Paraburkholderia Phytofirmans PsJN Research Articles

Manipulation of sward diversity is a more effective management strategy than addition of microbial inoculants in intensively managed grassland

Abstract Background and aims Diversifying grassland sward composition and application of microbial inoculants are potential alternative routes to facilitate enhanced nutrient acquisition by plants, but their relative effects have been rarely tested in grasslands. In a two-year field experiment, we investigated the impact of inoculants and sward types on forage yield, nutrient uptake, and the soil microbiome. Methods We implemented a fully factorial experiment with inoculants (eight levels; arbuscular mycorrhizal fungi (AMF), Paraburkholderia phytofirmans PsJN and Bacillus sp. P5 (P5), applied singly and in combination), and sward types (three levels: grass-only, grass and legume, mixture of grass, legume, and herb) as the two factors. Results In both years, there was a very strong effect of sward type, with the grass + legume and grass + legume + herb swards having much higher yields and nutrient uptake (N, P, K, S, Ca, Mg, Zn, Cu) than grass-only. Generally, there was no effect of the inoculants on yield and nutrient uptake, with limited exceptions involving AMF + P5. The best-performing microbial inoculant increased forage yield by 597 kg/ha/year, while switching from grass-only to one of the other sward types increased forage yield by 3932 kg/ha/year (grass + legume) and 4693 kg/ha/year (grass + legume + herb). The inoculants persisted in plots for > 1 year after application. Inoculants and sward type significantly affected the overall prokaryotic and fungal community structures. Conclusion Overall, under controlled field plot conditions, including legumes and herbs in a grass sward proved to be a far better farm-scale management strategy for increasing grassland forage yield and nutrient uptake than the application of microbial inoculants.

Metabolic changes in tomato plants caused by psychrotolerant Antarctic endophytic bacteria might be implicated in cold stress mitigation.

Climate change is responsible for mild winters and warm springs that can induce premature plant development, increasing the risk of exposure to cold stress with a severe reduction in plant growth. Tomato plants are sensitive to cold stress and beneficial microorganisms can increase their tolerance. However, scarce information is available on mechanisms stimulated by bacterial endophytes in tomato plants against cold stress. This study aimed to clarify metabolic changes stimulated by psychrotolerant endophytic bacteria in tomato plants exposed to cold stress and annotate compounds possibly associated with cold stress mitigation. Tomato seeds were inoculated with two bacterial endophytes isolated from Antarctic Colobanthus quitensis plants (Ewingella sp. S1.OA.A_B6 and Pseudomonas sp. S2.OTC.A_B10) or with Paraburkholderia phytofirmans PsJN, while mock-inoculated seeds were used as control. The metabolic composition of tomato plants was analyzed immediately after cold stress exposure (4°C for seven days) or after two and four days of recovery at 25°C. Under cold stress, the content of malondialdehyde, phenylalanine, ferulic acid, and p-coumaric acid was lower in bacterium-inoculated compared to mock-inoculated plants, indicating a reduction of lipid peroxidation and the stimulation of phenolic compound metabolism. The content of two phenolic compounds, five putative phenylalanine-derived dipeptides, and three further phenylalanine-derived compounds was higher in bacterium-inoculated compared to mock-inoculated samples under cold stress. Thus, psychrotolerant endophytic bacteria can reprogram polyphenol metabolism and stimulate the accumulation of secondary metabolites, like 4-hydroxybenzoic and salicylic acid, which are presumably involved in cold stress mitigation, and phenylalanine-derived dipeptides possibly involved in plant stress responses.

