Search Results (222)

Cotton Verticillium wilt (VW), caused by the soil-borne fungus Verticillium dahliae (V. dahliae), is a devastating disease that poses a serious threat to sustainable cotton production worldwide. Protein methylation plays a critical role in fungal adaptation to the host environment and manipulation of plant immunity. Protein arginine methyltransferases (PRMTs) are key enzymes catalyzing arginine methylation, yet their functions in V. dahliae pathogenicity remain largely unexplored. In this study, we identified VdPRMT4 in V. dahliae through homology-based screening. qRT-PCR analysis revealed that VdPRMT4 transcript levels were significantly increased during the early stages of V. dahliae infection in cotton. HIGS assays showed that silencing VdPRMT4 markedly alleviated cotton VW symptoms and reduced fungal biomass in cotton plants. Gene knockout and complementation experiments demonstrated that deletion of VdPRMT4 did not affect hyphal growth but significantly impaired sporulation capacity and severely attenuated pathogenicity on cotton. Transcriptomic analysis further indicated that loss of VdPRMT4 profoundly affected the metabolic pathways of V. dahliae, including protein processing in the endoplasmic reticulum, purine metabolism, and glycerolipid metabolism. Collectively, this study provides the first evidence that VdPRMT4 plays a critical role in stress adaptation and pathogenicity of V. dahliae, offering new insights into fungal pathogenesis and identifying potential targets for VW control. Full article

Crop losses driven by fungal pathogens remain a major constraint to global food production, reinforcing agriculture’s dependence on fungicide-based disease control. Soil acts as a long-term reservoir and key hotspot for the evolution and persistence of antifungal-resistant Fusarium. The intensive, prolonged use of overlapping single-site fungicides in agriculture strongly selects for both intrinsic and acquired resistance in soilborne Fusarium populations, contributing to major crop losses, food insecurity, and One Health concerns. This review synthesizes current knowledge on (i) target-site (CYP51, β-tubulin, cytochrome b, SDH, myosin-5) and non-target-site (ABC/MFS efflux, multidrug resistance, epigenetic regulation) resistance mechanisms across the genus Fusarium; (ii) the influence of management practices and fungicide characteristics and behaviour in soil in reshaping microbial communities and selecting for resistant Fusarium; (iii) the consequences for plant disease management and the limitations of practices like cultural and biological control; and (iv) innovative strategies for plant disease management, as well as the monitoring and detection of antifungal resistance in soils. These aspects show that soil reservoirs of antifungal-resistant Fusarium are compromising fungicide-based control and increasing risks across sectors, highlighting the urgent need for sustainable, multi-layered, integrated pest management strategies combined with robust, molecularly informed resistance monitoring. Full article

Traditional disease management, which is based on the application of synthetic chemical products, has negatively affected human health and the environment. A sustainable approach based on the application of natural compounds and microorganisms is potentially better for consumer health. Thus, the aim of this study was to evaluate the efficacy of plant-based and/or organic products against soilborne fungal pathogens of tomato. A preliminary in vitro experiment was performed to select potential putative inhibitory products (PIPs) and fungal pathogens that were then used in an in vivo experiment conducted inside a greenhouse that mimics real-world field conditions. For the greenhouse experiment, bergamot and pomegranate wastes and the commercial product EP5 were selected as the PIPs to control Agroathelia rolfsii, Fusarium oxysporum and Sclerotinia sclerotiorum growth. Each pot was artificially inoculated three days before the low-dose treatment, and one tomato seedling was transplanted into each pot four days after the treatment. Data regarding the phytosanitary status of the plants and roots, as well as their length and weight, were collected after 45 days, and the results obtained demonstrate that plant-derived products were able to mitigate fungal diseases, with pomegranate waste being the most effective. Also, the EP5 product, as a resistant inducer, was able to significantly improve the natural defense of tomato plants, resulting in it being the best PIP used. Mycological analyses were performed on the roots to assess the presence of inoculated fungal pathogens after natural product treatment. Overall, the results confirm that the PIPs are suitable for crop management, but the outcomes are variable. In general, pomegranate waste and EP5 significantly protected the roots against fungal attacks, while bergamot waste showed lower efficacy. This trend was not observed for plant length and weight, as the treated plants showed results similar to those of the untreated controls. In conclusion, natural products are a valid alternative to chemicals, as they demonstrate both efficacy and safety, but their potential should be further investigated in field trials. Full article

