Rice Sheath Rot Research Articles

Molecular and Morphological Identification of Sarocladium Species Causing Sheath Rot of Rice in Thailand and Their Division into Physiological Races.

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.

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

Rice sheath rot, caused by the fungus Sarocladium oryzae, poses a major threat to rice crops. This pathogen exhibits substantial variability in the field, yet limited information on its genetic diversity and population structure hampers the development of effective disease management strategies. In this study, hyper-variable Simple Sequence Repeats (HV-SSR) markers were employed for the first time to assess the genetic diversity of Sarocladium oryzae, collected from various rice cultivating regions in Odisha, Eastern India. The isolates were identified using both morphological and molecular criteria. A pathogenicity test was performed for all the isolates. A total of 2558 HV-SSRs with more than 10 repeat units were identified in the genome of S. oryzae. The most prevalent types of repeats were dinucleotides (26.8%), followed by trinucleotides (22.8%), tetranucleotides (8.67%), pentanucleotides (2.83%), and hexanucleotides (1.83%). A total of 150 HV-SSR primers were designed and 24 were randomly selected and validated, of which ten of them demonstrating polymorphism in the 87 isolates. These ten polymorphic hyper-variable SSR markers were subsequently used to assess the genetic diversity and population structure of Sarocladium oryzae isolates. The markers revealed a total of 32 alleles, with the number of alleles per locus varying from 2 to 4. Gene diversity ranged from 0.409 to 0.641, while the major allele frequency varied from 0.448 to 0.736. The Polymorphic Information Content (PIC) values ranged from 0.325 to 0.569, with an average of 0.457. Cluster analysis categorized the sheath rot isolates into three distinct major clusters. Principal coordinate analysis and structure analysis identified two genetic clusters within S. oryzae isolates. Analysis of molecular variance indicated that there was more genetic variation within populations (55%) and less variation among populations (45%). The findings of this study provide insights into the genetic diversity of S. oryzae in the rice-cultivating regions of Odisha, which can be used to develop more effective disease management strategies.

Assessment of rice sheath rot disease risk for its establishment in Southern Coastal states of India

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.

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.

Fusarium and Sarocladium Species Associated with Rice Sheath Rot Disease in Sub-Saharan Africa

Sarocladium and Fusarium species are commonly identified as causal agents of rice sheath rot disease worldwide. However, limited knowledge exists about their genetic, pathogenic, and toxigenic diversity in sub-Saharan African (SSA) countries, where an increasing incidence of this disease has been observed. In this study, seventy fungal isolates were obtained from rice plants displaying disease symptoms in rice research programs and farmer fields in Mali, Nigeria, and Rwanda. Thus, an extensive comparative analysis was conducted to assess their genetic, pathogenic, and toxigenic diversity. The Fusarium spp. were characterized using the translation elongation factor (EF-1α) region, while a concatenation of Internal Transcribed Spacer (ITS) and Actin-encoding regions were used to resolve Sarocladium species. Phylogenetic analysis revealed four Fusarium species complexes. The dominant complex in Nigeria was the Fusarium incarnatum-equiseti species complex (FIESC), comprising F. hainanense, F. sulawesiense, F. pernambucatum, and F. tanahbumbuense, while F. incarnatum was found in Rwanda. The Fusarium fujikuroi species complex (FFSC) was predominant in Rwanda and Mali, with species such as F. andiyazi, F. madaense, and F. casha in Rwanda and F. annulatum and F. nygamai in Mali. F. marum was found in Nigeria. Furthermore, Fusarium oxysporum species complex (FOSC) members, F. callistephi and F. triseptatum, were found in Rwanda and Mali, respectively. Two isolates of F. acasiae-mearnsii, belonging to the Fusarium sambucinum species complex (FSAMSC), were obtained in Rwanda. Isolates of Sarocladium, which were previously classified into three phylogenetic groups, were resolved into three species, which are attenuatum, oryzae, and sparsum. S. attenuatum was dominant in Rwanda, while S. oryzae and S. sparsum were found in Nigeria. Also, the susceptibility of FARO44, a rice cultivar released by Africa Rice Centre (AfricaRice), was tested against isolates from the four Fusarium species complexes and the three Sarocladium species. All isolates evaluated could induce typical sheath rot symptoms, albeit with varying disease development levels. In addition, liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to determine variation in the in vitro mycotoxins of the Fusarium species. Regional differences were observed in the in vitro mycotoxins profiling. Out of the forty-six isolates tested, nineteen were able to produce one to four mycotoxins. Notably, very high zearalenone (ZEN) production was specific to the two F. hainanense isolates from Ibadan, Nigeria, while Fusarium nygamai isolates from Mali produced high amounts of fumonisins. To the best of our knowledge, it seems that this study is the first to elucidate the genetic, pathogenic, and toxigenic diversity of Fusarium species associated with the rice sheath rot disease complex in selected countries in SSA.

