facilitated research investigating symbiotic plant-endophytic fungi interactions. Therefore, research on endophytic fungi can help discovery novel biomolecules for various biotechnological applications and develop a sustainable agriculture.

Trichoderma hamatum and Its Benefits

Trichoderma hamatum (Bonord.) Bainier (T. hamatum) belongs to Hypocreaceae family, Trichoderma genus. Trichoderma spp. are prominently known for their biocontrol activities and plant growth promotion. Hence, T. hamatum also possess several beneficial activities, such as antimicrobial activity, antioxidant activity, insecticidal activity, herbicidal activity, and plant growth promotion; in addition, it holds several other beneficial properties, such as resistance to dichlorodiphenyltrichloroethane (DDT) and degradation of DDT by certain enzymes and production of certain polysaccharide-degrading enzymes. Hence, the current review discusses the beneficial properties of T. hamatum and describes the gaps that need to be further considered in future studies, such as T. hamatum's potentiality against human pathogens and, in contrast, its role as an opportunistic human pathogen. Moreover, there is a need for substantial study on its antiviral and antioxidant activities.

Application of candidate endophytic fungi isolated from extreme desert adapted trees to mitigate the adverse effects of drought stress on maize (Zea mays L.)

The survival of plants under adverse conditions in desert habitats is related to microbial interactions, which can be an innovative strategy for reducing the effects of drought stress in colonized plants. In this study, two endophytic fungi, Trichoderma harzianum, and Fusarium solani, were recovered from the roots of trees in desert regions of Iran. A greenhouse experiment with two fungal agents (control, T. harzianum, F. solani, and T. harzianum + F. solani) and drought (100, 75, and 50% water-holding capacity) was performed on maize (Zea mays L.). Findings indicate that increasing drought levels negatively affect maize plant growth and physiological traits. However, the symbiotic relationship between fungal endophytes and maize roots increased fresh and dry biomass, root/shoot ratio, leaf area, relative water content, and membrane stability index compared with their control counterparts. Maize plants inoculated with endophytic fungi had 52.07, 40, 33.03, and 55.62% higher total phenolic, proline and soluble sugar concentrations, respectively than uninoculated controls. Photosynthetic parameters, including chlorophyll and carotenoid pigments, chlorophyll fluorescence, and gas exchange, were improved in the endophyte-treated plants. However, with increasing drought stress, maize plants colonized with endophytes, electrolyte leakage, and sub-stomatal CO2 concentrations decreased by 28.93% and 47.62%, respectively, compared to endophyte-free plants. When plants were exposed to higher levels of drought stress, endophytes were more effective in improving most parameters, and inoculation of maize seedlings with a combination of endophytes isolated from plants in harsh regions was more effective in increasing their tolerance to drought stress than individual inoculation of each fungus.

Reactive oxygen species and NADPH oxidase-encoding genes underly the plant growth and developmental responses to Trichoderma

The modulation of plant growth and development through reactive oxygen species (ROS) is a hallmark during the interactions with microorganisms, but how fungi and their molecules influence endogenous ROS production in the root remains unknown. In this report, we correlated the biostimulant effect of Trichoderma atroviride with Arabidopsis root development via ROS signaling. T. atroviride enhanced ROS accumulation in primary root tips, lateral root primordia, and emerged lateral roots as revealed by total ROS imaging through the fluorescent probe H2DCF-DA and NBT detection. Acidification of the substrate and emission of the volatile organic compound 6-pentyl-2H-pyran-2-one appear to be major factors by which the fungus triggers ROS accumulation. Besides, the disruption of plant NADPH oxidases, also known as respiratory burst oxidase homologs (RBOHs) including ROBHA, RBOHD, but mainly RBOHE, impaired root and shoot fresh weight and the root branching enhanced by the fungus in vitro. RbohE mutant plants displayed poor lateral root proliferation and lower superoxide levels than wild-type seedlings in both primary and lateral roots, indicating a role for this enzyme for T. atroviride-induced root branching. These data shed light on the roles of ROS as messengers for plant growth and root architectural changes during the plant-Trichoderma interaction.

