Rice is a staple food for more than half of the world population. It also plays a critical role in economy, particularly in Asia, where it is a primary food source. Enhancing rice growth is important, especially in facing increasing challenges such as climate change, soil degradation, and water scarcity. One emerging method to improve rice plant growth and resilience is application of endophytic fungi and also natural compounds as environmentally safe strategies for producing high quality agricultural products. Endophytic fungi such as Acrophialophora spp. and other beneficial microorganisms can significantly increase plant health and productivity via several modes of action, such as regulating phytohormones, nutrients uptake, stress resistance, biocontrol and plant growth-promoting properties. Synergy between beneficial microbes and natural compounds such as vitamins not only enhance plant growth but also contributes to greater crop resilience and yield stability, leading to a pivotal role in sustainable rice production. Despite the recognized plant growth-promoting properties of endophytic fungi and vitamins, the combined effects of Acrophialophora jodhpurensis and pyridoxine on rice growth and involvement of signaling pathways in their mode of action have not been previously investigated. In this study, jasmonate-deficient (JD) mutant Hebiba was used in all assays together with the wild type rice plants to determine the role of octadecanoid pathway in activation of plant growth factors by A. jodhpurensis and pyridoxine. Application of these treatments alone or in combination significantly increased rice growth factors at P ≤ 0.05 level. Highest increase of fresh and dry weights in both root (78 and 61

Rhizoctonia solani, a necrotrophic fungus with a wide host range, is responsible for various diseases on beans. Precise identification of R. solani is necessary for designing effective disease management strategies. In 2019, bean plants suspected to infection with R. solani were collected from farms in Fars and Razavi Khorasan provinces in Iran. The pathogen was identified as R. solani AG-11 based on morphological and molecular characteristics, and subsequently assessed for its pathogenicity, enzymatic activity, and the correlation between these factors. The isolates displayed different levels of virulence on Yaghoot beans, and Koch’s postulates were verified. Cellulase and pectinase activities were positively correlated with their pathogenicity. This research is the first worldwide report of R. solani AG-11 as a pathogen on bean plants, as well as investigation of its pathogenicity and enzymatic activity.

Diseases caused by various phytopathogens pose major threats to plant production, food security, and agricultural sustainability. Raising concerns about the environmental impact, phytopathogens resistance, and restrictions of synthetic chemicals application increased interest in plant-derived bioactive compounds as safer and sustainable alternatives. Among these natural compounds, flavonoids have emerged as promising metabolites due to their broad-spectrum antimicrobial properties and plant resistance inducers. This review provides an overview of current knowledge on using flavonoids in plant disease management, with particular emphasis on their modes of action and future application perspectives. Antimicrobial and protective effects of flavonoids against plant pathogens are investigated, including their ability to disrupt cell membrane, inhibit spore germination and mycelial growth, interfere with metabolic pathways, suppress virulence factors, modulate quorum sensing, and induce oxidative imbalance in target pathogens. In addition, the roles of flavonoids in enhancing host resistance via inducing plant defense pathways are discussed. Despite their considerable potential, practical use of flavonoids in crop protection remains constrained by issues such as limited stability, variable efficacy in the field conditions, and incomplete understanding of structure–activity relationships. The present review highlights advances in flavonoids application and integrated disease management, which help to overcome these limitations. Finally, research gaps and future directions are outlined for development of flavonoid-based plant protection strategies as effective and environmentally safe tools for sustainable agriculture.

Plants coexist with diverse fungal communities inhabiting both the rhizosphere and endosphere, forming dynamic interactions, which shape plant health and resilience. Recent studies reveal that these two fungal compartments are not functionally isolated but interconnected through complex signaling, metabolite exchange, and cooperative defense responses. Emerging evidence reveals that rhizospheric and endophytic fungi engage in dynamic crosstalk mediated by chemical signals and root exudates in the rhizosphere together with molecular exchanges which are involved in priming plant defense responses and secondary metabolism adjustments. This review synthesizes current knowledge on the mechanisms underlying the effects of rhizosphere dynamics on rhizospheric-endophytic fungal crosstalk and their collective roles in mediating plant tolerance or resistance to biotic and abiotic stresses. Ecological and molecular processes driving fungal recruitment, colonization, and communication, emphasizing their influence on plant immunity priming, hormonal modulation, and antioxidative systems are discussed. Advances in omics technologies have deepened understanding of the rhizosphere-endosphere continuum, revealing integrated networks which shape plant health under environmental constraints. The present review identifiees research gaps and proposes future directions for harnessing beneficial fungal networks in association with rhizosphere as sustainable tools for crop protection under changing climate conditions.