Prevalence of pathogens causing sheath rot of rice in North India and its management

Prevalence of pathogens causing sheath rot of rice in North India and its management

Short Communication: First report of Xanthomonas sacchari causing rice sheath rot disease in Lampung, Indonesia

Abstract. Ivayani, Widiastuti A, Suryanti, Suharjo R, Priyatmojo A. 2022. Short Communication: First report of Xanthomonas sacchari causing rice sheath rot disease in Lampung, Indonesia. Biodiversitas 23: 6463-6470. Rice sheath rot is recently reported as an emerging important rice disease in Indonesia, which can cause yield losses of up to 85%. Due to its potential loss, serious attention should be given on the disease. However, there is still limited information on the causal agent of the disease in Indonesia, especially from plant pathogenic bacteria. One bacterial isolate (LSE 33) was obtained from the sheath rot symptom of rice. Pathogenicity test revealed that bacteria produced symptoms that were similar to those obtained from the field. Based on the sequence analysis of 16S rRNA gene region, isolate LSE 33 was placed within group of the type strain and reference strains of Xanthomonas sacchari. Strain LSE 33 had 99.93% sequence similarity with Xanthomonas sacchari strain SAM 144 and strain AF 10 isolated from rice, and 99.35% similarity with strain LMG 471T isolated from sugarcane. To our knowledge, this is the first report of X. sacchari causing sheath rot on rice in Indonesia.

Identification of Unhealthy Leaves in Paddy by using Computer Vision based Deep Learning Model

India is one of the leading productions of Paddy. Compared to previous year Gross Domestic Product (GDP) Export rate of Paddy in the year 2021 has increased to around 33%. Paddy is the Major food production crop in India. Every crop is prone to many diseases throughout their lifespan. The disease can affect the crop at any stage of their growing phase. Early detection of disease is the only solution to reduce the damage. Early detection may reduce the damage caused and increase the quality as well as quantity of Production. Major disease which causes more damage in paddy production is Rice Blast, Brown Spot, Sheath Blight, Sheath Rot and False Smut. Early detection of these diseases can reduce the damage and increase the production value. Recent technology of computer vision and by using Deep learning model can accurately predict and diagnose the early symptom of diseases. We used Convolutional Neural Network classifier of deep learning model to predict the early symptom of disease in paddy. We compared four main classifier VGG16, VGG19, Inception-V3 and ResNet50, among these four Inception-V3 achieved a highest accuracy of 95.3%.

First Report of Fusarium Sheath Rot of Rice Caused by Fusarium incarnatum-equiseti Species Complex in the United States.

