Swimming motility, a virulence trait of Ralstonia solanacearum, is regulated by FlhDC and the plant host environment

Interactions with native microbial keystone taxa enhance the biocontrol efficiency of Streptomyces

BACKGROUND

Streptomyces spp. are known for producing bioactive compounds that suppress phytopathogens. However, previous studies have largely focused on their direct interactions with pathogens and plants, often neglecting their interactions with the broader soil microbiome. In this study, we hypothesized that these interactions are critical for effective pathogen control. We investigated a diverse collection of Streptomyces strains to select those with strong protective capabilities against tomato wilt disease caused by Ralstonia solanacearum. Leveraging a synthetic community (SynCom) established in our lab, alongside multiple in planta and in vitro co-cultivation experiments, as well as transcriptomic and metabolomic analyses, we explored the synergistic inhibitory mechanisms underlying bacterial wilt resistance facilitated by both Streptomyces and the soil microbiome.

RESULTS

Our findings indicate that direct antagonism by Streptomyces is not sufficient for their biocontrol efficacy. Instead, the efficacy was associated with shifts in the rhizosphere microbiome, particularly the promotion of two native keystone taxa, CSC98 (Stenotrophomonas maltophilia) and CSC13 (Paenibacillus cellulositrophicus). In vitro co-cultivation experiments revealed that CSC98 and CSC13 did not directly inhibit the pathogen. Instead, the metabolite of CSC13 significantly enhanced the inhibition efficiency of Streptomyces R02, a highly effective biocontrol strain in natural soil. Transcriptomic and metabolomic analyses revealed that CSC13's metabolites induced the production of Erythromycin E in Streptomyces R02, a key compound that directly suppressed R. solanacearum, as demonstrated by our antagonism tests.

CONCLUSIONS

Collectively, our study reveals how beneficial microbes engage with the native soil microbiome to combat pathogens, suggesting the potential of leveraging microbial interactions to enhance biocontrol efficiency. These findings highlight the significance of intricate microbial interactions within the microbiome in regulating plant diseases and provide a theoretical foundation for devising efficacious biocontrol strategies in sustainable agriculture. Video Abstract.

Exploring the multifaceted role of pehR in Ralstonia solanacearum pathogenesis: enzyme activity, motility, and biofilm formation

PehR is a transcriptional regulator among the various response regulators found in Ralstonia solanacearum, a bacterium that causes lethal wilt disease in over 450 plant species worldwide, including economically important crops such as tomato, chilli, and brinjal. PehR regulates the production of polygalacturonase, an extracellular enzyme that degrades plant cell walls, playing a significant role in bacterial wilt. Despite its significance, the precise function and regulatory mechanism of PehR in R. solanacearum are yet to be thoroughly investigated. The goal of this research is to better understand the role of PehR in R. solanacearum pathogenicity by identifying the genes and pathways that it regulates. By disrupting the pehR gene, we created the ΔpehR mutant of R. solanacearum F1C1, a strain isolated from Tezpur, Assam, India. Transcriptomic analysis revealed 667 differentially expressed genes (DEGs) in the ΔpehR mutant, with 320 upregulated and 347 downregulated compared to the wild-type F1C1 strain. GO and KEGG analyses indicated the downregulation of genes related to flagellum-dependent cell motility, membrane function, and amino acid degradation pathways in the ΔpehR mutant. EPS estimation, biochemical assays for biofilm production, motility, and enzymatic assays for cellulase and pectinase production were all used in the further characterization process. The ΔpehR mutant showed lower virulence in tomato seedlings compared to the wild-type F1C1 strain. The findings suggest that PehR could be a promising target for bacterial wilt disease control, as well as provide critical information for ensuring crop production safety around the world.

Bacillus licheniformisYB06: A Rhizosphere-Genome-Wide Analysis and Plant Growth-Promoting Analysis of a Plant Growth-Promoting Rhizobacterium Isolated from Codonopsis pilosula

Codonopsis pilosula, commonly known as Dangshen, is a valuable medicinal plant, but its slow growth and susceptibility to environmental stress pose challenges for its cultivation. In pursuit of sustainable agricultural practices to enhance the yield and quality of Dangshen, the present study isolated a bacterial strain exhibiting plant growth-promoting potential from the rhizosphere of C. pilosula. This strain was subsequently identified as Bacillus licheniformisYB06. Assessment of its plant growth-promoting attributes revealed the potential of B. licheniformis YB06 as a biofertilizer. Whole-genome sequencing of B. licheniformis YB06 revealed a genome size of 4,226,888 bp with a GC content of 46.22%, harboring 4325 predicted protein-coding sequences. Genomic analysis of B. licheniformis YB06 revealed a diverse array of genes linked to induced systemic resistance (ISR) and plant growth-promoting (PGP) traits, encompassing phytohormone production, nitrogen assimilation and reduction, siderophore biosynthesis, phosphate solubilization, biofilm formation, synthesis of PGP-related amino acids, and flagellar motility. Seed germination assays demonstrated the positive effects of B. licheniformis YB06 on the germination and growth of C. pilosula seedlings. Furthermore, we explored various fertilization regimes, particularly the B. licheniformis YB06-based biofertilizer, were investigated for their impact on the structure and diversity of the C. pilosula rhizosphere soil bacterial community. Our findings revealed that fertilization significantly impacted soil bacterial composition and diversity, with the combined application of B. licheniformis YB06-based biofertilizer and organic fertilizer exhibiting a particularly pronounced enhancement of rhizosphere bacterial community structure and diversity. This study represents the first report on the beneficial effects of B. licheniformis YB06 on both the growth of C. pilosula and the composition of its rhizosphere soil microbial community. These findings provide a theoretical foundation and practical guidance for the development of novel bio-organic compound fertilizers, thereby contributing to the sustainable cultivation of C. pilosula.

Biological Control of Avocado Branch Blight Caused by Lasiodiplodia theobromae Using Bacillus velezensis

In recent years, avocado branch blight has gradually become one of the major diseases causing mortality of avocado trees, which seriously affects the economic development of avocado planting regions. In order to investigate the cause of the disease, the pathogens were isolated from the interroot of avocado trees with the onset of the disease and identified as Lasiodiplodia theobromae. At the same time, three Bacillus velezensis strains, YK194, YK201, and YK268, with better antagonistic effects and high stability against L. theobromae, were isolated from the rhizospheric soil of healthy avocado plants. The results of branch experiments and field trials showed that the avocado leaves as well as branches treated with the strains YK194, YK201, and YK268 did not develop disease, and the incidence of avocado trees was significantly reduced. In the branch experiments, the biological control effect of the strains YK194, YK201, and YK268 reached 62.07, 52.70, and 72.45%, respectively. In the field experiments, it reached 63.85, 63.43, and 73.86%, respectively, which indicated that all these three strains possessed good biological control effects on avocado branch blight. Further investigation on the mechanism of action of antagonistic strains revealed that B. velezensis YK268 could produce lipopeptides, namely, surfactin, fengycin, and iturin, which could significantly inhibit the spore germination of L. theobromae. Consequently, these three isolates have potential as biocontrol agents against L. theobromae.

Phages enhance both phytopathogen density control and rhizosphere microbiome suppressiveness

Bacteriophages, viruses that specifically target plant pathogenic bacteria, have emerged as a promising alternative to traditional agrochemicals. However, it remains unclear how phages should be applied to achieve efficient pathogen biocontrol and to what extent their efficacy is shaped by indirect interactions with the resident microbiota. Here, we tested if the phage biocontrol efficacy of Ralstonia solanacearum phytopathogenic bacterium can be improved by increasing the phage cocktail application frequency and if the phage efficacy is affected by pathogen-suppressing bacteria already present in the rhizosphere. We find that increasing phage application frequency improves R. solanacearum density control, leading to a clear reduction in bacterial wilt disease in both greenhouse and field experiments with tomato. The high phage application frequency also increased the diversity of resident rhizosphere microbiota and enriched several bacterial taxa that were associated with the reduction in pathogen densities. Interestingly, these taxa often belonged to Actinobacteria known for antibiotics production and soil suppressiveness. To test if they could have had secondary effects on R. solanacearum biocontrol, we isolated Actinobacteria from Nocardia and Streptomyces genera and tested their suppressiveness to the pathogen in vitro and in planta. We found that these taxa could clearly inhibit R. solanacearum growth and constrain bacterial wilt disease, especially when combined with the phage cocktail. Together, our findings unravel an undiscovered benefit of phage therapy, where phages trigger a second line of defense by the pathogen-suppressing bacteria that already exist in resident microbial communities.

