Search Results (429)

In chili cultivation, obstacles to continuous cropping significantly compromise crop yield and soil health, whereas crop rotation can enhance the microbial environment of the soil and reduce disease incidence. However, its effects on the diversity of rhizosphere soil microbial communities are not clear. In this study, we analyzed the composition and characteristics of rhizosphere soil microbial communities under chili continuous cropping (CC) and chili–cotton crop rotation (CR) using high-throughput sequencing technology. CR treatment reduced the alpha diversity indices (including Chao1, Observed_species, and Shannon index) of bacterial communities and had less of an effect on fungal community diversity. Principal component analysis (PCA) revealed distinct compositional differences in bacterial and fungal communities between the treatments. Compared with CC, CR treatment has altered the structure of the soil microbial community. In terms of bacterial communities, the relative abundance of Firmicutes increased from 12.89% to 17.97%, while the Proteobacteria increased by 6.8%. At the genus level, CR treatment significantly enriched beneficial genera such as RB41 (8.19%), Lactobacillus (4.56%), and Bacillus (1.50%) (p < 0.05). In contrast, the relative abundances of Alternaria and Fusarium in the fungal community decreased by 6.62% and 5.34%, respectively (p < 0.05). Venn diagrams and linear discriminant effect size analysis (LEfSe) further indicated that CR facilitated the enrichment of beneficial bacteria, such as Bacillus, whereas CC favored enrichment of pathogens, such as Firmicutes. Fusarium solani MG6 and F. oxysporum LG2 are the primary chili root-rot pathogens. Optimal growth occurs at 25 °C, pH 6: after 5 days, MG6 colonies reach 6.42 ± 0.04 cm, and LG2 5.33 ± 0.02 cm, peaking in sporulation (p < 0.05). In addition, there are significant differences in the utilization spectra of carbon and nitrogen sources between the two strains of fungi, suggesting their different ecological adaptability. Integrated analyses revealed that CR enhanced soil health and reduced the root rot incidence by optimizing the structure of soil microbial communities, increasing the proportion of beneficial bacteria, and suppressing pathogens, providing a scientific basis for microbial-based soil management strategies in chili cultivation. Full article

Common bean (Phaseolus vulgaris L.) is a critical protein-rich legume supporting food and nutritional security globally. However, Fusarium wilt, caused by Fusarium solani, remains a major constraint to production, with yield losses reaching up to 84%. While biocontrol strategies have been explored, most microbial agents are sourced from mesophilic environments and show limited effectiveness under abiotic stress. Here, we report the isolation and characterization of extremophilic Bacillus spp. from the hypersaline Lake Bogoria, Kenya, and their biocontrol potential against F. solani. From 30 isolates obtained via serial dilution, 9 exhibited antagonistic activity in vitro, with mycelial inhibition ranging from 1.07–1.93 cm 16S rRNA sequencing revealed taxonomic diversity within the Bacillus genus, including unique extremotolerant strains. Molecular screening identified genes associated with the biosynthesis of antifungal metabolites such as 2,4-diacetylphloroglucinol, pyrrolnitrin, and hydrogen cyanide. Enzyme assays confirmed substantial production of chitinase (1.33–3160 U/mL) and chitosanase (10.62–28.33 mm), supporting a cell wall-targeted antagonism mechanism. In planta assays with the lead isolate (B7) significantly reduced disease incidence (8–35%) and wilt severity (1–5 affected plants), while enhancing root colonization under pathogen pressure. These findings demonstrate that extremophile-derived Bacillus spp. possess robust antifungal traits and highlight their potential as climate-resilient biocontrol agents for sustainable bean production in arid and semi-arid agroecosystems. Full article

