Endophytic fungi (EF) have emerged as promising modulators of plant growth and stress tolerance in agricultural ecosystems. This review synthesizes current knowledge on the role of EF in en-hancing crop adaptation to abiotic stress. Abiotic stresses, such as drought, salinity, and extreme temperatures, pose significant challenges to crop productivity worldwide. EF have shown re-markable potential in alleviating the adverse effects of these stresses. Through various mechanisms including synthesis of osmolytes, production of stress-related enzymes, and induction of plant de-fense mechanisms, EF enhance plant resilience to abiotic stressors. Moreover, EF promote nutrient uptake and modulate hormonal balance in plants, further enhancing stress tolerance. Recent ad-vancements in molecular techniques have facilitated the identification and characterization of stress-tolerant endophytic fungal strains, paving the way for their utilization in agricultural prac-tices. Furthermore, the symbiotic relationship between EF and plants offers ecological benefits, such as improved soil health and reduced dependence on chemical inputs. However, challenges remain in understanding the complex interactions between EF and host plants, as well as in scaling up their application in diverse agricultural systems. Future research should focus on elucidating the mechanisms underlying endophytic fungal-mediated stress tolerance and developing sustainable strategies for harnessing their potential in crop production.

In tobacco plants, symbiont endophytic fungi are widely distributed in all tissues where they play important roles. It is therefore important to determine the species distribution and characteristics of endophytic fungi in tobacco. Here, two parasitic fungi Leptosphaerulina chartarum and Curvularia trifolii were isolated and identified from normal tobacco tissue. We sequenced the mitogenomes of these two species and analysed their features, gene content, and evolutionary histories. The L. chartarum and C. trifolii mitochondrial genomes were 68,926 bp and 59,100 bp long circular molecules with average GC contents of 28.60% and 29.31%, respectively. The L. chartarum mitogenome contained 36 protein coding genes, 26 tRNA genes, and 2 rRNA genes (rrnL and rrnS), which were located on both strands. The C. trifolii mitogenome contained 26 protein coding genes, 29 tRNA genes, and 2 rRNA genes (rrnL and rrnS). The L. chartarum 26 tRNAs ranged from 70 bp to 84 bp in length, whereas the 29 tRNAs in C. trifolii ranged from 71 bp to 85 bp. L. chartarum and C. trifolii mtDNAs had an identical mitochondrial gene order and orientation and were phylogenetically identified as sisters. These data therefore provide an understanding of the gene content and evolutionary history of species within Pleosporales.

Bacterial endophytes interact closely with plant tissues and constitute an essential part of the plant microbiome. These interactions can promote plant growth and elicit specific defense responses against abiotic stresses and pathogen attacks. In this paper, we review the role of endophytic bacteria in modulating defenses of the host rendering the entire plant more resistant to pathogens and pests. The endophyte-induced resistance will probably introduce a new factor when consid-ering plant-pathogen interactions. The impact of the bacterial endosymbionts on the host leading to the priming state is also discussed since it confers a specific adaptation of the plant to the biotic threat.

Endophytic microbes are a ubiquitous group of plant-associated communities that colonize the intercellular or intracellular host tissues while giving numerous beneficial effects to the plants. All the plant species are thought to be associated with endophytes, majorly constituted with bacteria and fungi. During the last two decades, there has been a considerable movement toward the study of endophytes associated with coffee plants. In this review, the main consideration is given to address the coffee-associated endophytic bacteria and fungi, particularly their action on plant growth promotion and the biocontrol of pests. In addition, we sought to identify and analyze the gaps in available research. Additionally, the potential of endophytes to improve the quality of coffee seeds is briefly discussed. Even though there are limited studies on the subject, it has been well recognized the potentiality of coffee endophytes in plant growth promotion through enhancing nitrogen fixation, availability of minerals, nutrient absorption, secretion of phytohormones, and other bioactive metabolites. Further, the antagonistic effect against various coffee pathogenic bacteria, fungi, nematodes, and also insect pests lead to the protection of the crop. Furthermore, it is recognized that endophytes enhance the sensory characteristics of coffee as a new field of study.

