Aim: This study aimed to understand the Bacillus-mediated resistance against the sheath rot pathogen (Sarocladium oryzae) in rice, specifically focusing on the generation of reactive oxygen species (ROS), such as superoxide (O₂⁻) and hydrogen peroxide (H₂O₂), as an early defense response in rice sheaths treated with Bacillus bioformulations and subsequently challenged with S. oryzae. Study Design: An experimental design involving various Bacillus bioformulations (liquid and talc) applied as seed treatment, seedling dip, and foliar spray, followed by challenge inoculation with Sarocladium oryzae. Place and Duration of Study: The study was conducted as part of the research on Bacillus-mediated resistance in rice at ICAR-NRRI, Cuttack during 2021-2022. Methodology: Rice leaf sheaths were sampled at 0, 24, 48, 72, 96, 120, and 144 hours after pathogen inoculation. Treatments included liquid and talc formulations of Bacillus isolates (RBS-57, BS-5, RBS-3). Histochemical assays using nitro blue tetrazolium (NBT) for O₂⁻ and diaminobenzidine (DAB) for H₂O₂ were employed to detect and localize these reactive oxygen species. Results: Histochemical assays revealed an early and enhanced accumulation of both O₂⁻ and H₂O₂ in Bacillus-treated plants. The RBS-57 liquid formulation showed the highest O₂⁻ and H₂O₂ activities, peaking at 72 hours post-inoculation, which was significantly earlier and more intense than in control plants. This rapid and synchronized oxidative burst suggests an effective priming of host defense responses. H₂O₂ accumulation was confirmed by DAB staining, appearing as dark brown spots, and was observed exclusively in inoculated leaves, indicating a localized and pathogen-induced response. Similarly, O₂⁻ accumulation, visualized as intense blue spots with NBT solution, was higher in RBS-57 liquid bioformulation treatment, peaking at 72 hours, and was also localized to inoculated leaves. Chemical treatments resulted in significantly lower O₂⁻ activity compared to Bacillus treatments. Conclusion: The findings confirm the pivotal role of Bacillus-mediated ROS signaling in restricting Sarocladium oryzae infection in rice. The ability of Bacillus bioformulations to induce a rapid and intense oxidative burst positions them as valuable tools in developing sustainable and eco-friendly strategies for managing sheath rot disease, thereby contributing to global food security. In nutshell, this study highlights bacillus-based bioformulations as an eco-friendly and sustainable strategy for effective sheath rot disease management in rice.

Sheath rot (Sarocladium oryzae) of rice causes significant grain yield losses, warranting integrated, cost effective and eco-friendly management. With limited availability of highly resistant varieties, combining resistant / moderately resistant varieties with judicious and need based application of fungicides is a practical alternative. However, scarce information is available on the extent of yield losses in varieties with varied levels of resistance. This study evaluated yield losses in terms of 1000 grain weight (TGW) in rice varieties with varying resistance levels to sheath rot under protected conditions using fungicide azoxystrobin (11%) + tebuconazole (13.8%). It was observed that the differences in disease severity, AUDPC values and TGW loss were mainly attributed to the interaction effects among the treatment i.e. fungicide sprayed (protected) and fungicide non-sprayed (unprotected) treatment, and varieties & between varieties and years (P < 0.001). Plots with fungicidal application had a mean disease severity of 5.60% compared to 25.46% in untreated plots. Protected plots had a mean TGW of 24.80 g compared with 20.59 g in unprotected plots, reflecting a significant differences . Fungicide applications resulted in reduction of mean disease severity of 100, 74.03–97.57, 69.62–80.92, and 72.29–73.95% in resistant, moderately resistant, susceptible and highly susceptible varieties, respectively. A strong positive correlation was observed between disease severity and TGW loss during the cropping season 2019, 2020 and pooled data. The grain yield was enhanced, and crop loss models indicated good fitness with excellent predictive validity for estimating sheath rot impacts. As the first systematic assessment in northern region of India to systematically assess the impact of rice sheath rot. Its findings provide crucial insights into the interaction between fungicide treatments, varietal resistance, and disease dynamics, paving the way for more informed and effective management strategies in the region.Supplementary InformationThe online version contains supplementary material available at 10.1038/s41598-025-05104-y.

