Mechanistic insights into host adaptation, virulence and epidemiology of the phytopathogen Xanthomonas

Modularization of the type II secretion gene cluster from Xanthomonas euvesicatoria facilitates the identification of a structurally conserved XpsCLM assembly platform complex

Many bacterial pathogens depend on a type II secretion (T2S) system to secrete virulence factors from the periplasm into the extracellular milieu. T2S systems consist of an outer membrane secretin channel, a periplasmic pseudopilus and an inner membrane-associated assembly platform including a cytoplasmic ATPase. The components of T2S systems are often conserved in different bacterial species, however, the architecture of the assembly platform is largely unknown. Here, we analysed predicted assembly platform components of the Xps-T2S system from the plant-pathogenic bacterium Xanthomonas euvesicatoria. To facilitate these studies, we generated a modular xps-T2S gene cluster by Golden Gate assembly of single promoter and gene fragments. The modular design allowed the efficient deletion and replacement of T2S genes and the insertion of reporter fusions. Mutant approaches as well as interaction and crosslinking studies showed that the predicted assembly platform components XpsC, XpsL and XpsM form a trimeric complex which is essential for T2S and associates with the cytoplasmic ATPase XpsE and the secretin XpsD. Structural modeling revealed a similar trimeric architecture of XpsCLM homologs from Pseudomonas, Vibrio and Klebsiella species, despite overall low amino acid sequence similarities. In X. euvesicatoria, crosslinking and fluorescence microscopy studies showed that the formation of the XpsCLM complex is independent of the secretin and vice versa, suggesting that the assembly of the T2S system is a dynamic process which involves the association of preformed subcomplexes.

Xanthomonas oryzae Orphan Response Regulator EmvR Is Involved in Virulence, Extracellular Polysaccharide Production and Cell Motility

Bacteria have evolved a large number of two-component signalling systems (TCSs), which are typically composed of a histidine sensor kinase (HK) and a response regulator (RR), to sense environmental changes and modulate subsequent adaptive responses. Here, we describe the involvement of an orphan single-domain RR named EmvR in the virulence, extracellular polysaccharide (EPS) production and cell motilities of the bacterial leaf streak pathogen Xanthomonas oryzae pv. oryzicola (Xoc), which infects rice leaves mainly via stomata and wounds. Deletion of emvR in Xoc reduced virulence when using spraying inoculation but not when using infiltration inoculation. The emvR deletion mutant displayed weakened spreading and enhanced twitching. Additionally, although deletion of emvR did not significantly affect EPS production, overexpression of emvR significantly increased EPS production. Several standard assays revealed that EmvR physically interacts with PilB and represses its ATPase activity. Combining our data with previous findings that PilB provides the energy for type IV pilus (T4P) biogenesis, we conclude that EmvR plays a vital role in modulating Xoc T4P synthesis and in the early stage of Xoc infection through rice stomata. Moreover, our data reveal that EmvR can also interact with the HK of the TCS ColSXOCgx_4036/ColRXOCgx_4037, which positively and negatively affects Xoc spreading and twitching, respectively. We propose a 'one-to-two' TCS working model for the role of ColSXOCgx_4036, ColRXOCgx_4037, and EmvR in modulating Xoc motility.

Botanical-Based Strategies for Controlling Xanthomonas spp. in Cotton and Citrus: In Vitro and In Vivo Evaluation

Citrus canker, caused by Xanthomonas citri subsp. citri, and bacterial blight, caused by Xanthomonas citri subsp. malvacearum, results in substantial economic losses worldwide, and searching for new antibacterial agents is a critical challenge. In this study, regional isolates AE28 and RQ3 were obtained from characteristic lesions on Citrus limon and Gossypium hirsutum, respectively. Essential oils extracted by steam distillation from the fresh aerial parts of Pelargonium graveolens and Schinus molle exhibited complete (100%) inhibition of bacterial growth in vitro at a concentration of 1000 ppm, as determined by diffusion tests. To evaluate the potential of these essential oils for controlling Xanthomonas-induced diseases, in vivo assays were conducted on lemon leaves and cotton cotyledons inoculated with the regional AE28 and RQ3 strains. Two treatment approaches were tested: preventive application (24 h before inoculation) and curative application (24 h after inoculation). Preventive and curative treatments with P. graveolens essential oil significantly reduced citrus canker severity, whereas S. molle essential oil did not show a significant reduction compared to the control. In contrast, regardless of the treatment's timing, both essential oils effectively reduced bacterial blight severity in cotton cotyledons by approximately 1.5-fold. Gas chromatography-mass spectrometry (GC-MS) analysis identified geraniol and citronellol as the major components of P. graveolens essential oil, while limonene and t-cadinol were predominant in S. molle. These findings highlight the promising potential of botanical products as bactericidal agents, warranting further research to optimize their application and efficacy.

Entomopathogenic Bacteria Species and Toxins Targeting Aphids (Hemiptera: Aphididae): A Review

Aphids (Hemiptera: Aphididae) are cosmopolitan generalist pests of many agricultural crops. Their ability to reproduce rapidly through parthenogenesis allows them to quickly reach population sizes that are difficult to control. Their damage potential is further exacerbated when they act as vectors for plant pathogens, causing diseases in plants. Aphids are typically managed through the widespread use of insecticides, increasing the likelihood of short-term insecticide resistance. However, for the past few decades, entomopathogenic bacteria have been used as an alternative management strategy. Entomopathogenic bacteria have demonstrated their effectiveness for biologically suppressing insect pests, including aphids. In addition to identifying bacterial species that are pathogenic to aphids, research has been conducted on toxins such as Cry, Cyt, Vip, recombinant proteins, and other secondary metabolites with insecticidal activity. Most studies on aphids have been conducted in vitro, exposing them to an artificial diet contaminated with entomopathogenic bacteria or bacterial metabolites for periods ranging from 24 to 96 h. The discovery of new bacterial species with insecticidal potential, as well as the possibility of biotechnological applications through the genetic improvement of crops, will provide more alternatives for managing these agricultural pests in the future. This will also help address challenges related to field application.

Two TAL effectors of Xanthomonas citri promote pustule formation by directly repressing the expression of GRAS transcription factor in citrus

Citrus bacterial canker (CBC), caused by Xanthomonas citri subsp. citri (Xcc), poses a significant threat to the citrus industry. Xcc employs the transcription activator-like effector (TALE) PthA4 to target the major susceptibility (S) gene CsLOB1 in citrus, promoting host susceptibility to bacterial canker. However, the contribution of other Xcc TALEs, aside from PthA4, to virulence remains underexplored. In this study, we characterized two PthA1 variants, designated PthA5 and PthA6, which facilitate Xcc infection in susceptible citrus species by promoting the formation of hypertrophy and hyperplasia symptoms. Both PthA5 and PthA6 bind directly to effector-binding elements (EBEs) in the promoter of CsGRAS9, suppressing its expression. CsGRAS9 negatively regulates Xcc growth in citrus and contributes to CBC resistance. Notably, natural variations in the EBEs of the FhGRAS9 promoter, a homolog of CsGRAS9 in Hong Kong kumquat, prevent Xcc from affecting FhGRAS9 expression. Using the PTG/Cas9 system, we generated proCsGRAS9-edited sweet orange lines #18-2 and #23, which contain 86-bp and 62-bp deletions in the EBE regions of the CsGRAS9 promoter. These mutant lines showed enhanced CsGRAS9 expression and increased resistance to CBC during Xcc infection. Several GA-related genes and CsTAC1, regulated by CsGRAS9, were also identified. This is the first report that TALEs act as repressors of a resistance gene to confer host susceptibility.

Conserved immunomodulation and variation in host association by Xanthomonadales commensals in Arabidopsis root microbiota

Suppression of chronic Arabidopsis immune responses is a widespread but typically strain-specific trait across the major bacterial lineages of the plant microbiota. We show by phylogenetic analysis and in planta associations with representative strains that immunomodulation is a highly conserved, ancestral trait across Xanthomonadales, and preceded specialization of some of these bacteria as host-adapted pathogens. Rhodanobacter R179 activates immune responses, yet root transcriptomics suggest this commensal evades host immune perception upon prolonged association. R179 camouflage likely results from combined activities of two transporter complexes (dssAB) and the selective elimination of immunogenic peptides derived from all partners. The ability of R179 to mask itself and other commensals from the plant immune system is consistent with a convergence of distinct root transcriptomes triggered by immunosuppressive or non-suppressive synthetic microbiota upon R179 co-inoculation. Immunomodulation through dssAB provided R179 with a competitive advantage in synthetic communities in the root compartment. We propose that extensive immunomodulation by Xanthomonadales is related to their adaptation to terrestrial habitats and might have contributed to variation in strain-specific root association, which together accounts for their prominent role in plant microbiota establishment.