Evaluating the underlying physiological and molecular mechanisms in the system of rice intensification performance with Trichoderma-rice plant symbiosis as a model system

The system of rice intensification (SRI) is an extensively-researched and increasingly widely-utilized methodology for alleviating current constraints on rice production. Many studies have shown physiological and morphological improvements in rice plants induced by SRI management practices to be very similar to those that are associated with the presence of beneficial microbial endophytes in or around rice plants, especially their roots. With SRI methods, grain yields are increased by 25-100% compared to conventional methods, and the resulting plant phenotypes are better able to cope with biotic and abiotic stresses. SRI management practices have been shown to be associated with significant increases in the populations of certain microorganisms known to enhance soil health and plant growth, e.g., Azospirillum, Trichoderma, Glomus, and Pseudomonas. This article evaluates the effects of applying Trichoderma as a model microbe for assessing microbial growth-promotion, biological control activity, and modulation of gene expression under the conditions created by SRI practices. Information about the molecular changes and interactions associated with certain effects of SRI management suggests that these practices are enhancing rice plants' expression of their genetic potentials. More systematic studies that assess the effects of SRI methods respectively and collectively, compared with standard rice production methods, are needed to develop a more encompassing understanding of how SRI modifications of crops' growing environment elicit and contribute to more robust and more productive phenotypes of rice.

Trichoderma longibrachiatum Inoculation Improves Drought Resistance and Growth of Pinus massoniana Seedlings through Regulating Physiological Responses and Soil Microbial Community

Drought stress poses a serious threat to Pinus massoniana seedling growth in southern China. Trichoderma species, as beneficial microorganisms, have been widely used in agriculture to enhance plant growth and drought tolerance, but the interaction mechanisms remain unclear. To investigate the effect of drought-resistant Trichoderma longibrachiatum inoculation on P. massoniana growth under drought stress, the plant physiological indicators and rhizosphere microbiome diversity were measured to identify Trichoderma-activated mechanisms. Trichoderma longibrachiatum inoculation significantly promoted P. massoniana growth under drought treatment, and enhanced nitrogen, phosphorus, and potassium absorption compared with those of non-inoculated seedlings. Trichoderma longibrachiatum treatment alleviated the damage to cell membranes and needle tissue structure, and significantly increased antioxidant enzyme activities, osmotic substance contents, and photosynthesis in P. massoniana in response to drought stress. Soil nutrient contents, activities of sucrase, phosphatase, and urease as well as the relative abundances of the dominant genera Burkholderia, Rhodanobacter, and Trichoderma were elevated in the rhizosphere soil of P. massoniana inoculated with T. longibrachiatum under drought stress. A network analysis showed that certain crucial dominant taxa driven by T. longibrachiatum inoculation, including Penicillium, Trichoderma, Simplicillium, Saitozyma, Burkholderia, Bradyrhizobium, Sinomonas, and Mycobacterium, had more correlations with other microorganisms in the soil. Trichoderma longibrachiatum enhanced P. massoniana seedling growth under drought stress by regulating physiological responses and soil microbial community.

An insight into endophytic antimicrobial compounds: an updated analysis

Resistance in micro-organisms against antimicrobial compounds is an emerging phenomenon in the modern era as compared to the traditional world which brings new challenges to discover novel antimicrobial compounds from different available sources, such as, medicinal plants, various micro-organisms, like, bacteria, fungi, algae, actinomycetes, and endophytes. Endophytes reside inside the plants without exerting any harmful impact on the host plant along with providing ample of benefits. In addition, they are capable of producing diverse antimicrobial compounds similar to their host, allowing them to serve as useful micro-organism for a range of therapeutic purposes. In recent years, a large number of studies on the antimicrobial properties of endophytic fungi have been carried out globally. These antimicrobials have been used to treat various bacterial, fungal, and viral infections in humans. In this review, the potential of fungal endophytes to produce diverse antimicrobial compounds along with their various benefits to their host have been focused on. In addition, classification systems of endophytic fungi as well as the need for antimicrobial production with genetic involvement and some of the vital novel antimicrobial compounds of endophytic origin can further be utilized in the pharmaceutical industries for various formulations along with the role of nanoparticles as antimicrobial agents have been highlighted.

Identification of endophytic fungi with ACC deaminase-producing isolated from halophyte Kosteletzkya Virginica

