Enhanced in planta Fitness through Adaptive Mutations in EfpR, a Dual Regulator of Virulence and Metabolic Functions in the Plant Pathogen Ralstonia solanacearum

Transcriptomic profiling reveals host-specific evolutionary pathways promoting enhanced fitness in the plant pathogen Ralstonia pseudosolanacearum

The impact of host diversity on the genotypic and phenotypic evolution of broad-spectrum pathogens is an open issue. Here, we used populations of the plant pathogen Ralstonia pseudosolanacearum that were experimentally evolved on five types of host plants, either belonging to different botanical families or differing in their susceptibility or resistance to the pathogen. We investigated whether changes in transcriptomic profiles, associated with or independent of genetic changes, could occur during the process of host adaptation, and whether transcriptomic reprogramming was dependent on host type. Genomic and transcriptomic variations were established for 31 evolved clones that showed better fitness in their experimental host than the ancestral clone. Few genomic polymorphisms were detected in these clones, but significant transcriptomic variations were observed, with a large number of differentially expressed genes (DEGs). In a very clear way, a group of genes belonging to the network of regulation of the bacterial virulence such as efpR, efpH or hrpB, among others, were deregulated in several independent evolutionary lineages and appeared to play a key role in the transcriptomic rewiring observed in evolved clones. A double hierarchical clustering based on the 400 top DEGs for each clone revealed 2 major patterns of gene deregulation that depend on host genotype, but not on host susceptibility or resistance to the pathogen. This work therefore highlights the existence of two major evolutionary paths that result in a significant reorganization of gene expression during adaptive evolution and underscore clusters of co-regulated genes associated with bacterial adaptation on different host lines.

Novel mandelic acid derivatives suppress virulence of Ralstonia solanacearum via type III secretion system

BACKGROUND

Bacterial wilt induced by Ralstonia solanacearum is regarded as one of the most devastating diseases. However, excessive and repeated use of the same bactericides has resulted in development of bacterial resistance. Targeting bacterial virulence factors, such as type III secretion system (T3SS), without inhibiting bacterial growth is a possible assay to discover new antimicrobial agents.

RESULTS

In this work, identifying new T3SS inhibitors, a series of mandelic acid derivatives with 2-mercapto-1,3,4-thiazole moiety was synthesized. One of them, F-24, inhibited the transcription of hrpY gene significantly. The presence of this compound obviously attenuated hypersensitive response (HR) without inhibiting bacterial growth of R. solanacearum. The transcription levels of those typical T3SS genes were reduced to various degrees. The test of the ability of F-24 in protecting plants demonstrated that F-24 protected tomato plants against bacterial wilt without restricting the multiplication of R. solanacearum. The mechanism of this T3SS inhibition is through the PhcR-PhcA-PrhG-HrpB pathway.

CONCULSION

The screened F-24 could inhibit R. solanacearum T3SS and showed better inhibitory activity than previously reported inhibitors without affecting the growth of the strain, and F-24 is a compound with good potential in the control of R. solanacearum. © 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.

Ralstonia solanacearum: An Arsenal of Virulence Strategies and Prospects for Resistance

The group of strains constituting the Ralstonia solanacearum species complex (RSSC) is a prominent model for the study of plant-pathogenic bacteria because of its impact on agriculture, owing to its wide host range, worldwide distribution, and long persistence in the environment. RSSC strains have led to numerous studies aimed at deciphering the molecular bases of virulence, and many biological functions and mechanisms have been described to contribute to host infection and pathogenesis. In this review, we put into perspective recent advances in our understanding of virulence in RSSC strains, both in terms of the inventory of functions that participate in this process and their evolutionary dynamics. We also present the different strategies that have been developed to combat these pathogenic strains through biological control, antimicrobial agents, plant genetics, or microbiota engineering.

Tn-seq identifies Ralstonia solanacearum genes required for tolerance of plant immunity induced by exogenous salicylic acid

Ralstonia solanacearum, the causal agent of the devastating bacterial wilt disease, is of particular interest to the scientific community. The repertoire of type III effectors plays an important role in the evasion of plant immunity, but tolerance to plant immunity is also crucial for the survival and virulence of R. solanacearum. Nevertheless, a systematic study of R. solanacearum tolerance to plant immunity is lacking. In this study, we used exogenous salicylic acid (SA) to improve the immunity of tomato plants, followed by transposon insertion sequencing (Tn-seq) analysis and the identification of R. solanacearum genes associated with tolerance to plant immunity. Target gene deletion revealed that the lipopolysaccharide (LPS) production genes RS_RS02830, RS_RS03460, and RS_RS03465 are essential for R. solanacearum tolerance to plant immunity, and their expression is induced by plant immunity, thereby expanding our knowledge of the pathogenic function of R. solanacearum LPS. SA treatment increased the relative abundance of transposon insertion mutants of four genes, including two genes with unknown function, RS_RS11975 and RS_RS07760. Further verification revealed that deletion of RS_RS11975 or RS_RS07760 resulted in reduced in vivo competitive indexes but increased tolerance to plant immunity induced by SA treatment, suggesting that these two genes contribute to the trade-off between tolerance to plant immunity and fitness cost. In conclusion, this work identified and validated R. solanacearum genes required for tolerance to plant immunity and provided essential information for a more complete view of the interaction between R. solanacearum and the host plant.