Inoculation and tracking of beneficial microbes reveal they can establish in field-grown potato roots and decrease blemish diseases

In a three-year field study, we inoculated two potato varieties with a selection of four beneficial microbial strains (i.e. Rhizophagus irregularis MUCL41833, Trichoderma asperelloides A, Pseudomonas brassicacearum 3Re2-7 and Paraburkholderia phytofirmans PsJN), alone or in combination. Plants were grown under rainfed or irrigated conditions, and potato yield and development of several diseases were evaluated. The microbial inoculants were traced in the root system at different stages of crop development via molecular markers. Whatever the water supply, the inoculants had no effect on yield. Conversely, some of the inoculants were able to lower the incidence and/or severity of several blemish diseases, namely common scab-associated symptoms (CSAS) and silver scurf/black dot-associated symptoms (SSAS). Microbial consortia were more efficient in decreasing symptoms compared to single strain inoculations. The best control was obtained with the combination of R. irregularis and P. brassicacearum, which reduced the incidence of CSAS by 22% and severity of SSAS by 21%. Root tracking revealed that P. brassicacearum and P. phytofirmans PsJN were able to establish in the root system of the potato, while only P. brassicacearum was detected from emergence until flowering of the plants.

Control of Pierce's Disease of Grape with Paraburkholderia phytofirmans PsJN in the Field.

Replicated field studies were conducted to evaluate the factors that could influence the efficacy of Paraburkholderia phytofirmans PsJN for the control of Pierce's disease of grape, as well as to determine the extent to which disease control was systemic within plants. Topical applications of PsJN with an organosilicon surfactant was an effective way to introduce this bacterium under field conditions and provided similar levels of disease control as its mechanical inoculation. Disease incidence in inoculated shoots was often reduced two- to threefold when PsJN was inoculated a single time as much as 3 weeks before Xylella fastidiosa and up to 5 weeks after the pathogen. Inoculation of a shoot with PsJN greatly decreased the probability of any symptoms rather than reducing the severity of disease, suggesting a systemic protective response of individual shoots. Although the likelihood of disease symptoms on shoots inoculated with the pathogen on PsJN-treated plants was lower than on control plants inoculated only with the pathogen, the protection conferred by PsJN was not experienced by all shoots on a given plant. This suggested that any systemic resistance was spatially limited. Whereas the population size of PsJN increased to more than 106 cells/g and spread more than 1 m within 12 weeks after its inoculation alone into grape, its population size subsequently decreased greatly after about 5 weeks, and its distal dispersal in stems was restricted when co-inoculated with X. fastidiosa. PsJN may experience collateral damage from apparent host responses induced when both species are present.

Exopolysaccharide is required for motility, stress tolerance, and plant colonization by the endophytic bacterium Paraburkholderia phytofirmans PsJN.

Paraburkholderia phytofirmans PsJN is an endophytic bacterium and has been shown to promote the growth and health of many different plants. Exopolysaccharide (EPS) plays important roles in plant-bacteria interaction and tolerance to environmental stresses. However, the function of EPS in PsJN and its interaction with plants remain largely unknown. In this study, a deletion mutation of bceQ gene, encoding a putative flippase for the EPS biosynthesis, was introduced in the genome of PsJN. The ΔbceQ mutant produced a significantly lower level of EPS than the wild type strain in culture media. Compared to the wild type PsJN, the ΔbceQ mutant was more sensitive to desiccation, UV damage, salt (NaCl) and iron (FeCl3) stresses, and bacteriophage infection. More importantly, the mutation of bceQ decreased the endophytic colonization of PsJN in camelina (Camelina sativa) and pea (Camelina sativa) under plant drought stress conditions. To the best of our knowledge, this is the first report that EPS production is required for the maximal colonization of an endophytic bacterium in the plant tissues under stress conditions.

