The biocontrol agent Pseudomonas chlororaphis PA23 primes Brassica napus defenses through distinct gene networks

Transcriptome analysis unravels the biocontrol mechanism of Serratia plymuthica A30 against potato soft rot caused by Dickeya solani

Endophytic bacterium Serratia plymuthica A30 was identified as a superior biocontrol agent due to its effective colonization of potato tuber, tolerance to cold conditions, and strong inhibitory action against various soft rot pathogens, including Dickeya solani. We characterized transcriptome changes in potato tubers inoculated with S. plymuthica A30, D. solani, or both at the early and the late phases of interaction. At the early phase and in the absence of the pathogen, A30 influenced the microbial recognition system to initiate plant priming. In the presence of the pathogen alongside biocontrol strain, defense signaling was highly stimulated, characterized by the induction of genes involved in the detoxification system, reinforcement of cell wall structure, and production of antimicrobial metabolites, highlighting A30's role in enhancing the host resistance against pathogen attack. This A30-induced resistance relied on the early activation of jasmonic acid signaling and its production in tubers, while defense signaling mediated by salicylic acid was suppressed. In the late phase, A30 actively interferes with plant immunity by inhibiting stress- and defense-related genes expression. Simultaneously, the genes involved in cell wall remodeling and indole-3-acetic acid signaling were activated, thereby enhancing cell wall remodeling to establish symbiotic relationship with the host. The endophytic colonization of A30 coincided with the induction of genes involved in the biosynthesis and signaling of ethylene and abscisic acid, while downregulating those related to gibberellic acid and cytokinin. This combination suggested fitness benefits for potato tubers by preserving dormancy, and delaying sprouting, which affects durability of tubers during storage. This study contributes valuable insights into the tripartite interaction among S. plymuthica A30, D. solani, and potato tubers, facilitating the development of biocontrol system for soft rot pathogens under storage conditions.

Phenazines are involved in the antagonism of a novel subspecies of Pseudomonas chlororaphis strain S1Bt23 against Pythium ultimum

Long-term use of chemical fungicides to control plant diseases caused by fungi and oomycetes has led to pathogen resistance and negative impacts on public health and environment. There is a global search for eco-friendly methods and antagonistic bacteria are emerging as alternatives. We isolated a potent antagonistic bacterial strain (S1Bt23) from woodland soil in Québec, Canada. Taxonomic characterization by 16S rRNA, multi-locus sequence analysis, pairwise whole-genome comparisons, phylogenomics and phenotypic data identified strain S1Bt23 as a novel subspecies within Pseudomonas chlororaphis. In dual culture studies, strain S1Bt23 exhibited potent mycelial growth inhibition (60.2-66.7%) against Pythium ultimum. Furthermore, strain S1Bt23 was able to significantly bioprotect potato tuber slices from the development of necrosis inducible by P. ultimum. Annotations of the whole genome sequence of S1Bt23 revealed the presence of an arsenal of secondary metabolites including the complete phenazine biosynthetic cluster (phzABCDEFG). Thin-layer (TLC) and high-performance liquid (HPLC) chromatographic analyses of S1Bt23 extracts confirmed the production of phenazines, potent antifungal compounds. CRISPR/Cas9-mediated deletion of phzB (S1Bt23ΔphzB) or phzF (S1Bt23ΔphzF) gene abrogated phenazine production based on TLC and HPLC analyses. Also, S1Bt23ΔphzB and S1Bt23ΔphzF mutants lost antagonistic activity and bioprotection ability of potato tubers against P. ultimum. This demonstrated that phenazines are involved in the antagonistic activity of S1Bt23 against P. ultimum. Finally, based on genotypic and phenotypic data, we taxonomically conclude that S1Bt23 represents a novel subspecies for which the name Pseudomonas chlororaphis subsp. phenazini is proposed.

Formulations of synergistic microbial consortia for enhanced systemic resistance against Fusarium wilt in cumin

