Bacteria in the leaf ecosystem with emphasis on Pseudomonas syringae-a pathogen, ice nucleus, and epiphyte

Impact of microbial-based biopreparations on soil quality, plant health, and fruit chemistry in raspberry cultivation

Application of microbial-based biopreparations as a pre-harvest strategy offers a method to obtain sustainable agricultural practices and could be an important approach for advancing food science, promoting sustainability, and meeting global food market demands. The impact of a bacterial-fungal biopreparation mixture on soil-plant-microbe interactions, fruit chemical composition and yield of 7 raspberry clones was investigated by examining the structural and functional profiles of microbial communities within leaves, fruits, and soil. Biopreparation addition caused the enhancement of the microbiological utilization of specific compounds, such as d-mannitol, relevant in plant-pathogen interactions and overall plant health. The biopreparation treatment positively affected the nitrogen availability in soil (9-160%). The analysis of plant stress marker enzymes combined with the evaluation of fruit quality and chemical properties highlight changes inducted by the pre-harvest biopreparation application. Chemical analyses highlight biopreparations' role in soil and fruit quality improvement, promoting sustainable agriculture. This effect was dependent on tested clones, showing increase of soluble solid content in fruits, concentration of polyphenols or the sensory quality of the fruits. The results of the next-generation sequencing indicated increase in the effective number of bacterial species after biopreparation treatment. The network analysis showed stimulating effect of biopreparation on microbial communities by enhancing microbial interactions (increasing the number of network edges up to 260%) of and affecting the proportions of mutual relationships between both bacteria and fungi. These findings show the potential of microbial-based biopreparation in enhancing raspberry production whilst promoting sustainable practices and maintaining environmental homeostasis and giving inshght in holistic understanding of microbial-based approaches for advancing food science monitoring.

Pathogenicity, phylogenomic, and comparative genomic study of Pseudomonas syringae sensu lato affecting sweet cherry in California

To gain insights into the diversity of Pseudomonas syringae sensu lato affecting sweet cherry in California, we sequenced and analyzed the phylogenomic and genomic architecture of 86 fluorescent pseudomonads isolated from symptomatic and asymptomatic cherry tissues. Fifty-eight isolates were phylogenetically placed within the P. syringae species complex and taxonomically classified into five genomospecies: P. syringae pv. syringae, P. syringae, Pseudomonas cerasi, Pseudomonas viridiflava, and A. We annotated components of the type III secretion system and phytotoxin-encoding genes and correlated the data with pathogenicity phenotypes. Intact probable regulatory protein HrpR was annotated in the genomic sequences of all isolates of P. syringae pv. syringae, P. syringae, P. cerasi, and A. Isolates of P. viridiflava had atypical probable regulatory protein HrpR. Syringomycin and syringopeptin-encoding genes were annotated in isolates of all genomospecies except for A and P. viridiflava. All isolates of P. syringae pv. syringae caused cankers, leaf spots, and fruit lesions in the field. In contrast, all isolates of P. syringae and P. cerasi and some isolates of P. viridiflava caused only cankers. Isolates of genomospecies A could not cause any symptoms suggesting phytotoxins are essential for pathogenicity. On detached immature cherry fruit pathogenicity assays, isolates of all five genomospecies produced symptoms (black-dark brown lesions). However, symptoms of isolates of genomospecies A were significantly (P < 0.01) less severe than those of other genomospecies. We also mined for genes conferring resistance to copper and kasugamycin and correlated these data with in vitro antibiotic sensitivity tests.

IMPORTANCE

Comprehensive identification of phytopathogens and an in-depth understanding of their genomic architecture, particularly virulence determinants and antibiotic-resistant genes, are critical for several practical reasons. These include disease diagnosis, improved knowledge of disease epidemiology, pathogen diversity, and determination of the best possible management strategies. In this study, we provide the first report of the presence and pathogenicity of genomospecies Pseudomonas cerasi and Pseudomonas viridiflava in California sweet cherry. More importantly, we report a relatively high level of resistance to copper among the population of Pseudomonas syringae pv. syringae (47.5%). This implies copper cannot be effectively used to control bacterial blast and bacterial canker of sweet cherries. On the other hand, no isolates were resistant to kasugamycin, an indication that kasugamycin could be effectively used for the control of bacterial blast and bacterial canker. Our findings are important to improve the management of bacterial blast and bacterial canker of sweet cherries in California.

Hfq mediates transcriptome-wide RNA structurome reprogramming under virulence-inducing conditions in a phytopathogen

Although RNA structures play important roles in regulating gene expression, the mechanism and function of mRNA folding in plant bacterial pathogens remain elusive. Therefore, we perform dimethyl sulfate sequencing (DMS-seq) on the Pseudomonas syringae under nutrition-rich and -deficient conditions, revealing that the mRNA structure changes substantially in the minimal medium (MM) that tunes global translation efficiency (TE), thereby inducing virulence. This process is led by the increased expression of hfq, which is directly activated by transcription regulators RpoS and CysB. The co-occurrence of Hfq and RpoS in diverse bacteria and the deep conservation of Hfq Y25 is critical for RNA-mediated regulation and implicates the wider biological importance of mRNA structure and feedback loops in the control of global gene expression.

Characterization of selected phages for biocontrol of food-spoilage pseudomonads

Pseudomonas spp., such as P. fluorescens group, P. fragi, and P. putida, are the major psychrophilic spoilage bacteria in the food industry. Bacteriophages (phages) are a promising tool for controlling food-spoilage and food-poisoning bacteria; however, there are few reports on phages effective on food-spoilage bacteria such as Pseudomonas spp. In this study, 12 Pseudomonas phages were isolated from chicken and soil samples. Based on the host range and lytic activity at 30 °C and 4 °C and various combinations of phages, phages vB_PflP-PCS4 and vB_PflP-PCW2 were selected to prepare phage cocktails to control Pseudomonas spp. The phage cocktail consisting of vB_PflP-PCS4 and vB_PflP-PCW2 showed the strongest lytic activity and retarded regrowth of P. fluorescens and P. putida at 30 °C, 8 °C, and 4 °C at a multiplicity of infection of 100. Nucleotide sequence analysis of the genomic DNA indicated that vB_PflP-PCS4 and vB_PflP-PCW2 phages were lytic phages of the Podoviridae family and lacked tRNA, toxin, or virulence genes. A novel endolysin gene was found in the genomic DNA of phage vB_PflP-PCS4. The results of this study suggest that the phage cocktail consisting of vB_PflP-PCS4 and vB_PflP-PCW2 is a promising tool for the biocontrol of psychrophilic food-spoilage pseudomonads during cold storage and distribution.

Winter Rye Cover Crops Shelter Competent Squash Phyllosphere Bacteria to Reduce Pseudomonas syringae pv. lachrymans Growth and Angular Leaf Spot Symptoms

Cover crops, a soil conservation practice, can contribute to reducing disease pressure caused by Pseudomonas syringae, considered one of the most important bacterial plant pathogens. We recently demonstrated that the phyllosphere (leaf surface) bacterial community structure changed when squash (Cucurbita pepo) was grown with a rye (Secale cereale) cover crop treatment, followed by a decrease of angular leaf spot disease symptoms on squash caused by P. syringae pv. lachrymans. Application of biocontrol agents is a known agricultural practice to mitigate crop losses due to microbial disease. In this study, we tested the hypothesis that some phyllosphere bacteria promoted when squash is grown on cover crops could be isolated and used as a biocontrol agent to decrease angular leaf spot symptoms. We grew squash during a 2-year field experiment using four agricultural practices: bare soil, cover crops, chemically terminated cover crops, and plastic cover. We sampled squash leaves at three different dates each year and constructed a collection of cultivable bacterial strains isolated from squash leaves and rye cover crop material. Each isolated strain was identified by 16S rRNA gene sequencing and used in in vitro (Petri dish) pathogen growth and in vivo (greenhouse) symptom control assays. Four bacterial isolates belonging to the genera Pseudarthrobacter, Pseudomonas, Delftia, and Rhizobium were shown to inhibit P. syringae pv. lachrymans growth and angular leaf spot symptom development. Strikingly, the symptom control efficacy of all strains was stronger on older leaves. This study sheds light on the importance of bacterial isolation from cover crop sources to promote disease control. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Assessing the efficacy of phyllospheric growth-promoting and antagonistic bacteria for management of black rot disease of cauliflower incited by Xanthomonas campestris pv. campestris

The study aimed to assess the potential of phyllospheric bacterial strains isolated from cauliflower plants as biocontrol agents against black rot disease caused by Xanthomonas campestris pv. campestris, through both in vitro and in vivo evaluations. A total of 46 bacterial strains were isolated from healthy and infected cauliflower leaves of both resistant and susceptible plants, and evaluated them for various traits, including plant growth-promoting activities and in vitro antagonistic activity against Xanthomonas campestris pv. campestris. Further, a pot experiment was conducted with the susceptible cauliflower genotype (Pusa Sharad) and 10 selected phyllospheric bacterial isolates to assess their biocontrol efficacy against the disease. The results showed that 82.60% of phyllospheric bacterial isolates were positive for phosphate solubilization, 63.04% for ammonia production, 58.69% for HCN production, 36.95% for siderophore production, and 78.26% had the capacity to produce IAA. Out of the 46 isolates, 23 exhibited in vitro antagonistic activity against X. campestris pv. campestris and 10 isolates were selected for a pot experiment under glasshouse conditions based on their good plant growth-promoting activities and antagonistic assay. The results revealed that bacterial isolate CFLB-27 exhibited the highest biocontrol efficiency (65.41%), followed by CFLB-24 (58.30%), CFLB-31 (47.11%), and CFLB-26 (46.03%). These four isolates were identified as Pseudomonas fluorescens CFLB-27, Bacillus velezensis CFLB-24, Bacillus amyloliquefaciens CFLB-31, and Stenotrophomonas rhizophila CFLB-26. This study provides valuable insights into the potential of phyllospheric bacteria as an effective tool for disease management in sustainable agriculture.