Xanthomonas bundabergensis sp. nov., Xanthomonas medicagonis sp. nov. and Xanthomonas tesorieronis sp. nov.: three members of group 1 Xanthomonas

Between 1976 and 2010, four bacterial isolates were collected in New South Wales and Queensland, Australia, and stored as part of routine biosecurity surveillance. Recently, these historic isolates were analysed as part of a larger project to enhance the taxonomic accuracy of our culture collection and improve Australia's biosecurity preparedness. Three isolates were collected from Fragaria × ananassa, initially identified as Xanthomonas sp., and one from Medicago sativa, identified as Xanthomonas axonopodis subsp. alfalfae. In this study, we employed modern phenotypic and genomic techniques to further characterize these isolates. Matrix-assisted laser desorption ionization-time of flight MS biotyping and Biolog GEN III MicroPlates confirmed that they are members of the Xanthomonas genus but did not allow for species-level classification. Genome-relatedness indices and phylogenetic analysis confirmed that they were Xanthomonas and revealed that they represent three novel species. The maximum average nucleotide identity and digital DNA-DNA hybridization values observed when comparing the four isolates to all Xanthomonas type strains and each other were 93.9% and 50.7%, respectively. Pathogenesis assays confirmed that two of the isolates are not pathogenic to Fragaria, the plant from which they were isolated. Based on these findings, we propose the names Xanthomonas bundabergensis sp. nov. (DAR 80977T=ICMP 24943), Xanthomonas medicagonis sp. nov. (DAR 35659T=ICMP 24942) and Xanthomonas tesorieronis sp. nov. (DAR 34887T=ICMP 24940).

Hydroxycinnamic Acids Activate RpfB-Dependent Quorum Sensing Signal Turnover in Phytopathogen Xanthomonas campestris

Phytopathogen Xanthomonas campestris pv campestris (Xcc) uses various mechanisms, including the quorum sensing (QS) system, to regulate infection and colonize cruciferous host plants. Hydroxycinnamic acids (HCAs) are widely distributed in the plant kingdom, but their effect on the diffusible signaling factor family QS signal of Xcc remains unknown. In this study, we report that HCAs activate RpfB-dependent QS signal turnover via the sensor protein HepR, which in turn activates the HepABCD resistance-nodulation-division efflux pump to remove HCAs in Xcc. Exogenous addition of three HCAs induced DSF signal turnover during the late growth phase of Xcc in XYS medium. Furthermore, HCAs-induced DSF turnover was dependent on the DSF-degrading enzyme RpfB and the sensor HepR. Additionally, Xcc pumps HCAs through the HepABCD efflux pump. An electrophoretic mobility shift assay demonstrated that HCAs interfere with the binding of HepR to the Phep promoter. This work provides insight into the molecular interactions between Xcc and cruciferous plants.

Recent Advances in Sugarcane Leaf Scald Disease: Pathogenic Insights and Sustainable Management Approaches

Sugarcane, a key cash crop in tropical and subtropical regions, is primarily cultivated for sucrose and bioethanol. However, Sugarcane Leaf Scald Disease, caused by the Gram-negative bacterium Xanthomonas albilineans, significantly threatens global sugarcane production. This review examines the disease cycle, epidemics, host-pathogen interactions, integrated management strategies, and future prospects for combating leaf scald. It highlights advancements in understanding pathogenicity, immune responses, and sustainable management of bacterial plant diseases to enhance control and prevention efforts. An analysis of GenBank data revealed 21 strains of X. albilineans, with some featuring complete genome maps and varying guanine-cytosine (GC) content. Advanced genomic tools, including clustered regularly interspaced short palindromic repeats (CRISPR), and molecular techniques, such as polymerase chain reaction (PCR), enable accurate pathogen detection and facilitate the identification of resistance genes, aiding breeding programs. Recent progress in whole-genome sequencing and reduced costs have enabled the assembly of multiple X. albilineans genomes, enhancing bioinformatics analysis. Despite these advancements, research on the global genetic diversity of X. albilineans remains limited. Addressing this gap is crucial for developing more sustainable strategies to manage leaf scald, ensuring stable sugarcane yields and supporting global production. Further studies will strengthen efforts to mitigate this significant agricultural challenge.

Subtractive genome mining in Xanthomonas citri pv. citri strain 306 for identifying novel drug target proteins coupled with in-depth protein-protein interaction and coevolution analysis - A leap towards prospective drug design

Citrus canker poses a serious threat to a highly significant citrus fruit crop, this disease caused by one of the most destructive bacterial plant pathogens Xanthomonas citri pv. citri (Xcc). Bacterial plant diseases significantly reduce crop yields worldwide, making it more difficult to supply the growing food demand. The high levels of antibiotic resistance in Xcc strains are diminishing the efficacy of current control measures, necessitating the exploration of novel therapeutic targets to address the escalating antimicrobial resistance trend. Genome subtraction approach along with protein-protein network and coevolution analysis were used to identify potential drug targets in Xcc stain 306. The study involved retrieving the Xcc proteome from the UniProt database, eliminating paralogous proteins using CD-HIT (80 % identity cutoff), and selecting nonhomologous proteins through BLASTp (e-value <0.005). Essential proteins were identified using BLAST against the DEG (e-value cutoff 0.00001). 750 essential proteins were identified that are nonhomologous to citrus plant. Subsequent analyses included metabolic pathway assessment, subcellular localization prediction, and druggability analysis. Protein network analysis, coevolution analysis, protein active site identification was also performed. In conclusion, this study identified eight potential drug targets (GlmU, CheA, RmlD, GspE, FleQ, RpoN, Shk, SecB), highlighting RpoN, FleQ, and SecB as unprecedented targets for Xcc. These findings may contribute to the development of novel antimicrobial agents in the future that can efficiently control citrus canker disease.

Functional characterization, transcriptome and metabolome analyses reveal that pacR possesses multifaceted physiological roles in Xanthomonas campestris pathovar campestris

Xanthomonas campestris pathovar campestris (Xcc) is the pathogen responsible for causing black rot in cruciferous plants. In this study, we show that mutation of AAW18_RS04175 (pacR, encodes a hypothetical protein containing a domain of unknown function, DUF1631) of Xcc strain Xc17 had decreased bacterial attachment, exopolysaccharide production, hypersensitive response and virulence. Furthermore, the pacR mutant exhibited reduced cell membrane integrity and outer membrane vesicle production. Transcriptomic analysis indicated that 225 genes were differentially expressed following pacR mutation. These genes can be classified into various functional categories, such as the type three secretion system and membrane component. Among them, genes associated with attachment, exopolysaccharide synthesis, the type three secretion system, and nucleotide metabolism were further verified by quantitative RT-PCR. Metabolomic analysis showed that 81 and 132 metabolites in positive and negative modes, respectively, were altered after pacR mutation. Among the identified metabolites, some are known to belong to different pathways, such as biosynthesis of secondary metabolites, microbial metabolism in diverse environments, and nucleotide and purine metabolism, while others have not been previously documented in microbial systems. Additionally, the transcription initiation point of pacR was mapped, and promoter analysis indicated that pacR expression is influenced by different conditions. Taken together, our findings advance the understanding of PacR function and expression in Xcc and offer new insights into the role of the DUF1631-containing hypothetical protein in bacterial physiology.

Synthetic peptides bioactive against phytopathogens have lower impact on some beneficial bacteria: An assessment of peptides biosafety in agriculture

The emergence of bacterial resistance and the increasing restrictions on the use of agrochemicals are boosting the search for novel, sustainable antibiotics. Antimicrobial peptides (AMPs) arise as a new generation of antibiotics due to their effectiveness at low doses and biocompatibility. We compared the antimicrobial activity of four promising AMPs (CA-M, BP100, RW-BP100, and 3.1) against a collection of notorious phytopathogens, and quantified their impact on plant beneficial bacteria. Plant growth promoters (PGP) and biological control agents (BCA) were also included to study the feasibility of integrating AMPs with bio-based strategies to mitigate diseases impacts and promote crop production. Flow cytometry and fluorescence microscopy revealed that the AMPs' effects on the membrane integrity of both gram-negative and gram-positive strains were time- and concentration-dependent. Bacterial strains were separated into three groups of susceptibility to the AMPs. Group 1 was represented by the most sensitive, gram-negative phytopathogenic belonging to Xanthomonadales and Pseudomonadales and the gram-positive C. michiganensis subsp. michiganensis. Group 2 encompassed bacteria showing intermediate susceptibility, namely P. carotovorum subsp. carotovorum, P. cerasi, both phytopathogens, as well as the plant growth promoters P. fluorescens and P. putida. Finaly, Group 3 was represented by the bacteria with the lowest susceptibility to AMPs. It included beneficial bacteria (B. zhangzhouensis, B. subtilis, B. safensis, P. azotoformans), a phytopathogen (R. solanacearum), and a strain reported as able to act as both (P. aeruginosa). This work demonstrates that the minimum inhibitory concentrations (MICs) needed to act against the beneficial Bacillus and Pseudomonas strains were higher than those needed to produce bacteriostatic or bactericidal effects on the phytopathogens tested, hence supporting that these AMPs might be environmentally safe antibiotics with low likeliness of disrupting the beneficial microbial communities. The possibility of mixing these AMPs with BCA/PGP, in a combined biocontrol strategy, is also discussed.