The study aimed to understand the dynamic interplay between plants and their associated microbes to develop an efficient microbial consortium for managing Fusarium wilt of cumin. A total of 601 rhizospheric and endophytic bacteria and fungi were screened for antagonistic activity against Fusarium oxysporum f.sp. cumini (Foc). Subsequently, ten bacteria and ten fungi were selected for characterizing their growth promotion traits and ability to withstand abiotic stress. Furthermore, a pot experiment was conducted to evaluate the bioefficacy of promising biocontrol isolates-1F, 16B, 31B, and 223B in mono and consortium mode, focusing on disease severity, plant growth, and defense responses in cumin challenged with Foc. Promising isolates were identified as Trichoderma atrobruneum 15F, Pseudomonas sp. 2B, Bacillus amyloliquefaciens 9B, and Bacillus velezensis 32B. In planta, results revealed that cumin plants treated with consortia of 15F, 2B, 9B, and 32B showed highest percent disease control (76.35%) in pot experiment. Consortia of biocontrol agents significantly enhanced production of secondary metabolites and activation of antioxidant-defense enzymes compared to individual strain. Moreover, consortium treatments effectively reduced electrolyte leakage over the individual strain and positive control. The four-microbe consortium significantly enhanced chlorophyll (~ 2.74-fold), carotenoid content (~ 2.14-fold), plant height (~ 1.8-fold), dry weight (~ 1.96-fold), and seed yield (~ 19-fold) compared to positive control in pot experiment. Similarly, four microbe consortia showed highest percent disease control (72.2%) over the positive control in field trial. Moreover, plant growth, biomass, yield, and yield attributes of cumin were also significantly increased in field trial over the positive control as well as negative control.

Identification of receptor-like proteins induced by Sclerotinia sclerotiorum in Brassica napus

Heightening the resistance of plants to microbial infection is a widely concerned issue, especially for economical crops. Receptor-like proteins (RLPs), typically with tandem leucine-rich repeats (LRRs) domain, play a crucial role in mediating immune activation, being an indispensable constituent in the first layer of defense. Based on an analysis of orthologs among Brassica rapa, Brassica oleracea, and Brassica napus using Arabidopsis thaliana RLPs as a reference framework, we found that compared to A. thaliana, there were some obvious evolutionary diversities of RLPs among the three Brassicaceae species. BnRLP encoding genes were unevenly distributed on chromosomes, mainly on chrA01, chrA04, chrC03, chrC04, and chrC06. The orthologs of five AtRLPs (AtRLP3, AtRLP10, AtRLP17, AtRLP44, and AtRLP51) were highly conserved, but retrenchment and functional centralization occurred in Brassicaceae RLPs during evolution. The RLP proteins were clustered into 13 subgroups. Ten BnRLPs presented expression specificity between R and S when elicited by Sclerotinia sclerotiorum, which might be fabulous candidates for S. sclerotiorum resistance research.

Agronomic efficiency and genome mining analysis of the wheat-biostimulant rhizospheric bacterium Pseudomonas pergaminensis sp. nov. strain 1008T

Pseudomonas sp. strain 1008 was isolated from the rhizosphere of field grown wheat plants at the tillering stage in an agricultural plot near Pergamino city, Argentina. Based on its in vitro phosphate solubilizing capacity and the production of IAA, strain 1008 was formulated as an inoculant for bacterization of wheat seeds and subjected to multiple field assays within the period 2010-2017. Pseudomonas sp. strain 1008 showed a robust positive impact on the grain yield (+8% on average) across a number of campaigns, soil properties, seed genotypes, and with no significant influence of the simultaneous seed treatment with a fungicide, strongly supporting the use of this biostimulant bacterium as an agricultural input for promoting the yield of wheat. Full genome sequencing revealed that strain 1008 has the capacity to access a number of sources of inorganic and organic phosphorus, to compete for iron scavenging, to produce auxin, 2,3-butanediol and acetoin, and to metabolize GABA. Additionally, the genome of strain 1008 harbors several loci related to rhizosphere competitiveness, but it is devoid of biosynthetic gene clusters for production of typical secondary metabolites of biocontrol representatives of the Pseudomonas genus. Finally, the phylogenomic, phenotypic, and chemotaxonomic comparative analysis of strain 1008 with related taxa strongly suggests that this wheat rhizospheric biostimulant isolate is a representative of a novel species within the genus Pseudomonas, for which the name Pseudomonas pergaminensis sp. nov. (type strain 1008T = DSM 113453T = ATCC TSD-287T) is proposed.

cDNA Transcriptome of Arabidopsis Reveals Various Defense Priming Induced by a Broad-Spectrum Biocontrol Agent Burkholderia sp. SSG

