Search Results (87)

The genus Burkholderia encompasses both plant pathogenic and beneficial species, yet the genomic determinants underlying this lifestyle divergence remain poorly understood. Using 16S rRNA sequencing of 100 rice cultivars, our companion study demonstrated that resistant varieties are enriched in beneficial Burkholderiaceae, leading to the isolation of three phenotypically contrasting strains. Here, we present comparative genomic analyses of non-pathogenic biocontrol strain Burkholderia vietnamiensis J14EpLeaf2 and pathogenic strains Burkholderia gladioli A1EpSeed5 and Burkholderia cepacia J14Eple. Pathogenic strains possess significantly larger genomes (8.36–8.46 Mb) enriched in mobile genetic elements compared to the streamlined 6.95 Mb genome of B. vietnamiensis. CAZyme analysis revealed broader repertoires of glycoside hydrolases and polysaccharide lyases in pathogens, consistent with enhanced plant cell wall degradation. B. gladioli possesses a complete T3SS and expanded T6SS with 301 predicted effectors, while B. cepacia lacks structural T3SS genes but harbors 271 candidate effectors predicted to be secreted via alternative secretion pathways, compared to 180 in B. vietnamiensis. Notably, B. cepacia harbors cystic fibrosis-associated markers (cable pili, ZmpA/ZmpB), raising significant biosafety concerns that preclude its agricultural application. LC-MS validated IAA, ornibactin, and AHL production in B. vietnamiensis, supporting its plant growth-promoting and biocontrol functions. Computational PPI networks predicted distinct interaction landscapes requiring experimental validation. This study provides a genomic framework for distinguishing pathogenic from beneficial Burkholderia and supports B. vietnamiensis as a safe biocontrol agent while cautioning against B. cepacia J14Eple. Full article

Volatile organic compounds (VOCs) have garnered substantial research interest in recent years due to their biodegradability, low toxicity, and potent antimicrobial properties against various plant pathogens. As a typical herbivore-induced plant volatile (HIPV) elicited by Nilaparvata lugens (Brown planthopper, BPH), (E)-2-hexenal has been identified as a promising natural antimicrobial agent. In this study, we investigated the protective potential of (E)-2-hexenal against Rhizoctonia solani (R. solani) in rice, focusing on both its direct antifungal activity and host-mediated defense mechanisms. In vitro antifungal assays demonstrated that treatment with 100 μL/mL (E)-2-hexenal resulted in a 91.07% inhibition of R. solani mycelial growth after 48 h. Scanning electron microscopy (SEM) observation and chitinase activity analysis revealed that (E)-2-hexenal suppressed fungal growth by disrupting the structural integrity of the pathogen cell wall. Furthermore, 100 μL/mL (E)-2-hexenal effectively conferred protection to detached rice leaves. Whole-plant inoculation assays confirmed that (E)-2-hexenal pretreatment significantly alleviated disease symptoms and triggered systemic resistance in rice plants. Physiological and biochemical analyses showed that (E)-2-hexenal treatment enhanced the activities of defense-related enzymes, elevated hydrogen peroxide (H₂O₂) levels, and promoted the accumulation of defensive metabolites in rice leaves. HPLC-MS quantification further revealed significant increases in the endogenous levels of jasmonic acid (JA) and salicylic acid (SA). Transcriptomic KEGG pathway enrichment analysis indicated that differentially expressed genes (DEGs) were mainly involved in alpha-linolenic acid metabolism, diterpenoid biosynthesis, phenylpropanoid biosynthesis, plant–pathogen interaction, and plant hormone signal transduction. Collectively, these results suggest that (E)-2-hexenal enhances rice resistance to sheath blight disease via a dual-action mechanism: direct inhibition of fungal development and activation of host immune responses. Our findings highlight the potential application of (E)-2-hexenal and other VOCs in developing eco-friendly strategies for sustainable rice disease management. Full article