As a part of our ongoing research on endophytic fungi, we have isolated a sesterterpene mycotoxin, fusaproliferin (FUS), from Fusarium solani strain associated with the plant Aglaonema hookerianum Schott. FUS showed rapid and sub-micromolar IC₅₀ against pancreatic cancer cell lines. Time dependent survival analysis and microscopy imaging showed rapid morphological changes in cancer cell lines 4 hours after incubation with FUS. This provides a new chemical scaffold that can be further developed to obtain more potent synthetic agents against pancreatic cancer.

Endophytes are ubiquitous organisms that reside within plant organs and contribute to the growth and well-being of plants. Nevertheless, there is limited knowledge regarding the plant growth-promoting endophytes found in medicinal plants. Therefore, the aims of the present work were to isolate some endophytic bacteria associated with roots, stems, leaves and inflorescences of Aerva javanica, collected from the Shada Alasfal Mountain at Albaha region, Saudi Arabia. After that, they were screened for some of their direct and indirect plant growth-promoting mechanisms. Finally, based upon their internal transcribed spacer 16S rRNA gene sequencing, the isolates were identified. The results showed that the selected endophytes differentially produced IAA and ammonia, and solubilized phosphate as direct mechanisms. In addition, they had exhibited variable capacities to produce some lytic enzymes and HCN beside their antifungal activities. Furthermore, they showed abilities to tolerate some stress conditions. The bacterial endophytes were identified by molecular methods and belonged to the genera of Micrococcus, Enterobacter, Pseudomonas, Delftia and Bacillus. The findings of this study indicated that the bacterial endophytes isolated from Aerva javanica are possessing crucial functions to improve plant growth and could be utilized as biofertilizers or bioagents to establish a sustainable crop production system.

Almost fifty years after the introduction of antibiotics as an antimicrobial agent, we are facing an increasing number of multi-resistant microbials. The search for new antimicrobial compounds emerged as a promising alternative to treatments for diseases caused by microorganisms such as fungi and bacteria. Thus, endophytic fungi are gaining recognition for their varied metabolites that may possess antimicrobial properties. In our research, we isolated, from Calea pinnatifida, six endophytic fungi identified as Colletotrichum siamense, Colletotrichum karstii, Hypomontagnella barbarensis, Neopestalotiopsis clavispora, Nigrospora sacchari-officinarum and Annulohypoxylon moriforme. Analyses of microbial secondary metabolites by utilizing UHPLC-HR-ESI-MS/MS in conjunction with molecular networking, allowed the annotation of 9 compounds, 5 of them from GNPS spectral library match, and 4 from prediction-based on the molecular network, and allowed the isolation of two pairs of Acyl-tetronic acid derivatives distereoisomeric identified by NMR spectrum. In this sense, the present study underlines the value of endophytic fungi as a reservoir of potentially new antimicrobial agents.

The climate and its changes are major risk factors for agricultural activities because agricultural systems are highly affected by climatic factors such as temperature, rain, humidity, wind, and solar radiation. While some agricultural areas of the world are irrigated, the vast majority rely on natural rainfall patterns. Farmers will consume more water as a result of climate change and experience less water availability, resulting in a decrease in production capacity. As one of the most important natural phenomena affecting agricultural productivity, drought is a limiting environment for plant growth. The response of plants to water stress is complex and involves coordination between gene expression and its integration with hormones. It has been shown that bacteria have mechanisms to reduce water stress in these plant species and promote greater growth. The underlined mechanism involves root-to-shoot phenotypic changes in growth rate, architecture, hydraulic conductivity, water conservation, plant cell protection, and damage restoration through integrating phytohormones modulation, stress-induced enzymatic apparatus, and metabolites. This review demonstrates how plant growth-promoting bacteria can mitigate negative effects associated with water stress in plants and provide examples of technology conversion in agroecosystems.

