Search Results (2,559)

Picea schrenkiana is a keystone species in Central Asian ecosystems currently threatened by climate-driven disease outbreaks. Here, we investigated the causal agent of needle blight and characterized the associated microbial dynamics. By integrating tissue isolation, Koch’s postulates, and high-throughput amplicon sequencing across a disease severity level, we confirmed Lirula macrospora as the etiological agent. Community analysis revealed that disease severity is the primary driver of succession, with alpha diversity peaks at the moderate infection stage. Notably, the abundance of Lirula surged from 2.56% in healthy needles to 65.10% in severe cases, displacing the core endophyte Phaeococcomyces, while potentially beneficial bacteria like Sphingomonas showed only transient enrichment. Furthermore, cross-kingdom co-occurrence network analysis revealed marked topological restructuring whereby the system reached a complex ecological “tipping point” during moderate stage before undergoing significant simplification. As the disease progressed, L. macrospora shifted from a peripheral node to a central hub, effectively dismantling the native microbial network. We conclude that L. macrospora infection triggers a cascading collapse of the needle microbiome, driving a phase shift from a healthy homeostasis to a pathogen-dominated state. These findings elucidate the critical mechanisms of pathogen-microbiome interactions and provide a theoretical basis for the ecological management of P. schrenkiana forests. Full article

Emerging from millions of years of evolutionary optimization, Natural products (NPs) remain unique, unparalleled sources of bioactive scaffolds. Unlike synthetic molecules engineered around single therapeutic targets, NPs often exhibit multi-target, system-level bioactivity, aligned with the principles of network pharmacology, which modulates pathways in a coordinated, non-disruptive manner. This approach reduces resistance, buffers compensatory feedback loops, and enhances therapeutic resilience. Fungal endophytes represent one of the most chemically diverse and biologically sophisticated NP reservoirs known, producing polyketides, alkaloids, terpenoids, and peptides with intricate three-dimensional architectures and emergent bioactivity patterns that remain exceptionally difficult to design de novo. Advances in artificial intelligence (AI), machine learning, deep learning, and multi-omics integration have redefined the discovery landscape, transforming previously intractable fungal metabolomes and cryptic biosynthetic gene clusters (BGCs) into tractable, predictable, and engineerable systems. AI accelerates genome mining, metabolomic annotation, BGC-metabolite linking, structure prediction, and activation of silent pathways. Generative AI and diffusion models now enable de novo design of NP-inspired scaffolds while preserving biosynthetic feasibility, opening new opportunities for direct evolution, pathway refactoring, and precision biomanufacturing. This review synthesizes the chemical and biosynthetic diversity of major NP classes from fungal endophytes and maps them onto the rapidly expanding ecosystem of AI-driven tools. We outline how AI transforms NP discovery from empirical screening into a predictive, hypothesis-driven discipline with direct industrial implications for drug discovery and synthetic biology. By coupling evolutionarily refined chemistry with modern computational intelligence, the field is poised for a new era in which natural-product leads are not only rediscovered but systematically expanded, engineered, and industrialized to address urgent biomedical and sustainability challenges. Full article

As a fast-growing timber tree species with a wide cultivation area, poplar is facing the problem of declining economic benefits under long-term monoculture. Intercropping provides an effective solution. Using Illumina Miseq sequencing, we analyzed soil microbiomes under four patterns: poplar monoculture, and intercropping with amorpha fruticosa, black locust, or cassia seed. The results showed that the Alpha diversity index of intercropping area was significantly higher than that of single planting poplar area under intercropping and monoculture conditions. In the intercropping area, the highest species richness was the intercropping of poplar and black locust, and the lowest was the intercropping of poplar and amorpha fruticosa. The dominant microorganisms in the intercropping mode were Vicinamibacterales, and the fungi were Alternaia and Enterocarpus. In the single planting poplar area, a large number of bacteria gathered in the soil were Dongia and Alphaproteobacteria, and fungi were Fusarium and Mortierella. Functional prediction results showed that the biosynthetic function of ansamycin was the highest in the bacterial community. In the intercropping area, the functional abundance of methanol oxidation, sulfate respiration, sulfate compound respiration, nitrate denitrification, nitrite denitrification, and nitrous oxide denitrification was higher than that in the single planting poplar area. On the contrary, the abundance of methanotrophy function is lower than that of single planting poplar area. In the fungal community, the functional abundance of animal pathogens and the animal pathogen–dung saprotroph–endophyte–plant saprotroph–soil saprotroph–wood saprotroph group in the monoculture poplar area was higher than that in the three intercropping areas. In summary, the intercropping mode of poplar is better than the monoculture mode, and the species richness is the highest when poplar and black locust are intercropped. Therefore, the intercropping pattern of poplar and other tree species improved microbial community. This provides some theoretical guidance for the subsequent solution of continuous cropping obstacles in poplar. Full article

