Fungal endophytes are microorganisms that inhabit plant tissues without causing disease and emerge as critical mediators of plant stress tolerance, nutrient acquisition, and ecosystem resilience under diverse climate change scenarios. Their unique position within the host allows them to modulate physiological responses more closely than external microbiota. This review explores how endophytic fungi contribute to plant adaptation under climate-induced stresses such as heat, salinity, drought, pollution, and nutrient limitation, with a focus on molecular crosstalk, functional trait modules, and metabolic trade-offs. Key findings emphasize multilayered signaling systems, including MAMP/DAMP recognition, phytohormone regulation, immune tuning, ROS dynamics, and effector deployment, while emerging mechanisms such as cross-kingdom RNA and extracellular vesicle (EV)-mediated exchange are discussed as promising but currently limited in empirical validation within many endophytic systems. Endophytes also enhance nutrient exchange through conditional carbon-for-benefit trade and may shape rhizosphere microbiota and soil activities through plant-mediated inputs. Integrative multi-omics approaches provide predominantly correlational insights into the mechanistic basis of these effects, linking molecular function to ecosystem and community outcomes. These insights have potential applications in climate-resilient agriculture, phytoremediation, and ecosystem restoration; however, their large-scale implementation requires further field-based validation and context-specific assessment. Future priorities should focus on trait-based selection, ecological modeling, and biosafety evaluation to translate microbial functions into reliable field-level strategies that support sustainable crop performance under accelerating environmental stress.

It is currently unclear whether the mechanism of endophytic fungi improving the alkali tolerance of Hordeum bogdanii affects secondary metabolites. Unveiling this knowledge is crucial for understanding the tolerance mechanism of H. bogdanii to alkaline stress. The aim of this study was to investigate how endophytic fungi affect secondary metabolites of H. bogdanii under alkaline stress at different concentrations. Endophyte-infected (E +) and endophyte-free (E−) individuals of H. bogdanii were used as materials in this study. The method of indoor vermiculite aseptic planting was adopted. After mixed alkali stress treatment, the roots, stems, and leaves of the plants were collected to measure the indicators related to secondary metabolites. The results showed that endophytic fungi improved the alkali resistance of H. bogdanii by improving the related indicators of secondary metabolites. endophytic fungi significantly increased the contents of phosphorus, polyphenols, and alkaloids, and the activities of polyphenol oxidase and acid phosphatase, and significantly reduced flavonoid content. The content of polyphenols and alkaloids in stems, polyphenol oxidase activity in stems and leaves, and acid phosphatase activity in leaves were significantly affected. The findings of this study may aid in amplifying the alkali resistance mechanism of endophytic fungi to H. bogdanii as well as provide insights into improving the alkali resistance of other plants.