Almond decline and dieback have become significant challenges in newly established orchards, with symptoms including internal necrosis, canker, and external gummosis. This work aims to explore the potential fungal and bacterial causative agents through metabarcoding and traditional culture plate isolation across six almond cultivars. Our results emphasize the multifactorial nature of almond decline and dieback, with possible co-infections by opportunistic fungi and bacteria playing a central role. Classical isolation identified 47 fungal species or genera, including Diaporthe amygdali, Diplodia corticola, Phytophthora sp., and several Fusarium species. Almond metabarcoding revealed a more diverse microbial community, highlighting the prevalence of soilborne pathogens such as Neocosmospora rubicola, Dactylonectria estremocensis, and Plectosphaerella niemeijerarum. Soil metabarcoding suggested that these pathogens likely originate from nursery substrates or soils shared with other crops, such as olives and vineyards, that serve as a source of inoculum. ‘Soleta’ generally presented lower richness when compared to the other tested cultivars, suggesting a higher degree of biotic stress and decreased plant resilience. This study highlights the value of integrating NGS approaches to comprehensively study complex diseases and the need for further research on pathogen interactions and cultivar susceptibility for the future development of new sustainable, targeted management strategies in almond orchards. Full article

Root rot is one of the most serious diseases affecting Astragalus membranaceus, significantly reducing its yield and quality. This study focused on root rot in Astragalus membranaceus var. mongholicus. Pathogenic fungi were isolated and identified. The pathogenicity of seven strains of pathogenic fungi was verified according to Koch’s postulates. The inhibitory effects of eight classic fungicides and nine strains of biocontrol agents on the pathogenic fungi were determined using the mycelial growth rate method. Through morphological and ITS phylogenetic analyses, strains CDF5, CDF6, and CDF7 were identified as Fusarium oxysporum, while strains CDF1, CDF2, CDF3, and CDF4 were identified as Fusarium solani. Indoor virulence tests showed that, among the eight tested fungicides, carbendazim exhibited the strongest inhibitory effect on the mycelial growth of both F. oxysporum and F. solani, with a half-maximal effective concentration (EC₅₀) value of (0.44 ± 0.24) mg/mL, making it a highly promising chemical agent for the control of A. membranaceus var. mongholicus root rot. Among the nine biocontrol agents, KRS006 showed the best inhibitory effect against the seven pathogenic strains, with an inhibition rate ranging from 42.57% to 55.51%, and it can be considered a candidate strain for biological control. This study identified the biocontrol strain KRS006 and the chemical fungicide carbendazim as promising core agents for the biological and chemical control of A. membranaceus var. mongholicus root rot, respectively, providing a theoretical foundation for establishing a dual biocontrol–chemical control strategy. Based on the excellent performance of the biocontrol bacteria and fungicides in the pathogen control tests, future research should focus on field trials to verify the synergistic effect of this integrated control strategy and clarify the interaction mechanism between the antibacterial metabolites produced by the biocontrol bacteria KRS006 and carbendazim. Additionally, continuous monitoring of the evolution of Fusarium spp. resistance to carbendazim is critical to ensure the long-term sustainability of the integrated control system. Full article

Fusarioid fungi, members of the Nectriaceae within the Hypocreales (Ascomycota), exhibit diverse ecological roles and possess complex phylogenetic relationships, including endophytic, saprophytic, and pathogenic lifestyles. Among them, the genera Fusarium and Neocosmospora are particularly significant in agriculture and medicine. However, the boundaries between their species remain taxonomically contentious. In this study, 22 representative isolates from plant, fungal, and insect hosts were subjected to a polyphasic taxonomic approach that integrated morphological characterization, multilocus phylogenetic analyses, and phylogenomic analysis based on 4,941 single-copy orthologous genes. Consequently, five new species (F. dracaenophilum, F. puerense, F. wenshanense, N. alboflava, and N. fungicola) were described, and F. qiannanense and N. solani were recorded from new host species. The resulting phylogenomic tree topology was highly congruent with the multilocus phylogeny, providing robust support for the taxonomic distinction between Fusarium and Neocosmospora. This study provides new insights into the taxonomy of fusarioid fungi and has important implications for plant disease management, biodiversity conservation, and the study of fungal evolution. Full article