Plant endophytes, often termed the “second genome”, critically shape host adaptability. However, the complexity of their interactions, regulated by microbial traits, host species, and environment, has limited both our understanding of symbiosis and the application of beneficial endophytes. The symbiosis between locoweeds (Oxytropis and Astragalus species) and the endophyte Alternaria sect. Undifilum, which produces the neurotoxin swainsonine, serves as an ideal model for investigating these relationships. Through extensive national surveys (2021–2023) across China’s major locoweed habitats, combining field sampling with cultivation, molecular, quantitative, and modeling approaches, a central question emerged: To what extent are the distribution and function of this symbiosis shaped by the contemporary environment versus host evolutionary history? The results showed that: (1) Among 32 surveyed species of Oxytropis, Astragalus, and Sphaerophysa, the endophyte Alternaria sect. Undifilum colonized 11 species. In colonized plants, endophyte loads ranged from 0.02 to 58.87 pg/ng total DNA, and swainsonine concentrations varied from 0.00003% to 1.00%. (2) Environmental factors, rather than host phylogeny, were the key driver governing the geographical distribution and expression of the symbiosis. (3) Low temperature and drought stress regulated the symbiotic relationship and chemical defense through both direct effects on the symbionts and indirect pathways involving grazing pressure. This study demonstrates that the environment is the core force dominating the geographical pattern and functional expression of the locoweed–endophyte symbiosis at ecological scales. These findings provide new perspectives for understanding the general principles of plant–endophyte symbiosis and establish a scientific foundation for predicting and utilizing endophyte resources in changing environments. Full article

To evaluate the comprehensive ecological risks associated with transgenic plant residues, this study examined their impact on Eisenia fetida and their endogenous microorganisms. The results indicated that transgenic plant residues did not influence the survival or weight of E. fetida, but they significantly altered the microbial community structure at specific time points. Specifically, the diversity and structure of the fungal community exhibited significant changes on the 14th and 28th days after treatment. In contrast, the bacterial response was delayed, with 22 biomarkers, including Caproiciproducens, Lachnoclostridium, and Enterococcus, being specifically enriched on the 21st day. This study confirmed that transgenic plant residues can temporally reshape the microecology within E. fetida. The practical significance of this research lies in highlighting the importance of incorporating the microbiome into safety assessment frameworks, thereby providing a scientific foundation for developing more forward-looking ecological risk assessment standards. Full article

Vanda orchids are a commercially significant genus in the global floriculture industry, yet their cultivation often depends on substantial chemical fertilizer inputs, which raise both economic and environmental concerns. Endophytic bacteria offer a promising, sustainable alternative by promoting plant growth and enhancing nutrient acquisition. This study aimed to characterize native endophytic bacteria and assess their potential to improve nitrogen uptake and growth in Vanda orchids. Three potent nitrogen-fixing bacterial isolates (2R13, 3S19, and 3R14) were selected for this research. Through 16S rRNA sequencing, they were identified as Curtobacteriumcitreum, Stenotrophomonas panacihumi, and Bacillus subtilis, respectively. The efficacy of these isolates was evaluated in both controlled in vitro and practical greenhouse conditions using various dilution ratios. Scanning electron microscopy confirmed the successful colonization of isolate 3S19 within the root tissue of inoculated Vanda plantlets. The results revealed a significant interaction between the bacterial treatments and the growing environment. In vitro, isolate 3S19 applied at a 1:25 ratio yielded the highest total nitrogen content (12.46 mg g⁻¹ DW). Conversely, in the greenhouse experiment, isolates 2R13 and 3S19 were most effective at a 1:50 ratio, achieving nitrogen contents of 11.18 and 10.83 mg g⁻¹ DW. Furthermore, bacterial inoculation in the greenhouse generally led to significant improvements in plant growth parameters, including height, leaf count, and root development, compared to non-inoculated controls. These findings highlight the potential of these endophytic bacteria as effective biofertilizers for Vanda orchid cultivation. The contrasting outcomes between the two experimental settings underscore the critical importance of optimizing application rates based on specific environmental conditions to maximize benefits in commercial production. Full article