Bacterial volatile organic compounds attenuate pathogen virulence via evolutionary trade-offs

Volatile organic compounds (VOCs) produced by soil bacteria have been shown to exert plant pathogen biocontrol potential owing to their strong antimicrobial activity. While the impact of VOCs on soil microbial ecology is well established, their effect on plant pathogen evolution is yet poorly understood. Here we experimentally investigated how plant-pathogenic Ralstonia solanacearum bacterium adapts to VOC-mixture produced by a biocontrol Bacillus amyloliquefaciens T-5 bacterium and how these adaptations might affect its virulence. We found that VOC selection led to a clear increase in VOC-tolerance, which was accompanied with cross-tolerance to several antibiotics commonly produced by soil bacteria. The increasing VOC-tolerance led to trade-offs with R. solanacearum virulence, resulting in almost complete loss of pathogenicity in planta. At the genetic level, these phenotypic changes were associated with parallel mutations in genes encoding lipopolysaccharide O-antigen (wecA) and type-4 pilus biosynthesis (pilM), which both have been linked with outer membrane permeability to antimicrobials and plant pathogen virulence. Reverse genetic engineering revealed that both mutations were important, with pilM having a relatively larger negative effect on the virulence, while wecA having a relatively larger effect on increased antimicrobial tolerance. Together, our results suggest that microbial VOCs are important drivers of bacterial evolution and could potentially be used in biocontrol to select for less virulent pathogens via evolutionary trade-offs.

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.

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.

Sustainable natural bioresources in crop protection: antimicrobial hydroxycoumarins induce membrane depolarization-associated changes in the transcriptome of Ralstonia solanacearum

BACKGROUND

Ralstonia solanacearum is one of the most devastating pathogens affecting crop production worldwide. The hydroxycoumarins (umbelliferone, esculetin and daphnetin) represent sustainable natural bioresources on controlling plant bacterial wilt. However, the antibacterial mechanism of hydroxycoumarins against plant pathogens still remains poorly understood.

RESULTS

Here we characterized the effect of three hydroxycoumarins on the transcriptome of R. solanacearum. All three hydroxycoumarins were able to kill R. solanacearum, but their antibacterial activity impacted differently the bacterial transcriptome, indicating that their modes of action might be different. Treatment of R. solanacearum cultures with hydroxycoumarins resulted in a large number of differentially expressed genes (DEGs), involved in basic cellular functions and metabolic process, such as down-regulation of genes involved in fatty acid synthesis, lipopolysaccharides biosynthesis, RNA modification, ribosomal submits, oxidative phosphorylation and electrontransport, as well as up-regulation of genes involved in transcriptional regulators, drug efflux, and oxidative stress responses. Future studies based on in vitro experiments are proposed to investigate lipopolysaccharides biosynthesis pathway leading to R. solanacearum cell death caused by hydroxycoumarins. Deletion of lpxB substantially inhibited the growth of R. solanacearum, and reduced virulence of pathogen on tobacco plants.

CONCULSION

Our transcriptomic analyses show that specific hydroxycoumarins suppressed gene expression involved in fatty acid synthesis, RNA modification, ribosomal submits, oxidative phosphorylation and electrontransport. These findings provide evidence that hydroxycoumarins inhibit R. solanacearum growth through multi-target effect. Hydroxycoumarins could serve as sustainable natural bioresources against plant bacterial wilt through membrane destruction targeting the lipopolysaccharides biosynthesis pathway.

Genome-Wide Identification of Ralstonia solanacearum Genes Required for Survival in Tomato Plants