IMPORTANCE

Ralstonia solanacearum is a highly destructive plant-pathogenic bacterium with the ability to cause bacterial wilt in several crucial crop plants. Given the limitations of conventional chemical control methods, the use of bacterial viruses (phages) has been explored as an alternative biological control strategy. In this study, we show that increasing the phage application frequency can improve the density control of R. solanacearum, leading to a significant reduction in bacterial wilt disease. Furthermore, we found that repeated phage application increased the diversity of rhizosphere microbiota and specifically enriched Actinobacterial taxa that showed synergistic pathogen suppression when combined with phages due to resource and interference competition. Together, our study unravels an undiscovered benefit of phages, where phages trigger a second line of defense by the pathogen-suppressing bacteria present in resident microbial communities. Phage therapies could, hence, potentially be tailored according to host microbiota composition to unlock the pre-existing benefits provided by resident microbiota.

Recent advances in immuno-based methods for the detection of Ralstonia solanacearum

Ralstonia solanacearum (RS) is a widely recognized phytopathogenic bacterium which is responsible for causing devastating losses in a wide range of economically significant crops. Timely and accurate detection of this pathogen is pivotal to implementing effective disease management strategies and preventing crop losses. This review provides a comprehensive overview of recent advances in immuno-based detection methods for RS. The review begins by introducing RS, highlighting its destructive potential and the need for point-of-care detection techniques. Subsequently, it explores traditional detection methods and their limitations, emphasizing the need for innovative approaches. The main focus of this review is on immuno-based detection methods and it discusses recent advancements in serological detection techniques. Furthermore, the review sheds light on the challenges and prospects of immuno-based detection of RS. It emphasizes the importance of developing rapid, field-deployable assays that can be used by farmers and researchers alike. In conclusion, this review provides valuable insights into the recent advances in immuno-based detection methods for RS.

Antibacterial activity and action mechanism of curcusionol from Carex siderosticta Hance against Ralstonia nicotianae

BACKGROUND

Tobacco bacterial wilt is a typical soil-borne disease caused by Ralstonia nicotianae, which causes huge losses in tobacco production every year. The crude extract of Carex siderosticta Hance was shown to have antibacterial activity against R. nicotianae during our search, and the natural antibacterial components were sought after using bioassay-guided fractionation of the compounds.

RESULT

Ethanol extract of Carex siderosticta Hance with the minimum inhibitory concentration (MIC) value of 100 μg/mL against R. nicotianae in vitro. The potential of these compounds as antibactericides against R. nicotianae were assessed. Curcusionol (1), showed the highest antibacterial activity against R. nicotianae with MIC value of 12.5 μg/mL in vitro. In the protective effect tests, the control effect of curcusionol (1) was 92.31 and 72.60%, respectively, after application of 7 and 14 days, at a concentration of 1500 μg/mL, being comparable to that of streptomycin sulfate at a concentration of 500 μg/mL, confirming that curcusionol (1) showed the potential for the development of new antibacterial drugs. RNA-sequencing, scanning electron microscopy (SEM) and transmission electron microscopy (TEM) analysis confirmed that curcusionol mainly destroys R. nicotianae cell membrane structure and affects quorum sensing (QS) to inhibit pathogenic bacteria.

CONCLUSION

This study revealed that the antibacterial activity of Carex siderosticta Hance makes it a botanical bactericide against R. nicotianae, while curcusionol as lead structures for antibacterial development is obvious by its potent antibacterial activity. © 2023 Society of Chemical Industry.

PhcX Is a LqsR-family response regulator that contributes to Ralstonia solanacearum virulence and regulates multiple virulence factors

IMPORTANCE

The bacterial wilt caused by the soil-borne phytopathogen Ralstonia solanacearum is one of the most destructive crop diseases. To achieve a successful infection, R. solanacearum has evolved an intricate regulatory network to orchestrate the expression of an arsenal of virulence factors and fine-tune the allocation of energy. However, despite the wealth of knowledge gained in the past decades, many players and connections are still missing from the network. The importance of our study lies in the identification of PhcX, a novel conserved global regulator with critical roles in modulating the virulence and metabolism of R. solanacearum. PhcX affects many well-characterized regulators and exhibits contrasting modes of regulation from the central regulator PhcA on a variety of virulence-associated traits and genes. Our findings add a valuable piece to the puzzle of how the pathogen regulates its proliferation and infection, which is critical for understanding its pathogenesis and developing disease control strategies.

Transcriptomic analysis of Ralstonia solanacearum in response to antibacterial volatiles of Bacillus velezensis FZB42

Volatile organic compounds (VOCs), produced by a variety of microbial species and used as biological agents, have been demonstrated to play a significant role in controlling phytopathogens. In continuation of our previous studies, we aim to elucidate the underlying mechanisms and pathways involved in interactions between pathogens and microbial VOCs. In the current study, we tested how VOCs produced by Bacillus velezensis FZB42 affect the growth of Ralstonia solanacearum TBBS1 in vitro.Query The result showed that the colony growth of R. solanacearum was reduced with an inhibition rate of 0.83 ± 0.043 as compared to the control 1.7 ± 0.076, respectively. The number of viable cells of R. solanacearum was significantly decreased to 7.68 CFU/mL as compared to the control (9.02 CFU/mL). In addition, transcriptomic analysis of R. solanacearum in response to VOCs produced by FZB42 was performed to better understand the effect of VOCs on R. solanacearum. The transcriptional response of R. solanacearum to FZB42-VOCs was determined using an Illumina RNA-seq approach. The results revealed significant changes in the expression of 2094 R. solanacearum genes, including 593 upregulated and 1501 downregulated genes. To validate the RNA-seq results, the expression of 10 genes was quantified using RT-qPCR. Furthermore, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases were used to functionally annotate differentially expressed genes. Significant changes were observed in genes directly or indirectly related to virulence, including those related to bacterial invasion, motility, chemotaxis, and secretion systems. Overall, RNA-seq profiling provides new insights into the possible fundamental molecular mechanisms that are responsible for the reduction in growth and virulence of R. solanacearum upon application of FZB42-VOC.

RIN enhances plant disease resistance via root exudate-mediated assembly of disease-suppressive rhizosphere microbiota

The RIPENING-INHIBITOR (RIN) transcriptional factor is a key regulator governing fruit ripening. While RIN also affects other physiological processes, its potential roles in triggering interactions with the rhizosphere microbiome and plant health are unknown. Here we show that RIN affects microbiome-mediated disease resistance via root exudation, leading to recruitment of microbiota that suppress the soil-borne, phytopathogenic Ralstonia solanacearum bacterium. Compared with the wild-type (WT) plant, RIN mutants had different root exudate profiles, which were associated with distinct changes in microbiome composition and diversity. Specifically, the relative abundances of antibiosis-associated genes and pathogen-suppressing Actinobacteria (Streptomyces) were clearly lower in the rhizosphere of rin mutants. The composition, diversity, and suppressiveness of rin plant microbiomes could be restored by the application of 3-hydroxyflavone and riboflavin, which were exuded in much lower concentrations by the rin mutant. Interestingly, RIN-mediated effects on root exudates, Actinobacteria, and disease suppression were evident from the seedling stage, indicating that RIN plays a dual role in the early assembly of disease-suppressive microbiota and late fruit development. Collectively, our work suggests that, while plant disease resistance is a complex trait driven by interactions between the plant, rhizosphere microbiome, and the pathogen, it can be indirectly manipulated using "prebiotic" compounds that promote the recruitment of disease-suppressive microbiota.

Hexameric structure of the flagellar master regulator FlhDC from Cupriavidus necator and its interaction with flagellar promoter DNA

Bacterial flagella are assembled with ∼30 different proteins in a defined order via diverse regulatory systems. In gram-negative bacteria from the Gammaproteobacteria and Betaproteobacteria classes, the transcription of flagellar genes is strictly controlled by the master regulator FlhDC. In Gammaproteobacteria species, the FlhDC complex has been shown to activate flagellar expression by directly interacting with the promoter region in flagellar genes. To obtain the DNA-binding mechanism of FlhDC and determine the conserved and distinct structural features of Betaproteobacteria and Gammaproteobacteria FlhDCs that are necessary for their functions, we determined the crystal structure of Betaproteobacteria Cupriavidus necator FlhDC (cnFlhDC) and biochemically analyzed its DNA-binding capacity. cnFlhDC specifically recognized the promoter DNA of the class II flagellar genes flgB and flhB. cnFlhDC adopts a ring-like heterohexameric structure (cnFlhD₄C₂) and harbors two Zn-Cys clusters, as observed for Gammaproteobacteria Escherichia coli FlhDC (ecFlhDC). The cnFlhDC structure exhibits positively charged surfaces across two FlhDC subunits as a putative DNA-binding site. Noticeably, the positive patch of cnFlhDC is continuous, in contrast to the separated patches of ecFlhDC. Moreover, the ternary intersection of cnFlhD₄C₂ behind the Zn-Cys cluster forms a unique protruding neutral structure, which is replaced with a charged cavity in the ecFlhDC structure.

