Novel insights into rice innate immunity against bacterial and fungal pathogens

Host Metabolic Alterations Mediate Phyllosphere Microbes Defense upon Xanthomonas oryzae pv oryzae Infection

Rice bacterial leaf blight, caused by Xanthomonas oryzae pv oryzae (Xoo), is a significant threat to global food security. Although the microbiome plays an important role in protecting plant health, how the phyllosphere microbiome is recruited and the underlying disease resistance mechanism remain unclear. This study investigates how rice phyllosphere microbiomes respond to pathogen invasion through a comprehensive multiomics approach, exploring the mechanisms of microbial defense and host resistance. We discovered that Xoo infection significantly reshapes the physicosphere microbial community. The bacterial network became more complex, with increased connectivity and interactions following infection. Metabolite profiling revealed that l-ornithine was a key compound to recruiting three keystone microbes, Brevundimonas (YB12), Pantoea (YN26), and Stenotrophomonas (YN10). These microbes reduced the disease index by up to 67.6%, and these microbes demonstrated distinct defense mechanisms. Brevundimonas directly antagonized Xoo by disrupting cell membrane structures, while Pantoea and Stenotrophomonas enhanced plant immune responses by significantly increasing salicylic acid and jasmonic acid levels and activating defense-related enzymes. Our findings provide novel insights into plant-microbe interactions, demonstrating how host metabolic changes recruit and activate beneficial phyllosphere microbes to combat pathogenic invasion. This research offers promising strategies for sustainable agricultural practices and disease management.

Engineering rice genomes towards green super rice

Rice, cultivated for millennia across diverse geographical regions, has witnessed tremendous advancements in recent decades, epitomized by the emergence of Green Super Rice. These efforts aim to address challenges such as climate change, pest and disease threats, and sustainable agriculture. Driven by the advent of multiomics big data, breakthroughs in genomic tools and resources, hybrid rice breeding techniques, and the extensive utilization of green genes, rice genomes are undergoing delicate modifications to produce varieties with high yield, superior quality, enhanced nutrient efficiency, and resilience to pests and environmental stresses, leading to the development of green agriculture in China. Additionally, the utilization of wild relatives and the promotion of genomic breeding approaches have further enriched our understanding of rice improvement. In the future, international efforts to develop next-generation green rice varieties remain both challenging and imperative for the whole community.

Evolutionary and Epidemiological Insights from Historical and Modern Genomes of Xanthomonas oryzae pv. oryzicola, the Causal Agent of Bacterial Leaf Streak of Rice

Xanthomonas oryzae pv. oryzicola (Xoc) causes bacterial leaf streak (BLS) of rice. This disease represents a major constraint for rice production, which is a crop feeding more than half of the world's population. Xoc was first described in 1918 in the Philippines and is prevalent in southeast Asia. Today, BLS is also omnipresent in both East- and West-Africa, where the disease was first reported in the early 1980s. The appearance of Xoc in Africa decades after its first report in Asia suggests that the disease could have been introduced from Asia to Africa. Strict conservation of five transcription activator-like (TAL) effectors in whole-genome sequences of 10 strains of Xoc including three from West-Africa and seven from Asia also support this hypothesis. East-Africa, especially Madagascar, where the disease was first described in 1985 is located at the interface between Asia and Africa, hence representing an interesting region to explore the link between strains from Asia and West-Africa. In this study, we did the following: (i) reconstructed the genome of a historical Xoc strain from a herbarium specimen of rice showing symptoms of BLS that was sampled in Madagascar in 1931, 50 years before the first description of the disease, and (ii) sequenced nine new modern strains, including five from Madagascar and East-Africa. The analysis of those new genomes along with previously published ones shed light within the evolutionary and epidemiological history of Xoc. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

The pathogenicity-associated regulators participating in the regulatory cascade for RaxSTAB and RaxX in Xanthomonas oryzae pv. oryzae

The RaxX sulfopeptide, secreted via a type Ι secretion system, is crucial for activating XA21-mediated innate immunity in resistant rice lines bearing the XA21 receptor kinase. Certain pathogenicity-associated regulators that control the expression of the raxSTAB-raxX gene cluster have been functionally characterized, but the comprehensive regulatory cascade of RaxSTAB and RaxX in Xanthomonas oryzae pv. oryzae (Xoo) remains incompletely understood. Our investigation revealed that pathogenicity-associated regulators, including HrpG, HrpX, VemR, PhoR, and Clp, form a regulatory cascade governing the expression of the raxSTAB-raxX gene cluster. HrpG regulates the raxSTAB-raxX gene cluster transcription through the key regulator HrpX. VemR also participates in the transcription of the raxSTAB-raxX. The histidine kinase PhoR positively modulates raxSTAB-raxX expression, while the global regulator Clp directly binds the raxX promoter region to promote its transcription. These findings shed light on the intricate regulatory cascade of rax-related genes in Xoo, emphasizing the complex roles of pathogenicity-associated regulators within the pathogenic regulatory system.

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

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

Carbohydrate-active enzymes involved in rice cell wall metabolism

Plant cell walls are complex, multifunctional structures, built up of polysaccharides and proteins. The configuration and abundance of cell wall constituents determine cellular elongation and plant growth. The emphasis of this review is on rice, a staple crop with economic importance, serving as model for grasses/cereals. Recent advancements have contributed to a better understanding of the grass/cereal cell wall. This review brings together current knowledge of the organization and metabolism of the rice cell wall, and addresses gaps in the information regarding the cell wall and enzymes involved. Several cell wall fractions, including cellulose, mixed-linkage glucans, and glucuronoarabinoxylans, are well understood in rice and other grasses/grains. Conversely, there are still open questions and missing links in relation to xyloglucans, glucomannans, pectin, lignin, and arabinogalactan proteins. There is still a large and untapped potential to identify carbohydrate-active enzymes (CAZymes), to characterize their activity, and to elucidate their involvement in the metabolism of the mentioned cell wall fractions. This review highlights the involvement of carbohydrate-active enzymes in rice cell wall metabolism, providing an update of current understanding with the aim of demarcating research areas with potential for further investigations.

Phosphatidylcholine Transfer Protein OsPCTP Interacts with Ascorbate Peroxidase OsAPX8 to Regulate Bacterial Blight Resistance in Rice

Rice phosphatidylcholine transfer protein (PCTP), which contains a steroidogenic acute regulatory protein-related lipid transfer (START) domain, responds to bacterial blight disease. Overexpression of OsPCTP quantitatively enhances resistance to pathogen in rice, whereas depletion of it has the opposite effect. Further analysis showed that OsPCTP physically interacts with OsAPX8, a ROS scavenging enzyme, and influences ascorbate peroxidase enzymatic activity in vivo. In addition, the expression of pathogenesis-related genes PR1a, PR1b and PR10 were significantly induced in OsPCTP-OE plants compared with that in wild-type plants ZH11. Taken together, these results suggested that OsPCTP mediates bacterial blight resistance in rice through regulating the ROS defense pathway.

A protein elicitor PeVn1 from Verticillium nonalfalfae HW recognized as a MAMP triggers plant immunity response

Protein elicitors can induce plant systemic resistance to pathogens. The recognition of a potential elicitor activates intracellular signaling events, leading to plant resistance against pathogens. In this study, a novel protein elicitor was isolated from the culture filtrate of Verticillium nonalfalfae and named PeVn1, which can induce cell death in several plant species. The PeVn1 gene was then cloned and expressed in Escherichia coli. The recombinant protein PeVn1 triggers cell death in Nicotiana benthamiana in NbBAK1 and NbSOBIR1 dependent manner. Through bioassay analysis showed that the recombinant PeVn1 induced early defense induction events, such as reactive oxygen species burst, callose deposition and the activation of defense hormone signaling pathways and defense enzyme activities. Moreover, PeVn1 significantly enhanced resistance of Nicotiana benthamiana to Sclerotinia sclerotiorum, Botrytis cinerea and N. benthamiana mosaic virus and tomato to Pseudomonas syringae pv. Tomato DC3000. In conclusion, our study reveals that PeVn1 protein as a microbe-associated molecular pattern can induce plant immune responses, which provides a theoretical basis for the development of novel protein-induced disease resistance agents.