Activation of three targets by a TAL effector confers susceptibility to bacterial blight of cotton

Bacterial transcription activator-like effectors (TALEs) promote pathogenicity by activating host susceptibility (S) genes. To understand the pathogenicity and host adaptation of Xanthomonas citri pv. malvacearum (Xcm), we assemble the genome and the TALE repertoire of three recent Xcm Texas isolates. A newly evolved TALE, Tal7b, activates GhSWEET14a and GhSWEET14b, different from GhSWEET10 targeted by a TALE in an early Xcm isolate. Activation of GhSWEET14a and GhSWEET14b results in water-soaked lesions. Transcriptome profiling coupled with TALE-binding element prediction identify a pectin lyase gene as an additional Tal7b target, quantitatively contributing to Xcm virulence alongside GhSWEET14a/b. CRISPR-Cas9 gene editing supports the function of GhSWEETs in cotton bacterial blight and the promise of disrupting the TALE-binding site in S genes for disease management. Collectively, our findings elucidate the rapid evolution of TALEs in Xanthomonas field isolates and highlight the virulence mechanism wherein TALEs induce multiple S genes to promote pathogenicity.

Microbial inheritance through seed: a clouded area needs to be enlightened

Seed endophytes are actively used by the mother plant as both reservoir and vector of beneficial microbes. During seed dormancy endophytes experience significant physiochemical changes and only competent endophytes could colonise successfully in seeds and some of them act as obligate endophyte that are transmitted vertically across generations. The adaptive nature of endophytes allows them to switch lifestyles depending on environment and host conditions. In this review, instead of providing broad discussion on applicability of endophytes in plant growth improvement, the fundamental nature of endophytes, their survival strategies under stress conditions, transmittance, etc. have been broadly highlighted by collaborating recent discoveries and theories. We have also tried to differentiate endophyte with their pathogenic counterpart and their survival mechanism during seed dormancy stages. Critical analyses of physio-biochemical changes in seeds during maturation and parallel modifications of life styles of seed endophytes along with pathogens will enlighten the shaded part of seed-microbiome interactions. The mutualistic interrelations as well as their shipment towards pathogenic behaviour under stress are being discussed acutely. Finally, importances of conservation of seed microbiome to maintain seed quality and vigour have been pointed out. Throughout the manuscript, the knowledge gap on seed-microbiota have been mentioned, thus, in future, studies on these areas could help us to understand properly the actual role of endophytes for the betterment of maintaining seed quality and vigour.

Inhibition of Xanthomonas growth by bioactive volatiles from Pseudomonas sp. triggers remarkable changes in the phytopathogen transcriptome

Volatile organic compounds (VOCs) produced by microorganisms may have a noteworthy role in the control of plant pathogens. Xanthomonas are a well-studied group of phytobacteria that cause diverse diseases in economically important crops worldwide. Key species that infect sugarcane are X. albilineans (Xab) and X. axonopodis pv. vasculorum (Xav). Here, we investigated VOC-producing bacteria with antagonistic effects against Xab and Xav. We demonstrated that VOCs produced by Pseudomonas sp. V5-S-D11 was able to abolish the growth of these pathogens. A set of 32 VOCs was identified in the volatilome of V5-S-D11, with 10 showing a concentration-dependent inhibitory effect on both phytobacteria. Among them, dimethyl disulfide (DMDS), a volatile sulfur compound, has the potential to be biotechnologically explored in agriculture since it can improve plant growth and induce systemic resistance against plant pathogens. Interestingly, transcriptomic analysis of Xab treated with DMDS revealed several up-regulated metabolic pathways such as a two-component system, flagellar assembly, chemotaxis, and a bacterial secretion system. Although the ethanol (ETOH) used as DMDS solvent did not inhibit Xab growth, it triggered a similar up-regulation of some genes, indicating that this phytopathogen can deal with ETOH better than DMDS. Overall, this study explores the wide role of VOCs in the interactions with bacteria. Moreover, our results indicate that VOCs from Pseudomonas sp. may represent a novel biotechnological strategy to counteract diseases caused by Xanthomonas species and can be further exploited for sustainable approaches in agriculture.

The receptor MIK2 interacts with the kinase RKS1 to control quantitative disease resistance to Xanthomonas campestris

Molecular mechanisms underlying qualitative resistance have been intensively studied. In contrast, although quantitative disease resistance (QDR) is a common, durable, and broad-spectrum form of immune responses in plants, only a few related functional analyses have been reported. The atypical kinase Resistance related kinase 1 (RKS1) is a major regulator of QDR to the bacterial pathogen Xanthomonas campestris (Xcc) and is positioned in a robust protein-protein decentralized network in Arabidopsis (Arabidopsis thaliana). Among the putative interactors of RKS1 found by yeast two-hybrid screening, we identified the receptor-like kinase MDIS1-interacting receptor-like kinase 2 (MIK2). Here, using multiple complementary strategies including protein-protein interaction tests, mutant analysis, and network reconstruction, we report that MIK2 is a component of RKS1-mediated QDR to Xcc. First, by co-localization experiments, co-immunoprecipitation (Co-IP), and bimolecular fluorescence complementation, we validated the physical interaction between RKS1 and MIK2 at the plasma membrane. Using mik2 mutants, we showed that MIK2 is required for QDR and contributes to resistance to the same level as RKS1. Interestingly, a catalytic mutant of MIK2 interacted with RKS1 but was unable to fully complement the mik2-1 mutant phenotype in response to Xcc. Finally, we investigated the potential role of the MIK2-RKS1 complex as a scaffolding component for the coordination of perception events by constructing a RKS1-MIK2 centered protein-protein interaction network. Eight mutants corresponding to seven RKs in this network showed a strong alteration in QDR to Xcc. Our findings provide insights into the molecular mechanisms underlying the perception events involved in QDR to Xcc.

Pathogenomic Insights into Xanthomonas oryzae pv. oryzae's Resistome, Virulome, and Diversity for Improved Rice Blight Management

Oryza sativa (rice) is a major staple food targeted for increased production to achieve food security. However, increased production is threatened by several biotic and abiotic factors, of which bacterial blight disease caused by Xanthomonas oryzae pathovar oryzae is severe. Developing effective control strategies requires an up-to-date understanding of its pathogenomics. This study analyzes the genomes of 30 X. oryzae strains collected from rice-producing regions across five continents to identify genetic elements critical for its pathogenicity and adaptability and for an intraspecific diversity assessment using advanced genomics and bioinformatics tools. Resistome analysis revealed 28 distinct types of antibiotic resistance genes (ARGs), both innate and acquired, indicating a growing threat from multidrug-resistant X. oryzae strains. Sixteen virulent genes, including type III and VI secretion systems, motility genes, and effector proteins, were identified. A unique 'MexCD-OprJ' multidrug efflux system was detected in the Tanzanian strains, conferring resistance to multiple antibiotic classes. To curb further ARG emergence, there is a need to regulate the use of antibiotics for X. oryzae control and adopt resistant rice varieties. Transposable elements were also discovered to contribute to X. oryzae pathogenicity, facilitating the horizontal transfer of virulence genes. Pangenome analysis revealed intraspecific variation among the population, with 112 unique CDS having diverse functional roles. Strains registered in the Philippines had the most unique genes. Phylogenetic analysis confirmed the divergent evolution of X. oryzae. This study's results will aid in identifying more effective management strategies and biocontrol alternatives for sustainable rice production.