Ralstonia solanacearum is an extremely destructive phytopathogenic bacterium for which there is no effective control method. Though many pathogenic factors have been identified, the survival strategies of R. solanacearum in host plants remain unclear. Transposon insertion sequencing (Tn-seq) is a high-throughput genetic screening technology. This study conducted a Tn-seq analysis using the in planta environment as selective pressure to identify R. solanacearum genes required for survival in tomato plants. One hundred thirty genes were identified as putative genes required for survival in tomato plants. Sixty-three of these genes were classified into four Clusters of Orthologous Groups categories. The absence of genes that encode the outer membrane lipoprotein LolB (RS_RS01965) or the membrane protein RS_RS04475 severely decreased the in planta fitness of R. solanacearum. RS_RS09970 and RS_RS04490 are involved in tryptophan and serine biosynthesis, respectively. Mutants that lack RS_RS09970 or RS_RS04490 did not cause any wilt symptoms in susceptible tomato plants. These results confirmed the importance of genes related to "cell wall/membrane/envelope biogenesis" and "amino acid transport and metabolism" for survival in plants. The gene encoding NADH-quinone oxidoreductase subunit B (RS_RS10340) is one of the 13 identified genes involved in "energy production and conversion," and the Clp protease gene (RS_RS08645) is one of the 11 identified genes assigned to "posttranslational modification, protein turnover, and chaperones." Both genes were confirmed to be required for survival in plants. In conclusion, this study globally identified and validated R. solanacearum genes required for survival in tomato plants and provided essential information for a more complete view of the pathogenic mechanism of R. solanacearum. IMPORTANCE Tomato plant xylem is a nutritionally limiting and dynamically changing habitat. Studies on how R. solanacearum survives in this hostile environment are important for our full understanding of the pathogenic mechanism of this bacterium. Though many omics approaches have been employed to study in planta survival strategies, the direct genome-wide identification of R. solanacearum genes required for survival in plants is still lacking. This study performed a Tn-seq analysis in R. solanacearum and revealed that genes in the categories "cell wall/membrane/envelope biogenesis," "amino acid transport and metabolism," "energy production and conversion," "posttranslational modification, protein turnover, chaperones" and others play important roles in the survival of R. solanacearum in tomato plants.

Convergent Rewiring of the Virulence Regulatory Network Promotes Adaptation of Ralstonia solanacearum on Resistant Tomato

The evolutionary and adaptive potential of a pathogen is a key determinant for successful host colonization and proliferation but remains poorly known for most of the pathogens. Here, we used experimental evolution combined with phenotyping, genomics, and transcriptomics to estimate the adaptive potential of the bacterial plant pathogen Ralstonia solanacearum to overcome the quantitative resistance of the tomato cultivar Hawaii 7996. After serial passaging over 300 generations, we observed pathogen adaptation to within-plant environment of the resistant cultivar but no plant resistance breakdown. Genomic sequence analysis of the adapted clones revealed few genetic alterations, but we provide evidence that all but one were gain of function mutations. Transcriptomic analyses revealed that even if different adaptive events occurred in independently evolved clones, there is convergence toward a global rewiring of the virulence regulatory network as evidenced by largely overlapping gene expression profiles. A subset of four transcription regulators, including HrpB, the activator of the type 3 secretion system regulon and EfpR, a global regulator of virulence and metabolic functions, emerged as key nodes of this regulatory network that are frequently targeted to redirect the pathogen’s physiology and improve its fitness in adverse conditions. Significant transcriptomic variations were also detected in evolved clones showing no genomic polymorphism, suggesting that epigenetic modifications regulate expression of some of the virulence network components and play a major role in adaptation as well.

Experimental Evolution in Plant-Microbe Systems: A Tool for Deciphering the Functioning and Evolution of Plant-Associated Microbial Communities

In natural environments, microbial communities must constantly adapt to stressful environmental conditions. The genetic and phenotypic mechanisms underlying the adaptive response of microbial communities to new (and often complex) environments can be tackled with a combination of experimental evolution and next generation sequencing. This combination allows to analyse the real-time evolution of microbial populations in response to imposed environmental factors or during the interaction with a host, by screening for phenotypic and genotypic changes over a multitude of identical experimental cycles. Experimental evolution (EE) coupled with comparative genomics has indeed facilitated the monitoring of bacterial genetic evolution and the understanding of adaptive evolution processes. Basically, EE studies had long been done on single strains, allowing to reveal the dynamics and genetic targets of natural selection and to uncover the correlation between genetic and phenotypic adaptive changes. However, species are always evolving in relation with other species and have to adapt not only to the environment itself but also to the biotic environment dynamically shaped by the other species. Nowadays, there is a growing interest to apply EE on microbial communities evolving under natural environments. In this paper, we provide a non-exhaustive review of microbial EE studies done with systems of increasing complexity (from single species, to synthetic communities and natural communities) and with a particular focus on studies between plants and plant-associated microorganisms. We highlight some of the mechanisms controlling the functioning of microbial species and their adaptive responses to environment changes and emphasize the importance of considering bacterial communities and complex environments in EE studies.

