The volatile 6-pentyl-2H-pyran-2-one from Trichoderma atroviride regulates Arabidopsis thaliana root morphogenesis via auxin signaling and ETHYLENE INSENSITIVE 2 functioning

Linking a polyketide synthase gene cluster to 6-pentyl-alpha-pyrone, a Trichoderma metabolite with diverse bioactivities

BACKGROUND

Members of the fungal genus Trichoderma are well-known for their mycoparasitic and plant protecting activities, rendering them important biocontrol agents. One of the most significant specialized metabolites (SMs) produced by various Trichoderma species is the unsaturated lactone 6-pentyl-alpha-pyrone (6-PP). Although first identified more than 50 years ago and having pronounced antifungal and plant growth-promoting properties, the biosynthetic pathway of 6-PP still remains unresolved.

RESULTS

Here, we demonstrate that 6-PP is biosynthesized via the polyketide biosynthesis pathway. We identified Pks1, an iterative type I polyketide synthase, as crucial for its biosynthesis in Trichoderma atroviride, a species recognized for its prominent 6-PP production abilities. Phylogenetic and comparative genomic analyses revealed that the pks1 gene is part of a biosynthetic gene cluster conserved in those Trichoderma species that are known to produce 6-PP. Deletion of pks1 caused a complete loss of 6-PP production in T. atroviride and a significant reduction in antifungal activity against Botrytis cinerea and Rhizoctonia solani. Surprisingly, the absence of pks1 led to enhanced lateral root formation in Arabidopsis thaliana during interaction with T. atroviride. Transcriptomic analysis revealed co-regulation of pks1 with adjacent genes, including candidates coding for a C3H1-type zinc finger protein and lytic polysaccharide monooxygenase, suggesting coordination between 6-PP biosynthesis and environmental response mechanisms.

CONCLUSION

Our findings establish pks1 as an essential gene for 6-PP biosynthesis in T. atroviride, providing novel insights into the production of one of the most significant compounds of this mycoparasite. These findings may pave the way for the development of improved biocontrol agents and the application of 6-PP as potent biopesticide contributing to an eco-friendly and sustainable way of plant disease management.

4-Allylanisole Promotes the Root Growth of Arabidopsis thaliana by Inhibiting AtHDA9 Activity

This study elucidates the epigenetic mechanism through which 4-allylanisole, a key monoterpene in Foeniculum vulgare essential oils, regulates plant growth. Integrated RNA-Seq and ChIP-Seq analyses revealed 4-allylanisole enhances histone H3K9 acetylation (H3K9ac) at promoters of growth-related genes in Arabidopsis thaliana, concomitant with improved root development and biomass accumulation. Biochemical assays identified AtHDA9 histone deacetylase as the molecular target, showing 4-allylanisole directly inhibits its enzymatic activity through stable interactions with catalytic residues (Asp95, Phe202, Leu268, His174) confirmed by molecular docking and dynamics simulations. The suppressed deacetylation elevated endogenous indole-3-acetic acid (IAA) levels and amplified auxin signaling transduction. These findings establish a dual mechanism whereby 4-allylanisole epigenetically activates growth-related gene expression through H3K9ac accumulation while coordinately enhancing IAA biosynthesis and signaling. This work provides the first evidence of plant-derived volatile compounds regulating growth through histone modification-auxin crosstalk, proposing novel strategies for developing eco-friendly plant growth regulators.

A rhizobacterium-secreted protein induces lateral root development through the IAA34-PUCHI pathway

Lateral roots (LRs) can continuously forage water and nutrients from soil. In Arabidopsis thaliana, LR development depends on a canonical auxin signaling pathway involving the core transcription factors INDOLE-3-ACETIC ACIDs (IAAs) and AUXIN RESPONSE FACTORs (ARFs). In this study, we identified a protein, bacillolysin, secreted by the beneficial rhizobacterium Bacillus velezensis SQR9, that is able to stimulate LR formation of Arabidopsis. The receptor protein kinase C-TERMINALLY ENCODED PEPTIDE RECEPTOR2 (CEPR2) interacts with bacillolysin and plays a critical role in LR development. In the bacillolysin-regulated signaling pathway, the transcriptional repressor IAA34 interacts with PUCHI to activate downstream LATERAL ORGAN BOUNDARIES-DOMAIN33 (LBD33) expression, consequently inducing LR development. This study reveals interkingdom communication via a protein that mediates a novel pathway to induce LR development.

Root system architecture plasticity with beneficial rhizosphere microbes: Current findings and future perspectives

The rhizosphere microbiota, often referred to as the plant's "second genome" plays a critical role in modulating root system architecture (RSA). Despite this, existing methods to analyze root phenotypes in the context of root-microbe interactions remain limited, and the precise mechanisms affecting RSA by microbes are still not fully understood. This review comprehensively evaluates current root phenotyping techniques relevant to plant-microbe interactions, discusses their limitations, and explores future directions for integrating advanced technologies to elucidate microbial roles in altering RSA. Here, we summarized that microbial metabolite, primarily through auxin signaling pathways, drive root development changes. By harnessing advanced phenotyping tools, we aim to uncover more detailed mechanisms by which microbes modify RSA, providing valuable insights into strategies for optimizing nutrient uptake, bolstering food security, and enhancing resilience against climate-induced environmental stresses.

Sinomonas gamaensis NEAU-HV1 remodels the IAA14-ARF7/19 interaction to promote plant growth

Sinomonas species typically reside in soils or the rhizosphere and can promote plant growth. Sinomonas enrichment in rhizospheric soils is positively correlated with increases in plant biomass. However, the growth promotion mechanisms regulated by Sinomonas remain unclear. By using soil systems, we studied the growth-promoting effects of Sinomonas gamaensis NEAU-HV1 on various plants. Through a combination of phenotypic analyses and microscopic observations, the effects of NEAU-HV1 on root development were evaluated. We subsequently conducted molecular and genetic experiments to reveal the mechanism promoting lateral root (LR) development. We demonstrated that NEAU-HV1 significantly promoted the growth of lettuce, wheat, maize, peanut and Arabidopsis. This effect was associated with multiple beneficial traits, including phosphate solubilization, indole-3-acetic acid and 1-aminocyclopropane-1-carboxylic acid deaminase production and survival ability in the rhizosphere and within the inner tissue of roots. In addition, NEAU-HV1 could secrete metabolites to promote LR development by affecting auxin transport and signaling. Importantly, we found that the influence of auxin signaling may be attributed to the remodeling interaction between SOLITARY-ROOT (SLR)/IAA14 and ARF7/19, occurring independently of the auxin receptor TIR1/AFB2. Our results indicate that NEAU-HV1-induced LR formation is dependent on direct remodeling interactions between transcription factors, providing novel insights into plant-microbe interactions.