Rice is one of the vital staple food crops worldwide and it is affected by many fungal diseases. Among these, sheath rot disease caused by Sarocladium oryzae is emerging as a severe threat, leading to yield losses ranging from 10–85 %. Sheath rot disease of rice affects all the stages of the crop, but the disease is utmost critical in booting stage. It damages the boot leaf sheath that protects developing panicles, which delays or prevents panicle emergence. Grain production and quality are severely reduced. Discoloured, chaffy and sterile grains produced in the infected panicles. Survey was conducted in Thoothukudi district of Tamil Nadu during the period 2022 – 23. Ten isolates of S. oryzae were isolated using the infected samples collected. The isolate (So 5) obtained from Peikulam village of Sathankulam block (Lat. 8.51o N, Long. 77.85o E) was found to be the most virulent isolate. Morphological studies showed that the isolate So 5 recorded the maximum mycelial growth of 7.70 cm diameter after 20 days of inoculation in PDA medium. The pathogen produced white cottony aerial mycelial growth and cylindrical shape of conidia. The pathogen was molecularly confirmed as S. oryzae by comparing the similarities with the NCBI database (Accession No. OR298274). Screening of genotypes is essential to identify the resistant sources. One hundred rice genotypes were screened under natural and artificial conditions. The genotypes viz., Aryan 1102, Aryan 1203, Dhalaheera, Kattanoor, Navara black, Purpleputtu, Salem senna, Swarna and Varaprabha showed resistance in both conditions.

Rice sheath rot disease is one of the diseases that can significantly reduce rice plant productivity. This disease is complex as it can be caused by various types of pathogens. This study aimed to identify fungi associated with rice sheath rot disease based on morphological characteristics. Symptomatic rice sheaths were collected from several rice production centers in Lampung Province, followed by isolation and morphological characterization on the Potato Dextrose Agar (PDA) medium. Morphological identification was conducted based on macroscopic and microscopic characteristics, which were compared with relevant literature. The results of the study identified several fungi associated with rice sheath rot disease, including Sarocladium oryzae, Sarocladium sparsum, Fusarium bubalinum, Fusarium hainanense, Alternaria sp., and Curvularia sp.

Abstract Sarocladium oryzae is one of the rice sheath rot pathogens causing crop losses in several countries. This study aims to determine the optimal in-vitro factors for the growth of S. oryzae and test several rice varieties against S. oryzae infection. Six isolates of S. oryzae from different regions in Indonesia were used. The isolates underwent testing for light, pH, and temperature. Additionally, they were tested on five different rice varieties. The study showed that S. oryzae grows well with 12 hours of light/12 hours of darkness, pH 6, and a temperature of 25°C. It also sporulates heavily under continuous light, pH 6, and a temperature of 25°C. Ciherang, Inpari 30 and Mekongga rice varieties showed high disease severity against S. oryzae. The study demonstrates that S. oryzae grows and sporulates under optimal conditions, offering insights for controlling rice sheath rot disease and providing planting recommendations for affected areas.