Seashore mallow (Kosteletzkya virginica), as a noninvasive perennial halophytic oilseed-producing dicot, is native from the Gulf to the Atlantic coasts of the U.S. The purpose of our research was to investigate 1-aminocyclopropane-1carboxylic acid deaminase (ACCD) producing endophytic fungi from K.virginica. A total of 59 endophytic fungal strains, isolated from roots in K.virginica of seedlings, were grouped into 12 genera including in Penicillium, Aspergillus, Fusarium, Trichoderma, Rhizopycnis sp., Ceriporia Donk, Trametes sp., Schizophyllum commune sp., Alternaria, Cladosporium, Cylindrocarpon, and Scytalidium according to sequences of ITS. The ACD activity of 10 endophytic fungi isolated was detected. T.asperellum had the highest ACC deaminase activity among all 10 isolated genera of fungal strains, followed by T. viride. Dry weight and fresh weight of plant, plant height, root length, SOD activity, and chlorophyll content of wheat and soybean inoculated with T.asperellum or T. viride was increased compared with non-inoculated control plants under non salt or salt stress. Further analysis showed that T.asperellum or T.viride strains induced downregulation of the expression of ethylene synthesis-related genes such as ACC oxidase (ACO) and ACC synthase (ACS), thereby reducing ethylene synthesis and damage to plants under salt stress. These endophytic fungi can be used as alternative bioinoculants to increase crop yield in saline soil.

Photosynthetic electron transport rate and root dynamics of finger millet in response to Trichoderma harzianum

Finger millet (ragi) is the main food grain for many people, especially in the arid and semiarid regions of developing countries in Asia and Africa. The grains contain an exceptionally higher amount of Ca (>300 mg/100 g) when compared to other major cereals. For sustainable production of ragi in the current scenario of climate change, this study aimed to evaluate the impact of Trichoderma harzianum (TRI) on ragi performance. The performance of photosynthetic pigment pool, photosynthetic apparatus, and root dynamics of three varieties of ragi (PRM-1, PRM-701, and PRM-801) in response to four treatments viz., C (soil), S+ TRI (soil + Trichoderma), farmyard manure (soil+ FYM), and FYM+TRI (Soil + FYM + Trichoderma) were studied. Results have shown a significant increase in the photosynthetic pigment pool and optimized functional and structural integrity of the photosynthetic apparatus in response to the combination of farmyard manure (FYM) with TRI. Higher yield parameters viz., φ(Po) and φ(Eo), δ(Ro), efficiency ψ(Eo), performance indices - PI_abs and PI_total, and enhanced root canopy and biomass were observed in all three varieties. Improved electron transport from PSII to PSI, root canopy and biomass, may also suitably favor biological carbon sequestration to retain soil health and plant productivity in case grown in association with FYM and TRI.

Comparative Effectiveness of Filamentous Fungi in Biocontrol of Meloidogyne javanica and Activated Defense Mechanisms on Tomato

The nematicidal potential of five filamentous fungi as biological control agents (BCAs) against the root-knot nematode (RKN), Meloidogyne javanica, infecting tomato was assessed in vitro and in pot experiments. The five promising native taxa, namely Trichoderma longibrachiatum, T. harzainum, T. asperellum, Lecanicillium spp., and Metacordyceps chlamydosporia, were selected to compare their effectiveness against both chemical (Mocap, 10% ethoprophos) and biological (abamectin) nematicides on M. javanica reproduction indices and plant growth parameters. The stimulation of defense mechanisms was assessed by monitoring changes in the enzymatic activities of the polyphenol oxidase (PPO), peroxidase (POD), ascorbate peroxidase (APX), catalase (CAT), lipid peroxidation (MDA), phenols, and proteins content of tomato roots. The laboratory assays revealed that T. longibrachiatum, M. chlamydoporia, and Lecanicillium spp. seemed to be the most effective under laboratory conditions, with more than 60% of juvenile mortality. The egg infection rate was above 62%, and the egg hatching rate was below 32%. The direct parasitism by the five taxa was confirmed by scanning electron microscope observation. The results of this study found a similar parasitism mechanism for T. longibrachiatum, T. harzianum, and M. chlamydosporia, where their hyphae and spores adhered to the M. javanica juveniles cuticle layer and formed trapping rings around them. The pot experiment results showed that T. harzianum and Lecanicillium spp. enhanced the plant growth parameters. Trichoderma longibrachiatum, abamectin, and the ethoprophos-based nematicides effectively decreased the reproduction rates of the nematode. The Trichoderma species and M. chlamydosporia significantly reduced the gall index and female fecundity of RKN. The treatment with BCAs and chemical nematicides involved a significant increase in the antioxidant activities of nematode-infected plants. The ethoprophos and fungal treatments decreased the MDA and total phenols content compared with the nematode-infested seedlings. This paper analyzes the advancements made towards the effective and efficient biocontrol of M. javanica using different fungal taxa, especially T. longibrachiatum and M. chlamydosporia, and the implications of these advancements for sustainable agriculture and food security.