Fungal diseases, including sheath rot (Sarocladium oryzae), cause significant losses of yield and milling quality of rice (Oryza sativa). In August 2021, symptoms like sheath rot were observed on 20% of rice plants (cv. Presidio) in 1-hectare field in Eagle Lake, Texas. Initial lesions occurred on the upper flag leaf sheaths and were oblong or irregular oval, with gray to light brown centers, and a dark reddish-brown diffuse margin. Lesions enlarged, coalesced, and covered a large area of the sheath. Infection led to panicle rot with kernels turning dark brown. Unlike sheath rot, sheath infection also led to inside culm infection with irregular dark brown lesions. Infected tissue pieces were sterilized with 1% NaOCl for 2 min, followed by 75% ethanol for 30 s, washed in sterile H2O three times, air dried and incubated on PDA at 27℃. Fungal isolates were obtained from 15 diseased plant samples and their singled-spored fungal colonies were whitish, loosely floccose and produced light yellow pigmentation. On carnation leaf agar, macroconidia were slightly curved and tapered at the ends, with 3 to 5 septa, and measured 17.5 to 34.3 × 3.1 to 5.0 µm. Microconidia were ovoid, usually with 0 to 1 septum and were 4.0 to 15.5 × 2.5 to 4.5 µm. Spherical shaped chlamydospores were produced in chain. These morphological characteristics were consistent to those described for Fusarium incarnatum-equiseti species complex (O'Donnell et al. 2009), including F. incarnatum (Wang et al. 2021) and F. equiseti (Avila et al. 2019). For molecular identification, DNA of a representative isolate was extracted and ITS, LSU, and EF1 of the fungus were amplified using the primers of ITS1/ITS4 (Wang et al. 2014), D1/D2 domain region of LSU (Fell et al. 2000), and EF1 (Wang et al. 2014), respectively, and sequenced. The ITS sequence (OL344049) was 99.61% identical to F. incarnatum-equiseti species complex (FD_01692) in Fusarium-ID database and 99.61% identical to F. equiseti (LC514690, KY523100, MW016539) and F. incarnatum (MH979697) in NCBI database. The LSU sequence (OK559512) was 98.77% similar to F. equiseti (MN877913, MN368509) and F. incarnatum (MH877332, MH877326); the EF1 sequence (OK570044) was 99.27% similar to F. equiseti (MK278902) in NCBI database. A phylogenetic analysis based on the concatenated nucleotide sequences grouped this isolate in the F. incarnatum-equiseti species complex clade at 100% bootstrap support. To evaluate pathogenicity, a conidial suspension of 1 x 106 conidia/ml or sterilized water (the controls) was injected into the sheaths and young panicles of three rice plants (cv. Presidio) at boot. Treated plants were maintained in a greenhouse at 25 to 30℃. After 3 weeks, typical symptoms, like those observed in the field, developed on the inoculated plants but not on the controls. The same fungus was consistently re-isolated from the diseased plants. To our knowledge, this is the first report of Fusarium sheath rot caused by F. incarnatum-equiseti species complex in rice in the U. S. F. incarnatum-equiseti species complex has been reported to be associated with panicle infection in wild rice (O. latifolia) in Brazil (Tralamazza et al. 2021). F. incarnatum has also been reported to cause panicle rot in China (Wang et al. 2021). F. proliferatum has been reported to cause Fusarium sheath rot in India (Prabhukarthikeyan et al. 2021) and the U. S. (Cartwright et al. 1995). This research demonstrates the potential of different pathogens being involved in causing sheath rot of rice.

Fungi associated with rice sheath rot in Lampung, Indonesia

Rice sheath rot caused by some pathogens. It occurs in the upper leaf sheath that wraps the rice panicle, its major features are rotting, discoloration, sometimes affecting rice grain production. Lampung is an important rice-producing area in Indonesia. Currently, rice sheath rot in the area is reportedly caused by Fusarium sulawesiense and Fusarium hainanense. This study aimed to identify the rice sheath rot pathogen accurately by sampling locations at varying altitudes, plant ages, and varieties in Lampung Sampling was conducted in Lampung, infected plants were collected and the pathogen isolates were molecularly characterized on the basis of DNA sequence data for the internal transcribed spacer and translation elongation factor 1-α. Pathogenicity test results showed that 16 fungal isolates caused rice sheath rot. These isolates were identified as Sarocladium oryzae, Fusarium bubalinum, F. hainanense, Setophoma poaceicola, Curvularia geniculata, and Alternaria padwickii. This study is the first to report that S. poaceicola is a pathogen of rice sheath rot.

