Rice Fungal Pathogens Research Articles

Micro-scale screening of genetically modified Fusarium fujikuroi strain extends the apicidin family

Apicidins are a class of naturally occurring cyclic tetrapeptides produced by few strains within the Fusarium genus. These secondary metabolites have gained significant attention due to their antiprotozoal activity through HDAC inhibition, thereby highlighting their potential for the treatment of malaria. Predominantly, apicidins have been isolated from Fusarium semitectum, offering a deep insight into the biosynthetic pathway responsible for their formation. A similar biosynthetic gene cluster has also been identified in the rice pathogenic fungus F. fujikuroi, leading the discovery of three additional apicidins through genetic manipulation. Routine mass spectrometric screening of these compound-producing strains revealed another metabolite structurally related to previously studied apicidins. By optimizing culture conditions and developing an effective isolation method, we obtained a highly pure substance, whose chemical structure was fully elucidated using NMR and HRMS fragmentation. Further studies were conducted to determine cytotoxicity, antimalarial activity, and HDAC inhibitory activity of this new secondary metabolite alongside the previously known apicidins. This work not only expands the apicidin class with a new member but also provides extensive insights and comparative analysis of apicidin-like substances produced by F. fujikuroi.Graphical

Multiple Chitin- or Avirulent Strain-Triggered Immunity Induces Microbiome Reassembly in Rice.

Magnaporthe oryzae is one of the most important fungal pathogens of rice. Chitin and avirulent strains can induce two layers of immunity response, pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) and effector-triggered immunity (ETI), in rice with cognate R genes. However, little is known about the assembly of the rice microbiome induced by PTI and ETI in rice. In this study, we investigate the impact of continuous treatment of the avirulent M. oryzae strain with AvrPi9 and chitin on the bacterial endophytic community of rice varieties harboring resistant gene Pi9 and their antagonistic activity against rice blast fungus. Analysis of the 16S rRNA showed a significant increase in the diversity and microbial co-occurrence network complexity and the number of beneficial taxa-Bacillus, Pseudomonas, Microbacterium, and Stenotrophomonas spp.-following the chitin and avirulent strain treatments. The antifungal assay with bacterial endophytes recovered from the leaves showed few bacteria with antagonistic potential in rice treated with avirulent strains, suggesting that the sequential treatment of the avirulent strain decreased the antagonistic bacteria against M. oryzae. Moreover, we identified Bacillus safensis Ch_66 and Bacillus altitudinis Nc_68 with overall antagonistic activities in vivo and in vitro. Our findings provide a novel insight into rice microbiome assembly in response to different innate immunity reactions.

Characterization and evaluation of native Trichoderma harzianum P39 for biocontrol potentials against five seed-borne fungal pathogens of rice

Plant seeds can harbour pathogens that limits crop growth and productivity. This study isolated, characterised and evaluated native Trichoderma harzianum for antagonism against five (Alternaria alternata, Aspergillus oryzae, Bipolaris oryzae, Curvularia lunata and Fusarium verticillioides) fungal pathogens isolated from rice seeds. Evaluation was through simultaneous inoculation, a pathogen against the biocontrol agent, using the dual culture method in a PDA growth medium. Results confirmed the T. harzianum isolate had 98.27% pairwise identity with T. harzianum P39 (KX381171.1. accession number). The isolate showed increasing percentage inhibition, against all the pathogens, with increasing days after inoculation. The highest values ranged from 53.02%, A. oryzae to 70.06%, F. verticillioides (the least and most susceptible respectively). The overall inhibition percentages of A. alterata and B. oryzae (12th day after inoculation) were not significantly different from that of F. verticillioides. Trichoderma harzianum P39 can be formulated as biological seed dressing agent.