The Biocontrol Potential of Endophytic Trichoderma Fungi Isolated from Hungarian Grapevines, Part II, Grapevine Stimulation

In the first part of this two-piece publication, the isolation, identification and in vitro characterization of ten endophytic Trichoderma isolates were reported. Here we report the ability of two different mixes of some of these isolates (Trichoderma simmonsii, Trichoderma orientale and Trichoderma gamsii as well as of Trichoderma afroharzianum and T. simmonsii) to colonize and stimulate the growth of grapevines. Two commercial vineyards about 400 km away from the site of isolation were used as experimental fields, from which the strains of three Trichoderma species were re-isolated up to four years after rootstock soaking treatment with conidiospores, performed before planting. The treatments decreased the overall percentage of lost plants of about 30%, although a low number of lost plants (about 5%) were observed also in the control plot. For all cultivars and clones, the Trichoderma treatments significantly increased both the bud burst ratio and bud burst vigor index. In addition, the grape must parameters such as the Brix degrees, as well as the extract, the D-glucose and the D-fructose concentrations all appeared to be improved, suggesting a potentially higher ethanol content of the produced wine. We conclude that grapevine-endophytic Trichoderma isolates promote plant growth, which could be a useful feature for sustainable agriculture in general and integrated plant production in particular.

Trichoderma spp. Improves Flowering, Quality, and Nutritional Status of Ornamental Plants

Scientists all over the world conduct research to determine the influence of Trichoderma spp. on various groups of plants, mostly crops. However, there is little information on the influence of these fungi on ornamental plants. Therefore, the authors of this study analyzed the influence of Trichoderma spp. on the growth, flowering, quality, and nutritional status of ornamental plants. The research showed that Trichoderma spp. in this group of plants stimulate the elongation and thickening of shoots and the formation of leaves. These fungi also stimulate or inhibit leaf elongation. They also accelerate the flowering of plants, stimulate the elongation of inflorescence shoots and inflorescences, and the development of flowers. Apart from that, Trichoderma spp. positively influence the content of chlorophyll and carotenoids in leaves, and they stimulate the uptake of micro- and macroelements.

Rhizosphere inoculation of Nicotiana benthamiana with Trichoderma harzianum TRA1-16 in controlled environment agriculture: Effects of varying light intensities on the mutualism-parasitism interaction

Trichoderma spp., a genus of fast-growing and highly adaptable fungi that form symbiotic relationships with plant roots, rendering them ideal for practical use in controlled environment agriculture. Herein, this paper aims to understand how the Nicotiana benthamiana with inoculation of Trichoderma harzianum strain TRA1-16 responds to light intensity variation. Pot experiments were conducted under low and high light intensities (50 and 150 μmol·m^-2·s^-1, respectively) and microbial treatments. Plant growth, physio-biochemical attributes, activities of antioxidant enzymes, and phytohormones regulation were investigated. The results showed that for non-inoculated plants, the reduction in light intensity inhibited plant growth, nitrogen (N) and phosphorus (P) uptake, chlorophyll a/b, and carotenoid content. Trichoderma inoculation resulted in 1.17 to 1.51 times higher concentrations of available N and P in the soil than the non-inoculated group, with higher concentrations at high light intensity. Plant height, dry weight, nutrient uptake, and antioxidant activity were significantly increased after inoculation (p<0.05). However, the growth-promoting effect was less effective under low light conditions, with lower plant height and P content in plants. We suggested that when the light was attenuated, the mutualism of the Trichoderma turned into parasitism, slowing the growth of the host plant. The application of fungal inoculation techniques for plant growth promotion required coordination with appropriate light complementation. The mechanisms of coordination and interaction were proposed to be incorporated into the biological market theory.

Inoculation of Trichoderma asperelloides ameliorates aluminum stress-induced damages by improving growth, photosynthetic pigments and organic solutes in maize

