Rhizoctonia solani Kühn Pathophysiology: Status and Prospects of Sheath Blight Disease Management in Rice

Advances in breeding, biotechnology, and nanotechnological approaches to combat sheath blight disease in rice

Sheath blight, caused by the fungus Rhizoctonia solani, is a major problem that significantly impacts rice production and can lead to substantial yield losses. The disease has become increasingly problematic in recent years due to the widespread use of high-yielding semi-dwarf rice cultivars, dense planting, and heavy application of nitrogenous fertilizers. The disease has become more challenging to manage due to its diverse host range and the lack of resistant cultivars. Despite utilizing traditional methods, the problem persists without a satisfactory solution. Therefore, modern approaches, including advanced breeding, transgenic methods, genome editing using CRISPR/Cas9 technology, and nanotechnological interventions, are being explored to develop rice plants resistant to sheath blight disease. This review primarily focuses on these recent advancements in combating the sheath blight disease.

Synergistic Antifungal Activity of Green Synthesized Zinc Oxide Nanoparticles and Fungicide Against Rhizoctonia solani Causing Rice Sheath Blight Disease

The biosynthesis of metal oxide nanoparticles using leaf extract of medicinal plants is a promising substitute for the traditional chemical method. This work aimed to synthesize zinc oxide nanoparticles using a green approach from local "Dholkolmi" (Ipomoea carnea) leaf extract which is a medicinal plant growing outside the roads of different regions of Bangladesh. The biosynthesized zinc oxide nanoparticles (ZnONPs) were characterized using ultraviolet-visible spectroscopy, Fourier transform infrared spectroscopy, X-ray diffraction, particle size analyzer, zeta-potential, scanning electron microscopy-energy dispersive spectroscopy, field emission scanning electron microscopy, and transmission electron microscopy. The results of UV-visible spectrophotometers observed an absorption peak at 373 nm wavelength, which confirmed the synthesis of ZnONPs in the solution. ZnONP sizes determined by XRD, DLS, and TEM are approximately ~37 nm, 105.61 nm, and 19.66 nm, respectively. ZnONPs were present because of the strong oxygen and zinc signals in the EDX profile. Additionally, this research assessed the antifungal activity of the biosynthesized ZnONPs and as well as folicur-incorporated ZnONPs against Rhizoctonia solani by the poison bait technique. According to the result of this study, ZnONPs synthesized from Ipomoea carnea leaf extract showed no promising result against Rhizoctonia solani mycelial growth reduction. But folicur-incorporated ZnONPs revealed a significant finding with a maximum 100% inhibition of mycelial growth at 1:1 and 3:1 ratio of ZnONPs with folicur fungicide under in vitro conditions. In the net house experiment, folicur-incorporated ZnONPs at a 1:1 ratio of ZnONPs with folicur showed considerable disease inhibition (26.96% RLH) as compared to disease control (52.83% RLH). In the case of rainfed transplanted Aus (March-June), the highest percentage of RLH was recorded in disease control (64.61%), and the lowest RLH was found in folicur (24.79%) followed by a 1:1 ratio of ZnONPs with folicur (32.10%) in field condition. On the other hand, the highest percentage of RLH was recorded in disease control (65.31%) and the lowest RLH was found in folicur (18.14%) followed by a 1:1 ratio of ZnONPs with folicur (21.39%) in rainfed transplanted Aman (July-November) season. The findings of the in vitro and in vivo studies provided evidence that ZnONPs and folicur had a strong synergistic antifungal impact and may be employed as a possible rice sheath blight disease management agent.

Bacillus velezensis Y6, a Potential and Efficient Biocontrol Agent in Control of Rice Sheath Blight Caused by Rhizoctonia solani

Rice sheath blight is a serious disease caused by Rhizoctonia solani that reduces rice yield. Currently, there is a lack of efficient and environmentally friendly control methods. In this study, we found that Bacillus velezensis (B. velezensis) Y6 could significantly inhibit the growth of mycelium in Rhizoctonia solani, and its control efficiency against rice sheath blight was 58.67% (p < 0.01) in a pot experiment. Lipopeptides play an important role in the control of rice sheath blight by B. velezensis Y6, among which iturin and fengycin are essential, and iturin W, a novel lipopeptide in B. velezensis, plays a major role in lipopeptide antagonism to Rhizoctonia solani. In the field, we also found that inoculation with B. velezensis Y6 can increase rice yield (dry weight) by 11.75%. Furthermore, the transcriptome profiling results of the rice roots revealed that there were a total of 1227 differential genes (DEGs) regulated when treated with Y6, of which 468 genes were up-regulated and 971 genes were down-regulated in rice roots compared with the control. Among them, the DEGs were mainly distributed in biological processes (BP) and were mainly enriched in response to stimulus (GO:0050896), response to stress (GO:0006950), and response to abiotic stimulus (GO:0009628). According to the KEGG pathway analysis, there were 338 DEGs classified into 87 KEGG functional pathway categories. Compared with the control, a large number of enriched genes were distributed in phenylpropanoid biosynthesis (map00940), glutathione metabolism (map00480), glycolysis/gluconeogenesis (map00010), and amino sugar and nucleotide sugar metabolism (map00520). In summary, this investigation provides a new perspective for studying the molecular mechanism of B. velezensis in controlling rice sheath blight.

Thymol-a plant-based monoterpenoid phenol compound of an essential oil for the management of sheath blight disease of rice