Antimicrobial resistance in plant endophytes associated with poultry-manure application revealed by selective culture and whole genome sequencing

Poultry manure is widely used as organic fertilizer in agriculture during the cultivation of crops, but the persistent high-level use of antibiotics in poultry production has raised concerns about the selection for reservoirs of antimicrobial resistance genes (ARGs). Previous studies have shown that the addition of poultry manure can increase the abundance of genes associated with resistance to tetracyclines, aminoglycosides, fluoroquinolones, sulfonamides, bacitracin, chloramphenicol, and macrolide-lincosamide-streptogramin in soil and plants. Understanding the microbial populations that harbor these ARGs is important to identify microorganisms that could enter the human food chain. Here, we test the hypothesis that environmental exposure to poultry manure increases the occurrence of antimicrobial resistance (AMR) in plant endophytes using selective culture, phenotypic Antibiotic Susceptibility Testing (AST), phylogenetic analysis, and whole genome sequencing (WGS). Endophytes from poultry manure treated Sorghum bicolor (L.) Moench plant root and stem samples showed increased phenotypic and genotypic resistance against multiple antibiotics compared to untreated controls. Comparison of AMR phenotype-to-genotype relationships highlighted the detection of multi-drug resistant (MDR) plant endophytes, demonstrating the value of genomic surveillance for emerging drug-resistant pathogens. The increased occurrence of ARGs in poultry manure-exposed endophytes highlights the need for responsible antibiotic use in poultry and animal farming to reduce contamination of ecological niches and transgression into endophytic plant microbiome compartments. It also emphasizes the requirement for proper manure management practices and vigilance in monitoring and surveillance efforts to tackle the growing problem of antibiotic resistance and preserve the efficacy of antibiotics for human and veterinary medicine.

Effect of Plasma-Activated Water (PAW) Generated Using Non-Thermal Atmospheric Plasma on Phytopathogenic Bacteria

Plasma-activated water (PAW) exhibits potent antimicrobial properties attributed to the generation of diverse reactive oxygen and nitrogen species. This study assessed the effectiveness of PAW in vitro against phytopathogenic Xanthomonas arboricola and Pseudomonas syringae pv. syringae, which cause diseases on ornamental plants. Extending the plasma activation time of water and the incubation time of bacterial suspension in PAW increased the effectiveness of PAW. Treatments consisting of PAW activation using a power output of 200 W and a frequency of 50 Hz at different activation times and target population incubation times revealed significantly different effectiveness against P. syringae pv. syringae and X. arboricola. X. arboricola (reduction of 4.946 ± 0.20 log10 CFU/ml) was more sensitive to PAW inactivation than P. syringae pv. syringae (reduction of 3 ± 0.15 log10 CFU/ml). The plasma activation of water for 20 min followed by incubation of bacterial population for 180 min was proven to be the most effective treatment combination. The plasma activation time dose required to reduce the population by 90% was 7.47 ± 1.09 min for P. syringae pv. syringae and 4.45 ± 1.81 min for X. arboricola incubated for 180 min in PAW. The results of this study have the potential to further contribute to assessment of the effects of PAW on pathogen-infected plant tissues. In addition, the findings of this study could aid in further characterization of the reactive species formed during the plasma activation of water.

Genome sequence data for 61 isolates of Xanthomonas campestris pv. campestris from Brassica crops in Serbia

This Technical Resource describes genome sequencing data for 61 isolates of the bacterial pathogen Xanthomonas campestris pv. campestris collected from Brassica and Raphanus crops between 2010 and 2021 in Serbia. We present the raw sequencing reads and annotated contig-level genome assemblies and determine the races of ten isolates. The data can be used to test hypotheses and phylogeographic analyses and inform the design of informative molecular markers for population genetics studies. When combined with phenotypic data, they could be used to dissect relationships between genotypes and phenotypes such as host range and virulence. Finally, these genome sequences expand our inventory of plasmids known to reside in this pathogen.

Friends and Foes: Bacteria of the Hydroponic Plant Microbiome

Hydroponic greenhouses and vertical farms provide an alternative crop production strategy in regions that experience low temperatures, suboptimal sunlight, or inadequate soil quality. However, hydroponic systems are soilless and, therefore, have vastly different bacterial microbiota than plants grown in soil. This review highlights some of the most prevalent plant growth-promoting bacteria (PGPB) and destructive phytopathogenic bacteria that dominate hydroponic systems. A complete understanding of which bacteria increase hydroponic crop yields and ways to mitigate crop loss from disease are critical to advancing microbiome research. The section focussing on plant growth-promoting bacteria highlights putative biological pathways for growth promotion and evidence of increased crop productivity in hydroponic systems by these organisms. Seven genera are examined in detail, including Pseudomonas, Bacillus, Azospirillum, Azotobacter, Rhizobium, Paenibacillus, and Paraburkholderia. In contrast, the review of hydroponic phytopathogens explores the mechanisms of disease, studies of disease incidence in greenhouse crops, and disease control strategies. Economically relevant diseases caused by Xanthomonas, Erwinia, Agrobacterium, Ralstonia, Clavibacter, Pectobacterium, and Pseudomonas are discussed. The conditions that make Pseudomonas both a friend and a foe, depending on the species, environment, and gene expression, provide insights into the complexity of plant-bacterial interactions. By amalgamating information on both beneficial and pathogenic bacteria in hydroponics, researchers and greenhouse growers can be better informed on how bacteria impact modern crop production systems.

Host-Driven Selection, Revealed by Comparative Analysis of Xanthomonas Type III Secretion Effectoromes, Unveils Novel Recognized Effectors

Xanthomonas species are specialized plant pathogens, often exhibiting a narrow host range. They rely on the translocation of effector proteins through the type III secretion system to colonize their respective hosts. The effector arsenal varies among Xanthomonas spp., typically displaying species-specific compositions. This species-specific effector composition, collectively termed the effectorome, is thought to influence host specialization. We determined the plant host-derived effectoromes of more than 300 deposited genomes of Xanthomonas species associated with either Solanaceae or Brassicaceae hosts. Comparative analyses revealed clear species-specific effectorome signatures. However, Solanaceae or Brassicaceae host-associated effectorome signatures were not detected. Nevertheless, host biases in the presence or absence of specific effector classes were observed. To assess whether host-associated effector absence results from selective pressures, we introduced effectors unique to Solanaceae pathogens to X. campestris pv. campestris and effectors unique to Brassicaceae pathogens to X. euvesicatoria pv. euvesicatoria (Xeue) and evaluated if these introductions hindered virulence on their respective hosts. Introducing the effector XopI into X. campestris pv. campestris reduced virulence on white cabbage leaves without affecting localized or systemic colonization. Introducing the XopAC or XopJ5 effectors into Xeue reduced virulence and colonization on tomato but not on pepper. Additionally, XopAC and XopJ5 induced a hypersensitive response on tomato leaves when delivered by Xeue or through Agrobacterium-mediated transient expression, confirming recognition in tomato. This study demonstrates the role of host-derived selection in establishing species-specific effectoromes, identifying XopAC and XopJ5 as recognized effectors in tomato.

Biologically inspired nanoformulations for the control of bacterial canker pathogens Clavibacter michiganensis subsp. michiganensis and subsp. capsici

Clavibacter michiganensis subsp. michiganensis (Cmm) and C. michiganensis subsp. capsici (Cmc) are phytopathogenic bacteria that cause bacterial canker disease in tomatoes and peppers, respectively. Bacterial canker disease poses serious challenges to solanaceous crops, causing significant yield losses and economic costs. Effective management necessitates the development of sustainable control strategies employing nanobiotechnology. In this study, the antibacterial effects of four Aspergillus sojae-mediated nanoformulations, including cobalt oxide nanoparticles (Co3O4 NPs), zinc oxide nanoparticles (ZnO NPs), cobalt ferrite nanoparticles (CoFe2O4 NPs), and CoFe2O4/functionalized multi-walled carbon nanotube (fMWCNT) bionanocomposite, were evaluated against Cmm and Cmc. The diameters of the zone of inhibition of A. sojae-mediated Co3O4 NPs, ZnO NPs, CoFe2O4 NPs, and CoFe2O4/fMWCNT bionanocomposite against Cmm and Cmc were 23.60 mm, 22.09 mm, 27.65 mm, 22.51 mm, and 19.33 mm, 17.66 mm, 21.64 mm, 18.77 mm, respectively. The broth microdilution assay was conducted to determine the minimal inhibitory and bactericidal concentrations. The MICs of Co3O4 NPs, ZnO NPs, CoFe2O4 NPs, and CoFe2O4/fMWCNT bionanocomposite against Cmm were 2.50 mg/mL, 1.25 mg/mL, 2.50 mg/mL, and 2.50 mg/mL, respectively. While, their respective MBCs against Cmm were 5.00 mg/mL, 2.50 mg/mL, 5.00 mg/mL, and 5.00 mg/mL. The respective MICs of Co3O4 NPs, ZnO NPs, CoFe2O4 NPs, and CoFe2O4/fMWCNT bionanocomposite against Cmc were 2.50 mg/mL, 1.25 mg/mL, 5.00 mg/mL, and 5.00 mg/mL. While, their respective MBCs against Cmc were 5.00 mg/mL, 2.50 mg/mL, 10.00 mg/mL, and 10.00 mg/mL. The morphological and ultrastructural changes of Cmm and Cmc cells were observed using field-emission scanning and transmission electron microscopy before and after treatment with sub-minimal inhibitory concentrations of the nanoformulations. Nanoformulation-treated bacterial cells became deformed and disrupted, displaying pits, deep cavities, and groove-like structures. The cell membrane detached from the bacterial cell wall, electron-dense particles accumulated in the cytoplasm, cellular components disintegrated, and the cells were lysed. Direct physical interactions between the prepared nanoformulations with Cmm and Cmc cells might be the major mechanism for their antibacterial potency. Further research is required for the in vivo application of the mycosynthesized nanoformulations as countermeasures to combat bacterial phytopathogens.

