Inhibition of Xanthomonas fragariae, Causative Agent of Angular Leaf Spot of Strawberry, through Iron Deprivation

Microbial diversity and interactions: Synergistic effects and potential applications of Pseudomonas and Bacillus consortia

Microbial diversity and interactions in the rhizosphere play a crucial role in plant health and ecosystem functioning. Among the myriads of rhizosphere microbes, Pseudomonas and Bacillus are prominent players known for their multifaceted functionalities and beneficial effects on plant growth. The molecular mechanism of interspecies interactions between natural isolates of Bacillus and Pseudomonas in medium conditions is well understood, but the interaction between the two in vivo remains unclear. This paper focuses on the possible synergies between Pseudomonas and Bacillus associated in practical applications (such as recruiting beneficial microbes, cross-feeding and niche complementarity), and looks forward to the application prospects of the consortium in agriculture, human health and bioremediation. Through in-depth understanding of the interactions between Pseudomonas and Bacillus as well as their application prospects in various fields, this study is expected to provide a new theoretical basis and practical guidance for promoting the research and application of rhizosphere microbes.

Isolation and Characterization of Multi-Trait Plant Growth-Promoting Endophytic Bacteria from Scots Pine Tissues

Scots pine (Pinus sylvestris) is a globally significant tree species with considerable economic importance in forestry. A major challenge in afforestation, particularly in stressful environments, is growing seedlings with high viability and stress resistance. Recent studies suggest that Pseudomonas strains can alleviate stress and promote growth in crops, though limited evidence exists for trees. This study aimed to assess the plant growth-promoting (PGP) properties of Pseudomonas strains isolated from Scots pine stems using in vitro assays, and to evaluate their potential as bioinoculants through a two-year long field trial. From over sixty bacterial isolates originating from Scots pine stem tissues, only four were selected as being similar to Pseudomonas bacteria. Through 16S rRNA gene sequencing, the isolates were identified as Pseudomonas putida P57, Pseudomonas lurida P88 and 10-1, and Stenotrophomonas maltophilia P77. All isolates inhibited fungal pathogens Botrytis cinerea and Fusarium sporotrichiella, and exhibited PGP activities including nitrogen fixation and production of IAA (1.24-17.74 mg/l), ammonia (4.06-12.71 μM/ml), and siderophores, with the highest value of 1.44 ± 0.19 for the P. lurida P88 strain. Additionally, the Pseudomonas strains demonstrated phosphate solubilization capacity. We revealed that bioinoculation with strains P57 and P88 enhanced field germination of seeds by 35-45% and increased aerial biomass of two-year-old seedlings by 80-140%. Both strains adhered to seed surface and colonized roots and stems at levels of 2.4-3.2 log CFU/g fresh tissue up to two years post-inoculation. These findings highlight the potential of these bacterial strains as effective bioinoculants for improving Scots pine seedling growth under natural conditions.

Tannins as antimicrobial agents: Understanding toxic effects on pathogens

"Tannins" are compounds that belong to a group of secondary metabolites found in plants. They have a polyphenolic nature and exhibit active actions as first line defenses against invading pathogens. Several studies have demonstrated the multiple activities of tannins, highlighting their effectiveness as broad-spectrum antimicrobial agents. Tannins have reported as antibacterial, antifungal, and antiviral compounds by preventing enzymatic activities and inhibiting the synthesis of nucleic acids. Additionally, tannins primarily strengthen the plant cell wall, making it almost impenetrable to harmful pathogens. Most tannins are synthesized via the phenylpropanoid pathway to become secondary metabolites. Increased uptake of tannins has the potential to provide permanent immunity to subsequent infections by strengthening cell walls and producing antimicrobial compounds. Tannins also demonstrate a synergistic response with other defense-related molecules, such as phytoalexins and pathogenesis-related proteins, including antimicrobial peptides. Studying the mechanisms mediated by tannins on pathogen behaviors would be beneficial in stimulating plant defense against pathogens. This understanding could help explain the occurrence of diseases and outbreaks and enable potential mitigation in both natural and agricultural ecosystems.

Unraveling the functional genes present in rhizosphere microbiomes of Solanum lycopersicum

The microbiomes living in the rhizosphere soil of the tomato plant contribute immensely to the state of health of the tomato plant alongside improving sustainable agriculture. With the aid of shotgun metagenomics sequencing, we characterized the putative functional genes (plant-growth-promoting and disease-resistant genes) produced by the microbial communities dwelling in the rhizosphere soil of healthy and powdery mildew-diseased tomato plants. The results identified twenty-one (21) plant growth promotion (PGP) genes in the microbiomes inhabiting the healthy rhizosphere (HR) which are more predomiant as compared to diseased rhizosphere (DR) that has nine (9) genes and four (4) genes in bulk soil (BR). Likewise, we identified some disease-resistant genes which include nucleotide binding genes and antimicrobial genes. Our study revealed fifteen (15) genes in HR which made it greater in comparison to DR that has three (3) genes and three (3) genes in bulk soil. Further studies should be conducted by isolating these microorganisms and introduce them to field experiments for cultivation of tomatoes.