Sheath blight of rice is a global disease that significantly reduces rice yield. This study reports the antifungal activity of an active compound of essential oil, thymol, at different concentrations against Rhizoctonia solani (strain RS-Gvt). In vitro assay results indicated that thymol concentrations (0.5 mg mL-1 and 0.25 mg mL-1) completely inhibited (100%) the mycelial growth of RS-Gvt (p ≤ 0.01). Microscopic observations of thymol-treated mycelium of RS-Gvt at 0.0312 mg mL-1 and above concentrations, revealed a distorted mycelial morphology with deformed hyphae. Hyphae showed a bead-like appearance, reduction in size, and constriction of the hyphae at uneven points with increased hyphal density often entangling with each other. Further, an on-field experiment was conducted to study the field bio-efficacy of thymol for two consecutive Kharif seasons of 2022 and 2023 using a factorial RCBD design. The disease severity was measured as the percent disease index (PDI), and the results of two seasons were pooled. Pathogen (RS-Gvt) and thymol were inoculated in different combinations/methods as main treatments (M1-M3), and concentrations of thymol (0.0625-1.0 mg ML-1) as sub-treatments. The results indicated that all two factors significantly (P = 0.05) influenced the PDI and grain yield. The pooled data of two seasons indicated a significant difference between the main treatments (M1: RS-Gvt + thymol together; M2: thymol sprayed first followed by RS-Gvt; M3: RS-Gvt first followed by thymol spray) on PDI (53.39-59.67) and grain yield (4.16-4.75 t ha-1). M1 exhibited a lower PDI (53.39) and a higher grain yield (4.75 t ha-1) compared to M2 and M3, indicating a protective mode of action of thymol against sheath blight disease of rice. The sub-treatments have shown significant variation in PDI and grain yield. The PDI and grain yield ranged from 33.70 (at 1 mg mL-1) to 66.21 (at 0.0625 mg mL-1) and 4.18 (at 1 mg mL-1) to 5.26 (at 0.0625 mg mL-1) t ha-1, respectively, among the thymol concentrations. This indicates that increasing concentrations of thymol have negatively influenced the PDI and positively impacted the yield. Therefore, the spray of 1 mg mL-1 of thymol at the potential disease-infection stage is most effective in controlling the sheath blight disease of rice. This study provides an alternative green bioactive compound for controlling the sheath blight disease, and thymol can be included in developing eco-friendly integrated disease management practices. © 2024 Society of Chemical Industry.

Aspergillus cvjetkovicii protects against phytopathogens through interspecies chemical signalling in the phyllosphere

Resident microbiota produces small molecules that influence the chemical microenvironments on leaves, but its signalling roles in pathogen defence are not yet well understood. Here we show that Aspergillus cvjetkovicii, enriched in rice leaf microbiota, subverts Rhizoctonia solani infections via small-molecule-mediated interspecies signalling. 2,4-Di-tert-butylphenol (2,4-DTBP), identified as a key signalling molecule within the Aspergillus-enriched microbiota, effectively neutralizes reactive oxygen species-dependent pathogenicity by switching off bZIP-activated AMT1 transcription in R. solani. Exogenous application of A. cvjetkovicii and 2,4-DTBP demonstrated varying degrees of protective effects against R. solani infection in diverse crops, including cucumber, maize, soybean and tomato. In rice field experiments, they reduced the R. solani-caused disease index to 19.7-32.2%, compared with 67.2-82.6% in the control group. Moreover, 2,4-DTBP showed activity against other rice phytopathogens, such as Fusarium fujikuroi. These findings reveal a defensive strategy against phytopathogens in the phyllosphere, highlighting the potential of symbiotic microbiota-driven neutralization of pathogenicity.

Inhibition mechanism of Rhizoctonia solani by pectin-coated iron metal-organic framework nanoparticles and evidence of an induced defense response in rice

Nanocrop protectants have attracted much attention as sustainable platforms for controlling pests and diseases and improving crop nutrition. Here, we reported the fungicidal activity and disease inhibition potential of pectin-coated metal-iron organic framework nanoparticles (Fe-MOF-PT NPs) against rice stripe blight (RSB). An in vitro bacterial inhibition assay showed that Fe-MOF-PT NPs (80 mg/L) significantly inhibited mycelial growth and nucleus formation. The Fe-MOF-PT NPs adsorbed to the surface of mycelia and induced toxicity by disrupting cell membranes, mitochondria, and DNA. The results of a nontargeted metabolomics analysis showed that the metabolites of amino acids and their metabolites, heterocyclic compounds, fatty acids, and nucleotides and their metabolites were significantly downregulated after treatment with 80 mg/L NPs. The difference in metabolite abundance between the CK and Fe-MOF-PT NPs (80 mg/L) treatment groups was mainly related to nucleotide metabolism, pyrimidine metabolism, purine metabolism, fatty acid metabolism, and amino acid metabolism. The results of the greenhouse experiment showed that Fe-MOF-PT NPs improved rice resistance to R. solani by inhibiting mycelial invasion, enhancing antioxidant enzyme activities, activating the jasmonic acid signaling pathway, and enhancing photosynthesis. These findings indicate the great potential of Fe-MOF-PT NPs as a new RSB disease management strategy and provide new insights into plant fungal disease management.

The genome sequencing and comparative genomics analysis of Rhizoctonia solani reveals a novel effector family owning a uinque domain in Basidiomycetes

Rhizoctonia solani is a soil-borne pathogen with 14 anastomosis groups (AGs), and different subgroups are genetically diverse. However, the genetic factors contributing to the pathogenicity of the fungus have not been well characterized. In this study, the genome of R. solani AG1-ZJ was sequenced. As the result, a 41.57 Mb draft genome containing 12,197 putative coding genes was obtained. Comparative genomic analysis of 11 different AGs revealed conservation and unique characteristics between the AGs. Furthermore, a novel effector family containing a 68 amino acid conserved domain unique in basidiomycetous fungi was characterized. Two effectors containing the conserved domain in AG4-JY were identified, and named as RsUEB1 and RsUEB2. Furthermore, the spray-induced gene silencing strategy was used to generate a dsRNA capable of silencing the conserved domain sequence of RsUEB1 and RsUEB2. This dsRNA can significantly reduce the expression of RsUEB1 and RsUEB2 and the pathogenicity of AG4-JY on foxtail millet, maize, rice and wheat. In conclusion, this study provides significant insights into the pathogenicity mechanisms of R. solani. The identification of the conserved domain and the successful use of dsRNA silencing of the gene containing the conserved domain will offer a new strategy for controlling sheath blight in cereal crops.

