Sheath Brown Rot Research Articles

A review of bacterial diseases of rice and its management in Malaysia

Rice (Oryza sativa L.) is one of the staple foods in the world including Malaysia. Rice production has been affected due to disease infections that is usually destructive and cause many losses to rice productivity. The common bacterial diseases listed in Malaysia include bacterial leaf blight (BLB) (Xanthomonas oryzae pv. oryzae), bacterial leaf streak (BLS) (Xanthomonas oryzae pv. oryzicola), sheath brown rot (SBR) (Pseudomonas fuscovaginae) and bacterial panicle blight (BPB) (Burkholderia glumae). Currently, there is less information on the bacterial disease occurrence of rice in Malaysia. Hence, this study aimed to discuss the current report on the severity and the economic losses of rice production due to BLB, BLS, SBR and BPB in Malaysia and the possible management strategies to control the disease that consequently reduce the losses. In general, management strategies for bacterial diseases are challenging due to the lack of suitable chemical control that is not harmful to the environment and human health. Furthermore, other management strategies can be used to control these diseases such as cultural control and biological control. There is a need for the control method to be upgraded to reduce the occurrence of these diseases. All the information provided in this study may contribute as a useful tool for identification of the bacterial disease in paddy fields and as a source of effective strategies to control the disease before it becomes worse.

Versatile role of Pseudomonas fuscovaginae cyclic lipopeptides in plant and microbial interactions.

Pseudomonas fuscovaginae is the most prominent bacterial sheath rot pathogen, causing sheath brown rot disease in rice. This disease occurs worldwide and it is characterized by typical necrotic lesions on the sheath, as well as a reduction in the number of emitted panicles and filled grains. P. fuscovaginae has been shown to produce syringotoxin and fuscopeptin cyclic lipopeptides (CLPs), which have been linked to pathogenicity. In this study, we investigated the role of P. fuscovaginae UPB0736 CLPs in plant pathogenicity, antifungal activity and swarming motility. To do so, we sequenced the strain to obtain a single-contig genome and we constructed deletion mutants in the biosynthetic gene clusters responsible for the synthesis of CLPs. We show that UPB0736 produces a third CLP of 13 amino acids, now named asplenin, and we link this CLP with the swarming activity of the strain. We could then show that syringotoxin is particularly active against Rhizoctonia solani in vitro. By testing the mutants in planta we investigated the role of both fuscopeptin and syringotoxin in causing sheath rot lesions. We proved that the presence of these two CLPs considerably affected the number of emitted panicles, although their number was still significantly affected in the mutants deficient in both fuscopeptin and syringotoxin. These results reveal the importance of CLPs in P. fuscovaginae pathogenicity, but also suggest that other pathogenicity factors may be involved.

Commensal Pseudomonas fluorescens Strains Protect Arabidopsis from Closely Related Pseudomonas Pathogens in a Colonization-Dependent Manner.

ABSTRACTPlants form commensal associations with soil microorganisms, creating a root microbiome that provides benefits, including protection against pathogens. While bacteria can inhibit pathogens through the production of antimicrobial compounds in vitro, it is largely unknown how microbiota contribute to pathogen protection in planta. We developed a gnotobiotic model consisting of Arabidopsis thaliana and the opportunistic pathogen Pseudomonas sp. N2C3, to identify mechanisms that determine the outcome of plant-pathogen-microbiome interactions in the rhizosphere. We screened 25 phylogenetically diverse Pseudomonas strains for their ability to protect against N2C3 and found that commensal strains closely related to N2C3, including Pseudomonas sp. WCS365, were more likely to protect against pathogenesis. We used comparative genomics to identify genes unique to the protective strains and found no genes that correlate with protection, suggesting that variable regulation of components of the core Pseudomonas genome may contribute to pathogen protection. We found that commensal colonization level was highly predictive of protection, so we tested deletions in genes required for Arabidopsis rhizosphere colonization. We identified a response regulator colR, and two ColR-dependent genes with predicted roles in membrane modifications (warB and pap2_2), that are required for Pseudomonas-mediated protection from N2C3. We found that WCS365 also protects against the agricultural pathogen Pseudomonas fuscovaginae SE-1, the causal agent of bacterial sheath brown rot of rice, in a ColR-dependent manner. This work establishes a gnotobiotic model to uncover mechanisms by which members of the microbiome can protect hosts from pathogens and informs our understanding of the use of beneficial strains for microbiome engineering in dysbiotic soil systems.