Design, synthesis, X-ray crystal structure, and antimicrobial evaluation of novel quinazolinone derivatives containing the 1,2,4-triazole Schiff base moiety and an isopropanol linker

A series of novel quinazolinone derivatives (E1-E31) containing the 1,2,4-triazole Schiff base moiety and an isopropanol linker were designed, synthesized and assessed as antimicrobial agents in agriculture. All the target compounds were fully characterized by 1 H NMR, 13 C NMR, and high-resolution mass spectrometry (HRMS). Among them, the structure of compound E12 was further confirmed via single crystal X-ray diffraction method. The experimental results indicated that many compounds displayed good in vitro antibacterial efficacies against the tested phytopathogenic bacteria including Xanthomonas oryzae pv. oryzae (Xoo), Xanthomonas axonopodis pv. citri (Xac), and Ralstonia solanacearum (Rs). For example, compounds E3, E4, E10, E13, and E22 had EC50 (half-maximal effective concentration) values of 55.4, 39.5, 49.5, 53.5, and 57.4 µg/mL against Xoo, respectively, superior to the commercialized bactericide Bismerthiazol (94.5 µg/mL). In addition, the antibacterial efficacies of compounds E10 and E13 against Xac were about two times more effective than control Bismerthiazol, in terms of their EC50 values. Last, the antifungal assays showed that compounds E22 and E30 had the inhibition rates of 52.7% and 54.6% at 50 µg/mL against Gibberella zeae, respectively, higher than the commercialized fungicide Hymexazol (48.4%).

Identification of significant SNPs and candidate loci for blast disease resistance via GWAS and population structure analysis in ARC panel of Oryza sativa

Pyricularia (syn. Magnaporthe) oryzae is responsible for the blast disease in rice resulting in a greater extent of yield loss. However, some of the cultivars of rice have the ability to survive this devastating infection due to the presence of R (resistance) genes. Therefore, genome wide association study (GWAS) was undertaken using a panel of 400 rice landraces (ARC panel) and a set of filtered 38,723 single nucleotide polymorphisms (SNPs). The highest SNPs were mapped to chromosome 1 with a number of 4332 SNPs and lowest (2252) in chromosome 12. The ARC panel was evaluated phenotypically which revealed that 6% of the selected cultivars has resistance to rice blast disease with SES score of 1. The majority of the resistant cultivars belong to the group Asra of the panel. The population structure analysis was executed wherein three genetic subpopulations were identified namely RC1, RC2, RC3 and an admixture population constituting 48 accessions. Further, GWAS detected 15 significant association signal with P value in the range of 1.03E-05 to 1.03E-04, effect ranged from - 1.18 to 1.06, phenotypic variance explained was from 0 to 7.14%, R2 of 0.047 to 0.058, and minor allele frequency of 0.107 to 0.444. Eleven (Os01g39980, Os01g56130, Os01g67100, Os01g67110, Os03g41030, Os04g33310, Os07g42104, Os09g06464, Os09g08920, Os09g38800, Os12g37680) out of these 15 significant associations were identified as the candidate loci for the blast resistance in rice that will serve as an important genetic resistance source to be introgressed into an elite rice line in future breeding programs for deciphering blast resistance in rice. The GWAS study presented in this article helped to uncover significant gene regions which encode proteins to resist blast infection in rice plant. This is the first report on the GWAS analysis for blast resistance in unique landraces of rice from Northeast India employing single nucleotide polymorphism.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-024-01518-6.

Alfin-like (AL) transcription factor family in Oryza sativa L.: Genome-wide analysis and expression profiling under different stresses

Oryza sativa L. is the world's most essential and economically important food crop. Climate change and ecological imbalances make rice plants vulnerable to abiotic and biotic stresses, threatening global food security. The Alfin-like (AL) transcription factor family plays a crucial role in plant development and stress responses. This study comprehensively analyzed this gene family and their expression profiles in rice, revealing nine AL genes, classifying them into three distinct groups based on phylogenetic analysis and identifying four segmental duplication events. RNA-seq data analysis revealed high expression levels of OsALs in different tissues, growth stages, and their responsiveness to stresses. RT-qPCR data showed significant expression of OsALs in different abiotic stresses. Identification of potential cis-regulatory elements in promoter regions has also unveiled their involvement. Tertiary structures of the proteins were predicted. These findings would lay the groundwork for future research to reveal their molecular mechanism in stress tolerance and plant development.

Engineering disease-resistant plants with alternative translation efficiency by switching uORF types through CRISPR

Engineering disease-resistant plants can be a powerful solution to the issue of food security. However, it requires addressing two fundamental questions: what genes to express and how to control their expressions. To find a solution, we screen CRISPR-edited upstream open reading frame (uORF) variants in rice, aiming to optimize translational control of disease-related genes. By switching uORF types of the 5'-leader from Arabidopsis TBF1, we modulate the ribosome accessibility to the downstream firefly luciferase. We assume that by switching uORF types using CRISPR, we could generate uORF variants with alternative translation efficiency (CRISPR-aTrE-uORF). These variants, capable of boosting translation for resistance-associated genes and dampening it for susceptible ones, can help pinpoint previously unidentified genes with optimal expression levels. To test the assumption, we screened edited uORF variants and found that enhanced translational suppression of the plastic glutamine synthetase 2 can provide broad-spectrum disease resistance in rice with minimal fitness costs. This strategy, which involves modifying uORFs from none to some, or from some to none or different ones, demonstrates how translational agriculture can speed up the development of disease-resistant crops. This is vital for tackling the food security challenges we face due to growing populations and changing climates.

Resistance to Planthoppers and Southern Rice Black-Streaked Dwarf Virus in Rice Germplasms

The damage caused by the white-back planthopper (WBPH, Sogatella furcifera) and brown planthopper (BPH, Nilaparvata lugens), as well as southern rice black-streaked dwarf virus (SRBSDV), considerably decreases the grain yield of rice. Identification of rice germplasms with sufficient resistance to planthoppers and SRBSDV is essential to the breeding and deployment of resistant varieties and, hence, the control of the pests and disease. In this study, 318 rice accessions were evaluated for their reactions to the infestation of both BPH and WBPH at the seedling stage using the standard seed-box screening test method; insect quantification was further conducted at the end of the tillering and grain-filling stages in field trials. Accessions HN12-239 and HN12-328 were resistant to both BPH and WBPH at all tested stages. Field trials were conducted to identify resistance in the collection to SRBSDV based on the virus infection rate under artificial inoculation. Rathu Heenati (RHT) and HN12-239 were moderately resistant to SRBSDV. In addition, we found that WBPH did not penetrate stems with stylets but did do more probing bouts and xylem sap ingestion when feeding on HN12-239 than the susceptible control rice Taichung Native 1. The resistance of rice accessions HN12-239, HN12-328, and RHT to BPH, WBPH, and/or SRBSDV should be valuable to the development of resistant rice varieties.

Transcriptome analysis of differentially expressed genes in rice seedling leaves under different nitrate treatments on resistance to bacterial leaf blight

Nitrogen (N), as one of the most abundant mineral elements in rice, not only is the primary limiting factor for rice yield, but also impacts plant disease resistance by modulating plant morphology, regulating biochemical characteristics, as well as enhancing metabolic processes. Bacterial blight, a severe bacterial disease caused by Xanthomonas oryzae pv. oryzae (Xoo), significantly impairing rice yield and quality. Previous studies have shown that moderate application of nitrate nitrogen can improve plant disease resistance. However, further exploration is urgently required to investigate the involvement of the nitrate nitrogen signaling pathway in conferring resistance against bacterial leaf blight. In this study, we employed transcriptome sequencing to analyze the differentially expressed genes under various concentrations of nitrate supply duringrice bacterial blight infection. Our research reveals that nitrate nitrogen supply influences rice resistance to bacterial leaf blight. Through transcriptomic profiling of rice leaves inoculated under different nitrate nitrogen concentrations, we identified 4815 differentially expressed genes (DEGs) among four comparison groups, with notable differences in DEG enrichment between low and high nitrate nitrogen conditions, with some members of the NPF family implicated and we preliminarily elucidated the molecular regulatory network in which nitrate nitrogen participates in bacterial leaf blight resistance. Our findings provide a novel insight into a mechanism involving the nitrate nitrogen drive wider defense in rice.