Genetic diversity and pathogenicity of fungi associated with rice sheath rot in the Fogera plain, Northwest Ethiopia

AbstractSheath rot is a widespread rice disease that affects rice crops worldwide. It is particularly prevalent in Ethiopia, with the Fogera plains exhibiting the highest incidence and severity. However, the lack of reliable molecular‐level identification of rice fungal pathogens in Ethiopia has hindered the development of effective management practices. This study aimed to assess the diversity of fungal agents causing sheath rot disease in rice crops around the Fogera plains, Ethiopia, using both morphology and nucleotide sequences of the ITS1 rDNA region. Additionally, the pathogenicity of the isolates was evaluated using attached tiller assay methods. A total of 16 fungal isolates were recovered from diseased plant samples. Among these, five species; Phoma spp., Phoma herbarium, Epicoccum sorghinum, Epicoccum lantuscollum and Microdochium seminicola were identified and reported as new records of sheath rot disease in rice. The predominant genus was Phoma (75%) followed by Epicoccum (18.75%). The pathogenicity caused by E. sorghinum was particularly severe and significantly different from the symptoms caused by other isolates, resulting in a mean lesion length of 167.7 mm and a disease severity of 55.7%. These findings suggest that E. sorghinum is the most important rice pathogen in the region. Our results have identified the most predominant and pathogenic fungal species associated with sheath rot disease in the region. Importantly, this study marks the first report of sheath rot‐causing fungi identified in rice using the ITS rDNA‐sequencing technique in Ethiopia. Therefore, this research may contribute to the development of fungal disease management strategies in rice and provide evidence to initiate a rice breeding program focused on developing sheath‐rot‐resistant rice varieties.

Genetic analysis, purification and docking studies of trihydroxynaphthalene reductase involved in pathogenesis of rice pathogen, Curvularia lunata

Curvularia lunata causes black kernel disease in rice (Oryza sativa) kernel and enzyme, trihydroxynaphthalene reductase (3HNR) catalyzes a crucial reaction in melanin biosynthesis which aids in appressorium formation. However, the molecular mechanism of pathogenesis and characterization of 3HNR are poorly understood due to the limited research conducted on this pathosystem. Therefore, the C. lunata (GVBR1) was isolated from the diseased rice kernel and identified using microscopic, SEM and molecular methods. To elucidate the molecular mechanism of 3HNR, the C. lunata was treated with different concentrations of systemic fungicide tricyclazole and the gene expression of C. lunata trihydroxynaphthalene reductase (Cl3HNR) analyzed with different concentrations of tricyclazole treated, downregulated the Cl3HNR gene expression as compared to the control. Further, Cl3HNR was cloned into pGEX expression vector, heterologously expressed in Escherichia coli BL21 cells and the expressed protein corresponds to 28 kDa. The molecular docking and dynamic simulation revealed the interaction points within the active site of Cl3HNR. This study highlights the importance of the melanin biosynthetic gene involved in the pathogenesis of the rice fungal pathogen, C. lunata, which paves the way in developing the HNR enzyme inhibitor to control the rice disease.

A Relationship Prediction Method for Magnaporthe oryzae-Rice Multi-Omics Data Based on WGCNA and Graph Autoencoder.

Magnaporthe oryzae Oryzae (MoO) pathotype is a devastating fungal pathogen of rice; however, its pathogenic mechanism remains poorly understood. The current research is primarily focused on single-omics data, which is insufficient to capture the complex cross-kingdom regulatory interactions between MoO and rice. To address this limitation, we proposed a novel method called Weighted Gene Autoencoder Multi-Omics Relationship Prediction (WGAEMRP), which combines weighted gene co-expression network analysis (WGCNA) and graph autoencoder to predict the relationship between MoO-rice multi-omics data. We applied WGAEMRP to construct a MoO-rice multi-omics heterogeneous interaction network, which identified 18 MoO small RNAs (sRNAs), 17 rice genes, 26 rice mRNAs, and 28 rice proteins among the key biomolecules. Most of the mined functional modules and enriched pathways were related to gene expression, protein composition, transportation, and metabolic processes, reflecting the infection mechanism of MoO. Compared to previous studies, WGAEMRP significantly improves the efficiency and accuracy of multi-omics data integration and analysis. This approach lays out a solid data foundation for studying the biological process of MoO infecting rice, refining the regulatory network of pathogenic markers, and providing new insights for developing disease-resistant rice varieties.