Syringopeptin Contributes to the Virulence of Pseudomonas fuscovaginae, Based on sypA Biosynthesis Mutant Analysis.

Pseudomonas fuscovaginae, first reported from Japan in 1976, is now present in many agroecological regions around the world; it causes sheath brown rot of rice and is reported as a pathogen of a broad range of hosts. The pathogen can infect rice plants at all stages of growth and is known to cause significant losses due to grain discoloration, poor spike emergence and panicle sterility. Limited information is available on the virulence and mechanisms of pathogenicity for P. fuscovaginae. To address this, an analysis of genomes was conducted, which identified the presence of a gene showing homology to one of the genes contributing to syringopeptin synthetase (sypA) of P. syringae pv. syringae. To study the potential role of this gene in the virulence and pathogenicity of P. fuscovaginae, a site-specific mutation was created. Following inoculation of seeds and plantlets of rice and wheat with P. fuscovaginae wild types and their respective mutants, we demonstrated that the mutation significantly reduced virulence. This was evident on rice and wheat inoculated with mutants causing a significantly higher number of roots, length of roots and seedling height compared with their respective wild types. Characteristic disease symptoms of necrotic lesions were significantly less in rice seedlings infected with bacterial suspensions of mutants indicating a reduction in virulence. Chromatography analysis of bacterial exudates showed suppression of synthesis of metabolites analogous to syringopeptin in the mutants. These data demonstrate that the protein encoded by this sypA homolog gene is a major virulence determinant of P. fuscovaginae.

Development of plant-based emulsion formulations to control bacterial leaf blight and sheath brown rot of rice

Bacterial leaf blight (BLB) and sheath brown rot (SBR), caused by Xanthomonas oryzae pv. oryzae (Xoo) and Pseudomonas fuscovaginae, respectively, are bacterial diseases that lead to substantial yield losses in rice. Natural plant-based products represent a sustainable alternative to combat bacterial diseases due to their biodegradability and overall safety. However efficient ways of delivering them are crucial to their success. In an attempt to maximize the antibacterial properties of botanical bactericides for the control of these pathogens, this study evaluated the efficiency of different emulsion formulations of Piper sarmentosum extracts. The emulsion formulations were demonstrated to be effective in controlling BLB and SBR of rice in in vitro plate assays and in planta under glasshouse conditions. The observed in vitro inhibition of the bacterial pathogens and significant disease suppression in planta indicate that these plant extract formulations represent promising alternatives to be adopted in management strategies for controlling rice diseases.

Effect of antimicrobial activity from fermented mature coconut water to sheath brown rot of rice disease

Effect of antimicrobial activity from fermented mature coconut water to sheath brown rot of rice disease

Effect of antimicrobial activity from fermented mature coconut water to sheath brown rot of rice disease

Rotting of grains or sheaths caused by Pseudomonas fuscovaginae is common for mature plants and grains of seedlings. This study explored the effect of antimicrobial activity from fermented mature coconut water to understand better a certain kind of rotting in sheaths of rice plants screened against the pathogen. Fermented matured coconut water was extracted with methanol solvent demonstrated the highest activity with 20.02 mm of inhibition followed by water solvent with 10.10 mm of inhibition. Both negative controls for methanol and water-based extracts showed no inhibition activities towards the pathogen. Methanol extraction was then determined for minimal inhibitory concentration (MIC) and minimal bactericidal concentration (MBC). The finding indicated that 20% (v/v) concentration was recorded as MIC and 30% (v/v) concentration as MBC for this pathogen to reduce the disease lesion length significantly (P < 0.05). The findings from this study will be useful for agriculture related agencies in controlling the disease for a higher productivity of rice production.