Excess aluminum (Al) is a stressful condition that affects plant growth and yield quality. This study evaluates growth responses and changes in the contents of photosynthetic pigments and organic solute in maize (Zea mays L.) plants inoculated with Trichoderma asperelloides isolates (T01, T02, T74, T76, or T96) and treated with increasing doses of Al (0, 50, 100, 150, and 200 µM of Al). Uninoculated unstressed plants served as control. Absolute growth rate, root length, dry biomass (shoot, roots and total) and shoot:root ratio were significantly affected in Al-stressed maize plants inoculated with T. asperelloides. Also, chlorophylls (a, b and total) were significantly reduced, whereas carotenoids and anthocyanins increased in those plants. Except for carotenoids, all parameters increased in plants inoculated with T. asperelloides, especially T01 or T02 isolates. Anthocyanins increased by 50% in plants inoculated with T74 and treated with 100 or 150 µM Al as compared to control plants. Total soluble carbohydrates increased by 74% and 101% in plants inoculated with T74 and T76, respectively, and treated with 200 µM Al. Total free amino acids increased more than 50% in plants inoculated with T02 and treated with 150 and 200 µM Al. Free prolines increased by 90%, 145% and 165% in plants inoculated with T74 and treated 100, 150 and 200 µM Al, respectively, in comparison to the unstressed control plants. We concluded that T. asperelloides positively affected growth, photosynthetic pigments, and organic solutes of Al-stressed plants, especially those inoculated with T01, T02, or T74 isolates.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03310-3.

Trichoderma - genomes and genomics as treasure troves for research towards biology, biotechnology and agriculture

The genus Trichoderma is among the best studied groups of filamentous fungi, largely because of its high relevance in applications from agriculture to enzyme biosynthesis to biofuel production. However, the physiological competences of these fungi, that led to these beneficial applications are intriguing also from a scientific and ecological point of view. This review therefore summarizes recent developments in studies of fungal genomes, updates on previously started genome annotation efforts and novel discoveries as well as efforts towards bioprospecting for enzymes and bioactive compounds such as cellulases, enzymes degrading xenobiotics and metabolites with potential pharmaceutical value. Thereby insights are provided into genomes, mitochondrial genomes and genomes of mycoviruses of Trichoderma strains relevant for enzyme production, biocontrol and mycoremediation. In several cases, production of bioactive compounds could be associated with responsible genes or clusters and bioremediation capabilities could be supported or predicted using genome information. Insights into evolution of the genus Trichoderma revealed large scale horizontal gene transfer, predominantly of CAZyme genes, but also secondary metabolite clusters. Investigation of sexual development showed that Trichoderma species are competent of repeat induced point mutation (RIP) and in some cases, segmental aneuploidy was observed. Some random mutants finally gave away their crucial mutations like T. reesei QM9978 and QM9136 and the fertility defect of QM6a was traced back to its gene defect. The Trichoderma core genome was narrowed down to 7000 genes and gene clustering was investigated in the genomes of multiple species. Finally, recent developments in application of CRISPR/Cas9 in Trichoderma, cloning and expression strategies for the workhorse T. reesei as well as the use genome mining tools for bioprospecting Trichoderma are highlighted. The intriguing new findings on evolution, genomics and physiology highlight emerging trends and illustrate worthwhile perspectives in diverse fields of research with Trichoderma.

The diversity of rhizospheric bacterial communities associated with Trichoderma-treated rice fields

Microbial-based fertilizer has been widely used as a healthier and better alternative to agrochemical products. However, the effects of biofertilizers on the rhizospheric microbiota has rarely been investigated. Thus, the aim of this study was to investigate the effects of symbiotic fungus Trichoderma asperellum SL2-based inoculant on the soil bacterial population through next generation sequencing using a metabarcoding approach. The treatments plots were treated with T. asperellum SL2 spore suspension, while the control plots were treated with sterilized distilled water. The results showed similar bacterial microbiome profiles in the soil of control and T. asperellum SL2-treated plots. In conclusion, the application of the T. asperellum SL2 inoculant had not exerted negative impact towards the bacterial population as similar observation was reflected in control plots. Nonetheless, future research should be conducted to investigate the effects of repeated application of T. asperellum SL2 over a longer period on the rice microbiota communities.

Improvement in the physiological and biochemical performance of strawberries under drought stress through symbiosis with Antarctic fungal endophytes

Strawberry is one of the most widely consumed fruit, but this crop is highly susceptible to drought, a condition strongly associated with climate change, causing economic losses due to the lower product quality. In this context, plant root-associated fungi emerge as a new and novel strategy to improve crop performance under water-deficiency stress. This study aimed to investigate the supplementation of two Antarctic vascular plant-associated fungal endophytes, Penicillium brevicompactum and Penicillium chrysogenum, in strawberry plants to develop an efficient, effective, and ecologically sustainable approach for the improvement of plant performance under drought stress. The symbiotic association of fungal endophytes with strawberry roots resulted in a greater shoot and root biomass production, higher fruit number, and an enhanced plant survival rate under water-limiting conditions. Inoculation with fungal endophytes provokes higher photosynthetic efficiency, lower lipid peroxidation, a modulation in antioxidant enzymatic activity, and increased proline content in strawberry plants under drought stress. In conclusion, promoting beneficial symbiosis between plants and endophytes can be an eco-friendly strategy to cope with drought and help to mitigate the impact of diverse negative effects of climate change on crop production.