Paraburkholderia phytofirmans PsJN colonization of rice endosphere triggers an atypical transcriptomic response compared to rice native Burkholderia s.l. endophytes

The plant microbiome has recently emerged as a reservoir for the development of sustainable alternatives to chemical fertilizers and pesticides. However, the response of plants to beneficial microbes emerges as a critical issue to understand the molecular basis of plant-microbiota interactions. In this study, we combined root colonization, phenotypic and transcriptomic analyses to unravel the commonalities and specificities of the response of rice to closely related Burkholderia s.l. endophytes. In general, these results indicate that a rice-non-native Burkholderia s.l. strain, Paraburkholderia phytofirmans PsJN, is able to colonize the root endosphere while eliciting a markedly different response compared to rice-native Burkholderia s.l. strains. This demonstrates the variability of plant response to microbes from different hosts of origin. The most striking finding of the investigation was that a much more conserved response to the three endophytes used in this study is elicited in leaves compared to roots. In addition, transcriptional regulation of genes related to secondary metabolism, immunity, and phytohormones appear to be markers of strain-specific responses. Future studies need to investigate whether these findings can be extrapolated to other plant models and beneficial microbes to further advance the potential of microbiome-based solutions for crop production.

Gene regulatory networks with binary weights

An evolutionary computation framework to learn binary threshold networks is presented. Inspired by the recent trend of binary neural networks, where weights and activation thresholds are represented using 1 and -1 such that they can be stored in 1-bit instead of full precision, we explore this approach for gene regulatory network modeling. We test our method by inferring binary threshold networks of two regulatory network models: Quorum sensing systems in bacterium Paraburkholderia phytofirmans PsJN and the fission yeast cell-cycle. We considered differential evolution and particle swarm optimization for the simulations. Results for weights having only 1 and -1 values, and different activation thresholds are presented. Full binary threshold networks were found with minimum error (2 bits), whereas when the binary restriction is relaxed for the activation thresholds, networks with 0 bit error were found.

Plant-growth promotion by proteobacterial strains depends on the availability of phosphorus and iron in Arabidopsis thaliana plants.

Phosphorus (as phosphate, Pi) and iron (Fe) are critical nutrients in plants that are often poorly available in the soil and can be microbially affected. This work aimed to evaluate how plant-rhizobacteria interaction changes due to different Pi or Fe nutritional scenarios and to study the underlying molecular mechanisms of the microbial modulation of these nutrients in plants. Thus, three proteobacteria (Paraburkholderia phytofirmans PsJN, Azospirillum brasilense Sp7, and Pseudomonas putida KT2440) were used to inoculate Arabidopsis seeds. Additionally, the seeds were exposed to a nutritional factor with the following levels for each nutrient: sufficient (control) or low concentrations of a highly soluble source or sufficient concentrations of a low solubility source. Then, the effects of the combinatorial factors were assessed in plant growth, nutrition, and genetic regulation. Interestingly, some bacterial effects in plants depended on the nutrient source (e.g., increased aerial zones induced by the strains), and others (e.g., decreased primary roots induced by Sp7 or KT2440) occurred regardless of the nutritional treatment. In the short-term, PsJN had detrimental effects on plant growth in the presence of the low-solubility Fe compound, but this was not observed in later stages of plant development. A thorough regulation of the phosphorus content was detected in plants independent of the nutritional treatment. Nevertheless, inoculation with KT2440 increased P content by 29% Pi-deficiency exposed plants. Conversely, the inoculation tended to decrease the Fe content in plants, suggesting a competition for this nutrient in the rhizosphere. The P-source also affected the effects of the PsJN strain in a double mutant of the phosphate starvation response (PSR). Furthermore, depending on the nutrient source, PsJN and Sp7 strains differentially regulated PSR and IAA- associated genes, indicating a role of these pathways in the observed differential phenotypical responses. In the case of iron, PsJN and SP7 regulated iron uptake-related genes regardless of the iron source, which may explain the lower Fe content in inoculated plants. Overall, the plant responses to these proteobacteria were not only influenced by the nutrient concentrations but also by their availabilities, the elapsed time of the interaction, and the specific identities of the beneficial bacteria. Graphical AbstractThe effects of the different nutritional and inoculation treatments are indicated for plant growth parameters (A), gene regulation (B) and phosphorus and iron content (C). Figures created with BioRender.com with an academic license.