Potential of Trichoderma asperellum as a Growth Promoter in Hydroponic Lettuce Cultivated in a Floating-Root System

The genus Trichoderma is widely used in agriculture as a biological agent and biofertilizer, enhancing crop yield and quality. However, its use in hydroponic systems is limited. This study evaluated the potential of Trichoderma asperellum as a growth promoter for lettuce (Lactuca sativa L.) cv. Starfighter RZ in a floating-root hydroponic system (FHS). T. asperellum strains (TaMFP1 and TaMFP2) were isolated from soil and identified morphologically and molecularly. The experiment used a completely randomized design with the following four treatments (n = 4): root spraying with TaMFP1, TaMFP2, T. harzianum (Trichospore®), and uninoculated plants (control). After 30 days, morphological, biochemical, and quality parameters were analyzed. All Trichoderma treatments significantly increased plant height (19.0%), root length (25.7%), total fresh biomass (76.4%), total dry biomass (82.63%), and number of leaves (18.18%). The nitrate levels in leaves were unaffected by TaMFP1 and TaMFP2, while Trichospore® reduced the nitrate content by 24.94%. The foliar nitrogen content increased with specific treatments, though the phosphorus and magnesium levels decreased. Visual quality traits, including appearance and firmness, remained unchanged. T. asperellum strains TaMFP1 and TaMFP2 enhanced vegetative growth without compromising quality, demonstrating their potential as sustainable tools for hydroponic lettuce production in controlled environments.

Synthetic Microbial Communities Enhance Pepper Growth and Root Morphology by Regulating Rhizosphere Microbial Communities

Synthetic microbial community (SynCom) application is efficient in promoting crop yield and soil health. However, few studies have been conducted to enhance pepper growth via modulating rhizosphere microbial communities by SynCom application. This study aimed to investigate how SynCom inoculation at the seedling stage impacts pepper growth by modulating the rhizosphere microbiome using high-throughput sequencing technology. SynCom inoculation significantly increased shoot height, stem diameter, fresh weight, dry weight, chlorophyll content, leaf number, root vigor, root tips, total root length, and root-specific surface area of pepper by 20.9%, 36.33%, 68.84%, 64.34%, 29.65%, 27.78%, 117.42%, 35.4%, 21.52%, and 39.76%, respectively, relative to the control. The Chao index of the rhizosphere microbial community and Bray-Curtis dissimilarity of the fungal community significantly increased, while Bray-Curtis dissimilarity of the bacterial community significantly decreased by SynCom inoculation. The abundances of key taxa such as Scedosporium, Sordariomycetes, Pseudarthrobacter, norankSBR1031, and norankA4b significantly increased with SynCom inoculation, and positively correlated with indices of pepper growth. Our findings suggest that SynCom inoculation can effectively enhance pepper growth and regulate root morphology by regulating rhizosphere microbial communities and increasing key taxa abundance like Sordariomycetes and Pseudarthrobacter, thereby benefiting nutrient acquisition, resistance improvement, and pathogen resistance of crops to ensure sustainability.

Light Regulates Secreted Metabolite Production and Antagonistic Activity in Trichoderma

Secondary metabolism is one of the main mechanisms Trichoderma uses to explore and colonize new niches, and 6-pentyl-α-pyrone (6-PP) is an important secondary metabolite in this process. This work focused on standardizing a method to investigate the production of 6-PP. Ethanol and ethyl acetate were both effective solvents for quantifying 6-PP in solution and had limited solubility in potato-dextrose-broth media. The 6-PP extraction using ethyl acetate provided a rapid and efficient process to recover this metabolite. The 6-PP was readily produced during the development of Trichoderma atroviride growing in the dark, but light suppressed its production. The 6-PP was purified, and its spectrum by nuclear magnetic resonance and mass spectroscopy was identical to that of commercial 6-PP. Light also induced or suppressed other unidentified metabolites in several other species of Trichoderma. The antagonistic activity of T. atroviride was influenced by light, as suppression of plant pathogens was greater in the dark. The secreted metabolite production on potato-dextrose-agar was differentially regulated by light, indicating that Trichoderma produced several metabolites with antagonistic activity against plant pathogens. Light has an important influence on the secondary metabolism and antagonistic activity of Trichoderma, and this trait is of key relevance for selecting antagonistic Trichoderma strains for plant protection.

RAPID ALKALINIZATION FACTOR 22 is a key modulator of the root hair growth responses to fungal ethylene emissions in Arabidopsis

In Arabidopsis (Arabidopsis thaliana (L.) Heynh), exposure to volatile compounds (VCs) emitted by Penicillium aurantiogriseum promotes root hair (RH) proliferation and hyper-elongation through mechanisms involving ethylene, auxin, and photosynthesis signaling. In addition, this treatment enhances the levels of the small signaling peptide RAPID ALKALINIZATION FACTOR 22 (RALF22). Here, we used genetics to address the role of RALF22 in fungal VC-promoted RH growth and to identify the bioactive fungal VC. We found that RHs of ralf22 and feronia (fer-4) plants impaired in the expression of RALF22 and its receptor FERONIA, respectively, responded weakly to fungal VCs. Unlike in wild-type roots, fungal VC exposure did not enhance RALF22 transcript levels in roots of fer-4 and ethylene- and auxin-insensitive mutants. In ralf22 and fer-4 roots, this treatment did not enhance the levels of ERS2 transcripts encoding one member of the ethylene receptor family and those of some RH-related genes. RHs of ers2-1 and the rsl2rsl4 double mutants impaired in the expression of ERS2 and the ethylene- and auxin-responsive ROOT HAIR DEFECTIVE 6-LIKE 2 and 4 transcription factors, respectively, weakly responded to fungal VCs. Moreover, roots of plants defective in photosynthetic responsiveness to VCs exhibited weak RALF22 expression and RH growth responses to fungal VCs. VCs of ΔefeA strains of P. aurantiogriseum cultures impaired in ethylene synthesis weakly promoted RH proliferation and elongation in exposed plants. We conclude that RALF22 simultaneously functions as a transcriptionally regulated signaling molecule that participates in the ethylene, auxin, and photosynthesis signaling-mediated RH growth response to fungal ethylene emissions and regulation of ethylene perception in RHs.

Polyphasic Characterization of the Biocontrol Potential of a Novel Strain of Trichoderma atroviride Isolated from Central Mexico

This work describes the characterization of Trichoderma atroviride strain CMU-08, isolated from Michoacán, Mexico. CMU-08 demonstrated robust growth and conidiation across a temperature range from 16 to 32 °C and a pH range from 4 to 9 on potato dextrose agar (PDA) and malt extract agar (MEA) media. The strain is an efficient antagonist of six species of phytopathogenic fungi and oomycetes in PDA, MEA, and Vogel minimal medium (VMM). Antagonist mechanisms of CMU-08 included direct mycoparasitism observed in dual-culture assays, as well as antibiosis attributed to growth inhibition via both volatile and non-volatile metabolites, with the effectiveness varying depending on the test phytopathogen and culture medium. Extracellular filtrates (ECFs) recovered from liquid cultures of CMU-08 under basal and induced conditions using Botrytis cinerea cell walls significantly inhibited their growth at a concentration of 750 µg/mL. Moreover, in detached tomato leaf assays, these ECFs reduced foliar damage caused by B. cinerea by 24-34%. The volatile organic compounds (VOCs) produced by CMU-08 also exhibited substantial efficacy, reducing foliar damage by up to 50% in similar tests. Despite showing no basal extracellular chitinase enzymatic activity, CMU-08 demonstrated significant induction of this activity in cultures supplemented with B. cinerea and Fusarium sp. cell walls. Four genes encoding extracellular chitinases (chit33, chit36, ech42, and locus 217415) showed different dynamics of transcriptional regulation during the dual-culture confrontation of strain CMU-08 with B. cinerea and Fusarium sp., varying according to the phytopathogen and the interaction stage. The CMU-08 strain shows physiological versatility and employs a variety of antagonist mechanisms toward different species of phytopathogenic microorganisms, making it a good candidate for developing a biocontrol product for field application.