Metatranscriptomic Sequencing of Sheath Blight-Associated Isolates of Rhizoctonia solani Revealed Multi-Infection by Diverse Groups of RNA Viruses

Rice sheath blight, caused by the soil-borne fungus Rhizoctonia solani (teleomorph: Thanatephorus cucumeris, Basidiomycota), is one of the most devastating phytopathogenic fungal diseases and causes yield loss. Here, we report on a very high prevalence (100%) of potential virus-associated double-stranded RNA (dsRNA) elements for a collection of 39 fungal strains of R. solani from the rice sheath blight samples from at least four major rice-growing areas in the Philippines and a reference isolate from the International Rice Research Institute, showing different colony phenotypes. Their dsRNA profiles suggested the presence of multiple viral infections among these Philippine R. solani populations. Using next-generation sequencing, the viral sequences of the three representative R. solani strains (Ilo-Rs-6, Tar-Rs-3, and Tar-Rs-5) from different rice-growing areas revealed the presence of at least 36 viruses or virus-like agents, with the Tar-Rs-3 strain harboring the largest number of viruses (at least 20 in total). These mycoviruses or their candidates are believed to have single-stranded RNA or dsRNA genomes and they belong to or are associated with the orders Martellivirales, Hepelivirales, Durnavirales, Cryppavirales, Ourlivirales, and Ghabrivirales based on their coding-complete RNA-dependent RNA polymerase sequences. The complete genome sequences of two novel RNA viruses belonging to the proposed family Phlegiviridae and family Mitoviridae were determined.

Mangrove endophytic fungi: Biocontrol potential against Rhizoctonia solani and biofertilizers for fragrant rice cultivation

The mangrove ecosystem has emerged as a fascinating source for exploring novel bioresources which have multiple applications in modern agriculture. This study evaluates the potential applications of mangrove endophytic fungi (MEF), such as biocontrol agents against Rhizoctonia solani and as biofertilizers for improving the yield of fragrant rice variety Malaysian Rice Quality 76 (MRQ76). Through the antagonism assays, it is observed that among the 14 MEF studied, 4 fungal isolates (Colletotrichum sp. MEFN02, Aspergillus sp. MEFN06, Annulohypoxylon sp. MEFX02 and Aspergillus sp. MEFX10) exhibited promising antagonistic effect against the pathogen R. solani compared to the chemical fungicide (Benomyl). These isolates also revealed significant production of enzymes, phytochemicals, indoleacetic acid (40.96 mg/mL) and ammonia (32.54 mg/mL) and displayed tolerance to salt and temperature stress up to 2000 mM and >40 °C respectively. Furthermore, employing the germination and pathogenicity test, inoculation of these endophytes showed lower percentage of disease severity index (DSI%) against R. solani, ranging from (24 %-46 %) in MRQ76 rice seedlings. The in-vivo experiments of soil and seed inoculation methods conducted under greenhouse conditions revealed that these endophytes enhanced plant growth (8-15 % increase) and increased crop yield (≥50 %) in comparison to control treatments. The current findings provide valuable insights into eco-friendly, cost-effective and sustainable alternatives for addressing R. solani infection and improving the agronomic performance of the fragrant rice cultivar MRQ76, contributing to food security.

In vitro and in silico investigation of effects of antimicrobial peptides from Solanaceae plants against rice sheath blight pathogen Rhizoctinia solani

Rhizoctonia solani, the causative agent of sheath blight disease in rice, poses a significant threat to agricultural productivity. Traditional management approaches involving chemical fungicides have been effective but come with detrimental consequences for the ecosystem. This study aimed to investigate sustainable alternatives in the form of antifungal peptides derived from Solanaceous plant species as potential agents against R. solani. Peptide extracts were obtained using an optimized antimicrobial peptide (AMP) extraction method and desalted using the solid-phase extraction technique. The antifungal potential of peptide-rich extracts from Solanum tuberosum and Capsicum annum was assessed through in vitro tests employing the agar well diffusion method. Furthermore, peptide-protein docking analysis was performed on HPEPDOCK and HDOCK server; and molecular dynamics simulations (MDS) of 100 ns period were performed using the Gromacs 2020.4. The results demonstrated significant inhibition zones for both extracts at concentrations of 100 mg/mL. Additionally, the extracts of Solanum tuberosum and Capsicum annum had minimum inhibitory concentrations of 50 mg/mL and 25 mg/mL, respectively with minimum fungicidal concentrations of 25 mg/mL. Insights into the potential mechanisms of key peptides inhibiting R. solani targets were gleaned from in-silico studies. Notably, certain AMPs exhibited favorable free energy of binding against pathogenicity-related targets, including histone demethylase, sortin nexin, and squalene synthase, in protein-peptide docking simulations. Extended molecular dynamics simulations lasting 100 ns and MM-PBSA calculations were performed on select protein-peptide complexes. AMP10 displayed the most favorable binding free energy against all target proteins, with AMP3, AMP12b, AMP6, and AMP15 also exhibiting promising results against specific targets of R. solani. These findings underscore the potential of peptide extracts from S. tuberosum and C. annum as effective antifungal agents against rice sheath blight caused by R. solani.

Ca2+ affects the hyphal differentiation to sclerotia formation of Athelia rolfsii

RNA-Sequencing (RNA-Seq) and transcriptomic analyses have become powerful tools to study the developmental stages of fungal structures scuh as sclerotia. While RNA-Seq experiments have been set up for many important sclerotia- and microsclerotia-forming fungi, it has not been implemented to study Athelia rolfsii, which is one of the earliest fungi used in literature to uncover the roles of reactive oxygen species (ROS) in stimulating sclerotia formation. This study applied RNA-Seq to profile gene expression in four developmental stages of A. rolfsii sclerotia. Surprisingly, gene ontology and expression patterns suggested that most ROS-scavenging genes were not up-regulated in the stages from hyphal differentiation to the initial sclerotia stage. Using antioxidant and oxidant-amended culture assay, the results suggested none of the ascorbic acid, dithiothreitol (DTT), H2O2, or superoxide dismutase inhibitors [diethyldithiocarbamate (DETC), NaN3, and sodium dodecyl sulfate] affected the sclerotia number. Instead, only glutathione reduced the sclerotia number. Because glutathione has also been suggested to facilitate Ca2+ influx, therefore, glutathione culture assays with the combination of CaCl2, Ca2+-chelator egtazic acid, DETC, and H2O2 were tested on A. rolfsii, as well as two other fungi (Sclerotinia sclerotiorum and Macrophomina phaseolina) for comparison. Although the addition of CaCl2 caused sclerotia or microsclerotia reduction for all three fungi, the CaCl2-ROS interaction was only observed for S. sclerotiorum and M. phaseolina, but not A. rolfsi. Collectively, this study not only pointed out a conserved function of Ca2+ in suppressing fungal sclerotia and microsclerotia formation but also highlighted sclerotia formation of A. rolfsii being only sensitive to Ca2+ and independent of ROS stimuli.IMPORTANCEManagement for plant diseases caused by soil-borne fungal pathogens is challenging because many soil-borne fungal pathogens form sclerotia for long-term survival. Advanced understanding of the molecular and cellular mechanisms of sclerotia formation may provide novel insights to prevent these fungal residues in fields. This study discovered that Ca2+ acts as a negative signal cue to suppress sclerotia and microsclerotia formation in three economically important fungal pathogens. Moreover, the southern blight fungus Athelia rolfsii appears to be only regulated by Ca2+ but not reactive oxygen species. Accordingly, A. rolfsii can be a useful system for studying the detailed mechanism of Ca2+, and the applicability of Ca2+ in reducing sclerotia could be further assessed for disease management.