Sustainable Protocols for Cellulose Nanocrystals Synthesis from Tomato Waste and Their Antimicrobial Properties against Pseudomonas syringae pv. tomato

Nanotechnology is rapidly gaining ground in crop protection, with the growing quest for sustainable nanopesticides and nanocarriers for plant pathogen management. Among them, cellulose nanocrystals (CNC) are emerging as innovative agrofood-waste-derived antimicrobial materials. In this work, new chemical and enzymatic CNC extraction methods from tomato harvest residues were evaluated. The obtained nanomaterials were characterized and tested for their antimicrobial properties on Pseudomonas syringae pv. tomato (Pto), the causal agent of bacterial speck disease on tomato. Both protocols were efficient. The enzymatic extraction method was greener, producing purer CNC at slightly lower yield. The obtained CNC, although they weakly inhibited cell growth and did not promote reactive oxygen species (ROS) formation, provoked bacterial aggregation and the inhibition of biofilm production and swimming motility. Both protocols produced CNC with similar morpho-chemical features, as well as promising antimicrobial activity against plant bacterial pathogens, suggesting their potential role in sustainable crop protection strategies. The new protocols could be a valuable alternative to conventional methods.

Effect and mechanism of NaHS on tobacco bacterial wilt caused by Ralstonia solanacearum

Since its discovery as a third unique gaseous signal molecule, hydrogen sulfide (H₂S) has been extensively employed to resist stress and control pathogens. Nevertheless, whether H₂S can prevent tobacco bacterial wilt is unknown yet. We evaluated the impacts of the H₂S donor sodium hydrosulfide (NaHS) on the antibacterial activity, morphology, biofilm, and transcriptome of R. solanacearum to understand the effect and mechanism of NaHS on tobacco bacterial wilt. In vitro, NaHS significantly inhibited the growth of Ralstonia solanacearum and obviously altered its cell morphology. Additionally, NaHS significantly inhibited the biofilm formation and swarming motility of R. solanacearum, and reduced the population of R. solanacearum invading tobacco roots. In field experiments, the application of NaHS dramatically decreased the disease incidence and index of tobacco bacterial wilt, with a control efficiency of up to 89.49%. The application of NaHS also influenced the diversity and structure of the soil microbial community. Furthermore, NaHS markedly increased the relative abundances of beneficial microorganisms, which helps prevent tobacco bacterial wilt. These findings highlight NaHS's potential and efficacy as a powerful antibacterial agent for preventing tobacco bacterial wilt caused by R. solanacearum.

An RpoN-dependent PEP-CTERM gene is involved in floc formation of an Aquincola tertiaricarbonis strain

BACKGROUND

The floc is a characteristic of microbial aggregate growth, displaying cloudy suspensions in water. Floc formation has been demonstrated in a series of bacteria and the floc-forming bacteria play a crucial role in activated sludge (AS) process widely used for municipal sewage and industrial wastewater treatment over a century. It has been demonstrated that some exopolysaccharide biosynthesis genes and the sigma factor (sigma54 or rpoN) were required for floc forming in some bacteria. However, the mechanism underlying the floc formation stills need to be elucidated.

RESULTS

In this study, we demonstrate that a TPR (Tetratricopeptide repeats) protein-encoding gene prsT is required for floc formation of Aquincola tertiaricarbonis RN12 and an upstream PEP-CTERM gene (designated pepA), regulated by RpoN1, is involved in its floc formation but not swarming motility and biofilm formation. Overexpression of PepA could rescue the floc-forming phenotype of the rpoN1 mutant by decreasing the released soluble exopolysaccharides and increasing the bound polymers.

CONCLUSION

Our results indicate that the wide-spread PEP-CTERM proteins play an important role in the self-flocculation of bacterial cells and may be a component of extracellular polymeric substances required for floc-formation.

Getting to the root of Ralstonia invasion

Plant diseases caused by soilborne pathogens are a major limiting factor in crop production. Bacterial wilt disease, caused by soilborne bacteria in the Ralstonia solanacearum Species Complex (Ralstonia), results in significant crop loss throughout the world. Ralstonia invades root systems and colonizes plant xylem, changing plant physiology and ultimately causing plant wilting in susceptible varieties. Elucidating how Ralstonia invades and colonizes plants is central to developing strategies for crop protection. Here we review Ralstonia pathogenesis from root detection and attachment, early root colonization, xylem invasion and subsequent wilting. We focus primarily on studies in tomato from the last 5-10 years. Recent work has identified elegant mechanisms Ralstonia uses to adapt to the plant xylem, and has discovered new genes that function in Ralstonia fitness in planta. A picture is emerging of an amazingly versatile pathogen that uses multiple strategies to make its surrounding environment more hospitable and can adapt to new environments.

Genome-guided comparative in planta transcriptome analyses for identifying cross-species common virulence factors in bacterial phytopathogens

Plant bacterial disease is a complex outcome achieved through a combination of virulence factors that are activated during infection. However, the common virulence factors across diverse plant pathogens are largely uncharacterized. Here, we established a pan-genome shared across the following plant pathogens: Burkholderia glumae, Ralstonia solanacearum, and Xanthomonas oryzae pv. oryzae. By overlaying in planta transcriptomes onto the pan-genome, we investigated the expression profiles of common genes during infection. We found over 70% of identical patterns for genes commonly expressed by the pathogens in different plant hosts or infection sites. Co-expression patterns revealed the activation of a signal transduction cascade to recognize and respond to external changes within hosts. Using mutagenesis, we uncovered a relationship between bacterial virulence and functions highly conserved and shared in the studied genomes of the bacterial phytopathogens, including flagellar biosynthesis protein, C4-dicarboxylate ABC transporter, 2-methylisocitrate lyase, and protocatechuate 3,4-dioxygenase (PCD). In particular, the disruption of PCD gene led to attenuated virulence in all pathogens and significantly affected phytotoxin production in B. glumae. This PCD gene was ubiquitously distributed in most plant pathogens with high homology. In conclusion, our results provide cross-species in planta models for identifying common virulence factors, which can be useful for the protection of crops against diverse pathogens.

Mutation in phcA Enhanced the Adaptation of Ralstonia solanacearum to Long-Term Acid Stress

Bacterial wilt, caused by the plant pathogen Ralstonia solanacearum, occurs more severely in acidified soil according to previous reports. However, R. solanacearum cannot grow well in acidic environments under barren nutrient culture conditions, especially when the pH is lower than 5. With the worsening acidification of farmland, further determination of how R. solanacearum adapts to the long-term acidic environment is worthwhile. In this study, experimental evolution was applied to evaluate the adaptability and mechanism of the R. solanacearum experimental population responding to long-term acid stress. We chose the CQPS-1 strain as the ancestor, and minimal medium (MM medium) with different pH values as the culture environment to simulate poor soil. After 1500 generations of serial passage experiments in pH 4.9 MM, acid-adapted experimental strains (denoted as C49 strains) were obtained, showing significantly higher growth rates than the growth rates of control experimental strains (serial passage experiment in pH 6.5 MM, denoted as C65 strains). Competition experiments showed that the competitive indices (CIs) of all selected clones from C49 strains were superior to the ancestor in acidic environment competitiveness. Based on the genome variation analysis and functional verification, we confirmed that loss of function in the phcA gene was associated with the acid fitness gain of R. solanacearum, which meant that the inactivation of the PhcA regulator caused by gene mutation mediated the population expansion of R. solanacearum when growing in an acidic stress environment. Moreover, the swimming motility of acid evolution strains and the phcA deletion mutant was significantly enhanced compared to CQPS-1. This work provided evidence for understanding the adaptive strategy of R. solanacearum to the long-term acidic environment.

Comprehensive Analysis Reveals the Genetic and Pathogenic Diversity of Ralstonia solanacearum Species Complex and Benefits Its Taxonomic Classification

Ralstonia solanacearum species complex (RSSC) is a diverse group of plant pathogens that attack a wide range of hosts and cause devastating losses worldwide. In this study, we conducted a comprehensive analysis of 131 RSSC strains to detect their genetic diversity, pathogenicity, and evolution dynamics. Average nucleotide identity analysis was performed to explore the genomic relatedness among these strains, and finally obtained an open pangenome with 32,961 gene families. To better understand the diverse evolution and pathogenicity, we also conducted a series of analyses of virulence factors (VFs) and horizontal gene transfer (HGT) in the pangenome and at the single genome level. The distribution of VFs and mobile genetic elements (MGEs) showed significant differences among different groups and strains, which were consistent with the new nomenclatures of the RSSC with three distinct species. Further functional analysis showed that most HGT events conferred from Burkholderiales and played a great role in shaping the genomic plasticity and genetic diversity of RSSC genomes. Our work provides insights into the genetic polymorphism, evolution dynamics, and pathogenetic variety of RSSC and provides strong supports for the new taxonomic classification, as well as abundant resources for studying host specificity and pathogen emergence.