<i>In vitro</i> assessment of bacterial endophytes for antagonistic activity against <i>Magnaporthe oryzae</i> and <i>Cochliobolus miyabeanus</i> in rice

Rice is the global staple food, contributing over half of the world’s agricultural production. Excessive fungicide use in rice farming poses environmental, fungicide resistance, and beneficial microbial disruption concerns, making biocontrol, particularly bacteria, a promising biocontrol agent due to their rapid growth, ease of handling, and robust colonization attributes. Endophytes are endosymbionts residing within host plants, playing a pivotal role in plant health without inciting any pathogenic effects. In this study, we investigated the antagonistic potential of four characterized bacterial endophytic strains, viz., Bacillus velezensis strains A6 and P42, B. pseudomycoides HP3d and Paenibacillus polymyxa PGSS-1 against major foliar rice pathogens viz., Magnaporthe oryzae and Cochliobolus miyabeanus. Against M. oryzae, all the endophytic strains exhibited significant per cent inhibition (50.00-66.67%) and the highest inhibition of 66.67% was achieved by B. pseudomycoides strain HP3d, while the lowest inhibition of 50 and 51.11% was by B. velezensis strain A6, P42, and P. polymyxa PGSS1, respectively. These endophytes outperformed the positive control, P. fluorescens which showed 44.44% inhibition. Similarly, against C. miyabeanus, 31.25-43.75% inhibition was recorded, of which B. velezensis strain A6 exhibited the highest inhibition (43.75%), while B. velezensis strain P42 showed the lowest (31.25%). Furthermore, a double Petri dish assay was conducted to evaluate the volatile compounds produced by these endophytes against the two rice pathogens. It was observed that the volatile compounds produced by B. pseudomycoides strain HP3d and P. polymyxa strain PGSS1 significantly and effectively inhibited the growth of M. oryzae by 88.89% when compared to P. fluorescens (50.00%), whereas B. velezensis strain A6 showed the lowest inhibition (33.33%). Against the brown spot pathogen, C. miyabeanus, the endophytes demonstrated inhibition ranging from 56.25-87.50%, with B. pseudomycoides strain HP3d and P. fluorescens achieving the highest inhibition (87.50%) and B. velezensis strain P42 showing the lowest (56.25%). These results highlight the significant and varied inhibitory effects of volatile compounds released by these endophytes against fungal pathogens of rice. Overall, our findings highlight the promising biocontrol potential of these endophytic strains under in vitro conditions with B. pseudomycoides strain HP3d and P. polymyxa PGSS1 showing exceptional efficacy and they can be deployed in the field for the management of foliar fungal pathogens in rice.

Anti-inflammatory and Antiphytopathogenic Fungal Activity of 2,3-seco-Tirucallane Triterpenoids Meliadubins A and B from Melia dubia Cav. Barks with ChemGPS-NP and In Silico Prediction.

Two new rearranged 2,3-seco-tirucallane triterpenoids, meliadubins A (1) and B (2), along with four known compounds, 3-6, were isolated from the barks of Melia dubia Cav. Compound 2 exhibited a significant inflammatory inhibition effect toward superoxide anion generation in human neutrophils (EC50 at 5.54 ± 0.36 μM). It bound to active sites of a human inducible nitric oxide synthase (3E7G) through interactions with the residues of GLU377 and PRO350, which may benefit in reducing the neutrophilic inflammation effect. The ChemGPS-NP interpretation combined with bioactivity assay and in silico prediction results suggested 2 to be an agent for targeting iNOS with different mechanisms as compared to a selected set of current approved drugs. Moreover, compounds 1 and 2 showed remarkable inhibition against the rice pathogenic fungus Magnaporthe oryzae in a dose-dependent manner with IC50 values of 137.20 ± 9.55 and 182.50 ± 18.27 μM, respectively. Both 1 and 2 displayed interactions with the residue of TYR223, a key active site of trihydroxynaphthalene reductase (1YBV). The interpretation of 1 and 2 in the ChemGPS-NP physical-chemical property space indicated that both compounds are quite different compared to all members of a selected set of reference compounds. In light of demonstrated biological activity and in silico prediction experiments, both compounds possibly exhibited activity against phytopathogenic fungi via a novel mode of action.

