Search Results (910)

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

Armillaria mellea (A. mellea) serves as a crucial nutritional source for Gastrodia elata (GE) growth, and its origin directly influences the GE quality and yield. This study analyzed GE symbiotic with A. mellea from different sources using metabolomics and transcriptomics. Results demonstrated that Group A exhibited significant differences in metabolites and gene expression compared to other groups. Group A showed significantly higher accumulation of active components like gastrodin and p-hydroxybenzyl alcohol than others, but its yield was lower than Group B. Metabolomic analysis identified 2418 metabolites, while transcriptomic sequencing produced 964,110,904 clean reads, with 14,637 annotated transcripts. KEGG analysis revealed that Group A’s DEGs and DEMs were co-enriched in three key pathways, including flavonoid biosynthesis, phenylpropanoid biosynthesis, and plant hormone signal transduction, such as the positive regulatory roles of key genes (CHS, 4CL, MYC2) on metabolites such as hesperetin, ferulate, and jasmonic acid, respectively. The coordinated upregulation of gene–metabolite interactions in Group A GE may be closely related to the accumulation of major active components, indirectly suggesting the influence of the A. mellea source on metabolic and transcriptional response differences in GE. This study, centered on the host GE, indirectly deduces the association between A. mellea and GE, providing a theoretical basis for screening high-quality “fungus-GE” combinations. Further in-depth research and validation experiments will be conducted in conjunction with fungal omics. Full article

Ectomycorrhizal (ECM) symbiosis is a fundamental mutualism crucial for forest eco-system health. Its establishment is governed by sophisticated molecular dialogue preceding physical colonization. This review synthesizes this pre-colonization crosstalk, beginning with reciprocal signal exchange where root exudates trigger fungal growth, and fungal lipochitooligosaccharides activate host symbiotic programming, often via the common symbiosis pathway. Successful colonization requires fungi to navigate plant immunity. They employ effectors, notably mycorrhiza-induced small secreted proteins (MiSSPs), to suppress defenses, e.g., by stabilizing jasmonate signaling repressors or inhibiting apoplastic proteases, establishing a localized “mycorrhiza-induced resistance.” Concurrent structural adaptations, including fungal hydrophobins, expansins, and cell wall-modifying enzymes like chitin deacetylase, facilitate adhesion and apoplastic penetration. While this sequential model integrates immune suppression with structural remodeling, current understanding is predominantly derived from a limited set of model systems. Significant knowledge gaps persist regarding species-specific determinants in non-model fungi and hosts, the influence of environmental variability and microbiome interactions, and methodological challenges in capturing early signaling in situ. This review’s main contributions are: providing a synthesized sequential model of molecular crosstalk; elucidating the dual fungal strategy of simultaneous immune suppression and structural remodeling; and identifying crucial knowledge gaps regarding non-model systems and species-specific determinants, establishing a research roadmap with implications for forest management and ecosystem sustainability. Full article

Fusarium oxysporum f. sp. niveum is an increasingly threatening fungal pathogen that systemically colonizes watermelon plants and severely compromises their productivity by causing destructive vascular wilt disease. While its nonribosomal peptide synthetase NPS6 has been identified as a key virulence factor, the regulatory mechanisms through which it controls downstream gene networks to cause disease remain unclear. To elucidate this regulatory pathway, we constructed a ΔFW-NPS6 knockout mutant and conducted a comparative genome-wide analysis using RNA sequencing, with the wild-type strain as a control. The results revealed 66 NPS6-dependent differentially expressed genes, which were primarily associated with secondary-metabolite biosynthesis (e.g., genes encoding nonribosomal peptide synthetases like NPS2) and pathogen–host interactions (e.g., components of the MAPK signaling pathway), and were enriched in key pathogenic pathways. This finding reveals the virulence regulatory network mediated by NPS6, providing a direct theoretical foundation and crucial molecular targets for developing novel control strategies, such as targeted fungicides or genetic interventions, against Fusarium wilt in watermelon by highlighting NPS6 itself as a potential fungicide target and its downstream pathways (e.g., siderophore biosynthesis) as points for intervention. Full article