The genus Beauveria include important entomopathogenic and endophytic fungi, among them, Beauveria bassiana is the most studied species. However, there are few knowledge regarding their antimicrobial activity. The current research has been conducted to evaluate in vitro antagonistic activity of B. bassiana and the antimicrobial efficacy of its Exo and Endo metabolites against Bacillus cereus, B. megaterium, Clavibacter michiganensis (gram positive bacteria, G+ve), Xanthomonas campestris, Pseudomonas aeruginosa and P. fluorescence (gram negative bacteria, G-ve). In addition, Solid-phase microextraction (SPME) was coupled to Gas Chromatography-Mass Spectrometry (GC/MS) to qualitatively measure the volatile organic compounds (VOCs) metabolic profile of the most efficient studied isolate of B. bassiana. The obtained results showed that, the isolate UniB2439-3 has promising antibacterial effect against most of studied target bacteria. SPME-GC/MS analysis of VOCs revealed the presence of ethanol; butanal,2-methyl; 2,4-dimethyl-1-heptene; octane, 4-methyl and β-elemene as the main dominant bioactive compounds. The outgoing results explicated that the efficient isolate of B. bassiana can be potentially used as a biocontrol agent against several bacteria especially G+ve ones.

The genus Beauveria include important entomopathogenic and endophytic fungi, among them, B. bassiana is the most studied species. However, there are few knowledge regarding their antimicrobial activity. The current research has been conducted to evaluate in vitro antibacterial efficacy of five isolates of B. bassiana against Bacillus cereus, B. megaterium, B. mojavensis, Clavibacter michiganensis (gram positive bacteria, G+ve), Xanthomonas campestris, X. vesicatoria, Escherichia coli, Pseudomonas aeruginosa and P. fluorescence (gram negative bacteria, G-ve). In addition, chemical composition of the principal diffusible metabolites and volatile organic compounds (VOCs) of the most efficient studied isolate of B. bassiana has been carried out using GC-MS analysis. The obtained results showed that, the isolate UniB2439-3 has promising antibacterial effect against most of studied target bacteria. GC-MS analysis of diffusible metabolites detected the presence of hexanedioic acid, bis(2-ethylhexyl) ester as the main compound in the cell-free culture filtrate. Furthermore, GC-MS analysis of VOCs revealed the presence of ethanol; butanal,2-methyl; 2,4-dimethyl-1-heptene; octane, 4-methyl and β-elemene as the main dominant bioactive compounds. The outgoing results explicated that, the isolates of B. bassiana have promising antibacterial activity which could be correlated to their diffusible and VOCs metabolites. Therefore, the selected isolate can be potentially used as a biocontrol agent against several bacteria especially G+ve ones. Taking in consideration that the antibiotics are forbidden in agriculture in many countries worldwide, search for possible natural alternatives as efficient antimicrobial agents are highly interesting.

Plant endophytic fungi and rhizosphere soil fungi are often reported as biocontrol agents against plant pathogens or with plant growth promotion potential. Four treatments were performed in field and greenhouse experiments where cucumber plants were inoculated with Trichoderma harzianum and Fusarium oxysporum in 2022. The roots, stems and leaves of cucumber plants and their rhizosphere soil were collected twice individually from the field and greenhouse for isolation of cucumber endophytic and rhizosphere soil fungi. All 74 genera and 1275 fungal strains were sequenced by rDNA ITS. The PDA media yielded the highest number of genera isolated from cucumber plants, rhizosphere soil and both compared to other media. There were no significant differences among the 4 media for the isolation of cucumber endophytic fungi. The best media for isolating fungi from roots and stems were MRBA and PDA, respectively. PDA and CZA had higher isolation efficiency for the rhizosphere soil fungi than MRBA. The 28 fungal genera had high isolation efficiency, and the endophytic Trichoderma strains were best isolated by MEA. It is suggested that PDA can be used as a basic medium, and different media can be considered for specific fungal genera.