Antifungal Trait and Plant Growth Promotion Potential of Bacillus Spp. from Rhizosphere Soils of Black Aromatic Rice, ‘Chakhao’

Manipuri black aromatic rice, ‘Chakhao’, is a nutrient rich unique local rice cultivar of Manipur, India. Rhizosphere bacteria may have potential as antifungal agent and seedling growth promoter. Hence, the current investigation was aimed at screening, for the above traits, using bacteria, Bacillus spp., isolated from the soil of Rhizosphere of six Chakhao rice cultivars. Altogether, 323 bacterial isolates were obtained from the rhizospheric soils of 6 different cultivars of Chakhao, namely Chakhao Amubi (CA), Chakhao Poireiton (CP), Chakhao Sempak (CS), Chakhao Angoubi (CAng), Chakhao Angangbi (CR) and Chakhao Wairi (CW). All the rhizobacterial isolates were screened for antifungal activity against 5 rice fungal pathogens viz. Rhizoctonia solani (RS), Fusarium oxysporum (FO), Curvularia oryzae (CO), Pyricularia oryzae (PO) and Aspergillus niger (AN). The isolates were also subjected to PGP (plant growth promotion) assays such as ammonia, indole acetic acid (IAA), siderophore and 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase production, and phosphate solubilization. Of 323 isolates obtained, 64 were found to exhibit antifungal activity while 69 showed PGP traits. Twenty-five (25) isolates were found to be positive for both antifungal and PGP traits. Of 25 bioactive isolates, 4 (CR12, CW11, CA2 and CP2) potent isolates were shortlisted for further studies. The shortlisted potent isolates were subjected to quantitative estimation of PGP activities like phosphate solubilization, IAA and siderophore production. The strains could produce significant amount of IAA and siderophore and solubilize phosphate. Molecular characterization by 16S rDNA sequence analyses revealed the identity of the isolates: CR12: Bacillus subtilis (Accn. No.OM866257), CW11: Bacillus paralicheniformis (Accn. No.OM868047), CA2: Bacillus sp. CCMB1014 (Accn. No.OM868070) and CP2: Bacillus licheniformis (Accn. No.OM892495). Seedling vigor assays of the shortlisted potent strains were carried out on Chakhao Amubi rice. The isolates exhibited higher seedling vigor indices (CR12: 668.00, CA2: 618.66, CP2: 510.92 and CW11: 478.91) over the control (164.48). These rhizospheric strains have the potential to be developed as bioinoculants or biostimulants for enhancing Chakhao rice growth.

Potential of Bacillus spp. Isolated from Food Waste Compost for Controlling Rice Diseases

Bacterial leaf blight, bakanae and blast are severe, economically damaging rice diseases caused by Xanthomonas oryzae, Fusarium fujikuroi, and Magnaporthe oryzae, respectively. Bacillus spp. have been applied as bioactive, eco-friendly agents to control these diseases. In this study, five antagonistic strains isolated from food waste compost, namely B. subtilis strain BS, B. amyloliquefacien strain C2-1, B. tequilensis strain 1-BA, B. licheniformis strain 2-BA, and Lysinibacillus. sp strain 3-BA were tested for their efficacy againstrice diseases. The inhibition of X. oryzae was tested by paper disc diffusion, while the inhibitions of F. fujikuroi and M. oryzae were tested in dual cultures. It was found that B. amyloliquefacien strain C2-1 gave the widest clear zones. At 24 h, 48 h, 72 h and 7 days, the strain had produced zones of inhibition against X. oryzaeof 7.41±0.65, 7.9±0.20, 8.8±0.65 and 8.90±0.12 mm, respectively. B. amyloliquefacien strain C2-1 also reduced the growth of the fungal rice pathogens F. fujikuroi and M. oryzae, achieving 98.79% and 97.74% inhibitions, respectively. B. amyloliquefaciens strain C2-1 was also effective against X. oryzae, F. fujikuroi, and M. oryzae in the greenhouse. Fourteen days after spraying rice plants with the B. amyloliquefacien strain C2-1, infections with X. oryzae, F. fujikuroi, and M. oryzae were inhibited by 60%, 37%, and 25%, respectively. The results suggested that B. amyloliquefacien strain C2-1 can be used as a biocontrol agent against bacterial leaf blight, bakanae, and rice blast diseases.