Indirect reduction of Ralstonia solanacearum via pathogen helper inhibition

The rhizosphere microbiome forms a first line of defense against soilborne pathogens. To date, most microbiome enhancement strategies have relied on bioaugmentation with antagonistic microorganisms that directly inhibit pathogens. Previous studies have shown that some root-associated bacteria are able to facilitate pathogen growth. We therefore hypothesized that inhibiting such pathogen helpers may help reduce pathogen densities. We examined tripartite interactions between a model pathogen, Ralstonia solanacearum, two model helper strains and a collection of 46 bacterial isolates recovered from the tomato rhizosphere. This system allowed us to examine the importance of direct (effects of rhizobacteria on pathogen growth) and indirect (effects of rhizobacteria on helper growth) pathways affecting pathogen growth. We found that the interaction between rhizosphere isolates and the helper strains was the major determinant of pathogen suppression both in vitro and in vivo. We therefore propose that controlling microbiome composition to prevent the growth of pathogen helpers may become part of sustainable strategies for pathogen control.

Influence of Flagellin Polymorphisms, Gene Regulation, and Responsive Memory on the Motility of Xanthomonas Species That Cause Bacterial Spot Disease of Solanaceous Plants

Increasingly, new evidence has demonstrated variability in the epitope regions of bacterial flagellin, including in regions harboring the microbe-associated molecular patterns flg22 and flgII-28 that are recognized by the pattern recognition receptors FLS2 and FLS3, respectively. Additionally, because bacterial motility is known to contribute to pathogen virulence and chemotaxis, reductions in or loss of motility can significantly reduce bacterial fitness. In this study, we determined that variations in flg22 and flgII-28 epitopes allow some but not all Xanthomonas spp. to evade both FLS2- and FLS3-mediated oxidative burst responses. We observed variation in the motility for many isolates, regardless of their flagellin sequence. Instead, we determined that past growth conditions may have a significant impact on the motility status of isolates, because we could minimize this variability by inducing motility using chemoattractant assays. Additionally, motility could be significantly suppressed under nutrient-limited conditions, and bacteria could "remember" its prior motility status after storage at ultracold temperatures. Finally, we observed larger bacterial populations of strains with flagellin variants predicted not to be recognized by either FLS2 or FLS3, suggesting that these bacteria can evade flagellin recognition in tomato plants. Although some flagellin variants may impart altered motility and differential recognition by the host immune system, external growth parameters and gene expression regulation appear to have more significant impacts on the motility phenotypes for these Xanthomonas spp.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

The Regulatory Functions of σ54 Factor in Phytopathogenic Bacteria

σ⁵⁴ factor (RpoN), a type of transcriptional regulatory factor, is widely found in pathogenic bacteria. It binds to core RNA polymerase (RNAP) and regulates the transcription of many functional genes in an enhancer-binding protein (EBP)-dependent manner. σ⁵⁴ has two conserved functional domains: the activator-interacting domain located at the N-terminal and the DNA-binding domain located at the C-terminal. RpoN directly binds to the highly conserved sequence, GGN₁₀GC, at the −24/−12 position relative to the transcription start site of target genes. In general, bacteria contain one or two RpoNs but multiple EBPs. A single RpoN can bind to different EBPs in order to regulate various biological functions. Thus, the overlapping and unique regulatory pathways of two RpoNs and multiple EBP-dependent regulatory pathways form a complex regulatory network in bacteria. However, the regulatory role of RpoN and EBPs is still poorly understood in phytopathogenic bacteria, which cause economically important crop diseases and pose a serious threat to world food security. In this review, we summarize the current knowledge on the regulatory function of RpoN, including swimming motility, flagella synthesis, bacterial growth, type IV pilus (T4Ps), twitching motility, type III secretion system (T3SS), and virulence-associated phenotypes in phytopathogenic bacteria. These findings and knowledge prove the key regulatory role of RpoN in bacterial growth and pathogenesis, as well as lay the groundwork for further elucidation of the complex regulatory network of RpoN in bacteria.

Multiple Copies of flhDC in Paraburkholderia unamae Regulate Flagellar Gene Expression, Motility, and Biofilm Formation

FlhDC is a heterohexameric complex that acts as a master regulator of flagellar biosynthesis genes in numerous bacteria. Previous studies have identified a single flhDC operon encoding this complex. However, we found that two flhDC loci are present throughout Paraburkholderia, and two additional flhC copies are also present in Paraburkholderia unamae. Systematic deletion analysis in P. unamae of the different flhDC copies showed that one of the operons, flhDC1, plays the predominant role, with deletion of its genes resulting in a severe inhibition of motility and biofilm formation. Expression analysis using promoter-lacZ fusions and real-time quantitative PCR support the primary role of flhDC1 in flagellar gene regulation, with flhDC2 a secondary contributor. Phylogenetic analysis shows the presence of the flhDC1 and flhDC2 operons throughout Paraburkholderia. In contrast, Burkholderia and other bacteria only carry the copy syntenous with flhDC2. The variations in impact each copy of flhDC has on downstream processes indicate that regulation of FlhDC in P. unamae, and likely other Paraburkholderia species, is regulated at least in part by the presence of multiple copies of these genes. IMPORTANCE Motility is important in the colonization of plant roots by beneficial and pathogenic bacteria, with flagella playing essential roles in host cell adhesion, entrance, and biofilm formation. Flagellar biosynthesis is energetically expensive. Its complex regulation by the FlhDC master regulator is well studied in peritrichous flagella expressing enterics. We report the unique presence throughout Paraburkholderia of multiple copies of flhDC. In P. unamae, the flhDC1 copy showed higher expression and a greater effect on swim motility, flagellar development, and regulation of downstream genes, than the flhDC2 copy that is syntenous to flhDC in Escherichia coli and pathogenic Burkholderia spp. The flhDC genes have evolved differently in these plant-growth-promoting bacteria, giving an additional layer of complexity in gene regulation by FlhDC.

Pochonia chlamydosporia Isolate PC-170-Induced Expression of Marker Genes for Defense Pathways in Tomatoes Challenged by Different Pathogens

Pochonia chlamydosporia is a fungal parasite of nematode eggs. Studies have shown that some strains of Pochonia chlamydosporia can promote plant growth and induce plants’ systemic resistance to root-knot nematodes by colonizing in their roots. This study aimed to verify the effect of the PC-170 strain on tomato growth and systemic resistance. Split-root experiments were conducted to observe the systemic resistance induced by PC-170. To explore the defense pathway that was excited due to the colonization by PC-170, we tested the expression of marker genes for defense pathways, and used mutant lines to verify the role of plant defense pathways. Our results showed that PC-170 can colonize roots, and promotes growth. We found a role for jasmonic acid (JA) in modulating tomato colonization by PC-170. PC-170 can activate tomato defense responses to reduce susceptibility to infection by the root-knot nematode Meloidogyne incognita, and induced resistance to some pathogens in tomatoes. The marker genes of the defense pathway were significantly induced after PC-170 colonization. However, salicylic acid (SA)- and jasmonic acid (JA)-dependent defenses in roots were variable with the invasion of different pathogens. Defense pathways play different roles at different points in time. SA- and JA-dependent defense pathways were shown to cross-communicate. Different phytohormones have been involved in tomato plants’ responses against different pathogens. Our study confirmed that adaptive JA signaling is necessary to regulate PC-170 colonization and induce systemic resistance in tomatoes.

Preliminary Studies on the Antibacterial Mechanism of a New Plant-Derived Compound, 7-Methoxycoumarin, Against Ralstonia solanacearum

Ralstonia solanacearum (R. solanacearum) is one of the most devastating plant bacterial pathogens and leads to serious economic losses in crops worldwide. In this study, the antibacterial mechanism of 7-methoxycoumarin, a new coumarin antibiotic, was preliminarily investigated by the observation of symptoms and physical and biochemical analyses. The results showed that 7-methoxycoumarin significantly suppressed bacterial growth of R. solanacearum, with the minimum inhibitory concentration (MIC) and the minimum bactericidal concentration (MBC) values of 75 and 175 mg/L, respectively. Electron microscopy observations showed that the bacterial cell membrane was destroyed after 7-methoxycoumarin treatment. Biofilm formation of R. solanacearum was significantly suppressed by 7-methoxycoumarin at concentrations ranging from 25 to 100 mg/L. Furthermore, virulence-associated genes epsE, hrpG, and popA of R. solanacearum were significantly inhibited by 7-methoxycoumarin. The application of 7-methoxycoumarin effectively suppressed tobacco bacterial wilt progress in pot experiments, with relative control efficiencies of 83.61, 68.78, and 58.11% at 6, 8, and 10 days post inoculation, respectively.