To elucidate the potential of integrated multi-omics approaches for studying systemic mechanisms of mycorrhizal fungi in mediating plant-microbe interactions, this study employed the Tuber-inoculated Corylus system as a model to demonstrate how high-throughput profiling can investigate how fungal inoculation reshapes the rhizosphere microbial community and correlates with host metabolism. A pot experiment was conducted comparing inoculated (CTG) and non-inoculated (CK) plants, followed by integrated multi-omics analysis involving high-throughput sequencing (16S/ITS), functional prediction (PICRUSt2/FUNGuild), and metabolomics (UPLC-MS/MS). The results demonstrated that inoculation significantly restructured the fungal community, establishing Tuber as a dominant symbiotic guild and effectively suppressing pathogenic fungi. Although bacterial alpha diversity remained stable, the functional profile shifted markedly toward symbiotic support, including antibiotic biosynthesis and environmental adaptation. Concurrently, root metabolic reprogramming occurred, characterized by upregulation of strigolactones and downregulation of gibberellin A5, suggesting a potential “symbiosis-priority” strategy wherein carbon allocation shifted from structural growth to energy storage, and plant defense transitioned from broad-spectrum resistance to targeted regulation. Multi-omics correlation analysis further revealed notable associations between microbial communities and root metabolites, proposing a model in which Tuber acts as a core regulator that collaborates with the host to assemble a complementary micro-ecosystem. In summary, the integrated approach successfully captured multi-level changes, suggesting that Tuber-Corylus symbiosis constitutes a fungus-driven process that transforms the rhizosphere from a competitive state into a mutualistic state, thereby illustrating the role of mycorrhizal fungi as “ecosystem engineers” and providing a methodological framework for green agriculture research. Full article

The agave wilt associated with Fusarium oxysporum (Fox) is a major disease of blue agave (Agave tequilana Weber var. azul), used to produce “Tequila” in Mexico. Little is known about the A. tequilana-F. oxysporum interaction yet understanding defense mechanisms against the pathogen is necessary for control strategies. During early Fox infection, plants trigger defense mechanisms to interrupt the compatible interaction, while Fox’s pathogenesis mechanism interacts with plant response. This study evaluated plant defense mechanisms induced by Fox in A. tequilana and their interaction with fungal pathogenesis. For this, an A. tequilana pathogenic strain (FPA), and the non-A. tequilana pathogenic strains FNPA and FOL were utilized. Early defense mechanisms evaluated were hypersensitive response (HR) and cell wall strengthening in agave roots. Resistance mechanisms evaluated included pathogenesis-related proteins (PR proteins), phytoanticipins and phytoalexins. For early defense, induced HR was greater with FPA than other strains. Cell wall strengthening was found in agave roots, plants responded differentially to different strains. Initial response to FPA and FOL was similar in PR proteins, phytoalexins and phytoanticipins production. However, the response differentiated with FOL over time, indicating an incompatible interaction. The study identified effective and ineffective defense responses of A. tequilana to Fox infection, where FPA exhibited compatibility and caused unregulated ROS and PCD, early inhibition of PR activity, extensive lignification, and saponin detoxification. In contrast, this study unveiled incompatible interactions (FNPA and FOL) because of limited colonization, localized HR with suppressed ROS, early and sustained POX activation, significant callose accumulation, moderate lignification, and phenol–saponin dynamics that help in tissue containment and recovery. Full article

Fungal endophytes have emerged as a promising source of bioactive compounds with potent antifungal properties for plant disease management. This study aimed to isolate and characterize fungal endophytes from Antillean avocado (Persea americana var. americana) trees in the Colombian Caribbean, capable of producing bio-fungicide metabolites against Fusarium solani and Fusarium equiseti. For this, dual culture assays, liquid-state fermentation of endophytic isolates, and metabolite extractions were conducted. From 88 isolates recovered from leaves and roots, those classified within the Diaporthe genus exhibited the most significant antifungal activity. Some of their organic extracts displayed median inhibitory concentrations (IC₅₀) approaching 200 μg/mL. To investigate the mechanism of action, in silico studies targeting chitin synthase (CS) were performed, including homology models of the pathogens’ CS generated using Robetta, followed by molecular docking with Vina and interaction fingerprint similarity analysis of 15 antifungal metabolites produced by Diaporthe species using PROLIF. A consensus scoring strategy identified diaporxanthone A (12) and diaporxanthone B (13) as the most promising candidates, achieving scores up to 0.73 against F. equiseti, comparable to the control Nikkomycin Z (0.82). These results suggest that Antillean avocado endophytes produce bioactive metabolites that may inhibit fungal cell wall synthesis, offering a sustainable alternative for disease management. Full article

Coffea, a plant species of significant agricultural value used in coffee production, is a key commodity that supports the livelihoods of millions of people worldwide. However, coffee cultivation faces substantial threats from various pathogens, including Pseudomonas coronafaciens pv. garcae (Pcg), the causative agent of bacterial blight. This pathogen compromises coffee plant health, leading to reduced yields and plant death and impacting farmers and large-scale producers. Understanding the mechanisms underlying resistance to Pcg in the leaves of the resistant IAC 2211-6 Coffea arabica accession is crucial for developing effective control strategies. This study aimed to identify candidate biomarkers of resistance by comparing the leaf metabolome of (i) the resistant IAC 2211-6 and the susceptible IAC 125 RN Coffea arabica accessions and (ii) Pcg-infected and uninfected leaves. Untargeted metabolomics revealed distinct metabolic profiles between accessions. Flavonoids were more abundant in susceptible leaves. In contrast, resistant leaves showed increased levels of pipecolic acid ethyl ester, a structural derivative of a key systemic acquired resistance signal, and spiropreussione B, a compound associated with fungal endophytes. These findings highlight candidates potentially linked to resistance and suggest that systemic signaling and beneficial microbial interactions may contribute to resilience. Full article