Survey and Identification of Rice Diseases in South Gondar Zone, Amhara Region, Ethiopia

Disease surveys were conducted in rice grown districts of Libokemkem, Dera and Fogera in south Gondar zone in 2016 and 2017 cropping seasons. The study was designed to identify and record rice disease flora, their distribution in the districts, prioritize according to the importance and document for future use. Forty-six and 48 rice fields were assessed from nine Peasant Association (PA) in 2016 and 2017 cropping seasons, respectively. Rice diseases; Leaf blast, Panicle Blast, Brown spot, Sheath rot, Sheath brown rot, Sheath Blight, Bacterial blight, Rice Yellow Motile Virus, Kernel smut, Downy mildew were identified in 2016 cropping season and nine rice diseases: Leaf blast, Panicle Blast, Neck Blast, Node blast, Brown spot, Sheath rot, Sheath brown rot, Rice Yellow Motile Virus, Kernel smut were identified in 2017. The overall mean prevalence of sheath rot and sheath brown rot diseases were above 60%, while the others had prevalence below 21%. The incidences and severities of these two diseases were higher than the other diseases implying that both diseases were important. In the present studies many rice diseases were recorded in lowland ecosystem as compared to upland ecosystem. From the assessment X-jigna cultivar was more susceptible to rice disease and followed by Gumera. The results indicate that a sheath rot, and sheath brown rot, were important across the districts and years. Loss assessment studies should be initiated in order to know the yield damage caused by the diseases.

Quorum sensing and RsaM regulons of the rice pathogen Pseudomonas fuscovaginae.

Pseudomonas fuscovaginae (Pfv) is an emerging plant pathogen causing sheath brown rot in rice, as well as diseases in other gramineae food crops including maize, sorghum and wheat. Pfv possesses two conserved N-acyl homoserine lactone (AHL) quorum sensing (QS) systems called PfvI/R and PfsI/R, which are repressed by RsaL and RsaM, respectively. The two systems are not hierarchically organized and are involved in plant virulence. In this study the AHL QS PfsI/R, PfvI/R and RsaM regulons were determined by transcriptomic analysis. The PfsI/R system regulates 98 genes, whereas 26 genes are regulated by the PfvI/R AHL QS system; only two genes are regulated by both systems. RsaM, on the other hand, regulates over 400 genes: 206 are negatively regulated and 260 are positively regulated. More than half of the genes controlled by the PfsI/R system and 65 % by the PfvI/R system are also part of the RsaM regulon; this is due to RsaM being involved in the regulation of both systems. It is concluded that the two QS systems regulate a unique set of genes and that RsaM is a global regulator mediating the expression of different genes through the two QS systems as well as genes independently of QS.

Rice-Infecting Pseudomonas Genomes Are Highly Accessorized and Harbor Multiple Putative Virulence Mechanisms to Cause Sheath Brown Rot.

Sheath rot complex and seed discoloration in rice involve a number of pathogenic bacteria that cannot be associated with distinctive symptoms. These pathogens can easily travel on asymptomatic seeds and therefore represent a threat to rice cropping systems. Among the rice-infecting Pseudomonas, P. fuscovaginae has been associated with sheath brown rot disease in several rice growing areas around the world. The appearance of a similar Pseudomonas population, which here we named P. fuscovaginae-like, represents a perfect opportunity to understand common genomic features that can explain the infection mechanism in rice. We showed that the novel population is indeed closely related to P. fuscovaginae. A comparative genomics approach on eight rice-infecting Pseudomonas revealed heterogeneous genomes and a high number of strain-specific genes. The genomes of P. fuscovaginae-like harbor four secretion systems (Type I, II, III, and VI) and other important pathogenicity machinery that could probably facilitate rice colonization. We identified 123 core secreted proteins, most of which have strong signatures of positive selection suggesting functional adaptation. Transcript accumulation of putative pathogenicity-related genes during rice colonization revealed a concerted virulence mechanism. The study suggests that rice-infecting Pseudomonas causing sheath brown rot are intrinsically diverse and maintain a variable set of metabolic capabilities as a potential strategy to occupy a range of environments.