Horizontal gene transfer in plant microbiomes: integrons as hotspots for cross-species gene exchange

Plant microbiomes play important roles in plant health and fitness. Bacterial horizontal gene transfer (HGT) can influence plant health outcomes, driving the spread of both plant growth-promoting and phytopathogenic traits. However, community dynamics, including the range of genetic elements and bacteria involved in this process are still poorly understood. Integrons are genetic elements recently shown to be abundant in plant microbiomes, and are associated with HGT across broad phylogenetic boundaries. They facilitate the spread of gene cassettes, small mobile elements that collectively confer a diverse suite of adaptive functions. Here, we analysed 5,565 plant-associated bacterial genomes to investigate the prevalence and functional diversity of integrons in this niche. We found that integrons are particularly abundant in the genomes of Pseudomonadales, Burkholderiales, and Xanthomonadales. In total, we detected nearly 9,000 gene cassettes, and found that many could be involved in plant growth promotion or phytopathogenicity, suggesting that integrons might play a role in bacterial mutualistic or pathogenic lifestyles. The rhizosphere was enriched in cassettes involved in the transport and metabolism of diverse substrates, suggesting that they may aid in adaptation to this environment, which is rich in root exudates. We also found that integrons facilitate cross-species HGT, which is particularly enhanced in the phyllosphere. This finding may provide an ideal opportunity to promote plant growth by fostering the spread of genes cassettes relevant to leaf health. Together, our findings suggest that integrons are important elements in plant microbiomes that drive HGT, and have the potential to facilitate plant host adaptation.

Phylogenomic analyses and comparative genomics of Pseudomonas syringae associated with almond (Prunus dulcis) in California

We sequenced and comprehensively analysed the genomic architecture of 98 fluorescent pseudomonads isolated from different symptomatic and asymptomatic tissues of almond and a few other Prunus spp. Phylogenomic analyses, genome mining, field pathogenicity tests, and in vitro ice nucleation and antibiotic sensitivity tests were integrated to improve knowledge of the biology and management of bacterial blast and bacterial canker of almond. We identified Pseudomonas syringae pv. syringae, P. cerasi, and P. viridiflava as almond canker pathogens. P. syringae pv. syringae caused both canker and foliar (blast) symptoms. In contrast, P. cerasi and P. viridiflava only caused cankers, and P. viridiflava appeared to be a weak pathogen of almond. Isolates belonging to P. syringae pv. syringae were the most frequently isolated among the pathogenic species/pathovars, composing 75% of all pathogenic isolates. P. cerasi and P. viridiflava isolates composed 8.3 and 16.7% of the pathogenic isolates, respectively. Laboratory leaf infiltration bioassays produced results distinct from experiments in the field with both P. cerasi and P. syringae pv. syringae, causing significant necrosis and browning of detached leaves, whereas P. viridiflava conferred moderate effects. Genome mining revealed the absence of key epiphytic fitness-related genes in P. cerasi and P. viridiflava genomic sequences, which could explain the contrasting field and laboratory bioassay results. P. syringae pv. syringae and P. cerasi isolates harboured the ice nucleation protein, which correlated with the ice nucleation phenotype. Results of sensitivity tests to copper and kasugamycin showed a strong linkage to putative resistance genes. Isolates harbouring the ctpV gene showed resistance to copper up to 600 μg/ml. In contrast, isolates without the ctpV gene could not grow on nutrient agar amended with 200 μg/ml copper, suggesting ctpV can be used to phenotype copper resistance. All isolates were sensitive to kasugamycin at the label-recommended rate of 100μg/ml.

Applied microbiology of the phyllosphere

The phyllosphere, or plant leaf surface, represents a microbial ecosystem of considerable size, holding extraordinary biodiversity and enormous potential for the discovery of new products, tools, and applications in biotechnology, agriculture, medicine, and elsewhere. This mini-review highlights the applied microbiology of the phyllosphere as an original field of study concerning itself with the genes, gene products, natural compounds, and traits that underlie phyllosphere-specific adaptations and services that have commercial and economic value for current or future innovation. Examples include plant-growth-promoting and disease-suppressive phyllobacteria, probiotics and fermented foods that support human health, as well as microbials that remedy foliar contamination with airborne pollutants, residual pesticides, or plastics. Phyllosphere microbes promote plant biomass conversion into compost, renewable energy, animal feed, or fiber. They produce foodstuffs such as thickening agents and sugar substitutes, industrial-grade biosurfactants, novel antibiotics and cancer drugs, as well as enzymes used as food additives or freezing agents. Furthermore, new developments in DNA sequence-based profiling of leaf-associated microbial communities allow for surveillance approaches in the context of food safety and security, for example, to detect enteric human pathogens on leafy greens, predict plant disease outbreaks, and intercept plant pathogens and pests on internationally traded goods. KEY POINTS: • Applied phyllosphere microbiology concerns leaf-specific adaptations for economic value • Phyllobioprospecting searches the phyllosphere microbiome for product development • Phyllobiomonitoring tracks phyllosphere microbial profiles for early risk detection.

Occurrence of Pseudomonas syringae pvs. actinidiae, actinidifoliorum and Other P. syringae Strains on Kiwifruit in Northern Spain

Pseudomonas syringae pv. actinidiae (Psa), the agent causing bacterial canker of kiwifruit, has been present in the Principality of Asturias (PA), Northern Spain, since 2013, although with restricted distribution. In this study, 53 strains collected in kiwifruit orchards in PA during the period 2014-2020 were characterized by a polyphasic approach including biochemical and phylogenetic analysis. Thirty-three strains, previously identified by PCR as Psa, have been found to be a homogeneous group in phylogenetic analysis, which seems to indicate that there have been few introductions of the pathogen into the region. Two strains were confirmed as P. syringae pv. actinidifoliorum (Pfm), so this is the first report of Pfm in the PA. The remaining 18 strains were found to be close to P. avellanae and P. syringae pv. antirrhini or to strains described as Pfm look-alikes. Pathogenicity tests carried out on peppers with a selection of strains have shown that both Psa and Pfm caused clear damage, while the 18 atypical strains caused variable lesions. It would be necessary to carry out pathogenicity testing of atypical strains on kiwifruit plants to study the role of these strains in the kiwifruit pathosystem to evaluate their pathogenic potential in this crop.

Isolation, identification and pathogenicity of local entomopathogenic bacteria as biological control agents against the wild cochineal Dactylopius opuntiae (Cockerell) on cactus pear in Morocco

The Opuntia ficus-indica (L.) cactus, a crucial crop in Morocco, is threatened by the wild cochineal, Dactylopius opuntiae (Cockerell). The aim of this research was to investigate the efficacy of nine bacterial strains against both D. opuntiae nymphs and adults females applied individually or after black soap in the laboratory, greenhouse, and field conditions. Using the partial 16S ribosomal DNA, the bacterial isolates were identified as Pseudomonas koreensis, Pseudomonas sp., Burkholderia sp. and Bacillus sp. Under laboratory conditions, the insecticidal activity of P. koreensis strain 66Ms.04 showed the level mortality (88%) of adult females' at 108 CFU/mL, 7 days after application. At a concentration of 108 CFU/mL, P. koreensis strain 66Ms.04 and Pseudomonas sp. (strains 37 and 5) caused 100% nymphs mortality rate three days after application. Under greenhouse conditions, the use of P. koreensis strain 66Ms.04 at 108 CFU/mL following the application of black soap (60 g/L) demonstrated the maximum levels of females and nymphs' mortalities with 80 and 91.25%, respectively, after 8 days of treatment. In field conditions, the combined application of the P. koreensis strain 66Ms.04 at 108 CFU/mL with black soap at 60 g/L, for an interval of 7 days, significantly increased the mortality of adult females to 93.33% at 7 days after the second application. These findings showed that the combined treatment of P. koreensis strain 66Ms.04 with black soap can be a potent and eco-friendly pesticide against D. opuntiae.