Several species of Fusarium are reported to infect inflorescences of high-THC-containing cannabis (Cannabis sativa L.) plants grown in greenhouses in Canada. These include F. graminearum, F. sporotrichiodes, F. proliferatum, and, to a lesser extent, F. oxysporum and F. solani. The greatest concern surrounding the infection of cannabis by these Fusarium species, which cause symptoms of bud rot, is the potential for the accumulation of mycotoxins that may go undetected. In the present study, both naturally infected and artificially infected inflorescence tissues were tested for the presence of fungal-derived toxins using HPLC-MS/MS analysis. Naturally infected cannabis tissues were confirmed to be infected by both F. avenaceum and F. graminearum using PCR. Pure cultures of these two species and F. sporotrichiodes were inoculated onto detached inflorescences of two cannabis genotypes, and after 7 days, they were dried and assayed for mycotoxin presence. In these assays, all Fusarium species grew prolifically over the tissue surface. Tissues infected by F. graminearum contained 3-acetyl DON, DON, and zearalenone in the ranges of 0.13–0.40, 1.18–1.91, and 31.8 to 56.2 μg/g, respectively, depending on the cannabis genotype. In F. sporotrichiodes-infected samples, HT2 and T2 mycotoxins were present at 13.9 and 10.9 μg/g in one genotype and were lower in the other. In F. avenaceum-inoculated tissues, the mycotoxins enniatin A, enniatin A1, enniatin B, and enniatin B1 were produced at varying concentrations, depending on the isolate and cannabis genotype. Unexpectedly, these tissues also contained detectable levels of 3-acetyl DON, DON, and zearalenone, which was attributed to apre-existing natural infection by F. graminearum that was confirmed by RT-qPCR. Beauvericin was detected in tissues infected by F. avenaceum and F. sporotrichiodes, but not by F. graminearum. Naturally infected, dried inflorescences from which F. avenaceum was recovered contained beauvericin, enniatin A1, enniatin B, and enniatin B1 as expected. Uninoculated cannabis inflorescences were free of mycotoxins except for culmorin at 0.348 μg/g, reflecting pre-existing infection by F. graminearum. The mycotoxin levels were markedly different between the two cannabis genotypes, despite comparable mycelial colonization. Tall fescue plants growing in the vicinity of the greenhouse were shown to harbor F. avenaceum and F. graminearum, suggesting a likely external source of inoculum. Isolates of both species from tall fescue produced mycotoxins when inoculated onto cannabis inflorescences. These findings demonstrate that infection by F. graminearum and F. avenaceum, either from artificial inoculation or natural inoculum originating from tall fescue plants, can lead to mycotoxin accumulation in cannabis inflorescences. However, extensive mycelial colonization following prolonged incubation of infected tissues under high humidity conditions is required. Inoculations with Penicillium citrinum and Aspergillus ochraceus under these conditions produced no detectable mycotoxins. The mycotoxins alternariol and tentoxin were detected in several inflorescence samples, likely as a result of natural infection by Alternaria spp. Fusarium avenaceum is reported to infect cannabis inflorescences for the first time and produces mycotoxins in diseased tissues. Full article

Soilborne diseases cause losses of 45–70% in faba bean in Ethiopia. Studies were undertaken to define soilborne pathogens and their complexes in Ethiopia. First, the severity of root rot was assessed in 150 field sites across seven Ethiopian regions. Soil samples were collected, and the DNA of 29 pests and pathogens was quantified using a commercial quantitative PCR (qPCR) soil testing service. There was a very high incidence rate of Macrophomina phaseolina, as well as Pythium clades F and I. The other detected species in order of incidence included Fusarium redolens, Rhizoctonia solani, Aphanomyces euteiches, Phytophthora megasperma, Sclerotinia sclerotiorum and S. minor, and Verticillium dahliae, as well as low levels of Thielaviopsis basicola. Five anastomosis groups (AG) of R. solani, namely AG2.1, AG2.2, AG3, AG4, and AG5, were detected, of which AG2.2 and AG4 were most prevalent. We believe this is the first report of occurrence for Ethiopia of A. euteiches, Ph. megasperma, T. basicola, and the five AGs for R. solani. There were very high incidence rates of the foliar pathogens Botrytis cinerea, B. fabae, Didymella pinodes, and Phoma pinodella and of the nematode Pratylenchus thornei, followed by P. neglectus and P. penetrans. The root rot severity and distribution varied significantly across regions, as well as with soil types, soil pH, and soil drainage. Subsequently, metabarcoding of the soil DNA was undertaken using three primer pairs targeting fungi (ITS2), Fusarium species (TEF1 α), and Oomycetes (ITS1Oo). The ITS2 and TEF1α primers emphasized F. oxysporum as the most abundant soilborne fungal pathogen and highlighted F. ananatum, F. brachygibbosum, F. brevicaudatum, F. clavum, F. flagelliforme, F. keratoplasticum, F. napiforme, F. nelsonii, F. neocosmosporiellum, F. torulosum, and F. vanettenii as first reports of occurrence for Ethiopia. The ITS1Oo primer confirmed Pythium spp. as the most prevalent of all Oomycetes. Full article