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.

Biocontrol of strawberry Botrytis gray mold and prolong the fruit shelf-life by fumigant Trichoderma spp

Objectives To screen high active volatile organic compounds (VOCs)-producing Trichoderma isolates against strawberry gray mold caused by Botrytis cinerea, and to explore their antagonistic mode of action against the pathogen. VOCs produced by nine Trichoderma isolates (Trichoderma atroviride T1 and T3; Trichoderma harzianum T2, T4 and T5; T6, T7, T8 and T9 identified as Trichoderma asperellum in this work) significantly inhibited the mycelial growth (13.9-63.0% reduction) and conidial germination (17.6-96.3% reduction) of B. cinerea, the highest inhibition percentage belonged to VOCs of T7; in a closed space, VOCs of T7 shared 76.9% and 100% biocontrol efficacy against gray mold on strawberry fruits and detached leaves, respectively, prolonged the fruit shelf-life by 3 days in presence of B. cinerea, completely protected the leaves from B. cinerea infecting; volatile metabolites of T7 damaged the cell membrane permeability and integrity of B. cinerea, thereby inhibiting the mycelial growth and conidial germination. Gas chromatography-mass spectrometry (GC-MS) analysis revealed the VOCs contain 23 potential compounds, and the majority of these compounds were categorised as alkenes, alcohols, and esters, including PEA and 6PP, which have been reported as substances produced by Trichoderma spp. T. asperellum T7 showed high biofumigant activity against mycelial growth especially conidial germination of B. cinerea and thus protected strawberry fruits and leaves from gray mold, which acted by damaging the pathogen's plasma membrane and resulting in cytoplasm leakage, was a potential biofumigant for controlling pre- and post-harvest strawberry gray mold.

The decision for or against mycoparasitic attack by Trichoderma spp. is taken already at a distance in a prey-specific manner and benefits plant-beneficial interactions

BACKGROUND

The application of plant-beneficial microorganisms as bio-fertilizer and biocontrol agents has gained traction in recent years, as both agriculture and forestry are facing the challenges of poor soils and climate change. Trichoderma spp. are gaining popularity in agriculture and forestry due to their multifaceted roles in promoting plant growth through e.g. nutrient translocation, hormone production, induction of plant systemic resistance, but also direct antagonism of other fungi. However, the mycotrophic nature of the genus bears the risk of possible interference with other native plant-beneficial fungi, such as ectomycorrhiza, in the rhizosphere. Such interference could yield unpredictable consequences for the host plants of these ecosystems. So far, it remains unclear, whether Trichoderma is able to differentiate between plant-beneficial and plant-pathogenic fungi during the process of plant colonization.

RESULTS

We investigated whether Trichoderma spp. can differentiate between beneficial ectomycorrhizal fungi (represented by Laccaria bicolor and Hebeloma cylindrosporum) and pathogenic fungi (represented by Fusarium graminearum and Alternaria alternata) in different confrontation scenarios, including a newly developed olfactometer "race tube"-like system. Using two independent species, T. harzianum and T. atrobrunneum, with plant-growth-promoting and immune-stimulating properties towards Populus x canescens, our study revealed robustly accelerated growth towards phytopathogens, while showing a contrary response to ectomycorrhizal fungi. Transcriptomic analyses identified distinct genetic programs during interaction corresponding to the lifestyles, emphasizing the expression of mycoparasitism-related genes only in the presence of phytopathogens.

CONCLUSION

The findings reveal a critical mode of fungal community interactions belowground and suggest that Trichoderma spp. can distinguish between fungal partners of different lifestyles already at a distance. This sheds light on the entangled interactions of fungi in the rhizosphere and emphasizes the potential benefits of using Trichoderma spp. as a biocontrol agent and bio-fertilizer in tree plantations.

Revealing the Complex Interplay of Biostimulant Applications

Some biostimulant products provide proven benefits to plant production, potentially offering more environmentally friendly, sustainable, and natural inputs into production systems. However, the transference and predictability of known benefits between different growth environments, application protocols, and management systems are fraught with difficulty. In this study, we carried out carefully controlled glasshouse and in vitro assays with applications of humic acids, protein hydrolysates, and seaweed extract to compare the variability of biostimulant effects and dosage-dependent variations across diverse conditions, encompassing a sufficient range to comprehensively assess their full spectrum of impacts. The results demonstrated a clear trend of dosage-dependent effects with each biostimulant exhibiting a significant growth-promoting effect within a critical concentration range, but detrimental effects when the concentration fell outside this range. While substantial growth-promoting effects were observed under glasshouse conditions, biostimulant applications tended to be more sensitive and generally led to negative impacts in sterilised conditions. The combined use of biostimulants mostly resulted in detrimental and toxicological responses with only two combined treatments showing marginal synergistic effects. The findings demonstrated a complex interplay between biostimulants and the growth conditions of plants. Lack of knowledge of the indirect effects of different growth media may result in negative impacts of biostimulant applications and combinations of products outside narrow critical concentration ranges.

Trichoderma and Bacillus multifunctional allies for plant growth and health in saline soils: recent advances and future challenges

Saline soils pose significant challenges to global agricultural productivity, hindering crop growth and efficiency. Despite various mitigation strategies, the issue persists, underscoring the need for innovative and sustainable solutions. One promising approach involves leveraging microorganisms and their plant interactions to reclaim saline soils and bolster crop yields. This review highlights pioneering and recent advancements in utilizing multi-traits Trichoderma and Bacillus species as potent promoters of plant growth and health. It examines the multifaceted impacts of saline stress on plants and microbes, elucidating their physiological and molecular responses. Additionally, it delves into the role of ACC deaminase in mitigating plant ethylene levels by Trichoderma and Bacillus species. Although there are several studies on Trichoderma-Bacillus, much remains to be understood about their synergistic relationships and their potential as auxiliaries in the phytoremediation of saline soils, which is why this work addresses these challenges.

Uncovering the multifaceted properties of 6-pentyl-alpha-pyrone for control of plant pathogens

Some volatile organic compounds (VOCs) produced by microorganisms have the ability to inhibit the growth and development of plant pathogens, induce the activation of plant defenses, and promote plant growth. Among them, 6-pentyl-alpha-pyrone (6-PP), a ketone produced by Trichoderma fungi, has emerged as a focal point of interest. 6-PP has been isolated and characterized from thirteen Trichoderma species and is the main VOC produced, often accounting for >50% of the total VOCs emitted. This review examines abiotic and biotic interactions regulating the production of 6-PP by Trichoderma, and the known effects of 6-PP on plant pathogens through direct and indirect mechanisms including induced systemic resistance. While there are many reports of 6-PP activity against plant pathogens, the vast majority have been from laboratory studies involving only 6-PP and the pathogen, rather than glasshouse or field studies including a host plant in the system. Biopesticides based on 6-PP may well provide an eco-friendly, sustainable management tool for future agricultural production. However, before this can happen, challenges including demonstrating disease control efficacy in the field, developing efficient delivery systems, and determining cost-effective application rates must be overcome before 6-PP's potential for pathogen control can be turned into reality.