Genetic Causes of Non-pathogenic Pseudomonas syringae pv. actinidiae Isolates in Kiwifruit Orchards

Bacterial canker disease has become the largest threat to kiwifruit cultivation and production. A monomorphic subpopulation of Pseudomonas syringae pv. actinidiae biovar 3 (Psa3) is responsible for the pandemic worldwide. Diversity in pathogenicity has been found in the pandemic subpopulation and in other Psa3 subpopulations causing epidemics in China. However, the genetic bases have not yet been elucidated. In this study, 117 Psa3 isolates were identified by Psa- and Psa3-specific primers, and evaluated for pathogenicity. Three isolates G4, G40, and S2 are not pathogenic to kiwifruit and do not elicit hypersensitivity responses (HRs) in non-host Nicotiana benthamiana leaves. Two isolates, G25 and G35, exhibited attenuated HR-eliciting activity in non-host N. benthamiana, but they exhibited greatly and slightly reduced pathogenicity in host plants, respectively. The genomes of the five isolates were sequenced and compared with closely related isolates revealed by MLVA and whole-genome typing methods. The candidate genetic loci responsible for the changes in pathogenicity and HR elicitation, were further evaluated by allele replacement experiments. We found that the three non-pathogenic isolates were formed due to the independent, identical insertion events of ISPsy36 transposon in the hrpR gene, encoding a key regulator of type III secretion system (T3SS) and type III effectors (T3Es). In the symptomatic sample from which G4 was isolated, 27% HR negative isolates were detected. In isolate G25, transposon insertion of ISPsy32 at the non-coding sequence upstream of the hrpR gene was detected, similar to a previously reported low-virulent Psa3 strain M227. In isolate G35, we detected disruptions of T3Es hopBB1-1 and hopBB1-2, which induce HR in N. benthamiana leaves revealed by Agrobacterium tumefaciens infiltration. These phenotype-changed isolates were formed at low frequencies during the course of pathogen infection in host plants, supported by the binding assay of ISPsy32 and the non-coding DNA sequences upstream of the hrpR gene, the co-isolation of the virulent isolates belonging to the same MLVA clade, and the low levels of transcription of the transposon genes. Taken together, in terms of short-term field evolution, transposon insertions in the T3SS-related genes resulted in the formation of non-pathogenic and low-virulent Psa3 isolates.

Consequences of adaptation of TAL effectors on host susceptibility to Xanthomonas

Transcription activator-like effectors (TALEs) are virulence factors of Xanthomonas that induce the expression of host susceptibility (S) genes by specifically binding to effector binding elements (EBEs) in their promoter regions. The DNA binding specificity of TALEs is dictated by their tandem repeat regions, which are highly variable between different TALEs. Mutation of the EBEs of S genes is being utilized as a key strategy to generate resistant crops against TALE-dependent pathogens. However, TALE adaptations through rearrangement of their repeat regions is a potential obstacle for successful implementation of this strategy. We investigated the consequences of TALE adaptations in the citrus pathogen Xanthomonas citri subsp. citri (Xcc), in which PthA4 is the TALE required for pathogenicity, whereas CsLOB1 is the corresponding susceptibility gene, on host resistance. Seven TALEs, containing two-to-nine mismatching-repeats to the EBE_PthA4 that were unable to induce CsLOB1 expression, were introduced into Xcc pthA4:Tn5 and adaptation was simulated by repeated inoculations into and isolations from sweet orange for a duration of 30 cycles. While initially all strains failed to promote disease, symptoms started to appear between 9–28 passages in four TALEs, which originally harbored two-to-five mismatches. Sequence analysis of adapted TALEs identified deletions and mutations within the TALE repeat regions which enhanced putative affinity to the CsLOB1 promoter. Sequence analyses suggest that TALEs adaptations result from recombinations between repeats of the TALEs. Reintroduction of these adapted TALEs into Xcc pthA4:Tn5 restored the ability to induce the expression of CsLOB1, promote disease symptoms and colonize host plants. TALEs harboring seven-to-nine mismatches were unable to adapt to overcome the incompatible interaction. Our study experimentally documented TALE adaptations to incompatible EBE and provided strategic guidance for generation of disease resistant crops against TALE-dependent pathogens.

Mutation of the EBEs of susceptibility (S) genes via genome editing and utilization of naturally occurring EBE variants have been used to generate disease resistant plants. However, TALE adaptations may lead to resistance loss, limiting the long-term efficacy of the strategy.

We utilized an experimental evolution approach to test TALEs adaptations in the Xanthomonas citri-citrus pathosystem using designer TALEs that cannot recognize the EBE of host targets. We identified adaptive TALE mutations and deletions that occurred during less than 30 cycles of repeated infections, which reconstituted the virulence on the host. Adaptive variants originated from TALEs that harbored a small number of mismatches (≤5) to the EBE, whereas designer TALEs that harbored larger number of mismatches (≥7) to the EBE failed to adapt in the duration of this study. Our study experimentally demonstrates adaptive rearrangements of TALEs during host adaptation and suggests that the potential durability in the resistance of modified crops should be a significant factor to be considered prior to their introduction into the field.