The genetic and physiological basis of Arabidopsis thaliana tolerance to Pseudomonas viridiflava

The opportunistic pathogen Pseudomonas viridiflava colonizes > 50 agricultural crop species and is the most common Pseudomonas in the phyllosphere of European Arabidopsis thaliana populations. Belonging to the P. syringae complex, it is genetically and phenotypically distinct from well-characterized P. syringae sensu stricto. Despite its prevalence, we lack knowledge of how A. thaliana responds to its native isolates at the molecular level. Here, we characterize the host response in an A. thaliana - P. viridiflava pathosystem. We measured host and pathogen growth in axenic infections and used immune mutants, transcriptomics, and metabolomics to determine defense pathways influencing susceptibility to P. viridiflava infection. Infection with P. viridiflava increased jasmonic acid (JA) levels and the expression of ethylene defense pathway marker genes. The immune response in a susceptible host accession was delayed compared with a tolerant one. Mechanical injury rescued susceptibility, consistent with an involvement of JA. The JA/ethylene pathway is important for suppression of P. viridiflava, yet suppression capacity varies between accessions. Our results shed light on how A. thaliana can suppress the ever-present P. viridiflava, but further studies are needed to understand how P. viridiflava evades this suppression to spread broadly across A. thaliana populations.

Influence of plasma-treated air on surface microbial communities on freshly harvested lettuce

Plant-based foods like lettuce are an important part of the human diet and worldwide industry. On a global scale, the number of food-associated illnesses increased in the last decades. Conventional lettuce sanitation methods include cleaning either with tap or chloritized water. Beside these water-consuming strategies, physical plasma is an innovative and effective possibility for food sanitation. Recent studies with plasma-treated water showed an effective reduction of the microbial load. Plasma-processed air (PPA) is another great opportunity to reduce the microbial load and save water. To test the efficiency of PPA, the surface microbiome of treated lettuce was analyzed via proliferation assays with special agars, live/dead assays and tests for respiratory activity of the microorganisms. PPA showed a reduction of the colony forming units (CFU/mL) on all tested microbial groups (Gram-negative and Gram-positive bacteria, yeasts and molds). These results were supported by the live/dead assay. For further insights, the PPA-ingredients were detected with Fourier Transformation Infrared Spectroscopy (FTIR), which revealed NO2, NO and N2O5 as the main reactive species in the PPA. In the future, PPA could be an outstanding, on-demand sanitation step for higher food safety standards, especially in situations where humidity and high temperature should be avoided.

Transcription factor PbbZIP4 is targeted for proteasome-mediated degradation by the ubiquitin ligase PbATL18 to influence pear's resistance to Colletotrichum fructicola by regulating the expression of PbNPR3

Pear anthracnose caused by Colletotrichum fructicola is one of the main fungal diseases in all pear-producing areas. The degradation of ubiquitinated proteins by the 26S proteasome is a regulatory mechanism of eukaryotes. E3 ubiquitin ligase is substrate specific and is one of the most diversified and abundant enzymes in the regulation mechanism of plant ubiquitination. Although numerous studies in other plants have shown that the degradation of ubiquitinated proteins by the 26S proteasome is closely related to plant immunity, there are limited studies on them in pear trees. Here, we found that an E3 ubiquitin ligase, PbATL18, interacts with and ubiquitinates the transcription factor PbbZIP4, and this process is enhanced by C. fructicola infection. PbATL18 overexpression in pear callus enhanced resistance to C. fructicola infection, whereas PbbZIP4 overexpression increased sensitivity to C. fructicola infection. Silencing PbATL18 and PbbZIP4 in Pyrus betulaefolia seedlings resulted in opposite effects, with PbbZIP4 silencing enhancing resistance to C. fructicola infection and PbATL18 silencing increasing sensitivity to C. fructicola infection. Using yeast one-hybrid screens, an electrophoretic mobility shift assay, and dual-luciferase assays, we demonstrated that the transcription factor PbbZIP4 upregulated the expression of PbNPR3 by directly binding to its promoter. PbNPR3 is one of the key genes in the salicylic acid (SA) signal transduction pathway that can inhibit SA signal transduction. Here, we proposed a PbATL18-PbbZIP4-PbNPR3-SA model for plant response to C. fructicola infection. PbbZIP4 was ubiquitinated by PbATL18 and degraded by the 26S proteasome, which decreased the expression of PbNPR3 and promoted SA signal transduction, thereby enhancing plant C. fructicola resistance. Our study provides new insights into the molecular mechanism of pear response to C. fructicola infection, which can serve as a theoretical basis for breeding superior disease-resistant pear varieties.

Response of microbial communities in the phyllosphere ecosystem of tobacco exposed to the broad-spectrum copper hydroxide

Copper hydroxide is a broad-spectrum copper fungicide, which is often used to control crop fungal and bacterial diseases. In addition to controlling targeted pathogens, copper hydroxide may also affect other non-targeted microorganisms in the phyllosphere ecosystem. At four time points (before spraying, and 5, 10 and 15 days after fungicide application), the response of diseased and healthy tobacco phyllosphere microorganisms to copper hydroxide stress was studied by using Illumina high-throughput sequencing technology, and Biolog tools. The results showed that the microbiome communities of the healthy group were more affected than the disease group, and the fungal community was more sensitive than the bacterial community. The most common genera in the disease group were Alternaria, Boeremia, Cladosporium, Pantoea, Ralstonia, Pseudomonas, and Sphingomonas; while in the healthy group, these were Alternaria, Cladosporium, Symmetrospora, Ralstonia, and Pantoea. After spraying, the alpha diversity of the fungal community decreased at 5 days for both healthy and diseased groups, and then showed an increasing trend, with a significant increase at 15 days for the healthy group. The alpha diversity of bacterial community in healthy and diseased groups increased at 15 days, and the healthy group had a significant difference. The relative abundance of Alternaria and Cladosporium decreased while that of Boeremia, Stagonosporopsis, Symmetrospora, Epicoccum and Phoma increased in the fungal communities of healthy and diseased leaves. The relative abundance of Pantoea decreased first and then increased, while that of Ralstonia, Pseudomonas and Sphingomonas increased first and then decreased in the bacterial communities of healthy and diseased leaves. While copper hydroxide reduced the relative abundance of pathogenic fungi Alternaria and Cladosporium, it also resulted in the decrease of beneficial bacteria such as Actinomycetes and Pantoea, and the increase of potential pathogens such as Boeremia and Stagonosporopsis. After treatment with copper hydroxide, the metabolic capacity of the diseased group improved, while that of the healthy group was significantly suppressed, with a gradual recovery of metabolic activity as the application time extended. The results revealed changes in microbial community composition and metabolic function of healthy and diseased tobacco under copper hydroxide stress, providing a theoretical basis for future studies on microecological protection of phyllosphere.

Light cues induce protective anticipation of environmental water loss in terrestrial bacteria

The ecological significance of light perception in nonphotosynthetic bacteria remains largely elusive. In terrestrial environments, diurnal oscillations in light are often temporally coupled to other environmental changes, including increased temperature and evaporation. Here, we report that light functions as an anticipatory cue that triggers protective adaptations to tolerate a future rapid loss of environmental water. We demonstrate this photo-anticipatory stress tolerance in leaf-associated Pseudomonas syringae pv. syringae (Pss) and other plant- and soil-associated pseudomonads. We found that light influences the expression of 30% of the Pss genome, indicating that light is a global regulatory signal, and this signaling occurs almost entirely via a bacteriophytochrome photoreceptor that senses red, far-red, and blue wavelengths. Bacteriophytochrome-mediated light control disproportionally up-regulates water-stress adaptation functions and confers enhanced fitness when cells encounter light prior to water limitation. Given the rapid speed at which water can evaporate from leaf surfaces, such anticipatory activation of a protective response enhances fitness beyond that of a reactive stress response alone, with recurring diurnal wet-dry cycles likely further amplifying the fitness advantage over time. These findings demonstrate that nonphotosynthetic bacteria can use light as a cue to mount an adaptive anticipatory response against a physiologically unrelated but ecologically coupled stress.

Ill Communication: Host Metabolites as Virulence-Regulating Signals for Plant-Pathogenic Bacteria

Plant bacterial pathogens rely on host-derived signals to coordinate the deployment of virulence factors required for infection. In this review, I describe how diverse plant-pathogenic bacteria detect and respond to plant-derived metabolic signals for the purpose of virulence gene regulation. I highlight examples of how pathogens perceive host metabolites through membrane-localized receptors as well as intracellular response mechanisms. Furthermore, I describe how individual strains may coordinate their virulence using multiple distinct host metabolic signals, and how plant signals may positively or negatively regulate virulence responses. I also describe how plant defenses may interfere with the perception of host metabolites as a means to dampen pathogen virulence. The emerging picture is that recognition of host metabolic signals for the purpose of virulence gene regulation represents an important primary layer of interaction between pathogenic bacteria and host plants that shapes infection outcomes.