The Identification and Gene Mapping of Spotted Leaf Mutant spl43 in Rice

Our study investigates the genetic mechanisms underlying the spotted leaf phenotype in rice, focusing on the spl43 mutant. This mutant is characterized by persistent reddish-brown leaf spots from the seedling stage to maturity, leading to extensive leaf necrosis. Using map-based cloning, we localized the responsible locus to a 330 Kb region on chromosome 2. We identified LOC_Os02g56000, named OsRPT5A, as the causative gene. A point mutation in OsRPT5A, substituting valine for glutamic acid, was identified as the critical factor for the phenotype. Functional complementation and the generation of CRISPR/Cas9-mediated knockout lines in the IR64 background confirmed the central role of OsRPT5A in controlling this trait. The qPCR results from different parts of the rice plant revealed that OsRPT5A is constitutively expressed across various tissues, with its subcellular localization unaffected by the mutation. Notably, we observed an abnormal accumulation of reactive oxygen species (ROS) in spl43 mutants by examining the physiological indexes of leaves, suggesting a disruption in the ROS system. Complementation studies indicated OsRPT5A's involvement in ROS homeostasis and catalase activity regulation. Moreover, the spl43 mutant exhibited enhanced resistance to Xanthomonas oryzae pv. oryzae (Xoo), highlighting OsRPT5A's role in rice pathogen resistance mechanisms. Overall, our results suggest that OsRPT5A plays a critical role in regulating ROS homeostasis and enhancing pathogen resistance in rice.

Carbon nanosol promotes plant growth and broad-spectrum resistance

Carbon nanosol (CNS) is a carbon-based nanomaterial capable of promoting plant growth while the underlying mechanism involved in this process remains unknown. This study demonstrates that CNS promotes rice seedling growth under restricted concentrations. Macroelement transporter mutants were investigated to further investigate the CNS-mediated promotion of rice seedling growth. The genetic and physiological findings revealed that nitrate transporter 1.1B (NRT1.1B) and ammonium transporter 1 (AMT1) mutants inhibited the CNS-induced growth development of rice seedlings, whereas potassium transporter (AKT1) and phosphate transporter 8 (PT8) did not exhibit any inhibitory effects. Further investigations demonstrated the inhibition of CNS-mediated growth promotion via glutamine synthetase 1;1 (gs1;1) mutants. Additionally, the administration of CNS resulted in enhanced accumulation of chlorophyll in plants, and the promotion of CNS-induced growth was inhibited by yellow-green leaf 8 (YGL8) mutants and the chlorophyll biosynthetic gene divinyl reductase (DVR) mutants. According to these findings, the CNS promotes plant growth by stimulating chlorophyll biosynthesis. Furthermore, the presence of CNS enhanced the ability of rice to withstand blast, sheath blight (ShB), and bacterial blight. The nrt1.1b, amt1, dvr, and ygl8 mutants did not exhibit a broad spectrum effect. The positive regulation of broad-spectrum resistance in rice by GS1;1 suggests the requirement of N assimilation for CNS-mediated broad-spectrum resistance. In addition, an in vitro assay demonstrated that CNS inhibits the growth of pathogens responsible for blast, ShB, and bacterial blight, namely Magnaporthe oryzae, Rhizoctonia solani AG1-IA, and Xanthomonas oryzae pv. Oryzae, respectively. CNS application may also induce broad-spectrum resistance against bacterial and fungal pathogens, indicating that in addition to its antifungal and antibacterial properties, CNS application may also stimulate N assimilation. Collectively, the results indicate that CNS may be a potential nano-therapeutic agent for improved plant growth promotion while also providing broad-spectrum resistance.

Structural insight into subunit F of respiratory chain complex I from Xanthomonas oryzae pv. oryzae inhibition by parthenolide

BACKGROUND

Bacterial leaf blight caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most serious diseases of rice, and there is a lack of bactericides for controlling this disease. We previously found parthenolide (PTL) is a potential lead for developing bactericides against Xoo, and subunit F of respiratory chain complex I (NuoF) is an important target protein of PTL. However, the binding modes of PTL with NuoF need further elucidation.

RESULTS

In this study, we obtained the crystal structure of Xoo NuoEF (complex of subunit E and F of respiratory chain complex I) with a resolution of 2.36 Å, which is the first report on the protein structure of NuoEF in plant-pathogenic bacteria. The possible binding sites of PTL with NuoF (Cys105 and Cys187) were predicted with molecular docking and mutated into alanine using a base mismatch method. The mutated proteins were expressed in Escherichia coli and purified with affinity chromatography. The binding abilities of PTL with mutated proteins were investigated via pull-down assay and BIAcore analysis, which revealed that double mutation of Cys105 and Cys187 in NuoF severely affected the binding ability of PTL with NuoF. In addition, the binding modes were further simulated with combined quantum mechanical/molecular mechanical calculations, and the results indicated that PTL may have a stronger binding with Cys105 than Cys187.

CONCLUSION

NuoEF protein structure of Xoo was resolved, and Cys105 and Cys187 in NuoF are important binding sites of PTL. This study further clarified the action mechanism of PTL against Xoo, and will promote the innovation of bactericides targeting Xoo complex I. © 2024 Society of Chemical Industry.

Novel Sulfoximine Derivatives Containing Cyanoguanidine and Nitroguanidine Moieties: Design, Synthesis, and Bioactivities

A total of 32 novel sulfoximines bearing cyanoguanidine and nitroguanidine moieties were designed and synthesized by a rational molecule design strategy. The bioactivities of the title compounds were evaluated and the results revealed that some of the target compounds possessed excellent antifungal activities against six agricultural fungi, including Sclerotinia sclerotiorum, Fusarium graminearum, Phytophthora capsici, Botrytis cinerea, Rhizoctonia solani, and Pyricularia grisea. Among them, compounds 8e1 and 8e4 exhibited significant efficacy against P. grisea with EC50 values of 2.72 and 2.98 μg/mL, respectively, which were much higher than that of commercial fungicides boscalid (47.95 μg/mL). Interestingly, in vivo assays determined compound 8e1 possessed outstanding activity against S. sclerotiorum with protective and curative effectiveness of 98 and 95.6% at 50 μg/mL, which were comparable to those of boscalid (93.2, 91.9%). The further preliminary mechanism investigation disclosed that compound 8e1 could damage the structure of the cell membrane of S. sclerotiorum, increase its permeability, and suppress its growth. Overall, the findings enhanced that these novel sulfoximine derivatives could be potential lead compounds for the development of new fungicides.

Natural product guvermectin inhibits guanosine 5'-monophosphate synthetase and confers broad-spectrum antibacterial activity

Bacterial diseases caused substantial yield losses worldwide, with the rise of antibiotic resistance, there is a critical need for alternative antibacterial compounds. Natural products (NPs) from microorganisms have emerged as promising candidates due to their potential as cost-effective and environmentally friendly bactericides. However, the precise mechanisms underlying the antibacterial activity of many NPs, including Guvermectin (GV), remain poorly understood. Here, we sought to explore how GV interacts with Guanosine 5'-monophosphate synthetase (GMPs), an enzyme crucial in bacterial guanine synthesis. We employed a combination of biochemical and genetic approaches, enzyme activity assays, site-directed mutagenesis, bio-layer interferometry, and molecular docking assays to assess GV's antibacterial activity and its mechanism targeting GMPs. The results showed that GV effectively inhibits GMPs, disrupting bacterial guanine synthesis. This was confirmed through drug-resistant assays and direct enzyme inhibition studies. Bio-layer interferometry assays demonstrated specific binding of GV to GMPs, with dependency on Xanthosine 5'-monophosphate. Site-directed mutagenesis identified key residues crucial for the GV-GMP interaction. This study elucidates the antibacterial mechanism of GV, highlighting its potential as a biocontrol agent in agriculture. These findings contribute to the development of novel antibacterial agents and underscore the importance of exploring natural products for agricultural disease management.