It was of great practical significance to repair the toxicity of salt stress environment to soybean seedlings and maintain the balance between agricultural production and ecological environment in the Yellow River valley of China. ‘Xudou 20’ was used as the experimental material, a large-scale planting variety in the old Yellow River basin. Endophytes 131 and 137 isolated from soybean root nodule were taken as the research objects, and the soybean plants were cultivated by pot culture in intelligent artificial incubator. Salt stress group, bacteria suspension group and control group were set up to study the effects of inoculation treatments on the activities of superoxide dismutase (SOD) and catalase (CAT) of soybean seedlings under different NaCl stress. The results showed that when inoculated with endophyte 131 bacterial suspension and cultured for 14 days, the SOD activity was the highest (14.89 U•g−1•FW) at the salt concentration 50 mmol•L-1. When inoculated with 131 bacterial suspension (2:1) and cultured for 28 days, the SOD activity reached the highest (0.94 ug-1FW) at the salt concentration of 50 mmol•L-1, and the CAT activity amounted to the highest (1910 U•g−1•min−1). The 16S rDNA sequencing and phylogenetic analysis showed that the most similar strain of strain 137 was Bacillus cereus, and the most similar strain of strain 131 was Enterobacter ludwigii. Therefore, the activities of SOD and CAT in soybean seedlings inoculated with endophytes 131 and 137 increased at different degrees under salt stress, which could effectively alleviate the damage of salt stress environment to plants, and thus improve the stress resistance of plants.

Members of the Fusarium oxysporum species complex (FOSC) has the capacity to specialize into host-specific pathogens known as formae speciales through horizontal gene transfer between pathogenic and endophytic individuals. To this day, the origin of these formae speciales and the genetic determinants dictating the switch from endophytic to pathogenic Fusarium oxysporum (Fox) are still unknown. F. oxysporum f. sp. vanillae (Fov), member of FOSC, is the causal agent of root and stem rot disease, representing the main phytosanitary problem in vanilla plantations worldwide. Here we analyzed the RNA-seq libraries resulting from the interaction vanilla-Fov at early and late stages of the infection, and what we initially identified as control in a previous study, detecting the presence of Fox endophytes. We identified virulence, hypervirulence, sporulation, conidiation, necrosis, and production of fusaric acid as key processes taking place during Fov-vanilla interaction. Through comparison with endophytic Fox, we found that Fov can infect vanilla thanks to the presence of pathogenicity islands and genomic regions associated with supernumerary chromosomes. These play a central role as carriers of genes involved with pathogenic activity and could have being obtained by Fov through horizontal gene transfer. We also found that, unlike other pathogenic members of FOSC, Fov do not use Secreted in Xylem proteins (SIX) to infect vanilla.

Cadmium (Cd) is a heavy metal that suppresses plant growth; however, application of endophytic bacteria can increase resistance of plants against Cd, as well as improve plant growth. Two bacterial endophytic strains were isolated from Solanum nigrum and were identified as Serratia sp. AI001 and Enterobacter sp. AI002 by 16S DNA sequencing. Strains AI001 and AI002, tolerated up to 25 mg/mL Cd in broth culture and showed phosphate solubilization potential in Pikovskaya agar medium. AI001 and AI002 produced indole-3-acetic acid, which was confirmed by gas spectrometry-mass chromatography. Brassica plants stressed with 0, 5, 15, and 25 mg/L Cd showed significant decrease in plant growth, chlorophyll content and biomass, and significant increase in Cd dose-dependent electrolyte leakage. Inoculation of strain AI001 or AI002 significantly enhanced the plant growth attributes of shoot length, root length, chlorophyll content, and biomass as compared to those in uninoculated plants. Reduced glutathione contents in plants stressed with different concentrations of Cd also increased with inoculation of AI001 and AI002. The reason of Cd resistance enhancement in plants by inocula could be due to their greater plant growth promoting activities as well as their antioxidative response.