Metabolic resource overlap impacts competition among phyllosphere bacteria

The phyllosphere is densely colonised by microbial communities, despite sparse and heterogeneously distributed resources. The limitation of resources is expected to drive bacterial competition resulting in exclusion or coexistence based on fitness differences and resource overlap between individual colonisers. We studied the impact of resource competition by determining the effects of different bacterial colonisers on the growth of the model epiphyte Pantoea eucalypti 299R (Pe299R). Resource overlap was predicted based on genome-scale metabolic modelling. By combining results of metabolic modelling and pairwise competitions in the Arabidopsis thaliana phyllosphere and in vitro, we found that ten resources sufficed to explain fitness of Pe299R. An effect of both resource overlap and phylogenetic relationships was found on competition outcomes in vitro as well as in the phyllosphere. However, effects of resource competition were much weaker in the phyllosphere when compared to in vitro experiments. When investigating growth dynamics and reproductive success at the single-cell resolution, resource overlap and phylogenetic relationships are only weakly correlated with epiphytic Pe299R reproductive success, indicating that the leaf's spatial heterogeneity mitigates resource competition. Although the correlation is weak, the presence of competitors led to the development of Pe299R subpopulations that experienced different life histories and cell divisions. In some in planta competitions, Pe299R benefitted from the presence of epiphytes despite high resource overlap to the competitor strain suggesting other factors having stronger effects than resource competition. This study provides fundamental insights into how bacterial communities are shaped in heterogeneous environments and a framework to predict competition outcomes.

Predictive Population Dynamics of Escherichia coli O157:H7 and Salmonella enterica on Plants: a Mechanistic Mathematical Model Based on Weather Parameters and Bacterial State

Weather affects key aspects of bacterial behavior on plants but has not been extensively investigated as a tool to assess risk of crop contamination with human foodborne pathogens. A novel mechanistic model informed by weather factors and bacterial state was developed to predict population dynamics on leafy vegetables and tested against published data tracking Escherichia coli O157:H7 (EcO157) and Salmonella enterica populations on lettuce and cilantro plants. The model utilizes temperature, radiation, and dew point depression to characterize pathogen growth and decay rates. Additionally, the model incorporates the population level effect of bacterial physiological state dynamics in the phyllosphere in terms of the duration and frequency of specific weather parameters. The model accurately predicted EcO157 and S. enterica population sizes on lettuce and cilantro leaves in the laboratory under various conditions of temperature, relative humidity, light intensity, and cycles of leaf wetness and dryness. Importantly, the model successfully predicted EcO157 population dynamics on 4-week-old romaine lettuce plants under variable weather conditions in nearly all field trials. Prediction of initial EcO157 population decay rates after inoculation of 6-week-old romaine plants in the same field study was better than that of long-term survival. This suggests that future augmentation of the model should consider plant age and species morphology by including additional physical parameters. Our results highlight the potential of a comprehensive weather-based model in predicting contamination risk in the field. Such a modeling approach would additionally be valuable for timing field sampling in quality control to ensure the microbial safety of produce. IMPORTANCE Fruits and vegetables are important sources of foodborne disease. Novel approaches to improve the microbial safety of produce are greatly lacking. Given that bacterial behavior on plant surfaces is highly dependent on weather factors, risk assessment informed by meteorological data may be an effective tool to integrate into strategies to prevent crop contamination. A mathematical model was developed to predict the population trends of pathogenic E. coli and S. enterica, two major causal agents of foodborne disease associated with produce, on leaves. Our model is based on weather parameters and rates of switching between the active (growing) and inactive (nongrowing) bacterial state resulting from prevailing environmental conditions on leaf surfaces. We demonstrate that the model has the ability to accurately predict dynamics of enteric pathogens on leaves and, notably, sizes of populations of pathogenic E. coli over time after inoculation onto the leaves of young lettuce plants in the field.

Development of the Pseudomonas syringae pv. morsprunorum Biofilm Monitored in Real Time Using Attenuated Total Reflection Fourier Transform Infrared Measurements in a Flow Cell Chamber

Biofilms of sessile Pseudomonas syringae cells formed on top of plant host's leaves or fruits allow surviving harsh environmental conditions (desiccation) and improve their resistance to antibacterial treatments of crops. A better understanding of these biofilms can help minimize their effect on harvests. In the present study, infrared attenuated total reflection spectroscopy coupled with optical and confocal laser scanning microscopy has been applied for the first time to analyze Pseudomonas syringae pathovar morsprunorum biofilm development in real time. The biofilm development was observed within a spectral window 4000-800 cm^-1 under constant flow conditions for 72 h. The kinetics of representative integrated band areas (nucleic acids with polysaccharides at 1141-1006 cm^-1, amino acid side chains with free fatty acids at 1420-1380 cm^-1, proteins at 1580-1490 cm^-1, and lipids with proteins at 2935-2915 cm^-1) were analyzed with regard to the observed biofilm structure and the following P. syringae biofilm developmental stages were attributed: The inoculation phase, washing of weakly attached bacteria closely followed by recolonization of the vacated surface, the restructuration phase, and finally the maturation phase.

Detection, Diagnosis, and Preventive Management of the Bacterial Plant Pathogen Pseudomonas syringae

Plant diseases caused by the pathogen Pseudomonas syringae are serious problems for various plant species worldwide. Accurate detection and diagnosis of P. syringae infections are critical for the effective management of these plant diseases. In this review, we summarize the current methods for the detection and diagnosis of P. syringae, including traditional techniques such as culture isolation and microscopy, and relatively newer techniques such as PCR and ELISA. It should be noted that each method has its advantages and disadvantages, and the choice of each method depends on the specific requirements, resources of each laboratory, and field settings. We also discuss the future trends in this field, such as the need for more sensitive and specific methods to detect the pathogens at low concentrations and the methods that can be used to diagnose P. syringae infections that are co-existing with other pathogens. Modern technologies such as genomics and proteomics could lead to the development of new methods of highly accurate detection and diagnosis based on the analysis of genetic and protein markers of the pathogens. Furthermore, using machine learning algorithms to analyze large data sets could yield new insights into the biology of P. syringae and novel diagnostic strategies. This review could enhance our understanding of P. syringae and help foster the development of more effective management techniques of the diseases caused by related pathogens.

Oxidative response of rice (Oryza sativa L.) seedlings to quinolone antibiotics and its correlation with phyllosphere microbes and antibiotic resistance genes

With the increasing use of veterinary antibiotics, quinolone antibiotics may enter farmland systems after livestock manure has been composted. However, the phytotoxicity mechanism of antibiotics in crops is still unclear. In this study, the oxidative responses of rice (Oryza sativa L.) seedlings to three typical quinolone antibiotics and their underlying mechanisms were investigated. The bioconcentration factor values were 1.47, 0.55, and 0.23 in the levofloxacin, enrofloxacin and norfloxacin treatment, respectively. The inhibitory effects on rice seedlings were in the order of levofloxacin > enrofloxacin > norfloxacin, which may be due to the high uptake of levofloxacin. The H₂O₂ level, MDA content, and ion leakage rate increased significantly (p < 0.05), and cell plasmolysis was observed, showing that antibiotics can cause membrane lipid peroxidation and damage the cell membrane structure. Antioxidant enzyme activities (superoxide dismutase, catalase, and peroxidase) changed with the antibiotic concentration. Integrated biomarker response analysis showed that levofloxacin caused the greatest oxidative stress in rice seedlings. Transcriptomic analysis identified 5880 differentially expressed genes, and these were annotated as 20 biological functions; the greatest abundances were cellular and metabolic processes, cell part, and membrane part and organelle; SOD and CAT related genes were up-regulated. The richness and diversity of the phyllosphere microbial community decreased significantly (p < 0.05) and the microbiome changed at the phylum and genus levels. The H₂O₂ level was correlated with changes in phyllosphere microbial communities. The number of antibiotic resistance genes (ARGs) and mobile genetic elements decreased, while their abundance increased. In conclusion, enrofloxacin exposure not only affects the microbial community but may also affect the ARGs carried by microbes. The relative abundance of MGEs and ARGs was significantly positively correlated (R² = 0.760, p = 0.0148), indicating that MGEs can significantly promote the spread of ARGs.

Plant-exuded chemical signals induce surface attachment of the bacterial pathogen Pseudomonas syringae

Many plant pathogenic bacteria suppress host defenses by secreting small molecule toxins or immune-suppressing proteins into host cells, processes that likely require close physical contact between pathogen and host. Yet, in most cases, little is known about whether phytopathogenic bacteria physically attach to host surfaces during infection. Here we report that Pseudomonas syringae pv. tomato strain DC3000, a Gram-negative bacterial pathogen of tomato and Arabidopsis, attaches to polystyrene and glass surfaces in response to chemical signals exuded from Arabidopsis seedlings and tomato leaves. We characterized the molecular nature of these attachment-inducing signals and discovered that multiple hydrophilic metabolites found in plant exudates, including citric acid, glutamic acid, and aspartic acid, are potent inducers of surface attachment. These same compounds were previously identified as inducers of P. syringae genes encoding a type III secretion system (T3SS), indicating that both attachment and T3SS deployment are induced by the same plant signals. To test if surface attachment and T3SS are regulated by the same signaling pathways, we assessed the attachment phenotypes of several previously characterized DC3000 mutants, and found that the T3SS master regulator HrpL was partially required for maximal levels of surface attachment, whereas the response regulator GacA, a negative regulator of T3SS, negatively regulated DC3000 surface attachment. Together, our data indicate that T3SS deployment and surface attachment by P. syringae may be co-regulated by the same host signals during infection, possibly to ensure close contact necessary to facilitate delivery of T3SS effectors into host cells.