Lactic acid induced defense responses in tobacco against Phytophthora nicotianae

Induced resistance is considered an eco-friendly disease control strategy, which can enhance plant disease resistance by inducing the plant's immune system to activate the defense response. In recent years, studies have shown that lactic acid can play a role in plant defense against biological stress; however, whether lactic acid can improve tobacco resistance to Phytophthora nicotianae, and its molecular mechanism remains unclear. In our study, the mycelial growth and sporangium production of P. nicotianae were inhibited by lactic acid in vitro in a dose-dependent manner. Application of lactic acid could reduce the disease index, and the contents of total phenol, salicylic acid (SA), jasmonic acid (JA), lignin and H2O2, catalase (CAT) and phenylalanine ammonia-lyase (PAL) activities were significantly increased. To explore this lactic acid-induced protective mechanism for tobacco disease resistance, RNA-Seq analysis was used. Lactic acid enhances tobacco disease resistance by activating Ca2+, reactive oxygen species (ROS) signal transduction, regulating antioxidant enzymes, SA, JA, abscisic acid (ABA) and indole-3-acetic acid (IAA) signaling pathways, and up-regulating flavonoid biosynthesis-related genes. This study demonstrated that lactic acid might play a role in inducing resistance to tobacco black shank disease; the mechanism by which lactic acid induces disease resistance includes direct antifungal activity and inducing the host to produce direct and primed defenses. In conclusion, this study provided a theoretical basis for lactic acid-induced resistance and a new perspective for preventing and treating tobacco black shank disease.

Improvement of Broad-Spectrum Disease-Resistant Rice by the Overexpression of BSR1 via a Moderate-Strength Constitutive Promoter and a Pathogen-Inducible Promoter

Conferring crops with resistance to multiple diseases is crucial for stable food production. Genetic engineering is an effective means of achieving this. The rice receptor-like cytoplasmic kinase BSR1 mediates microbe-associated molecular pattern-induced immunity. In our previous study, we demonstrated that rice lines overexpressing BSR1 under the control of the maize ubiquitin promoter exhibited broad-spectrum resistance to rice blast, brown spot, leaf blight, and bacterial seedling rot. However, unfavorable phenotypes were observed, such as a decreased seed germination rate and a partial darkening of husked rice. Herein, we present a strategy to address these unfavorable phenotypes using an OsUbi7 constitutive promoter with moderate expression levels and a pathogen-inducible PR1b promoter. Rice lines expressing BSR1 under the influence of both promoters maintained broad-spectrum disease resistance. The seed germination rate and coloration of husked rice were similar to those of the wild-type rice.

The OsICS1 is directly regulated by OsWRKY6 and increases resistance against Xanthomonas oryzae pv. oryzae

KEY MESSAGE

OsICS1 but not OsICS1-L mediates the rice response to Xoo inoculation, with its overexpression increasing resistance against this pathogen. OsICS1 but not OsICS-L is directly upregulated by OsWRKY6. Rice (Oryza sativa) is a staple crop for about half of the global population and is particularly important in the diets of people living in Asia, Latin America, and Africa. This crop is continually threatened by bacterial leaf blight disease caused by Xanthomonas oryzae pv. oryzae (Xoo), which drastically reduces yields; therefore, it is needed to elucidate the plant's resistance mechanisms against Xoo. Isochorismate synthase (ICS1) generates salicylic acid (SA) and increases resistance against bacterial disease. The OsICS1 is differently annotated in rice genome databases and has not yet been functionally characterized in the context of Xoo infection. Here, we report that the expression of the OsICS1 is directly regulated by OsWRKY6 and increases plant resistance against Xoo. Inoculation with Xoo increased the expression of OsICS1 but not that of the long variant of OsICS1 (OsICS1-L). OsWRKY6 directly activated the OsICS1 promoter but not the OsICS1-L promoter. OsICS1 overexpression in rice increased resistance against Xoo through the induction of SA-dependent bacterial defense genes. These data show that OsICS1 promotes resistance against Xoo infection.

A critical review on bioaerosols-dispersal of crop pathogenic microorganisms and their impact on crop yield

Bioaerosols are potential sources of pathogenic microorganisms that can cause devastating outbreaks of global crop diseases. Various microorganisms, insects and viroids are known to cause severe crop diseases impeding global agro-economy. Such losses threaten global food security, as it is estimated that almost 821 million people are underfed due to global crisis in food production. It is estimated that global population would reach 10 billion by 2050. Hence, it is imperative to substantially increase global food production to about 60% more than the existing levels. To meet the increasing demand, it is essential to control crop diseases and increase yield. Better understanding of the dispersive nature of bioaerosols, seasonal variations, regional diversity and load would enable in formulating improved strategies to control disease severity, onset and spread. Further, insights on regional and global bioaerosol composition and dissemination would help in predicting and preventing endemic and epidemic outbreaks of crop diseases. Advanced knowledge of the factors influencing disease onset and progress, mechanism of pathogen attachment and penetration, dispersal of pathogens, life cycle and the mode of infection, aid the development and implementation of species-specific and region-specific preventive strategies to control crop diseases. Intriguingly, development of R gene-mediated resistant varieties has shown promising results in controlling crop diseases. Forthcoming studies on the development of an appropriately stacked R gene with a wide range of resistance to crop diseases would enable proper management and yield. The article reviews various aspects of pathogenic bioaerosols, pathogen invasion and infestation, crop diseases and yield.

GERWR: Identifying the Key Pathogenicity- Associated sRNAs of Magnaporthe Oryzae Infection in Rice Based on Graph Embedding and Random Walk With Restart

Rice blast, caused by Magnaporthe oryzae(M.oryzae), is a destructive rice disease that reduces rice yield by 10% to 30% annually. It also affects other cereal crops such as barley, wheat, rye, millet, sorghum, and maize. Small RNAs (sRNAs) play an essential regulatory role in fungus-plant interaction during the fungal invasion, but studies on pathogenic sRNAs during the fungal invasion of plants based on multi-omics data integration are rare. This paper proposes a novel approach called Graph Embedding combined with Random Walk with Restart (GERWR) to identify pathogenic sRNAs based on multi-omics data integration during M.oryzae invasion. By constructing a multi-omics network (MRMO), we identified 29 pathogenic sRNAs of rice blast fungus. Further analysis revealed that these sRNAs regulate rice genes in a many-to-many relationship, playing a significant regulatory role in the pathogenesis of rice blast disease. This paper explores the pathogenic factors of rice blast disease from the perspective of multi-omics data analysis, revealing the inherent connection between pathogenic factors of different omics. It has essential scientific significance for studying the pathogenic mechanism of rice blast fungus, the rice blast fungus-rice model system, and the pathogen-host interaction in related fields.