Accurate and early detection of plant diseases is essential for effective management and the advancement of sustainable smart agriculture. However, building large annotated datasets for disease classification is often costly and time-consuming, requiring expert input. To address this challenge, this study explores the integration of few-shot learning with hyperspectral imaging to detect four major fungal diseases in tomato plants: Alternaria alternata, Alternaria solani, Botrytis cinerea, and Fusarium oxysporum. Following inoculation, hyperspectral images were captured every other day from Day 1 to Day 7 post inoculation. The proposed hybrid method includes three main steps: (1) preprocessing of hyperspectral image cubes, (2) deep feature extraction using the EfficientNet model, and (3) classification using Manhattan distance within a few-shot learning framework. This combination leverages the strengths of both spectral imaging and deep learning for robust detection with minimal data. The few-shot learning approach achieved high detection accuracies of 85.73%, 80.05%, 90.33%, and 82.09% for A. alternata, A. solani, B. cinerea, and F. oxysporum, respectively, based on data collected on Day 7 post inoculation using only three training images per class. Accuracy improved over time, reflecting the progressive nature of symptom development and the model’s adaptability with limited data. Notably, A. alternata and B. cinerea were reliably detected by Day 3, while A. solani and F. oxysporum reached dependable detection levels by Day 5. Routine visual assessments showed that A. alternata and B. cinerea developed visible symptoms by Day 5, whereas A. solani and F. oxysporum remained asymptomatic until Day 7. The model’s ability to detect infections up to two days before visual symptoms emerged highlights its value for pre-symptomatic diagnosis. These findings support the use of few-shot learning and hyperspectral imaging for early, accurate disease detection, offering a practical solution for precision agriculture and timely intervention. Full article

Fusarium wilt, caused by Fusarium solani, is a devastating disease that leads to significant losses in ginger (Zingiber officinale) crops worldwide. To explore the molecular mechanisms underlying F. solani infection and disease progression, we performed a comparative transcriptome analysis of ginger rhizomes during storage, comparing inoculated and non-inoculated samples. A total of 647 and 6398 DEGs were identified in the 1.5- and 2-day infection groups, respectively. KEGG analysis revealed that most DEGs were enriched in the plant–pathogen interaction pathway, with both PTI and ETI being activated. Six DEGs in this pathway were validated by qRT-PCR at two time points, showing a strong correlation with FPKM values from the transcriptome data. Furthermore, transient expression analysis in Nicotiana benthamiana leaves demonstrated that overexpressing ZoCEBiP1 helped scavenge excess ROS, thereby reducing disease severity. Transcriptional profiling of DEGs in the plant–pathogen interaction pathway revealed significant changes in genes involved in ROS and NO metabolism. In F. solani-infected ginger rhizomes, levels of H₂O₂ and O₂⁻ were elevated, along with increased activities of antioxidant enzymes (POD, CAT, SOD, and APX) and higher NO content and NOS activity. These findings elucidated the early defense response of ginger rhizomes to F. solani infection and provided insights for developing effective strategies to manage fungal diseases. Full article