Mechanism Analysis of OsZF8-Mediated Regulation of Rice Resistance to Sheath Blight

Transcription factors are key molecules involved in transcriptional and post-transcriptional regulation in plants and play an important regulatory role in resisting biological stress. In this study, we identified a regulatory factor, OsZF8, mediating rice response to Rhizoctonia solani (R. solani) AG1-IA infection. The expression of OsZF8 affects R. solani rice infection. OsZF8 knockout and overexpressed rice plants were constructed, and the phenotypes of mutant and wild-type (WT) plants showed that OsZF8 negatively regulated rice resistance to rice sheath blight. However, it was speculated that OsZF8 plays a regulatory role at the protein level. The interacting protein PRB1 of OsZF8 was screened using the yeast two-hybrid and bimolecular fluorescence complementation test. The results showed that OsZF8 effectively inhibited PRB1-induced cell death in tobacco cells, and molecular docking results showed that PRB1 had a strong binding effect with OsZF8. Further, the binding ability of OsZF8-PRB1 to ergosterol was significantly reduced when compared with the PRB1 protein. These findings provide new insights into elucidating the mechanism of rice resistance to rice sheath blight.

Oschib1 gene encoding a GH18 chitinase confers resistance against sheath blight disease of rice caused by Rhizoctonia solani AG1-IA

Sheath blight disease of rice caused by Rhizoctonia solani AG1-IA, is a major fungal disease responsible for huge loss to grain yield and quality. The major limitation of achieving persistent and reliable resistance against R. solani is the governance of disease resistance trait by many genes. Therefore, functional characterization of new genes involved in sheath blight resistance is necessary to understand the mechanism of resistance as well as evolving effective strategies to manage the disease through host-plant resistance. In this study, we performed RNA sequencing of six diverse rice genotypes (TN1, BPT5204, Vandana, N22, Tetep, and Pankaj) from sheath and leaf tissue of control and fungal infected samples. The approach for identification of candidate resistant genes led to identification of 352 differentially expressed genes commonly present in all the six genotypes. 23 genes were analyzed for RT-qPCR expression which helped identification of Oschib1 showing differences in expression level in a time-course manner between susceptible and resistant genotypes. The Oschib1 encoding classIII chitinase was cloned from resistant variety Tetep and over-expressed in susceptible variety Taipei 309. The over-expression lines showed resistance against R. solani, as analyzed by detached leaf and whole plant assays. Interestingly, the resistance response was correlated with the level of transgene expression suggesting that the enzyme functions in a dose dependent manner. We report here the classIIIb chitinase from chromosome10 of rice showing anti-R. solani activity to combat the dreaded sheath blight disease.

Methionine biosynthetic genes and methionine sulfoxide reductase A are required for Rhizoctonia solani AG1-IA to cause sheath blight disease in rice

Rhizoctonia solani is a polyphagous necrotrophic fungal pathogen that causes sheath blight disease in rice. It deploys effector molecules as well as carbohydrate-active enzymes and enhances the production of reactive oxygen species for killing host tissues. Understanding R. solani ability to sustain growth under an oxidative-stress-enriched environment is important for developing disease control strategies. Here, we demonstrate that R. solani upregulates methionine biosynthetic genes, including Rs_MET13 during infection in rice, and double-stranded RNA-mediated silencing of these genes impairs the pathogen's ability to cause disease. Exogenous treatment with methionine restores the disease-causing ability of Rs_MET13-silenced R. solani and facilitates its growth on 10 mM H2O2-containing minimal-media. Notably, the Rs_MsrA gene that encodes methionine sulfoxide reductase A, an antioxidant enzyme involved in the repair of oxidative damage of methionine, is upregulated upon H2O2 treatment and also during infection in rice. Rs_MsrA-silenced R. solani is unable to cause disease, suggesting that it is important for the repair of oxidative damage in methionine during host colonization. We propose that spray-induced gene silencing of Rs_MsrA and designing of antagonistic molecules that block MsrA activity can be exploited as a drug target for effective control of sheath blight disease in rice.

Deciphering core microbiota in rhizosphere soil and roots of healthy and Rhizoctonia solani-infected potato plants from various locations

Black scurf caused by Rhizoctonia solani severely affects potato production. Through amplification of V3-V4 and ITS1-5f variable regions of 16S and internal transcribed spacer (ITS) rRNA, the study was based on the location (Kunming, Qujing, and Zhaotong), plant components (rhizosphere soil and roots), and sample types (healthy and diseased) to assess the diversity of bacterial and fungal communities. We found plant components significantly influence microbial diversity, with rhizosphere soil being more diverse than roots, and the microbial community in the root is mainly derived from the rhizosphere soil. Moreover, the rhizosphere soil and roots of healthy potato plants exhibit greater microbial diversity compared to those of potato plants infected by Rhizoctonia solani. Bacterial phyla Actinobacteriota and Acidobacteriota were enriched in rhizosphere soil compared to that of roots, whereas Proteobacteria and Cyanobacteria showed the opposite trend. Fungal phylum Ascomycota was found in low relative abundance in rhizosphere soil than in roots, whereas Basidiomycota showed the opposite trend. Bacterial genera including Streptomyces, Lysobacter, Bacillus, Pseudomonas, Ensifer, Enterobacter, and the Rhizobium group (Allorhizobium, Neorhizobium, Pararhizobium, Rhizobium), along with fungal genera such as Aspergillus, Penicillium, Purpureocillium, and Gibberella moniliformis, have the potential ability of plant growth promotion and disease resistance. However, most fungal species and some bacterial species are pathogenic to potato and could provide a conducive environment for black scurf infection. Interaction within the bacterial network increased in healthy plants, contrasting with the trend in the fungal network. Our findings indicate that R. solani significantly alters potato plant microbial diversity, underscoring the complexity and potential interactions between bacterial and fungal communities for promoting potato plant health and resistance against black scurf.