Complete Genome Sequence of the Ice-Nucleation-Active Pseudomonas syringae Strain MUP17, Isolated from the Frost-Damaged Barley Cultivar Hordeum vulgare cv. La Trobe

Pseudomonas syringae MUP17 was isolated from Western Australian frost-damaged barley. The MUP17 complete genome contained a 5,850,185-bp single circular chromosome with a GC content of 59.12%. IMG/M genome annotation identified 5,012 protein-coding genes, 1 of which encoded an ice-nucleation protein containing 19 occurrences of a highly repetitive PF00818 domain.

Complete Genome Sequence of the Ice-Nucleation-Active Pseudomonas syringae Strain MUP20, Isolated from Frost-Damaged Wheat (Triticum aestivum cv. Scepter) in Western Australia

Pseudomonas syringae MUP20 was isolated from Western Australian frost-damaged wheat. The MUP20 complete genome contained a 6,045,198-bp single circular chromosome with a GC content of 59.03%. IMG/M genome annotation identified 5,245 protein-coding genes, 1 of which encoded an ice nucleation protein containing 20 occurrences of a highly repetitive PF00818 domain.

Complete Genome Sequence of the Ice-Nucleation-Active Pseudomonas syringae pv. pisi Isolate MUP32, Isolated from Frost-Damaged Pea (Pisum sativum subsp. arvense cv. Dundale) in New South Wales

The genome of Pseudomonas syringae MUP32, which was isolated from frost-damaged pea in New South Wales, Australia, is tripartite and contains a circular chromosome (6,032,644 bp) and two plasmids (61,675 and 54,993 bp). IMG/M genome annotation identified 5,370 protein-coding genes, one of which encoded an ice-nucleation protein with 19 repetitive PF00818 domains.

Characterization of Pseudomonas syringae Strains Associated with Shoot Blight of Raspberry and Blackberry in Serbia

During May 2016, severe blight symptoms were observed in several raspberry and blackberry fields in Serbia. In total, 22 strains were isolated: 16 from symptomatic raspberry shoots, 2 from asymptomatic raspberry leaves, and 4 from symptomatic blackberry shoots. Additionally, eight raspberry strains, isolated earlier from two similar outbreaks, were included in the study. Pathogenicity of the strains was confirmed on detached raspberry and blackberry shoots by reproducing the symptoms of natural infection. The strains were Gram-negative, fluorescent on King's medium B, ice nucleation positive, and utilized glucose oxidatively. All strains were levan positive, oxidase negative, nonpectolytic, arginine dihydrolase negative, and induced hypersensitivity in tobacco leaves (LOPAT + - - - +, Pseudomonas group Ia). Furthermore, all strains liquefied gelatin and hydrolyzed aesculin but did not show tyrosinase activity or utilize tartrate (GATTa + + - -). Tentative identification using morphology, LOPAT, GATTa, and ice-nucleating ability tests suggested that isolated strains belong to Pseudomonas syringae. The syrB gene associated with syringomycin production was detected in all strains. DNA fingerprints with REP, ERIC, and BOX primers generated identical profiles for 29 strains, except for strain KBI 222, which showed a unique genomic fingerprint. In all, 9 of 10 selected strains exhibited identical sequences of four housekeeping genes: gyrB, rpoD, gapA, and gltA. Five nucleotide polymorphisms were found in strain KBI 222 at the rpoD gene locus only. In the phylogenetic tree based on a concatenated sequence of all four housekeeping genes, strains clustered within phylogroup 2 (i.e., genomospecies 1) of the P. syringae species complex, with pathotype strains of P. syringae pv. aceris and P. syringae pv. solidagae as their closest relatives. There was no correlation between genotype and geographic origin, particular outbreak, host, or cultivar.

Effect of temperature and humidity on dynamics and transmission of Pseudomonas amygdali pv. lachrymans aerosols

Cucumber angular leaf spot (ALS) disease, caused by Pseudomonas amygdali pv. lachrymans (Pal), is an emerging disease with a high incidence that causes severe damage to cucumber worldwide. Bacterial aerosols play a crucial role in the epidemiology of greenhouse ALS disease. However, little is known about the influence of temperature and relative humidity (RH) on the dynamics of Pal in aerosols. A study was conducted to investigate the relationships between the concentration of Pal aerosols and their dependence on temperature and RH in aerosol chambers and greenhouses. The results demonstrated that temperature and RH are both significant factors influencing the release amount, survival time and infectivity of Pal in aerosols, while RH has a greater influence on particle size than temperature across the range of conditions tested. The release amount and survival time of Pal in aerosols under high RH (95%) and low temperature (≤ 25°C) conditions were significantly higher than those under low RH (35%) and high temperature (35°C) conditions. The highest release amount of Pal aerosol (96 CFU/m³) and highest survival rate (98.41%) were found at 18°C and 95% RH, while the highest disease index (DI = 60.9) caused by Pal aerosol was found at 25°C and 95% RH. In addition, Pal aerosols presented a larger diameter (4.7->7.0 μm) under high RH (95% RH) than under dry conditions (≤ 65% RH). These findings will play a crucial role in elucidating the influence of environmental parameters on the dynamics and transmission of Pal in aerosols. Based on our findings, preliminary recommendations for controlling airborne Pal spread involve controlling air temperature and RH, which will contribute to the effective alleviation and control of cucumber ALS disease.

Identification and Characterization of Pseudomonas syringae pv. syringae, a Causative Bacterium of Apple Canker in Korea

In the present investigation, bacterial isolates from infected apple trees causing apple canker during winter were studied in the northern Gyeongbuk Province, Korea. The pathogen was identified as Pseudomonas syringae pv. syringae (Pss) through various physiological and biochemical characterization assays such as BIOLOG, gas chromatography of fatty acid methyl esters, and 16S rRNA. Bioassays for the production of phytotoxins were positive for syringopeptin and syringomycin against Bacillus megaterium and Geotrichum candidum, respectively. The polymerase chain reaction (PCR) method enabled the detection of toxin-producing genes, syrB1, and sypB in Pss. The differentiation of strains was performed using LOPAT and GATTa tests. Pss further exhibited ice nucleation activity (INA) at a temperature of -0.7°C, indicating an INA+ bacterium. The ice-nucleating temperature was -4.7°C for a non-treated control (sterilized distilled water), whereas it was -9.6°C for an INA- bacterium Escherichia coli TOP10. These methods detected pathogenic strains from apple orchards. Pss might exist in an apple tree during ice injury, and it secretes a toxin that makes leaves yellow and cause canker symptoms. Until now, Korea has not developed antibiotics targeting Pss. Therefore, it is necessary to develop effective disease control to combat Pss in apple orchards. Pathogenicity test on apple leaves and stems showed canker symptoms. The pathogenic bacterium was re-isolated from symptomatic plant tissue and confirmed as original isolates by 16S rRNA. Repetitive element sequence-based PCR and enterobacterial repetitive intergenic consensus PCR primers revealed different genetic profiles within P. syringae pathovars. High antibiotic susceptibility results showed the misreading of mRNA caused by streptomycin and oxytetracycline.

Genomic and functional analysis of phage-mediated horizontal gene transfer in Pseudomonas syringae on the plant surface

Many strains of Pseudomonas colonise plant surfaces, including the cherry canker pathogens, Pseudomonas syringae pathovars syringae and morsprunorum. We have examined the genomic diversity of P. syringae in the cherry phyllosphere and focused on the role of prophages in transfer of genes encoding Type 3 secreted effector (T3SE) proteins contributing to the evolution of virulence. Phylogenomic analysis was carried out on epiphytic pseudomonads in the UK orchards. Significant differences in epiphytic populations occurred between regions. Nonpathogenic strains were found to contain reservoirs of T3SE genes. Members of P. syringae phylogroups 4 and 10 were identified for the first time from Prunus. Using bioinformatics, we explored the presence of the gene encoding T3SE HopAR1 within related prophage sequences in diverse P. syringae strains including cherry epiphytes and pathogens. Results indicated that horizontal gene transfer (HGT) of this effector between phylogroups may have involved phage. Prophages containing hopAR1 were demonstrated to excise, circularise and transfer the gene on the leaf surface. The phyllosphere provides a dynamic environment for prophage-mediated gene exchange and the potential for the emergence of new more virulent pathotypes. Our results suggest that genome-based epidemiological surveillance of environmental populations will allow the timely application of control measures to prevent damaging diseases.