Investigation of the antibacterial activity of benziothiazolinone against Xanthomonas oryzae pv. oryzae

Plant pathogenic bacteria can cause numerous diseases for higher plants and result in severe reduction of crop yield. Introduction of new bactericides can always effectively control these plant diseases. Benziothiazolinone (BIT) is a novel fungicide registered in China for the control of plant fungal diseases, however, its anti-bacterial activity is not well studied. The results of activity tests showed that BIT exhibited stronger inhibitory activity against bacteria, particularly for Xanthomonas oryzae pv. oryzae (Xoo) (EC50 = 0.17 μg/mL), which was superior than that of the tested fungi in vitro. BIT also exhibited excellent protective and curative activity against rice bacterial leaf blight (BLB) caused by Xoo with the control efficacies of 71.37% and 91.64% at 600 μg/mL, respectively. After treatment with BIT, Xoo cell surface became wrinkled and the cell shape was distorted with extruding cellular content. It was also found that BIT decreased DNA synthesis and affected the biofilm formation and motility of Xoo cells. However, no significant change in the protein content was observed. Moreover, the results of quantitative real-time PCR also showed that expressions of several genes related to DNA synthesis, biofilm formation and motility of Xoo cells were down- or up-regulated, which further proved the anti-bacterial activity of BIT in influencing the biological properties of Xoo. Additionally, BIT also enhanced the activity of phenylalanine ammonia lyase (PAL), a plant defense enzyme. Taken together, benziothiazolinone might be served as an alternative candidate for the control of BLB.

Peroxisome dynamics determines host-derived ROS accumulation and infectious growth of the rice blast fungus

IMPORTANCE

The interplay between plant and pathogen is a dynamic process, with the host's innate defense mechanisms serving a crucial role in preventing infection. In response to many plant pathogen infections, host cells generate the key regulatory molecule, reactive oxygen species (ROS), to limit the spread of the invading organism. In this study, we reveal the effects of fungal peroxisome dynamics on host ROS homeostasis, during the rice blast fungus Magnaporthe oryzae infection. The elongation of the peroxisome appears contingent upon ROS and links to the accumulation of ROS within the host and the infectious growth of the pathogen. Importantly, we identify a peroxisomal 3-ketoacyl-CoA thiolase, MoKat2, responsible for the elongation of the peroxisome during the infection. In response to host-derived ROS, the homodimer of MoKat2 undergoes dissociation to bind peroxisome membranes for peroxisome elongation. This process, in turn, inhibits the accumulation of host ROS, which is necessary for successful infection. Overall, our study is the first to highlight the intricate relationship between fungal organelle dynamics and ROS-mediated host immunity, extending the fundamental knowledge of pathogen-host interaction.

XanFur, a novel Fur protein induced by H2O2, positively regulated by the global transcriptional regulator Clp and required for the full virulence of Xanthomonas oryzae pv. oryzae in rice

IMPORTANCE

Although Xanthomonas oryzae pv. oryzae (Xoo) has been found to be a bacterial pathogen causing bacterial leaf blight in rice for many years, the molecular mechanisms of the rice-Xoo interaction has not been fully understood. In this study, we found that XanFur of Xoo is a novel ferric uptake regulator (Fur) protein conserved among major pathogenic Xanthomonas species. XanFur is required for the virulence of Xoo in rice, and likely involved in regulating the virulence determinants of Xoo. The expression of xanfur is induced by H2O2, and positively regulated by the global transcriptional regulator Clp. Our results reveal the function and regulation of the novel virulence-related Fur protein XanFur in Xoo, providing new insights into the interaction mechanisms of rice-Xoo.

Fine mapping and candidate gene analysis of qSB12YSB, a gene conferring major quantitative resistance to rice sheath blight

KEY MESSAGE

qSB12YSB, a major quantitative sheath blight resistance gene originated from rice variety YSBR1 with good breeding potential, was mapped to a 289-Kb region on chromosome 12. Sheath blight (ShB), caused by Rhizoctonia solani kühn, is one of the most serious global rice diseases. Rice resistance to ShB is a typical of quantitative trait controlled by multiple quantitative trait loci (QTLs). Many QTLs for ShB resistance have been reported while only few of them were fine-mapped. In this study, we identified a QTL on chromosome 12, in which the qSB12YSB resistant allele shows significant ShB resistance, by using 150 BC4 backcross inbred lines employing the resistant rice variety YSBR1 as the donor and the susceptible variety Lemont (LE) as the recurrent parent. We further fine-mapped qSB12YSB to a 289-kb region by generating 34 chromosomal segment substitution lines and identified a total of 18 annotated genes as the most likely candidates for qSB12YSB after analyzing resequencing and transcriptomic data. KEGG analysis suggested that qSB12YSB might activate secondary metabolites biosynthesis and ROS scavenging system to improve ShB resistance. qSB12YSB conferred significantly stable resistance in three commercial rice cultivars (NJ9108, NJ5055 and NJ44) in field trials when introduced through marker assisted selection. Under severe ShB disease conditions, qSB12YSB significantly reduced yield losses by up to 13.5% in the LE background, indicating its great breeding potential. Our results will accelerate the isolation of qSB12YSB and its utilization in rice breeding programs against ShB.

Streptomyces as a promising biological control agents for plant pathogens

Plant diseases caused by pathogenic microorganisms in agriculture present a considerable obstacle, resulting in approximately 30-40% crop damage. The use of conventional techniques to manage these microorganisms, i.e., applying chemical pesticides and antimicrobials, has been discovered to have adverse effects on human health and the environment. Furthermore, these methods have contributed to the emergence of resistance among phytopathogens. Consequently, it has become imperative to investigate natural alternatives to address this issue. The Streptomyces genus of gram-positive bacteria is a potentially viable natural alternative that has been extensively researched due to its capacity to generate diverse antimicrobial compounds, such as metabolites and organic compounds. Scientists globally use diverse approaches and methodologies to extract new bioactive compounds from these bacteria. The efficacy of bioactive compounds in mitigating various phytopathogens that pose a significant threat to crops and plants has been demonstrated. Hence, the Streptomyces genus exhibits potential as a biological control agent for combating plant pathogens. This review article aims to provide further insight into the Streptomyces genus as a source of antimicrobial compounds that can potentially be a biological control against plant pathogens. The investigation of various bioactive compounds synthesized by this genus can enhance our comprehension of their prospective utilization in agriculture.

Novel broad-spectrum bacteriophages against Xanthomonas oryzae and their biocontrol potential in rice bacterial diseases

Bacterial leaf blight (BLB) and bacterial leaf streak (BLS)-caused by Xanthomonas oryzae pv. oryzae (Xoo) and Xanthomonas oryzae pv. oryzicola (Xoc), respectively-are two major bacterial diseases that threaten the safe production of rice, one of the most important food crops. Bacteriophages are considered potential biocontrol agents against rice bacterial pathogens, due to their host specificity and environmental safety. It is common for BLB and BLS to occur together in fields, which highlights the need for broad-spectrum phages capable of infecting both Xoo and Xoc. In this study, two lytic broad-spectrum phages (pXoo2106 and pXoo2107) that can infect various strains of Xoo and Xoc were assessed. Both phages belong to the class Caudoviricetes and one of them to the family Autographiviridae, while the other belongs to an unclassified family. Two phages alone or combined in a phage cocktail could effectively inhibit Xoo and Xoc growth in vitro. In an in vivo biocontrol experiment, the phage cocktail reduced the total CFU and significantly eased the symptoms caused by Xoo or Xoc. Our results suggest that pXoo2106 and pXoo2107 have a broad-spectrum host range targeting different X. oryzae strains, and have strong biocontrol potential in field applications against both BLB and BLS.

Wall-associated kinase BrWAK1 confers resistance to downy mildew in Brassica rapa

The plant cell wall is the first line of defence against physical damage and pathogen attack. Wall-associated kinase (WAK) has the ability to perceive the changes in the cell wall matrix and transform signals into the cytoplasm, being involved in plant development and the defence response. Downy mildew, caused by Hyaloperonospora brassicae, can result in a massive loss in Chinese cabbage (Brassica rapa L. ssp. pekinensis) production. Herein, we identified a candidate resistant WAK gene, BrWAK1, in a major resistant quantitative trait locus, using a double haploid population derived from resistant inbred line T12-19 and the susceptible line 91-112. The expression of BrWAK1 could be induced by salicylic acid and pathogen inoculation. Expression of BrWAK1 in 91-112 could significantly enhance resistance to the pathogen, while truncating BrWAK1 in T12-19 increased disease susceptibility. Variation in the extracellular galacturonan binding (GUB) domain of BrWAK1 was found to mainly confer resistance to downy mildew in T12-19. Moreover, BrWAK1 was proved to interact with BrBAK1 (brassinosteroid insensitive 1 associated kinase), resulting in the activation of the downstream mitogen-activated protein kinase (MAPK) cascade to trigger the defence response. BrWAK1 is the first identified and thoroughly characterized WAK gene conferring disease resistance in Chinese cabbage, and the plant biomass is not significantly influenced by BrWAK1, which will greatly accelerate Chinese cabbage breeding for downy mildew resistance.