English

Rice sheath rot disease is one of the obstacles in Fogera plain of rain-fed rice production system. A cultivar called X-Jigna has been used by small scale farmers based on mono-cropping system for over two decades. This production system contributed to the disease occurrence and adversely impacted the production and productivity. So far, there were no any effective measures taken as research remedies in the rain-fed production areas. Since the disease is seed-borne, recently, effective seed treatment methods were identified and evaluated at farmers’ fields. Partial budget analysis was employed to estimate economic costs and benefits to realize the seed treatment methods were economically viable or not. The yield responses from fungicide and hot water treatments were higher than the control check. Marginal rate of return of hot water and fungicide treatment methods were higher than untreated production. Sensitivity analysis was used to evaluate the resistance and responses to the changes in prices and yields of new production method. The result shows that marginal rate of return was declining with an increasing price change of fungicide. Marginal rate of return was highly sensitive to decreasing level of yields but not strongly sensitive to the different level of price changes of fungicide. When farmers change their production method from use of untreated to treated seed, the yield loses could be dramatically decreased and marginal rate of return were considerably increased. The result ascertained that seed treatment methods were found to be effective, economically feasible and highly recommended for rice producing farmers. Key words: Break-even price, break-even yield, cost-benefit, marginal rate of return, partial budget analysis, seed treatment, sensitivity analysis, sheath rot disease.

Negatively Regulated Aerobactin and Desferrioxamine E by Fur in Pantoea ananatis Are Required for Full Siderophore Production and Antibacterial Activity, but Not for Virulence.

Pantoea ananatis is an emerging plant pathogen that causes disease in economically important crops such as rice, corn, onion, melon, and pineapple, and it also infects humans and insects. In this study, we identified biosynthetic gene clusters of aerobactin and desferrioxamine E (DFO-E) siderophores by using the complete genome of P. ananatis PA13 isolated from rice sheath rot. P. ananatis PA13 exhibited the strongest antibacterial activity against Erwinia amylovora and Yersinia enterocolitica (Enterobacterales). Mutants of aerobactin or DFO-E maintained antibacterial activity against E. amylovora and Y. enterocolitica, as well as in a siderophore activity assay. However, double aerobactin and DFO-E gene deletion mutants completely lost siderophore and antibacterial activity. These results reveal that both siderophore biosynthetic gene clusters are essential for siderophore production and antibacterial activity in P. ananatis PA13. A ferric uptake regulator protein (Fur) mutant exhibited a significant increase in siderophore production, and a Fur-overexpressing strain completely lost antibacterial activity. Expression of the iucA, dfoJ, and foxA genes was significantly increased in the Δfur mutant background, and expression of these genes returned to wild-type levels after fur compensation. These results indicate that Fur negatively regulates aerobactin and DFO-E siderophores. However, siderophore production was not required for P. ananatis virulence in plants, but it appears to be involved in the microbial ecology surrounding the plant environment. This study is the first to report the regulation and functional characteristics of siderophore biosynthetic genes in P. ananatis. IMPORTANCE Pantoea ananatis is a bacterium that causes diseases in several economically important crops, as well as in insects and humans. This bacterium has been studied extensively as a potentially dangerous pathogen due to its saprophytic ability. Recently, the types, biosynthetic gene clusters, and origin of the siderophores in the Pantoea genus were determined by using genome comparative analyses. However, few genetic studies have investigated the characteristics and functions of siderophores in P. ananatis. The results of this study revealed that the production of aerobactin and desferrioxamine E in the rice pathogen P. ananatis PA13 is negatively regulated by Fur and that these siderophores are essential for antibacterial activity against Erwinia amylovora and Yersinia enterocolitica (Enterobacterales). However, siderophore production was not required for P. ananatis virulence in plants, but it appears to be involved in the microbial ecology surrounding the plant environment.