This study was performed to identify Botrytis species pathogenic on strawberry and investigate effect of Ferula gummosa essential oil (EO) against Botrytis spp. The infected plant samples were collected in Khorasan Razavi province from strawberry fruits with gray mold disease symptoms. Following purification of the fungi, of the 54 isolates, 53 isolates were identified as B. cinerea and 1 isolate belonged to B. pelargonii based on morphological and molecular (ITS and RPB2 sequences) identification. The EO obtained from F. gummosa at 125, 250, 500, 750 and 1000 μg mL-1 concentrations showed significant antifungal effect on mycelial growth of B. cinerea and B. pelargonii in a dose dependent manner. Also, the EO at all concentrations tested strongly inhibited spore germination of B. cinerea and B. pelargonii. Treatment with the EO at EC50 concentration significantly reduced the sclerotia production of B. cinerea and B. pelargonii. Light and electron microscopy observations showed that F. gummosa EO at EC50 concentration caused morphological changes in the fungal structures. This EO reduced the activity of cell wall degrading enzymes, such as cellulase and pectinase produced by both fungal species. A total of 22 compounds were identified in the EO by gas chromatography-mass spectrometry. The major compounds of F. gummosa EO were β-Pinene (% 37.7), γ-Terpinene (% 21) and a-pinene (% 12). Moreover, the F. gummosa EO at 500, 750 and 1000 μg mL-1 concentrations considerably reduced the disease severity and infection of strawberry fruits by B. cinerea and B. pelargonii. According to the results of this study, inhibitory effect of F. gummosa EO was impressive in controlling strawberry postharvest gray mold disease. This is the first report on inhibitory ability of F. gummosa EO against strawberry postharvest gray mold disease, which can be suggested as a preserver coating for the fruits to extend their shelf life during storage period.

Plants adjust their physiology, biology and phenotype to survive in various environmental situations and organize their responses to unfavorable conditions. Phenotypic and physiologic flexibility of various plant species may be mediated by numerous microorganisms, including endophytic fungi. These beneficial fungi are capable of increasing plant growth via either enhancing plant immunity to biotic and abiotic environmental stimuli, or by producing growth-stimulating factors such as phytohormones. Phytohormones have vital roles in plant resistance mechanisms and can be considered as growth regulators via their prominent effect on plant metabolism. Exogenous use of various hormones can increase plant growth factors and decrease harmful effects of environmental stresses. Recent investigations revealed that phytohormones production or regulation by beneficial fungi could be critical metabolic engineering targets for activating plant resistance to environmental stimuli. Signaling pathways involved in phytohormones biosynthesis and mechanisms related to this process have been identified using numerous biochemical and molecular approaches. This review is focused on production and regulation of some phytohormones by endophytic fungi and current knowledge on the vital role of these small biological molecules in increasing immunity responses in plants exposed to environmental cues. Therefore, the present review can be useful for plant pathologists, physiologists and environmental microbiologists for designing novel and effective strategies to develop broad-spectrum microbial inoculants supporting plant growth and organic crop production under unfavorable conditions. Focus on exploring cytomolecular and biochemical mechanisms involved in the effect of fungi and other beneficial microbes on producing or regulating phytohormone levels in plant tissues seems to be interesting subjects for future research.