Unveiling the Genetic Tapestry: Exploring Rhizoctonia solani AG-3 Anastomosis Groups in Potato Crops across Borders

The current study was carried out to screen 10 isolates (ARS-01-ARS-10) of Rhizoctonia. solani from potato tubers cv. Kuroda, which were collected from various potato fields in Multan, Pakistan. The isolates were found to be morphologically identical, as the hyphae exhibit the production of branches at right angles and acute angles often accompanied by septum near the emerging branches. Anastomosis grouping showed that these isolates belonged to AG-3. A pathogenicity test was performed against the susceptible Kuroda variety and among the isolates, ARS-05 exhibited the highest mean severity score of approximately 5.43, followed by ARS-09, which showed a mean severity score of about 3.67, indicating a moderate level of severity. On the lower end of the severity scale, isolates ARS-06 and ARS-07 displayed mean severity scores of approximately 0.53 and 0.57, respectively, suggesting minimal symptom severity. These mean severity scores offer insights into the varying degrees of symptom expression among the different isolates of R. solani under examination. PCoA indicates that the severe isolate causing black scurf on the Kuroda variety was AG-3. A comprehensive analysis of the distribution, genetic variability, and phylogenetic relationships of R. solani anastomosis groups (AGs) related to potato crops across diverse geographic regions was also performed to examine AG prevalence in various countries. AG-3 was identified as the most widespread group, prevalent in Sweden, China, and the USA. AG-5 showed prominence in Sweden and the USA, while AG-2-1 exhibited prevalence in China and Japan. The phylogenetic analysis unveiled two different clades: Clade I comprising AG-3 and Clade II encompassing AG-2, AG-4, and AG-5, further subdivided into three subclades. Although AGs clustered together regardless of origin, their genetic diversity revealed complex evolutionary patterns. The findings pave the way for region-specific disease management strategies to combat R. solani's impact on potato crops.

Development of activation-tagged gain-of-functional mutants in indica rice line (BPT 5204) for sheath blight resistance

BACKGROUND

The development of sheath blight (ShB) resistance varieties has been a challenge for scientists for long time in rice. Activation tagging is an efficient gain-of-function mutation approach to create novel phenotypes and to identify their underlying genes. In this study, a mutant population was developed employing activation tagging in the recalcitrant indica rice (Oryza sativa L.) cv. BPT 5204 (Samba Mahsuri) through activation tagging.

METHODS AND RESULTS

In this study, we have generated more than 1000 activation tagged lines in indica rice, from these mutant population 38 (GFP- RFP+) stable Ds plants were generated through germinal transposition at T2 generation based on molecular analysis and seeds selected on hygromycin (50 mg/L) containing medium segregation analyses confirmed that the transgene inherited as mendelian segregation ratio of 3:1 (3 resistant: 1 susceptible). Of them, five stable activation tagged Ds lines (M-Ds-1, M-Ds-2, M-Ds-3, M-Ds-4 and M-Ds-5) were selected based on phenotypic observation through screening for sheath blight (ShB) resistance caused by fungal pathogen Rhizoctonia solani (R. solani),. Among them, M-Ds-3 and M-Ds-5 lines showed significant resistance for ShB over other tagged lines and wild type (WT) plants. Furthermore, analysed for launch pad insertion through TAIL-PCR results and mapped on corresponding rice chromosomes. Flanking sequence and gene expression analysis revealed that the upregulation of glycoside hydrolase-OsGH or similar to Class III chitinase homologue (LOC_Os08g40680) in M-Ds-3 and a hypothetical protein gene (LOC_Os01g55000) in M-Ds-5 are potential candidate genes for sheath blight resistance in rice.

CONCLUSION

In the present study, we developed Ac-Ds based ShB resistance gain-of-functional mutants through activation tagging in rice. These activation tagged mutant lines can be excellent sources for the development of ShB resistant cultivars in rice.

Genome and transcriptome sequencing of Trichoderma harzianum T4, an important biocontrol fungus of Rhizoctonia solani, reveals genes related to mycoparasitism

Trichoderma harzianum is a well-known biological control strain and a mycoparasite of Rhizoctonia solani. To explore the mechanisms of mycoparasitism, the genome and transcriptome of T. harzianum T4 were both assembled and analyzed in this study. The genome of T. harzianum T4 was assembled into 106 scaffolds, sized 41.25 Mb, and annotated with a total of 8118 predicted genes. We analyzed the transcriptome of T. harzianum T4 against R. solani in a dual culture in three culture periods: before contact (BC), during contact (C), and after contact (AC). Transcriptome sequencing identified 1092, 1222, and 2046 differentially expressed genes (DEGs), respectively. These DEGs, which are involved in pathogen recognition and signal transduction, hydrolase, transporters, antibiosis, and defense-related functional genes, are significantly upregulated in the mycoparasitism process. The results of genome and transcriptome analysis indicated that the mycoparasitism process of T. harzianum T4 was very complex. T. harzianum successfully recognizes and invades host cells and kills plant pathogens by regulating various DEGs at different culture periods. The relative expression levels of the 26 upregulated DEGs were confirmed by RT-qPCR to validate the reliability of the transcriptome data. The results provide insight into the molecular mechanisms underlying T. harzianum T4's mycoparasitic processes, and they provide a potential molecular target for the biological control mechanism of T. harzianum T4.

Characterization of heteropolysaccharides from Rhizoctonia solani AG1 IA cell wall and comparison of their effect on inducing plant defense

Rhizoctonia solani (R. solani) is an important pathogenic fungus that causes symptoms of sheath blight, and the polysaccharide-rich cell wall plays a major role in plant-pathogen interactions. However, the composition and structure of its cell wall polysaccharides are insufficiently understood, and its specific function in plant-pathogen interactions is unknown, which makes effective control of sheath blight difficult at present. Herein, five cell wall polysaccharides (WF-1, WF-2, CAF-1, HAF-1 and HAF 2-1) were sequentially extracted by boiling water, cold and hot alkali from R. solani AG1 IA. They were heteropolysaccharides containing mainly glucose, mannose and galactose and less fucose, with molecular weights above 1100 kDa. These five polysaccharides mainly composed of →4)-Glcp-(1→, →6)-Glcp-(1→, →4,6)-Glcp-(1→, →3,4)-Glcp-(1→, and Manp-(1→. Several polysaccharides, except WF-1, showed different induced resistance degrees on rice plant, with HAF 2-1 having the most significant effect. Further analysis using NMR confirmed that the backbone of HAF 2-1 mainly consisted of →4)-α-D-Glcp-(1→ and →6)-α-D-Glcp-(1→ with branches of →4,6)-D-Glcp-(1→. HAF 2-1 enhance the resistance of rice against R. solani through salicylic acid (SA)-mediated immune signaling pathway. This work improves our knowledge of the cell wall polysaccharides in plant pathogens and facilitates the study of pathogenic mechanisms and effective disease control.