English

The sheath rot rice disease is known to be associated to Pseudomonas fuscovaginae and a recent study on the symptomatic of sheath rot revealed that this bacterial pathogen is abundant in highland rice ecology cultivation in Burundi. From asymptomatic samples of sheath rice, a collection of bacterial isolates and culturable microbiome have been carried out. A comparison between the culturable microbiome and total microbiome was made. Phenotypic assays in vitro on the bacterial isolates were performed after identification at the genus level of each bacterial isolate by sequencing of 16S RNA gene. A bacterial isolate belonging to Alcaligenes genus has antibacterial activity against the rice sheath rot pathogen P. fuscovaginae in vitro conditions.   Key words: Pseudomonas fuscovaginae, sheath rot, microbiome, Alcaligenes species.

Metabolomic and Transcriptomic Changes Induced by Potassium Deficiency During Sarocladium oryzae Infection Reveal Insights into Rice Sheath Rot Disease Resistance

Rice sheath rot disease caused by Sarocladium oryzae (S. oryzae) infection is an emerging disease, and infection can cause yield losses of 20–85%. Adequate potassium (K) application is a feasible strategy for rice tolerance to S. oryzae infection. However, little is known about the metabolic mechanisms regulated by K that allow rice to cope better with S. oryzae infection. The present study performed a comparative metabolome and transcriptome analysis of rice with different K nutrition statuses before and upon S. oryzae infection. Sarocladium oryzae infection triggered a hydrogen peroxide (H2O2) burst, and K starvation aggravated the accumulation of H2O2 in the flag leaf sheath (FLS), which resulted in lipid peroxidation. Likewise, K deficiency altered the lipid homeostasis of the host plants by hyperaccumulation of 1-alkyl-2-acylglycerophosphoethanolamine. K starvation decreased the content of glycoglycerolipids including monogalactosyldiacyglycerol and digalactosyldoacylglycerol during S. oryzae infection, which destroyed the stability of bilayer membranes. In contrast, sufficient K supply increased antioxidant-related transcript expression (for example, the genes related to glutathione-S-transferase biosynthesis were upregulated), which activated the antioxidant systems. Additionally, upon S. oryzae infection, K starvation amplified the negative impacts of S. oryzae infection on flag leaf photosynthetic potential. These results provide new insight into the role of K in alleviating S. oryzae infection. Adequate K supply decreased the negative impacts of sheath rot disease on rice growth by alleviating lipid peroxidation and maintaining lipid homeostasis.

History of Sheath Rot Disease in Indonesia and Disease Severity in Two Rice Production Centres of West Java

The observation conducted from 2000 to 2018 found that rice sheath rot has become an emerging disease in several regions. The disease was able to reduce quality and quantity of rice yield. This research objective was to study the history and status of rice sheath rot caused by Sarocladium oryzae. Data was obtained from literature study, farmer interview, and field survey. Data were used to calculate disease incidence followed by visual observation of the symptoms caused by this disease. Identification of sheath rot pathogen was done using microscopic and molecular techniques using specific primers. Rice sheath rot was first reported in Indonesia as a minor disease in 1987 and has only currently become an important disease. This fungus generally causes rice sheath rot in Karawang and Cianjur Regency. Disease incidence of rice sheath rot was 12.56% without considering the varieties at all generative growth stages. Average disease incidence on all rice varieties observed was 12.64%, except for IR 42 (0%). The level of rice plants damage due to rice sheath rot in Cianjur was higher than Karawang with average disease incidence of 11.58% and 9.27%, respectively. Rice sheath rot symptoms have often been found in the last 10 years with average level of damage of 3%‒18% and yield loss of 10%-15%. This disease has proven to be important and has become a challenge in rice cultivation. The fungus that infect rice plants in Karawang and Cianjur had different morphotypes, namely KP, KP2, KP3, PW3, and PW03. The amplification results showed that all fungal isolates were S. oryzae.