Demonstrating the Applicability of Proton Transfer Reaction Mass Spectrometry to Quantify Volatiles Emitted by the Mycoparasitic Fungus Trichoderma atroviride in Real Time: Monitoring of Trichoderma-Based Biopesticides

The present study aims to explore the potential application of proton transfer reaction time-of-flight mass spectrometry (PTR-ToF-MS) for real-time monitoring of microbial volatile organic compounds (MVOCs). This investigation can be broadly divided into two parts. First, a selection of 14 MVOCs was made based on previous research that characterized the MVOC emissions of Trichoderma atroviride, which is a filamentous fungus widely used as a biocontrol agent. The analysis of gas-phase standards using PTR-ToF-MS allowed for the categorization of these 14 MVOCs into two groups: the first group primarily undergoes nondissociative proton transfer, resulting in the formation of protonated parent ions, while the second group mainly undergoes dissociative proton transfer, leading to the formation of fragment ions. In the second part of this investigation, the emission of MVOCs from samples of T. atroviride was continuously monitored over a period of five days using PTR-ToF-MS. This also included the first quantitative online analysis of 6-amyl-α-pyrone (6-PP), a key MVOC emitted by T. atroviride. The 6-PP emissions of T. atroviride cultures were characterized by a gradual increase over the first two days of cultivation, reaching a plateau-like maximum with volume mixing ratios exceeding 600 ppbv on days three and four. This was followed by a marked decrease, where the 6-PP volume mixing ratios plummeted to below 50 ppbv on day five. This observed sudden decrease in 6-PP emissions coincided with the start of sporulation of the T. atroviride cultures as well as increasing intensities of product ions associated with 1-octen-3-ol and 3-octanone, whereas both these MVOCs were previously associated with sporulation in T. atroviride. The study also presents the observations and discussion of further MVOC emissions from the T. atroviride samples and concludes with a critical assessment of the possible applications and limitations of PTR-ToF-MS for the online monitoring of MVOCs from biological samples in real time.

Trichoderma-secreted anthranilic acid promotes lateral root development via auxin signaling and RBOHF-induced endodermal cell wall remodeling

Trichoderma spp. have evolved the capacity to communicate with plants by producing various secondary metabolites (SMs). Nonhormonal SMs play important roles in plant root development, while specific SMs from rhizosphere microbes and their underlying mechanisms to control plant root branching are still largely unknown. In this study, a compound, anthranilic acid (2-AA), is identified from T. guizhouense NJAU4742 to promote lateral root development. Further studies demonstrate that 2-AA positively regulates auxin signaling and transport in the canonical auxin pathway. 2-AA also partly rescues the lateral root numbers of CASP1pro:shy2-2, which regulates endodermal cell wall remodeling via an RBOHF-induced reactive oxygen species burst. In addition, our work reports another role for microbial 2-AA in the regulation of lateral root development, which is different from its better-known role in plant indole-3-acetic acid biosynthesis. In summary, this study identifies 2-AA from T. guizhouense NJAU4742, which plays versatile roles in regulating plant root development.

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.

Papiliotrema flavescens, a plant growth-promoting fungus, alters root system architecture and induces systemic resistance through its volatile organic compounds in Arabidopsis

The current trend in agricultural development is the establishment of sustainable agricultural systems. This involves utilizing and implementing eco-friendly biofertilizers and biocontrol agents as alternatives to conventional fertilizers and pesticides. A plant growth-promoting fungal strain, that could alter root system architecture and promote the growth of Arabidopsis seedlings in a non-contact manner by releasing volatile organic compounds (VOCs) was isolated in this study. 26S rDNA sequencing revealed that the strain was a yeast-like fungus, Papiliotrema flavescens. Analysis of plant growth-promoting traits revealed that the fungus could produce indole-3-acetic acid and ammonia and fix nitrogen. Transcriptome analysis in combination with inhibitor experiments revealed that P. flavescens VOCs triggered metabolic alterations, promoted auxin accumulation and distribution in the roots, and coordinated ethylene signaling, thus inhibiting primary root elongation and inducing lateral root formation in Arabidopsis. Additionally, transcriptome analysis and fungal infection experiments confirmed that pretreatment with P. flavescens stimulated the defense response of Arabidopsis to boost its resistance to the pathogenic fungus Botrytis cinerea. Solid-phase microextraction, which was followed by gas chromatography-mass spectrometry analysis, identified three VOCs (acetoin, naphthalene and indole) with significant plant growth-promoting attributes. Their roles were confirmed using further pharmacological experiments and upregulated expression of auxin- and ethylene-related genes. Our study serves as an essential reference for utilizing P. flavescens as a potential biological fertilizer and biocontrol agent.

Inferring co-expression networks of Arabidopsis thaliana genes during their interaction with Trichoderma spp

Fungi of the Trichoderma genus are called "biostimulants" because they promote plant growth and development and induce disease resistance. We used conventional transcriptome and gene co-expression analyses to understand the molecular response of the plant Arabidopsis thaliana to inoculation with Trichoderma atroviride or Trichoderma virens. The transcriptional landscape of the plant during the interaction with these fungi showed a reduction in functions such as reactive oxygen species production, defense mechanisms against pathogens, and hormone signaling. T. virens, as opposed to T. atroviride, was more effective at downregulating genes related to terpenoid metabolism, root development, and chemical homeostasis. Through gene co-expression analysis, we found functional gene modules that closely link plant defense with hypoxia. Notably, we found a transcription factor (locus AT2G47520) with two functional domains of interest: a DNA-binding domain and an N-terminal cysteine needed for protein stability under hypoxia. We hypothesize that the transcription factor can bind to the promoter sequence of the GCC-box that is connected to pathogenesis by positioned weight matrix analysis.

Location: root architecture structures rhizosphere microbial associations

Root architectural phenotypes are promising targets for crop breeding, but root architectural effects on microbial associations in agricultural fields are not well understood. Architecture determines the location of microbial associations within root systems, which, when integrated with soil vertical gradients, determines the functions and the metabolic capability of rhizosphere microbial communities. We argue that variation in root architecture in crops has important implications for root exudation, microbial recruitment and function, and the decomposition and fate of root tissues and exudates. Recent research has shown that the root microbiome changes along root axes and among root classes, that root tips have a unique microbiome, and that root exudates change within the root system depending on soil physicochemical conditions. Although fresh exudates are produced in larger amounts in root tips, the rhizosphere of mature root segments also plays a role in influencing soil vertical gradients. We argue that more research is needed to understand specific root phenotypes that structure microbial associations and discuss candidate root phenotypes that may determine the location of microbial hotspots within root systems with relevance to agricultural systems.

Signal communication during microbial modulation of root system architecture

Every living organism on Earth depends on its interactions with other organisms. In the rhizosphere, plants and microorganisms constantly exchange signals and influence each other's behavior. Recent studies have shown that many beneficial rhizosphere microbes can produce specific signaling molecules that affect plant root architecture and therefore could have substantial effects on above-ground growth. This review examines these chemical signals and summarizes their mechanisms of action, with the aim of enhancing our understanding of plant-microbe interactions and providing references for the comprehensive development and utilization of these active components in agricultural production. In addition, we highlight future research directions and challenges, such as searching for microbial signals to induce primary root development.