Light modulates important physiological features of Ralstonia pseudosolanacearum during the colonization of tomato plants

Ralstonia pseudosolanacearum GMI1000 (Rpso GMI1000) is a soil-borne vascular phytopathogen that infects host plants through the root system causing wilting disease in a wide range of agro-economic interest crops, producing economical losses. Several features contribute to the full bacterial virulence. In this work we study the participation of light, an important environmental factor, in the regulation of the physiological attributes and infectivity of Rpso GMI1000. In silico analysis of the Rpso genome revealed the presence of a Rsp0254 gene, which encodes a putative blue light LOV-type photoreceptor. We constructed a mutant strain of Rpso lacking the LOV protein and found that the loss of this protein and light, influenced characteristics involved in the pathogenicity process such as motility, adhesion and the biofilms development, which allows the successful host plant colonization, rendering bacterial wilt. This protein could be involved in the adaptive responses to environmental changes. We demonstrated that light sensing and the LOV protein, would be used as a location signal in the host plant, to regulate the expression of several virulence factors, in a time and tissue dependent way. Consequently, bacteria could use an external signal and Rpsolov gene to know their location within plant tissue during the colonization process.

Dynamic expression of Ralstonia solanacearum virulence factors and metabolism-controlling genes during plant infection

BACKGROUND

Ralstonia solanacearum is the causal agent of bacterial wilt, a devastating plant disease responsible for serious economic losses especially on potato, tomato, and other solanaceous plant species in temperate countries. In R. solanacearum, gene expression analysis has been key to unravel many virulence determinants as well as their regulatory networks. However, most of these assays have been performed using either bacteria grown in minimal medium or in planta, after symptom onset, which occurs at late stages of colonization. Thus, little is known about the genetic program that coordinates virulence gene expression and metabolic adaptation along the different stages of plant infection by R. solanacearum.

RESULTS

We performed an RNA-sequencing analysis of the transcriptome of bacteria recovered from potato apoplast and from the xylem of asymptomatic or wilted potato plants, which correspond to three different conditions (Apoplast, Early and Late xylem). Our results show dynamic expression of metabolism-controlling genes and virulence factors during parasitic growth inside the plant. Flagellar motility genes were especially up-regulated in the apoplast and twitching motility genes showed a more sustained expression in planta regardless of the condition. Xylem-induced genes included virulence genes, such as the type III secretion system (T3SS) and most of its related effectors and nitrogen utilisation genes. The upstream regulators of the T3SS were exclusively up-regulated in the apoplast, preceding the induction of their downstream targets. Finally, a large subset of genes involved in central metabolism was exclusively down-regulated in the xylem at late infection stages.

CONCLUSIONS

This is the first report describing R. solanacearum dynamic transcriptional changes within the plant during infection. Our data define four main genetic programmes that define gene pathogen physiology during plant colonisation. The described expression of virulence genes, which might reflect bacterial states in different infection stages, provides key information on the R. solanacearum potato infection process.

Elucidation of antibacterial effect of calcium chloride against Ralstonia pseudosolanacearum race 4 biovar 3 infecting ginger (Zingiber officinale Rosc.)

Bacterial wilt incited by Ralstonia pseudosolanacearum (Rps) race 4 biovar 3 is a serious threat to ginger (Zingiber officinale Rosc.) cultivation throughout the ginger growing tracts and warrants effective remedial measures since most of the strategies failed at field level implementation. After a series of experiments, calcium chloride was found to be effective against Rps both in vitro and in planta and its prophylactic effect has been successfully demonstrated under field conditions. CaCl2 at a concentration of > 2% significantly inhibited Rps under in vitro conditions. Calcium is an important nutritional element imparts a major role in plant disease resistance, and numerous studies have demonstrated the mitigating effect of calcium for disease management. CaCl2 being inhibitory to Rps, the mechanism of inhibition by CaCl2 against Rps was elucidated by a series of in vitro assays including swarming motility and biofilm formation. Direct inhibition was also studied using Scanning Electron Microscopy (SEM). The minimum bactericidal concentration and minimum inhibitory concentration were found to be around 3% while the EC 90 value was found to be 2.25%. The SEM analysis revealed the destruction of cell structure by making perforations on the cell surface. CaCl2 at the targeted concentrations inhibited biofilm formation as well as swarming motility of Rps. These findings suggest that CaCl2 exhibits strong antibacterial activity against Rps and has the potential to be used as an effective bactericide for Rps in managing bacterial wilt in ginger.

Tyrosine Nitration of Flagellins: a Response of Sinorhizobium meliloti to Nitrosative Stress

Rhizobia are bacteria which can either live as free organisms in the soil or interact with plants of the legume family with, as a result, the formation of root organs called nodules in which differentiated endosymbiotic bacteria fix atmospheric nitrogen to the plant's benefit. In both lifestyles, rhizobia are exposed to nitric oxide (NO) which can be perceived as a signaling or toxic molecule. NO can act at the transcriptional level but can also modify proteins by S-nitrosylation of cysteine or nitration of tyrosine residues. However, only a few molecular targets of NO have been described in bacteria and none of them have been characterized in rhizobia. Here, we examined tyrosine nitration of Sinorhizobium meliloti proteins induced by NO. We found three tyrosine-nitrated proteins in S. meliloti grown under free-living conditions, in response to an NO donor. Two nitroproteins were identified by mass spectrometry and correspond to flagellins A and B. We showed that one of the nitratable tyrosines is essential to flagellin function in motility.IMPORTANCE Rhizobia are found as free-living bacteria in the soil or in interaction with plants and are exposed to nitric oxide (NO) in both environments. NO is known to have many effects on animals, plants, and bacteria where only a few molecular targets of NO have been described so far. We identified flagellin A and B by mass spectrometry as tyrosine-nitrated proteins in Sinorhizobium meliloti in vivo We also showed that one of the nitratable tyrosines is essential to flagellin function in motility. The results enhanced our understanding of NO effects on rhizobia. Identification of bacterial flagellin nitration opens a new possible role of NO in plant-microbe interactions.

The LysR-Type Transcriptional Regulator CrgA Negatively Regulates the Flagellar Master Regulator flhDC in Ralstonia solanacearum GMI1000

The invasion and colonization of host plants by the destructive pathogen Ralstonia solanacearum rely on its cell motility, which is controlled by multiple factors. Here, we report that the LysR-type transcriptional regulator CrgA (RS_RS16695) represses cell motility in R. solanacearum GMI1000. CrgA possesses common features of a LysR-type transcriptional regulator and contains an N-terminal helix-turn-helix motif as well as a C-terminal LysR substrate-binding domain. Deletion of crgA results in an enhanced swim ring and increased transcription of flhDC In addition, the ΔcrgA mutant possesses more polar flagella than wild-type GMI1000 and exhibits higher expression of the flagellin gene fliC Despite these alterations, the ΔcrgA mutant did not have a detectable growth defect in culture. Yeast one-hybrid and electrophoretic mobility shift assays revealed that CrgA interacts directly with the flhDC promoter. Expressing the β-glucuronidase (GUS) reporter under the control of the crgA promoter showed that crgA transcription is dependent on cell density. Soil-soaking inoculation with the crgA mutant caused wilt symptoms on tomato (Solanum lycopersicum L. cv. Hong yangli) plants earlier than inoculation with the wild-type GMI1000 but resulted in lower disease severity. We conclude that the R. solanacearum regulator CrgA represses flhDC expression and consequently affects the expression of fliC to modulate cell motility, thereby conditioning disease development in host plants.IMPORTANCE Ralstonia solanacearum is a widely distributed soilborne plant pathogen that causes bacterial wilt disease on diverse plant species. Motility is a critical virulence attribute of R. solanacearum because it allows this pathogen to efficiently invade and colonize host plants. In R. solanacearum, motility-defective strains are markedly affected in pathogenicity, which is coregulated with multiple virulence factors. In this study, we identified a new LysR-type transcriptional regulator (LTTR), CrgA, that negatively regulates motility. The mutation of the corresponding gene leads to the precocious appearance of wilt symptoms on tomato plants when the pathogen is introduced using soil-soaking inoculation. This study indicates that the regulation of R. solanacearum motility is more complex than previously thought and enhances our understanding of flagellum regulation in R. solanacearum.

The involvement of the Type Six Secretion System (T6SS) in the virulence of Ralstonia solanacearum on brinjal

Ralstonia solanacearum is an important soil-borne plant pathogen which causes bacterial wilt in a large number of crops. Bacterial Type Six Secretion System (T6SS) is known to participate in pathogenesis, bacterial interaction and inter-bacterial competition. Contribution of T6SS in the virulence of R. solanacearum on eggplant (Solanum melongena L) is studied. In this study, five T6SS gene (ompA, vgrG3, hcp, tssH and tssM) mutants have been developed by insertional mutagenesis and the virulence of the mutants was evaluated on eggplant. In general, the T6SS mutants showed significant reduction of wilt on eggplant. R. solanacearum mutant of ompA gene significantly reduced the wilt from day five through day eight in petiole inoculation. In soil drench inoculation, R. solanacearum mutant of vgrG3 gene reduced the wilt on eggplant and was significantly different throughout the experimental period. Other mutants, viz., tssH, tssM and hcp, also reduced the wilt during the initial stages of disease development. This is the first report on the role of T6SS genes, ompA, vgrG3, hcp and tssH on virulence of R. solanacearum.