This study aimed to develop biofumigation strategies against chestnut fruit rot caused by Botryosphaeria dothidea. An endophytic strain, FPYF2509, was isolated from Castanea mollissima fruit and identified as Trichoderma nordicum using morphological and phylogenetic (tef1, rpb2) analyses. Antifungal volatile organic compounds (VOCs) were analyzed using headspace solid-phase microextraction and gas chromatography–mass spectrometry during dual-culture interactions with pathogens. The volatiles from the interaction exhibited to inhibit pathogen growth. Particularly an induced myrtenol, demonstrated strongly biofumigation activity in vitro, with a lowest observed effect concentration of 0.02 µL/mL, minimum inhibitory concentration and a minimum fungicidal concentration of 0.2 µL/mL against B. dothidea. In vivo, fumigation with 0.2 µL/mL myrtenol significantly reduced disease incidence from 83.3% to 17.39%, achieving a 79.1% control efficacy. This work presents endophytic T. nordicum FPYF2509 as a promising biocontrol agent and identifies myrtenol, of fungal interaction origin, as a novel and effective mycofumigant for postharvest disease management. Full article

Endophytic fungi enhance plant growth and stress resilience, yet their molecular roles in the roots of the endangered tree Phoebe bournei remain unclear. A comparative RNA-seq analysis was performed on root transcriptomes from wild, endophyte-colonized adult trees (OT) and axenically grown seedlings (ST). Unmapped reads were analyzed against the NCBI nucleotide (NT) database using BLASTN (v2.17.0), revealing Rhizophagus irregularis as the predominant endophytic fungus. Differential expression analysis identified 5891 DEGs, which were significantly enriched in pathways related to plant–pathogen interactions, phenylpropanoid biosynthesis, plant hormone signal transduction, and MAPK signaling. Key upregulated genes included PbMPK3, PbCML42, PbCML41.2, and PbGSTU28, suggesting enhanced ROS scavenging, calcium signaling, and defense activation. RT-qPCR validation confirmed the transcriptomic trends for selected genes. Our findings reveal that root endophytic fungi modulate a coordinated network involving immune priming, phytohormone regulation, and redox homeostasis, thereby supporting root development and enhancing resistance to biotic and abiotic stresses in P. bournei. This study provides foundational molecular insights into beneficial plant–endophyte interactions and identifies candidate genes that are valuable for the conservation and breeding of this threatened species. Full article

Drought stress severely limits wheat growth, development and yield. Endophytic fungi play a crucial role in plant growth and drought resistance. In agricultural production, they hold significant application potential as biocontrol agents capable of mitigating drought-induced damage. However, the mechanisms underlying changes in endophytic fungal community structure under drought stress remain unclear. Our study employed amplicon sequencing to investigate the structure of endophytic fungal communities in wheat roots under different water treatments, comparing structural and functional changes between different treatments. Results revealed that drought stress led to the greatest accumulation of relative abundance in the phylum Ascomycota (86.4%). At the genus level, Stachybotrys (increase 994.2%), Fusarium (increase 94.6%) and Aspergillus (increase 295.6%) showed the most significant increases in relative abundance. Co-occurrence network and Sankey diagram analysis revealed that wheat roots formed a drought-specific endophytic fungal community centered around Stachybotrys, Fusarium and Aspergillus, which indirectly enhanced crop drought tolerance. Our findings provide a theoretical foundation for future agricultural strategies to improve crop drought resistance through precise regulation of microbial communities. Full article