Ammopiptanthus mongolicus is the only evergreen broadleaf shrub and constructive species in the northwest desert of China (Hu et al. 2021). It also is listed as one of the national second-class endangered plants. Ammopiptanthus mongolicus has a good effect of water conservation, windbreak and sand fixation because its deep root system (Zhou et al. 2012; Dong et al. 2023). A large number of dead plants of Ammopiptanthus mongolicus were found in Etuoke county, Inner Mongolia Autonomous Region, China (40°4'28″-40°4'34″ N, 106°53'5″-106°53'31″ E). In September 2023, the investigation and research in the region found that the incidence of diseased plants in this field was about 30%, and for individual plant, the incidence of diseased branches was about 60%. The leaves of diseased branches initially became from green to yellow and then wilt and fall. Eventually the plant dies. (Figure 1). The miter cut of the root showed that the root steles of diseased plants had obvious black and brown color (Figure 2). For isolation, the 30 tissue blocks (10×10 mm) of from 10 symptomatic roots diseased were surface sterilized with 70% ethanol for 3 minutes and sodium hypochlorite (2.5% available chlorine) for 5 minutes, and rinsed three times with sterilized distilled water. Then, these tissue blocks were placed on potato dextrose agar (PDA) medium, and incubated from 3 to 5 days at 25°C. After 3 days on PDA, the surface of the colony was rough, the color were white-pink at the beginning, and deep purple pigment were produced in the later stage, making the colony bluish-purple to gray-purple, their undersides were bluish-purple. Mycelia were white. After 7 days on SNA, Microconidia were typical of the clavicular type, 8.5 ± 2.5 μm × 2.3 ± 0.2 μm(×400). Microconidia were usually very long conidial chains, sometimes the spore chain collapses and the conidia clump together to form an approximate pseudocephaly. The macroconidia were slender and long, slightly falcate or straight, 42.8 ± 3.4 μm × 3.8 ± 0.7 μm(×400) (Figure 4). Species identity was confirmed by sequencing the EF1-α gene (EF1 and EF2 primers)(O'Donnell et al. 1998), RPB1 (F5 and G2R primers)(O'Donnell et al. 2022) and RPB2 (5F2 and 11AR)(O'Donnell et al. 2022). The amplified sequences of a representative isolate (AmP10) have deposited in GenBank with accession number OR594338 (EF1-α), OR841329 (RPB1) and OR841331 (RPB2). Thee results of pairwise alignment in Fusarioid-ID datebase(Crous et al. 2021) showed that EF1-α sequence was 99.54% similarity and 89.96% overlap to the corresponding sequence KF499582 of ex-epitype CBS 218.76 of Fusarium verticillioides, Fusarium fujikuroi species complex (FFSC, previously GFSC) (Lecellier et al. 2014), RPB1 sequence was 100% similarity and 100% overlap to the corresponding sequence MW402638 of ex-epitype CBS 218.76 of Fusarium verticillioides, Fusarium fujikuroi species complex (FFSC, previously GFSC) (Yilmaz et al. 2021), RPB2 sequence was 99.94% similarity and 87.83% overlap to the corresponding sequence MW928835 of ex-epitype CBS 218.76 of Fusarium verticillioides, Fusarium fujikuroi species complex (FFSC, previously GFSC) (Crous et al. 2021). Moreover, the result of polyphasic identification in Fusarioid-ID datebase also showed EF1-α, RPB1 and RPB2 sequences were 100% similarity to the corresponding sequences of ex-epitype CBS 218.76 of Fusarium verticillioides, Fusarium fujikuroi species complex (FFSC, previously GFSC). To test the pathogenicity, the healthy green seedlings (64 days old) were planted into plastic pots containing sterilized soil in the greenhouse after the seeds of Ammopiptanthus mongolicus were surface sterilized with 70% ethanol for 3 minutes and 2.5% sodium hypochlorite for 3 minutes. The roots of 3 seedlings were inoculated with 1×106 /ml of the conidial suspension, and another 3 used as controls with inoculated sterile water. Then, all pots were placed in a greenhouse maintained at 18°C to 25°C. After incubation for 3-5 days, the typical symptoms similar to the symptoms in the field (Figure 5), brown root steles (Figure 6), developed on the plants inoculated with conidial suspension, whereas no symptoms were observed on the control plants. The same pathogen was consistently reisolated from the inoculated roots and confirmed as Fusarium verticillioides based on morphological and molecular analyses. To our knowledge, this is the first report of Fusarium verticillioides on Ammopiptanthus mongolicus in China. This study provides a basis for identifying pathogens causing blight on Ammopiptanthus mongolicus and managing the disease.

Ammopiptanthus mongolicus is the only evergreen broad-leaved shrub in the desert region of Northwest China, which is one of the dominant species in the desert vegetation of the region, playing an important role in maintaining the stability of the local desert ecosystem. A. mongolicus is also very hardy and drought resistant and can survive extreme temperatures (Liu et al. 2013; Yang et al. 2022). The large-scale death of A. mongolicus could cause desertification in the region. Two months after the discovery of Fusarium verticillioides causing blight on A. mongolicus in Etuoke county, Inner Mongolia Autonomous Region in September 2023 (Yang et al. 2024), a large number of A. mongolicus plants with symptoms of blights were found in Lingwu city, Ningxia Hui Autonomous Region, China (106.442368°E, 37.734026°N) in November 2023. The incidence of diseased plants in this field was about 30%. The field symptoms in Lingwu city were similar to those observed in Etuoke county. The diseased leaves initially turned yellow, then wilted and dehisced, eventually resulting in plant death (Figure 1). The roots of the diseased plants were cut diagonally and the central cylinder showed a brown color (Figure 2). In order to investigate whether the death of A. mongolicus was caused by the same pathogen as those identified previously, 30 roots were collected from 10 diseased plants. After rinsing and surface sterilization (70% ethanol for 3 min and 2.5% NaClO for 5 min, rinsed 3 times with sterile distilled water), diseased tissues (10×10 mm) were placed on potato dextrose agar (PDA) (3 pieces per plate) and incubated from 3 to 5 days at 25°C. The strain AmP5 was isolated and used for further study. After 3 days on PDA medium, fungal colonies were white to milky, the undersides of the cultures were yellowish to orange-brown (Figure 3). After 7 days on synthetic nutrient-poor agar (SNA), microconidia were ovoidal or with a rounded apex and truncate base, 10.5 ± 1.5 μm × 1.6 ± 0.2 μm (×400). The macroconidia were slightly curved or arcuate, 40.5 ± 3.5 μm × 5 ± 0.5 μm (×400) (Figure 4) (Šišić et al. 2018). The pathogen was confirmed to be Neocosmospora pisi by multigene phylogenetic analysis of TEF, RPB1 and RPB2 genes using primers EF1/EF2, F5/G2R and 5F2/11AR, respectively (O'Donnell et al. 2022). The sequences of PCR products were deposited in GenBank with accession numbers OR944631 (RPB1), OR988086 (TEF) and OR988087 (RPB2), respectively. The results of pairwise alignment in Fusarioid-ID database (Crous et al. 2021) showed 99.84% similarity and 83.96% overlap of the EF1-α sequence to the corresponding sequence LR583636 of ex-epitype CBS 123669 of Neocosmospora pisi (syn. Fusarium solani f. sp. pisi), 99.72% similarity and 85.66% overlap of the RPB1 sequence to the corresponding sequence MW834242 of ex-epitype CBS 123669 of N. pisi, and 99.47% similarity and 78.26% overlap of RPB2 sequence to the corresponding sequence LR583862 of ex-epitype CBS 123669 of N. pisi. Moreover, the result of polyphasic identification in the Fusarioid-ID database also showed EF1-a, RPB1, and RPB2 sequences had 99.15% similarity to the corresponding sequences of CBS 1233669. The pathogenicity of AmP5 was tested on potted 64 days old seedlings A. mongolicus plants. The roots of 3 seedlings were inoculated with conidial suspension (1×106 /ml), and another 3 used as controls were inoculated with sterile water, by gently peeling off the soil around the roots during inoculation, and pouring the conidial suspension around the roots (10 ml/seedling). All plants were placed in a growth chamber at 18-25℃ (10 h light; 14 h dark). After incubation for 3-5 days, the symptoms similar to those observed in the field (Figure 5), including brown rot of steles (Figure 6), developed on plants inoculated with conidial suspension, whereas no symptoms were observed on the control plants. The same pathogen was reisolated from inoculated roots and confirmed as N. pisi based on morphological and molecular analyses (TEF, RPB1 and RPB2). To our knowledge, this is the first report of blight on A. mongolicus caused by N. pisi in China. This study also indicates that blight on A. mongolicus can be caused by different fungal pathogens. Blight caused by different pathogens may have different in terms of control measures and pathogenic mechanisms, so the study of blight caused by different pathogens is of profound value.