Rice WRKY13 TF protein binds to motifs in the promoter region to regulate downstream disease resistance-related genes.

In plants, pathogen resistance is brought about by the binding of certain transcription factor (TF) proteins to the cis-elements of certain target genes. These cis-elements are present upstream in the motif of the promoters of each gene. This ensures the binding of a specific TF to a specific promoter, therefore regulating the expression of that gene. Therefore, the study of each promoter sequence of all the rice genes would help identify the target genes of a specific TF. Rice 1kb upstream promoter sequences of 55,986 annotated genes were analyzed using the Perl program algorithm to detect WRKY13 binding motifs (bm). The resulting genes were grouped using Gene Ontology and gene set enrichment analysis. A gene with more than 4 TF bm in their promoter was selected. Ten genes reported to have a role in rice disease resistance were selected for further analysis. Cis-acting regulatory element analysis was carried out to find the cis-elements and confirm the presence of the corresponding motifs in the promoter sequences of these genes. The 3D structure of WRKY13 TF and the corresponding ten genes were built, and the interacting residues were determined. The binding capacity of WRKY13 to the promoter of these selected genes was analyzed using docking studies. WRKY13 was considered for docking analysis based on the prior reports of autoregulation. Molecular dynamic simulations provided more details regarding the interactions. Expression data revealed the expression of the genes that helped provide the mechanism of interaction. Further co-expression network helped to characterize the interaction of these selected disease resistance-related genes with the WRKY13 TF protein. This study suggests downstream target genes that are regulated by the WRKY13 TF. The molecular mechanism involving the gene network regulated by WRKY13 TF in disease resistance against rice fungal pathogens is explored.

Transcriptional Regulation of Autophagy-Related Genes by Sin3 Negatively Modulates Autophagy in Magnaporthe oryzae.

Autophagy is a conserved degradation and recycling pathway in eukaryotes and is important for their normal growth and development. An appropriate status of autophagy is crucial for organisms which is tightly regulated both temporally and continuously. Transcriptional regulation of autophagy-related genes (ATGs) is an important layer in autophagy regulation. However, the transcriptional regulators and their mechanisms are still unclear, especially in fungal pathogens. Here, we identified Sin3, a component of the histone deacetylase complex, as a transcriptional repressor of ATGs and negative regulator of autophagy induction in the rice fungal pathogen Magnaporthe oryzae. A loss of SIN3 resulted in upregulated expression of ATGs and promoted autophagy with an increased number of autophagosomes under normal growth conditions. Furthermore, we found that Sin3 negatively regulated the transcription of ATG1, ATG13, and ATG17 through direct occupancy and changed levels of histone acetylation. Under nutrient-deficient conditions, the transcription of SIN3 was downregulated, and the reduced occupancy of Sin3 from those ATGs resulted in histone hyperacetylation and activated their transcription and in turn promoted autophagy. Thus, our study uncovers a new mechanism of Sin3 in modulating autophagy through transcriptional regulation. IMPORTANCE Autophagy is an evolutionarily conserved metabolic process and is required for the growth and pathogenicity of phytopathogenic fungi. The transcriptional regulators and precise mechanisms of regulating autophagy, as well as whether the induction or repression of ATGs is associated with autophagy level, are still poorly understood in M. oryzae. In this study, we revealed that Sin3 acts as a transcriptional repressor of ATGs to negatively regulate autophagy level in M. oryzae. Under the nutrient-rich conditions, Sin3 inhibits autophagy with a basal level through directly repressing the transcription of ATG1-ATG13-ATG17. Upon nutrient-deficient treatment, the transcriptional level of SIN3 would decrease and dissociation of Sin3 from those ATGs associates with histone hyperacetylation and activates their transcriptional expression and in turn contributes to autophagy induction. Our findings are important as we uncover a new mechanism of Sin3 for the first time to negatively modulate autophagy at the transcriptional level in M. oryzae.