Type III Secretion System Repressor RhpR Induces GrlP, a Glycine-Rich Outer Membrane Lipoprotein with Functions in Regulating the Periplasmic Space and Pleiotropic Responses

The two-component system RhpRS was initially identified as a regulator of genes encoding the type III secretion system (T3SS) in Pseudomonas syringae. Phosphorylated RhpR (P-RhpR) negatively regulates the T3SS genes by repressing the hrpR promoter, but directly activates the expression of a small gene named here as grlp. Here, we show that grlp is expressed higher in rich medium than in minimal medium in P. s. pv. tomato DC3000 and encodes a glycine rich lipoprotein (GrlP) located in the outer membrane (OM). The grlp gene has a pleiotropic effect on bacterial behaviors such as reductions in pathogenicity, swimming motility, biofilm formation, tolerance to various stresses and antibiotics, and long-term survival when overexpressed, but induces these responses when it is deleted in P. s. pv. tomato DC3000. Overexpression of grlp increases the size of periplasm while deletion of grlp decreases the periplasmic space. Further, GrlP interacts with OprI, the ortholog of E. coli OM lipoprotein Lpp, a key player in determining the size of periplasm and mechanic stiffness of the OM by tethering the OM to peptidoglycan (PG) in periplasm. As periplasmic space and OM mechanics play central roles in regulating bacterial physiology, we speculate that GrlP probably imposes its functions on bacterial physiology by regulating the periplasmic space and OM mechanics. These findings suggest that the T3SS gene regulation is closely coordinated with bacterial cell envelope properties by RhpRS in P. syringe. IMPORTANCE The OM of Gram-negative bacteria is the most front line in contact with extracellular milieu. OM is not only a protective layer, but also a structure that determines the envelope stiffness. Recent evidence indicated that components determining the periplasmic space and cross-links of lipopolysaccharide on the OM play key roles in regulating the mechanical properties of the OM. However, whether the OM composition and mechanical properties are coordinated with the expression of the T3SS genes is unknown. Here, we found that the two-component system (TCS) regulator P-RhpR, a direct repressor of the T3SS regulator hrpRS operon, directly activates the expression of the OM lipoprotein gene grlp bearing a function in regulating the periplasmic space. This finding suggests a coordination between the OM properties and the T3SS gene regulation and reveals a new target for control of the T3SS gene expression and bacterial pathogenicity.

Prevention of Stomatal Entry as a Strategy for Plant Disease Control against Foliar Pathogenic Pseudomonas Species

The genus Pseudomonas includes some of the most problematic and studied foliar bacterial pathogens. Generally, in a successful disease cycle there is an initial epiphytic lifestyle on the leaf surface and a subsequent aggressive endophytic stage inside the leaf apoplast. Leaf-associated bacterial pathogens enter intercellular spaces and internal leaf tissues by natural surface opening sites, such as stomata. The stomatal crossing is complex and dynamic, and functional genomic studies have revealed several virulence factors required for plant entry. Currently, treatments with copper-containing compounds, where authorized and admitted, and antibiotics are commonly used against bacterial plant pathogens. However, strains resistant to these chemicals occur in the fields. Therefore, the demand for alternative control strategies has been increasing. This review summarizes efficient strategies to prevent bacterial entry. Virulence factors required for entering the leaf in plant-pathogenic Pseudomonas species are also discussed.

Natural variation and drought-induced differences in metabolite profiles of red oak-leaf and Romaine lettuce play a role in modulating the interaction with Salmonella enterica

Nutrients on produce surfaces are vital for successful enteric pathogen colonisation. In this study, we investigated natural variation in metabolite profiles of Romaine 'Parris Island Cos' and red oak-leaf lettuce 'Mascara' under regular and restricted watering conditions. We also investigated the impact of plant drought stress on the Salmonella - lettuce association. Salmonella Newport and Typhimurium were able to persist at higher levels on regularly watered Romaine than red oak-leaf lettuce. Drought treatment to lettuce impaired epiphytic Salmonella association, with S. Newport and Typhimurium being differentially affected. A higher log reduction of both serotypes was measured on drought-subjected red oak-leaf lettuce plants than controls, but S. Typhimurium was unaffected on water deficit-treated Romaine lettuce (p < 0.05). To assess Salmonella interaction with leaf surface metabolites, leaf washes collected from both cultivars were inoculated and found to be able to support S. Newport growth, with higher levels of Salmonella retrieved from Romaine washes (p < 0.05). The lag phase of S. Newport in washes from water restricted red oak-leaf lettuce was prolonged in relation to regularly-watered controls (p < 0.05). Untargeted plant metabolite profiling using electrospray ionization time-of-flight mass spectrometry (ESI-TOF-MS) revealed natural variation between Romaine and red oak-leaf lettuce profiles for leaf tissue and leaf washes. Metabolite profile shifts were detected in both lettuce types in response to drought stress, but more unique peaks were detected in red oak-leaf than Romaine lettuce after drought treatment. Variation between the two cultivars was in part attributed to naturally higher levels of flavonoids and anthocyanins in red oak-leaf lettuce compared to Romaine. Moreover, red oak-leaf, but not Romaine lettuce, responded to drought by inducing the accumulation of proline, phenolics, flavonoids and anthocyanins. Drought stress, therefore, enhanced the functional food properties of red oak-leaf lettuce. Salmonella growth dynamics in lettuce leaf washes suggested that natural variation and drought-induced changes in metabolite profiles in lettuce could partly explain the differential susceptibility of various lettuce types to Salmonella, although the primary or secondary metabolites mediating this effect remain unknown. Regulated mild water stress should be investigated as an approach to lower Salmonella contamination risk in suitable lettuce cultivars, while simultaneously boosting the health beneficial quality of lettuce.

A Recipe for Success: Three Key Strategies Used by Aphids and Pseudomonas syringae to Colonize the Phyllosphere

Aphids and Pseudomonas syringae are a permanent challenge for agriculture, causing severe losses to the crop industry worldwide. Despite the obvious phylogenetic distance between them, both have become predominant colonizers of the plant kingdom. In this study, we reviewed three key steps of spread and colonization that aphids and P. syringae have mastered to successfully colonize the phyllosphere. These steps involve (i) plant-to-plant movement for locating new nutritional sources, (ii) disruption and modification of the apoplast to facilitate nutrient acquisition, and (iii) suppression of host defenses through effector proteins. In addition, we will provide insights about the direct interaction between aphids and P. syringae and how this yet underrated phenomenon could bring new ecological implications for both organisms beyond their pathogenicity.

In vitro studies of biofilm-forming Bacillus strains, biocontrol agents isolated from the maize phyllosphere

We aimed to assess how biofilm formation by three Bacillus isolates was affected by changes in temperature, water potential, growth media, time, and the combinations between these factors. The strains had been selected as potential biological control agents (BCAs) in earlier studies, and they were identified as B. subtilis and B. velezensis spp. through 16 rRNA sequencing and MALDI-TOF MS. Maize leaves (ML) were used as one of the growth media, since they made it possible to simulate the nutrient content in the maize phyllosphere, from which the bacteria were originally isolated. The strains were able to form biofilm both in ML and biofilm-inducing MSgg after 24, 48, and 72 h. Biofilm development in the form of pellicles and architecturally complex colonies varied morphologically from one strain to another and depended on the conditions mentioned above. In all cases, colonies and pellicles were less complex when both temperature and water potential were lower. Scanning electron microscopy (SEM) revealed that changing levels of complexity in pellicles were correlated with those in colonies. Statistical analyses found that the quantification of biofilm produced by the isolates was influenced by all the conditions tested. In terms of motility (which may contribute to biofilm formation), swimming and swarming were possible for all strains in 0.3 and 0.7% agar, respectively. A more in-depth understanding of how abiotic factors influence biofilm formation can contribute to a more effective use of these biocontrol strains against pathogens in the maize phyllosphere.

RNA-seq Gene Profiling Reveals Transcriptional Changes in the Late Phase during Compatible Interaction between a Korean Soybean Cultivar (Glycine max cv. Kwangan) and Pseudomonas syringae pv. syringae B728a

Soybean (Glycine max (L) Merr.) provides plant-derived proteins, soy vegetable oils, and various beneficial metabolites to humans and livestock. The importance of soybean is highly underlined, especially when carbon-negative sustainable agriculture is noticeable. However, many diseases by pests and pathogens threaten sustainable soybean production. Therefore, understanding molecular interaction between diverse cultivated varieties and pathogens is essential to developing disease-resistant soybean plants. Here, we established a pathosystem of the Korean domestic cultivar Kwangan against Pseudomonas syringae pv. syringae B728a. This bacterial strain caused apparent disease symptoms and grew well in trifoliate leaves of soybean plants. To examine the disease susceptibility of the cultivar, we analyzed transcriptional changes in soybean leaves on day 5 after P. syringae pv. syringae B728a infection. About 8,900 and 7,780 differentially expressed genes (DEGs) were identified in this study, and significant proportions of DEGs were engaged in various primary and secondary metabolisms. On the other hand, soybean orthologs to well-known plant immune-related genes, especially in plant hormone signal transduction, mitogen-activated protein kinase signaling, and plant-pathogen interaction, were mainly reduced in transcript levels at 5 days post inoculation. These findings present the feature of the compatible interaction between cultivar Kwangan and P. syringae pv. syringae B728a, as a hemibiotroph, at the late infection phase. Collectively, we propose that P. syringae pv. syringae B728a successfully inhibits plant immune response in susceptible plants and deregulates host metabolic processes for their colonization and proliferation, whereas host plants employ diverse metabolites to protect themselves against infection with the hemibiotrophic pathogen at the late infection phase.