Abstract: Thermophilic fungi constitute an interesting study model for understanding ecologi-cal mechanisms of adaptation in diverse environments and have attractive toolboxes with a wide range of biotechnological applications. This work describes for the first time an endophytic and thermophilic strain of Aspergillus brasiliensis that was isolated in the crater of the active volcano "El Chichonal" in Mexico. The average temperature of the collection site was around 60 °C and the soil pH was moderately acidic. The complete genome of A. brasiliensis E_15.1 was sequenced and assembled in about 37 Mb of genomic DNA. We performed a comprehensive phylogenomic anal-ysis for the precise taxonomic identification of this species as a novel strain of Aspergillus brasil-iensis. Likewise, the predicted coding sequences were classified according to various functions including Carbohydrate-Active Enzymes (CAZymes), biosynthetic gene clusters of secondary metabolites (BGCs), and metabolic pathways associated with plant growth promotion. Among the functional traits identified was the degradation of chitin, chitooligosaccharides, xylan, and cellulose, as well as the biosynthesis of clavaric acid, a triterpene with antitumor activity due to its ability to inhibit Farnesyl-protein transferase. In addition to the genomic analysis, a set of en-zymatic assays confirmed the thermostability of extracellular xylanases, cellulases of A. brasili-ensis E_15.1. Our findings suggest that the enzymatic repertoire of A. brasiliensis E_15.1 has a high potential for industrial application due to its thermostability and can promote plant growth at high temperatures. Finally, this strain constitutes an interesting source of terpenoids with pharmacological activity.

Soil improvement methods can result in changes in the microbial community in blueberry soil. However, there have been few reports on the impacts of different soil improvement methods on the microbial function, particularly on endophytic microbe. In this study, we analyzed the response of microbial community composition, microbial function and nitrogen (N) cycle to different improvement methods using high throughput sequencing. We aimed to investigate the best soil improvement method from a microbial perspective. The results showed that the highest microbial diversity was observed in the T4 treatment (peat combined with mushroom bran), followed by the T2 treatment (peat combined with acidified rice husk) both in the rhizosphere and roots. The dominant phyla were Proteobacteria and Actinobacteria, which were most abundance in the T4 and T1 (peat combined with sulfur) treatments in the rhizosphere soil, respectively, but showed the opposite trend in the root endophytic bacterial community. Interestingly, Acidobacterium and Paludibaculum, belonging to the Acidobacteria phylum, were found to have the highest influence according to the correlation network analysis. And these bacteria were most abundant in the T2 treatment in the rhizosphere soil. The rhizosphere soil microbial communities were clustered into two categories: one for T1 and T2 treatments, and another for T3 (mushroom bran) and T4 treatments. Compared to the other treatments, the T1 treatment had the most significant impact on microbial functional pathways in the blueberry roots. T2 treatment promoted the growth of N fixation functional bacteria both in the rhizosphere soil and roots. At the module level, the T2 treatment increased the relative abundance of N fixation and decreased the relative abundance of assimilating nitrate reduction reaction (ANRA), dissimilating nitrate reduction reaction (DNRA), denitrification and completed nitrification in the blueberry rhizosphere soil. Additionally, the T2 treatment increased the abundance of root endophytic microbes involved in N fixation. Overall, our findings suggest that the addition of peat combined with acidified rice husk is the optimal soil improvement method for blueberry cultivation.