Genome-Scale Investigation of the Metabolic Determinants Generating Bacterial Fastidious Growth

Xylella fastidiosa is one of the most important threats to plant health worldwide, causing disease in the Americas on a range of agricultural crops and trees, and recently associated with a critical epidemic affecting olive trees in Europe. A main challenge for the detection of the pathogen and the development of physiological studies is its fastidious growth, as the generation time can vary from 10 to 100 h for some strains. This physiological peculiarity is shared with several human pathogens and is poorly understood. We performed an analysis of the metabolic capabilities of X. fastidiosa through a genome-scale metabolic model of the bacterium. This model was reconstructed and manually curated using experiments and bibliographical evidence. Our study revealed that fastidious growth most probably results from different metabolic specificities such as the absence of highly efficient enzymes or a global inefficiency in virulence factor production. These results support the idea that the fragility of the metabolic network may have been shaped during evolution to lead to the self-limiting behavior of X. fastidiosa.

High proliferation rate and robustness are vital characteristics of bacterial pathogens that successfully colonize their hosts. The observation of drastically slow growth in some pathogens is thus paradoxical and remains unexplained. In this study, we sought to understand the slow (fastidious) growth of the plant pathogen Xylella fastidiosa. Using genome-scale metabolic network reconstruction, modeling, and experimental validation, we explored its metabolic capabilities. Despite genome reduction and slow growth, the pathogen’s metabolic network is complete but strikingly minimalist and lacking in robustness. Most alternative reactions were missing, especially those favoring fast growth, and were replaced by less efficient paths. We also found that the production of some virulence factors imposes a heavy burden on growth. Interestingly, some specific determinants of fastidious growth were also found in other slow-growing pathogens, enriching the view that these metabolic peculiarities are a pathogenicity strategy to remain at a low population level.

IMPORTANCEXylella fastidiosa is one of the most important threats to plant health worldwide, causing disease in the Americas on a range of agricultural crops and trees, and recently associated with a critical epidemic affecting olive trees in Europe. A main challenge for the detection of the pathogen and the development of physiological studies is its fastidious growth, as the generation time can vary from 10 to 100 h for some strains. This physiological peculiarity is shared with several human pathogens and is poorly understood. We performed an analysis of the metabolic capabilities of X. fastidiosa through a genome-scale metabolic model of the bacterium. This model was reconstructed and manually curated using experiments and bibliographical evidence. Our study revealed that fastidious growth most probably results from different metabolic specificities such as the absence of highly efficient enzymes or a global inefficiency in virulence factor production. These results support the idea that the fragility of the metabolic network may have been shaped during evolution to lead to the self-limiting behavior of X. fastidiosa.

Experimental Evolution of Legume Symbionts: What Have We Learnt?

Rhizobia, the nitrogen-fixing symbionts of legumes, are polyphyletic bacteria distributed in many alpha- and beta-proteobacterial genera. They likely emerged and diversified through independent horizontal transfers of key symbiotic genes. To replay the evolution of a new rhizobium genus under laboratory conditions, the symbiotic plasmid of Cupriavidus taiwanensis was introduced in the plant pathogen Ralstonia solanacearum, and the generated proto-rhizobium was submitted to repeated inoculations to the C. taiwanensis host, Mimosa pudica L.. This experiment validated a two-step evolutionary scenario of key symbiotic gene acquisition followed by genome remodeling under plant selection. Nodulation and nodule cell infection were obtained and optimized mainly via the rewiring of regulatory circuits of the recipient bacterium. Symbiotic adaptation was shown to be accelerated by the activity of a mutagenesis cassette conserved in most rhizobia. Investigating mutated genes led us to identify new components of R. solanacearum virulence and C. taiwanensis symbiosis. Nitrogen fixation was not acquired in our short experiment. However, we showed that post-infection sanctions allowed the increase in frequency of nitrogen-fixing variants among a non-fixing population in the M. pudica-C. taiwanensis system and likely allowed the spread of this trait in natura. Experimental evolution thus provided new insights into rhizobium biology and evolution.

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.

Modulation of Quorum Sensing as an Adaptation to Nodule Cell Infection during Experimental Evolution of Legume Symbionts