The plant host environment influences competitive interactions between bacterial pathogens

Bacteria compete for resources in diverse environments using an array of antagonistic strategies, including the production of narrow-spectrum protein antibacterials termed bacteriocins. Although significant research has focused on bacteriocin-mediated dynamics in culture environments, little research has explored bacteriocin-mediated dynamics within a host context, particularly in plant environments. Here, we show that a bacterial plant pathogen, Pseudomonas syringae pv. syringae (Psy), expresses a bacteriocin both in culture and in leaf apoplast when co-inoculated with a bacteriocin-sensitive competitor, P. syringae pv. phaseolicola (Pph). Although there is an observable negative effect of the bacteriocin on the Pph population at most time points both in culture and in the leaf apoplast, a bacteriocin-mediated benefit to Psy was only observed when the producing strain was co-infiltrated at a low population frequency (1:9) into the leaf apoplast. At 6 days post-infiltration, Psy achieved an eightfold population increase compared to a bacteriocin-deficient mutant in the apoplast. No bacteriocin-mediated benefit for Psy was observed under the culture conditions tested. Additionally, we found that the bacteriocin-mediated benefit for Psy was dependent on the Type III Secretion System. Taken together, our results demonstrate that the fitness benefit of bacteriocin-mediated antagonism is influenced by interactions within the host plant.

Weather stressors correlate with Escherichia coli and Salmonella enterica persister formation rates in the phyllosphere: a mathematical modeling study

Enteric pathogens can enter a persister state in which they survive exposure to antibiotics and physicochemical stresses. Subpopulations of such phenotypic dormant variants have been detected in vivo and in planta in the laboratory, but their formation in the natural environment remains largely unexplored. We applied a mathematical model predicting the switch rate to persister cell in the phyllosphere to identify weather-related stressors associated with E. coli and S. enterica persister formation on plants based on their population dynamics in published field studies from the USA and Spain. Model outputs accurately depicted the bi-phasic decay of bacterial population sizes measured in the lettuce and spinach phyllosphere in these studies. Predicted E. coli persister switch rate on leaves was positively and negatively correlated with solar radiation intensity and wind velocity, respectively. Likewise, predicted S. enterica persister switch rate correlated positively with solar radiation intensity; however, a negative correlation was observed with air temperature, relative humidity, and dew point, factors involved in water deposition onto the phylloplane. These findings suggest that specific environmental factors may enrich for dormant bacterial cells on plants. Our model quantifiably links persister cell subpopulations in the plant habitat with broader physical conditions, spanning processes at different granular scales.

Predictive modeling of Pseudomonas syringae virulence on bean using gradient boosted decision trees

Pseudomonas syringae is a genetically diverse bacterial species complex responsible for numerous agronomically important crop diseases. Individual P. syringae isolates are assigned pathovar designations based on their host of isolation and the associated disease symptoms, and these pathovar designations are often assumed to reflect host specificity although this assumption has rarely been rigorously tested. Here we developed a rapid seed infection assay to measure the virulence of 121 diverse P. syringae isolates on common bean (Phaseolus vulgaris). This collection includes P. syringae phylogroup 2 (PG2) bean isolates (pathovar syringae) that cause bacterial spot disease and P. syringae phylogroup 3 (PG3) bean isolates (pathovar phaseolicola) that cause the more serious halo blight disease. We found that bean isolates in general were significantly more virulent on bean than non-bean isolates and observed no significant virulence difference between the PG2 and PG3 bean isolates. However, when we compared virulence within PGs we found that PG3 bean isolates were significantly more virulent than PG3 non-bean isolates, while there was no significant difference in virulence between PG2 bean and non-bean isolates. These results indicate that PG3 strains have a higher level of host specificity than PG2 strains. We then used gradient boosting machine learning to predict each strain’s virulence on bean based on whole genome k-mers, type III secreted effector k-mers, and the presence/absence of type III effectors and phytotoxins. Our model performed best using whole genome data and was able to predict virulence with high accuracy (mean absolute error = 0.05). Finally, we functionally validated the model by predicting virulence for 16 strains and found that 15 (94%) had virulence levels within the bounds of estimated predictions. This study strengthens the hypothesis that P. syringae PG2 strains have evolved a different lifestyle than other P. syringae strains as reflected in their lower level of host specificity. It also acts as a proof-of-principle to demonstrate the power of machine learning for predicting host specific adaptation.

Pseudomonas syringae is a genetically diverse Gammaproteobacterial species complex responsible for numerous agronomically important crop diseases. Strains in the P. syringae species complex are frequently categorized into pathovars depending on pathogenic characteristics such as host of isolation and disease symptoms. Common bean pathogens from P. syringae are known to cause two major diseases: (1) pathovar phaseolicola strains from phylogroup 3 cause halo blight disease, characterized by large necrotic lesions surrounded by a chlorotic zone or halo of yellow tissue; and (2) pathovar syringae strains from phylogroup 2 causes bacterial spot disease, characterized by brown leaf spots. While halo blight can cause serious crop losses, bacterial spot disease is generally of minor agronomic concern. Recently, statistical genetic and machine learning approaches have been applied to genomic data to identify genes underlying traits of interest or predict the outcome of host-microbe interactions. Here, we apply machine learning to P. syringae genomic data to predict virulence on bean. We first characterized the virulence of P. syringae isolates on common bean using a seed infection assay and then applied machine learning to the genomic data from the same strains to generate a predictive model for virulence on bean. We found that machine learning models built with k-mers from either full genome data or virulence factors could predict bean virulence with high accuracy. We also confirmed prior work showing that phylogroup 3 halo blight pathogens display a stronger degree of phylogenetic clustering and host specificity compared to phylogroup 2 brown spot pathogens. This works serves as a proof-of-principle for the power of machine learning for predicting host specificity and may find utility in agricultural diagnostic microbiology.

RsmA3 modulates RpoS through the RetS-Gac-Rsm signaling pathway in response to H2 O2 stress in the phytopathogen Pseudomonas syringae

Reactive oxygen species are a fatal challenge to the plant pathogenic bacterium Pseudomonas syringae. In this study, we reveal that the global regulatory protein RsmA3 from the RetS-Gac/Rsm signaling pathway modulates RpoS in the early-log growth phase in the P. syringae wild-type strain MB03, thereby regulating oxidative tolerance to H₂ O₂ and ultimately affecting pathogenicity to the host plant. Following increased H₂ O₂ by external addition or endogenous induction by menadione, the resistance of the mutant strain ΔretS to H₂ O₂ is significantly enhanced due to rapid increases in the transcription of Rsm-related non-coding small RNAs (nc sRNAs), a sigma factor RpoS, and H₂ O₂ -detoxifying enzymes. Moreover, the ΔretS mutant is significantly less pathogenic in cucumber leaves. Seven Rsm-related nc sRNAs (namely, rsmZ, rsmY, and rsmX_1-5 ) show functional redundancy in the RetS-Gac-Rsm signaling pathway. External addition of H₂ O₂ stimulates increases in the transcription of both rsmY and rsmZ. Thus, we propose a regulatory model of the RetS-Gac-Rsm signaling pathway in P. syringae MB03 for the regulation of H₂ O₂ tolerance and phytopathogenicity in the host plant.

Community Structure of Phyllosphere Bacteria in Different Cultivars of Fingered Citron (Citrus medica 'Fingered') and Their Correlations With Fragrance

In recent years, plant metabolomics and microbiome studies have suggested that the synthesis and secretion of plant secondary metabolites are affected by microbial-host symbiotic interactions. In this study, six varieties of fingered citron (Citrus medica 'Fingered') are sampled to study their phyllosphere bacterial communities and volatile organic compounds (VOCs). High-throughput sequencing is used to sequence the V5-V7 region of the 16S rRNA of the fingered citron phyllosphere bacteria, and the results showed that Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes were the dominant bacterial phylum in the phyllosphere of fingered citron. There were significant differences in the phyllosphere bacteria community between XiuZhen and the remaining five varieties. The relative abundance of Actinomycetospora was highest in XiuZhen, and Halomonas, Methylobacterium, Nocardioides, and Pseudokineococcus were also dominant. Among the remaining varieties, Halomonas was the genus with the highest relative abundance, while the relative abundances of all the other genera were low. Headspace solid-phase microextraction (HS-SPME) and gas chromatography-mass spectrometry (GC-MS) were used to analyze and identify the aroma compounds of six different fingered citron, and a total of 76 aroma compounds were detected in six varieties. Pinene, geraniol, and linalool were found to be the primary VOCs that affect the aroma of fingered citron based on relative odor activity value. The correlation analysis showed 55 positive and 60 negative correlations between the phyllosphere bacterial flora and aroma compounds of fingered citron. The top 10 genera in the relative abundance were all significantly associated with aroma compounds. This study provides deep insight into the relation between bacteria and VOCs of fingered citron, and this may better explain the complexity of the analysis of bacterial and metabolic interactions.