High-quality complete genome sequence of Xanthomonas oryzae pv. oryzicola (Xoc) strain HB8

Here, we report a high-quality genome of Xanthomonas oryzae pv. oryzicola (Xoc) strain HB8, which causes bacterial leaf streaks in rice. The genome size of HB8 is 4,800,100 bp, with a GC content of 64.03%, which serves as an important resource for the study of the Xanthomonas-rice pathosystem.

CRISPR/Cas9-mediated simultaneous mutation of three salicylic acid 5-hydroxylase (OsS5H) genes confers broad-spectrum disease resistance in rice

Salicylic acid (SA) is an essential plant hormone that plays critical roles in basal defence and amplification of local immune responses and establishes resistance against various pathogens. However, the comprehensive knowledge of the salicylic acid 5-hydroxylase (S5H) in rice-pathogen interaction is still elusive. Here, we reported that three OsS5H homologues displayed salicylic acid 5-hydroxylase activity, converting SA into 2,5-dihydroxybenzoic acid (2,5-DHBA). OsS5H1, OsS5H2, and OsS5H3 were preferentially expressed in rice leaves at heading stage and responded quickly to exogenous SA treatment. We found that bacterial pathogen Xanthomonas oryzae pv. oryzae (Xoo) strongly induced the expression of OsS5H1, OsS5H2, and OsS5H3. Rice plants overexpressing OsS5H1, OsS5H2, and OsS5H3 showed significantly decreased SA contents and increased 2,5-DHBA levels, and were more susceptible to bacterial blight and rice blast. A simple single guide RNA (sgRNA) was designed to create oss5h1oss5h2oss5h3 triple mutants through CRISPR/Cas9-mediated gene mutagenesis. The oss5h1oss5h2oss5h3 exhibited stronger resistance to Xoo than single oss5h mutants. And oss5h1oss5h2oss5h3 plants displayed enhanced rice blast resistance. The conferred pathogen resistance in oss5h1oss5h2oss5h3 was attributed to the significantly upregulation of OsWRKY45 and pathogenesis-related (PR) genes. Besides, flg22-induced reactive oxygen species (ROS) burst was enhanced in oss5h1oss5h2oss5h3. Collectively, our study provides a fast and effective approach to generate rice varieties with broad-spectrum disease resistance through OsS5H gene editing.

Risk of Pesticides Mixtures in Rice to Birds and Humans in Iran

Rice is a staple in the diet of nearly half of the world's population. As with most crops, pesticides are used as a tool to increase crop yield in rice farming. This study investigated the residues of 14 organophosphate insecticides and 2 herbicides in rice cultivated at five locations in the southwest of Iran. The pesticide residues were then used to estimate the risk that they may pose to the health of bird and human consumers. The rice samples from the five locations contained residues from 10 to 13 pesticides. Of the 16 pesticides measured, the mean concentration of 12 pesticides exceeded the maximum residue limit set by the Iranian National Standards Organization at two or more of the sampling sites. The greatest total exceedance (sum of all pesticides detected in rice) of the species sensitivity distributions constructed for birds was 0.74% and the level of concern set for the assessment was an exceedance ≥ 5%, which suggests a relatively low risk to birds. For human consumers, no single pesticide measured in rice samples posed a considerable risk. However, when considering the mixture of pesticides present in rice samples, the cumulative risk exceeded the level of concern in all samples from all sites. The margin of safety for the mixture of pesticides present in rice samples ranged from 5.8 to 29.1, with 1 being the level of concern. The results of this study indicate that efforts need to be made to mitigate the exposure of human consumers to pesticides present in rice cultivated in Iran. This study also highlights the need to collect data on pesticides residues in other crop cultivated in Iran.

An updated review on oral protein-based antigen vaccines efficiency and delivery approaches: a special attention to infectious diseases

Various infectious agents affect human health via the oral entrance. The majority of pathogens lack approved vaccines. Oral vaccination is a convenient, safe and cost-effective approach with the potential of provoking mucosal and systemic immunity and maintaining individual satisfaction. However, vaccines should overcome the intricate environment of the gastrointestinal tract (GIT). Oral protein-based antigen vaccines (OPAVs) are easier to administer than injectable vaccines and do not require trained healthcare professionals. Additionally, the risk of needle-related injuries, pain, and discomfort is eliminated. However, OPAVs stability at environmental and GIT conditions should be considered to enhance their stability and facilitate their transport and storage. These vaccines elicit the local immunity, protecting GIT, genital tract and respiratory epithelial surfaces, where numerous pathogens penetrate the body. OPAVs can also be manipulated (such as using specific incorporated ligand and receptors) to elicit targeted immune response. However, low bioavailability of OPAVs necessitates development of proper protein carriers and formulations to enhance their stability and efficacy. There are several strategies to improve their efficacy or protective effects, such as incorporation of adjuvants, enzyme inhibitors, mucoadhesive or penetrating devices and permeation enhancers. Hence, efficient delivery of OPAVs into GIT require proper delivery systems mainly including smart target systems, probiotics, muco-adhesive carriers, lipid- and plant-based delivery systems and nano- and microparticles.

Improvement of resistance to rice blast and bacterial leaf streak by CRISPR/Cas9-mediated mutagenesis of Pi21 and OsSULTR3;6 in rice (Oryza sativa L.)

Rice (Oryza sativa L.) is a staple food in many countries around the world, particularly in China. The production of rice is seriously affected by the bacterial leaf streak and rice blast, which can reduce rice yield or even cause it to fail to be harvested. In this study, susceptible material 58B was edited by CRISPR/Cas9, targeting a target of the Pi21 gene and a target of the effector-binding element (EBE) of the OsSULTR3;6 gene, and the mutants 58b were obtained by Agrobacterium-mediated method. The editing efficiency of the two targets in the T₀ generation was higher than 90.09%, the homozygous mutants were successfully selected in the T₀ generation, and the homozygous mutation rate of each target was higher than 26.67%. The expression of the edited pi21 and EBE of Ossultr3;6 was significantly reduced, and the expression of defense responsive genes was significantly upregulated after infected with rice blast. The lesion areas of rice blast and bacterial leaf streak were significantly reduced in 58b, and the resistance of both was effectively improved. Furthermore, the gene editing events did not affect the agronomic traits of rice. In this study, the resistance of 58b to rice blast and bacterial leaf streak was improved simultaneously. This study provides a reference for using Clustered Regularly Interspaced Short Palindromic Repeats/Cas9 (CRISPR/Cas9) to accelerate the improvement of rice varieties and the development of new materials for rice breeding.

Calcium-binding protein OsANN1 regulates rice blast disease resistance by inactivating jasmonic acid signaling

Rice blast, caused by the fungal pathogen Magnaporthe oryzae, is one of the most devastating diseases in rice (Oryza sativa L.). Plant annexins are calcium- and lipid-binding proteins that have multiple functions; however, the biological roles of annexins in plant disease resistance remain unknown. Here, we report a rice annexin gene, OsANN1 (Rice annexin 1), that was induced by M. oryzae infection and negatively regulated blast disease resistance in rice. By yeast 2-hybrid screening, we found that OsANN1 interacted with a cytochrome P450 monooxygenase, HAN1 ("HAN" termed "chilling" in Chinese), which has been reported to catalyze the conversion of biologically active jasmonoyl-L-isoleucine (JA-Ile) to the inactive form 12-hydroxy-JA-Ile. Pathogen inoculation assays revealed that HAN1 was also a negative regulator in rice blast resistance. Genetic evidence showed that OsANN1 acts upstream of HAN1. OsANN1 stabilizes HAN1 in planta, resulting in the inactivation of the endogenous biologically active JA-Ile. Taken together, our study unravels a mechanism where an OsANN1-HAN1 module impairs blast disease resistance via inactivating biologically active JA-Ile and JA signaling in rice.