Root rot, a globally devastating disease of common bean (Phaseolus vulgaris L.), remains a major constraint on bean production across China. Despite its agricultural impact, the pathogen complex associated with this disease has been poorly characterized in most provinces. To address this critical knowledge gap, we conducted nationwide surveys during 2016–2018, systematically sampling 1–10 symptomatic plants from each of 121 (2016) and 170 (2018) field sites across 17 provinces in China’s major vegetable production regions. Isolates obtained from symptomatic root tissues underwent morphological screening, followed by molecular identification using partial sequences of EF1-α for Fusarium species and ITS regions for other genera. Pathogenicity of representative isolates was subsequently confirmed through controlled greenhouse assays. This integrated approach revealed fourteen fungal and oomycete genera, with Fusarium (predominantly F. oxysporum and F. solani) and Rhizoctonia (R. solani) emerging as the most prevalent pathogens. Notably, pathogen composition exhibited significant regional variation and underwent temporal shifts across developmental stages. Additionally, F. oxysporum, F. solani, and R. solani demonstrated significant interspecies associations with frequent co-occurrence in bean root rot systems. Collectively, this first comprehensive characterization of China’s common bean root rot complex not only clarifies spatial–temporal pathogen dynamics but also provides actionable insights for developing region- and growth stage-specific management strategies, particularly through targeted control of dominant pathogens during key infection windows. Full article

In recent years, the excessive use of pesticides has raised environmental and health concerns, which has led to research into natural alternatives. Essential oils may represent a sustainable solution to this problem. In this study, essential oils from Thymbra capitata (L.) Cav., Eucalyptus globulus Labill, and Mentha piperita L. were analyzed by GC–MS and tested in vitro using the poisoned food technique against six olive pathogen fungi: Alternaria sp., Arthrinium marii, Colletotrichum acutatum, Fomitiporia mediterranea, Fusarium solani, and Verticillium dahliae. T. capitata essential oil (0.1 g/L) showed the highest antifungal activity when compared to E. globulus and M. piperita essential oils, which exhibited significantly lower efficacy against the tested olive phytopathogenic fungi. GC–MS analysis revealed that carvacrol is the main compound (76.1%) in T. capitata essential oil. A comparison of the inhibitory effect of T. capitata essential oil (0.1 g/L) and carvacrol (0.07 g/L) on selected fungal strains showed similar results, with carvacrol slightly more effective, although the differences were mostly statistically insignificant, except for C. acutatum. To the authors knowledge, this is the first study demonstrating the inhibitory effect of Thymbra capitata essential oil against A. marii and F. mediterranea. The results of this study represent a basis for the development of new biochemical biopesticides based on T. capitata essential oil as a useful tool for the contrast of some fungal olive tree diseases. Full article

Cepharanthine (CEP) is a natural bisbenzylisoquinoline alkaloid known for its antibacterial, antiviral, and anti-inflammatory activities. Its antifungal effect, however, has not been well studied. In this work, we used machine learning-based virtual screening with Random Forest, Neural Network, and Support Vector Machine models to identify potential inhibitors of Fusarium solani. CEP was selected as a candidate and tested experimentally. The results showed that it inhibited the growth of Fusarium solani, Fusarium proliferatum, Fusarium oxysporum, Alternaria alternata, and Botrytis cinerea. It also reduced the sporulation and spore germination of Fusarium solani and disrupted its redox balance. Transcriptome analysis showed changes in gene expression related to basic metabolic pathways. Molecular docking suggested that CEP binds to the FsCFEM1 protein, and molecular dynamics simulations confirmed stable binding, with key roles for residues THR748 and LEU950. These results suggest that CEP is a potential bio-based antifungal agent and provide novel insights into its mechanism against Fusarium solani. Full article

The glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene plays a pivotal role in the glycolysis/gluconeogenesis process, contributing significantly to glycosyl donor synthesis, plant growth and development, and stress responses. Gastrodia elata Bl., a heterotrophic plant in the Orchidaceae family, has its dried tubers used as the traditional Chinese medicine. This study identified three GeGAPDH genes in G. elata, all encoding basic, stable, hydrophilic proteins. Phylogenetic analysis and subcellular localization predictions categorized GeGAPDH1 as a plastid subtype, while GeGAPDH2 and GeGAPDH3 were classified as cytoplasmic subtypes. Prokaryotic expression experiments demonstrated successful expression of the GeGAPDH1 protein in Escherichia coli, which exhibited significant GAPDH enzymatic activity. Subcellular localization experiments showed that GeGAPDH1 was localized in the plastid. Expression analysis indicated that the three GeGAPDH genes were predominantly expressed in tubers. Under low-temperature stress, although the total GAPDH enzyme activity in tubers did not change significantly, the expression of GeGAPDH1 was significantly up-regulated, while GeGAPDH2 and GeGAPDH3 were significantly down-regulated. This suggests that different subtypes of GeGAPDH may regulate cold resistance through different pathways. Upon pathogen infection, the GeGAPDH gene family exhibited pathogen-specific regulatory patterns. During infection by Fusarium oxysporum, both the expression levels of all three GeGAPDH genes and the total GAPDH enzyme activity in tubers increased significantly; however, F. solani infection induced a significant increase in total GAPDH enzyme activity without significant changes in gene expression. These results suggest that the GeGAPDH gene family may respond to different pathogen infections through transcriptional or translational regulation mechanisms. This study systematically identified and characterized the GeGAPDH gene family in G. elata, providing a theoretical foundation for understanding the functional differentiation of GAPDH in heterotrophic plants. Full article

Lanzhou lily is a plant native to China with high edible, medicinal, and ornamental value that is relatively susceptible to Fusarium wilt. In this study, the application of Trichoderma longibrachiatum SMF2 (TlSMF2) effectively controlled Lanzhou lily wilt disease caused by Fusarium oxysporum and F. solani. TlSMF2 and the antimicrobial peptaibols trichokonins (TKs) produced by TlSMF2 inhibited the mycelial growth and spore germination of these two pathogens. Transcriptome analysis revealed that the TKs-induced defense responses of Lanzhou lily were mainly related to the production of plant hormones and defense enzymes. In detail, TKs treatment increased the levels of salicylic acid (SA) and jasmonic acid (JA) and the expression of their related genes and upregulated the activities of chitinase and phenylalanine ammonia-lyase (PAL). Moreover, TKs caused the induction of LzWRKY26 and LzWRKY75, which is highly homologous to LrWRKY3 that positively regulates Lilium regale resistance to F. oxysporum. LzWRKY26 expression was also induced by SA and MeJA treatments and F. oxysporum infection, which was consistent with the findings that many cis-acting elements associated with phytohormones and stress responses are present in the promoter region of LzWRKY26. Therefore, the biocontrol mechanisms of TlSMF2 against Lanzhou lily wilt disease involve substrate competition and toxicity against pathogens, as well as the induction of systemic resistance in plants. Our results highlight a promising biological control agent for soil-borne fungal diseases and offer deeper insights into the biocontrol mechanisms of TlSMF2. Full article

This study investigates the main insects and endophytic fungi that promote the formation of agarwood in Aquilaria sinensis (Lour.) Spreng. and elucidates the effects and mechanisms of different ‘insect + fungus’ combinations on agarwood formation. The results showed that 16 strains of endophytic fungi were isolated from A. sinensis. Fusarium solani, Penicillium chrysogenum, Fusarium equiseti, and Phaeoacremonium alvesii were identified as dominant fungi promoting agarwood formation, while Nadezhdiella cantori was recognized as the dominant insect facilitating this process. The optimal ‘insect + fungus’ combination was Nadezhdiella cantori + Fusarium equiseti. The average agarotetrol contents were 0.046% and 0.054% in February and June, respectively, which were significantly higher than those in cold drilling, fungal-only, and insect-only treatments. RNA sequencing revealed 23,801 differentially expressed unigenes in cjYB1Z4 (optimal combination) versus control BMZ. Upregulated unigenes were enriched in isoflavone biosynthesis, flavonoid biosynthesis, and sesquiterpenoid and triterpene biosynthesis. Fifty sesquiterpene-related differential unigenes encoded seven key enzymes in the MVA pathway, seven key enzymes in the MEP pathway, and seven terpene synthases. Co-expression network analysis indicated that transcription factors (e.g., WRKY33, ABF, WRKY2) potentially regulate agarwood sesquiterpene formation. This work elucidates preliminary effects and molecular mechanisms of insect- and fungi-induced agarwood formation in A. sinensis, advancing agarwood induction technology. Full article