Organic acid is one of the important components in plant roots and root exudates, which plays an important role in nutrient activation, changing soil microbial activity and alleviating metal element toxicity stress. To study the effect of endophytic fungi infection on the organic acid contents of plants, this study used the grass species Hordeum bogdanii, Endophytic Fungi (E+) and without endophytic fungi (E-) H. bogdanii grasses from Wensu County, Xinjiang Province, China, as test materials H. bogdanii plants were grown hydroponically and treated with 0, 50 and 150 mmol/L mixed alkali (Na2CO3:NaHCO3 = 1:1) for 1 and 21 h. Root exudates and fresh root samples were collected for determination the organic acid contents of malic acid, shikimic acid, citric acid, and oxalic acid. The results showed that under alkali stress, the oxalic acid content in roots and root exudates of E + and E- plants decreased. The contents of citric acid and shikimic acid in roots and root exudates of E + and E- plants increased first and then decreased. Malic acid content in root exudates did not change significantly, and malic acid content in roots increased with the increase of alkali stress time. Among them, the organic acid content of H. bogdanii E + plants was significantly higher than that of uninfected E- plants, indicating that endophytic fungi under alkali stress were helpful to increase the root exudates of H. bogdanii grass and the accumulation of malic acid, shikimic acid, citric acid and oxalic acid content in the root. The most obvious change was oxalic acid content, and there was interaction between endophytic fungi and alkali treatment. It indicated that endophytic fungi could increase the secretion of organic acids from plants under alkali stress, which was conducive to the survival of plants in alkaline soil.

Ammopiptanthus mongolicus is a rare tertiary relic evergreen broad-leaved shrub that is seriously threatened by Fusarium wilt disease caused by Fusarium verticillioides. Mycorrhiza is a widely occurring symbiotic association of plant roots with arbuscular mycorrhizal fungi. To explore the relationship between wilt disease in A. mongolicus and arbuscular mycorrhiza, fungal communities in the roots and rhizosphere of healthy and diseased plants were analyzed using high-throughput sequencing technology based on specific primer amplicons. Arbuscular mycorrhizal fungal communities in roots were more strongly affected by Fusarium wilt disease than those in the rhizosphere. Wilt disease had no effect on α-diversity indices (Shannon and Simpson) in both the roots and rhizosphere soil, or on the phylogenetic diversity index (Pd) and richness indices (Chao, Ace and Sobs) in rhizosphere soil. However, it had a significant effect on the phylogenetic diversity index (Pd) and richness indices (Chao and Sobs) of arbuscular mycorrhizal fungal communities in the roots. Wilt disease increased the abundance of the genus Sclerocystis and decreased the abundance of Glomus. Arbuscular mycorrhizal fungal communities in diseased plants showed greater co-occurrence network complexity in both rhizosphere soil and roots. In terms of the ecological processes driving arbuscular mycorrhizal fungal community assembly, drift was intensified by wilt disease in both rhizosphere soil and roots. This study revealed the effect of wilt disease on arbuscular mycorrhizal fungal communities in the rhizosphere soil and roots of A. mongolicus. These findings provide important theoretical support and core AMF resources for the ecological prevention and control of A. mongolicus wilt disease.