Burkholderia sp. SSG is a potent biological control agent. Even though its survival on the leaf surface declined rapidly, SSG provided extended, moderate plant protection from a broad spectrum of pathogens. This study used Arabidopsis Col-0 and its mutants, eds16-1, npr1-1, and pad4-1 as model plants and compared treated plants with non-treated controls to elucidate whether SSG triggers plant defense priming. Only eds16-1 leaves with SSG became purplish, suggesting the involvement of salicylic acid (SA) in SSG-induced priming. cDNA sequencing of Col-0 plants and differential gene expression analysis identified 120 and 119 differentially expressed genes (DEGs) at 6- and 24-h post-treatment (hpt) with SSG, respectively. Most of these DEGs encoded responses to biotic and abiotic stimuli or stresses; four DEGs had more than two isoforms. A total of 23 DEGs were shared at 6 and 24 hpt, showing four regulation patterns. Functional categorization of these shared DEGs, and 44 very significantly upregulated DEGs revealed that SSG triggered various defense priming mechanisms, including responses to phosphate or iron deficiency, modulation of defense-linked SA, jasmonic acid, ethylene, and abscisic acid pathways, defense-related gene regulation, and chromatin modification. These data support that SSG is an induced systemic resistance (ISR) trigger conferring plant protection upon pathogen encounter.

Whole-Genome Sequence of Pseudomonas sp. Strain MM211, Isolated from Soil in Langenfeld, Germany

Here, we present the genome sequence of Pseudomonas sp. strain MM211, which was isolated from garden soil. The complete circular genome consists of a 5,281,862-bp chromosome, with a GC content of 61.5%.

Physiological, proteomic, and metabolomic analysis provide insights into Bacillus sp.-mediated salt tolerance in wheat

Herein, the inoculation with strain wp-6 promoted the growth of wheat seedlings by improving the energy production and conversion of wheat seedlings and alleviating salt stress. Soil salinization decreases crop productivity due to high toxicity of sodium ions to plants. Plant growth-promoting rhizobacteria (PGPR) have been demonstrated to alleviate salinity stress. However, the mechanism of PGPR in improving plant salt tolerance remains unclear. In this study, physiological analysis, proteomics, and metabolomics were applied to investigate the changes in wheat seedlings under salt stress (150 mM NaCl), both with and without plant root inoculation with wp-6 (Bacillus sp.). Under salt stress, root inoculation with strain wp-6 increased plant biomass (57%) and root length (25%). The Na⁺ content was reduced, while the K⁺ content and K⁺/Na⁺ ratio were increased. The content of malondialdehyde was decreased by 31.94% after inoculation of wp-6 under salt stress, while the content of proline, soluble sugar, and soluble protein were increased by 7.48%, 12.34%, and 4.12%, respectively. The peroxidase, catalase, and superoxide dismutase activities were increased after inoculation of wp-6 under salt stress. Galactose metabolism, phenylalanine metabolism, caffeine metabolism, ubiquinone and other terpenoid-quinone biosynthesis, and glutathione metabolism might play an important role in promoting the growth of salt-stressed wheat seedlings after the inoculation with wp-6. Interaction analysis of differentially expressed proteins and metabolites found that energy production and transformation-related proteins and six metabolites (D-arginine, palmitoleic acid, chlorophyllide b, rutin, pheophorbide a, and vanillylamine) were mainly involved in the growth of wheat seedlings after the inoculation with wp-6 under salt stress. Furthermore, correlation analysis found that inoculation with wp-6 promotes the growth of salt-stressed wheat seedlings mainly through regulating amino acid metabolism and porphyrin and chlorophyll metabolism. This study provides an eco-friendly method to increase agricultural productivity and paves a way to sustainable agriculture.

Draft Genome Sequences of Pseudomonas spp. Isolated from Berry Surfaces in Commercial Cranberry Bogs in Massachusetts, USA

The surfaces of plants are colonized by a rich diversity of microbes but are largely unexplored. Here, we present the draft genome sequences of five Pseudomonas spp. isolated from cultivated cranberry fruit surfaces. Although the isolates represent four different species, their genomes all contain conserved iron sequestration and uptake genes.

Benefits to Plant Health and Productivity From Enhancing Plant Microbial Symbionts