In Vitro Antifungal Activity of Dihydrochelerythrine and Proteomic Analysis in Ustilaginoidea virens

Dihydrochelerythrine (DHCHE) is an isoquinoline compound, which has distinct antifungal activity and can induce apoptosis. The antifungal activity of DHCHE against five rice pathogenic fungi was studied in vitro. At the concentration of 7.5 mg/L, DHCHE exhibited the highest efficacy among tested compounds in inhibiting mycelium growth, with an inhibition rate of 68.8% in Ustilaginoidea virens, which was approximately 2.4 times of that of validamycin (28.7%). After exposure to DHCHE, transmission electron micrographs revealed spores showed incomplete organelles, malformed cell walls and nuclear membranes, as well as irregular lipid spheres. Reactive oxygen species accumulation in treated spores was markedly higher than that in control spores. DHCHE induced cell damage increased in a dose-dependent manner, as indicated by the decrease in mitochondrial membrane potential and initiation of apoptosis. The differences of expression levels of Fip1, ACP1, PMS2 and COX13 that are important for oxidative phosphorylation and mismatch repair pathway were significant, which may be some of the reasons for the induction of apoptosis in DHCHE-treated U. virens. The protein levels of Fip1, ACP1, PMS2 and COX13 agreed with protein fold change ratio from parallel reaction monitoring Gene Ontology terms and Kyoto Encyclopedia of Genes and Genomes pathway of differentially expressed proteins were further analyzed. These findings will help to elucidate the mechanisms associated with antifungal and pro-apoptotic effects of DHCHE on U. virens, thereby aiding the potential development of novel pesticides.

Long-term fertilization suppresses rice pathogens by microbial volatile compounds

Microbial volatile organic compounds (VOCs) can suppress plant pathogens. Although fertilization strongly affects soil microbial communities, the influence of fertilization on microbial VOC-mediated suppression of pathogens has not been elucidated. Soil was sampled from a paddy field that had been subjected to the following treatments for 30 years: a no-fertilizer control, mineral fertilization (NPK), NPK combined with rice straw (NPK + S), NPK combined with chicken manure (70% NPK + 30% M). Then, within a laboratory experiment, pathogens were exposed to VOCs without physical contact to assess the impact of VOCs emitted from paddy soils on in vitro growth of the fungal rice pathogens: Pyricularia oryzae and Rhizoctonia solani. The VOCs emitted from soil reduced the mycelial biomass of P. oryzae and R. solani by 36–51% and 10–30%, respectively, compared to that of the control (no soil; no VOCs emission). Overall, the highest suppression of P. oryzae and R. solani was in the NPK and NPK + S soils, which emitted more quinones, phenols, and low alcohols than NPK + M soils. The abundances of quinones and phenols in the soil air were maximal in the NPK-fertilized soil because the low ratio of dissolved organic carbon and Olsen-P increased the population of key species such as Acidobacteriae, Anaerolineae, and Entorrhizomycetes. The abundance of alcohols was minimum in the NPK + S fertilized soil because the high SOC content decreased the population of Sordariomycetes. In conclusion, mineral fertilization affects bacterial and fungal VOC emissions, thereby suppressing the growth of R. solani and P. oryzae.

Antagonistic activity of wild growing mushrooms against various fungal rice pathogen.