Is Endophytic Colonization of Host Plants a Method of Alleviating Drought Stress? Conceptualizing the Hidden World of Endophytes

In the wake of changing climatic conditions, plants are frequently exposed to a wide range of biotic and abiotic stresses at various stages of their development, all of which negatively affect their growth, development, and productivity. Drought is one of the most devastating abiotic stresses for most cultivated crops, particularly in arid and semiarid environments. Conventional breeding and biotechnological approaches are used to generate drought-tolerant crop plants. However, these techniques are costly and time-consuming. Plant-colonizing microbes, notably, endophytic fungi, have received increasing attention in recent years since they can boost plant growth and yield and can strengthen plant responses to abiotic stress. In this review, we describe these microorganisms and their relationship with host plants, summarize the current knowledge on how they “reprogram” the plants to promote their growth, productivity, and drought tolerance, and explain why they are promising agents in modern agriculture.

Fungal endophytes of Brassicaceae: Molecular interactions and crop benefits

Brassicaceae family includes an important group of plants of great scientific interest, e.g., the model plant Arabidopsis thaliana, and of economic interest, such as crops of the genus Brassica (Brassica oleracea, Brassica napus, Brassica rapa, etc.). This group of plants is characterized by the synthesis and accumulation in their tissues of secondary metabolites called glucosinolates (GSLs), sulfur-containing compounds mainly involved in plant defense against pathogens and pests. Brassicaceae plants are among the 30% of plant species that cannot establish optimal associations with mycorrhizal hosts (together with other plant families such as Proteaceae, Chenopodiaceae, and Caryophyllaceae), and GSLs could be involved in this evolutionary process of non-interaction. However, this group of plants can establish beneficial interactions with endophytic fungi, which requires a reduction of defensive responses by the host plant and/or an evasion, tolerance, or suppression of plant defenses by the fungus. Although much remains to be known about the mechanisms involved in the Brassicaceae-endophyte fungal interaction, several cases have been described, in which the fungi need to interfere with the GSL synthesis and hydrolysis in the host plant, or even directly degrade GSLs before they are hydrolyzed to antifungal isothiocyanates. Once the Brassicaceae-endophyte fungus symbiosis is formed, the host plant can obtain important benefits from an agricultural point of view, such as plant growth promotion and increase in yield and quality, increased tolerance to abiotic stresses, and direct and indirect control of plant pests and diseases. This review compiles the studies on the interaction between endophytic fungi and Brassicaceae plants, discussing the mechanisms involved in the success of the symbiosis, together with the benefits obtained by these plants. Due to their unique characteristics, the family Brassicaceae can be seen as a fruitful source of novel beneficial endophytes with applications to crops, as well as to generate new models of study that allow us to better understand the interactions of these amazing fungi with plants.

Endophytic Trichoderma spp. can protect strawberry and privet plants from infection by the fungus Armillaria mellea

Armillaria mellea is an important fungal pathogen worldwide, affecting a large number of hosts in the horticulture and forestry industries. Controlling A. mellea infection is expensive, labour intensive and time-consuming, so a new, environmentally friendly management solution is required. To this effect, endophytic Trichoderma species were studied as a potential protective agent for Armillaria root rot (ARR) in strawberry and privet plants. A collection of forty endophytic Trichoderma isolates were inoculated into strawberry (Fragaria × ananassa) plants and plant growth was monitored for two months, during which time Trichoderma treatment had no apparent effect. Trichoderma-colonised strawberry plants were then inoculated with A. mellea and after three months plants were assessed for A. mellea infection. There was considerable variation in ARR disease levels between plants inoculated with different Trichoderma spp. isolates, but seven isolates reduced ARR below the level of positive controls. These isolates were further tested for protective potential in Trichoderma-colonized privet (Ligustrum vulgare) plants where five Trichoderma spp. isolates, including two highly effective Trichoderma atrobrunneum isolates, were able to significantly reduce levels of disease. This study highlights the potential of plants pre-colonised with T. atrobrunneum for effective protection against A. mellea in two hosts from different plant families.