Rice sheath blight caused by Rhizoctonia solani is one of the most destructive diseases of rice. Bixafen has been proposed as a promising control agent with moderate resistance risk; however, its cellular mode of action remains unclear. Therefore, this study investigated the antifungal mechanism of bixafen from the perspective of programmed cell death (PCD). Bioassays showed that bixafen strongly inhibited R. solani, with a median effective concentration (EC₅₀) of 1.16 μg/mL. Morphologically, bixafen induced hyphae collapse, vacuolization, chromatin aggregation, and mitochondrial disruption. Transcriptome analysis further revealed that bixafen significantly altered the expression of genes involved in the tricarboxylic acid cycle and PCD pathways. In addition, bixafen, at the concentration of EC₅₀, triggered ROS accumulation accompanied by increased malondialdehyde (MDA) levels. These oxidative effects led to mitochondrial damage, characterized by loss of membrane potential, reduced Tomm20 expression, and decreased Aco-2 activity. Subsequently, bixafen activated apoptosis, as evidenced by induction of the mitochondria-associated inducer of death (AMID), down-regulation of Bcl-2, and DNA fragmentation. Moreover, bixafen also induced autophagy by reducing p62 and increasing Beclin-1 expression, which suggests the clearance of damaged mitochondria. Collectively, these results demonstrated that bixafen induced mitochondrial-dependent apoptosis and autophagy in R. solani, which provided novel insights into its cellular antifungal mechanism and supported its potential as a PCD-targeted fungicide. Full article

Rice production experiences significant losses due to fungal diseases, particularly rice sheath blight caused by Rhizoctonia solani. Despite the intensive and continuous use of synthetic fungicides, diseases severity has not reduced and control has become increasingly challenging; therefore, the search for environmentally friendly and sustainable products has intensified. Here, we conducted a chemical characterization of Xylopia frutescens and using in silico analysis evaluated the interaction of their two major compounds with lectin protein site of R. solani. In vitro tests using increasing concentrations of essential oil against R. solani were performed. Subsequently, in four varieties of rice, five concentrations of X. frutescens essential oils were applied and evaluated the phytotoxicity effect as well the potential of Xylopia frutescens essential oil for controlling, both preventively and curatively, rice sheath blight. We further investigate the selectivity of this essential oil towards the non-target organism, Trichoderma asperellum. Our analysis revealed that trans-pinocarveol and myrtenal are the main compounds of X. frutescens essential oil and interact with the lectin of R. solani, supporting the antifungal properties of X. frutescens essential oil. In in vitro conditions, the highest tested concentrations of X. frutescens essential oil inhibited the pathogen’s sclerotia and mycelial growth. Under greenhouse conditions, the treatments caused low phytotoxicity and effectively reduced disease severity when applied, both preventively and curatively. Furthermore, the biocontrol agent T. asperellum exhibited tolerance to X. frutescens essential oil. Collectively, our findings demonstrate the potential of X. frutescens essential oil for the development of botanical fungicides capable of controlling R. solani without harming beneficial non-target organisms such as T. asperellum. Full article

Rapid and accurate phenotypic screening of rice germplasms is crucial for identifying potential sources of rice sheath blight resistance. However, visual and/or caliper-based estimations of coalescing, necrotic, diseased lesions of rice sheath blight (ShB)-infected plants are time-consuming, labor-intensive, and subject to human rater subjectivity. Here, we propose the use of RGB images and image processing techniques to quantify ShB disease progression in terms of lesion height and diseased area. To be specific, we developed a Pixel Color- and Coordinate-based K-Means Clustering (PCC-KMC) algorithm utilizing the Mahalanobis distance metric, aimed at accurately segmenting symptomatic and non-symptomatic regions within rice stem images. The performance of PCC-KMC, combined with manual classification of the segmented regions, was evaluated using Lin’s concordance correlation coefficient (${\rho }_c$) by comparing its results to visual measurements of ShB lesion height (cm) and to lesion/diseased area (cm₂) measured using ImageJ. Low bias (C_b) and high precision (r) were observed for absolute lesion height (C_b = 0.93, r = 0.94) and absolute symptomatic area (C_b = 0.98, r = 0.97) studies. Furthermore, to automatically classify the segmented regions produced by the PCC-KMC algorithm, we employed a convolutional neural network (CNN). Unlike conventional CNNs that require fixed-size image inputs, our CNN is designed to take the RGB histogram of each segmented region (a 1000 by 3 representation) as input and determine whether the region corresponds to ShB infection. This design effectively handles the arbitrary sizes and irregular shapes of segmentation regions generated by PCC-KMC. Our CNN was trained based on an 85%:15% composition for the training and testing dataset from a total of 168 ShB-infected stem sample images, recording 92% accuracy and 0.21 loss. PCC-KMC-CNN also showed high accuracy and precision for the absolute lesion height (C_b = 0.86, r = 0.90) and absolute diseased area (C_b = 0.99, r = 0.97) studies, indicating that PCC-KMC combined with automatic CNN-based classification performs very effectively. These results demonstrate that the potential of our methodology to serve as an alternative to the traditional visual-based ShB disease severity assessment and can be considered to be utilized for lab-scale, high-throughput phenotyping of rice ShB. Full article