Enhanced Rice Resistance to Sheath Blight through Nitrate Transporter 1.1B Mutation without Yield Loss under NH4+ Fertilization

Nitrogen fertilization can promote rice yield but decrease resistance to sheath blight (ShB). In this study, the nitrate transporter 1.1b (nrt1.1b) mutant that exhibited less susceptibility to ShB but without compromising yield under NH4+ fertilization was screened. NRT1.1B's regulation of ShB resistance was independent of the total nitrogen concentration in rice under NH4+ conditions. In nrt1.1b mutant plants, the NH4+ application modulated auxin signaling, chlorophyll content, and phosphate signaling to promote ShB resistance. Furthermore, the findings indicated that NRT1.1B negatively regulated ShB resistance by positively modulating the expression of H+-ATPase gene OSA3 and phosphate transport gene PT8. The mutation of OSA3 and PT8 promoted ShB resistance by increasing the apoplastic pH in rice. Our study identified the ShB resistance mutant nrt1.1b, which maintained normal nitrogen use efficiency without compromising yield.

Evaluation of Morpho-Physiological and Yield-Associated Traits of Rice (Oryza sativa L.) Landraces Combined with Marker-Assisted Selection under High-Temperature Stress and Elevated Atmospheric CO2 Levels

Rice (Oryza sativa L.) is an important cereal crop worldwide due to its long domestication history. North-Eastern India (NEI) is one of the origins of indica rice and contains various native landraces that can withstand climatic changes. The present study compared NEI rice landraces to a check variety for phenological, morpho-physiological, and yield-associated traits under high temperatures (HTs) and elevated CO2 (eCO2) levels using molecular markers. The first experiment tested 75 rice landraces for HT tolerance. Seven better-performing landraces and the check variety (N22) were evaluated for the above traits in bioreactors for two years (2019 and 2020) under control (T1) and two stress treatments [mild stress or T2 (eCO2 550 ppm + 4 °C more than ambient temperature) and severe stress or T3 (eCO2 750 ppm + 6 °C more than ambient temperature)]. The findings showed that moderate stress (T2) improved plant height (PH), leaf number (LN), leaf area (LA), spikelets panicle-1 (S/P), thousand-grain weight (TGW), harvest index (HI), and grain production. HT and eCO2 in T3 significantly decreased all genotypes' metrics, including grain yield (GY). Pollen traits are strongly and positively associated with spikelet fertility at maturity and GY under stress conditions. Shoot biomass positively affected yield-associated traits including S/P, TGW, HI, and GY. This study recorded an average reduction of 8.09% GY across two seasons in response to the conditions simulated in T3. Overall, two landraces-Kohima special and Lisem-were found to be more responsive compared to other the landraces as well as N22 under stress conditions, with a higher yield and biomass increment. SCoT-marker-assisted genotyping amplified 77 alleles, 55 of which were polymorphic, with polymorphism information content (PIC) values from 0.22 to 0.67. The study reveals genetic variation among the rice lines and supports Kohima Special and Lisem's close relationship. These two better-performing rice landraces are useful pre-breeding resources for future rice-breeding programs to increase stress tolerance, especially to HT and high eCO2 levels under changing climatic situations.

Study on the metabolic process of phthalic acid driven proliferation of Rhizoctonia solani

Introduction

Continuous cropping obstacle seriously affects the quality and yield of Salvia miltiorrhiza, and the synergistic effect of root exudates and rhizosphere pathogenic microorganisms may be an important cause of continuous cropping obstacle. This study aimed to explore the effects of representative organic acids on the growth and metabolism of specific microorganisms in the S. miltiorrhiza rhizosphere soil under continuous cropping, and clarify its mechanism.

Methods

The effect of phthalic acid (PA) on the growth and metabolism of Rhizoctonia solani was evaluated by mycelial growth inhibition method. Ultra-high performance liquid chromatography and tandem mass spectrometry were used to identify the differential metabolites of R. solani induced by exogenous PA.

Results

PA exerted a concentration-dependent effect on mycelial growth, biomass, intracellular polysaccharides con-tent, and total protein content in R. solani. A total of 1773 metabolites and 1040 differential metabolites were identified in the blank medium (CK), Fungi (CK + fungi), and PA-Fungi (CK + fungi + acid) groups. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the differential metabolites were mainly involved in the sugar, lipid, and protein metabolic pathways related to stable membrane structure and cell growth.

Discussion

The proliferation and metabolism network of R. solani induced by PA was proposed, and the enhancement of sugar, lipid, and amino acid metabolism was presumed to be related to the active resistance of cells to organic acid stress. These results offer new in-sights into the effects of PA metabolism on promoting R. solani proliferation, and provide theoretical support for further optimizing the rhizosphere microecological environment of Salvia miltiorrhiza continuous cropping soil and reducing continuous cropping obstacle.