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.

Root phenotypes for improved nitrogen capture

Background

Suboptimal nitrogen availability is a primary constraint for crop production in low-input agroecosystems, while nitrogen fertilization is a primary contributor to the energy, economic, and environmental costs of crop production in high-input agroecosystems. In this article we consider avenues to develop crops with improved nitrogen capture and reduced requirement for nitrogen fertilizer.

Scope

Intraspecific variation for an array of root phenotypes has been associated with improved nitrogen capture in cereal crops, including architectural phenotypes that colocalize root foraging with nitrogen availability in the soil; anatomical phenotypes that reduce the metabolic costs of soil exploration, improve penetration of hard soil, and exploit the rhizosphere; subcellular phenotypes that reduce the nitrogen requirement of plant tissue; molecular phenotypes exhibiting optimized nitrate uptake kinetics; and rhizosphere phenotypes that optimize associations with the rhizosphere microbiome. For each of these topics we provide examples of root phenotypes which merit attention as potential selection targets for crop improvement. Several cross-cutting issues are addressed including the importance of soil hydrology and impedance, phenotypic plasticity, integrated phenotypes, in silico modeling, and breeding strategies using high throughput phenotyping for co-optimization of multiple phenes.

Conclusions

Substantial phenotypic variation exists in crop germplasm for an array of root phenotypes that improve nitrogen capture. Although this topic merits greater research attention than it currently receives, we have adequate understanding and tools to develop crops with improved nitrogen capture. Root phenotypes are underutilized yet attractive breeding targets for the development of the nitrogen efficient crops urgently needed in global agriculture.

[Ecological and biological benefits of the cosmopolitan fungus Trichoderma spp. in agriculture: A perspective in the Mexican countryside]

There is currently an extensive record of scientific studies on the general characteristics of filamentous fungus Trichoderma spp., which demonstrates its wide range of interrelation in ecosystems and its fungal activity that benefits the agricultural sector and agroindustry, as well as its importance in the preservation and restoration of the soil microbiota. The success of the biological and ecological benefits of Trichoderma is due to its reproductive capacity, as well as its efficiency in the use of soil nutrients; the efficacy of the genus has been reported against a variety of phytopathogenic fungi, as well as the potential to synthesize and release enzymes (cellulases, xylanases, and chitinases) that have been implemented in agroindustrial bioprocesses. It has also been reported that various species of Trichoderma spp. can produce auxins and gibberellin-type growth regulators, reported as growth promoters of some agricultural crops; however, their most relevant fact is their ability to prevail at certain doses of 'agrotoxic' active ingredients and contribute studies regarding processes for obtaining biofuel and bioremediation of the agricultural soil. In this overview, a general description of the current and relevant studies of the different subspecies of Trichoderma and their contribution in agriculture is made, presenting results obtained in vitro, in greenhouses and in the field. This analysis will serve as a starting point for future research in Mexico, specifically on the genus Trichoderma and its benefits for the Mexican countryside.

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.

Biostimulants and environmental stress mitigation in crops: A novel and emerging approach for agricultural sustainability under climate change

Pesticide and fertilizer usage is at the center of agricultural production to meet the demands of an ever-increasing global population. However, rising levels of chemicals impose a serious threat to the health of humans, animals, plants, and even the entire biosphere because of their toxic effects. Biostimulants offer the opportunity to reduce the agricultural chemical footprint owing their multilevel, beneficial properties helping to make agriculture more sustainable and resilient. When applied to plants or to the soil an increased absorption and distribution of nutrients, tolerance to environmental stress, and improved quality of plant products explain the mechanisms by which these probiotics are useful. In recent years, the use of plant biostimulants has received widespread attention across the globe as an ecologically acceptable alternative to sustainable agricultural production. As a result, their worldwide market continues to grow, and further research will be conducted to broaden the range of the products now available. Through this review, we present a current understanding of biostimulants, their mode of action and their involvement in modulating abiotic stress responses, including omics research, which may provide a comprehensive assessment of the crop's response by correlating molecular changes to physiological pathways activated under stress conditions aggravated by climate change.

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.

Effect of the Nonpathogenic Strain Fusarium oxysporum FO12 on Fe Acquisition in Rice (Oryza sativa L.) Plants

Rice (Oryza sativa L.) is a very important cereal worldwide, since it is the staple food for more than half of the world's population. Iron (Fe) deficiency is among the most important agronomical concerns in calcareous soils where rice plants may suffer from this deficiency. Current production systems are based on the use of high-yielding varieties and the application of large quantities of agrochemicals, which can cause major environmental problems. The use of beneficial rhizosphere microorganisms is considered a relevant sustainable alternative to synthetic fertilizers. The main goal of this study was to determine the ability of the nonpathogenic strain Fusarium oxysporum FO12 to induce Fe-deficiency responses in rice plants and its effects on plant growth and Fe chlorosis. Experiments were carried out under hydroponic system conditions. Our results show that the root inoculation of rice plants with FO12 promotes the production of phytosiderophores and plant growth while reducing Fe chlorosis symptoms after several days of cultivation. Moreover, Fe-related genes are upregulated by FO12 at certain times in inoculated plants regardless of Fe conditions. This microorganism also colonizes root cortical tissues. In conclusion, FO12 enhances Fe-deficiency responses in rice plants, achieves growth promotion, and reduces Fe chlorosis symptoms.

Guided analysis of ambient ionization mass spectrometry data with the MQ_Assistant

RATIONALE

Ambient ionization mass spectrometry (AIMS) delivers realistic data from samples in their native state. In addition, AIMS methods reduce time and costs for sample preparation and have less environmental impact. However, AIMS data are often complex and require substantial processing before interpretation.

METHODS

We developed an interactive R script for guided mass spectrometry (MS) data processing. The "MQ_Assistant" is based on MALDIquant, a popular R package for MS data processing. In each step, the user can try and preview the effect of chosen parameters before deciding on the values with the best result and proceeding to the next stage. The outcome of the MQ_Assistant is a feature matrix that can be further analyzed in R and statistics tools such as MetaboAnalyst.

RESULTS

Using 360 AIMS example spectra, we demonstrate the step-by-step processing for creating a feature matrix. In addition, we show how to visualize the results of three biological replicates of a plant-microbe interaction between Arabidopsis and Trichoderma as a heatmap using R and upload them to MetaboAnalyst. The final parameter set can be saved for reuse in MALDIquant workflows of similar data.

CONCLUSIONS

The MQ_Assistant helps novices and experienced users to develop workflows for (AI)MS data processing. The interactive procedure supports the quick finding of appropriate settings. These parameters can be exported and reused in future projects. The stepwise operation with visual feedback also suggests the use of the MQ_Assistant in education.