Rice is a vital staple food crop widely cultivated across diverse Asian agroclimatic zones. However, in recent years, the emergence of sheath rot disease, caused by Sarocladium oryzae, has severely impacted rice yields, devastating approximately half of rice production. Traditional methods of controlling plant diseases often have harmful effects on the environment and have led to the development of pathogenic resistance to various agrochemicals. In contrast, endophytes have shown great promise in managing plant diseases while enhancing plant growth and yield. The seed-associated endophyte Bacillus lichiniformis has demonstrated remarkable efficacy, exhibiting a 76.47% inhibition rate against S. oryzae. Beyond its antibiotic properties, this endophyte also promotes biostimulant activities, including the production of indole-3-acetic acid (IAA), siderophores, and the utilization of ammonia (NH3). Additionally, the analysis of secondary metabolites using gas chromatography-mass spectrometry (GC-MS) revealed a diverse array of compounds, including 9,12-Octadecadienoic acid (Z, Z)-TMS derivatives, Elaidic acid-TMS, Bis(2-ethylhexyl) phthalate, Caproic acid-TMS, Diethyl phthalate, Ricinoleic acid-2TMS derivatives, Mandelic acid-2TMS, and others. These compounds exhibit significant antifungal, antiviral, larvicidal, and antibacterial activities against various plant pathogens, highlighting the potential of Bacillus lichiniformis as a sustainable and effective biocontrol agent in rice cultivation. This research underscores the critical role of endophytes in promoting sustainable agricultural practices, offering an environmentally friendly alternative to chemical control methods while effectively combating emerging plant diseases.

Rice sheath rot, caused by Sarocladium oryzae, is a devastating disease threatening rice production worldwide, with yield losses ranging from 9.6 per cent to 85 per cent. Conventional reliance on synthetic fungicides has raised concerns about environmental sustainability and health safety, prompting the exploration of eco-friendly alternatives. This study investigates the in vitro efficacy of native antagonistic bio-agents, specifically Trichoderma spp. and Pseudomonas spp., against Sarocladium oryzae. Rhizospheric soil samples were collected to isolate and identify bio-agents, which were then tested using the dual culture method. Results revealed significant pathogen inhibition, with Trichoderma isolate Tr-1 achieving the highest inhibition rate (76.72%) among the Trichoderma isolates and in Pseudomonas isolates Ps-1 (61.21%) showed the significant inhibition. These findings highlight the potential of native bio-agents as sustainable, environmentally friendly alternatives to chemical fungicides, offering a promising strategy for integrated disease management in rice cultivation and advancing organic farming practices.

Fig. S1. Phylogenetic tree inferred from a Maximum Likelihood (RAxML) analysis based on a concatenated alignment of ITS, and LSU sequences of 706 strains representing Bionectriaceae and outgroups. Numbers at branches indicate support values (RAxML-BS) above 50 %. The new species are printed in red font and new combinations in blue font and the ingroup genera highlighted with coloured boxes. Strains with a type status are indicated with “T”. The tree is rooted to Bullanockia australis (CBS 142093), Flammocladiella aceris (CBS 138906), F. anomiae (CBS 142775), F. decora (CBS 142776), Stromatonectria caraganae (CBS 125579, CBS 127387), Tilachlidium brachiatum (CBS 505.67, CBS 363.97) and Xanthonectria pseudopeziza (CBS 140160, CBS 141245). The scale bar represents the expected number of changes per site. &lt;br /&gt;Fig. S2. Phylogenetic tree inferred from a Maximum Likelihood (RAxML) analysis based on a concatenated alignment of ITS, LSU, RPB2, and TEF1 sequences of 751 strains representing Bionectriaceae and allied families in Hypocreales and outgroups. Numbers at branches indicate support values (RAxML-BS) above 50 %. The new species are printed in red font and new combinations in blue font and the ingroup genera highlighted with coloured boxes. Strains with a type status are indicated with “T”. The tree is rooted to Paracremonium inflatum (CBS 485.77), Sarocladium oryzae (CBS 180.74), S. zeae (CBS 800.69), and Xenoacremonium recifei (CBS 137.35). The scale bar represents the expected number of changes per site. &lt;br /&gt;Table S1. Strains used in this study with details of their host, location, and GenBank accessions numbers.