Loss of a Premature Stop Codon in the Rice Wall-Associated Kinase 91 (WAK91) Gene Is a Candidate for Improving Leaf Sheath Blight Disease Resistance

Leaf sheath blight disease (SB) of rice caused by the soil-borne fungus Rhizoctonia solani results in 10-30% global yield loss annually and can reach 50% under severe outbreaks. Many disease resistance genes and receptor-like kinases (RLKs) are recruited early on by the host plant to respond to pathogens. Wall-associated receptor kinases (WAKs), a subfamily of receptor-like kinases, have been shown to play a role in fungal defense. The rice gene WAK91 (OsWAK91), co-located in the major SB resistance QTL region on chromosome 9, was identified by us as a candidate in defense against rice sheath blight. An SNP mutation T/C in the WAK91 gene was identified in the susceptible rice variety Cocodrie (CCDR) and the resistant line MCR010277 (MCR). The consequence of the resistant allele C is a stop codon loss, resulting in an open reading frame with extra 62 amino acid carrying a longer protein kinase domain and additional phosphorylation sites. Our genotype and phenotype analysis of the parents CCDR and MCR and the top 20 individuals of the double haploid SB population strongly correlate with the SNP. The susceptible allele T is present in the japonica subspecies and most tropical and temperate japonica lines. Multiple US commercial rice varieties with a japonica background carry the susceptible allele and are known for SB susceptibility. This discovery opens the possibility of introducing resistance alleles into high-yielding commercial varieties to reduce yield losses incurred by the sheath blight disease.

Genome-Wide Identification and Analysis of Collar Region-Preferential Genes in Rice

The collar region plays a crucial role in leaf angle formation and plant architecture, which is important for improving crop yield given the challenges of diminishing arable land and changing environmental conditions. To determine collar region-preferential genes (CRPGs) affecting plant architecture and crop yield, we conducted genome-wide transcriptomic analysis. By integrating our RNA sequencing data with public rice anatomical expression data, we identified 657 CRPGs. Verification involved testing six randomly selected CRPGs, all of which exhibited collar-preferential expression. The functional significance of CRPGs was assessed via Gene Ontology enrichment analysis, utilizing MapMan and KEGG, and literature analysis provided additional information for characterized CRPGs. Our findings revealed links between manipulating leaf angle and phytohormone-related pathways and stress responses. Moreover, based on the CRPGs, five transcription factors downstream of the liguleless 1 (LG1) gene were identified. Overall, the identified CRPGs provide potential targets for further research and breeding applications aimed at improving crop productivity by manipulating leaf architecture.

Transcriptomic Response of Clonostachys rosea Mycoparasitizing Rhizoctonia solani

Clonostachys rosea is an important mycoparasitism biocontrol agent that exhibits excellent control efficacy against numerous fungal plant pathogens. Transcriptomic sequencing may be used to preliminarily screen mycoparasitism-related genes of C. rosea against fungal pathogens. The present study sequenced and analyzed the transcriptome of C. rosea mycoparasitizing a Basidiomycota (phylum) fungal pathogen, Rhizoctonia solani, under three touch stages: the pre-touch stage, touch stage and after-touch stage. The results showed that a number of genes were differentially expressed during C. rosea mycoparasitization of R. solani. At the pre-touch stage, 154 and 315 genes were up- and down-regulated, respectively. At the touch stage, the numbers of up- and down-regulated differentially expressed genes (DEGs) were 163 and 188, respectively. The after-touch stage obtained the highest number of DEGs, with 412 and 326 DEGs being up- and down-regulated, respectively. Among these DEGs, ABC transporter-, glucanase- and chitinase-encoding genes were selected as potential mycoparasitic genes according to a phylogenetic analysis. A comparative transcriptomic analysis between C. rosea mycoparasitizing R. solani and Sclerotinia sclerotiorum showed that several DEGs, including the tartrate transporter, SDR family oxidoreductase, metallophosphoesterase, gluconate 5-dehydrogenase and pyruvate carboxylase, were uniquely expressed in C. rosea mycoparasitizing R. solani. These results significantly expand our knowledge of mycoparasitism-related genes in C. rosea and elucidate the mycoparasitism mechanism of C. rosea.

Screening bacterial isolates for biocontrol of sheath blight in rice plants

Sheath blight (Rhizoctonia solani) causes significant yield losses in rice (Oryza sativa L.). Its sustainable management needs an efficient biocontrol agent. The objective was to screen bacterial isolates as an antagonist to R. solani and identify the most efficient ones as sheath blight suppressors under greenhouse conditions. Two assays (E1 and E2) were performed in a completely randomized design with three replications. E1 tested 21 bacterial isolates antagonists to R. solani in vitro. E2 was conducted under greenhouse conditions, with rice cultivar BRS Pampeira sown in plastic pots (7 kg) containing fertilized soil. Sixty old plants were inoculated with a segment of a toothpick containing fragments of R. solani, followed by spray inoculation of a bacterial suspension (108 CFU/mL). The severity of the disease was determined by calculating the relative lesion size formed on the colm. Isolates BRM32112 (Pseudomonas nitroreducens), BRM65929 (Priestia megaterium), and BRM65919 (Bacillus cereus) reduced R. solani colony radial growth by 92.8, 77.56, and 75.56%, respectively while BRM63523 (Serratia marcescens), BRM65923 and BRM65916 (P. megaterium) and BRM65919 (B. cereus) with 23.45, 23.37, 23.62, and 20.17 cm, respectively were effective at suppressing sheath blight in greenhouse, indicating their potential as a biofungicide for sheath blight suppression.

Comparative Study of Three Biological Control Agents and Two Conventional Fungicides against Coriander Damping-off and Root Rot Caused by Rhizoctonia solani

The in vitro and in vivo efficacy of three biocontrol agents, Trichoderma viride, Pseudomonas fluorescence, and Bacillus subtilis, were tested against Rhizoctonia solani (AG-4) infection compared to two conventional fungicides (Rizolex-T 50%wettable powder and Amistar 25%). Antifungal enzyme activity was assayed in the culture filtrate of the biocontrol agents. The impact of the tested biocontrol agents on the induction of the coriander immune system was investigated against R. solani by assessing the resistance-related enzymes and compounds in biocontrol agent-treated plants compared with the control. The obtained results revealed that all tested biocontrol agents significantly reduced the linear growth of R. solani, and T. viride recorded the highest inhibition percentage. This could be linked to the ability of T. viride to produce higher activities of antimicrobial enzymes, i.e., cellulase, chitinase, and protease, compared to P. fluorescence and B. subtilis. Applying the tested biocontrol agents significantly alleviated pre- and post-emergence damping-off and root rot/wilt diseases of infected coriander compared with untreated plants. The tested biocontrol agents exhibited significantly higher germination percentage and vigor index of the coriander than the tested fungicides. The tested biocontrol agents significantly minimized the reduction of photosynthetic pigments induced by R. solani. In addition, the results showed a significant increase in enzymes/molecules (i.e., phenylalanine, catalase, peroxidase, catalase, superoxide dismutase, phenylalanine ammonia-lyase, phenolics, ascorbic acids, and salicylic acid) involved directly and indirectly in coriander resistance to R. solani. The principal component analysis of the recorded data recommended the role of the high accumulation of oxidative parameters (hydrogen peroxide and lipid peroxidation) and the inhibition of phenolic compounds in the downregulation of coriander resistance against R. solani. The heatmap analysis results revealed that biocontrol agents, especially Trichoderma, enhanced the resistance against R. solani via the stimulation of salicylic acid, phenolics, and antioxidant enzymes. Overall, the data recommended the efficacy of biocontrol agents, especially T. viride, against R. solani infecting coriander plants, which could be an efficient and a safer alternative to conventional fungicides.