Allelic variations of ClACO gene improve nitrogen uptake via ethylene-mediated root architecture in watermelon

KEY MESSAGE

The ClACO gene encoding 1-aminocyclopropane-1-carboxylate oxidase enabled highly efficient 15N uptake in watermelon. Nitrogen is one of the most essential nutrient elements that play a pivotal role in regulating plant growth and development for crop productivity. Elucidating the genetic basis of high nitrogen uptake is the key to improve nitrogen use efficiency for sustainable agricultural productivity. Whereas previous researches on nitrogen absorption process are mainly focused on a few model plants or crops. To date, the causal genes that determine the efficient nitrogen uptake of watermelon have not been mapped and remains largely unknown. Here, we fine-mapped the 1-aminocyclopropane-1-carboxylate oxidase (ClACO) gene associated with nitrogen uptake efficiency in watermelon via bulked segregant analysis (BSA). The variations in the ClACO gene led to the changes of gene expression levels between two watermelon accessions with different nitrogen uptake efficiencies. Intriguingly, in terms of the transcript abundance of ClACO, it was concomitant with significant differences in ethylene evolutions in roots and root architectures between the two accessions and among the different genotypic offsprings of the recombinant BC2F1(ZJU132)-18. These findings suggest that ethylene as a negative regulator altered nitrogen uptake efficiency in watermelon by controlling root development. In conclusion, our current study will provide valuable target gene for precise breeding of 'green' watermelon varieties with high-nitrogen uptake efficiencies.

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

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

Microbial volatile compounds (MVCs): an eco-friendly tool to manage abiotic stress in plants

Microbial volatile compounds (MVCs) are produced during the metabolism of microorganisms, are widely distributed in nature, and have significant applications in various fields. To date, several MVCs have been identified. Microbial groups such as bacteria and fungi release many organic and inorganic volatile compounds. They are typically small odorous compounds with low molecular masses, low boiling points, and lipophilic moieties with high vapor pressures. The physicochemical properties of MVCs help them to diffuse more readily in nature and allow dispersal to a more profound distance than other microbial non-volatile metabolites. In natural environments, plants communicate with several microorganisms and respond differently to MVCs. Here, we review the following points: (1) MVCs produced by various microbes including bacteria, fungi, viruses, yeasts, and algae; (2) How MVCs are effective, simple, efficient, and can modulate plant growth and developmental processes; and (3) how MVCs improve photosynthesis and increase plant resistance to various abiotic stressors.

Trichoderma Species from Soil of Pernambuco State, Brazil

Trichoderma is an important fungal genus, known mainly for its potential for the biological control of phytopathogens. Accurate identification of these fungi is essential for research and applications involving them, to be addressed correctly. The objectives of this study were to isolate, identify, and report the species richness of Trichoderma species that occur in the soil of different regions of Pernambuco, Brazil. DNA sequences of portions of the translation elongation factor 1-α (TEF1) gene region were generated for 56 isolates of Trichoderma, obtained from the Zona da Mata, Agreste, and Sertão regions of Pernambuco. According to the phylogenetic analysis based on these sequences, these fungi belong to two Sections-Trichoderma (35 isolates) and Pachybasidium (21 isolates). These fungi have been resolved in nine species, including Trichoderma afroharzianum, Trichoderma asperelloides, Trichoderma asperellum, Trichoderma koningiopsis, and five possible new species to be confirmed in further studies. This study shows that the soils of Pernambuco host a diversity of Trichoderma species and consequently of biological resources with potential for application in agriculture.

Trichoderma virens exerts herbicidal effect on Arabidopsis thaliana via modulation of amino acid metabolism

Trichoderma virens is a plant beneficial fungus well-known for its biocontrol, herbicidal and growth promotion activity. Earlier, we identified HAS (HA-synthase, a terpene cyclase) and GAPDH (glyceraldehyde-3-phosphate dehydrogenase) to be involved in the production of multiple non-volatiles and non-volatile+volatile metabolites, respectively. The present study delineates the function of HAS and GAPDH in regulating herbicidal activity, using the model plant Arabidopsis thaliana. Under axenic conditions, rosette-biomass of seedlings co-cultivated with ΔHAS (HAS^R) and ΔGAPDH (GAPDH^R) was higher than WT-Trichoderma (WT^R) as well as non-colonized control (NoT^R), even though the root colonization ability was reduced. However, HAS^R biomass was still higher than those of GAPDH^R, indicating that blocking volatiles will not provide any additional contribution over non-volatile metabolites for Trichoderma-induced herbicidal activity. LC-MS analysis revealed that loss of herbicidal activity of ΔHAS/ΔGAPDH was associated with an increase in the levels of amino acids, which coincided with reduced expression levels of amino-acid catabolism and anabolism related genes in HAS^R/GAPDH^R. RNAi-mediated suppression of an oxidoreductase gene, VDN5, specifically prevented viridin-to-viridiol conversion. Additionally, vdn5 mimics ΔHAS, in terms of amino-acid metabolism gene expression and partially abolishes the herbicidal property of WT-Trichoderma. Thus, the study provides mechanistic frame-work for better utilization of Trichoderma virens for biocontrol purposes, balancing between plant growth promotion and herbicidal activity.

Assessment of Tunisian Trichoderma Isolates on Wheat Seed Germination, Seedling Growth and Fusarium Seedling Blight Suppression

Beneficial microorganisms, including members of the Trichoderma genus, are known for their ability to promote plant growth and disease resistance, as well as being alternatives to synthetic inputs in agriculture. In this study, 111 Trichoderma strains were isolated from the rhizospheric soil of Florence Aurore, an ancient wheat variety that was cultivated in an organic farming system in Tunisia. A preliminary ITS analysis allowed us to cluster these 111 isolates into three main groups, T. harzianum (74 isolates), T. lixii (16 isolates) and T. sp. (21 isolates), represented by six different species. Their multi-locus analysis (tef1, translation elongation factor 1; rpb2, RNA polymerase B) identified three T. afroharzianum, one T. lixii, one T. atrobrunneum and one T. lentinulae species. These six new strains were selected to determine their suitability as plant growth promoters (PGP) and biocontrol agents (BCA) against Fusarium seedling blight disease (FSB) in wheat caused by Fusarium culmorum. All of the strains exhibited PGP abilities correlated to ammonia and indole-like compound production. In terms of biocontrol activity, all of the strains inhibited the development of F. culmorum in vitro, which is linked to the production of lytic enzymes, as well as diffusible and volatile organic compounds. An in planta assay was carried out on the seeds of a Tunisian modern wheat variety (Khiar) by coating them with Trichoderma. A significant increase in biomass was observed, which is associated with increased chlorophyll and nitrogen. An FSB bioprotective effect was confirmed for all strains (with Th01 being the most effective) by suppressing morbid symptoms in germinated seeds and seedlings, as well as by limiting F. culmorum aggressiveness on overall plant growth. Plant transcriptome analysis revealed that the isolates triggered several SA- and JA-dependent defense-encoding genes involved in F. culmorum resistance in the roots and leaves of three-week-old seedlings. This finding makes these strains very promising in promoting growth and controlling FSB disease in modern wheat varieties.