Dichloromethane extract (DCM) of Scutellaria luteocaerulea root has inhibitory effect against Fusarium culmorum and Fusarium pseudograminearum. This DCM fraction caused cell membrane damage in the hyphal cells of Fusarium spp. and decreased fungal biomass. The fraction induced apoptosis in hyphal cells of both pathogens via increasing accumulation of hydrogen peroxide (H2O2), hydroxyl radicals (.OH), and nitrogen dioxide (NO2). The DCM fraction reduced antioxidant activity in both pathogens. Application of the DCM fraction via seed treatment and wheat head spraying reduced the disease severity, deoxynivalenol (DON) accumulation, and expression of the tri5 gene in both fungi causing Fusarium head blight (FHB). The High Performance Liquid Chromatography (HPLC) method was used to separate microfractions of the DCM fraction, and thirty microfractions were obtained. Similar microfractions were combined using thin-layer chromatography (TLC) and 8 microfractions were created. These microfractions were assessed for antifungal activity at 100 μg mL−1 concentration in vitro. Among them, F5 microfraction showed the best antifungal effect against both pathogens. Also, an analytical method based on the liquid chromatography-mass spectrometry (LC-MS) analysis was used to identify secondary metabolites of the F5 microfraction. Therefore, the DCM fraction of S. luteocaerulea might be used for plant protection against FHB disease.

Dichlomethane (DCM) extract from the roots of Scutellaria luteocaerulea (skullcap) showed in vitro antifungal activity against Fusarium pseudograminearum and Fusarium culmorum, with IC50 values of 550 and 450 μg mL-1, respectively. Additionally, the effects of S. luteocaerulea on hyphal structures of the pathogens, spore germination, and mycelial growth were studied. According to the data obtained, the extract of S. luteocaerulea inhibited spore germination and mycelial growth of both pathogens tested. Additionally, the pathogens hyphae and spores were deformed when treated with the extract of S. luteocaerulea. Induced apoptotic characteristics were detected in both pathogens via the addition of the DCM fraction of S. luteocaerulea into the culture. The DCM fraction of S. luteocaerulea induced the production of reactive oxygen species (ROS) in both pathogens, as a characteristic of apoptosis. Activities of cell wall degrading enzymes (CWDEs) and production of deoxynivalenol (DON) were reduced. Also, the effect of the DCM fraction of S. luteocaerulea was investigated on the severity of Fusarium crown rot (FCR) and Fusarium head blight (FHB) diseases caused by both fungi on bread wheat. Plants treated with the DCM fraction of S. luteocaerulea showed an increased 1000-grain weight and decreased disease progress in greenhouse conditions. High performance liquid chromatography (HPLC) analysis revealed that the fraction had high concentration of wogonin. Therefore, the DCM fraction obtained from S. luteocaerulea could potentially be used in the future to protect wheat plants against F. pseudograminearum and F. culmorum.

The growing global food demand necessitates sustainable agricultural practices that minimize environmental impact while ensuring high yields. Synthetic pesticides, while crucial for crop protection, raise concerns about environmental contamination, resistance development, and harm to non-target organisms. Carbonates and bicarbonates (e.g., NaHCO3, KHCO3, CaCO3) offer a promising, Generally Recognized as Safe (GRAS) alternative for integrated pest and disease management and abiotic stress mitigation. These compounds exhibit broad-spectrum efficacy against diverse fungal, oomycete, bacterial, and insect pathogens, including the clubroot protist (Plasmodiophora brassicae). Their direct antimicrobial mechanisms involve disrupting pathogen cell membranes and walls, inducing osmotic stress, and altering pH, which leads to pathogen death. Beyond direct toxicity, carbonates and bicarbonates also elicit plant defenses, inducing systemic acquired resistance (SAR) and stimulating defense enzymes (e.g., peroxidase, polyphenol oxidase). Furthermore, they enhance soil health by raising pH, improving nutrient availability, structure, and water retention, while reducing heavy metal bioavailability. These soil improvements increase plant resilience to drought, salinity, and metal toxicity, with potential benefits also arising from improved stomatal regulation. Recent advancements have introduced carbonate nanoparticles as nano-fungicides and biostimulants, offering enhanced efficacy at lower application rates. Integrating carbonates/bicarbonates into Integrated pest management (IPM) programs, especially in combination with biocontrol agents and other beneficial salts, demonstrates synergistic effects and reduces reliance on conventional pesticides. However, further research is needed to elucidate detailed molecular mechanisms, assess long-term soil impacts, optimize application methods (e.g., foliar sprays, soil amendments, nanoformulations), and evaluate compatibility with other agrochemicals. Addressing these knowledge gaps will enable the full potential of these sustainable compounds for resilient and food-secure agriculture.