Life on a leaf: the epiphyte to pathogen continuum and interplay in the phyllosphere

Epiphytic microbes are those that live for some or all of their life cycle on the surface of plant leaves. Leaf surfaces are a topologically complex, physicochemically heterogeneous habitat that is home to extensive, mixed communities of resident and transient inhabitants from all three domains of life. In this review, we discuss the origins of leaf surface microbes and how different biotic and abiotic factors shape their communities. We discuss the leaf surface as a habitat and microbial adaptations which allow some species to thrive there, with particular emphasis on microbes that occupy the continuum between epiphytic specialists and phytopathogens, groups which have considerable overlap in terms of adapting to the leaf surface and between which a single virulence determinant can move a microbial strain. Finally, we discuss the recent findings that the wheat pathogenic fungus Zymoseptoria tritici spends a considerable amount of time on the leaf surface, and ask what insights other epiphytic organisms might provide into this pathogen, as well as how Z. tritici might serve as a model system for investigating plant-microbe-microbe interactions on the leaf surface.

Antisense Oligonucleotide as a New Technology Application for CsLOB1 Gene Silencing Aiming at Citrus Canker Resistance

Citrus canker disease, caused by Xanthomonas citri subsp. citri, poses a significant threat to global citrus production. The control of the disease in the field relies mainly on the use of conventional tools such as copper compounds, which are harmful to the environment and could lead to bacterial resistance. This scenario stresses the need for new and sustainable technologies to control phytopathogens, representing a key challenge in developing studies that translate basic into applied knowledge. During infection, X. citri subsp. citri secretes a transcriptional activator-like effector that enters the nucleus of plant cells, activating the expression of the canker susceptibility gene LATERAL ORGAN BOUNDARIES 1 (LOB1). In this study, we explored the use of antisense oligonucleotides (ASOs) with phosphorothioate modifications to transiently inhibit the gene expression of CsLOB1 in Citrus sinensis. We designed and validated three potential ASO sequences, which led to a significant reduction in disease symptoms compared with the control. The selected ASO3-CsLOB1 significantly decreased the expression level of CsLOB1 when delivered through two distinct delivery methods, and the reduction of the symptoms ranged from approximately 15 to 83%. Notably, plants treated with ASO3 did not exhibit an increase in symptom development over the evaluation period. This study highlights the efficacy of ASO technology, based on short oligonucleotide chemically modified sequences, as a promising tool for controlling phytopathogens without the need for genetic transformation or plant regeneration. Our results demonstrate the potential of ASOs as a biotechnological tool for the management of citrus canker disease.

Exploring the Global Trends of Bacillus, Trichoderma and Entomopathogenic Fungi for Pathogen and Pest Control in Chili Cultivation

Chili, renowned globally and deeply ingrained in various cultures. Regrettably, the onset of diseases instigated by pests and pathogens has inflicted substantial losses on chili crops, with some farms experiencing complete production decimation. Challenges confronting chili cultivation include threats from pathogenic microbes like Xanthomonas, Fusarium, Phytophthora, Verticillium, Rhizoctonia, Colletotrichium and Viruses, alongside pests such as whiteflies, mites, thrips, aphids, and fruit flies. While conventional farming practices often resort to chemical pesticides to combat these challenges, their utilization poses substantial risks to both human health and the environment. In response to this pressing issue, this review aims to evaluate the potential of microbe-based biological control as eco-friendly alternatives to chemical pesticides for chili cultivation. Biocontrol agents such as Bacillus spp., Trichoderma spp., and entomopathogenic fungi present safer and more environmentally sustainable alternatives to chemical pesticides. However, despite the recognised potential of biocontrol agents, research on their efficacy in controlling the array of pests and pathogens affecting chili farming remains limited. This review addresses this gap by evaluating the efficiency of biocontrol agents, drawing insights from existing studies conducted in other crop systems, regarding pest and pathogen management. Notably, an analysis of Scopus publications revealed fewer than 30 publications in 2023 focused on these three microbial agents. Intriguingly, India, as the world's largest chili producer, leads in the number of publications concerning Bacillus spp., Trichoderma spp., and entomopathogenic fungi in chili cultivation. Further research on microbial agents is imperative to mitigate infections and reduce reliance on chemical pesticides for sustainable chili production.

CRISPR/Cas9-generated mutations in a sugar transporter gene reduce cassava susceptibility to bacterial blight

Bacteria from the genus Xanthomonas are prolific phytopathogens that elicit disease in over 400 plant species. Xanthomonads carry a repertoire of specialized proteins called transcription activator-like (TAL) effectors that promote disease and pathogen virulence by inducing the expression of host susceptibility (S) genes. Xanthomonas phaseoli pv. manihotis (Xpm) causes bacterial blight on the staple food crop cassava (Manihot esculenta Crantz). The Xpm effector TAL20 induces ectopic expression of the S gene Manihot esculenta Sugars Will Eventually be Exported Transporter 10a (MeSWEET10a), which encodes a sugar transporter that contributes to cassava bacterial blight (CBB) susceptibility. We used CRISPR/Cas9 to generate multiple cassava lines with edits to the MeSWEET10a TAL20 effector binding site and/or coding sequence. In several of the regenerated lines, MeSWEET10a expression was no longer induced by Xpm, and in these cases, we observed reduced CBB disease symptoms post Xpm infection. Because MeSWEET10a is expressed in cassava flowers, we further characterized the reproductive capability of the MeSWEET10a promoter and coding sequence mutants. Lines were crossed to themselves and to wild-type plants. The results indicated that expression of MeSWEET10a in female, but not male, flowers is critical to produce viable F1 seed. In the case of promoter mutations that left the coding sequence intact, viable F1 progeny were recovered. Taken together, these results demonstrate that blocking MeSWEET10a induction is a viable strategy for decreasing cassava susceptibility to CBB and that ideal lines will contain promoter mutations that block TAL effector binding while leaving endogenous expression of MeSWEET10a unaltered.

Isolation and Characterization of Two Novel Genera of Jumbo Bacteriophages Infecting Xanthomonas vesicatoria Isolated from Agricultural Regions in Mexico

Bacterial spot is a serious disease caused by several species of Xanthomonas affecting pepper and tomato production worldwide. Since the strategies employed for disease management have been inefficient and pose a threat for environmental and human health, the development of alternative methods is gaining relevance. The aim of this study is to isolate and characterize lytic phages against Xanthomonas pathogens. Here, we isolate two jumbo phages, named XaC1 and XbC2, from water obtained from agricultural irrigation channels by the enrichment technique using X. vesicatoria as a host. We determined that both phages were specific for inducing the lysis of X. vesicatoria strains, but not of other xanthomonads. The XaC1 and XbC2 phages showed a myovirus morphology and were classified as jumbo phages due to their genomes being larger than 200 kb. Phylogenetic and comparative analysis suggests that XaC1 and XbC2 represent both different and novel genera of phages, where XaC1 possesses a low similarity to other phage genomes reported before. Finally, XaC1 and XbC2 exhibited thermal stability up to 45 °C and pH stability from 5 to 9. All these results indicate that the isolated phages are promising candidates for the development of formulations against bacterial spot, although further characterization is required.

A cyclic di-GMP-binding adaptor protein interacts with a N5-glutamine methyltransferase to regulate the pathogenesis in Xanthomonas citri subsp. citri

The second messenger cyclic diguanylate monophosphate (c-di-GMP) regulates a wide range of bacterial behaviours through diverse mechanisms and binding receptors. Single-domain PilZ proteins, the most widespread and abundant known c-di-GMP receptors in bacteria, act as trans-acting adaptor proteins that enable c-di-GMP to control signalling pathways with high specificity. This study identifies a single-domain PilZ protein, XAC3402 (renamed N5MapZ), from the phytopathogen Xanthomonas citri subsp. citri (Xcc), which modulates Xcc virulence by directly interacting with the methyltransferase HemK. Through yeast two-hybrid, co-immunoprecipitation and immunofluorescent staining, we demonstrated that N5MapZ and HemK interact directly under both in vitro and in vivo conditions, with the strength of the protein-protein interaction decreasing at high c-di-GMP concentrations. This finding distinguishes N5MapZ from other characterized single-domain PilZ proteins, as it was previously known that c-di-GMP enhances the interaction between those single-domain PilZs and their protein partners. This observation is further supported by the fact that the c-di-GMP binding-defective mutant N5MapZR10A can interact with HemK to inhibit the methylation of the class 1 translation termination release factor PrfA. Additionally, we found that HemK plays an important role in Xcc pathogenesis, as the deletion of hemK leads to extensive phenotypic changes, including reduced virulence in citrus plants, decreased motility, production of extracellular enzymes and stress tolerance. Gene expression analysis has revealed that c-di-GMP and the HemK-mediated pathway regulate the expression of multiple virulence effector proteins, uncovering a novel regulatory mechanism through which c-di-GMP regulates Xcc virulence by mediating PrfA methylation via the single-domain PilZ adaptor protein N5MapZ.