First Report of Sheath Brown Rot of Rice Caused by Pseudomonas fuscovaginae in Korea

First Report of Sheath Brown Rot of Rice Caused by <i>Pseudomonas fuscovaginae</i> in Korea

Phenotypic Characterization and Molecular Identification of Malaysian Pseudomonas fuscovaginae Isolated from Rice Plants

Sheath Brown Rot (SBR) is one of the most important diseases that affect rice plant. The disease cause rots to the sheaths, panicles and leaves of rice plant. The disease also contaminating rice seeds through grain’s discoloration thus leads in reduction of rice production. In this study, 50 bacteria isolates that fluoresced under UV illumination on King’s B Selective (KBS) medium were obtained. Out of 50 isolates, 25 isolates were positive for both Hypersensitivity Reaction (HR) and pathogenicity tests. They also showed positive results for several biochemical reactions such as oxidase, arginine dihydrolase and trehalose utilization tests. Based on the preliminary tests, all isolates have been identified as Pseudomonas fuscovaginae (P. fuscovaginae). The 16S rDNA sequence analysis showed that all the isolates had 97-99% sequence similarities to Pseudomonas fuscovaginae in the GenBank database. This result was also supported by the constructed phylogenetic tree with the Acidivorax avenae outgroup. It was noted that all 25 isolates originated from the same node with the P. fuscovaginae group. The findings on characteristics of P. fuscovaginae in Peninsular Malaysia hopefully can be used in future studies especially on Malaysian P. fuscovaginae biology and their control.

Chemical composition of Piper sarmentosum extracts and antibacterial activity against the plant pathogenic bacteria Pseudomonas fuscovaginae and Xanthomonas oryzae pv. oryzae

Piper sarmentosum is a cultivated plant that also grows wildly in the South East Asian region. It is well known for its medicinal properties and a variety of active chemical constituents. The control potential of the plant extract against bacterial leaf blight caused by Xanthomonas oryzae and sheath brown rot of rice caused by Pseudomonas fuscovaginae was evaluated. The aqueous methanol extracts of fruits and leaves of P. sarmentosum were chemically analyzed using gas-chromatography mass-spectrometry (GC-MS). The results gave the highest best matches of 28 compounds (80.2% of total extracts) in the leaf extract and 24 compounds (89.1% of total extracts) in the fruit extract. The flavonoid fraction 4H-pyran-4-one,2,3-dihydro-3,5-dihydroxy-6-methyl- (DDMP) was found to be the major component which constitutes a complex natural product that has been of recent medicinal interest. The extract of the fruit had IC50 of 28.08 and 8.41 mg ml−1 against P. fuscovaginae and X. oryzae, respectively, while the leaf extract had IC50 of 10.42 and 24.69 mg ml−1 against P. fuscovaginae and X. oryzae, respectively.

Identification of virulence associated loci in the emerging broad host range plant pathogen Pseudomonas fuscovaginae.