Plant Growth Promotion and Heat Stress Amelioration in Arabidopsis Inoculated with Paraburkholderia phytofirmans PsJN Rhizobacteria Quantified with the GrowScreen-Agar II Phenotyping Platform.

High temperatures inhibit plant growth. A proposed strategy for improving plant productivity under elevated temperatures is the use of plant growth-promoting rhizobacteria (PGPR). While the effects of PGPR on plant shoots have been extensively explored, roots-particularly their spatial and temporal dynamics-have been hard to study, due to their below-ground nature. Here, we characterized the time- and tissue-specific morphological changes in bacterized plants using a novel non-invasive high-resolution plant phenotyping and imaging platform-GrowScreen-Agar II. The platform uses custom-made agar plates, which allow air exchange to occur with the agar medium and enable the shoot to grow outside the compartment. The platform provides light protection to the roots, the exposure of it to the shoots, and the non-invasive phenotyping of both organs. Arabidopsis thaliana, co-cultivated with Paraburkholderia phytofirmans PsJN at elevated and ambient temperatures, showed increased lengths, growth rates, and numbers of roots. However, the magnitude and direction of the growth promotion varied depending on root type, timing, and temperature. The root length and distribution per depth and according to time was also influenced by bacterization and the temperature. The shoot biomass increased at the later stages under ambient temperature in the bacterized plants. The study offers insights into the timing of the tissue-specific, PsJN-induced morphological changes and should facilitate future molecular and biochemical studies on plant-microbe-environment interactions.

Individual competence predominates over host nutritional status in Arabidopsis root exudate-mediated bacterial enrichment in a combination of four Burkholderiaceae species

BackgroundRhizosphere microorganisms play a crucial role in plant health and development. Plant root exudates (PRE) are a complex mixture of organic molecules and provide nutritional and signaling information to rhizosphere microorganisms. Burkholderiaceae species are non-abundant in the rhizosphere but exhibit a wide range of plant-growth-promoting and plant-health-protection effects. Most of these plant-associated microorganisms have been studied in isolation under laboratory conditions, whereas in nature, they interact in competition or cooperation with each other. To improve our understanding of the factors driving growth dynamics of low-abundant bacterial species in the rhizosphere, we hypothesized that the growth and survival of four Burkholderiaceae strains (Paraburkholderia phytofirmans PsJN, Cupriavidus metallidurans CH34, C. pinatubonensis JMP134 and C. taiwanensis LMG19424) in Arabidopsis thaliana PRE is affected by the presence of each other.ResultsDifferential growth abilities of each strain were found depending on plant age and whether PRE was obtained after growth on N limitation conditions. The best-adapted strain to grow in PRE was P. phytofirmans PsJN, with C. pinatubonensis JMP134 growing better than the other two Cupriavidus strains. Individual strain behavior changed when they succeeded in combinations. Clustering analysis showed that the 4-member co-culture grouped with one of the best-adapted strains, either P. phytofirmans PsJN or C. pinatubonensis JMP134, depending on the PRE used. Sequential transference experiments showed that the behavior of the 4-member co-culture relies on the type of PRE provided for growth.ConclusionsThe results suggest that individual strain behavior changed when they grew in combinations of two, three, or four members, and those changes are determined first by the inherent characteristics of each strain and secondly by the environment.

Comparative effect of seed treatment with thyme essential oil and Paraburkholderia phytofirmans on growth, photosynthetic capacity, grain yield, δ15N and δ13C of durum wheat under drought and heat stress