Several species of saprophytic filamentous fungi are able of disrupting the life cycle of certain soil-born parasites that are of veterinary and agronomy importance, offering a promising sustainable control alternative. This study consisted of designing an experimental model, using catnip (Nepeta cataria) trays to simulate a vegetated environment for evaluating the parasiticidal activity of Mucor circinelloides, Trichoderma atrobrunneum, and Duddingtonia flagrans. Fungal spores were added to treated trays before adding feces with protozoan (Eimeria spp.), and gastrointestinal nematodes (roundworms, strongyles), and untreated-control water. No differences in plant growth or vigor, regardless of fungal presence, were observed, confirming the safety of these biological agents for vegetation. In the control trays, the viability of parasites ranged from 50% to 85%. In the treated trays, the viability of Eimeria and roundworms decreased by 40–100%, and the strongyle egg counts were reduced by 74% within 15 days. It is concluded that the vegetated tray model effectively simulates field conditions and provides a reliable platform for evaluating fungal efficacy against the free-living stages of parasites, offering a versatile tool for future research on soil-borne pathogens affecting animals and plants. Full article

High-density apple (Malus domestica Borkh.) orchards yield fruits as early as three years after planting but nutrient inputs and availability are paramount to a successful orchard; sustainable practices that balance tree growth and production with environmental concerns are not widely available. In this three-year study, we implemented a split-plot design in three orchards across the Mid-Atlantic region of the USA to evaluate integrated soil management approaches that combine locally sourced carbon-based organic mulch with fertilizers on rhizosphere microbes and tree growth. Bacterial and fungal communities were sampled at the end of the first and third growing seasons in addition to soil and tree-related physicochemical properties. Mulch treatment showed the most significant effect on both the bacterial and fungal groups. Most of these changes reflect the increase in soil organic matter and the increase in carbon cycling. Sequence variants belonging to Flavobacteria and Cytophaga were enriched by the mulch application. A key result from this project is the suppression of the relative abundance of potential soil-borne plant fungal pathogens in all orchards in all years. Additionally, arbuscular mycorrhizal fungi were enriched under the mulch treatment. Microbial shifts accompanying the mulch treatments supported higher trunk cross-sectional areas by the third sampling year that increased by 33.5%. Fertilizer treatments had less pronounced effects on microbial communities. These results highlight the potential for using sustainable, integrated nutrient management strategies to promote healthy orchard soils and support vigorous tree growth while reducing fungal pathogens. Our work will contribute to regional and location-specific fertilizer recommendations for apple producers. Full article

Greenhouse cultivation enables year-round vegetable production and high yields through precise environmental regulation. Yet, the same stable microclimate that promotes crop growth also favors the proliferation of pests and diseases. This review synthesizes current knowledge on how greenhouse climate variables govern pest and disease epidemiology in tomato, cucumber, and sweet pepper. Only greenhouse-based studies were included to ensure direct relevance to protected horticulture. Microclimatic stability determines infection probability, vector behavior, and host susceptibility. Warm, humid conditions promote fungal and bacterial pathogens, whereas dry, high vapor pressure deficit (VPD) environments favor mites and thrips and enhance virus transmission. Species-specific traits further modulate vulnerability. Tomato is dominated by virus–bacterium complexes and foliar/stem fungal diseases, cucumber by phytopathogenic fungi favored by high relative humidity (RH) and soilborne pathogens, and sweet pepper by virus–vector systems and long-cycle fungal infections. Temperature exerts the strongest influence, while RH and VPD jointly regulate surface moisture and vector activity. Light intensity and spectral composition also affect pest orientation and fungal sporulation. Integrating environmental sensing, biological control, and adaptive climate regulation offers a pathway toward preventive, climate-smart Integrated Pest Management (IPM). The review highlights the emerging role of climate-informed decision-support systems (DSSs) and the need for greenhouse-specific datasets to improve pest and disease forecasting. Full article

Soil fungi play a pivotal role in maintaining ecosystem functions and regulating plant health. Although plant root traits can significantly impact the abundance and diversity of different fungal groups, the mechanism by which plant root strategies drive the assembly of soil fungal guilds remains limited. Utilizing Root Economics Space theory, this study investigates how four green manures (hairy vetch, rye, radish, and rapeseed) with contrasting root functional strategies (along the ‘fast–slow’ and ‘outsourcing–DIY’ axes) regulate the composition and functional structure of soil fungal communities. Community characteristics of three functional guilds (plant pathogens, saprophytes, and arbuscular mycorrhizal fungi), as well as relationships between these communities and plant root traits, were evaluated using a combination of Illumina high-throughput sequencing, functional annotation, and multivariate statistical analysis. Overall, different root strategies were associated with distinct fungal community patterns, potentially related to differences in root-derived resource inputs and soil properties. The ‘slow’ and ‘DIY’ strategies were associated with lower relative abundance of plant pathogenic fungi and higher relative abundance of saprotrophic fungi, whereas the ‘fast’ and ‘outsourcing’ strategies were associated with higher relative abundance of plant pathogens and AMF. These findings suggest that root functional strategies may help explain variation in fungal guild composition under different green manure species. From a practical perspective, the results provide a basis for selecting green manure species to help manage soil-borne disease risk, regulate beneficial soil microbial communities, and support more sustainable soil management in agricultural production. Full article