Metabarcoding reveals response of rice rhizosphere bacterial community to rice bacterial leaf blight

Rice bacterial leaf blight (BLB) is a major disease affecting cultivated rice and caused by the bacterium Xanthomonas oryzae pv. oryzae (Xoo). It is well established that rhizosphere microorganisms could help improve the adaptability of plants to biotic stresses. However, it is still unclear about the response mechanism of rice rhizosphere microbial community to BLB infection. Here, we used 16S rRNA gene amplicon sequencing to explore the effect of BLB on the rice rhizosphere microbial community. The results show that the alpha diversity index of the rice rhizosphere microbial community decreased significantly at the onset of BLB and then gradually recovered to normal levels. Beta diversity analysis indicated that BLB significantly affected community composition. In addition, there were significant differences in the taxonomic composition between healthy and diseased groups. For example, ceretain genera were more abundant in diseased rhizospheres, namely Streptomyces, Sphingomonas, and Flavobacterium, among others. In addition, the size and complexity of the rhizosphere co-occurrence network increased after disease onset compared to healthy groups. Also, hub microbe Rhizobiaceae and Gemmatimonadaceae were identified in the diseased rhizosphere co-occurrence network, and these hub microbes played an important role in maintaining network stability. In conclusion, our results provide important insights into the rhizosphere microbial community response to BLB and also provide important data and ideas in using rhizosphere microbes to control BLB.

Phage combination alleviates bacterial leaf blight of rice (Oryza sativa L.)

Rice bacterial leaf blight (BLB) is the most destructive bacterial diseases caused by Xanthomonas oryzae pv. oryzae (Xoo). Phages have been proposed as a green and efficient strategy to kill bacterial pathogens in crops, however, the mechanism of action of phages in the control of phyllosphere bacterial diseases remain unclear. Here, the glasshouse pot experiment results showed that phage combination could reduce the disease index by up to 64.3%. High-throughput sequencing technology was used to analyze the characteristics of phyllosphere microbiome changes and the results showed that phage combinations restored the impact of pathogen invasion on phyllosphere communities to a certain extent, and increased the diversity of bacterial communities. In addition, the phage combination reduced the relative abundance of epiphytic and endophytic Xoo by 58.9% and 33.9%, respectively. In particular, Sphingomonas and Stenotrophomonas were more abundant. According to structural equation modeling, phage combination directly and indirectly affected the disease index by affecting pathogen Xoo biomass and phage resistance. In summary, phage combination could better decrease the disease index. These findings provide new insights into phage biological control of phyllosphere bacterial diseases, theoretical data support, and new ideas for agricultural green prevention and control of phyllosphere diseases.

Effects of temperature and microwave on the stability of the blast effector complex APikL2A/sHMA25 as determined by molecular dynamics analyses

Magnaporthe oryzae is the causal agent of rice blast, and understanding how abiotic stress affects the resistance of plants to this disease is useful for designing disease control strategies. In this paper, the effects of temperature and microwave irradiation on the effector complex comprising APikL2A from M. oryzae and sHMA25 from foxtail millet were investigated by molecular dynamics simulations using the GROMACS software package. While the structure of APikL2A/sHMA25 remained relatively stable in a temperature range of 290 K (16.85 °C) to 320 K (46.85 °C), the concave shape of the temperature-dependent binding free energy curve indicated that there was maximum binding affinity between APikL2A and sHMA25 at 300 K-310 K. This coincided with the optimum infectivity temperature, thus suggesting that coupling of the two polypeptides may play a role in the infection process. A strong oscillating electric field destroyed the structure of APikL2A/sHMA25, although it was stable and not susceptible to weak electric fields.

Identification and fine mapping of a new bacterial blight resistance gene, Xa43(t), in Zhangpu wild rice (Oryza rufipogon)

Bacterial blight (BB) is currently considered one of the most serious rice diseases and is caused by Xanthomonas oryzae pv. oryzae (Xoo). Numerous studies have shown that breeding resistant rice varieties is one of the most effective methods to prevent BB, and it is important to identify and isolate more BB resistance (R) genes from different rice resources. Using a map-based approach, we identified a new QTL/gene, Xa43(t), from ZhangPu wild rice, which was highly resistant to the BB isolate PX099. We performed bulked segregant analysis combined with candidate gene prediction to identify the candidate gene. The Xa43(t) gene was narrowed down to a 29-kb region containing four putative genes. More importantly, the candidate gene Xa43(t) did not affect the main agronomic traits of rice. We also identified a widely applicable molecular marker, namely Inde1-18, which co-segregates with the Xa43(t) gene. The Xa43(t) gene is a new broad-spectrum BB resistance gene without identified alleles and has good application prospects for rice disease resistance breeding.

Current trends in management of bacterial pathogens infecting plants

Plants are continuously challenged by different pathogenic microbes that reduce the quality and quantity of produce and therefore pose a serious threat to food security. Among them bacterial pathogens are known to cause disease outbreaks with devastating economic losses in temperate, tropical and subtropical regions throughout the world. Bacteria are structurally simple prokaryotic microorganisms and are diverse from a metabolic standpoint. Bacterial infection process mainly involves successful attachment or penetration by using extracellular enzymes, type secretion systems, toxins, growth regulators and by exploiting different molecules that modulate plant defence resulting in successful colonization. Theses bacterial pathogens are extremely difficult to control as they develop resistance to antibiotics. Therefore, attempts are made to search for innovative methods of disease management by the targeting bacterial virulence and manipulating the genes in host plants by exploiting genome editing methods. Here, we review the recent developments in bacterial disease management including the bioactive antimicrobial compounds, bacteriophage therapy, quorum-quenching mediated control, nanoparticles and CRISPR/Cas based genome editing techniques for bacterial disease management. Future research should focus on implementation of smart delivery systems and consumer acceptance of these innovative methods for sustainable disease management.

Population structure of Pyricularia oryzae on rice in Vietnam reveals diversified populations with four pandemic and two endemic clusters

We characterized the genetic structure of 609 strains of Pyricularia oryzae, the fungal pathogen causing rice blast disease, in three main regions in Vietnam using microsatellites (SSR) markers. From the 447 distinct multilocus genotypes identified, six genetic clusters were defined, all of them showing elevated genetic and genotypic diversities. Four of these clusters were related to rice-attacking lineages already described at the worldwide scale, whereas the two remaining clusters were endemic to Vietnam. Strains were unevenly distributed into the six clusters depending on their groups of rice variety (indica / japonica) or type of varieties (traditional / modern) of origin, but none of the clusters was specifically related to these two factors. The highest diversity of blast population was found in Northern mountainous area, and the lowest in Red River Delta in both term of genetic diversity and gene diversity. Hierarchical AMOVAs confirmed that all three factors considered (rice variety group, type of variety origin and geography) significantly contributed to the population structure of P. oryzae in Vietnam, with highest contribution from rice variety group. Mating types were unevenly distributed among clusters. Combined with results of female fertility and linkage disequilibirum, we hypothesized that clonal reproduction probably occurred in all clusters, but that sexual reproduction likely took place at least in some restricted areas in the Northern mountainous area for strains belonging to the cluster related to the previously described recombinant lineage (worldwide lineage 1). Our study pictures the genetic diversity, population structure and reproductive mode of the blast fungus in central and north Vietnam, and shows that the observed population structure is explained by several factors, the most important one being the variability of rice variety. All these new information might help for elaborating appropriate strategies to controlling the blast disease.