Seed mycoflora poses significant challenges to rice production, leading to substantial economic losses. Red rice seed samples of seven Indian landraces, Chohartu, Deval, Gosha, Jattu, Karad 21-1, Karad 21-3 and Matali, were collected from different districts of Himachal Pradesh, India. The presence of mycoflora associated with seed-borne fungi and their impact on seed health were evaluated using two methods: agar plate method and blotter paper method. A total of nine fungal species including Fusarium sp., Bipolaris oryzae, Alternaria padwickii, Curvularia lunata, Sarocladium oryzae, Trichoderma sp., Rhizoctonia solani, Rhizopus stolonifer and Aspergillus niger were isolated, identified and morphologically characterised based on colony growth, mycelial features, conidial structures and spores. The highest seed infections were recorded with Fusarium spp., Curvularia lunata and Bipolaris oryzae and the least with Alternaria padwickii and Rhizoctonia solani. Seeds showed that the fungi had a variable effect on seed quality parameters like seed germination, shoot length, root length and seedling vigour index. It was observed that the ‘Matali’ landrace showed the most detrimental effects on all these parameters. Hence, this study underscores the requirement of thorough seed examination to reduce the effects of seed mycoflora associated with red rice seeds, which could affect rice production.

Rice sheath rot caused by the fungus Sarocladium oryzae, has become a highly destructive rice disease with a high variability in yield loss levels. Therefore, sheath rot disease can be effectively managed through crop improvement strategies viz., discovery of resistance sources from varieties, germplasm, landraces, wild genetic resources and further deploying them in breeding programmes. In this study, we evaluated 338 NSN-1 rice cultures for their resistance to sheath rot at ZARS V.C. farm Mandya during Kharif 2023with HR-12 as a susceptible check under natural and artificially inoculated conditions and disease severity was assessed using a 0-9 disease scoring scale. Our results revealed considerable variations in sheath rot resistance among the NSN-1 rice cultures. Several lines exhibited different levels of resistance, Out of 338, seven NSN-1 cultures were found immune with no disease (viz., NSN-1-4612, NSN-1-4628, NSN-1-4502, NSN-1-4304, NSN-1-5310, NSN-1-4138 and Rasi). One NSN-1-5815 line showed resistance reaction with less than one per cent disease, suggesting their potential for deployment in breeding programs aimed at developing sheath rot resistant rice varieties. These findings contribute to the ongoing efforts to enhance the resistance of rice cultivars to sheath rot, thereby ensuring the sustainability of paddy cultivation.

Sheath rot and dirty panicle are some of the major diseases of rice in Thailand. The diseases are traditionally considered to be caused by the pathogen Sarocladium oryzae and damage and lower both the quantity and quality of rice grain. In this study, 32 fungal isolates collected from the central and northeastern regions of Thailand were analysed phylogenetically using three molecular markers (ITS, D1/D2 of 28S rDNA and ACT) and physiological races were determined on 10 differential rice cultivars. We found that S. oryzae is not the only causal agent of sheath rot in Thailand, but S. attenuatum was also found. Despite having similar morphological features, the phylogenetic analysis recognised 11 of 32 isolates as S. attenuatum and the remaining isolates as S. oryzae. This is the first report of S. attenuatum causing sheath rot of rice in Thailand in addition to S. oryzae. Evaluation of physiological races revealed high pathogenic diversity of the two species. Thus, 16 and 11 physiological races were recorded from 21 isolates of S. oryzae and 11 isolates of S. attenuatum, respectively. These results indicate that both S. oryzae and S. attenuatum are the causal agents of rice sheath rot and dirty panicle in Thailand and that they are pathologically diverse.