Clubroot caused by Plasmodiophora brassicae is a devastating soil-borne disease of oilseed rape, and physiological race differentiation of the pathogen greatly hinders disease control. The differential regulatory mechanisms of different P. brassicae races on the rhizosphere microecology remain unclear. This study aimed to reveal the race-specific effects of P. brassicae on the rhizosphere microenvironment, microbial community and nitrogen cycling of oilseed rape. A pot inoculation experiment was conducted with two typical races from Sichuan Province (race 4 CZ and race 2 KD), combined with soil physicochemical determination, high-throughput sequencing and functional prediction. The results showed that CZ exhibited a higher infection rate but a lower disease index than KD. Both races significantly decreased soil pH and reshaped soil nutrient profiles. Notably, CZ treatment caused a more pronounced pH decrease and was characterized by NH₄⁺-N accumulation, whereas KD treatment was dominated by NO₃⁻-N enrichment. Bacterial alpha diversity was increased by both races, following the order KD > CZ > CK. In contrast, fungal alpha diversity was decreased by both races, showing the pattern CK > KD > CZ. Distinct rhizosphere microbial community structures were formed under different race infections, and both races reduced the abundance of nitrogen-fixing bacteria and related functional genes. These findings indicate that distinct P. brassicae races shape race-specific rhizosphere microenvironments by differentially regulating soil acidification, nutrient availability and nitrogen-cycling functional microorganisms, thereby driving divergent pathogenic outcomes. This study is the first to reveal differential regulation of the rhizosphere microecology by distinct physiological races of P. brassicae, offering new insights for region-specific management of clubroot disease. Full article

Astragalus membranaceus suffers severe yield and quality losses due to root rot caused by Fusarium solani. To address this, we analyzed the root-associated microbial communities of healthy and diseased plants in northwest China using high-throughput sequencing. Combining community analysis with pot experiments and transcriptomic profiling, we elucidated the molecular mechanisms by which the biocontrol fungus Purpureocilliu lilacinum BP2-7 suppresses root rot. Root rot reshaped root-associated microbial structure, affecting fungal diversity more than bacterial diversity. The antagonistic effect of P. lilacinum BP2-7 against F. solani reached 71.43% in plate assays and 63.7% control efficacy in pot experiments, representing the first report of P. lilacinum application for managing root rot in A. membranaceus. Transcriptomic analysis revealed that P. lilacinum BP2-7 promotes the transition of plants from a damaged to a recovering state by modulating translation and metabolic processes, and enhancing protein homeostasis, while moderately downregulating defense-related responses to alleviate pathogen-induced excessive defense mechanisms. Additionally, twenty candidate genes involved in the direct inhibition of F. solani were identified, suggesting a role in enhancing host resistance. This study supports eco-friendly biocontrol strategies and advances understanding of plant–microbe interactions for managing soil-borne diseases in other important crops. Full article

Sclerotinia sclerotiorum is a soilborne fungal pathogen, and it is a major threat to lettuce production, causing lettuce drop. This study evaluated the antifungal effectiveness of five essential oils (EOs) (Rosmarinus officinalis, R. officinalis var. verbenone, Lavandula hybrida, Origanum majorana, and Thymus vulgaris) at 0.1%, 1%, and 10%, along with their phytotoxic effect in the field on three different crops (lettuce, tomato, and chard) following foliar application. T. vulgaris EO completely inhibited S. sclerotiorum mycelial growth at all tested concentrations. R. officinalis, L. hybrida, and O. majorana also showed full inhibition at 1% and 10%, while R. officinalis var. verbenone achieved 80–100% inhibition. R. officinalis had the least phytotoxic effects, with only a minimal effect on chard at 1%. R. officinalis var. verbenone caused low/moderate phytotoxicity in lettuce and chard but had no toxic effect on tomato. L. hybrida and O. majorana had moderate to low effects, while T. vulgaris was the most phytotoxic, significantly affecting lettuce and tomato at 1%. Further field trials are needed to define EO application protocols toward sustainable lettuce drop management without risks of phytotoxicity. Full article