The olive tree hosts diverse endophytic fungi that may contribute to plant protection and growth. In this study, a preliminary screening of olive-associated fungal endophytes was conducted. A total of 67 fungal endophytes were isolated from the leaves and roots of the Greek cultivars Amfissa and Kalamon and identified using morphological and molecular approaches; 28 representative strains were selected for functional evaluation. Dual culture assays revealed substantial antagonistic activity against major phytopathogens, with growth inhibition ranging from 19.05% to 100%. Notably, strains F.KALl.8 and F.AMFr.15 showed the strongest suppression across pathogens. Interaction phenotyping revealed all major interaction types (A, B, C) and subtype C1/C2, with several strains producing pigmentation zone lines or hyphal ridges at contact sites. The assessment of plant growth-related effects using Arabidopsis thaliana as a model system showed that three strains (F.AMFr.15, F.KALr.4, F.KALr.38A) significantly increased seedling biomass (up to ~16% above the control), whereas nine strains caused severe growth reduction and disease symptoms. Beneficial strains also altered root architecture, inhibiting primary root elongation while inducing extensive lateral root formation. Collectively, these findings highlight the functional diversity of olive-associated fungal endophytes and identify promising candidate strains, particularly F.AMFr.15 (identified as Clonostachys sp.), for further host-specific validation as potential biological control and plant growth-promoting agents. Full article

Fungal pathogens, including Colletotrichum gloeosporioides and Pestalotiopsis spp., are significant threats to global cacao production. Understanding their varying responses to novel antifungal agents is crucial for developing sustainable plant protection strategies. This study investigated the quantitative morphological responses and isolate-specific sensitivity of three cacao pathogen isolates (one Pestalotiopsis sp. and two C. gloeosporioides) to four novel bio-based phenolic-branched fatty acids and their corresponding amides derived from renewable feedstocks. We observed a high degree of isolate-specific susceptibility. A phenol-branched soy oil-derived fatty amide (PhSOAM) proved most potent, significantly inhibiting the growth of Pestalotiopsis sp. and one C. gloeosporioides isolate. In contrast, the second C. gloeosporioides isolate displayed complete insensitivity to all tested compounds, highlighting significant intraspecific variation. Notably, quantitative image analysis revealed that PhSOAM uniquely altered fungal colony morphology by significantly increasing the length-to-width ratio, suggesting a mechanism of action involving the disruption of polarized growth. Multivariate analyses and machine learning models (R² up to 0.74) effectively classified these responses, identifying the specific pathogen-compound pairing as the most critical determinant of the interaction outcome. This work not only highlights the potential of bio-based amides but also establishes a powerful analytical framework, combining morphological profiling with predictive modeling, to gain deeper insights into the complex, isolate-specific nature of fungal–antifungal interactions. Full article

The aim of this study was to determine fungal diversity and composition in an area of high host diversity and identify the organisms involved in the appearance of symptoms in Pinus needles. Asymptomatic and symptomatic live needle samples were obtained from different Pinus spp. in an arboretum with confirmed presence of brown spot needle blight. The samples were analysed using high-throughput sequencing of fungal ITS2rDNA. Ascomycota dominated all samples, with Lophodermium as the most abundant genus, although it showed lower representation in symptomatic needles. Other genera with recognised pathogenic potential, including Lecanosticta, Pestalotiopsis, Cyclaneusma, Rhizosphaera, Neophysalospora, and Cenangium, were also detected, whereas the Dothistroma genus was absent despite its presence in the region. Alpha diversity was higher in asymptomatic needles, with a significant difference only for the Shannon index, while Bray–Curtis dissimilarity revealed significant shifts in community composition between needle types. Functional guilds were dominated by pathotroph–saprotroph trophic mode, and the functional guild ‘plant pathogen’ was the most abundant across samples. These findings identify fungal genera associated with symptomatic and asymptomatic needles and provide guidance for future targeted isolation and detailed morphological and molecular identification using more resolutive techniques, enabling a deeper understanding of pathogenic community presence and their potential synergistic interactions. Full article