Compounds from rhizosphere microbes that promote plant growth

The rhizosphere is the soil-plant interface colonized by bacterial and fungal species that exert growth-promoting and adaptive benefits. The plant-bacteria relationships rely upon the perception of volatile organic compounds (VOCs), canonical phytohormones such as auxins and cytokinins, and the bacterial quorum sensing-related N-acyl-L-homoserine lactones and cyclodipeptides. On the other hand, plant-beneficial Trichoderma fungi emit highly active VOCs, including 6-pentyl-2H-pyran-2-one (6-PP), and β-caryophyllene, which contribute to plant morphogenesis, but also into how these microbes spread over roots or live as endophytes. Here, we describe recent findings concerning how compounds from beneficial bacteria and fungi affect root architecture and advance into the signaling events that mediate microbial recognition.

Comparative physiological and transcriptome analysis provide insights into the inhibitory effect of 6-pentyl-2H-pyran-2-one on Clarireedia jacksonii

Clarireedia spp. is a destructive phytopathogenic fungus that causes turf dollar spot of bent-grass, leading to widespread lawn death. In this study, we explored the antifungal capability of 6-pentyl-2H-pyran-2-one (6PP), a natural metabolite volatilized by microorganisms, which plays an important role in the biological control of turfgrass dollar spot. However, the mechanisms by which 6PP inhibits Clarireedia jacksonii remain unknown. In the present study, C. jacksonii mycelial growth was inhibited by the 6PP treatment and the 6PP treatment damaged cell membrane integrity, causing an increase in relative conduc-tivity. Furthermore, physiological and biochemistry assay showed that 6PP treatment can enhance reactive oxygen species (ROS) levels, malondialdehyde (MDA) content obviously increased with 6PP exposure, increased alchohol dehydrogenase (ADH) and depleted acetalde-hyde dehydrogenase (ALDH), and activated the activities of many antioxidant enzymes in C. jacksonii. Gen Ontology and Kyoto Encyclopedia of Genes and Genomes analysis revealed that some genes in C. jacksonii after 6PP treatment related to integrity of the cell wall and membrane, and oxidative stress were significantly downregulated. It is worth mentioning that the fatty acid degradation pathway is significantly upregulated, with an increase in ATP content and ATP synthase activity, which may promote fungal cell apoptosis. Moreover, we found that the expression of ABC transporters, and glutathione metabolism encoding genes were increased to respond to external stimuli. Taken together, these findings revealed the potential antifungal mechanism of 6PP against Clarireedia spp., which also provides a theoretical basis for the commercial utilization of 6PP as a green pesticide in the future.

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

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

Strain improvement of Trichoderma harzianum for enhanced biocontrol capacity: Strategies and prospects

In the control of plant diseases, biocontrol has the advantages of being efficient and safe for human health and the environment. The filamentous fungus Trichoderma harzianum and its closely related species can inhibit the growth of many phytopathogenic fungi, and have been developed as commercial biocontrol agents for decades. In this review, we summarize studies on T. harzianum species complex from the perspective of strain improvement. To elevate the biocontrol ability, the production of extracellular proteins and compounds with antimicrobial or plant immunity-eliciting activities need to be enhanced. In addition, resistance to various environmental stressors should be strengthened. Engineering the gene regulatory system has the potential to modulate a variety of biological processes related to biocontrol. With the rapidly developing technologies for fungal genetic engineering, T. harzianum strains with increased biocontrol activities are expected to be constructed to promote the sustainable development of agriculture.

The involvement of AtMKK1 and AtMKK3 in plant-deleterious microbial volatile compounds-induced defense responses

Plant-deleterious microbial volatiles activate the transactivation of hypoxia, MAMPs and wound responsive genes in Arabidopsis thaliana. AtMKK1 and AtMKK3 are involved in the plant-deleterious microbial volatiles-induced defense responses. Microbial volatile compounds (mVCs) are a collection of volatile metabolites from microorganisms with biological effects on all living organisms. mVCs function as gaseous modulators of plant growth and plant health. In this study, the defense events induced by plant-deleterious mVCs were investigated. Enterobacter aerogenes VCs lead to growth inhibition and immune responses in Arabidopsis thaliana. E. aerogenes VCs negatively regulate auxin response and transport gene expression in the root tip, as evidenced by decreased expression of DR5::GFP, PIN3::PIN3-GFP and PIN4::PIN4-GFP. Data from transcriptional analysis suggests that E. aerogenes VCs trigger hypoxia response, innate immune responses and metabolic processes. In addition, the transcript levels of the genes involved in the synthetic pathways of antimicrobial metabolites camalexin and coumarin are increased after the E. aerogenes VCs exposure. Moreover, we demonstrate that MKK1 serves as a regulator of camalexin biosynthesis gene expression in response to E. aerogenes VCs, while MKK3 is the regulator of coumarin biosynthesis gene expression. Additionally, MKK1 and MKK3 mediate the E. aerogenes VCs-induced callose deposition. Collectively, these studies provide molecular insights into immune responses by plant-deleterious mVCs.

Cell-free microbial culture filtrates as candidate biostimulants to enhance plant growth and yield and activate soil- and plant-associated beneficial microbiota

In this work we compiled information on current and emerging microbial-based fertilization practices, especially the use of cell-free microbial culture filtrates (CFs), to promote plant growth, yield and stress tolerance, and their effects on plant-associated beneficial microbiota. In addition, we identified limitations to bring microbial CFs to the market as biostimulants. In nature, plants act as metaorganisms, hosting microorganisms that communicate with the plants by exchanging semiochemicals through the phytosphere. Such symbiotic interactions are of high importance not only for plant yield and quality, but also for functioning of the soil microbiota. One environmentally sustainable practice to increasing crop productivity and/or protecting plants from (a)biotic stresses while reducing the excessive and inappropriate application of agrochemicals is based on the use of inoculants of beneficial microorganisms. However, this technology has a number of limitations, including inconsistencies in the field, specific growth requirements and host compatibility. Beneficial microorganisms release diffusible substances that promote plant growth and enhance yield and stress tolerance. Recently, evidence has been provided that this capacity also extends to phytopathogens. Consistently, soil application of microbial cell-free culture filtrates (CFs) has been found to promote growth and enhance the yield of horticultural crops. Recent studies have shown that the response of plants to soil application of microbial CFs is associated with strong proliferation of the resident beneficial soil microbiota. Therefore, the use of microbial CFs to enhance both crop yield and stress tolerance, and to activate beneficial soil microbiota could be a safe, efficient and environmentally friendly approach to minimize shortfalls related to the technology of microbial inoculation. In this review, we compile information on microbial CFs and the main constituents (especially volatile compounds) that promote plant growth, yield and stress tolerance, and their effects on plant-associated beneficial microbiota. In addition, we identify challenges and limitations for their use as biostimulants to bring them to the market and we propose remedial actions and give suggestions for future work.

Microbial Volatile Organic Compounds: An Alternative for Chemical Fertilizers in Sustainable Agriculture Development

Microorganisms are exceptional at producing several volatile substances called microbial volatile organic compounds (mVOCs). The mVOCs allow the microorganism to communicate with other organisms via both inter and intracellular signaling pathways. Recent investigation has revealed that mVOCs are chemically very diverse and play vital roles in plant interactions and microbial communication. The mVOCs can also modify the plant's physiological and hormonal pathways to augment plant growth and production. Moreover, mVOCs have been affirmed for effective alleviation of stresses, and also act as an elicitor of plant immunity. Thus, mVOCs act as an effective alternative to various chemical fertilizers and pesticides. The present review summarizes the recent findings about mVOCs and their roles in inter and intra-kingdoms interactions. Prospects for improving soil fertility, food safety, and security are affirmed for mVOCs application for sustainable agriculture.