In the context of global challenges such as climate change, soil degradation, and food security, understanding the modes of action of Plant Growth-Promoting Microorganisms (PGPMs), their formulation, and their application is crucial and can be more focused in future research projects. This editorial paper aims to elucidate diverse modes of action employed by different types of PGPMs, including nitrogen fixation, phosphorus solubilization, production or regulation of phytohormones, and plant protection against environmental and biotic stresses as demonstrated and discussed in the Special Issue entitled "Plant Growth-Promoting Microorganisms: new insights and the way forward".

Grapes have high economic importance and are recognized as one of the key plant species cultivated across the globe, including Iran. However, this plant is sensitive to a wide range of pathogens. Bunch rot disease, caused by Alternaria spp. stands out as one of the most critical and damaging grape diseases, worldwide. This disease has significant economic losses for producers, every year. In addition, the toxic metabolites produced by this fungus pose a serious threat to fruit yield, marketability, human and animal health. However, identification of Alternaria species causing the bunch rot disease has not been done in Iran, and no grape cultivars with complete resistance to this destructive disease have been identified, so far. Thus, identifying virulence factors of the pathogens, analyzing the resistance levels in grapevines, and examining the plant's defense responses to the disease are essential steps in creating novel and effective strategies for disease management. Therefore, the objectives of this study were to identify Alternaria species responsible for bunch rot disease, to assess pathogenicity levels and various virulence factors associated with the fungal pathogens, and to determine resistance level of various grape cultivars against Alternaria spp. obtained from this plant in Iran. The samples were collected from grape berries exhibiting typical symptoms of the disease from vineyards in Khorasan-Razavi province of Iran. Morphological identification of the fungi was performed on potato carrot agar (PCA) medium. Three species of Alternaria were identified, including A. alternata, A. tenuissima, and A. destruens. For molecular identification, the ITS1 and ITS4 primers were utilized, followed by sequence analysis. Alternaria alternata was found to be the most prevalent species, while A. destruens was the least frequently obtained species. Three grape cultivars were examined to investigate pathogenicity of the fungal isolates and evaluate resistance levels of the host cultivars. Among the cultivars tested, Sahebi exhibited the highest resistance, while Fakhri was the most susceptible cultivar. The research revealed different degrees of virulence and aggressiveness among the fungal isolates. Isolates of A. alternata and A. destruens showed the highest pathogenicity levels. Analysis of cell wall degrading enzymes revealed that the isolates with higher pathogenicity had higher enzyme activity. This study is the first report of Alternaria spp. responsible for bunch rot disease in Iran. Also, this is the first global report of A. destruens pathogenic on grapes and exploration of the relationship between pathogenicity factors and pathogenesis of Alternaria spp. affecting grapes.

Strawberry (Fragaria x ananassa) is one of the most important fruit crops, worldwide. In June 2023, strawberry fruits with pink mould symptoms were collected from a storage facility in Khorasan Razavi province of Iran. Trichothecium roseum was isolated from symptomatic fruit and identified through morphological characteristics. Molecular identification was carried out based on the internal transcribed spacer (ITS) region of ribosomal DNA (rDNA) using ITS1 and ITS4 primers. Pathogenicity was confirmed according to Koch's postulates. Cell wall-degrading enzyme secretion was investigated as a potential factor in fungal pathogenicity. The results of morphological identification, ITS analysis and pathogenicity test indicated that the causal agent was T. roseum. Enzyme activity assays revealed that T. roseum obtained from strawberry with a high level of aggressiveness was able to secrete cellulase and pectinase. To our knowledge, this is the first report of post-harvest pink mould of strawberry caused by T. roseum in Iran.