LAMP-based foldable microdevice platform for the rapid detection of Magnaporthe oryzae and Sarocladium oryzae in rice seed

Rice blast (caused by Magnaporthe oryzae) and sheath rot diseases (caused by Sarocladium oryzae) are the most predominant seed-borne pathogens of rice. The detection of both pathogens in rice seed is essential to avoid production losses. In the present study, a microdevice platform was designed, which works on the principles of loop-mediated isothermal amplification (LAMP) to detect M. oryzae and S. oryzae in rice seeds. Initially, a LAMP, polymerase chain reaction (PCR), quantitative PCR (qPCR), and helicase dependent amplification (HDA) assays were developed with primers, specifically targeting M. oryzae and S. oryzae genome. The LAMP assay was highly efficient and could detect the presence of M. oryzae and S. oryzae genome at a concentration down to 100 fg within 20 min at 60 °C. Further, the sensitivity of the LAMP, HDA, PCR, and qPCR assays were compared wherein; the LAMP assay was highly sensitive up to 100 fg of template DNA. Using the optimized LAMP assay conditions, a portable foldable microdevice platform was developed to detect M. oryzae and S. oryzae in rice seeds. The foldable microdevice assay was similar to that of conventional LAMP assay with respect to its sensitivity (up to 100 fg), rapidity (30 min), and specificity. This platform could serve as a prototype for developing on-field diagnostic kits to be used at the point of care centers for the rapid diagnosis of M. oryzae and S. oryzae in rice seeds. This is the first study to report a LAMP-based foldable microdevice platform to detect any plant pathogens.

Survival of the fittest: how the rice microbial community forces Sarocladium oryzae into pathogenicity.

The fungus Sarocladium oryzae (Sawada) causes rice sheath rot and produces the phytotoxins cerulenin and helvolic acid. Both toxins show antimicrobial activity but only helvolic acid production in the rice sheath correlates with virulence. Sarocladium oryzae isolates that differ in their toxin production were used to study their interaction with the rice culturable bacterial endophyte community. The diversity and community structure was defined in the edge of sheath rot lesions, followed by a null model-based co-occurrence analysis to discover pairwise interactions. Non-random pairs were co-cultured to study the nature of the interactions and the role of the toxins herein. Compared to healthy sheaths, endophyte diversity strongly increased when infected with the least virulent S. oryzae isolates producing low amounts of toxins. Virulent S. oryzae isolates did not affect diversity but caused strong shifts in species composition. The endophyte community of healthy rice plants was dominated by B. cereus. This bacterium was enriched in lesions produced by low-virulent S. oryzae isolates and caused hyphal lysis. Contrarily, helvolic acid producers eliminated this bacterium from the sheath endosphere. We conclude that S. oryzae needs to produce antibiotics to defend itself against antagonistic rice endophytes to successfully colonize and infect the rice sheath.

Auxin, Abscisic Acid and Jasmonate Are the Central Players in Rice Sheath Rot Caused by Sarocladium oryzae and Pseudomonas fuscovaginae

Sheath rot is an emerging rice disease that causes severe yield losses worldwide. The main causal agents are the toxin producers Sarocladium oryzae and Pseudomonas fuscovaginae. The fungus S. oryzae produces helvolic acid and cerulenin and the bacterium P. fuscovaginae produces cyclic lipopeptides. Helvolic acid and the lipopeptide, fuscopeptin, inhibit membrane-bound H+-ATPase pumps in the rice plant. To manage rice sheath rot, a better understanding of the host response and virulence strategies of the pathogens is required. This study investigated the interaction of the sheath rot pathogens with their host and the role of their toxins herein. Japonica rice was inoculated with high- and low-helvolic acid-producing S. oryzae isolates or with P. fuscovaginae wild type and fuscopeptin mutant strains. During infection, cerulenin, helvolic acid and the phytohormones abscisic acid, jasmonate, auxin and salicylic acid were quantified in the sheath. In addition, disease severity and grain yield parameters were assessed. Rice plants responded to high-toxin-producing S. oryzae and P. fuscovaginae strains with an increase in abscisic acid, jasmonate and auxin levels. We conclude that, for both pathogens, toxins play a core role during sheath rot infection. S. oryzae and P. fuscovaginae interact with their host in a similar way. This may explain why both sheath rot pathogens cause very similar symptoms despite their different nature.