Antagonistic potential of six soil fungi viz., Aspergillus flavus Link., A. fumigatus Fresen., A. niger Tiegh., Penicillium sp., Trichoderma harzianum Refat. and T. viride Pers. against eight pathogenic fungi viz., Alternaria alternata (Fr.) Keissler, Curvularia lunata (Wakker) Boedijn, Drechslera oryzae Breda de Haan (Subramanian and Jain), Fusarium moniliforme Sheldon, F. solani (Mart.) Sacc. Microdochium oryzae (Hashloka and Yokogi) Sam. and Hal., Pestalotiopsis guepinii (Desm.) Stay. and Sarocladium oryzae (Sawada) W. Gams and D. Hawks of rice were evaluated. In colony interaction, the highest growth inhibition (88%) was observed owing to T. harzianum against Alternaria alternata.Volatile substances from soil fungi inhibited the radial growth of the test pathogens which varied from 8.33 to 57.36%.The highest inhibition (57.36%) was found owing to T. harzianum against P. guepinii. The inhibition of mycelial growth of the test pathogens ranged from 29.05 to 64.5% owing to non volatile substances of the soil fungi. The highest mycelial growth inhibition was observed owing to T. harzianum against C. lunata. Trichoderma harzianum may be exploited commercially to control rice pathogens. Bangladesh J. Bot. 53(1): 101-108, 2024 (March)

Unravelling genetic diversity and population structure of Sarocladium oryzae causing sheath rot disease in rice using hyper-variable SSR markers

Screening of rice genotypes against sheath rot of rice caused by Sarocladium oryzae

Sheath rot of rice has become an emerging disease in most of the rice-growing areas of north India, so the resistant varieties against sheath rot need to be developed. An effort was made to identify resistance sources against the disease caused by three different pathogens viz., Sarocladium oryzae, Fusarium verticillioides, and Fusarium fujikuroi in the region. Fifty advanced promising rice germplasm lines were inoculated with three pathogens associated with disease using the grain insertion method at the boot stage. Two lines RYT 3836 and RYT 3920 showed moderately resistant reaction to all three pathogens inoculated. RYT 3886 was resistant to both F. verticillioides &amp; F. fujikuroi while RYT 3884 was resistant to F. fujikuroi only. However, none of the evaluated lines possessed resistance for S. oryzae.

Rice sheath rot (Sarocladium oryzae) is an emerging disease in all rice ecosystems and considered as one of the major threats to rice production. For development of precise management strategies spatial distribution of infection risk is essential to ascertain epidemic nature of the disease. For risk estimation, temperature-based infection model has been designed and disease risk estimated as the monthly cumulative value of the daily infection index. Geo-spatial distribution of infection risk has been assessed for the coastal rice ecosystems based on 39 years of weather data and two years (2018 and 2019) of surveyed ground truth. Infection risk was noted to be higher in kharif than rabi season and the eastern coast was identified as hotspot. Yearly variation estimates has indicated rabi rice is likely to be vulnerable to climate change arising due to temperature rise. Infection risk prediction based on critical weather factor is useful in germplasm, fungicide evaluation along with development of management strategies.

Penyakit busuk pelepah merupakan salah satu penyakit penting pada tanaman padi. Penyakit ini dapat menyebabkan kehilangan hasil sampai 85%. Penyakit busuk pelepah disebabkan oleh jamur Sarocladium oryzae. Penelitian ini bertujuan untuk menguji ketahanan beberapa varietas padi terhadap jamur S. oryzae penyebab penyakit busuk pelepah. Penelitian dilakukan dari Agustus 2021 sampai Maret 2022 di rumah kaca Fakultas Pertanian Universitas Lampung. Empat varietas yang diuji yaitu Ciherang, Inpari 32, IR 64, dan Inpari Nutri-Zinc. Peubah yang diamati yaitu keterjadian dan keparahan penyakit. Pengamatan dilakukan selama 56 hari (8 minggu). Percobaan dilakukan dalam rancangan acak lengkap (RAL) dengan 4 (empat) perlakuan dan 6 (enam) ulangan, dan masing-masing unit percobaan terdiri dari 8 batang dalam 1 rumpun padi. Hasil penelitian menunjukkan bahwa gejala penyakit hasil inokulasi buatan sama dengan gejala penyakit yang ditemukan di lapang, yaitu berupa bercak coklat hingga kehitaman pada pelepah daun bendera. Masa inkubasi penyakit busuk pelepah berkisar 6,7-7,2 hari setelah inokulasi dengan masa inkubasi terpanjang terjadi pada varietas IR 64. Keterjadian dan keparahan penyakit pada semua varietas tidak berbeda nyata pada 8 minggu setelah inokulasi. Hasil penghitungan nilai laju infeksi dan penghitungan AUDPC (Area Under Disease Progress Curve) pada semua varietas menunjukkan tidak berbeda nyata. Hal ini menunjukkan bahwa varietas Ciherang, Inpari 32, IR 64, dan Inpari Nutri-Zinc memiliki tingkat ketahanan yang sama terhadap infeksi jamur S. oryzae.