Research progress on iron uptake pathways and mechanisms of foodborne microorganisms and their application in the food sector

Iron is one of the essential nutrients for almost all microorganisms. Under iron-limited conditions, bacteria can secrete siderophores to the outside world to absorb iron for survival. This process requires the coordinated action of energy-transducing proteins, transporters, and receptors. The spoilage factors of some spoilage bacteria and the pathogenic mechanism of pathogenic bacteria are also closely related to siderophores. Meanwhile, some siderophores have also gradually evolved toward beneficial aspects. First, a variety of siderophores are classified into three aspects. In addition, representative iron uptake systems of Gram-negative and Gram-positive bacteria are described in detail to understand the common and specific pathways of iron uptake by various bacteria. In particular, the causes of siderophore-induced bacterial pathogenicity and the methods and mechanisms of inhibiting bacterial iron absorption under the involvement of siderophores are presented. Then, the application of siderophores in the food sector is mainly discussed, such as improving the food quality of dairy products and meat, inhibiting the attack of pathogenic bacteria on food, improving the plant growth environment, and promoting plant growth. Finally, this review highlights the unresolved fate of siderophores in the iron uptake system and emphasizes further development of siderophore-based substitutes for traditional drugs, new antibiotic-resistance drugs, and vaccines in the food and health sectors.

Effect of ozonated water, mancozeb, and thiophanate-methyl on the phyllosphere microbial diversity of strawberry

Phyllosphere microorganisms are closely linked to plant health. This study investigated the effect of ozonated water, mancozeb, and thiophanate-methyl on phyllosphere microorganisms in strawberry plants of the "Hongyan" variety. Sequencing analysis of the phyllosphere bacterial and fungal communities was performed using 16S rRNA gene fragment and ITS1 region high-throughput sequencing after spraying ozonated water, mancozeb, thiophanate-methyl, and clear water. Proteobacteria, Actinobacteria, and Firmicutes were the dominant bacterial phyla in strawberry. The relative abundance of Proteobacteria (82.71%) was higher in the ozonated water treatment group than in the other treatment groups, while the relative abundance of Actinobacteria (9.38%) was lower than in the other treatment groups. The strawberry phyllosphere fungal communities were mainly found in the phyla Basidiomycota and Ascomycota. The relative abundance of Basidiomycota was highest in the ozonated water treatment group (81.13%), followed by the mancozeb treatment group (76.01%), while the CK group only had an abundance of 43.38%. The relative abundance of Ascomycota was lowest in the ozonated water treatment group (17.98%), 23.12% in the mancozeb treatment group, 43.39% in the thiophanate-methyl treatment group, and 55.47% in the CK group. Pseudomonas, Halomonas, and Nesterenkonia were the dominant bacterial genera on strawberry surfaces, while Moesziomyces, Aspergillus, and Dirkmeia were the dominant fungal genera. Ozonated water was able to significantly increase the richness of bacteria and fungi and decrease fungal diversity. However, bacterial diversity was not significantly altered. Ozonated water effectively reduced the relative abundance of harmful fungi, such as Aspergillus, and Penicillium, and enriched beneficial bacteria, such as Pseudomonas and Actinomycetospora, more effectively than mancozeb and thiophanate-methyl. The results of the study show that ozonated water has potential as a biocide and may be able to replace traditional agents in the future to reduce environmental pollution.

Pseudomonas putida and its close relatives: mixing and mastering the perfect tune for plants

Abstract

Plant growth–promoting rhizobacteria (PGPR) are a group of microorganisms of utmost interest in agricultural biotechnology for their stimulatory and protective effects on plants. Among the various PGPR species, some Pseudomonas putida strains combine outstanding traits such as phytohormone synthesis, nutrient solubilization, adaptation to different stress conditions, and excellent root colonization ability. In this review, we summarize the state of the art and the most relevant findings related to P. putida and its close relatives as PGPR, and we have compiled a detailed list of P. putida sensu stricto, sensu lato, and close relative strains that have been studied for their plant growth–promoting characteristics. However, the mere in vitro analysis of these characteristics does not guarantee correct plant performance under in vivo or field conditions. Therefore, the importance of studying adhesion and survival in the rhizosphere, as well as responses to environmental factors, is emphasized. Although numerous strains of this species have shown good performance in field trials, their use in commercial products is still very limited. Thus, we also analyze the opportunities and challenges related to the formulation and application of bioproducts based on these bacteria.

Key points

•The mini-review updates the knowledge on Pseudomonas putida as a PGPR.

• Some rhizosphere strains are able to improve plant growth under stress conditions.

• The metabolic versatility of this species encourages the development of a bioproduct.