Over millions of years, changes have occurred in regulatory circuitries in response to genome reorganization and/or persistent changes in environmental conditions. How bacteria optimize regulatory circuitries is crucial to understand bacterial adaptation. Here, we analyzed the experimental evolution of the plant pathogen Ralstonia solanacearum into legume symbionts after the transfer of a natural plasmid encoding the essential mutualistic genes. We showed that the Phc quorum sensing system required for the virulence of the ancestral bacterium was reconfigured to improve intracellular infection of root nodules induced by evolved Ralstonia A single mutation in either the PhcB autoinducer synthase or the PhcQ regulator of the sensory cascade tuned the kinetics of activation of the central regulator PhcA in response to cell density so that the minimal stimulatory concentration of autoinducers needed for a given response was increased. Yet, a change in the expression of a PhcA target gene was observed in infection threads progressing in root hairs, suggesting early programming for the late accommodation of bacteria in nodule cells. Moreover, this delayed switch to the quorum sensing mode decreased the pathogenicity of the ancestral strain, illustrating the functional plasticity of regulatory systems and showing how a small modulation in signal response can produce drastic changes in bacterial lifestyle.IMPORTANCE Rhizobia are soil bacteria from unrelated genera able to form a mutualistic relationship with legumes. Bacteria induce the formation of root nodules, invade nodule cells, and fix nitrogen to the benefit of the plant. Rhizobial lineages emerged from the horizontal transfer of essential symbiotic genes followed by genome remodeling to activate and/or optimize the acquired symbiotic potential. This evolutionary scenario was replayed in a laboratory evolution experiment in which the plant pathogen Ralstonia solanacearum successively evolved the capacities to nodulate Mimosa pudica and poorly invade, then massively invade, nodule cells. In some lines, the improvement of intracellular infection was achieved by mutations modulating a quorum sensing regulatory system of the ancestral strain. This modulation that affects the activity of a central regulator during the earliest stages of symbiosis has a huge impact on late stages of symbiosis. This work showed that regulatory rewiring is the main driver of this pathogeny-symbiosis transition.

Phage combination therapies for bacterial wilt disease in tomato

Bacteriophages have been proposed as an alternative to pesticides to kill bacterial pathogens of crops. However, the efficacy of phage biocontrol is variable and poorly understood in natural rhizosphere microbiomes. We studied biocontrol efficacy of different phage combinations on Ralstonia solanacearum infection in tomato. Increasing the number of phages in combinations decreased the incidence of disease by up to 80% in greenhouse and field experiments during a single crop season. The decreased incidence of disease was explained by a reduction in pathogen density and the selection for phage-resistant but slow-growing pathogen strains, together with enrichment for bacterial species that were antagonistic toward R. solanacearum. Phage treatment did not affect the existing rhizosphere microbiota. Specific phage combinations have potential as precision tools to control plant pathogenic bacteria.

Spontaneous mutations in a regulatory gene induce phenotypic heterogeneity and adaptation of Ralstonia solanacearum to changing environments

An evolution experiment with the bacterial plant pathogen Ralstonia solanacearum revealed that several adaptive mutations conferring enhanced fitness in plants arose in the efpR gene encoding a regulator of virulence and metabolic functions. In this study, we found that an efpR mutant systematically displays colonies with two morphotypes: the type S ('smooth', similar to the wild type) and the type EV ('efpR variant'). We demonstrated that the efpH gene, a homologue of efpR, plays a key role in the control of phenotypic heterogeneity, the ΔefpR-ΔefpH double mutant being stably locked into the EV type. Using mixed infection assays, we demonstrated that the type EV is metabolically more proficient than the type S and displays fitness gain in specific environments, whereas the type S has a better fitness into the plant environment. We provide evidence that this efpR-dependent phenotypic heterogeneity is a general feature of strains of the R. solanacearum species complex and could occur in natural conditions. This study highlights the potential role of phenotypic heterogeneity in this plant pathogen as an adaptive trait to changing environments.

The pleiotropic Legionella transcription factor LvbR links the Lqs and c-di-GMP regulatory networks to control biofilm architecture and virulence

The causative agent of Legionnaires' disease, Legionella pneumophila, colonizes amoebae and biofilms in the environment. The opportunistic pathogen employs the Lqs (Legionella quorum sensing) system and the signalling molecule LAI-1 (Legionella autoinducer-1) to regulate virulence, motility, natural competence and expression of a 133 kb genomic "fitness island", including a putative novel regulator. Here, we show that the regulator termed LvbR is an LqsS-regulated transcription factor that binds to the promoter of lpg1056/hnox1 (encoding an inhibitor of the diguanylate cyclase Lpg1057), and thus, regulates proteins involved in c-di-GMP metabolism. LvbR determines biofilm architecture, since L. pneumophila lacking lvbR accumulates less sessile biomass and forms homogeneous mat-like structures, while the parental strain develops more compact bacterial aggregates. Comparative transcriptomics of sessile and planktonic ΔlvbR or ΔlqsR mutant strains revealed concerted (virulence, fitness island, metabolism) and reciprocally (motility) regulated genes in biofilm and broth respectively. Moreover, ΔlvbR is hyper-competent for DNA uptake, defective for phagocyte infection, outcompeted by the parental strain in amoebae co-infections and impaired for cell migration inhibition. Taken together, our results indicate that L. pneumophila LvbR is a novel pleiotropic transcription factor, which links the Lqs and c-di-GMP regulatory networks to control biofilm architecture and pathogen-host cell interactions.