Tools for adapting to a complex habitat: G-protein coupled receptors in Trichoderma

Sensing the environment and interpretation of the received signals are crucial competences of living organisms in order to properly adapt to their habitat, succeed in competition and to reproduce. G-protein coupled receptors (GPCRs) are members of a large family of sensors for extracellular signals and represent the starting point of complex signaling cascades regulating a plethora of intracellular physiological processes and output pathways in fungi. In Trichoderma spp. current research involves a wide range of topics from enzyme production, light response and secondary metabolism to sexual and asexual development as well as biocontrol, all of which require delicate balancing of resources in response to the environmental challenges or biotechnological needs at hand, which are crucially impacted by the surroundings of the fungi and their intercellular signaling cascades triggering a precisely tailored response. In this review we summarize recent findings on sensing by GPCRs in Trichoderma, including the function of pheromone receptors, glucose sensing by CSG1 and CSG2, regulation of secondary metabolism by GPR8 and impacts on mycoparasitism by GPR1. Additionally, we provide an overview on structural determinants, posttranslational modifications and interactions for regulation, activation and signal termination of GPCRs in order to inspire future in depth analyses of their function and to understand previous regulatory outcomes of natural and biotechnological processes modulated or enabled by GPCRs.

Immunomodulatory Molecular Mechanisms of Luffa cylindrica for Downy Mildews Resistance Induced by Growth-Promoting Endophytic Fungi

Downy mildew (DM), caused by P. cubensis, is harmful to cucurbits including luffa, with increased shortcomings associated with its control through cultural practices, chemical fungicides, and resistant cultivars; there is a prompt need for an effective, eco-friendly, economical, and safe biocontrol approach. Current research is therefore dealt with the biocontrol of luffa DM1 through the endophytic fungi (EF) consortium. Results revealed that T. harzianum (ThM9) and T. virens (TvA1) showed pathogen-dependent inducible metabolic production of squalene and gliotoxins by higher gene expression induction of SQS1/ERG9 (squalene synthase) and GliP (non-ribosomal peptide synthetase). Gene expression of lytic enzymes of EF was also induced with subsequently higher enzyme activities upon confrontation with P. cubensis. EF-inoculated luffa seeds showed efficient germination with enhanced growth potential and vigor of seedlings. EF-inoculated plants showed an increased level of growth-promoting hormone GA with higher gene expression of GA2OX8. EF-pre-inoculated seedlings were resistant to DM and showed an increased GSH content and antioxidant enzyme activities (SOD, CAT, POD). The level of MDA, H2O2, REL, and disease severity was reduced by EF. ACC, JA, ABA, and SA were overproduced along with higher gene expression of LOX, ERF, NCED2, and PAL. Expression of defense-marker genes (PPO, CAT2, SOD, APX, PER5, LOX, NBS-LRR, PSY, CAS, Ubi, MLP43) was also modulated in EF-inoculated infected plants. Current research supported the use of EF inoculation to effectively escalate the systemic immunity against DM corresponding to the significant promotion of induced systemic resistance (ISR) and systemic acquired resistance (SAR) responses through initiating the defense mechanism by SA, ABA, ET, and JA biosynthesis and signaling pathways in luffa.

Effects of Vermicompost Substrates and Coconut Fibers Used against the Background of Various Biofertilizers on the Yields of Cucumis melo L. and Solanum lycopersicum L

Vermicompost has been promoted as a viable substrate component owing to its physicochemical properties, nutrient richness, and status as an excellent soil improver. It is considered the best organic fertilizer and is more eco-friendly than chemical fertilizers. Plant-growth-promoting microorganisms (PGPMs) are defined as plant biofertilizers that improve nutritional efficiency—that is, they transform nutrients within substrates from organic to inorganic forms, making them available for plants. The main objective of this research study is to evaluate the effects of the application of three PGPM microbial consortia on different mixtures of organic substrates based on vermicompost (V) and coconut fiber (CF) on two different horticultural crops. We performed a yield analysis and drainage nutrient tests and determined the plant nutritional status and enzymatic activity in organic substrates based on the two crops, Cucumis melo L. and Solanum lycopersicum L. A multivariate analysis of variance and principal component analysis was conducted using substrate types and PGPMs as factors. Differences (p < 0.05) in yield, dehydrogenase activity, the nutrient concentrations in a petiole sap, and drainage were observed at 30, 60, 75, and 90 days after transplant. PGPMs such as Trichoderma sp. and plant-growth-promoting rhizobacteria (PGPR) in organic substrates (40V + 60CF) can significantly improve the nutritional status of plants for use in organic soilless container agriculture. Biofertilization with PGPMs and suitable mixtures of organic substrates together with aqueous extracts (tea) of vermicompost, as nutrient solutions applied by fertigation, has allowed us to achieve an adequate level of production through environmentally friendly techniques. The results obtained allowed us to affirm that it was possible to replace conventional fertilization using chemical products and ensure adequate crop nutrition by supplying the main macronutrients.