Beauveria bassiana can colonize plants, acting against insect pests and promoting plant growth. This study evaluated how different fungal inoculation methods affected Eucalyptus grandis growth and the foraging behavior of ants. An isolate (LPP 139) was identified as B. bassiana based on ITS sequences. Seedlings were submitted to three inoculation methods using fungal suspensions at 1 × 10⁸ conidia mL⁻¹: (1) soil drenching at sowing (SD), (2) soil drenching 20 days after sowing (20SD), and (3) foliar spraying 20 days after sowing (20F) when compared to controls. SD treatment enhanced plant height (mean 25 cm with a 31.6% increase compared to the controls; p = 0.0353) and shoot fresh weight (mean 1.5 g, a 50% increase; p = 0.0154), while 20SD increased leaf number (141.4% increase; p = 0.0419). The 20F treatment increased leaf number (287.9% compared to the controls; p = 0.0006), shoot weight (mean fresh weight 1.5 g, a 50% increase; p = 0.0213 and mean dry weight 0.7 g, a 75% increase; p = 0.0236), and reduced leaf-cutting ant foraging (mean 26 cm², a reduction of 53.6%; p = 0.0134). These findings highlight the dual action of B. bassiana, promoting plant growth and reducing the activity of ants. Full article

Fungal extracts have been reported to exert diverse biological activities, including anti-inflammatory, antibacterial, and antiviral effects. However, the anti-coronaviral properties of fungal extracts remain largely unexplored. In this study, we demonstrated that the Penicillium compactum extract (PCE) inhibits the replication of human coronavirus. RD cells were infected with human coronavirus and subsequently treated with PCE. PCE treatment reduced the expression of viral proteins and ameliorated virus-induced cytopathic effects. In addition, PCE markedly decreased viral RNA levels in both the cells and the conditioned medium. Finally, we confirmed that PCE treatment reduced the production of infectious viral particles. Collectively, these findings indicate that PCE exhibits potent antiviral activity against human coronavirus. Full article

Brachiaria decumbens is a high-yielding forage grass of major economic value in tropical regions. The root endophytic fungus Piriformospora indica is widely recognized for promoting plant growth and stress tolerance, yet its effects on B. decumbens remain poorly characterized. Here, we profiled root responses to P. indica colonization at 10 days after inoculation (dais; early stage) and 20 dais (late stage) during symbiosis establishment. Colonization was confirmed by phenotypic and physiological assessments, with inoculated plants showing enhanced root growth; colonized roots exhibited higher activities of catalase (CAT), superoxide dismutase (SOD), and peroxidase (POD), along with increased indole-3-acetic acid (IAA) levels, whereas malondialdehyde (MDA), jasmonic acid (JA), and the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) were reduced. Transcriptome and metabolomic profiling identified 1884 and 1077 differentially expressed genes (DEGs) and 2098 and 1509 differentially accumulated metabolites (DAMs) at 10 dais (Pi10d vs. CK10d) and 20 dais (Pi20d vs. CK20d), respectively, and 3355 DEGs and 2314 DAMs between stages (Pi20d vs. Pi10d). Functional enrichment highlighted key pathways related to secondary metabolism, carbohydrate metabolism, and lipid biosynthesis. Differentially expressed transcription factors spanned multiple families, including MYB, AP2/ERF, MADS-box, and bZIP, consistent with broad transcriptional reprogramming during symbiosis establishment. Integrative multi-omics analysis further highlighted phenylpropanoid biosynthesis and α-linolenic acid metabolism as consistently co-enriched pathways, suggesting coordinated shifts in gene expression and metabolite accumulation across colonization stages. Collectively, these results provide a multi-layered resource and a framework for mechanistic dissection of the P. indica–B. decumbens interaction. Full article