Plants exist in close association with uncountable numbers of microorganisms around, on, and within them. Some of these endophytically colonize plant roots. The colonization of roots by certain symbiotic strains of plant-associated bacteria and fungi results in these plants performing better than plants whose roots are colonized by only the wild populations of microbes. We consider here crop plants whose roots are inhabited by introduced organisms, referring to them as Enhanced Plant Holobionts (EPHs). EPHs frequently exhibit resistance to specific plant diseases and pests (biotic stresses); resistance to abiotic stresses such as drought, cold, salinity, and flooding; enhanced nutrient acquisition and nutrient use efficiency; increased photosynthetic capability; and enhanced ability to maintain efficient internal cellular functioning. The microbes described here generate effects in part through their production of Symbiont-Associated Molecular Patterns (SAMPs) that interact with receptors in plant cell membranes. Such interaction results in the transduction of systemic signals that cause plant-wide changes in the plants' gene expression and physiology. EPH effects arise not only from plant-microbe interactions, but also from microbe-microbe interactions like competition, mycoparasitism, and antibiotic production. When root and shoot growth are enhanced as a consequence of these root endophytes, this increases the yield from EPH plants. An additional benefit from growing larger root systems and having greater photosynthetic capability is greater sequestration of atmospheric CO2. This is transferred to roots where sequestered C, through exudation or root decomposition, becomes part of the total soil carbon, which reduces global warming potential in the atmosphere. Forming EPHs requires selection and introduction of appropriate strains of microorganisms, with EPH performance affected also by the delivery and management practices.

A Consortium of Pseudomonas aeruginosa and Trichoderma harzianum for Improving Growth and Induced Biochemical Changes in Fusarium Wilt Infected Bananas

Fusarium wilt of banana cannot be effectively controlled by current control strategies. The most virulent form that caused major losses in the banana production is Fusarium oxysporum f. sp. cubense Tropical Race 4 (Foc-TR4). Biocontrol of Foc-TR4 using microbial antagonists offers a sustainable and eco-friendly alternative. A consortium of biocontrol agents (BCAs), Pseudomonas aeruginosa DRB1 and Trichoderma harzianum CBF2 was formulated into pesta granules, talc powder, alginate beads and liquid bioformulations. Previous study indicated bioformulations containing both BCAs successfully reduced the disease severity of Foc-TR4. To date, the biocontrol mechanism and plant growth promoting (PGP) traits of a consortium of BCAs on infected bananas have not been explored. Therefore, the study was undertaken to investigate the effect of a consortium of DRB1 and CBF2 in the growth and biochemical changes of Foc-TR4 infected bananas. Results indicated pesta granules formulation produced bananas with higher biomass (fresh weight: 388.67 g), taller plants (80.95 cm) and larger leaves (length: 39.40 cm, width: 17.70 cm) than other bioformulations. Applying bioformulations generally produced plants with higher chlorophyll (392.59 μg/g FW-699.88 μg/g FW) and carotenoid contents (81.30 μg/g FW-120.01 μg/g FW) compared to pathogen treatment (chlorophyll: 325.96 μg/g FW, carotenoid: 71.98 μg/g FW) which indicated improved vegetative growth. Bioformulation-treated plants showed higher phenolic (49.58-93.85 μg/g FW) and proline contents (54.63 μg/g FW-89.61 μg/g FW) than Foc-TR4 treatment (phenolic: 46.45 μg/g FW, proline: 28.65 μg/g FW). The malondialdehylde (MDA) content was lower in bioformulation treatments (0.49 Nm/g FW-1.19 Nm/g FW) than Foc-TR4 treatment (3.66 Nm/g FW). The biochemical changes revealed that applying bioformulations has induced host defense response by increasing phenolic and proline contents which reduced root damage caused by Foc-TR4 resulting in lower MDA content. In conclusion, applying bioformulations containing microbial consortium is a promising method to improve growth and induce significant biochemical changes in bananas leading to the suppression of Foc-TR4.

Activation tagging identifies Arabidopsis transcription factor AtMYB68 for heat and drought tolerance at yield determining reproductive stages

Heat stress occurring at reproductive stages can result in significant and permanent damage to crop yields. However, previous genetic studies in understanding heat stress response and signaling were performed mostly on seedling and plants at early vegetative stages. Here we identify, using a developmentally defined, gain-of-function genetic screen with approximately 18 000 Arabidopsis thaliana activation-tagged lines, a mutant that maintained productive seed set post-severe heat stress during flowering. Genome walking indicated this phenotype was caused by the insertion of 35S enhancers adjacent to a nuclear localized transcription factor AtMYB68. Subsequent overexpression analysis confirmed that AtMYB68 was responsible for the reproductive heat tolerance of the mutant. Furthermore, these transgenic Arabidopsis plants exhibited enhanced abscisic acid sensitivity at and post-germination, reduced transpirational water loss during a drought treatment, and enhanced seed yield under combined heat and drought stress during flowering. Ectopic expression of AtMYB68 in Brassica napus driven either by 35S or by heat-inducible promoter recapitulated the enhanced reproductive heat stress and drought tolerance phenotypes observed in the transgenic Arabidopsis. The improvement to heat stress is likely due to enhanced pollen viability observed in the transgenic plants. More importantly, the transgenic canola showed significant yield advantages over the non-transgenic controls in multiple locations, multiple season field trials under various drought and heat stress conditions. Together these results suggest that AtMYB68 regulate plant stress tolerance at the most important yield determining stage of plant development, and is an effective target for crop yield protection under current global climate volatility.