BackgroundPseudomonas fuscovaginae (Pfv) is an emerging plant pathogen of rice and also of other gramineae plants. It causes sheath brown rot disease in rice with symptoms that are characterized by brown lesions on the flag leaf sheath, grain discoloration and sterility. It was first isolated as a high altitude pathogen in Japan and has since been reported in several countries throughout the world. Pfv is a broad host range pathogen and very little is known about its virulence mechanisms.ResultsAn in planta screen of 1000 random independent Tn5 genomic mutants resulted in the isolation of nine mutants which showed altered virulence. Some of these isolates are mutated for functions which are known to be virulence associated factors in other phytopathogenic bacteria (eg. pil gene, phytotoxins and T6SS) and others might represent novel virulence loci.ConclusionsBeing an emerging pathogen worldwide, the broad host range pathogen Pfv has not yet been studied for its virulence functions. The roles of the nine loci identified in the in planta screen are discussed in relation to pathogenicity of Pfv. In summary, this article reports a first study on the virulence of this pathogen involving in planta screening studies and suggests the presence of several virulence features with known and novel functions in the Pseudomonas group of bacteria.Electronic supplementary materialThe online version of this article (doi:10.1186/s12866-014-0274-7) contains supplementary material, which is available to authorized users.

Development of a Genomics-Based LAMP (Loop-Mediated Isothermal Amplification) Assay for Detection ofPseudomonas fuscovaginaefrom Rice

The vast amount of data available through next-generation sequencing technology is facilitating the design of diagnostic marker systems. This study reports the use of draft genome sequences from the bacterial plant pathogen Pseudomonas fuscovaginae, the cause of sheath brown rot of rice, to describe the genetic diversity within a worldwide collection of strains representing the species. Based on a comparative analysis with the draft sequences, primers for a loop-mediated isothermal amplification (LAMP) assay were developed to identify P. fuscovaginae. The assay reported here reliably differentiated strains of P. fuscovaginae isolated from rice from a range of other bacteria that are commonly isolated from rice and other plants using a primer combination designated Pf8. The LAMP assay identified P. fuscovaginae purified DNA, live or heat-killed cells from pure cultures, and detected the bacterium in extracts or exudates from infected host plant material. The P. fuscovaginae LAMP assay is a suitable diagnostic tool for the glasshouse and laboratory and could be further developed for in-field surveys.

Genome Sequence of the Rice Pathogen Pseudomonas fuscovaginae CB98818

Pseudomonas fuscovaginae is a phytopathogenic bacterium causing bacterial sheath brown rot of cereal crops. Here, we present the draft genome sequence of P. fuscovaginae CB98818, originally isolated from a diseased rice plant in China. The draft genome will aid in epidemiological studies, comparative genomics, and quarantine of this broad-host-range pathogen.

Bacterial pathogens of rice in the Kingdom of Cambodia and description of a new pathogen causing a serious sheath rot disease

A study of rice diseases in Cambodia from 2005 to 2007 showed widespread occurrence of diseases caused by Acidovorax avenae subsp. avenae, Burkholderia gladioli, B. cepacia and Pantoea ananatis. This is the first report of these pathogens in Cambodia. Additionally, a pseudomonad causing a widespread disease similar to sheath brown rot (caused by Pseudomonas fuscovaginae) was isolated. The studied strains were pathogenic to rice cvs Sen Pidau and IR 66, producing similar, though slightly less severe, symptoms to those observed in the field. Based on comparative 16S rDNA gene sequence analysis, combined with cell wall fatty acid analysis and metabolic profiles, the isolated strains were allocated to the genus Pseudomonas. The novel species were differentiated from Pseudomonas fuscovaginae and P. putida by their inability to metabolize d‐fructose, d‐galactose, d‐galactonic acid lactone, d‐galacturonic acid, d‐glucosaminic acid, d‐glucuronic acid, p‐hydroxy phenylacetic acid, d‐saccharic acid and urocanic acid. The major fatty acids were C16:0, summed feature 3 (C16:1ω7c and C16:1ω6c) and summed feature 8 (C18:1ω7c), representing 80% of the total. Partial 16S rRNA gene sequences (1460 bp) were identical, except for two nucleotide changes amongst the six strains. Alignment of the causal strains within type‐culture databases revealed similarities of 99·7% with Pseudomonas parafulva AJ 2129T, 99·2% with P. fulva IAM 1592T, 98·9% with P. plecoglossicidia FPC 951T, and 98·1% with P. fuscovaginae MAFF 301177T. On the basis of data from this polyphasic study, it is proposed that the unknown strains isolated from rice represent a novel species of the genus Pseudomonas.