Expression of Ralstonia solanacearum type III secretion system is dependent on a novel type 4 pili (T4P) assembly protein (TapV) but is T4P independent

Type IV pili (T4P) are virulence factors in various pathogenic bacteria of animals and plants that play important roles in twitching motility, swimming motility, biofilm formation, and adhesion to host cells. Here, we genetically characterized functional roles of a putative T4P assembly protein TapV (Rsc1986 in reference strain GMI1000) and its homologue Rsp0189, which shares 58% amino acid identity with TapV, in Ralstonia solanacearum. Deletion of tapV, but not rsp0189, resulted in significantly impaired twitching motility, swimming motility, and adhesion to tomato roots, which are consistent as phenotypes of the pilA mutant (a known R. solanacearum T4P-deficient mutant). However, unlike the pilA mutant, the tapV mutant produced more biofilm than the wild-type strain. Our gene expression studies revealed that TapV, but not Rsp0189, is important for expression of a type III secretion system (T3SS, a pathogenicity determinant of R. solanacearum) both in vitro and in planta, but it is T4P independent. We further revealed that TapV affected the T3SS expression via the PhcA-TapV-PrhG-HrpB pathway, consistent with previous reports that PhcA positively regulates expression of pilA and prhG. Moreover, deletion of tapV, but not rsp0189, significantly impaired the ability to migrate into and colonize xylem vessels of host plants, but there was no alteration in intercellular proliferation of R. solanacearum in tobacco leaves, which is similar to the pilA mutant. The tapV mutant showed significantly impaired virulence in host plants. This is the first report on the impact of T4P components on the T3SS, providing novel insights into our understanding of various biological functions of T4P and the complex regulatory pathway of T3SS in R. solanacearum.

Regulators of nitric oxide signaling triggered by host perception in a plant pathogen

The rhizosphere interaction between plant roots or pathogenic microbes is initiated by mutual exchange of signals. However, how soil pathogens sense host signals is largely unknown. Here, we studied early molecular events associated with host recognition in Fusarium graminearum, an economically important fungal pathogen that can infect both roots and heads of cereal crops. We found that host sensing prior to physical contact with plant roots radically alters the transcriptome and triggers nitric oxide (NO) production in F. graminearum We identified an ankyrin-repeat domain containing protein (FgANK1) required for host-mediated NO production and virulence in F. graminearum In the absence of host plant, FgANK1 resides in the cytoplasm. In response to host signals, FgANK1 translocates to the nucleus and interacts with a zinc finger transcription factor (FgZC1), also required for specific binding to the nitrate reductase (NR) promoter, NO production, and virulence in F. graminearum Our results reveal mechanistic insights into host-recognition strategies employed by soil pathogens.

Genome analysis of plant growth-promoting rhizobacterium Pseudomonas chlororaphis subsp. aurantiaca JD37 and insights from comparasion of genomics with three Pseudomonas strains

Pseudomonas chlororaphis subsp. aurantiaca strain JD37 is a plant growth-promoting rhizobacterium (PGPR), which has important biotechnological features such as plant growth promotion, rhizosphere colonization and biocontrol activities. In present study, the genome sequence of JD37 was obtained and comparative genomic analysis were performed to explore unique features of the JD37 genome and its relationship with other Pseudomonas PGPR: P. chlororaphis PA23, P. protegens Pf-5 and P. aeruginosa M18. JD37 possessed a single circular chromosome of 6,702,062 bp in length with an average GC content of 62.75 %. No plasmid was detected in JD37. A total of 5003 functional proteins of JD37 were predicted according to the clusters of orthologous groups (COGs) database. The JD37 genome consisted of various genes involved in plant growth promotion, biocontrol activities and defense responses. Genes involved in the rhizosphere colonization and motility were also found in the genome of JD37, suggesting the common plant growth-promoting traits in PGPR. The identified resistance genes (e.g. those related to metal resistance, antibiotics, and osmotic and temperature-shock) and secondary metabolite biosynthesis revealed the pathways for metabolites it produced. Data presented in present study further provided valuable information on its molecular genetics and adaptive capacity in the rhizosphere niche.

The cold shock family gene cspD3 is involved in the pathogenicity of Ralstonia solanacearum CQPS-1 to tobacco

Cold shock proteins (Csps) are small and highly conserved proteins that have target RNA- and DNA-binding activities. Csps play roles in different cellular processes and show functional redundancy. Ralstonia solanacearum, the agent of bacterial wilt, has 4 or 5 Csps based on genome analysis. However, the functions of all Csps in R. solanacearum remain unclear. According to phylogenetic analysis, the Csps from R. solanacearum are clustered into a group with CspD from E. coli. Here, we studied the role of CspD3, which was closer to CspD of E. coli in the phylogenetic tree. A cspD3 deletion strain was constructed to assess its effect on the phenotype of R. solanacearum, including growth, biofilm formation, motility, and virulence. The results showed that cspD3 of R. solanacearum was not necessary for normal growth, cold-shock adaptation, or biofilm formation. However, deletion of cspD3 in R. solanacearum CQPS-1 led to increased swimming motility, and the mean diameters of swimming haloes produced by the ΔcspD3 mutant were 1.3-fold larger than those produced by wild-type strain and 1.2-fold larger than those produced by the complemented strain. More importantly, the virulence of the cspD3 deletion mutant on susceptible tobacco plants was significantly attenuated compared to the wild-type strain. At 20 days after inoculation, the disease index of the ΔcspD3 mutant was 2.27, which was reduced by 1.6-fold relative to the wild-type strain. To assess the molecular response influenced by cspD3, the expressions of the main motility-associated genes and virulence-associated genes including flgM, fliA, pehS, pehR, hrpG, xpsR, and prhI in R. solanacearum were measured. The results showed that the expressions of hrpG, xpsR, and prhI were significantly decreased in cspD3 deletion mutant. Collectively, our findings showed that Csps are involved in the regulation of motility and virulence in R. solanacearum.

A LysR-Type Transcriptional Regulator LcrX Is Involved in Virulence, Biofilm Formation, Swimming Motility, Siderophore Secretion, and Growth in Sugar Sources in Xanthomonas axonopodis Pv. glycines

Xanthomonas axonopodis pv. glycines (Xag) is a Gram-negative bacterium that causes bacterial pustule disease in soybean. To acclimate to new environments, the expression of genes in bacteria is controlled directly or indirectly by diverse transcriptional factors. Among them, LysR type transcriptional regulators are well-characterized and abundant in bacteria. In a previous study, comparative proteomic analysis revealed that LysR type carbohydrate-related transcriptional regulator in Xag (LcrX) was more abundant in XVM2, which is a minimal medium, compared with a rich medium. However, the functions of LcrX in Xag have not been characterized. In this study, we generated an LcrX-overexpressing strain, Xag(LcrX), and the knockout mutant strain, XagΔlcrX(EV), to elucidate the functions of LcrX. Bacterial multiplication of Xag(LcrX) in soybean was significantly impaired, indicating that LcrX is related to virulence. Comparative proteomic analysis revealed that LcrX is mainly involved in carbohydrate metabolism/transport and inorganic ion transport/metabolism. Based on the results of proteomics analysis, diverse phenotypic assays were carried out. A gel electrophoresis mobility shift assay demonstrated that LcrX specifically bound to the putative promoter regions of genes encoding putative fructose 1,6-bisphosphatase and protease. Through a 96-well plate assay under various conditions, we confirmed that the growth of Xag(LcrX) was dramatically affected in the presence of various carbon sources, while the growth of XagΔlcrX(EV) was only slightly changed. Biofilm formation activity was reduced in Xag(LcrX) but enhanced in XagΔlcrX(EV). The production of siderophores was also decreased in Xag(LcrX) but not altered in XagΔlcrX(EV). In contrast, LcrX was not associated with exopolysaccharide production, protease activity, or bacterial motility. These findings provide new insights into the functions of a carbohydrate-related transcriptional regulator in Xag.

Involvement of a PadR regulator PrhP on virulence of Ralstonia solanacearum by controlling detoxification of phenolic acids and type III secretion system

Ralstonia solanacearum can metabolize ferulic acid (FA) and salicylic acid (SA), two representative phenolic acids, to protect it from toxicity of phenolic acids. Here, we genetically demonstrated a novel phenolic acid decarboxylase regulator (PadR)-like regulator PrhP as a positive regulator on detoxification of SA and FA in R. solanacearum. Although the ability to degrade SA and FA enhances the infection process of R. solanacearum toward host plants, PrhP greatly contributes to the infection process besides degradation of SA and FA. Our results from the growth assay, promoter activity assay, RNA-seq and qRT-PCR revealed that PrhP plays multiple roles in the virulence of R. solanacearum: (1) positively regulates expression of genes for degradation of SA and FA; (2) positively regulates expression of genes encoding type III secretion system (T3SS) and type III effectors both in vitro and in planta; (3) positively regulates expression of many virulence-related genes, such as the flagella, type IV pili and cell wall degradation enzymes; and (4) is important for the extensive proliferation in planta. The T3SS is one of the essential pathogenicity determinants in many pathogenic bacteria, and PrhP positively regulates its expression mediated with the key regulator HrpB but through some novel pathway to HrpB in R. solanacearum. This is the first report on PadR regulators to regulate the T3SS and it could improve our understanding of the various biological functions of PadR regulators and the complex regulatory pathway on T3SS in R. solanacearum.