The excessive use of synthetic chemicals in agriculture demands sustainable alternatives to combat crop-affecting microorganisms. Plant-derived secondary metabolites have garnered attention as promising candidates with antimicrobial properties. This study investigates the antimicrobial potential of tobacco plants, specifically non-commercial accessions Nic 1015 (“TI 1341”) and BHmN, recognized for their rich bioactive compounds. Our objectives encompassed the extraction of leaf surface compounds and the assessment of their in vitro antimicrobial activity against crop-damaging microorganisms. Ethanol-based extracts, abundant in diterpenes, were meticulously analyzed. Notably, BHmN contained cis-abienol, while both accessions featured α-CBT diol, as confirmed by thin-layer chromatography (TLC) and high-performance liquid chromatography (HPLC). TLC-Bioautography and microdilution assays unveiled substantial antifungal activity. The growth inhibition percentages correlated with extract concentrations, highlighting the pivotal role of diterpenes. These extracts exhibited pronounced efficacy against Rhizoctonia solani and Stemphylium solani but displayed relatively weaker activity against Sarocladium oryzae. Notably, Nic 1015 extract demonstrated remarkable antifungal activity at a minimal concentration of 78 µg·mL−1, while cis-abienol and sclareol inhibited the growth of Fusarium graminearum and Alternaria alternata. Additionally, the extracts demonstrated in vitro antibacterial activity against common plant culture contaminants, Bacillus licheniformis and Stenotrophomonas maltophilia. In conclusion, the findings underscore the potential of these extracts as effective tools for controlling pathogenic fungi and bacterial contaminants in plant in vitro cultures. Harnessing plant-derived secondary metabolites, especially those from tobacco leaf surface, presents a sustainable and eco-friendly strategy to mitigate the detrimental impact of microorganisms on agricultural crops, promising a greener alternative to synthetic chemical products.

Induction of defense-related enzymes and enhanced disease resistance in rice against Sarocladium oryzae by Bacillus cereus RBS-57

Abstract Sheath rot is one of the most destructive emerging diseases of rice in Asia and a significant loss (20–85%) to rice production is caused by this disease under temperate agro-climatic conditions of Kashmir. Disease is more prevalent in higher belts of valley where Japonica rice cultivation is more common. Also, late-maturing varieties are more likely to be attacked by sheath rot disease of rice. Information regarding the occurrence and distribution of any pathogen and its variability in the field is very much essential to devise a suitable disease management programme against the particular pathogen. The isolates of Sarocladium oryzae tested in the present study exhibited considerable variation in cultural characteristics, morphology and pathogenicity. The resistant sources for sheath rot disease of rice were identified among the temperate germplasm of rice under a relatively high inoculum concentration and disease pressure of all the variable isolates of S. oryzae. Among 219 rice genotypes screened for resistance against S. oryzae under field conditions, 42 genotypes were further evaluated under controlled epiphytotic conditions against all the 18 isolates of S. oryzae. Four genotypes (SKUA-354, ORN-V4, GS-183, GS357) were finally selected with high resistance against sheath rot disease of rice which can be utilized as potential donors for the development of disease-resistant varieties of rice against sheath rot.