Rice blast, caused by the fungal pathogen Pyricularia oryzae, remains one of the most destructive diseases threatening global rice production. Although the deployment of resistant cultivars is widely regarded as the most effective and sustainable control strategy, resistance based solely on host genetics often has limited durability due to the rapid adaptation of the pathogen. Increasing evidence suggests that plant-associated microbial communities contribute to host health and disease resistance, yet the role of seed-associated microbiota in shaping rice blast resistance remains insufficiently understood. In this study, we investigated seed endophytic bacterial communities across multiple indica–japonica hybrid rice varieties from the Yongyou series that exhibit contrasting levels of resistance to rice blast. By integrating amplicon sequencing, we identified distinct seed bacterial assemblages associated with blast-resistant and blast-susceptible varieties were identified. Notably, the microbial communities in blast-resistant varieties exhibited significantly higher Shannon index, with a median value of 3.478 compared to 2.654 in susceptible varieties (p < 0.001), indicating a greater diversity and more balanced community structure compared to those in susceptible varieties. Several bacterial taxa consistently enriched in resistant varieties showed negative ecological associations with P. oryzae, both at the local scale and across publicly available global metagenomic datasets. These findings indicate that seed endophytic bacterial communities are non-randomly structured in relation to host resistance phenotypes and may contribute to rice blast resistance through persistent ecological interactions with the pathogen. This work highlights the potential importance of seed-associated microbiota as intrinsic components of varietal resistance and provides a microbial perspective for improving durable disease resistance in rice breeding programs. Full article

Black point (BP) and Fusarium-damaged kernels are common disorders affecting wheat grains worldwide. While the negative impact of Fusarium head blight (FHB) on yield and grain quality is well established, the biological significance of BP remains debated. This study evaluated the effects of BP on yield-related traits and seedling performance of winter wheat and compared them with the effects of FHB. Four winter wheat cultivars (Mercedes, Adina, Steffi, and LG Mocca) were examined under field and laboratory conditions. Fusarium infection was induced by artificial inoculation with Fusarium culmorum, whereas BP was assessed under natural field conditions using non-inoculated control plants. Fusarium infection significantly reduced thousand-grain weight (up to 46%) and grain number per ear (up to 35%). In contrast, BP was not associated with yield reduction. Grain with BP symptoms showed a 10–30% higher thousand-grain weight compared with BP-free grain. Seedlings originating from BP-affected seeds exhibited equal or improved biometric traits and a higher vigor index. Phytopathological analysis showed that Alternaria spp. dominated the endophytic mycoflora of both BP-affected and BP-free seeds. These results indicate that, under the conditions of this study, BP did not negatively affect wheat yield or seedling vigor and differed fundamentally from the damaging effects of FHB, highlighting the importance of distinguishing BP from Fusarium-related damage in wheat production. Full article

Drought stress is a major abiotic factor limiting global crop productivity by disrupting cellular homeostasis, impairing photosynthesis, and restricting metabolic activity. Plant-associated microorganisms, including rhizobacteria, endophytes, and arbuscular mycorrhizal fungi, play key roles in enhancing drought resilience through molecular, biochemical, and physiological mechanisms. These beneficial microbes modulate phytohormone biosynthesis, enhance osmolyte accumulation, increase organic acid exudation, and activate ROS-scavenging antioxidant pathways. Microbe-mediated regulation of aquaporins, heat shock proteins, and root system architecture further improves water-use efficiency, hydraulic conductance, and stress acclimation. Advances in microbial genomics and systems biology have revealed the molecular drivers of plant–microbe synergism, enabling the development of tailored microbial consortia and next-generation bioinoculants. Complementarily, genetic and genome-guided modulation of drought-responsive regulatory hubs including transcription factors (e.g., DREBs, NACs, MYBs, and bZIPs), signal transducers (e.g., MAPKs and CDPKs), and protective proteins enhances adaptive plasticity under water deficit conditions. This review integrates current molecular insights into drought-induced perturbations in plants and highlights the convergence of microbial interventions and genome-guided strategies in reinforcing drought tolerance. Emphasizing mechanistic frameworks, scalable microbial technologies, and molecular breeding approaches, this work underscores their potential to improve crop resilience in increasingly water-limited environments. Full article