Screening of Rice Germplasms for Their Resistance against Sheath Rot Disease (Sarocladium oryzae) at Fogera, Ethiopia

Sheath rot of rice, Sarocladium oryzae [(Sawada) W. Gams & D. Hawksw], is currently regarded as one of the most serious rice diseases in Fogera plains. Varietal resistance is the most cost-effective and eco-friendly management strategy for the small-scale farmers. An investigation was conducted to identify resistant sources among rice germplasm introductions that could be employed in varietal development program. Eighty germplasms along four checks were evaluated in field trials for two years at two locations arranged in an augmented design. Results indicated that three immune germplasms (SCRID014-1-1-1-1, SCRID037-4-2-2-5-2 and YUNLU N0.33) were found to be suitable for resistant variety development. The remaining, germplasms were found to exhibit different levels of reactions, of which 27 resistant, 35 moderately resistant, 13 moderately susceptible and two susceptible, with PSI ranging between 1.48–56.17%. The immune germplasms perform better than the standard check varieties in all agronomic and phenological traits considered. Based on these results, the high yielder immune germplasms could be used to develop resistant varieties so as to meet the farmers’ requirement, as far as rice production is concerned.

Input-based assessment on integrated pest management for transplanted rice (Oryza sativa) in India

Globally, India ranks second in terms of area planted under rice (Oryza sativa) and its production as well. Potential to yield is dented due to a lack of inbuilt resistance to different biotic stresses as discernible in ~1000 rice cultivars across the country. Farmers usually rely on applying pesticides that result in several environmental adversities apart from rejection of export consignments due to the presence of chemical residue in grains. Yield losses due to pests of rice in tropical Asia range 25–43%. There is a need to explore alternative integrated input-based management options for judicious use of chemicals with optimal combinations of non-chemical interventions to improve productivity and profitability of rice culture. Field trials were conducted in split-split plot design at Chinsurah, West Bengal during three consecutive rainy (kharif) seasons (2013-15) in transplanted rice. The exploratory objectives were to assess different interventions for alleviating crop biotic stresses and obtaining precise estimate of grain yield as well as economic advantages, and to devise a cost-effective recommendation on need-based integrated pest management (IPM) in transplanted rice. Green manuring with 45-day old Sesbania crop showed a significant (P < 0.05) reduction in infestation of leaf folder, stem borer, sheath rot, sheath blight, false smut, brown spot and bacterial leaf blight of rice compared to control. Both the herbicide (pretilachlor)-treated and green (Sesbania)-manured plots displayed a significant (P < 0.05) suppression of weeds. The diseases (sheath rot, sheath blight, brown spot) of rice were significantly (P < 0.05) reduced by all the treatments targeted for better crop management as evidenced from the sub-sub plots. Rice diseases were best managed by seed treatment with carbendazim 50% WP @ 1.0 g a.i./kg seed, and the effect was more pronounced when the crop was green manured. Significantly (P < 0.05) higher grain yield of rice was recorded with Sesbania manuring, which was as good (P < 0.05) as pre-emergence application of pretilachlor. The herbicide application provided the highest (2.03) incremental benefit-cost ratio (IBCR) among the main plot treatments. Seed treatment with carbendazim followed by (fb) seed bed application of Pseudomonas fluorescens in combination with green manuring prior to rice transplanting in main field fb sequential sprays of chlorantraniliprole 0.4% GR (20 DAT), chlorantraniliprole 18.5% SC (40 DAT) and validamycin 3% L (50 DAT) on the standing crop provided the highest (5656 kg/ha) grain yield with a lower (2.02) IBCR. Contrastingly, only seed treatment with carbendazim recorded the highest (73.85) IBCR. Lower pest incidence and higher grain yields did not fetch greater economic return as apparent from the current investigation. Considering quantifiable and economic impact of inputs, their need-based usage would be a cost-effective proposition to take care of dominant pests in transplanted rice. No comprehensive investigation made such a target-based IPM of most influential crop pests of rice for realizing higher productivity and profitability.