A Multilocus Sequence Typing Scheme for Rapid Identification of Xanthomonas citri Based on Whole-Genome Sequencing Data

Xanthomonas citri is a plant-pathogenic bacterium associated with a diverse range of host plant species. It has undergone substantial reclassification and currently consists of 14 different subspecies or pathovars that are responsible for a wide range of plant diseases. Whole-genome sequencing (WGS) provides a cutting-edge advantage over other diagnostic techniques in epidemiological and evolutionary studies of X. citri because it has a higher discriminatory power and is replicable across laboratories. WGS also allows for the improvement of multilocus sequence typing (MLST) schemes. In this study, we used genome sequences of Xanthomonas isolates from the NCBI RefSeq database to develop a seven-gene MLST scheme that yielded 19 sequence types (STs) that correlated with phylogenetic clades of X. citri subspecies or pathovars. Using this MLST scheme, we examined 2,911 Xanthomonas species assemblies from NCBI GenBank and identified 15 novel STs from 37 isolates that were misclassified in NCBI. In total, we identified 545 X. citri assemblies from GenBank with 95% average nucleotide identity to the X. citri type strain, and all were classified as one of the 34 STs. All MLST classifications correlated with a phylogenetic position inferred from alignments using 92 conserved genes. We observed several instances where strains from different pathovars formed closely related monophyletic clades and shared the same ST, indicating that further investigation of the validity of these pathovars is required. Our MLST scheme described here is a robust tool for rapid classification of X. citri pathovars using WGS and a powerful method for further comprehensive taxonomic revision of X. citri pathovars.

Xanthomonas as a Model System for Studying Pathogen Emergence and Evolution

In this review, we highlight studies in which whole-genome sequencing, comparative genomics, and population genomics have provided unprecedented insights into past and ongoing pathogen evolution. These include new understandings of the adaptive evolution of secretion systems and their effectors. We focus on Xanthomonas pathosystems that have seen intensive study and improved our understanding of pathogen emergence and evolution, particularly in the context of host specialization: citrus canker, bacterial blight of rice, and bacterial spot of tomato and pepper. Across pathosystems, pathogens appear to follow a pattern of bursts of evolution and diversification that impact host adaptation. There remains a need for studies on the mechanisms of host range evolution and genetic exchange among closely related but differentially host-specialized species and to start moving beyond the study of specific strain and host cultivar pairwise interactions to thinking about these pathosystems in a community context.

Synthesis, Structural Characterization, and Biological Activities of 1,3,4- Thiadiazole Derivatives Containing Sulfonylpiperazine Structures

To develop novel bacterial biofilm inhibiting agents, a series of 1,3,4-thiadiazole derivatives containing sulfonylpiperazine structures were designed, synthesized, and characterized using 1H nuclear magnetic resonance (1H NMR), 13C nuclear magnetic resonance (13C NMR), and high-resolution mass spectrometry. Meanwhile, their biological activities were evaluated, and the ensuing structure-activity relationships were discussed. The bioassay results showed the substantial antimicrobial efficacy exhibited by most of the compounds. Among them, compound A24 demonstrated a strong efficacy with an EC50 value of 7.8 μg/mL in vitro against the Xanthomonas oryzae pv. oryzicola (Xoc) pathogen, surpassing commercial agents thiodiazole copper (31.8 μg/mL) and bismerthiazol (43.3 μg/mL). Mechanistic investigations into its anti-Xoc properties revealed that compound A24 operates by increasing the permeability of bacterial cell membranes, inhibiting biofilm formation and cell motility, and inducing morphological changes in bacterial cells. Importantly, in vivo tests showed its excellent protective and curative effects on rice bacterial leaf streak. Besides, molecular docking showed that the hydrophobic effect and hydrogen-bond interactions are key factors between the binding of A24 and AvrRxo1-ORF1. Therefore, these results suggest the utilization of 1,3,4-thiadiazole derivatives containing sulfonylpiperazine structures as a bacterial biofilm inhibiting agent, warranting further exploration in the realm of agrochemical development.

Bacillus Strains as Effective Biocontrol Agents Against Phytopathogenic Bacteria and Promoters of Plant Growth

Modern crop production relies on the application of chemical pesticides and fertilizers causing environmental and economic challenges. In response, less environmentally impactful alternatives have emerged such as the use of beneficial microorganisms. These microorganisms, particularly plant growth-promoting bacteria (PGPB), have demonstrated their ability to enhance plant growth, protect against various stresses, and reduce the need for chemical inputs. Among the PGPB, Bacillus species have garnered attention due to their adaptability and commercial potential. Recent reports have highlighted Bacillus strains as biocontrol agents against phytopathogenic bacteria while concurrently promoting plant growth. We also examined Bacillus plant growth-promoting abilities in Arabidopsis thaliana seedlings. In this study, we assessed the potential of various Bacillus strains to control diverse phytopathogenic bacteria and inhibit quorum sensing using Chromobacterium violaceum as a model system. In conclusion, our results suggest that bacteria of the genus Bacillus hold significant potential for biotechnological applications. This includes developments aimed at reducing agrochemical use, promoting sustainable agriculture, and enhancing crop yield and protection.

Antibiotic Resistance in Plant Pathogenic Bacteria: Recent Data and Environmental Impact of Unchecked Use and the Potential of Biocontrol Agents as an Eco-Friendly Alternative

The economic impact of phytopathogenic bacteria on agriculture is staggering, costing billions of US dollars globally. Pseudomonas syringae is the top most phytopathogenic bacteria, having more than 60 pathovars, which cause bacteria speck in tomatoes, halo blight in beans, and so on. Although antibiotics or a combination of antibiotics are used to manage infectious diseases in plants, they are employed far less in agriculture compared to human and animal populations. Moreover, the majority of antibiotics used in plants are immediately washed away, leading to environmental damage to ecosystems and food chains. Due to the serious risk of antibiotic resistance (AR) and the potential for environmental contamination with antibiotic residues and resistance genes, the use of unchecked antibiotics against phytopathogenic bacteria is not advisable. Despite the significant concern regarding AR in the world today, there are inadequate and outdated data on the AR of phytopathogenic bacteria. This review presents recent AR data on plant pathogenic bacteria (PPB), along with their environmental impact. In light of these findings, we suggest the use of biocontrol agents as a sustainable, eco-friendly, and effective alternative to controlling phytopathogenic bacteria.

The Global Transcription Regulator XooClp Governs Type IV Pili System-Mediated Bacterial Virulence by Directly Binding to TFP-Chp Promoters to Coordinate Virulence Associated Functions

Type IV pili (TFP) play a crucial role in the sensing of the external environment for several bacteria. This surface sensing is essential for the lifestyle transitions of several bacteria and involvement in pathogenesis. However, the precise mechanisms underlying TFP's integration of environmental cues, particularly in regulating the TFP-Chp system and its effects on Xanthomonas physiology, social behavior, and virulence, remain poorly understood. In this study, we focused on investigating Clp, a global transcriptional regulator similar to CRP-like proteins, in Xanthomonas oryzae pv. oryzae, a plant pathogen. Our findings reveal that Clp integrates environmental cues detected through diffusible signaling factor (DSF) quorum sensing into the TFP-Chp regulatory system. It accomplishes this by directly binding to TFP-Chp promoters in conjunction with intracellular levels of cyclic-di-GMP, a ubiquitous bacterial second messenger, thereby controlling TFP expression. Moreover, Clp-mediated regulation is involved in regulating several cellular processes, including the production of virulence-associated functions. Collectively, these processes contribute to host colonization and disease initiation. Our study elucidates the intricate regulatory network encompassing Clp, environmental cues, and the TFP-Chp system, providing insights into the molecular mechanisms that drive bacterial virulence in Xanthomonas spp. These findings offer valuable knowledge regarding Xanthomonas pathogenicity and present new avenues for innovative strategies aimed at combating plant diseases caused by these bacteria. [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.