Flowering, Nutritional Status, and Content of Chloroplast Pigments in Leaves of Gladiolus hybridus L. ‘Advances Red’ after Application of Trichoderma spp

In this study, we attempt to assess the influence of Trichoderma spp. on the flowering and nutritional status of Gladiolus hybridus L. ‘Advances Red’, as well as on the content of chlorophyll a + b and carotenoids in the leaves. During both years of the experiment, there was a treatment in which Trichoderma fungi were not used (control), and in another treatment, plants were treated with these fungi. After five weeks of cultivation, when leaf apexes were visible above the surface of the substrate, each plant was irrigated with a suspension (20 mL) of mix of Trichoderma spp. (T. viride Schumach-Tv14, T. harzianum Rifai-Thr2, T. hamatum/Bonord/Bainier-Th15). The treatment of the plants Trichoderma-spp. improved their uptake of macro- (P, K and Ca) and micronutrients (Zn, Fe and B), and increased the chlorophyll a + b and carotenoids in their leaves. Trichoderma spp. accelerated the flowering of Gladiolus hybridus L. ‘Advances Red’ by 10–14 days. The fungi stimulated the elongation of inflorescence shoots and inflorescences, in which the number of flowers increased, but flower diameter did not change. Trichoderma spp. improved the nutrients uptake, chlorophyll a + b and carotenoids, and flowering; hence, Trichoderma spp. treatment is suggested for enhancing inflorescence and inflorescence shoots in Gladiolus hybridus.

Unraveling the Genome Sequence of Plant Growth Promoting Aspergillus niger (CSR3) Provides Insight into the Synthesis of Secondary Metabolites and Its Comparative Genomics

Aspergillus niger strain CSR3 is an endophytic fungus that regulates plant endogenous hormones, secondary metabolites, and promotes plant growth during abiotic stress conditions. In this study, we sequenced the genome of A. niger (CSR3) and compared it with previously available A. niger strains. The final genome assembly was 35.8 Mb in size, consisting of 23 scaffolds with N50 scaffold length of 2.4 Mb. A total of 12,442 protein coding genes, 270 tRNA, and 57 rRNA were predicted in the CSR3 genome. We used comparative genomic analysis to provide insights into the genome's evolution and to elucidate the adaptive genomic signatures for bioactive secondary metabolite biosynthesis, hormones biosynthesis, and plant growth promoting activities. We also analyzed the transposable elements (TEs), simple sequence repeats (SSRs), CAZymes families, genes involved in gibberellin biosynthesis, and secondary metabolite clusters in the CSR3 genome. A total of 21 secondary metabolite biosynthesis gene clusters were detected, with 18 essential enzymes involved in the mevalonate pathway (MVA). The repeat analysis revealed about 3431 SSR, 274 TEs, and 205 inverted repeats (IR). Further gene family analysis revealed that 124 gene families were gained, whereas 125 gene families were lost in CSR3 genome, compared to A. niger ASM151534V and A. niger ASM285V2 genomes. The results improve our understanding of the CSR3 genome and will assist in future investigations on the genetic basis of A. niger CSR3, including the identification of CSR3 phytostimulant properties.

Microbial Contributions for Rice Production: From Conventional Crop Management to the Use of 'Omics' Technologies

Rice, the main staple food for about half of the world's population, has had the growth of its production stagnate in the last two decades. One of the ways to further improve rice production is to enhance the associations between rice plants and the microbiome that exists around, on, and inside the plant. This article reviews recent developments in understanding how microorganisms exert positive influences on plant growth, production, and health, focusing particularly on rice. A variety of microbial species and taxa reside in the rhizosphere and the phyllosphere of plants and also have multiple roles as symbiotic endophytes while living within plant tissues and even cells. They alter the morphology of host plants, enhance their growth, health, and yield, and reduce their vulnerability to biotic and abiotic stresses. The findings of both agronomic and molecular analysis show ways in which microorganisms regulate the growth, physiological traits, and molecular signaling within rice plants. However, many significant scientific questions remain to be resolved. Advancements in high-throughput multi-omics technologies can be used to elucidate mechanisms involved in microbial-rice plant associations. Prospectively, the use of microbial inoculants and associated approaches offers some new, cost-effective, and more eco-friendly practices for increasing rice production.