AbstractAbiotic stresses such as drought and heat constitute one of the major constraints to global crop production, and climate change will worsen the scenario. There is growing interest in investigating the application of biostimulants to palliate yield losses due to the impact of drought and heat stress. This study focuses on assessing the impact of coating seeds with either thyme essential oil or Paraburkholderia phytofirmans PsJN strain on agronomic performance of durum wheat subjected to contrasting levels of irrigation. For this aim, the Tunisian durum wheat genotype Karim was cultivated in a field experiment in a semi‐arid climate, with two supplemental irrigation levels (SI): moderate drought stress (100% SI) and severe drought stress (50% SI). The impact of the seed coating technique was assessed on grain yield (GY) and its agronomic components (spikes/m2, straw yield [SY], 1,000 kernel weight [TKW] and the harvest index [HI]) across two consecutive crop seasons; 2015–16 and 2016–17. In addition, the effect on leaf nitrogen and carbon isotope composition (δ15N, δ13C) and nitrogen and carbon contents of leaves at grain filling was also assessed in the 2016–17 season. The two seed coating treatments (SCTs) enhanced GY, SY, spikes/m2, TKW and HI under both moderate stress (100% SI) and severe stress (50% SI). The positive effect of the SCTs on GY and agronomic yield components was more marked under the combined heat–water stress conditions of the first season (2015–16). In general, thyme oil enhanced vegetative growth, tillering and tiller fertility, while, PsJN had a positive effect, more centred on the grain filling stage. Under moderate stress, both SCTs decreased δ15N and δ13C at grain filling and straw N content at harvest, illustrating a better carbon and nitrogen uptake and mobilisation. Under severe water stress, both SCTs induced higher leaf total N, and lower δ13C, and leaf total C at grain filling. The effect on physiological traits and carbon and nitrogen metabolism is discussed. The findings emphasise a practical implication of these biostimulants.

Humic Acid Enhances the Growth of Tomato Promoted by Endophytic Bacterial Strains Through the Activation of Hormone-, Growth-, and Transcription-Related Processes.

Plant growth-promoting bacteria (PGPB) are promising alternatives in the reduction of the use of chemical fertilizers. Likewise, humic acid (HA) can improve plant growth and/or the establishment of endophytic PGPB. Although the effects of PGPB colonization or HA treatment have been studied separately, little information is available on plant response to the combined applications of PGPB and HA. Thus, the aim of this work was to understand the physiological effects, bacterial colonization and transcriptional responses activated by endophytic bacterial strains in tomato roots and shoots in the absence (control condition) and presence of HA (HA condition). Tomato shoot length was promoted by seed inoculation with Paraburkholderia phytofirmans PsJN, Pantoea agglomerans D7G, or Enterobacter sp. 32A in the presence of HA, indicating a possible complementation of PGPB and HA effects. Tomato colonization by endophytic bacterial strains was comparable in the control and HA condition. The main transcriptional regulations occurred in tomato roots and the majority of differentially expressed genes (DEGs) was upregulated by endophytic bacterial strains in the HA condition. Half of the DEGs was modulated by two or three strains as possible common reactions to endophytic bacterial strains, involving protein metabolism, transcription, transport, signal transduction, and defense. Moreover, strain-specific tomato responses included the upregulation of signal transduction, transcription, hormone metabolism, protein metabolism, secondary metabolism, and defense processes, highlighting specific traits of the endophyte-tomato interaction. The presence of HA enhanced the upregulation of genes related to signal transduction, hormone metabolism, transcription, protein metabolism, transport, defense, and growth-related processes in terms of number of involved genes and fold change values. This study provides detailed information on HA-dependent enhancement of growth-related processes stimulated by endophytic bacterial strains in tomato plants and reports the optimized dosages, complementation properties and gene markers for the further development of efficient PGPB- and HA-based biostimulants.

Evaluating the combined effect of a systemic phenylpyrrole fungicide and the plant growth-promoting rhizobacteria Paraburkholderia phytofirmans (strain PsJN::gfp2x) against the grapevine trunk pathogen Neofusicoccum parvum.