Xanthomonas rydalmerensis sp. nov., a non-pathogenic member of Group 1 Xanthomonas

Five bacterial isolates were isolated from Fragaria × ananassa in 1976 in Rydalmere, Australia, during routine biosecurity surveillance. Initially, the results of biochemical characterisation indicated that these isolates represented members of the genus Xanthomonas. To determine their species, further analysis was conducted using both phenotypic and genotypic approaches. Phenotypic analysis involved using MALDI-TOF MS and BIOLOG GEN III microplates, which confirmed that the isolates represented members of the genus Xanthomonas but did not allow them to be classified with respect to species. Genome relatedness indices and the results of extensive phylogenetic analysis confirmed that the isolates were members of the genus Xanthomonas and represented a novel species. On the basis the minimal presence of virulence-associated factors typically found in genomes of members of the genus Xanthomonas, we suggest that these isolates are non-pathogenic. This conclusion was supported by the results of a pathogenicity assay. On the basis of these findings, we propose the name Xanthomonas rydalmerensis, with DAR 34855T = ICMP 24941 as the type strain.

Exopolysaccharide Production and Precipitation Method as a Tool to Study Virulence Factors

Acidovorax avenae subsp. avenae (Aaa) is the causal agent of red stripe in sugarcane, a disease characterized by two forms: leaf stripe and top rot. Despite the importance of this disease, little is known about Aaa virulence factors (VFs) and their function in the infection process. Among the different array of VFs exerted by phytopathogenic bacteria, exopolysaccharides (EPSs) often confer a survival advantage by protecting the cell against abiotic and biotic stresses, including host defensive factors. They are also main components of the extracellular matrix involved in cell-cell recognition, surface adhesion, and biofilm formation. EPS composition and properties have been well studied for some plant pathogenic bacteria; nevertheless, there is no knowledge about Aaa-EPS. In this work, we describe a simple and reliable method for EPS production, precipitation, and quantification based on cold precipitation after ethanol addition, which will allow to study EPS characteristics of different Aaa strains and to evaluate the association among EPS (e.g., amount, composition, viscosity) and Aaa pathogenicity.

Regulatory Effects of Diverse DSF Family Quorum-Sensing Signals in Plant-Associated Bacteria

Numerous bacterial species employ diffusible signal factor (DSF)-based quorum sensing (QS) as a widely conserved cell-cell signaling communication system to collectively regulate various behaviors crucial for responding to environmental changes. cis-11-Methyl-dodecenoic acid, known as DSF, was first identified as a signaling molecule in Xanthomonas campestris pv. campestris. Subsequently, many structurally related molecules have been identified in different bacterial species. This review aims to provide an overview of current understanding regarding the biosynthesis and regulatory role of DSF signals in both pathogenic bacteria and a biocontrol bacterium. Recent studies have revealed that the DSF-based QS system regulates antimicrobial factor production in a cyclic dimeric GMP-independent manner in the biocontrol bacterium Lysobacter enzymogenes. Additionally, the DSF family signals have been found to be involved in suppressing plant innate immunity. The discovery of these diverse signaling mechanisms holds significant promise for developing novel strategies to combat stubborn plant pathogens. [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.

A disease predictive model based on epidemiological factors for the management of bacterial leaf blight of rice

Abstract Rice is a widely consumed staple food for a large part of the world’s human population. Approximately 90% of the world’s rice is grown in Asian continent and constitutes a staple food for 2.7 billion people worldwide. Bacterial leaf blight (BLB) caused by Xanthomonas oryzae pv. oryzae is one of the devastating diseases of rice. A field experiment was conducted during the year 2016 and 2017 to investigate the influence of different meteorological parameters on BLB development as well as the computation of a predictive model to forecast the disease well ahead of its appearance in the field. The seasonal dataset of disease incidence and environmental factors was used to assess five rice varieties/ cultivars (Basmati-2000, KSK-434, KSK-133, Super Basmati, and IRRI-9). The accumulated effect of two year environmental data; maximum and minimum temperature, relative humidity, wind speed, and rainfall, was studied and correlated with disease incidence. Average temperature (maximum & minimum) showed a negative significant correlation with BLB disease and all other variables; relative humidity, rainfall, and wind speed had a positive correlation with BLB disease development on individual varieties. Stepwise regression analysis was performed to indicate potentially useful predictor variables and to rule out incompetent parameters. Environmental data from the growing seasons of July to October 2016 and 2017 revealed that, with the exception of the lowest temperature, all environmental factors contributed to disease development throughout the cropping season. A disease prediction multiple regression model was developed based on two-year data (Y = 214.3-3.691 Max T-0.508 Min T + 0.767 RH + 2.521 RF + 5.740 WS), which explained 95% variability. This disease prediction model will not only help farmers in early detection and timely management of bacterial leaf blight disease of rice but may also help reduce input costs and improve product quality and quantity. The model will be both farmer and environmentally friendly.

Whole-genome sequencing and comparative genome analysis of Xanthomonas fragariae YM2 causing angular leaf spot disease in strawberry

Background

Angular leaf spot disease caused by plant pathogenic bacterium Xanthomonas fragariae seriously threatens strawberry crop production globally.

Methods

In this study, we sequenced the whole genome of X. fragariae YM2, isolated from Yunnan Province, China. In addition, we performed a comparative genome analysis of X. fragariae YM2 with two existing strains of X. fragariae YL19 and SHQP01 isolated from Liaoning and Shanghai, respectively.

Results

The results of Nanopore sequencing showed that X. fragariae YM2 comprises one single chromosome with a contig size of 4,263,697 bp, one plasmid contig size of 0.39 Mb, a GC content ratio of 62.27%, and 3,958 predicted coding genes. The genome of YM2 comprises gum, hrp, rpf, and xps gene clusters and lipopolysaccharide (LPS), which are typical virulence factors in Xanthomonas species. By performing a comparative genomic analysis between X. fragariae strains YM2, YL19, and SHQP01, we found that strain YM2 is similar to YL19 and SHQP01 regarding genome size and GC contents. However, there are minor differences in the composition of major virulence factors and homologous gene clusters. Furthermore, the results of collinearity analysis demonstrated that YM2 has lower similarity and longer evolutionary distance with YL19 and SHQP01, but YL19 is more closely related to SHQP01.

Conclusions

The availability of this high-quality genetic resource will serve as a basic tool for investigating the biology, molecular pathogenesis, and virulence of X. fragariae YM2. In addition, unraveling the potential vulnerabilities in its genetic makeup will aid in developing more effective disease suppression control measures.

Derivative of cinnamic acid inhibits T3SS of Xanthomonas oryzae pv. oryzae through the HrpG-HrpX regulatory cascade

Bacterial leaf blight (BLB) caused by Xanthomonas oryzae pv. oryzae (Xoo) has a significant impact on rice yield and quality worldwide. Traditionally, bactericide application has been commonly used to control this devastating disease. However, the overuse of fungicides has led to a number of problems such as the development of resistance and environmental pollution. Therefore, the development of new methods and approaches for disease control are still urgent. In this paper, a series of cinnamic acid derivatives were designed and synthesized, and three novel T3SS inhibitors A10, A12 and A20 were discovered. Novel T3SS inhibitors A10, A12 and A20 significantly inhibited the hpa1 promoter activity without affecting Xoo growth. Further studies revealed that the title compounds A10, A12 and A20 significantly impaired hypersensitivity in non-host plant tobacco leaves, while applications on rice significantly reduced symptoms of bacterial leaf blight. RT-PCR showed that compound A20 inhibited the expression of T3SS-related genes. In summary, this work exemplifies the potential of the title compound as an inhibitor of T3SS and its efficacy in the control of bacterial leaf blight.

Seed biopriming for sustainable agriculture and ecosystem restoration

The utilization of microbial inoculants in the realm of sustainable agricultural and ecosystem restoration has witnessed a surge in recent decades. This rise is largely attributed to advancements in our understanding of plant-microbe interactions, the urgency to reduce the dependence on agrochemicals and the growing societal demand for sustainable strategies in ecosystem management. However, despite the rapid growth of bio-inoculants sector, certain limitations persist concerning their efficacy and performance under the field condition. Here, we propose that seed biopriming, an effective microbial inoculant technique integrating both biological agents (the priming of beneficial microbes on seeds) and physiological aspects (hydration of seeds for improved metabolically activity), has a significant potential to mitigate these limitations. This method increases the protection of seeds against soil-borne pathogens and soil pollutants, such as salts and heavy metals, while promoting germination rate and uniformity, leading to overall improved primary productivity and soil health. Furthermore, we argue that a microbial coating on seeds can facilitate transgenerational associations of beneficial microbes, refine plant and soil microbiomes, and maintain soil legacies of beneficial microflora. This review article aims to improve our understanding of the seed biopriming approach as a potent and valuable tool in achieving sustainable agriculture and successful ecosystem restoration.