Paddy is an important crop in Malaysia. There are various pathogens able to infect paddy causing a loss in yield's production. In this study, dual culture method, volatile organic compound (VOC) analysis, and non-volatile compound analysis were used to assess the ability of mushroom to control fungal rice pathogens including Curvularia lunata, Bipolaris panici-miliacei, and Nigrospora sp. Four mushroom isolates were further analysed for their antagonistic activity against rice pathogen. The highest percentage inhibition of radial growth (PIRG) was recorded between 45.55 and 73.68% observed in isolate 42b. The 4 isolates with the highest PIRG based on the dual culture analysis were then tested for their production of VOCs and non-volatile compound. Internal transcribed spacer (ITS) region analysis of the 4 mushroom isolates revealed their identity as Coprinellus disseminates (isolate 12b), Marasmiellus palmivorus (isolate 42b), Trametes maxima (isolate 56e), and Lentinus sajor-caju (isolate 60a). This study showed that mushroom isolates have the potential of antagonistic effect on various fungal rice pathogens tested by the production of secondary metabolites and mycoparasitic interaction.

Metatranscriptomic Analysis Reveals Rich Mycoviral Diversity in Three Major Fungal Pathogens of Rice

In recent years, three major fungal diseases of rice, i.e., rice blast, rice false smut, and rice-sheath blight, have caused serious worldwide rice-yield reductions and are threatening global food security. Mycoviruses are ubiquitous in almost all major groups of filamentous fungi, oomycetes, and yeasts. To reveal the mycoviral diversity in three major fungal pathogens of rice, we performed a metatranscriptomic analysis of 343 strains, representing the three major fungal pathogens of rice, Pyricularia oryzae, Ustilaginoidea virens, and Rhizoctonia solani, sampled in southern China. The analysis identified 682 contigs representing the partial or complete genomes of 68 mycoviruses, with 42 described for the first time. These mycoviruses showed affinity with eight distinct lineages: Botourmiaviridae, Partitiviridae, Totiviridae, Chrysoviridae, Hypoviridae, Mitoviridae, Narnaviridae, and Polymycoviridae. More than half (36/68, 52.9%) of the viral sequences were predicted to be members of the families Narnaviridae and Botourmiaviridae. The members of the family Polymycoviridae were also identified for the first time in the three major fungal pathogens of rice. These findings are of great significance for understanding the diversity, origin, and evolution of, as well as the relationship between, genome structures and functions of mycoviruses in three major fungal pathogens of rice.

Antagonistic feature displayed by endophytic bacteria consortium for control rice pathogens

Rhizoctonia solani and Xanthomonas oryzae pv. oryzae (Xoo) are important pathogens causing severe damage on rice. It makes severe damage and is required for the management of the disease. One of the management of the disease is the use of endophytic bacteria. The purpose of this study was to determine the compatibility of endophytic bacteria as consortium, to examine the potency of the endophytic bacteria consortium against R. solani and Xoo and to understand the mechanism of inhibition of endophytic bacteria consortium against R. solani and Xoo. Assessment on the compatibility between endophytic bacteria was performed in a petridish using streak method. The endophytic bacterial consortium antagonism test against rice pathogenic fungi and bacteria was carried out in a completely randomized design with 2 treatments and 15 replications. The variables observed were the compatibility of endophytic bacteria, the percentage of inhibition and the zone of inhibition. The mechanism of inhibition was observed from changes in the form of pathogenic fungi and bacteriostatic or bactericidal. The results showed that among 12 compatible endophytic bacteria as constituents of the consortium, five isolates of endophytic bacteria showed strong and very strong growth with the other isolates. These isolates from Petanahan Kebumen, Karangwangkal Purwokerto and Sumbang Banyumas. The consortium of endophytic bacteria was able to suppress the growth of R. solani by 57.14% with antibiosis mechanism causing swelling of the mycelium and formed a red pigment. The endophytic bacteria consortium inhibited the growth of Xoo by 15 mm with a bacteriostatic antibiosis mechanism. Consortium endophytic bacteria can be used as an alternative to control plant diseases which also has the opportunity to be formulated and applied to plants.