Endophytic fungi are a diverse group of microorganisms that colonize the inter- or intracellular spaces of plants for mutual benefits. The interactions with a host plant and other microbiomes are multidimensional and play a crucial role in the production of secondary metabolites. We screened bioactive compounds present in the extracts of Aspergillus flavus, an endophytic fungus isolated from the roots of the medicinal grass Cynodon dactylon, for its anticancer potential. Ethyl acetate extract from isolated A. flavus showed significant cytostatic effects (IC50: 16.25 μg mL−1) against breast cancer cells (MCF-7). Morphology of cells and DAPI stained nuclei along with the results of flow cytometry annexin V/PI assay suggested apoptosis to be the main process leading to cells’ death. While investigating the mechanism that triggers apoptosis, we found that the extract of A. flavus increased ROS generation and caused loss of mitochondrial membrane potential of MCF-7 cells. To identify the metabolites that might be responsible for the anticancer effect, the extract was examined using gas chromatography-mass spectrometry (GC-MS). Interestingly, nine phytochemicals were found to have potential inhibitory effects of anti-apoptotic protein (Bcl-2) in the breast cancer cells. In the in silico molecular docking and molecular dynamics simulation studies revealed that two compounds: 2,4,7-Trinitrofluorenone and 3alpha, 5alpha-Cyclo-ergosta-7,9(11),22t-triene-6beta-ol exhibited significant binding affinities (-9.20, and -9.50 Kcal mol-1, respectively) against Bcl-2 along with binding stability and intermolecular interactions of its ligand-Bcl-2 complexes. Overall, the study found that the endophytic A. flavus from C. dactylon contains plant-like bioactive compounds that have a promising effect in breast cancer.

Endophytic bacteria, especially those participate in nitrogen fixation, play critical roles in supplying essential nutrients for legume plant growth. Compared to the numerous bacterial microbiome reports targeting legume roots and nodules, little is known about embryonic bacteria that facilitate plant nutrient utilization after seed germination. Here, we collected and investigated endophytic bacterial microbiomes in edible pea (Pisum sativum) embryos using five representative cultivars and a pea sprout control. Twenty-six nitrogen-fixing bacteria (NFBs) were isolated from pea embryos, with three strains found in fresh pea (FGP) and snow pea (SP) exhibiting the strongest nitrogenase activity. Some NFB isolates are also potassium-solubilizing bacteria (KSBs) or phosphorus-solubilizing bacteria (PSBs) utilizing inorganic and/or organic phosphorus. All 26 NFBs showed variable levels of indole-3-acetic acid (IAA) secretion. The nutrient-solubilizing NFBs identified in our research are valuable resources for biofertilizer development. At the microbiome level, high-throughput 16S ribosomal RNA (rRNA) sequencing of 40 bacterial collections from pea embryos revealed similar community structures and species abundances and diversities in most samples. Our embryo-derived endophytic bacterial pool provides a microbiome platform for seed dormancy and germination research of edible peas.

The emergence of new plant diseases is an increasingly important concern. Climate change is likely to be among the factors causing most of the emerging diseases endangering forest and tree heritage around the world. Such diseases may be caused by latent pathogens or microorganisms cryptically associated with plants. The shift from a non-pathogenic to a pathogenic stage may depend on physiological alterations of the host, environmental changes and/or stress factors. In some woods of the Salento peninsula (Apulia region, Italy) sudden declines of holm oak plants (Quercus ilex L.) have been observed since 2016. The morphological and molecular characterization of representative fungal isolates associated with canker and necrosis in declining plants indicated that these isolates belong to the Botryosphaeriaceae family, and the most frequent species were Diplodia corticola and Diplodia quercivora, followed by Neofusicoccum vitifusiforme. In artificially inoculated young holm oak plants, both D. corticola and D. quercivora species produced intense and severe subcortical and leaf margin necrosis. N. vitifusiforme, although less aggressive, induced the same symptoms. Our research in addition to confirm the involvement of D. corticola in olm oak decline, represents the first report of D. quercivora as a new pathogen on Quercus ilex in Italy. Furthermore, to the best of our knowledge, we also found N. vitifusiforme as a new pathogen on Q. ilex for the first time.