Chalcidoids (Hymenoptera: Chalcidoidea), the most important natural enemies of parasitoids, serve as a pivotal factor in the regulation and management of pest populations. Microbiotas mediate interactions among plants, herbivores, and natural enemies and shape host immunity, parasitoid development, and gall formation; however, the niche-specific diversity and functions of tritrophic parasitoid–host–gall systems remain unclear. Focusing on leaf galls induced on twisted willow (Salix matsudana f. tortuosa) by the willow-galling sawfly Euura viminalis and on two chalcidoids, Eurytoma aethiops and Aprostocetus sp., we profiled bacterial and fungal microbiomes across plant surfaces, gall lumen, host larval tissues, and parasitoids using HTAS. Fungal diversity peaked on parasitoids but was depleted in the gall lumen and host tissues; bacterial richness showed the opposite trend, peaking in the gall lumen and decreasing on parasitoids. In networks contrasted by kingdom, fungi showed positive interface-hub connectivity (Cladosporium, Alternaria), whereas bacteria showed negative hub-mediated associations (Pseudomonas, Acinetobacter), indicating habitat-specific replacements: exposed niches favored transport, two-component, secretion–motility and energy functions, whereas the gall lumen reduced transport/motility but selectively retained N/S metabolism; and in host tissues, information processing and nitrogen respiration were highlighted. These results inform microbiome-guided parasitoid biocontrol. Full article

The plant microbiome plays important roles in plant growth and resistance, but its assembly and affecting factors have not been fully studied for most of the agricultural plants. In this study, the endophytic mycobiota of the leaves and roots and the rhizosphere soils of five pummelo varieties were profiled based on the amplicon sequencing of the fungal internal transcribed spacer (ITS). The fungal richness and diversity were significantly different among the compartments, but not among the pummelo varieties. The composition and structure of the endophytic mycobiota of the compartments were significantly different across all five pummelo varieties. These suggest that the variety effect is weaker than the compartment effect, but still significant in shaping the pummelo mycobiota. Specifically, the dominant leaf endophytic fungal taxa (e.g., Fusarium and Zasmidium), and the root selection of fungal genera from the rhizosphere soils, were significantly different among the varieties. And also, the variety effect is more significant in shaping the leaf endophytic mycobiota than those of the roots. Finally, the pummelo varieties also showed some consistent alterations on the endophytic mycobiota, such as the root enrichment of Exophiala species. Our study indicates that the endophytic mycobiota of pummelos is significantly and interactively affected by plant variety and compartment effects, and suggests some fungi of interest for further tests. Full article

Urban parks are key to urban ecosystems, where soil microbe-plant-soil interactions sustain ecosystem services. Using high-throughput sequencing and multivariate statistics, this study explored how plant species diversity affects soil microbial community structure, functional diversity, and environmental drivers. Results showed that fungal and bacterial OTUs differed across plant diversity gradients, with Ascomycota (fungi) and Actinobacteriota/Proteobacteria (bacteria) dominant. Soil organic carbon (SOC) was positively correlated with Verrucomicrobia, while Acidobacteriota increased with lower SOC. Fungi were more sensitive to pH than bacteria. Partial Least Squares Path Modeling (PLS-PM) indicated that plant diversity was significantly positively associated with fungal community structure and was indirectly associated with bacterial diversity via soil factors (e.g., SOC, pH), with fungal community variation more explained than bacterial. Higher plant diversity was associated with elevated SOC and a higher relative abundance of putative nutrient-cycling taxa (e.g., Rhizobium), suggesting a potential enhancement of soil nutrient cycling capacity. This study demonstrates that plant diversity shapes microbial communities directly and via soil properties, highlighting synergistic effects. We propose arbor-shrub-herb composite vegetation in urban forest management to optimize microbial habitats and ecological services. Full article

Diet and living environments exert a profound influence on gut microbiota composition. This study presents the first comprehensive characterization of fecal bacteria, fungi, and protozoa in wild (WA) (n = 10) and captive (DA) (n = 11) wapiti (Cervus canadensis) in China. Results reveal distinct microbial profiles between the two groups. In wild wapiti, Escherichia-Shigella and UCG-005 were the dominant bacterial genera, while Succinivibrio and Treponema predominated in captive individuals. Among fungi, Agaricus and Preussia were most abundant in wild wapiti, whereas Xeromyces was identified in captive ones. For protozoa, Heteromita was the primary genus in wild wapiti, while Heteromita, Entamoeba, and Eimeria were the main genera in captive wapiti. Functional predictions further underscored these differences. In wild wapiti, bacterial and fungal functions were primarily associated with carbon metabolism and the pyruvate cycle, with mutualistic interactions prevailing among bacteria, fungi, and protozoa. Conversely, captive wapiti exhibited functional profiles centered on lipopolysaccharide and amino acid metabolism, also characterized by mutualistic coexistence among microbial communities. These findings highlight the significant impact of dietary composition on the gut microbiome. In summary, wild wapiti appear to possess a superior capacity for plant fiber utilization. These findings provide valuable data for the health management of farmed wapiti and their adaptability in natural habitats. Full article