Rice sheath blight caused by Rhizoctonia solani is a devastating global rice disease. This study aimed to isolate biocontrol bacteria from the medicinal plant Bletilla striata for managing the disease. Strain A1 demonstrated the strongest antagonistic activity, with a 91.92% inhibition rate against R. solani in vitro. It also exhibited a broad antifungal spectrum against ten plant pathogenic fungi. Morphological and molecular (16S rRNA and recA genes) analysis identified strain A1 as Pseudomonas koreensis. In detached leaf assays, lesion length was significantly reduced. Pot and field trials showed control efficacies of 65.54% and 72.53%, respectively, comparable to the chemical agent Jinggangmycin. Strain A1 secreted extracellular enzymes (protease, β-1,3-glucanase), siderophores, and auxin (IAA), and possessed phosphate-solubilizing and nitrogen-fixing capabilities. The strain significantly enhanced the activities of key defense enzymes (POD, PAL, PPO, CAT, SOD) in rice. Furthermore, both its sterile culture filtrate and the corresponding crude ethyl acetate extract exhibited strong, direct suppression of R. solani growth. LC-MS analysis identified potential antifungal compounds, including Pseudomonic Acid, Artemisinin, and Tetradecane, in the extract. In conclusion, P. koreensis A1 is a promising biocontrol and plant growth-promoting candidate for sustainable management of rice sheath blight. Full article

This study investigated the effects of different water management practices on the growth, yield, and grain quality of rice grown under environmentally friendly farming methods in Apgok-Ri, Gungnyu-Myeon, Uiryeong-Gun, from 2022 to 2024. Treatments included mid-season drainage for 2, 3, or 4 weeks (2MD, 3MD, 4MD), followed by either low-level water management (MD-1) or alternate wetting and drying (MD-2), with continuous flooding (CF) as the control. The rice variety was machine-transplanted on 9–10 June, and organic fertilizer (90 kg N/ha) was applied as a basal dressing. Water treatments were initiated in mid-July each year. The highest yield was consistently recorded in the 2MD-2 treatment, with 5.85, 5.74, and 5.38 tons/ha from 2022 to 2024, representing 15.0%, 14.5%, and 7.8% increases over CF, respectively. On average, alternate irrigation (MD-2) resulted in higher yields than low-level water management (MD-1) by 1.19–5.90%. Grain quality was also highest in 2MD-2, showing the greatest percentage of ripened grains each year, whereas CF had the highest proportion of immature and unripe grains. Crude protein content in brown rice was lowest in 3MD-2 (6.12%), followed by 2MD-2 (7.51%). Incidences of major diseases such as sheath blight, rice blast, panicle blight, and bacterial grain blight were highest in the CF treatment. Rice leaf blight was not significantly different in 2022, but was most prevalent in CF in 2023 and 2024. There were no major differences in brown planthopper and false smut incidence, although false smut peaked in CF in 2024. These findings suggest that 2-week mid-season drainage followed by alternate irrigation (2MD-2) is an effective strategy to improve yield, grain quality, and disease resistance in sustainable rice farming systems. Full article

Improving the efficacy of microbial biocontrol agents is a pivotal strategy for sustainable management of rice blast and sheath blight caused by Pyricularia oryzae and Rhizoctonia solani, respectively, in Vietnam. In this study, Trichoderma sp. TVN-A0 and Trichoderma sp. TVN-H0 were irradiated by gamma to generate mutants for screening the enhanced antagonistic activity against P. oryzae and R. solani. The potential mutants were screened by antifungal metabolite production via the cellophane membrane assay (I_CM), antagonistic performance through dual culture confrontation assays (I_DC), volatile organic compound bioassays (I_VOCs), and chitinase activity. As a result, among five potential mutants derived from each wild-type strain (AM1-AM5 and HM1-HM5), mutant AM2 originated from TVN-A0, and mutant HM2 derived from TVN-H0 demonstrated the highest inhibition rates and chitinase activities. The AM2 exhibited I_CM of 96.71% against R. solani, 92.57% against P. oryzae, I_DC of 87.76%, and I_VOCs of 83.57%, while HM2 possessed I_CM of 95.33% against R. solani, 85.28% against P. oryzae, I_DC of 91.24%, and I_VOCs of 79.33%. The genetic differences among mutants and their parents were investigated by RAPD. The non-GMO AM2 and HM2 mutants are promising candidates for biocontrol of the diseases caused by P. oryzae and R. solani in Vietnam. Full article