Crp-Like Protein Plays Both Positive and Negative Roles in Regulating the Pathogenicity of Bacterial Pustule Pathogen Xanthomonas axonopodis pv. glycines

The global regulator Crp-like protein (Clp) is positively involved in the production of virulence factors in some of the Xanthomonas spp. However, the functional importance of Clp in X. axonopodis pv. glycines has not been investigated previously. Here, we showed that deletion of clp led to significant reduction in the virulence of X. axonopodis pv. glycines in soybean, which was highly correlated with the drastic reductions in carbohydrates utilization, extracellular polysaccharide (EPS) production, biofilm formation, cell motility, and synthesis of cell wall degrading enzymes (CWDEs). These significantly impaired properties in the clp mutant were completely rescued by a single-copy integration of the wild-type clp into the mutant chromosome via homologous recombination. Interestingly, overexpression of clp in the wild-type strain resulted in significant increases in cell motility and synthesis of the CWDEs. To our surprise, significant reductions in carbohydrates utilization, EPS production, biofilm formation, and the protease activity were observed in the wild-type strain overexpressing clp, suggesting that Clp also plays a negative role in these properties. Furthermore, quantitative reverse transcription polymerase chain reaction analysis suggested that clp was positively regulated by the diffusible signal factor-mediated quorum-sensing system and the HrpG/HrpX cascade. Taken together, our results reveal that Clp functions as both activator and repressor in multiple biological processes in X. axonopodis pv. glycines that are essential for its full virulence.

The RSc0454-Encoded FAD-Linked Oxidase Is Indispensable for Pathogenicity in Ralstonia solanacearum GMI1000

Ralstonia solanacearum is the causal agent of bacterial wilt disease. Here, we report that a large FAD-linked oxidase encoded by RSc0454 in GMI1000 is required for pathogenicity. The FAD-linked oxidase encoded by RSc0454 is composed of 1,345 amino acids, including DUF3683, lactate dehydrogenase (LDH), and succinate dehydrogenase (SDH) domains. The RSc0454 protein showed both LDH and SDH activities. To investigate its role in pathogenicity, a deletion mutant of the RSc0454 gene was constructed in GMI1000, which was impaired in its ability to cause bacterial wilt disease in tomato. A single DUF3683, LDH, or SDH domain was insufficient to restore bacterial pathogenicity. Mutagenesis of the RSc0454 gene did not affect growth rate but caused cell aggregation at the bottom of the liquid nutrient medium, which was reversed by exogenous applications of lactate, fumarate, pyruvate, and succinate. qRT-PCR and promoter LacZ fusion experiments demonstrated that RSc0454 gene transcription was induced by lactate and fumarate (both substrates of LDH). Compared with the downregulation of the succinate dehydrogenase gene sdhBADC and the lactate dehydrogenase gene ldh, RSc0454 gene transcription was enhanced in planta. This suggests that the oxidase encoded by RSc0454 was involved in a redox balance, which is in line with the different living conditions of R. solanacearum.

Identification by Tn-seq of Dickeya dadantii genes required for survival in chicory plants

The identification of the virulence factors of plant-pathogenic bacteria has relied on the testing of individual mutants on plants, a time-consuming process. Transposon sequencing (Tn-seq) is a very powerful method for the identification of the genes required for bacterial growth in their host. We used this method in a soft-rot pathogenic bacterium to identify the genes required for the multiplication of Dickeya dadantii in chicory. About 100 genes were identified showing decreased or increased fitness in the plant. Most had no previously attributed role in plant-bacterium interactions. Following our screening, in planta competition assays confirmed that the uridine monophosphate biosynthesis pathway and the purine biosynthesis pathway were essential to the survival of D. dadantii in the plant, as the mutants ∆carA, ∆purF, ∆purL, ∆guaB and ∆pyrE were unable to survive in the plant in contrast with the wild-type (WT) bacterium. This study also demonstrated that the biosynthetic pathways of leucine, cysteine and lysine were essential for bacterial survival in the plant and that RsmC and GcpA were important in the regulation of the infection process, as the mutants ∆rsmC and ∆gcpA were hypervirulent. Finally, our study showed that D. dadantii flagellin was glycosylated and that this modification conferred fitness to the bacterium during plant infection. Assay by this method of the large collections of environmental pathogenic strains now available will allow an easy and rapid identification of new virulence factors.

Various antibacterial mechanisms of biosynthesized copper oxide nanoparticles against soilborne Ralstonia solanacearum

The substantial antimicrobial efficacy of nanoparticles against phytopathogens has been extensively investigated for advanced agricultural applications. However, few reports have focused on soilborne pathogenic bacteria. The aim of this study was to obtain sustainably synthesized copper oxide nanoparticles (CuONPs) using papaya leaf extracts and investigate the bactericidal activity of these CuONPs against Ralstonia solanacearum, the cause of bacterial wilt, under laboratory and greenhouse conditions. The results showed that CuONPs possessed strong antibacterial activity and that all R. solanacearum were killed after exposure to 250 μg mL-1 CuONPs. CuONPs could interact with bacterial cells to prevent biofilm formation, reduce swarming motility and disturb ATP production. Ultrastructural observations by transmission electron microscopy (TEM) revealed that after interactions with CuONPs, bacterial cells suffered significantly from nanomechanical damage to the cytomembrane, accompanied by the absorption of multiple nanoparticles. In addition, molecular studies identified the downregulation mechanism of a series of genes involving pathogenesis and motility. The control efficiency of CuONPs in tobacco bacterial wilt disease management under greenhouse conditions was verified by root irrigation application, demonstrating that as-prepared CuONPs significantly reduced the disease occurrence and disease index. Our studies focused on developing biosynthesized nanoparticles as a biocompatible alternative for soilborne disease management.

Plant-like bacterial expansins play contrasting roles in two tomato vascular pathogens

Expansin proteins, which loosen plant cell walls, play critical roles in normal plant growth and development. The horizontal acquisition of functional plant-like expansin genes in numerous xylem-colonizing phytopathogenic bacteria suggests that bacterial expansins may also contribute to virulence. To investigate the role of bacterial expansins in plant diseases, we mutated the non-chimeric expansin genes (CmEXLX2 and RsEXLX) of two xylem-inhabiting bacterial pathogens, the Actinobacterium Clavibacter michiganensis ssp. michiganensis (Cmm) and the β-proteobacterium Ralstonia solanacearum (Rs), respectively. The Cmm ΔCmEXLX2 mutant caused increased symptom development on tomato, which was characterized by more rapid wilting, greater vascular necrosis and abundant atypical lesions on distant petioles. This increased disease severity correlated with larger in planta populations of the ΔCmEXLX2 mutant, even though the strains grew as well as the wild-type in vitro. Similarly, when inoculated onto tomato fruit, ΔCmEXLX2 caused significantly larger lesions with larger necrotic centres. In contrast, the Rs ΔRsEXLX mutant showed reduced virulence on tomato following root inoculation, but not following direct petiole inoculation, suggesting that the RsEXLX expansin contributes to early virulence at the root infection stage. Consistent with this finding, ΔRsEXLX attached to tomato seedling roots better than the wild-type Rs, which may prevent mutants from invading the plant's vasculature. These contrasting results demonstrate the diverse roles of non-chimeric bacterial expansins and highlight their importance in plant-bacterial interactions.

An Innovative Root Inoculation Method to Study Ralstonia solanacearum Pathogenicity in Tomato Seedlings

In this study, we report Ralstonia solanacearum pathogenicity in the early stages of tomato seedlings by an innovative root inoculation method. Pathogenicity assays were performed under gnotobiotic conditions in microfuge tubes by employing only 6- to 7-day-old tomato seedlings for root inoculation. Tomato seedlings inoculated by this method exhibited the wilted symptom within 48 h and the virulence assay can be completed in 2 weeks. Colonization of the wilted seedlings by R. solanacearum was confirmed by using gus staining as well as fluorescence microscopy. Using this method, mutants in different virulence genes such as hrpB, phcA, and pilT could be clearly distinguished from wild-type R. solanacearum. The method described here is economic in terms of space, labor, and cost as well as the required quantity of bacterial inoculum. Thus, the newly developed assay is an easy and useful approach for investigating virulence functions of the pathogen at the seedling stage of hosts, and infection under these conditions appears to require pathogenicity mechanisms used by the pathogen for infection of adult plants.