Progress in rice sheath blight resistance research

Rice sheath blight (ShB) disease poses a major threat to rice yield throughout the world. However, the defense mechanisms against ShB in rice remain largely unknown. ShB resistance is a typical quantitative trait controlled by multiple genes. With the rapid development of molecular methods, many quantitative trait loci (QTLs) related to agronomic traits, biotic and abiotic stresses, and yield have been identified by genome-wide association studies. The interactions between plants and pathogens are controlled by various plant hormone signaling pathways, and the pathways synergistically or antagonistically interact with each other, regulating plant growth and development as well as the defense response. This review summarizes the regulatory effects of hormones including auxin, ethylene, salicylic acid, jasmonic acid, brassinosteroids, gibberellin, abscisic acid, strigolactone, and cytokinin on ShB and the crosstalk between the various hormones. Furthermore, the effects of sugar and nitrogen on rice ShB resistance, as well as information on genes related to ShB resistance in rice and their effects on ShB are also discussed. In summary, this review is a comprehensive description of the QTLs, hormones, nutrition, and other defense-related genes related to ShB in rice. The prospects of targeting the resistance mechanism as a strategy for controlling ShB in rice are also discussed.

Relationship between antioxidant enzymes and sclerotial formation of Pleurotus tuber-regium under abiotic stress

In order to explore the relationship between sclerotial formation and antioxidant enzymes under abiotic stresses, the effects of abiotic stresses including temperature, pH value, osmotic pressure, limited nitrogen, and hydrogen peroxide (H₂O₂) on the activities of antioxidant enzymes, ascorbate peroxidase (APX), superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) in Pleurotus tuber-regium were studied. Meanwhile, the sclerotial formation under these abiotic stress conditions was also investigated. It was found that low temperature, weak alkaline, appropriate osmotic stress, and H₂O₂ can promote sclerotial formation, and sclerotial formation always tended to occur when the activities of antioxidant enzymes were at a high value. During the prolonged low temperature stress, SOD acted mainly in the early stage of stress, while POD and CAT had higher activity in the middle and late stage. Moreover, the reverse transcription quantitative polymerase chain reaction (RT-qPCR) results showed that SOD.193 and POD.535 were significantly down-regulated in sclerotia, and CAT.1115 and POD.401 were up-regulated instead. These antioxidant enzyme genes played an important role in the sclerotial formation under low temperature stress. It is strongly suggested that antioxidant enzymes and abiotic stresses are closely related to sclerotial formation in P. tuber-regium. KEY POINTS: • Low temperature and H2O2 can promote sclerotial formation. • Sclerotia are more likely to form under high antioxidant enzyme activity. • POD.401, POD.535, SOD.193, and CAT.1115 are important for sclerotial formation.

Elevated CO2 and temperature under future climate change increase severity of rice sheath blight

Sheath blight (ShB), caused by Rhizoctonia solani, is one of the major threats to rice (Oryza sativa L.) production. However, it is not clear how the risk of rice ShB will respond to elevated CO₂ and temperature under future climate change. Here, we conducted, field experiments of inoculated R. solani under combinations of two CO₂ levels (ambient and enriched up to 590 μmol mol^-1) and two temperature levels (ambient and increased by 2.0°C) in temperature by free-air CO₂ enrichment (T-FACE) system for two cultivars (a susceptible cultivar, Lemont and a resistant cultivar, YSBR1). Results indicate that for the inoculation of plants with R. solani, the vertical length of ShB lesions for cv. Lemont was significantly longer than that for cv. YSBR1 under four CO₂ and temperature treatments. The vertical length of ShB lesions was significantly increased by elevated temperature, but not by elevated CO₂, for both cultivars. The vertical length of ShB lesions under the combination of elevated CO₂ and elevated temperature was increased by 21-38% for cv. Lemont and by -1-6% for cv. YSBR1. A significant increase in MDA level was related to a significant increase in the vertical length of ShB lesions under the combination of elevated CO₂ and elevated temperature. Elevated CO₂ could not compensate for the negative effect of elevated temperature on yield of both cultivars under future climate change. Rice yield and biomass were further decreased by 2.0-2.5% and 2.9-4.2% by an increase in the severity of ShB under the combination of elevated CO₂ and elevated temperature. Thus, reasonable agronomic management practices are required to improve both resistance to ShB disease and grain yield for rice under future climate change.

Oxalactam A, a Novel Macrolactam with Potent Anti-Rhizoctonia solani Activity from the Endophytic Fungus Penicillium oxalicum

A novel macrolactam named oxalactam A (1), three known dipeptides (2-4) as well as other known alkaloids (5-7) were obtained from the endophytic fungus Penicillium oxalicum, which was derived from the tuber of Icacina trichantha (Icacinaceae). All chemical structures were established based on spectroscopic data, chemical methods, ECD calculations, and ¹³C-DP4+ analysis. Among them, oxalactam A (1) is a 16-membered polyenic macrolactam bearing a new skeleton of 2,9-dimethyl-azacyclohexadecane core and exhibited potent anti-Rhizoctonia solani activity with a MIC value of 10 μg/mL in vitro. The plausible biosynthetic pathway of 1 was also proposed via the alanyl protecting mechanism. Notably, three dipeptides (2-4) were first identified from the endophytic fungus P. oxalicum and the NMR data of cyclo(L-Trp-L-Glu) (2) was reported for the first time. In addition, the binding interactions between compound 1 and the sterol 14α-demethylase enzyme (CYP51) were studied by molecular docking and dynamics technologies, and the results revealed that the 16-membered polyenic macrolactam could be a promising CYP51 inhibitor to develop as a new anti-Rhizoctonia solani fungicide.