Characterization of antifungal metabolite phenazine from rice rhizosphere fluorescent pseudomonads (FPs) and their effect on sheath blight of rice

We have shown, the outcome of antifungal activity of phenazine derivatives which is produced by fluorescent pseudomonads (FPs) for the control of sheath blight of rice. A total of 50 fluorescent pseudomonads (FPs) were isolated from rice rhizosphere. Off which, 36 FPs exhibited antagonistic activity against Rhizoctonia solani, Macrophomina phaseolina, Fusarium oxysporum, Alternaria alternata and Sclerotium rolfsii up to 70–80% compared to control by dual culture method. BOX-PCR analyses of antagonistic isolates indicated that two phylogenetic group, where group I consisted of 28 isolates and eight isolates belongs to group II. Among 36 FPs, a total of 10 FPs revealed that the presence of phenazine derivatives on thin layer chromatography (TLC), which is coincided with that of authentic phenazine with R_f value 0.57. Similar to TLC analysis, antibiotic encoding gene phenazine-1-carboxamide (PCN) was detected in 10 FPs by PCR analysis with respective primer. Among, PCN detected isolates of FPs, a significant biocontrol potential possessing isolate designated as VSMKU1 and it was showed prominent antifungal activity against R. solani and other tested fungal pathogens. Hence, the isolate VSMKU1 was selected for further studies. The selected isolate VSMKU1 was identified as Pseudomonas aeruginosa by 16S rDNA sequence analysis. The antifungal metabolite phenazine like compound produced by VSMKU1 was confirmed by UV, FT-IR and HPLC analysis. The phenazine compound from VSMKU1 significantly arrest the growth of R. solani compared to carbendazim by well diffusion method. The detached leaf assay showed remarkable inhibition of lesion height 80 to 85% by the treatments of culture (VSMKU1), cell free culure filtrate and phenazine like compound compared to control and other treatments was observed in detached leaves of rice. These results emphasized that VSMKU1 isolate can be used as an alternative potential biocontrol agent against sheath blight of rice, instead of using commercial fungicide such as validamycin and carbendazim which cause environmental pollution and health hazards.

Enhancement and improvement of selenium in soil to the resistance of rape stem against Sclerotinia sclerotiorum and the inhibition of dissolved organic matter derived from rape straw on mycelium

Sclerotinia stem rot (SSR), caused by Sclerotinia sclerotiorum (S. sclerotiorum), one of the most destructive diseases in many crops including Brassica napus L. The extensive use of fungicides to control S. sclerotiorum caused severe damage to the environment in the long term. Increasing study reported that selenium (Se) is a beneficial element for plant by promoting growth and enhancing disease resistance. In this study, it was found that Se in soil shortened lesion length by 19.14% on rape stem infected with S. sclerotiorum. While resistance mechanism of rape stem against S. sclerotiorum remains unknown. Transcriptomic analysis of rape stem was performed and the results indicated that genes related to antifungal pathways were up-regulated. Moreover, metabonomic analysis was carried out to study the inhibitive effect of the dissolved organic matter derived from rape straw with Se pretreatment in soil (RSDOM_Se) on S. sclerotiorum mycelium, results showed that RSDOM_Se caused severe damage to energy metabolism of mycelium. Further study indicated that RSDOM_Se decreased the pathogenicity of mycelium on rape leaves significantly, and enhanced content of chlorophyII, carotenoids, OD phenol and activities of phenylalanine ammonia-lyase (PAL), polyphenol oxidase (PPO) in rape leaves, which suggested that RSDOM_Se plays a positive role in regulating oxidative stress responses of plant when infected with S. sclerotiorum. In addition, when compared with dimcthachlon (DIM) treatment alone, DIM combined with RSDOM_Se resulted in higher inhibition on mycelial growth of S. sclerotiorum (the inhibition ratio of nearly 60%). Results in this study suggested that Se enhanced the resistance of rape stem against S. sclerotiorum because of the up-regulated genes related to antifungal pathways, and RSDOM_Se improved the mycelial growth inhibition and decreased the pathogenicity of mycelium on rape leaves. Overall, Se as well as Se-enrich byproducts, possessed great potential to be developed as ecological fungicides for controlling S. sclerotiorum.