To scientifically assess the effects of environmentally friendly fumigants on soil microbial communities, soils from a 7-year continuous cropping tomato greenhouse were studied, with unfumigated soil used as the control (CK). Rhizosphere soil samples treated with dazomet (DZ), metam sodium (MS) and calcium cyanamide (CC) were collected at the seedling recovery and fruiting stages. The influences of different fumigants and growth stages on soil microbial communities, tomato yield and soil-borne diseases were investigated. The results indicated that soil fumigation significantly decreased microbial community richness and diversity at the seedling recovery stage, which gradually recovered at the fruiting stage. The variation trends of microbial relative abundance at the phylum and genus levels differed among the treatments at both stages. At the phylum level, Actinobacteria and Proteobacteria were the dominant bacterial phyla, and Ascomycota was the dominant fungal phylum. Genus-level clustering revealed that the bacterial communities under MS and CC were similar to those under CK at the fruiting stage, whereas the fungal communities under all the fumigation treatments were significantly distinct from those under CK. Fumigation effectively inhibited pathogenic genera, including Amesia, Fusarium, Rhizopus and Ascobolus, at the seedling recovery stage, but some pathogens recovered at the fruiting stage. The relative abundance of Fusarium in the MS treatment increased to 8.25%. DZ treatment performed optimally: it increased beneficial genera such as Bacillus and Streptomyces at the seedling recovery stage, suppressed harmful genera, including Amesia and Fusarium, and further enriched Remersonia at the fruiting stage. Fumigation significantly improved tomato yield and reduced the incidence of soil-borne diseases. The yield of CC was the highest, at 35.41% greater than that of CK, but it was not significantly different from that of DZ in terms of cost. In conclusion, the DZ treatment had the best overall effect. Full article

Allyl isothiocyanate (AITC) is effective as a bio-based fumigant in controlling soil-borne diseases; however, the selective pressure it exerts on soil microecology and evolutionary dynamics remains inadequately characterized. This study systematically investigated the remodeling effects of continuous AITC fumigation on soil microbial communities, functional genes, and functional strains by integrating metagenomic analysis and pure culture techniques. Results demonstrate that AITC drives directional selection from “sensitive” to “tolerant” microorganisms. Fungal communities exhibit greater cumulative damage than bacterial communities, with the proportion of significantly suppressed fungi increasing linearly from 9.3% at baseline to 35.7%. At the genus level, sensitive groups were predominantly enriched in pathogen-associated genera, e.g., Pseudomonas and Xanthomonas, whereas tolerant groups, represented by Bacillus and Streptomyces, maintained ecological dominance under continuous stress. Functionally, AITC induced differential evolution of functional gene repertoires. Nitrogen cycle genes (e.g., amoC) exhibited high negative sensitivity, with significant downregulation by 20%, whereas the TCA core module in the carbon cycle exhibited strong robustness. Virulence assays confirmed EC₅₀ values for tolerant beneficial bacteria (Bacillus spp.) (>40 mg·L⁻¹) were significantly higher than those for pathogens (1.3–7.9 mg/L). This study established a microbial “sensitive-tolerant” response framework under AITC stress, revealing the core potential of endogenous tolerant strains for the precise ecological restoration of fumigated soils. Full article

Chili pepper (Capsicum annuum L.) is a globally significant economic crop, however long-term continuous cropping often induces multifaceted constraints including soil nutrient depletion, rhizosphere microbial imbalance, and pathogen accumulation, which collectively exacerbate soil-borne diseases and substantially reduce yield. Incorporating rice (Oryza sativa L.) into rotation increases the diversity of the cultivation environment and represents a cost-effective strategy to mitigate continuous-cropping obstacles. Therefore, evaluating and elucidating the role and underlying mechanisms of the chili pepper–rice rotation system in improving soil conditions and alleviating continuous cropping obstacles in chili pepper holds significant importance. This study conducted a two-year field experiment from 2023 to 2024, setting up chili pepper–rice rotation (RVR) and chili continuous cropping (CCV) treatments, to systematically analyze the effects of chili pepper–rice rotation on chili pepper yield, disease occurrence, soil nutrients, and rhizosphere microbial communities. Across 2023–2024, RVR significantly reduced the incidence of bacterial wilt and root rot, increasing yield by 10.60% in 2023 and by 61.07% in 2024 relative to CCV. Analysis of soil physicochemical properties revealed that RVR significantly promoted the accumulation of available nitrogen, phosphorus, and potassium in the soil, as well as enhanced nutrient-acquisition enzyme activity, effectively alleviating the carbon and phosphorus limitations faced by rhizosphere microorganisms. Rhizosphere microbial analysis indicated that under the RVR treatment, the abundance of pathogen-associated taxa such as Ralstonia and Fusarium significantly decreased. The co-occurrence network modularity increased, and the negative cohesion of pathogens was strengthened, thereby inhibiting pathogen expansion. Further random forest and correlation analyses demonstrated that RVR significantly contributed to yield formation by optimizing fungal metabolic pathways, such as galactose degradation, sulfate reduction, and L-tryptophan degradation. In conclusion, the chili pepper–rice rotation significantly alleviates continuous cropping obstacles and enhances yield by improving nutrient supply and regulating microbial community composition, as well as the topological structure and functional relationships of their co-occurrence networks, particularly by strengthening the role of fungi in community function and metabolic regulation. This study provides a theoretical basis for the biological and soil regulation of pepper continuous cropping obstacles and offers a feasible pathway for sustainable cultivation and green control strategies. Full article