Sheath blight (ShB), caused by the necrotrophic fungus Rhizoctonia solani (R. solani), poses severe threats to global rice production. Developing a resistant variety with an ShB-resistance gene is one of most efficient and economical approaches to control the disease. Here, we identified a highly conserved chloroplast-localized stem-loop-binding protein encoding gene (OsCSP41b), which shows great potential in developing an ShB-resistant variety. OsCSP41b-knockout mutants exhibit chlorotic leaves and increased ShB susceptibility, whereas OsCSP41b-overexpressing lines (CSP41b-OE) display significantly enhanced resistance to R. solani, as well as to drought, and salinity stresses. Notably, CSP41b-OE lines present a completely comparable grain yield to the wild type (WT). Transcriptomic analyses reveal that chloroplast transcripts and photosynthesis-associated genes maintain observably elevated stability in CSP41b-OE plants versus WT plants following R. solani infection, which probably accounts for the enhanced ShB resistance of CSP41b-OE. Our findings nominate the OsCSP41b gene as a promising molecular target for developing a rice variety with stronger resistance to both R. solani and multi-abiotic stresses. Full article

Sheath blight (ShB), caused by the necrotrophic fungus Rhizoctonia solani, is one of the most serious rice diseases worldwide. In this study, we successfully grafted salicylic acid (SA) onto mesoporous silica nanoparticles through an amide-bond coupling method, forming functionalized MSN-SA nanoparticles. Physicochemical characterization showed that the MSN-SA nanoparticles were spherical, with an average particle size of approximately 30 nm and an SA loading rate of around 7.21%. The assessment of ShB resistance revealed that both SA and MSN-OH treatments were capable of inducing resistance to a certain extent. When SA and MSN-OH were applied in combination, the resistance was further augmented, indicating an additive effect between them. Intriguingly, MSN-SA treatment (50% in Lemont) exhibited a higher and more durable control efficacy compared with SA + MSN-OH treatment (33%). Moreover, field experiments demonstrated that the MSN-SA was safe for rice, and under severe disease conditions, it could recover 16.7% of the yield loss, thus highlighting its substantial application value. Further transcriptome analysis and physicochemical assays suggested that MSN-SA released SA in a slow and continuous manner, thus persistently activating the immune response, and that MSN-SA integrated the effects of SA and MSN-OH, thereby enhancing the ShB resistance. Altogether, our results provide new perspectives and a novel nanomaterial-based immune elicitor for the green control of ShB. Full article

Transcription factors are pivotal molecules involved in transcriptional and post-transcriptional regulation in plants, playing a crucial role in combating biological stress. Here, we have characterized a regulatory factor, OsbHLH34, which governs the response of rice to infection by Rhizoctonia solani AG1-IA. The expression of OsbHLH34 significantly impacts the susceptibility of rice to Rhizoctonia solani infection. Through the generation of OsbHLH34 knockout and overexpressing rice plants, we observed that OsbHLH34 acts as a positive regulator of rice resistance against rice sheath blight. The average lesion area of overexpression plants was 14.3%, the average lesion area of wildtype plants was 36%, and the average lesion area of mutant plants was 67.6%. Transcriptome and qRT-PCR analysis showed that OsbHLH34 regulates OsERF34, which is a key transcription factor for ethylene biosynthesis and resistance to sheath blight. By employing yeast one-hybrid and dual luciferase assays, we demonstrated that OsbHLH34 directly interacts with the promoter of OsERF34, thereby activating its transcription. Both in vitro and in vivo experiments confirmed OsERF34 as a direct target of OsbHLH34. These findings not only enhance our understanding of the molecular mechanisms underpinning rice disease resistance but also offer novel targets for the improvement of rice disease resistance through breeding strategies. Full article