The additional PRC2 subunit and Sin3 histone deacetylase complex are required for the normal distribution of H3K27me3 occupancy and transcriptional silencing in Magnaporthe oryzae.

Development in higher organisms requires proper gene silencing, partially achieved through trimethylation of lysine 27 on histone H3 (H3K27me3). However, how the normal distribution of this modification is established and maintained and how it affects gene expression remains unclear, especially in fungi. Polycomb repressive complex 2 (PRC2) catalyses H3K27me3 to assemble transcriptionally repressed facultative heterochromatin and is crucial in animals, plants, and fungi. Here, we report on the critical role of an additional PRC2 subunit in the normal distribution of H3K27me3 occupancy and the stable maintenance of gene repression in the rice fungal pathogen Magnaporthe oryzae. P55, identified as an additional PRC2 subunit, is physically associated with core subunits of PRC2 and is required for a complete level of H3K27me3 modification. Loss of P55 caused severe global defects in the normal distribution of H3K27me3 and transcriptional reprogramming on the H3K27me3-occupied genes. Furthermore, we found that the Sin3 histone deacetylase complex was required to sustain H3K27me3 occupancy and stably maintain gene repression by directly interacting with P55. Our results revealed a novel mechanism by which P55 and Sin3 participate in the normal distribution of facultative heterochromatic modifications and the stable maintenance of gene repression in eukaryotes.

Characterization of novel extracellular polymeric substances produced by Bacillus velezensis P1 for potential biotechnological applications

AbstractBacillus velezensis (B. velezensis) P1 released huge amount of exopolymeric substances (EPS), and its EPS was extracted and characterized. The extracted EPS strongly inhibited (88%–91%) the growth of two serious rice fungal pathogens. The main component of the EPS was protein (44%). Fourier transform infrared spectra of the EPS revealed a complex structure that contained sufficient negatively charged functional groups for the zeta potential of the compound to be highly negative (−33.83 mV). Scanning electron microscope images revealed plate‐like particles with smooth, clean surfaces. The EPS showed high degrees of whiteness (L* = 94.56) and crystallinity (87%), and was thermally stable up to 500°C. Flocculation activity in a kaolin dispersion was optimal at an EPS concentration of 12 mg L−1. The EPS preferred an alkaline condition, with the highest flocculation activity (76%) observed at pH 10. The EPS produced by B. velezensis P1 could be a potential material for applying in agriculture and industry.

Production of the plant hormone gibberellin by rhizobia increases host legume nodule size.

Plant-associated microbes have evolved the ability to independently produce gibberellin (GA) phytohormones as a mechanism to influence their host. Indeed, GA was first discovered as a metabolite from the fungal rice pathogen Gibberella fujikuroi, which uses it as a virulence factor. Though some bacterial plant pathogens similarly use GA to promote infection, symbiotic nitrogen-fixing bacteria (rhizobia), which inhabit the root nodules of legumes, also can produce GA, suggesting a role in symbiosis. The bacterial GA biosynthetic operon has been identified, but in rhizobia this typically no longer encodes the final metabolic gene (cyp115), so that these symbionts can only produce the penultimate intermediate GA9. Here, we demonstrate that soybean (Glycine max) expresses functional GA 3-oxidases (GA3ox) within its nodules, which have the capability to convert GA9 produced by the enclosed rhizobial symbiont Bradyrhizobium diazoefficiens to bioactive GA4. This rhizobia-derived GA is demonstrated to cause an increase in nodule size and decrease in the number of nodules. The increase in individual nodule size correlates to greater numbers of bacterial progeny within a nodule, thereby providing a selective advantage to rhizobia that produce GA during the rhizobia-legume symbiosis. The expression of GA3ox in nodules and resultant nodulation effects of the GA product suggests that soybean has co-opted control of bioactive GA production, and thus nodule size, for its own benefit. Thus, our results suggest rhizobial GA biosynthesis has coevolved with host plant metabolism for cooperative production of a phytohormone that influences nodulation in a mutually beneficial manner.