The genus Acrophialophora is a thermotolerant fungus, which is widely distributed in temperate and tropical zones. This fungus is classified in Ascomycota and belongs to the Chaetomiaceae family and the genera of Parathielavia, Pseudothielavia and Hyalosphaerella are closely related to Acrophialophora. For this genus have been reported 28 species so far, which two species of Acrophialophora jodhpurensis and Acrophialophora teleoafricana produce only sexual phase and other species produce asexual form. Therefore, producing both sexual and asexual forms were not reported by any species. Many applications were reported by some species in agriculture, pharmacy and industry. Production of enzymes, antimicrobial metabolites and plant growth-promoting factors were reported by some species. The species of A. nainiana is used in the industries of textile, fruit juice, pulp and paper due to extracellular enzyme production. Also, other species produce extracellular enzymes that can be used in various industries. The species Acrophialophora are used in the composting industry due to the production of various enzymes and to be thermotolerant. In addition, some species were isolated from hostile environmental conditions. Therefore has been suggested that it can be used for mycoremediation. Also, antimicrobial metabolites of Acrophialophora have been reported to be effective against human and plant pathogens. In contrast to the beneficial effects described, the Acrophialophora pathogenicity has been rarely reported. Two species A. fusispora and A. levis are opportunistic fungi and have been reported as pathogens in humans, animals and plants. Currently, the development and applications of Acrophialophora species have increased more than past. To our knowledge, there is no report with comprehensive information on the species of Acrophialophora, which include their disadvantage and beneficial effects, particularly in agriculture. Therefore, it seems necessary to pay more in-depth attention to the application of this genus as a beneficial fungus in agriculture, pharmaceutical and industry. This review is focused on the history, phylogeny, morphology, valuable roles of Acrophialophora and pathogenicity.

Tomato (Solanum lycopersicum L.) holds significant importance as a primary vegetable crop globally. In this research, the extracellular green-synthesis of silver nanoparticles was accomplished by using some Gram positive bacteria. Three isolates including KM59, SM88, and KM93 exhibited the highest nanoparticle biosynthesis activity. The isolates were identified according to colony morphology and the 16S rRNA gene sequence identities, as Streptomyces spp. The obtained AgNPs were characterized by TEM and exhibited various shapes, including hexagonal, pentagonal, spherical, and triangular. The MIC for Ralstonia solanacearum was determined to be 25, 6.25, and 25 µg/mL for the AgNPs93, AgNPs88, and AgNPs59, respectively. The MIC of AgNPs93, AgNPs88, and AgNPs59 against Xanthomonas campestris was assessed at concentrations of 25, 12.5, and 50 µg/mL, respectively. In the case of Alternaia alternata, the MIC for AgNPs93 and AgNPs59 was found to be 50 µg/mL, while for AgNPs88, it was 25 µg/mL. Furthermore, the MIC of AgNPs88 against Rhizoctonia solani was determined to be 12.5 µg/mL, whereas for AgNPs93, it was 25 µg/mL, and for AgNPs59, it was 50 µg/mL. Disease index was reduced (AgNPs88 demonstrated the most potent inhibitory effect, whereas AgNPs59 displayed the least inhibitory effect) when tomato plants inoculated with fungal and bacterial pathogens treated with the AgNPs at MIC concentrations. The cytotoxicity of AgNPs on the B16F10 cancer cell lines determined by the means of MTT assay. Biosynthesis of AgNPs using Actinobacteria is an eco-friendly process. In agriculture, medical sciences, and industry, process optimization can become a valuable technology for mass production.

Isolates of Rhizoctonia solani (AG-3 PT, AG-4 HG-I, AG-4 HG-II) and one binucleate Rhizoctonia sp. (BNR) belonging to AG-Bb were investigated for pathogenicity on tomato cultivar Mobil. The BNR isolate revealed the lowest virulence and it was used as biocontrol agent against R. solani AG-4 HG-II, which showed the highest virulence on tomato. Inoculation of tomato plants with the hypovirulent BNR isolate reduced the disease symptoms of R. solani and induced resistance. Resistance induction was observed not only on the plants simultaneously inoculated with BNR and R. solani, but also when the plants were inoculated by the BNR and R. solani with time intervals. The peroxidase (POX), superoxide dismutase (SOD) and catalase (CAT) activities and expression levels of the corresponding genes in tomato plants increased after R. solani or BNR inoculation. The highest level of antioxidant activities and expression of their genes, lignin and callose formation were observed in the plants inoculated with the BNR and R. solani, simultaneously. The BNR inoculation reduced H2O2 accumulation. The highest level of priming was observed for the POX among other antioxidants tested via application of the BNR. Treatment with potassium cyanide (as a POX inhibitor) reduced basal resistance and BNR-induced resistance (BNR-IR) via reduction of lignification and callose deposition in tomato plants. These findings demonstrated the role of antioxidant enzymes, mainly the POX, in both basal resistance and BNR-IR. Therefore, redox state and antioxidants are involved in cell wall strengthening via lignin and callose formation, as important defense components which decrease the pathogen progress in plant tissues.