Sheath blight (ShB) causes severe yield loss in rice. Previously, we demonstrated that the sugar will eventually be exported and the transporter 11 (SWEET11) mutation significantly improved rice resistance to ShB, but it caused severe defects in seed development. The present study found that WRKY36 and PIL15 directly activate SWEET11 to negatively regulate ShB. Interestingly, WRKY36 interacted with PIL15, WRKY36 and PIL15 directly activates miR530 to negatively regulate seed development. WRKY36 interacted with a key BR signaling transcription factor WRKY53. AOS2 is an effector protein from Rhizoctonia solani (R. solani) that interacts with WRKY53. Interestingly, AOS2 also interacts with WRKY36 and PIL15 to activate SWEET11 for sugar nutrition for R. solani. These data collectively suggest that WRKY36–PIL15 negatively regulates ShB resistance and seed development via the activation of SWEET11 and miR530, respectively. In addition, WRKY36 and PIL15 are the partners of the effector protein AOS2 by which R. solani hijacks sugar nutrition from rice. Full article

Rhizoctonia solani is a basidiomycete phytopathogenic fungus that causes rapid necrosis in a wide range of crop species, leading to substantial agricultural losses worldwide. The species complex is divided into 13 anastomosis groups (AGs) based on hyphal fusion compatibility and further subdivided by culture morphology. While R. solani classifications were shown to be independent of host specificity, it remains unclear whether different R. solani isolates share similar virulence mechanisms. Here, we investigated the infectivity of Japanese R. solani isolates on Brachypodium distachyon and barley. Two isolates, AG-1 IA (from rice) and AG-4 HG-I+II (from cauliflower), infected leaves of both plants, but only AG-4 HG-I+II infected roots. B. distachyon accessions Bd3-1 and Gaz-4 and barley cultivar ‘Morex’ exhibited enhanced resistance to both isolates compared to B. distachyon Bd21 and barley cultivars ‘Haruna Nijo’ and ‘Golden Promise’. During AG-1 IA infection, but not AG-4 HG-I+II infection, resistant Bd3-1 and Morex induced genes for salicylic acid (SA) and N-hydroxypipecolic acid (NHP) biosynthesis. Pretreatment with SA or NHP conferred resistance to AG-1 IA, but not AG-4 HG-I+II, in susceptible B. distachyon Bd21 and barley Haruna Nijo. On the leaves of susceptible Bd21 and Haruna Nijo, AG-1 IA developed extensive mycelial networks with numerous infection cushions, which are specialized infection structures well-characterized in rice sheath blight. In contrast, AG-4 HG-I+II formed dispersed mycelial masses associated with underlying necrosis. We propose that the R. solani species complex encompasses at least two distinct infection strategies: AG-1 IA exhibits a hemibiotrophic lifestyle, while AG-4 HG-I+II follows a predominantly necrotrophic strategy. Full article

Rice sheath blight (RSB), caused by the pathogenic fungus Rhizoctonia solani, poses a significant threat to global food security. The defense mechanisms employed by rice against RSB are not well understood. In our study, we analyzed the interactions between rice and R. solani by comparing the phenotypic changes, ROS content, and metabolite variations in both tolerant and susceptible rice varieties during the early stages of fungal infection. Notably, there were distinct phenotypic differences in the response to R. solani between the tolerant cultivar Zhengdao22 (ZD) and the susceptible cultivar Xinzhi No.1 (XZ). We observed that the activities of five defense-related enzymes in both tolerant and susceptible cultivars changed dynamically from 0 to 72 h post-infection with R. solani. In particular, the activities of superoxide dismutase and peroxidase were closely associated with resistance to RSB. Metabolomic analysis revealed 825 differentially accumulated metabolites (DAMs) between the tolerant and susceptible varieties, with 493 DAMs responding to R. solani infection. Among these, lipids and lipid-like molecules, organic oxygen compounds, phenylpropanoids and polyketides, organoheterocyclic compounds, and organic acids and their derivatives were the most significantly enriched. One DAM, P-coumaraldehyde, which responded to R. solani infection, was found to effectively inhibit the growth of R. solani, Magnaporthe grisea, and Ustilaginoidea virens. Additionally, multiple metabolic pathways, including amino acid metabolism, carbohydrate metabolism, metabolism of cofactors and vitamins, and metabolism of terpenoids and polyketides, are likely involved in RSB resistance. Our research provides valuable insights into the molecular mechanisms underlying the interaction between rice and R. solani. Full article