A new chemical control strategy for grapevine trunk diseases (GTDs) is to develop site-targeted fungicides to protect grapevine vascular tissues. Due to the complexity of GTDs, the effectiveness of a single method is limited. Investigation of the interactions between chemical and biological agents is an essential requirement for integrated control strategies. The effect of a phloem-mobile derivative of the fungicide fenpiclonil (SM 26) in combined use with the plant growth-promoting rhizobacteria, Paraburkholderia phytofirmans PsJN on the Neofusicoccum parvum strain Bourgogne (NpB) was evaluated. SM 26 was found to be translocated to the shoot apices and roots of grapevines through both xylem and phloem after foliage application. In vitro studies demonstrated that SM 26 exhibited no inhibitory effect on the growth of PsJN and could be largely absorbed into the bacterial cells. In vivo evaluation showed that the combined use of SM 26 and PsJN was the most effective following artificial inoculation of NpB on the stems of rooted Chardonnay and Sauvignon cuttings. Finally, the expression of defence-related genes, including the genes associated with secondary metabolism (ANTS, PAL, STS, Vv17.3), defence proteins (GLUC, PR1, PGIP), redox status (GTS1) and ethylene synthesis (ACC), was found to be strongly upregulated in PsJN + SM 26 cotreated plants compared to non-treated plants (controls), especially for Chardonnay. The systemic profungicide SM 26 interacts with the biocontrol agent PsJN to stimulate some plant defence responses, and their combined use may present a potential integrated control strategy against GTDs. © 2020 Society of Chemical Industry.

Reconstruction of a gene regulatory network of the induced systemic resistance defense response in Arabidopsis using boolean networks

BackgroundAn important process for plant survival is the immune system. The induced systemic resistance (ISR) triggered by beneficial microbes is an important cost-effective defense mechanism by which plants are primed to an eventual pathogen attack. Defense mechanisms such as ISR depend on an accurate and context-specific regulation of gene expression. Interactions between genes and their products give rise to complex circuits known as gene regulatory networks (GRNs). Here, we explore the regulatory mechanism of the ISR defense response triggered by the beneficial bacterium Paraburkholderia phytofirmans PsJN in Arabidopsis thaliana plants infected with Pseudomonas syringae DC3000. To achieve this, a GRN underlying the ISR response was inferred using gene expression time-series data of certain defense-related genes, differential evolution, and threshold Boolean networks.ResultsOne thousand threshold Boolean networks were inferred that met the restriction of the desired dynamics. From these networks, a consensus network was obtained that helped to find plausible interactions between the genes. A representative network was selected from the consensus network and biological restrictions were applied to it. The dynamics of the selected network showed that the largest attractor, a limit cycle of length 3, represents the final stage of the defense response (12, 18, and 24 h). Also, the structural robustness of the GRN was studied through the networks’ attractors.ConclusionsA computational intelligence approach was designed to reconstruct a GRN underlying the ISR defense response in plants using gene expression time-series data of A. thaliana colonized by P. phytofirmans PsJN and subsequently infected with P. syringae DC3000. Using differential evolution, 1000 GRNs from time-series data were successfully inferred. Through the study of the network dynamics of the selected GRN, it can be concluded that it is structurally robust since three mutations were necessary to completely disarm the Boolean trajectory that represents the biological data. The proposed method to reconstruct GRNs is general and can be used to infer other biologically relevant networks to formulate new biological hypotheses.

Impact of Paraburkholderia phytofirmans PsJN on Grapevine Phenolic Metabolism.

Phenolic compounds are implied in plant-microorganisms interaction and may be induced in response to plant growth-promoting rhizobacteria (PGPRs). Among PGPR, the beneficial bacterium Paraburkholderia phytofirmans PsJN was previously described to stimulate the growth of plants and to induce a better adaptation to both abiotic and biotic stresses. This study aimed to investigate the impact of PsJN on grapevine secondary metabolism. For this purpose, gene expression (qRT-PCR) and profiling of plant secondary metabolites (UHPLC-UV/DAD-MS QTOF) from both grapevine root and leaves were compared between non-bacterized and PsJN-bacterized grapevine plantlets. Our results showed that PsJN induced locally (roots) and systemically (leaves) an overexpression of PAL and STS and specifically in leaves the overexpression of all the genes implied in phenylpropanoid and flavonoid pathways. Moreover, the metabolomic approach revealed that relative amounts of 32 and 17 compounds in roots and leaves, respectively, were significantly modified by PsJN. Once identified to be accumulated in response to PsJN by the metabolomic approach, antifungal properties of purified molecules were validated in vitro for their antifungal effect on Botrytis cinerea spore germination. Taking together, our findings on the impact of PsJN on phenolic metabolism allowed us to identify a supplementary biocontrol mechanism developed by this PGPR to induce plant resistance against pathogens.