Members of the genus Fusarium are considered highly destructive pathogens of common beans (Phaseolus vulgaris). This study aimed to identify the causal agent of the disease, confirm its pathogenicity following Koch’s postulates, and investigate the extracellular enzymes of F. solani. After conducting a field survey on common bean plants in Khorasan Razavi Province in August and September of 2021 and 2022 and isolating fungi, the isolates were identified as F. solani f. sp. phaseoli based on morphological traits and molecular analysis of the internal transcribed spacer region. Pathogenicity tests revealed the isolates causing symptoms such as yellowing, rotting, and wilting on common bean seedlings (cv. Derakhshan). Moreover, extracellular destructive enzymes, including pectinase and cellulase, were quantitatively assessed. The isolates exhibited cellulase activity more quickly and at higher levels than pectinase. Our findings indicated that the enzymes are key in inducing disease symptoms in the host plant.

Aim To investigate antifungal activity of the extract and major metabolite of the endophytic fungus Acrophialophora jodhpurensis (belonging to Chaetomiaceae) against crown and root rot caused by Rhizoctonia solani (teleomorph: Thanatephorus cucumeris), as an important pathogen of tomato.Methods and Results The endophytic fungus A. jodhpurensis, has high inhibitory effect against R. solani AG4-HG II in vitro and in vivo. The media conditions were optimized for production of the endophyte's metabolites. The highest amounts of secondary metabolites were produced at pH 7, 30 degrees C temperature, and in the presence of 0.5% glucose, 0.033% sodium nitrate, and 1 gl-1 asparagine as the best carbon, nitrogen, and amino acid sources, respectively. The mycelia were extracted by methanol and the obtained extract was submitted to various chromatography techniques. Phytochemical analysis via thin-layer chromatography (TLC) and nuclear magnetic resonance (NMR) spectroscopy showed that ergosterol peroxide was the major component in the extract of this endophyte. Antifungal activities of the methanolic extract and ergosterol peroxide in the culture media were studied against R. solani. Minimum inhibitory concentrations of the extract and ergosterol peroxide against the pathogen were 600 and 150 mu g ml-1, respectively. Ergosterol peroxide revealed destructive effects on the pathogen structures in microscopic analyses and induced sclerotia production. Histochemical analyses revealed that it induced apoptosis in the mycelia of R. solani via superoxide production and cell death. Application of ergosterol peroxide in the leaf disc assay reduced the disease severity in tomato leaves.Conclusions Antifungal metabolites produced by A. jodhpurensis, such as ergosterol peroxide, are capable of controlling destructive Rhizoctonia diseases on tomato.

Chemical fungicides are commonly used to manage fungal plant diseases, which can cause toxicity in nontarget organisms, environmental pollution, resistance development in pathogen populations, and concerns for human health. As a result, biocontrol can be considered an effective and environmentally benign approach to controlling various phytopathogens. As a result, using beneficial yeasts may provide plant defense against diseases. Furthermore, several yeast-based products are used to protect various plant species, particularly fruits, from postharvest fungal degradation as well as to increase the shelf life of other food goods. These successful applications suggest that numerous yeasts can be used as novel and effective alternatives to hazardous chemical fungicides in the pre- and postharvest management of plant diseases. Due to their antagonistic abilities, undemanding cultivation requirements, and biosafety concerns, many of these unicellular fungi have been considered for biocontrol applications. The biological control mechanisms employed by yeasts against phytopathogens are mainly unknown so far, and there are plenty of prospects for the progress of commercial yeast-based products that can be used in protecting various plant species. These are interesting topics for future trends. Furthermore, yeast application is environmentally safe, and the eco-friendliness of these fungal microorganisms leads to their suitability for practical uses in the fields, with no major ecological concerns when compared to today's more aggressive disease management strategies, such as the use of synthetic agrochemicals. Here, we review fundamental research on characterization, beneficial effects, and direct and indirect modes of action of yeast against fungal pathogens. Furthermore, the potential of yeasts for commercial biocontrol usage and the scarcity of detailed studies on the biocontrol mechanisms of various yeast species and registered yeast-based biocontrol products, including green nanoparticles, are discussed in this chapter.