In Vivo Low-Temperature Plasma Ionization Mass Spectrometry (LTP-MS) Reveals Regulation of 6-Pentyl-2H-Pyran-2-One (6-PP) as a Physiological Variable during Plant-Fungal Interaction

Volatile organic compounds (VOCs) comprises a broad class of small molecules (up to ~300 g/mol) produced by biological and non-biological sources. VOCs play a vital role in an organism's metabolism during its growth, defense, and reproduction. The well-known 6-pentyl-α-pyrone (6-PP) molecule is an example of a major volatile biosynthesized by Trichoderma atroviride that modulates the expression of PIN auxin-transport proteins in primary roots of Arabidopsis thaliana during their relationship. Their beneficial relation includes lateral root formation, defense induction, and increased plant biomass production. The role of 6-PP has been widely studied due to its relevance in this cross-kingdom relationship. Conventional VOCs measurements are often destructive; samples require further preparation, and the time resolution is low (around hours). Some techniques enable at-line or real-time analyses but are highly selective to defined compounds. Due to these technical constraints, it is difficult to acquire relevant information about the dynamics of VOCs in biological systems. Low-temperature plasma (LTP) ionization allows the analysis of a wide range of VOCs by mass spectrometry (MS). In addition, LTP-MS requires no sample preparation, is solvent-free, and enables the detection of 6-PP faster than conventional analytical methods. Applying static statistical methods such as Principal Component Analysis (PCA) and Discriminant Factorial Analysis (DFA) leads to a loss of information since the biological systems are dynamic. Thus, we applied a time series analysis to find patterns in the signal changes. Our results indicate that the 6-PP signal is constitutively emitted by T. atroviride only; the signal shows high skewness and kurtosis. In A. thaliana grown alone, no signal corresponding to 6-PP is detected above the white noise level. However, during T. atroviride-A. thaliana interaction, the signal performance showed reduced skewness and kurtosis with high autocorrelation. These results suggest that 6-PP is a physiological variable that promotes homeostasis during the plant-fungal relationship. Although the molecular mechanism of this cross-kingdom control is still unknown, our study indicates that 6-PP has to be regulated by A. thaliana during their interaction.

Structures and Biological Activities of Secondary Metabolites from Trichoderma harzianum

The biocontrol fungus Trichoderma harzianum, from both marine and terrestrial environments, has attracted considerable attention. T. harzianum has a tremendous potential to produce a variety of bioactive secondary metabolites (SMs), which are an important source of new herbicides and antibiotics. This review prioritizes the SMs of T. harzianum from 1988 to June 2022, and their relevant biological activities. Marine-derived SMs, especially terpenoids, polyketides, and macrolides compounds, occupy a significant proportion of natural products from T. harzianum, deserving more of our attention.

Assessing the Various Antagonistic Mechanisms of Trichoderma Strains against the Brown Root Rot Pathogen Pyrrhoderma noxium Infecting Heritage Fig Trees

A wide range of phytopathogenic fungi exist causing various plant diseases, which can lead to devastating economic, environmental, and social impacts on a global scale. One such fungus is Pyrrhoderma noxium, causing brown root rot disease in over 200 plant species of a variety of life forms mostly in the tropical and subtropical regions of the globe. The aim of this study was to discover the antagonistic abilities of two Trichoderma strains (#5001 and #5029) found to be closely related to Trichoderma reesei against P. noxium. The mycoparasitic mechanism of these Trichoderma strains against P. noxium involved coiling around the hyphae of the pathogen and producing appressorium like structures. Furthermore, a gene expression study identified an induced expression of the biological control activity associated genes in Trichoderma strains during the interaction with the pathogen. In addition, volatile and diffusible antifungal compounds produced by the Trichoderma strains were also effective in inhibiting the growth of the pathogen. The ability to produce Indole-3-acetic acid (IAA), siderophores and the volatile compounds related to plant growth promotion were also identified as added benefits to the performance of these Trichoderma strains as biological control agents. Overall, these results show promise for the possibility of using the Trichoderma strains as potential biological control agents to protect P. noxium infected trees as well as preventing new infections.

Volatile Organic Compound (VOC) Profiles of Different Trichoderma Species and Their Potential Application

Fungi emit a broad spectrum of volatile organic compounds (VOCs), sometimes producing species-specific volatile profiles. Volatilomes have received over the last decade increasing attention in ecological, environmental and agricultural studies due to their potential to be used in the biocontrol of plant pathogens and pests and as plant growth-promoting factors. In the present study, we characterised and compared the volatilomes from four different Trichoderma species: T. asperellum B6; T. atroviride P1; T. afroharzianum T22; and T. longibrachiatum MK1. VOCs were collected from each strain grown both on PDA and in soil and analysed using proton transfer reaction quadrupole interface time-of-flight mass spectrometry (PTR-Qi-TOF-MS). Analysis of the detected volatiles highlighted a clear separation of the volatilomes of all the four species grown on PDA whereas the volatilomes of the soil-grown fungi could be only partially separated. Moreover, a limited number of species-specific peaks were found and putatively identified. In particular, each of the four Trichoderma species over-emitted somevolatiles involved in resistance induction, promotion of plant seed germination and seedling development and antimicrobial activity, as 2-pentyl-furan, 6PP, acetophenone and p-cymene by T. asperellum B6, T. atroviride P1, T. afroharzianum T22 and T. longibrachiatum MK1, respectively. Their potential role in interspecific interactions from the perspective of biological control is briefly discussed.

Metabolites derived from fungi and bacteria suppress in vitro growth of Gnomoniopsis smithogilvyi, a major threat to the global chestnut industry

INTRODUCTION

Chestnut rot caused by the fungus Gnomoniopsis smithogilvyi is a disease present in the world's major chestnut growing regions. The disease is considered a significant threat to the global production of nuts from the sweet chestnut (Castanea sativa). Conventional fungicides provide some control, but little is known about the potential of biological control agents (BCAs) as alternatives to manage the disease.

OBJECTIVE

Evaluate whether formulated BCAs and their secreted metabolites inhibit the in vitro growth of G. smithogilvyi.

METHODS

The antifungal potential of BCAs was assessed against the pathogen through an inverted plate assay for volatile compounds (VOCs), a diffusion assay for non-volatile compounds (nVOCs) and in dual culture. Methanolic extracts of nVOCs from the solid medium were further evaluated for their effect on conidia germination and were screened through an LC-MS-based approach for antifungal metabolites.

RESULTS

Isolates of Trichoderma spp., derived from the BCAs, significantly suppressed the pathogen through the production of VOCs and nVOCs. The BCA from which Bacillus subtilis was isolated was more effective in growth inhibition through the production of nVOCs. The LC-MS based metabolomics on the nVOCs derived from the BCAs showed the presence of several antifungal compounds.

CONCLUSION

The results show that G. smithogilvyi can be effectively controlled by the BCAs tested and that their use may provide a more ecological alternative for managing chestnut rot. The in vitro analysis should now be expanded to the field to assess the effectiveness of these alternatives for chestnut rot management.