Insights into plant-beneficial traits of probiotic Pseudomonas chlororaphis isolates

Pseudomonas chlororaphisisolates have been studied intensively for their beneficial traits.P. chlororaphisspecies function as probiotics in plants and fish, offering plants protection against microbes, nematodes and insects. In this review, we discuss the classification ofP. chlororaphisisolates within four subspecies; the shared traits include the production of coloured antimicrobial phenazines, high sequence identity between housekeeping genes and similar cellular fatty acid composition. The direct antimicrobial, insecticidal and nematocidal effects ofP. chlororaphisisolates are correlated with known metabolites. Other metabolites prime the plants for stress tolerance and participate in microbial cell signalling events and biofilm formation among other things. Formulations ofP. chlororaphisisolates and their metabolites are currently being commercialized for agricultural use.

Investigation of the quorum-sensing regulon of the biocontrol bacterium Pseudomonas chlororaphis strain PA23

Pseudomonas chlororaphis strain PA23 is a biocontrol agent capable of protecting canola from stem rot disease caused by the fungal pathogen Sclerotinia sclerotiorum. PA23 produces several inhibitory compounds that are under control of a complex regulatory network. Included in this cascade is the PhzRI quorum sensing (QS) system, which plays an essential role in PA23 biocontrol, as well as CsaRI and AurRI, which have not yet been characterized in PA23. The focus of the current study was to employ RNA sequencing to explore the spectrum of PA23 genes under QS control. In this work, we investigated genes under the control of the main QS transcriptional regulator, PhzR, as well as those differentially expressed in an AHL-deficient strain, PA23-6863, which constitutively expresses an AiiA lactonase, rendering the strain QS defective. Transcriptomic profiling revealed 545 differentially expressed genes (365 downregulated; 180 upregulated) in the phzR mutant and 534 genes (382 downregulated; 152 upregulated) in the AHL-deficient PA23-6863. In both strains, decreased expression of phenazine, pyrrolnitrin, and exoprotease biosynthetic genes was observed. We have previously reported that QS activates expression of these genes and their encoded products. In addition, elevated siderophore and decreased chitinase gene expression was observed in the QS-deficient stains, which was confirmed by phenotypic analysis. Inspection of the promoter regions revealed the presence of "phz-box" sequences in only 58 of the 807 differentially expressed genes, suggesting that much of the QS regulon is indirectly regulated. Consistent with this notion, 41 transcriptional regulators displayed altered expression in one or both of the QS-deficient strains. Collectively, our findings indicate that QS governs expression of approximately 13% of the PA23 genome affecting diverse functions ranging from secondary metabolite production to general metabolism.

Characterization of Rhodopseudomonas palustris population dynamics on tobacco phyllosphere and induction of plant resistance to Tobacco mosaic virus

Although many biocontrol bacteria can be used to improve plant tolerance to stresses and to promote plant growth, the hostile environmental conditions on plant phyllosphere and the limited knowledge on bacterial colonization on plant phyllosphere minimized the beneficial effects produced by the biocontrol bacteria. Rhodopseudomonas palustris strain GJ-22 is known as a phyllosphere biocontrol agent. In this paper, we described detailed processes of strain GJ-22 colony establishment at various colonization stages. Four different types of bacterial colonies, Type 1, scattered single cells; Type 2, small cell clusters; Type 3, small cell aggregates; and Type 4, large cell aggregates, were observed in the course of bacterial colonization. We categorized bacterial colonization into four phases, which were, Phase I: bacterial colony exists as Type 1 and cell population reduced quickly; Phase II: Type 1 evolved into Type 2 and cell population remained steady; Phase III: Type 3 arose and replaced Type 2, and cell population expanded slowly; and Phase IV: Type 3 matured into Type 4 and cell population increased quickly. We have shown that the preferable location sites of bacterial aggregates on leaf phyllosphere are grooves between plant epidermal cells. Analyses of expressions of plant defence-related genes showed that, starting from Phase III, bacterial cells in the Type 3 and Type 4 colonies produced unidentified signals to induce host defence against Tobacco mosaic virus infection. In addition, we determined the crucial role of aggregates formation of GJ-22 cell on plant phyllosphere in terms of bacterial cell stress tolerance and ISR (induced systemic resistance) priming. To our knowledge, this is the first report focused on the colonization process of a phyllosphere biocontrol agent and gave a clear description on the morphological shift of bacterial colony on phyllosphere.

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.