Complete genome sequence of the sesame pathogen Ralstonia solanacearum strain SEPPX 05

Ralstonia solanacearum is a soil-borne phytopathogen associated with bacterial wilt disease of sesame. R. solanacearum is the predominant agent causing damping-off from tropical to temperate regions. Because bacterial wilt has decreased the sesame industry yield, we sequenced the SEPPX05 genome using PacBio and Illumina HiSeq 2500 systems and revealed that R. solanacearum strain SEPPX05 carries a bipartite genome consisting of a 3,930,849 bp chromosome and a 2,066,085 bp megaplasmid with 66.84% G+C content that harbors 5,427 coding sequences. Based on the whole genome, phylogenetic analysis showed that strain SEPPX05 is grouped with two phylotype I strains (EP1 and GMI1000). Pan-genomic analysis shows that R. solanacearum is a complex species with high biological diversity and was able to colonize various environments during evolution. Despite deletions, insertions, and inversions, most genes of strain SEPPX05 have relatively high levels of synteny compared with strain GMI1000. We identified 104 genes involved in virulence-related factors in the SEPPX05 genome and eight absent genes encoding T3Es of GMI1000. Comparing SEPPX05 with other species, we found highly conserved secretion systems central to modulating interactions of host bacteria. These data may provide important clues for understanding underlying pathogenic mechanisms of R. solanacearum and help in the control of sesame bacterial wilt.

Metabolomics of tomato xylem sap during bacterial wilt reveals Ralstonia solanacearum produces abundant putrescine, a metabolite that accelerates wilt disease

Ralstonia solanacearum thrives in plant xylem vessels and causes bacterial wilt disease despite the low nutrient content of xylem sap. We found that R. solanacearum manipulates its host to increase nutrients in tomato xylem sap, enabling it to grow better in sap from infected plants than in sap from healthy plants. Untargeted GC/MS metabolomics identified 22 metabolites enriched in R. solanacearum-infected sap. Eight of these could serve as sole carbon or nitrogen sources for R. solanacearum. Putrescine, a polyamine that is not a sole carbon or nitrogen source for R. solanacearum, was enriched 76-fold to 37 µM in R. solanacearum-infected sap. R. solanacearum synthesized putrescine via a SpeC ornithine decarboxylase. A ΔspeC mutant required ≥ 15 µM exogenous putrescine to grow and could not grow alone in xylem even when plants were treated with putrescine. However, co-inoculation with wildtype rescued ΔspeC growth, indicating R. solanacearum produced and exported putrescine to xylem sap. Intriguingly, treating plants with putrescine before inoculation accelerated wilt symptom development and R. solanacearum growth and systemic spread. Xylem putrescine concentration was unchanged in putrescine-treated plants, so the exogenous putrescine likely accelerated disease indirectly by affecting host physiology. These results indicate that putrescine is a pathogen-produced virulence metabolite.

Recruitment of a Lineage-Specific Virulence Regulatory Pathway Promotes Intracellular Infection by a Plant Pathogen Experimentally Evolved into a Legume Symbiont

Ecological transitions between different lifestyles, such as pathogenicity, mutualism and saprophytism, have been very frequent in the course of microbial evolution, and often driven by horizontal gene transfer. Yet, how genomes achieve the ecological transition initiated by the transfer of complex biological traits remains poorly known. Here, we used experimental evolution, genomics, transcriptomics and high-resolution phenotyping to analyze the evolution of the plant pathogen Ralstonia solanacearum into legume symbionts, following the transfer of a natural plasmid encoding the essential mutualistic genes. We show that a regulatory pathway of the recipient R. solanacearum genome involved in extracellular infection of natural hosts was reused to improve intracellular symbiosis with the Mimosa pudica legume. Optimization of intracellular infection capacity was gained through mutations affecting two components of a new regulatory pathway, the transcriptional regulator efpR and a region upstream from the RSc0965-0967 genes of unknown functions. Adaptive mutations caused the downregulation of efpR and the over-expression of a downstream regulatory module, the three unknown genes RSc3146-3148, two of which encoding proteins likely associated to the membrane. This over-expression led to important metabolic and transcriptomic changes and a drastic qualitative and quantitative improvement of nodule intracellular infection. In addition, these adaptive mutations decreased the virulence of the original pathogen. The complete efpR/RSc3146-3148 pathway could only be identified in the genomes of the pathogenic R. solanacearum species complex. Our findings illustrate how the rewiring of a genetic network regulating virulence allows a radically different type of symbiotic interaction and contributes to ecological transitions and trade-offs.

A Single Regulator Mediates Strategic Switching between Attachment/Spread and Growth/Virulence in the Plant Pathogen Ralstonia solanacearum

The PhcA virulence regulator in the vascular wilt pathogen Ralstonia solanacearum responds to cell density via quorum sensing. To understand the timing of traits that enable R. solanacearum to establish itself inside host plants, we created a ΔphcA mutant that is genetically locked in a low-cell-density condition. Comparing levels of gene expression of wild-type R. solanacearum and the ΔphcA mutant during tomato colonization revealed that the PhcA transcriptome includes an impressive 620 genes (>2-fold differentially expressed; false-discovery rate [FDR], ≤0.005). Many core metabolic pathways and nutrient transporters were upregulated in the ΔphcA mutant, which grew faster than the wild-type strain in tomato xylem sap and on dozens of specific metabolites, including 36 found in xylem. This suggests that PhcA helps R. solanacearum to survive in nutrient-poor environmental habitats and to grow rapidly during early pathogenesis. However, after R. solanacearum reaches high cell densities in planta, PhcA mediates a trade-off from maximizing growth to producing costly virulence factors. R. solanacearum infects through roots, and low-cell-density-mode-mimicking ΔphcA cells attached to tomato roots better than the wild-type cells, consistent with their increased expression of several adhesins. Inside xylem vessels, ΔphcA cells formed aberrantly dense mats. Possibly as a result, the mutant could not spread up or down tomato stems as well as the wild type. This suggests that aggregating improves R. solanacearum survival in soil and facilitates infection and that it reduces pathogenic fitness later in disease. Thus, PhcA mediates a second strategic switch between initial pathogen attachment and subsequent dispersal inside the host. PhcA helps R. solanacearum optimally invest resources and correctly sequence multiple steps in the bacterial wilt disease cycle.

Ralstonia solanacearum is a destructive soilborne crop pathogen that wilts plants by colonizing their water-transporting xylem vessels. It produces its costly virulence factors only after it has grown to a high population density inside a host. To identify traits that this pathogen needs in other life stages, we studied a mutant that mimics the low-cell-density condition. This mutant (the ΔphcA mutant) cannot sense its own population density. It grew faster than and used many nutrients not available to the wild-type bacterium, including metabolites present in tomato xylem sap. The mutant also attached much better to tomato roots, and yet it failed to spread once it was inside plants because it was trapped in dense mats. Thus, PhcA helps R. solanacearum succeed over the course of its complex life cycle by ensuring avid attachment to plant surfaces and rapid growth early in disease, followed by high virulence and effective dispersal later in disease.

RpoN2- and FliA-regulated fliTX is indispensible for flagellar motility and virulence in Xanthomonas oryzae pv. oryzae

Background

Bacterial blight of rice caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most important crop diseases in the world. More insights into the mechanistic regulation of bacterial pathogenesis will help us identify novel molecular targets for developing effective disease control strategies. A large flagellar gene cluster is regulated under a three-tiered hierarchy by σ⁵⁴ factor RpoN2 and its activator FleQ, and σ²⁸ factor FliA. A hypothetical protein gene fliTX is located upstream of rpoN2, however, how it is regulated and how it is related to bacterial behaviors remain to be elucidated.

Results

Sequence alignment analysis indicated that FliTX in Xoo is less well conserved compared with FliT proteins in Escherichia coli, Salmonella typhimurium, and Pseudomonas fluorescens. Co-transcription of fliTX with a cytosolic chaperone gene fliS and an atypical PilZ-domain gene flgZ in an operon was up-regulated by RpoN2/FleQ and FliA. Significantly shorter filament length and impaired swimming motility were observed in ∆fliTX compared with those in the wildtype strain. ∆fliTX also demonstrated reduced disease lesion length and in planta growth in rice, attenuated ability of induction of hypersensitive response (HR) in nonhost tobacco, and down-regulation of type III secretion system (T3SS)-related genes. In trans expression of fliTX gene in ∆fliTX restored these phenotypes to near wild-type levels.

Conclusions

This study demonstrates that RpoN2- and FliA-regulated fliTX is indispensible for flagellar motility and virulence and provides more insights into mechanistic regulation of T3SS expression in Xoo.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-017-1083-6) contains supplementary material, which is available to authorized users.