The Ralstonia solanacearum csp22 peptide, but not flagellin-derived peptides, is perceived by plants from the Solanaceae family

Ralstonia solanacearum, the causal agent of bacterial wilt disease, is considered one of the most destructive bacterial pathogens due to its lethality, unusually wide host range, persistence and broad geographical distribution. In spite of the extensive research on plant immunity over the last years, the perception of molecular patterns from R. solanacearum that activate immunity in plants is still poorly understood, which hinders the development of strategies to generate resistance against bacterial wilt disease. The perception of a conserved peptide of bacterial flagellin, flg22, is regarded as paradigm of plant perception of invading bacteria; however, no elicitor activity has been detected for R. solanacearum flg22. Recent reports have shown that other epitopes from flagellin are able to elicit immune responses in specific species from the Solanaceae family, yet our results show that these plants do not perceive any epitope from R. solanacearum flagellin. Searching for elicitor peptides from R. solanacearum, we found several protein sequences similar to the consensus of the elicitor peptide csp22, reported to elicit immunity in specific Solanaceae plants. A R. solanacearum csp22 peptide (csp22Rsol ) was indeed able to trigger immune responses in Nicotiana benthamiana and tomato, but not in Arabidopsis thaliana. Additionally, csp22Rsol treatment conferred increased resistance to R. solanacearum in tomato. Transgenic A. thaliana plants expressing the tomato csp22 receptor (SlCORE) gained the ability to respond to csp22Rsol and became more resistant to R. solanacearum infection. Our results shed light on the mechanisms for perception of R. solanacearum by plants, paving the way for improving current approaches to generate resistance against R. solanacearum.

How Ralstonia solanacearum Exploits and Thrives in the Flowing Plant Xylem Environment

The plant wilt pathogen Ralstonia solanacearum thrives in the water-transporting xylem vessels of its host plants. Xylem is a relatively nutrient-poor, high-flow environment but R. solanacearum succeeds there by tuning its own metabolism and altering xylem sap biochemistry. Flow influences many traits that the bacterium requires for pathogenesis. Most notably, a quorum sensing system mediates the pathogen's major transition from a rapidly dividing early phase that voraciously consumes diverse food sources and avidly adheres to plant surfaces to a slower-growing late phase that can use fewer nutrients but produces virulence factors and disperses effectively. This review discusses recent findings about R. solanacearum pathogenesis in the context of its flowing in planta niche, with emphasis on R. solanacearum metabolism in plants.

Parallels between experimental and natural evolution of legume symbionts

The emergence of symbiotic interactions has been studied using population genomics in nature and experimental evolution in the laboratory, but the parallels between these processes remain unknown. Here we compare the emergence of rhizobia after the horizontal transfer of a symbiotic plasmid in natural populations of Cupriavidus taiwanensis, over 10 MY ago, with the experimental evolution of symbiotic Ralstonia solanacearum for a few hundred generations. In spite of major differences in terms of time span, environment, genetic background, and phenotypic achievement, both processes resulted in rapid genetic diversification dominated by purifying selection. We observe no adaptation in the plasmid carrying the genes responsible for the ecological transition. Instead, adaptation was associated with positive selection in a set of genes that led to the co-option of the same quorum-sensing system in both processes. Our results provide evidence for similarities in experimental and natural evolutionary transitions and highlight the potential of comparisons between both processes to understand symbiogenesis.

It is unclear if experimental evolution is a good model for natural processes. Here, Clerissi et al. find parallels between the evolution of symbiosis in rhizobia after horizontal transfer of a plasmid over 10 million years ago and experimentally evolved symbionts.

Involvement of ralfuranones in the quorum sensing signalling pathway and virulence of Ralstonia solanacearum strain OE1-1

The soil-borne, plant-pathogenic Ralstonia solanacearum strain OE1-1 produces and secretes methyl 3-hydroxymyristate (3-OH MAME) as a quorum sensing (QS) signal, which contributes to its virulence. A global virulence regulator, PhcA, functioning through the QS system, positively regulates the expression of ralA, which encodes furanone synthase, to produce aryl-furanone secondary metabolites, ralfuranones. A ralfuranone-deficient mutant (ΔralA) is weakly virulent when directly inoculated into tomato xylem vessels. To investigate the functions of ralfuranones, we analysed R. solanacearum transcriptome data generated by RNA sequencing technology. ΔralA expressed phcB, which is associated with 3-OH MAME production, and phcA at levels similar to those in strain OE1-1. In addition, ΔralA exhibited down-regulated expression of more than 90% of the QS positively regulated genes, and up-regulated expression of more than 75% of the QS negatively regulated genes. These results suggest that ralfuranones affect the QS feedback loop. Ralfuranone supplementation restored the ability of ΔralA cells to aggregate. In addition, ralfuranones A and B restored the swimming motility of ΔralA to wild-type levels. However, the application of exogenous ralfuranones did not affect the production of the major exopolysaccharide, EPS I, in ΔralA. Quantitative real-time polymerase chain reaction assays revealed that the deletion of ralA results in the down-regulated expression of vsrAD and vsrBC, which encode a sensor kinase and a response regulator, respectively, in the two-component regulatory systems that influence EPS I production. The application of ralfuranone B restored the expression of these two genes. Overall, our findings indicate that integrated signalling via ralfuranones influences the QS and virulence of R. solanacearum.