Modular (de)construction of complex bacterial phenotypes by CRISPR/nCas9-assisted, multiplex cytidine base-editing

CRISPR/Cas technologies constitute a powerful tool for genome engineering, yet their use in non-traditional bacteria depends on host factors or exogenous recombinases, which limits both efficiency and throughput. Here we mitigate these practical constraints by developing a widely-applicable genome engineering toolset for Gram-negative bacteria. The challenge is addressed by tailoring a CRISPR base editor that enables single-nucleotide resolution manipulations (C·G → T·A) with >90% efficiency. Furthermore, incorporating Cas6-mediated processing of guide RNAs in a streamlined protocol for plasmid assembly supports multiplex base editing with >85% efficiency. The toolset is adopted to construct and deconstruct complex phenotypes in the soil bacterium Pseudomonas putida. Single-step engineering of an aromatic-compound production phenotype and multi-step deconstruction of the intricate redox metabolism illustrate the versatility of multiplex base editing afforded by our toolbox. Hence, this approach overcomes typical limitations of previous technologies and empowers engineering programs in Gram-negative bacteria that were out of reach thus far.

Rapid engineering of bacterial genomes is a requisite for both fundamental and applied studies. Here the authors develop an enhanced, broad-host-range cytidine base editor that enables multiplexed and efficient genome editing of Gram-negative bacteria.

Phyllosphere Microorganisms: Sources, Drivers, and Their Interactions with Plant Hosts

The leaves of plants are colonized by various microorganisms. In comparison to the rhizosphere, less is known about the characteristics and ecological functions of phyllosphere microorganisms. Phyllosphere microorganisms mainly originate from soil, air, and seeds. The composition of phyllosphere microorganisms is mainly affected by ecological and abiotic factors. Phyllosphere microorganisms execute multiple ecological functions by influencing leaf functions and longevity, seed mass, fruit development, and homeostasis of host growth. A plant can respond to phyllosphere microorganisms by secondary metabolite secretion and its immune system. Meanwhile, phyllosphere microorganisms play an important role in ecological stability and environmental safety assessment. However, as a result of the instability of the phyllosphere environment and the poor cultivability of phyllosphere microorganisms in the current research, there are still many limitations, such as the lack of insight into the mechanisms of plant-microorganism interactions, the roles of phyllosphere microorganisms in plant growth processes, the responses of phyllosphere microorganisms to plant metabolites, etc. This review summarizes the latest progress made in the research of the phyllosphere in recent years. This is beneficial for deepening our understanding of phyllosphere microorganisms and promoting the research of plant-atmosphere interactions, plant pathogens, and plant biological control.

Could Bacillus biofilms enhance the effectivity of biocontrol strategies in the phyllosphere?

Maize (Zea mays L.), a major crop in Argentina and a staple food around the world, is affected by the emergence and re-emergence of foliar diseases. Agrochemicals are the main control strategy nowadays, but they can cause resistance in insects and microbial pathogens and have negative effects on the environment and human health. An emerging alternative is the use of living organisms, i.e. microbial biocontrol agents, to suppress plant pathogen populations. This is a risk-free approach when the organisms acting as biocontrol agents come from the same ecosystem as the foliar pathogens they are meant to antagonize. Some epiphytic microorganisms may form biofilm by becoming aggregated and attached to a surface, as is the case of spore-forming bacteria from the genus Bacillus. Their ability to sporulate and their tolerance to long storage periods make them a frequently used biocontrol agent. Moreover, the biofilm that they create protects them against different abiotic and biotic factors and helps them to acquire nutrients, which ensures their survival on the plants they protect. This review analyzes the interactions that the phyllosphere-inhabiting Bacillus genus establishes with its environment through biofilm, and how this lifestyle could serve to design effective biological control strategies.

Grape Cultivar Features Differentiate the Grape Rhizosphere Microbiota

Rhizosphere microflora are key determinants that contribute to plant growth and productivity, which are involved in improving the uptake of nutrients, regulation of plants' metabolisms and activation of plants' responses against both biotic and abiotic stresses. However, the structure and diversity of the grape rhizosphere microbiota remains poorly described. To gain a detailed understanding of the assembly of rhizosphere microbiota, we investigated the rhizosphere microbiota of nine grape varieties in northern China by high-throughput sequencing. We found that the richness and diversity of bacterial and fungal community networking in the root compartments were significantly influenced by the grape variety. The bacterial linear discriminant analysis showed that Pseudomonas and Rhizobium, which were considered as potential plant-growth-promoting bacteria, were more enriched in Pinot noir, and Nitrosospira was enriched in Gem. The fungal linear discriminant analysis showed that Fusarium was more enriched in Longan, Sporormiella was more enriched in Merlot, Gibberella and Pseudallescheria were more enriched in Gem and Mortierella was more abundant in Cabernet Sauvignon. The 16S rRNA functional prediction indicated that no significance differentiates among the grape varieties. Understanding the rhizosphere soil microbial diversity characteristics of different grape varieties could provide the basis for exploring microbial associations and maintaining the health of grapes.

Pseudomonas syringae addresses distinct environmental challenges during plant infection through the coordinated deployment of polysaccharides

Prior to infection, phytopathogenic bacteria face a challenging environment on the plant surface, where they are exposed to nutrient starvation and abiotic stresses. Pathways enabling surface adhesion, stress tolerance, and epiphytic survival are important for successful plant pathogenesis. Understanding the roles and regulation of these pathways is therefore crucial to fully understand bacterial plant infections. The phytopathogen Pseudomonas syringae pv. tomato (Pst) encodes multiple polysaccharides that are implicated in biofilm formation, stress survival, and virulence in other microbes. To examine how these polysaccharides impact Pst epiphytic survival and pathogenesis, we analysed mutants in multiple polysaccharide loci to determine their intersecting contributions to epiphytic survival and infection. In parallel, we used qRT-PCR to analyse the regulation of each pathway. Pst polysaccharides are tightly coordinated by multiple environmental signals. Nutrient availability, temperature, and surface association strongly affect the expression of different polysaccharides under the control of the signalling protein genes ladS and cbrB and the second messenger cyclic-di-GMP. Furthermore, functionally redundant, combinatorial phenotypes were observed for several polysaccharides. Exopolysaccharides play a role in mediating leaf adhesion, while α-glucan and alginate together confer desiccation tolerance. Our results suggest that polysaccharides play important roles in overcoming environmental challenges to Pst during plant infection.

Identification of the Genes of the Plant Pathogen Pseudomonas syringae MB03 Required for the Nematicidal Activity Against Caenorhabditis elegans Through an Integrated Approach

Nematicidal potential of the common plant pathogen Pseudomonas syringae has been recently identified against Caenorhabditis elegans. The current study was designed to investigate the detailed genetic mechanism of the bacterial pathogenicity by applying comparative genomics, transcriptomics, mutant library screening, and protein expression. Results showed that P. syringae strain MB03 could kill C. elegans in the liquid assay by gut colonization. The genome of P. syringae MB03 was sequenced and comparative analysis including multi locus sequence typing, and genome-to-genome distance placed MB03 in phylogroup II of P. syringae. Furthermore, comparative genomics of MB03 with nematicidal strains of Pseudomonas aeruginosa (PAO1 and PA14) predicted 115 potential virulence factors in MB03. However, genes for previously reported nematicidal metabolites, such as phenazine, pyochelin, and pyrrolnitrin, were found absent in the MB03 genome. Transcriptomics analysis showed that the growth phase of the pathogen considerably affected the expression of virulence factors, as genes for the flagellum, glutamate ABC transporter, phoP/phoQ, fleS/fleR, type VI secretion system, and serralysin were highly up-regulated when stationary phase MB03 cells interacted with C. elegans. Additionally, screening of a transposon insertion mutant library led to the identification of other nematicidal genes such as acnA, gltP, oprD, and zapE. Finally, the nematicidal activity of selected proteins was confirmed by heterologous expression in Escherichia coli.

Response of Tomato-Pseudomonas Pathosystem to Mild Heat Stress

Higher plants suffer from mild heat stress when temperatures increase by 5 °C above optimum growth temperatures. This produces changes at the cellular and metabolic levels, allowing plants to adapt to heat conditions. This study investigated an increase of 5 °C above the optimum growth temperature (26 °C) of tomato plants in the tomato–Pseudomonas syringae pv. tomato pathosystem. A temperature increase above 26 °C affects plant development, the defensive pathways activated against Pseudomonas syringae pv. tomato strain DC3000 (PstDC3000), and the bacterial growth and virulence machinery. The results demonstrated that tomato plants were able to acclimate to mild heat stress, showing no symptoms of damage. Moreover, plants subjected to a 5 °C increase (T31 °C plants) showed higher basal levels of metabolites such as proline and putrescine, which probably act as compatible osmolytes. This demonstrates their importance as key components of thermotolerance. When grown under mild heat stress, plants were less susceptible to PstDC3000 and showed increased accumulation of abscisic acid, jasmonic acid-isoleucine, and spermine. In addition, the temperature increase negatively affected the infectivity of PstDC3000. Inhibition of the genes responsible for quorum sensing establishment and synthesis of flagellin and coronatine was observed in bacteria extracted from T31 °C plants. Analysis of the genes involved in the synthesis of the type III secretion system indicates the important role of this system in bacterial growth under these conditions. As the known resistance mechanisms involved in the defense against PstDC3000 were not activated, the changes in its virulence mechanisms under high temperatures may explain the lower infection observed in the T31 °C plants.