Seed Coating with Thyme Essential Oil or Paraburkholderia phytofirmans PsJN Strain: Conferring Septoria Leaf Blotch Resistance and Promotion of Yield and Grain Isotopic Composition in Wheat

Septoria leaf blotch (SLB) is considered one of the most devastating diseases affecting global wheat production. Biostimulant application is among the modern approaches in plant protection to overcome the impact of SLB’s fungicide resistance. In this manner, the effect of coating seeds with thyme essential oil or Paraburkholderia phytofirmansPsJN strain on SLB severity and yield components (spikes/m2, straw yield (SY), grain yield (GY) and thousand kernel weight (TKW)) were assessed under field conditions for 3 years. The effect on physiological traits and nitrogen and carbon isotope composition (δ15Ngrain, δ13Cgrain) and nitrogen and carbon content (Ngrain, Cgrain) of grains was assessed in one year of study. The increasing SLB severity decreased all yield components, increased δ15Ngrain and Cgrain content and slightly decreased δ13Cgrain as the resulting effect of Z.tritici inducing stomatal opening and leaf necrosis. Across the years, both treatments alleviated the SLB adverse impact by reducing SLB severity, increasing spikes/m2, SY, GY and TKW. Both treatments ameliorated grain quality by increasing Cgrain content and decreasing δ13Cgrain and δ15Ngrain. The difference between the performance of thyme oil or PsJN strain in terms of intensity and stability is discussed and considered to be linked to the different triggered systemic resistance and the associated amount of costs deriving from resource allocation towards defense processes.

Gene networks underlying the early regulation of Paraburkholderia phytofirmans PsJN induced systemic resistance in Arabidopsis.

Plant defense responses to biotic stresses are complex biological processes, all governed by sophisticated molecular regulations. Induced systemic resistance (ISR) is one of these defense mechanisms where beneficial bacteria or fungi prime plants to resist pathogens or pest attacks. In ISR, the defense arsenal in plants remains dormant and it is only triggered by an infection, allowing a better allocation of plant resources. Our group recently described that the well-known beneficial bacterium Paraburkholderia phytofirmans PsJN is able to induce Arabidopsis thaliana resistance to Pseudomonas syringae pv. tomato (Pst) DC3000 through ISR, and that ethylene, jasmonate and salicylic acid are involved in this protection. Nevertheless, the molecular networks governing this beneficial interaction remain unknown. To tackle this issue, we analyzed the temporal changes in the transcriptome of PsJN-inoculated plants before and after being infected with Pst DC3000. These data were used to perform a gene network analysis to identify highly connected transcription factors. Before the pathogen challenge, the strain PsJN regulated 405 genes (corresponding to 1.8% of the analyzed genome). PsJN-inoculated plants presented a faster and stronger transcriptional response at 1-hour post infection (hpi) compared with the non-inoculated plants, which presented the highest transcriptional changes at 24 hpi. A principal component analysis showed that PsJN-induced plant responses to the pathogen could be differentiated from those induced by the pathogen itself. Forty-eight transcription factors were regulated by PsJN at 1 hpi, and a system biology analysis revealed a network with four clusters. Within these clusters LHY, WRKY28, MYB31 and RRTF1 are highly connected transcription factors, which could act as hub regulators in this interaction. Concordantly with our previous results, these clusters are related to jasmonate, ethylene, salicylic, acid and ROS pathways. These results indicate that a rapid and specific response of PsJN-inoculated plants to the virulent DC3000 strain could be the pivotal element in the protection mechanism.