Soybean root rot, caused by diverse soil-borne pathogens, is a major constraint on production worldwide, with yield losses ranging from 10 to 60% under epidemic conditions. Symptomatic plants were collected from three locations in Harbin, Heilongjiang Province, China, and 23 fungal isolates were recovered using standard tissue isolation procedures. Integrated morphological characterization and rDNA-ITS sequencing identified these isolates as three Fusarium species: F. oxysporum (18 isolates, 78%), F. equiseti (3 isolates, 13%), and F. brachygibbosum (2 isolates, 9%). Pathogenicity assays following Koch’s postulates confirmed F. oxysporum as the predominant and most aggressive pathogen in this region. To identify resistance resources, 200 soybean germplasm accessions adapted to Northeast China were screened using an etiolated seedling hypocotyl inoculation method with Fusarium oxysporum isolate A3 (DSI = 68.5) as the test pathogen. Disease severity indices exhibited a continuous distribution (mean = 52.84, range = 0–100), suggesting quantitative inheritance. Accessions were classified as highly resistant (13, 6.5%), resistant (40, 20%), moderately susceptible (67, 33.5%), susceptible (43, 21.5%), or highly susceptible (37, 18.5%). To explore potential molecular mechanisms underlying resistance, RT-qPCR analysis was performed on two extreme genotypes—a highly resistant line (H9477F5, DSI = 15.3) and a highly susceptible line (HN91, DSI = 88.7) at 1, 3, and 5 days post-inoculation. The resistant line maintained consistently higher expression of positive regulators GmFER and GmSOD1, with GmFER reaching 15.89-fold induction at day 3. Conversely, expression of negative regulators GmJAZ1 and GmTAP1 remained lower in the resistant line, with susceptible plants showing 5.62-fold higher GmJAZ1 expression at day 3. These findings provide characterized pathogen isolates, resistant germplasm resources (53 accessions with HR or R classifications), and preliminary molecular insights that may inform breeding strategies for improving root rot resistance in Northeast China. Full article

Sorghum (Sorghum bicolor L. Moench) is a major cereal crop cultivated in semi-arid regions, but its yield is often constrained by soilborne fungal pathogens that affect plant growth and grain quality. This study explored how Trichoderma-based bioinoculants restructure the structure and functional composition of fungal communities in distinct sorghum compartments (soil, root, seed, and stem) using ITS amplicon sequencing. Two cultivars, Kalatur and Foehn, were evaluated under control and inoculated conditions. Alpha diversity indices revealed that inoculation reduced overall fungal richness and evenness, particularly in seed and stem tissues, while selectively enhancing beneficial taxa. Beta diversity analyses (PERMANOVA, p < 0.01) confirmed significant treatment-driven shifts in community composition. LEfSe analysis identified Trichoderma and Mortierella as biomarkers of inoculated samples, whereas Fusarium, Alternaria, and Penicillium predominated in controls. The enrichment of saprotrophic and symbiotrophic taxa in treated samples, coupled with the decline of pathogenic genera, indicates a transition toward functionally beneficial microbial assemblages. These results demonstrate that Trichoderma bioinoculants not only suppress fungal pathogens but also promote the establishment of beneficial ecological groups contributing to plant and soil health. The present work provides insight into the mechanisms through which microbial inoculants modulate host-associated fungal communities, supporting their use as sustainable tools for crop protection and microbiome management in sorghum-based agroecosystems. Full article