The OsBDR1-MPK3 module negatively regulates blast resistance by suppressing the jasmonate signaling and terpenoid biosynthesis pathway

Receptor-like kinases (RLKs) may initiate signaling pathways by perceiving and transmitting environmental signals to cellular machinery and play diverse roles in plant development and stress responses. The rice genome encodes more than one thousand RLKs, but only a small number have been characterized as receptors for phytohormones, polypeptides, elicitors, and effectors. Here, we screened the function of 11 RLKs in rice resistance to the blast fungus Magnaporthe oryzae (M. oryzae) and identified a negative regulator named BDR1 (Blast Disease Resistance 1). The expression of BDR1 was rapidly increased under M. oryzae infection, while silencing or knockout of BDR1 significantly enhanced M. oryzae resistance in two rice varieties. Protein interaction and kinase activity assays indicated that BDR1 directly interacted with and phosphorylated mitogen-activated kinase 3 (MPK3). Knockout of BDR1 compromised M. oryzae-induced MPK3 phosphorylation levels. Moreover, transcriptome analysis revealed that M. oryzae-elicited jasmonate (JA) signaling and terpenoid biosynthesis pathway were negatively regulated by BDR1 and MPK3. Mutation of JA biosynthetic (allene oxide cyclase (AOC)/signaling (MYC2) genes decreased rice resistance to M. oryzae. Besides diterpenoid, the monoterpene linalool and the sesquiterpene caryophyllene were identified as unique defensive compounds against M. oryzae, and their biosynthesis genes (TPS3 and TPS29) were transcriptionally regulated by JA signaling and suppressed by BDR1 and MPK3. These findings demonstrate the existence of a BDR1-MPK3 cascade that negatively mediates rice blast resistance by affecting JA-related defense responses.

Assembling highly repetitive Xanthomonas TALomes using Oxford Nanopore sequencing

BACKGROUND

Most plant-pathogenic Xanthomonas bacteria harbor transcription activator-like effector (TALE) genes, which function as transcriptional activators of host plant genes and support infection. The entire repertoire of up to 29 TALE genes of a Xanthomonas strain is also referred to as TALome. The DNA-binding domain of TALEs is comprised of highly conserved repeats and TALE genes often occur in gene clusters, which precludes the assembly of TALE-carrying Xanthomonas genomes based on standard sequencing approaches.

RESULTS

Here, we report the successful assembly of the 5 Mbp genomes of five Xanthomonas strains from Oxford Nanopore Technologies (ONT) sequencing data. For one of these strains, Xanthomonas oryzae pv. oryzae (Xoo) PXO35, we illustrate why Illumina short reads and longer PacBio reads are insufficient to fully resolve the genome. While ONT reads are perfectly suited to yield highly contiguous genomes, they suffer from a specific error profile within homopolymers. To still yield complete and correct TALomes from ONT assemblies, we present a computational correction pipeline specifically tailored to TALE genes, which yields at least comparable accuracy as Illumina-based polishing. We further systematically assess the ONT-based pipeline for its multiplexing capacity and find that, combined with computational correction, the complete TALome of Xoo PXO35 could have been reconstructed from less than 20,000 ONT reads.

CONCLUSIONS

Our results indicate that multiplexed ONT sequencing combined with a computational correction of TALE genes constitutes a highly capable tool for characterizing the TALomes of huge collections of Xanthomonas strains in the future.

The NAC transcription factor ONAC083 negatively regulates rice immunity against Magnaporthe oryzae by directly activating transcription of the RING-H2 gene OsRFPH2-6

NAC transcription factors (TFs) play critical roles in plant immunity by modulating the expression of downstream genes via binding to specific cis-elements in promoters. Here, we report the function and regulatory network of a pathogen- and defense phytohormone-inducible NAC TF gene, ONAC083, in rice (Oryza sativa) immunity. ONAC083 localizes to the nucleus and exhibits transcriptional activation activity that depends on its C-terminal region. Knockout of ONAC083 enhances rice immunity against Magnaporthe oryzae, strengthening pathogen-induced defense responses, and boosting chitin-induced pattern-triggered immunity (PTI), whereas ONAC083 overexpression has opposite effects. We identified ONAC083-binding sites in the promoters of 82 genes, and showed that ONAC083 specifically binds to a conserved element with the core sequence ACGCAA. ONAC083 activated the transcription of the genes OsRFPH2-6, OsTrx1, and OsPUP4 by directly binding to the ACGCAA element. OsRFPH2-6, encoding a RING-H2 protein with an N-terminal transmembrane region and a C-terminal typical RING domain, negatively regulated rice immunity against M. oryzae and chitin-triggered PTI. These data demonstrate that ONAC083 negatively contributes to rice immunity against M. oryzae by directly activating the transcription of OsRFPH2-6 through the ACGCAA element in its promoter. Overall, our study provides new insight into the molecular regulatory network of NAC TFs in rice immunity.

Exploration of Fungicidal Activity and Mode of Action of Ferimzone Analogs

Lead discovery and molecular target identification are important for developing novel pesticides. Scaffold hopping, an effective approach of modern medicinal and agrochemical chemistry for a rational design of target molecules, is aiming to design novel molecules with similar structures and similar/better biological performance. Herein, 24 new ferimzone derivatives were designed and synthesized by a scaffold-hopping strategy. In vitro bioassays indicated that compound 5o showed similar potency to ferimzone against Cercospora arachidicola and 2-fold higher potency than ferimzone against Alternaria solani. Compounds 5q, 6a, and 6d displayed fungicidal activity with EC₅₀ values ranging from 1.17 to 3.84 μg/mL against Rhizoctonia solani, and compounds 5q and 6a displayed 1.6-1.8-fold higher activity than ferimzone against Fusarium graminearum. The in vivo bioassays at 200 μg/mL indicated that compound 5q was more potent than ferimzone against Pyricularia oryzae (90% vs 70% efficacy, respectively). Density functional theory (DFT) calculations elucidated the structure-energy relationship. Although the mode of action of ferimzone is still unclear, studies suggested that compound 5q significantly inhibited the growth and reproduction of R. solani, and its energy metabolism pathways (e.g., starch, sucrose, lipids, and glutathione) were seriously downregulated after a 5q treatment.

A Proteomics Insight into Advancements in the Rice-Microbe Interaction

Rice is one of the most-consumed foods worldwide. However, the productivity and quality of rice grains are severely constrained by pathogenic microbes. Over the last few decades, proteomics tools have been applied to investigate the protein level changes during rice-microbe interactions, leading to the identification of several proteins involved in disease resistance. Plants have developed a multi-layered immune system to suppress the invasion and infection of pathogens. Therefore, targeting the proteins and pathways associated with the host's innate immune response is an efficient strategy for developing stress-resistant crops. In this review, we discuss the progress made thus far with respect to rice-microbe interactions from side views of the proteome. Genetic evidence associated with pathogen-resistance-related proteins is also presented, and challenges and future perspectives are highlighted in order to understand the complexity of rice-microbe interactions and to develop disease-resistant crops in the future.

Membrane component ergosterol builds a platform for promoting effector secretion and virulence in Magnaporthe oryzae

The plasma membrane (PM) functions as a physical border between the extracellular and cytoplasmic environments that contribute to the interaction between host plants and pathogenic fungi. As a specific sterol constituent in the cell membrane, ergosterol plays a significant role in fungal development. However, the role of ergosterol in the infection of the rice blast fungus Magnaporthe oryzae remains unclear. In this study, we found that a sterol reductase, MoErg4, is involved in ergosterol biosynthesis and the regulation of plasma membrane integrity in M. oryzae. We found that defects in ergosterol biosynthesis disrupt lipid raft formation in the PM and cause an abnormal distribution of the t-soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) protein MoSso1, inhibiting its interaction with the v-SNARE protein MoSnc1. In addition, we found that MoSso1-MoSnc1 interaction is important for biotrophic interface complex development and cytoplasmic effector protein secretion. Our findings suggested that ergosterol-enriched lipid rafts constitute a platform for interactions among various SNARE proteins that are required for the development and pathogenicity of M. oryzae.