Bacteria Associated with Acute Oak Decline: Where Did They Come From? We Know Where They Go

Acute oak decline is a high-impact disease causing necrotic lesions on the trunk, crown thinning and the eventual death of oak. Four bacterial species are associated with the lesions-Brenneria goodwinii, Gibbsiella quercinecans, Rahnella victoriana and Lonsdalea Britannica-although an epi-/endophytic lifestyle has also been suggested for these bacteria. However, little is known about their environmental reservoirs or their pathway to endophytic colonisation. This work aimed to investigate the ability of the four AOD-associated bacterial species to survive for prolonged periods within rhizosphere soil, leaves and acorns in vitro, and to design an appropriate method for their recovery. This method was trialled on field samples related to healthy and symptomatic oaks. The in vitro study showed that the majority of these species could survive for at least six weeks within each sample type. Results from the field samples demonstrated that R. victoriana and G. quercinecans appear environmentally widespread, indicating multiple routes of endophytic colonisation might be plausible. B. goodwinii and L. britannica were only identified from acorns from healthy and symptomatic trees, indicating they may be inherited members of the endophytic seed microbiome and, despite their ability to survive outside of the host, their environmental occurrence is limited. Future research should focus on preventative measures targeting the abiotic factors of AOD, how endophytic bacteria shift to a pathogenic cycle and the identification of resilient seed stock that is less susceptible to AOD.

RNase D Is Involved in 5S rRNA Degradation and Exopolysaccharide Production in Xanthomonas campestris pv. campestris

Ribonucleases (RNases) play critical roles in RNA metabolism and are collectively essential for cell viability. However, most knowledge about bacterial RNases comes from the studies on Escherichia coli; very little is known about the RNases in plant pathogens. The crucifer black rot pathogen Xanthomonas campestris pv. campestris (Xcc) encodes 15 RNases, but none of them has been functionally characterized. Here, we report the physiological function of the exoribonuclease RNase D in Xcc and provide evidence demonstrating that the Xcc RNase D is involved in 5S rRNA degradation and exopolysaccharide (EPS) production. Our work shows that the growth and virulence of Xcc were not affected by deletion of RNase D but were severely attenuated by RNase D overexpression. However, deletion of RNase D in Xcc resulted in a significant reduction in EPS production. In addition, either deletion or overexpression of RNase D in Xcc did not influence the tRNAs tested, inconsistent with the finding in E. coli that the primary function of RNase D is to participate in tRNA maturation and its overexpression degrades tRNAs. More importantly, deletion, overexpression, and in vitro enzymatic analyses revealed that the Xcc RNase D degrades 5S rRNA but not 16S and 23S rRNAs that share an operon with 5S rRNA. Our results suggest that Xcc employs RNase D to realize specific modulation of the cellular 5S rRNA content after transcription and maturation whenever necessary. The finding expands our knowledge about the function of RNase D in bacteria.

Complete Genome Sequence Resource for Xanthomonas hortorum Isolated from Greek Oregano

In spring 2019, necrotic leaf spots were detected on Greek oregano (Origanum vulgare var. hirtum) plants in a commercial greenhouse operation. An isolate was recovered from the diseased plants. Partial 16S ribosomal RNA sequencing and multilocus sequence analysis revealed that the isolate was a Xanthomonas sp. but proved insufficient to identify the species with certainty. Therefore, whole-genome sequencing using both Nanopore and Illumina technologies was performed. Here, we report the complete and annotated genome sequence of Xanthomonas hortorum strain 108, which was originally isolated from Greek oregano in Long Island, NY, U.S.A.

Plant Stomata: An Unrealized Possibility in Plant Defense against Invading Pathogens and Stress Tolerance

Stomata are crucial structures in plants that play a primary role in the infection process during a pathogen's attack, as they act as points of access for invading pathogens to enter host tissues. Recent evidence has revealed that stomata are integral to the plant defense system and can actively impede invading pathogens by triggering plant defense responses. Stomata interact with diverse pathogen virulence factors, granting them the capacity to influence plant susceptibility and resistance. Moreover, recent studies focusing on the environmental and microbial regulation of stomatal closure and opening have shed light on the epidemiology of bacterial diseases in plants. Bacteria and fungi can induce stomatal closure using pathogen-associated molecular patterns (PAMPs), effectively preventing entry through these openings and positioning stomata as a critical component of the plant's innate immune system; however, despite this defense mechanism, some microorganisms have evolved strategies to overcome stomatal protection. Interestingly, recent research supports the hypothesis that stomatal closure caused by PAMPs may function as a more robust barrier against pathogen infection than previously believed. On the other hand, plant stomatal closure is also regulated by factors such as abscisic acid and Ca2+-permeable channels, which will also be discussed in this review. Therefore, this review aims to discuss various roles of stomata during biotic and abiotic stress, such as insects and water stress, and with specific context to pathogens and their strategies for evading stomatal defense, subverting plant resistance, and overcoming challenges faced by infectious propagules. These pathogens must navigate specific plant tissues and counteract various constitutive and inducible resistance mechanisms, making the role of stomata in plant defense an essential area of study.

Xanthomonas euvesicatoria-Specific Bacteriophage BsXeu269p/3 Reduces the Spread of Bacterial Spot Disease in Pepper Plants

The present study was focused on the pathosystem pepper plants (Capsicum annuum L.)-phytopathogenic bacterium X. euvesicatoria (wild strain 269p)-bacteriophage BsXeu269p/3 and the possibility of bacteriophage-mediated biocontrol of the disease. Two new model systems were designed for the monitoring of the effect of the phage treatment on the infectious process in vivo. The spread of the bacteriophage and the pathogen was monitored by qPCR. A new pair of primers for phage detection via qPCR was designed, as well as probes for TaqMan qPCR. The epiphytic bacterial population and the potential bacteriolytic effect of BsXeu269p/3 in vivo was observed by SEM. An aerosol-mediated transmission model system demonstrated that treatment with BsXeu269p/3 reduced the amount of X. euvesicatoria on the leaf surface five-fold. The needle-pricking model system showed a significant reduction of the amount of the pathogen in infectious lesions treated with BsXeu269p/3 (av. 59.7%), compared to the untreated control. We found that the phage titer is 10-fold higher in the infection lesions but it was still discoverable even in the absence of the specific host in the leaves. This is the first report of in vivo assessment of the biocontrol potential of locally isolated phages against BS pathogen X. euvesicatoria in Bulgaria.

The Effects of Gluconacin on Bacterial Tomato Pathogens and Protection against Xanthomonas perforans, the Causal Agent of Bacterial Spot Disease

As agricultural practices become more sustainable, adopting more sustainable practices will become even more relevant. Searching for alternatives to chemical compounds has been the focus of numerous studies, and bacteriocins are tools with intrinsic biotechnological potential for controlling plant diseases. We continued to explore the biotechnological activity of the bacteriocin Gluconacin from Gluconacetobacter diazotrophicus, PAL5 strain, by investigating this protein's antagonism against important tomato phytopathogens and demonstrating its effectiveness in reducing bacterial spots caused by Xanthomonas perforans. In addition to this pathogen, the bacteriocin Gluconacin demonstrated bactericidal activity in vitro against Ralstonia solanacearum and Pseudomonas syringae pv. tomato, agents that cause bacterial wilt and bacterial spots, respectively. Bacterial spot control tests showed that Gluconacin reduced disease severity by more than 66%, highlighting the biotechnological value of this peptide in ecologically correct formulations.

The Role of Iron in Phytopathogenic Microbe-Plant Interactions: Insights into Virulence and Host Immune Response

Iron is an essential element required for the growth and survival of nearly all forms of life. It serves as a catalytic component in multiple enzymatic reactions, such as photosynthesis, respiration, and DNA replication. However, the excessive accumulation of iron can result in cellular toxicity due to the production of reactive oxygen species (ROS) through the Fenton reaction. Therefore, to maintain iron homeostasis, organisms have developed a complex regulatory network at the molecular level. Besides catalyzing cellular redox reactions, iron also regulates virulence-associated functions in several microbial pathogens. Hosts and pathogens have evolved sophisticated strategies to compete against each other over iron resources. Although the role of iron in microbial pathogenesis in animals has been extensively studied, mechanistic insights into phytopathogenic microbe-plant associations remain poorly understood. Recent intensive research has provided intriguing insights into the role of iron in several plant-pathogen interactions. This review aims to describe the recent advances in understanding the role of iron in the lifestyle and virulence of phytopathogenic microbes, focusing on bacteria and host immune responses.