Control of primary metabolism by a virulence regulatory network promotes robustness in a plant pathogen

Robustness is a key system-level property of living organisms to maintain their functions while tolerating perturbations. We investigate here how a regulatory network controlling multiple virulence factors impacts phenotypic robustness of a bacterial plant pathogen. We reconstruct a cell-scale model of Ralstonia solanacearum connecting a genome-scale metabolic network, a virulence macromolecule network, and a virulence regulatory network, which includes 63 regulatory components. We develop in silico methods to quantify phenotypic robustness under a broad set of conditions in high-throughput simulation analyses. This approach reveals that the virulence regulatory network exerts a control of the primary metabolism to promote robustness upon infection. The virulence regulatory network plugs into the primary metabolism mainly through the control of genes likely acquired via horizontal gene transfer, which results in a functional overlay with ancestral genes. These results support the view that robustness may be a selected trait that promotes pathogenic fitness upon infection.

Identification of Cyclic Dipeptides from Escherichia coli as New Antimicrobial Agents against Ralstonia Solanacearum

Ralstonia solanacearum is a causative agent of bacterial wilt in many important crops throughout the world. How to control bacterial wilt caused by R. solanacearum is a major problem in agriculture. In this study, we aim to isolate the biocontrol agents that have high efficacy in the control of bacterial wilt. Three new bacterial strains with high antimicrobial activity against R. solanacearum GMI1000 were isolated and identified. Our results demonstrated that these bacteria could remarkably inhibit the disease index of host plant infected by R. solanacearum. It was indicated that strain GZ-34 (CCTCC No. M 2016353) showed an excellent protective effect to tomato under greenhouse conditions. Strain GZ-34 was characterized as Escherichia coli based on morphology, biochemistry, and 16S rRNA analysis. We identified that the main antimicrobial compounds produced by E. coli GZ-34 were cyclo(l-Pro-d-Ile) and cyclo(l-Pro-l-Phe) using electrospray ionization mass spectrometry (ESI-MS) and nuclear magnetic resonance (NMR) analysis. The two active compounds also interfered with the expression levels of some pathogenicity-contributors of R. solanacearum. Furthermore, cyclo(l-Pro-l-Phe) effectively inhibited spore formation of Magnaporthe grisea, which is a vital pathogenesis process of the fungal pathogen, suggesting cyclic dipeptides from E. coli are promising potential antimicrobial agents with broad-spectrum activity to kill pathogens or interfere with their pathogenesis.

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.

Modulation of Inter-kingdom Communication by PhcBSR Quorum Sensing System in Ralstonia solanacearum Phylotype I Strain GMI1000

Ralstonia solanacearum is a ubiquitous soil-borne plant pathogenic bacterium, which frequently encounters and interacts with other soil cohabitants in competition for environmental niches. Ralsolamycin, which is encoded by the rmy genes, has been characterized as a novel inter-kingdom interaction signal that induces chlamydospore development in fungi. In this study, we provide the first genetic evidence that the rmy gene expression is controlled by the PhcBSR quorum sensing (QS) system in strain GMI1000. Mutation of phcB could lead to significant reduction of the expression levels of the genes involved in ralsolamycin biosynthesis. In addition, both the phcB and rmy mutants were attenuated in induction of chlamydospore formation in Fusarium oxysporum f. cubense and diminished in the ability to compete with the sugarcane pathogen Sporisorium scitamineum. Agreeable with the pattern of QS regulation, transcriptional expression analysis showed that the transcripts of the rmy genes were increased along with the increment of the bacterial population density. Taken together, the above findings provide new insights into the regulatory mechanisms that the QS system involves in governing the ralsolamycin inter-kingdom signaling system.

Codon optimization underpins generalist parasitism in fungi

The range of hosts that parasites can infect is a key determinant of the emergence and spread of disease. Yet, the impact of host range variation on the evolution of parasite genomes remains unknown. Here, we show that codon optimization underlies genome adaptation in broad host range parasites. We found that the longer proteins encoded by broad host range fungi likely increase natural selection on codon optimization in these species. Accordingly, codon optimization correlates with host range across the fungal kingdom. At the species level, biased patterns of synonymous substitutions underpin increased codon optimization in a generalist but not a specialist fungal pathogen. Virulence genes were consistently enriched in highly codon-optimized genes of generalist but not specialist species. We conclude that codon optimization is related to the capacity of parasites to colonize multiple hosts. Our results link genome evolution and translational regulation to the long-term persistence of generalist parasitism.