Sheath Brown Rot Disease of Rice Caused by Pseudomonas Fuscovaginae in the Peninsular Malaysia

Relative to the established and well known rice diseases, sheath brown rot caused by Pseudomonas fuscovaginae can be considered new but getting widespread and serious all over the world. Our research was aimed to monitor and quantify the incidence and importance of the disease in Malaysia. A series of field monitoring and sampling were conducted to quantify the incidence and severity of the disease. Laboratory analysis of the collected diseased plant was done to identify the causal organism. Disease resistance screening of selected rice cultivars were also conducted to overcome the problem. The disease was found to become more important,prevalent and widely spread throughout rice growing areas in Peninsular Malaysia. Infected plants in the field became yellowish,lower leaf sheaths turned light or dark brown, while grains produced by an infected plant were discoloured, malformed and empty. The highest disease incidence was recorded in the state of Pahang (62%) and Selangor (62%), while the most severe infection was recorded in Pahang (55%) and Terengganu (61%). The evaluations of varietal resistance evaluation showed that the pathogen naturally infected all tested rice varieties at different levels of infection. Several rice varieties i.e. MR240, MR243, MR244, MR245, MR246, MR248 and MR249, classified as moderately resistant to the disease, could be recommended for planting in the next planting season.

Polyphasic identification ofPseudomonas fuscovaginaecausing sheath and glume lesions on rice in Australia

Pathogenic fluorescent pseudomonads associated with sheath brown rot disease symptoms on near-mature rice were characterised by a polyphasic study. Twelve strains of Pseudomonas fuscovaginae from the International Collection of Microorganisms from Plants (ICMP), which represent those strains lodged in several world culture collections, were used for comparison. Two strains, ICMP 9997 and 9999, were considered to have no similarity at all to P. fuscovaginae and a further two strains, ICMP11283 and 11284, were considered, by fatty acid analysis, to be more closely related to P. putida. These two strains were related to P. marginalis according to Biolog, and to P. tolaasii according to 16s and rpoB data. The Australian rice isolates were all identified as P. putida Biotype A by fatty acid analysis or as P. asplenii (4 isolates), P. fuscovaginae (2 isolates) or P. fluorescens (1 isolate) by Biolog. Sequencing of the 16s rRNA gene placed the rice isolates with P. fuscovaginae and P. asplenii, whereas rpoB gene sequence analysis showed a higher similarity to P. fuscovaginae than to P. asplenii. This is the first report of P. fuscovaginae in Australia.

First report of sheath brown rot of rice in China and characterization of the causal organism by phenotypic tests and Biolog

A bacterial disease of rice was observed in autumn of 1998-99 in the fields of Jiaxing and Yuhang, Zhejiang Province, China. Oblong to irregular dark green and water-soaked lesions occurred on the sheath, which later became gray-brown or brown surrounded by an effuse dark brown margin. With severe infection, the entire leaf sheath became necrotic and dried out. The panicles withered. Glumes of panicle emerging from the infected sheath exhibited water-soaked lesions that turned light brown. Grains of infected panicles were discolored, deformed, or empty. No bacterial ooze was produced from any part of the infected plant. The disease was first discovered in Japan in the 1950s. Since then, it has been reported in Southeast Asia, South America, and Africa, but not previously in China (Tanii et al 1976, Xie 1996). However, an epiphytic bacterium isolated from a weed was identified as Pseudomonas fuscovaginae in central China in 1986 but not from rice (Duan and Fang 1986). We therefore determined the causal organism and compared it with P. fuscovaginae , the causal organism of sheath brown rot of rice, and other related bacteria.