Paraburkholderia phytofirmans PsJN-Plants Interaction: From Perception to the Induced Mechanisms.

The use of plant-associated bacteria has received many scientific and economic attention as an effective and alternative method to reduce the chemical pesticides use in agriculture. The genus Burkholderia includes at least 90 species including pathogenic strains, plant pathogens, as well as plant beneficial species as those related to Paraburkholderia, which has been reported to be associated with plants and exerts a positive effect on plant growth and fitness. Paraburkholderia phytofirmans PsJN, a beneficial endophyte able to colonize a wide range of plants, is an established model for plant-associated endophytic bacteria. Indeed, in addition to its plant growth promoting ability, it can also induce plant resistance against biotic as well as abiotic stresses. Here, we summarized an inventory of knowledge on PsJN-plant interaction, from the perception to the resistance mechanisms induced in the plant by a way of the atypical colonization mode of this endophyte. We also have carried out an extensive genome analysis to identify all gene clusters which contribute to the adaptive mechanisms under different environments and partly explaining the high ecological competence of P. phytofirmans PsJN.

Linkage of the Nit1C gene cluster to bacterial cyanide assimilation as a nitrogen source.

A genetic linkage between a conserved gene cluster (Nit1C) and the ability of bacteria to utilize cyanide as the sole nitrogen source was demonstrated for nine different bacterial species. These included three strains whose cyanide nutritional ability has formerly been documented (Pseudomonas fluorescens Pf11764, Pseudomonas putida BCN3 and Klebsiella pneumoniae BCN33), and six not previously known to have this ability [Burkholderia (Paraburkholderia) xenovorans LB400, Paraburkholderia phymatum STM815, Paraburkholderia phytofirmans PsJN, Cupriavidus (Ralstonia) eutropha H16, Gluconoacetobacter diazotrophicus PA1 5 and Methylobacterium extorquens AM1]. For all bacteria, growth on or exposure to cyanide led to the induction of the canonical nitrilase (NitC) linked to the gene cluster, and in the case of Pf11764 in particular, transcript levels of cluster genes (nitBCDEFGH) were raised, and a nitC knock-out mutant failed to grow. Further studies demonstrated that the highly conserved nitB gene product was also significantly elevated. Collectively, these findings provide strong evidence for a genetic linkage between Nit1C and bacterial growth on cyanide, supporting use of the term cyanotrophy in describing what may represent a new nutritional paradigm in microbiology. A broader search of Nit1C genes in presently available genomes revealed its presence in 270 different bacteria, all contained within the domain Bacteria, including Gram-positive Firmicutes and Actinobacteria, and Gram-negative Proteobacteria and Cyanobacteria. Absence of the cluster in the Archaea is congruent with events that may have led to the inception of Nit1C occurring coincidentally with the first appearance of cyanogenic species on Earth, dating back 400-500 million years.

A Boolean network model of bacterial quorum-sensing systems

There are several mathematical models to represent gene regulatory networks, one of the simplest is the Boolean network paradigm. In this paper, we reconstruct a regulatory network of bacterial quorum-sensing systems, in particular, we consider Paraburkholderia phytofirmans PsJN which is a plant growth promoting bacteria that produces positive effects in horticultural crops like tomato, potato and grape. To learn the regulatory network from temporal expression pattern of quorum-sensing genes at root plants, we present a methodology that considers the training of perceptrons for each gene and then the integration into one Boolean regulatory network. Using the proposed approach, we were able to infer a regulatory network model whose topology and dynamic exhibited was helpful to gain insight on the quorum-sensing systems regulation mechanism. We compared our results with REVEAL and Best-Fit extension algorithm, showing that the proposed neural network approach obtained a more biologically meaningful network and dynamics, demonstrating the effectiveness of the proposed method.