Agrobacterium tumefaciens fitness genes involved in the colonization of plant tumors and roots

Agrobacterium tumefaciens colonizes the galls (plant tumors) it causes, and the roots of host and nonhost plants. Transposon-sequencing (Tn-Seq) was used to discover A.tumefaciens genes involved in reproductive success (fitness genes) on Solanum lycopersicum and Populus trichocarpa tumors and S.lycopersicum and Zea mays roots. The identified fitness genes represent 3-8% of A. tumefaciens genes and contribute to carbon and nitrogen metabolism, synthesis and repair of DNA, RNA and proteins and envelope-associated functions. Competition assays between 12 knockout mutants and wild-type confirmed the involvement of 10 genes (trpB, hisH, metH, cobN, ntrB, trxA, nrdJ, kamA, exoQ, wbbL) in A.tumefaciens fitness under both tumor and root conditions. The remaining two genes (fecA, noxA) were important in tumors only. None of these mutants was nonpathogenic, but four (hisH, trpB, exoQ, ntrB) exhibited impaired virulence. Finally, we used this knowledge to search for chemical and biocontrol treatments that target some of the identified fitness pathways and report reduced tumorigenesis and impaired establishment of A.tumefaciens on tomato roots using tannic acid or Pseudomonas protegens, which affect iron assimilation. This work revealed A.tumefaciens pathways that contribute to its competitive survival in plants and highlights a strategy to identify plant protection approaches against this pathogen.

Involvement of the MxtR/ErdR (CrbS/CrbR) Two-Component System in Acetate Metabolism in Pseudomonas putida KT2440

MxtR/ErdR (also called CrbS/CrbR) is a two-component system previously identified as important for the utilization of acetate in Vibrio cholerae and some Pseudomonas species. In addition, evidence has been found in Pseudomonas aeruginosa for a role in regulating the synthesis and expression, respectively, of virulence factors such as siderophores and RND transporters. In this context, we investigated the physiological role of the MxtR/ErdR system in the soil bacterium Pseudomonas putida KT2440. To that end, mxtR and erdR were individually deleted and the ability of the resulting mutants to metabolize different carbon sources was analyzed in comparison to wild type. We also assessed the impact of the deletions on siderophore production, expression of mexEF-oprN (RND transporter), and the biocontrol properties of the strain. Furthermore, the MxtR/ErdR-dependent expression of putative target genes and binding of ErdR to respective promoter regions were analyzed. Our results indicated that the MxtR/ErdR system is active and essential for acetate utilization in P. putida KT2440. Expression of scpC, pp_0354, and acsA-I was stimulated by acetate, while direct interactions of ErdR with the promoter regions of the genes scpC, pp_0354, and actP-I were demonstrated by an electromobility shift assay. Finally, our results suggested that MxtR/ErdR is neither involved in regulating siderophore production nor the expression of mexEF-oprN in P. putida KT2440 under the conditions tested.

Host-Pathogen Interactions between Xanthomonas fragariae and Its Host Fragaria × ananassa Investigated with a Dual RNA-Seq Analysis

Strawberry is economically important and widely grown, but susceptible to a large variety of phytopathogenic organisms. Among them, Xanthomonas fragariae is a quarantine bacterial pathogen threatening strawberry productions by causing angular leaf spots. Using whole transcriptome sequencing, the gene expression of both plant and bacteria in planta was analyzed at two time points, 12 and 29 days post inoculation, in order to compare the pathogen and host response between the stages of early visible and of well-developed symptoms. Among 28,588 known genes in strawberry and 4046 known genes in X. fragariae expressed at both time points, a total of 361 plant and 144 bacterial genes were significantly differentially expressed, respectively. The identified higher expressed genes in the plants were pathogen-associated molecular pattern receptors and pathogenesis-related thaumatin encoding genes, whereas the more expressed early genes were related to chloroplast metabolism as well as photosynthesis related coding genes. Most X. fragariae genes involved in host interaction, recognition, and pathogenesis were lower expressed at late-phase infection. This study gives a first insight into the interaction of X. fragariae with its host. The strawberry plant changed gene expression in order to consistently adapt its metabolism with the progression of infection.

Genetic and structural determinants on iron assimilation pathways in the plant pathogen Xanthomonas citri subsp. citri and Xanthomonas sp

Iron is a vital nutrient to bacteria, not only in the basal metabolism but also for virulent species in infection and pathogenicity at their hosts. Despite its relevance, the role of iron in Xanthomonas citri infection, the etiological agent of citrus canker disease, is poorly understood in contrast to other pathogens, including other members of the Xanthomonas genus. In this review, we present iron assimilation pathways in X. citri including the ones for siderophore production and siderophore-iron assimilation, proven to be key factors to virulence in many organisms like Escherichia coli and Xanthomonas campestris. Based on classical iron-related proteins previously characterized in E. coli, Pseudomonas aeruginosa, and also Xanthomonadaceae, we identified orthologs in X. citri and evaluated their sequences, structural characteristics such as functional motifs, and residues that support their putative functions. Among the identified proteins are TonB-dependent receptors, periplasmic-binding proteins, active transporters, efflux pumps, and cytoplasmic enzymes. The role of each protein for the bacterium was analyzed and complemented with proteomics data previously reported. The global view of different aspects of iron regulation and nutrition in X. citri virulence and pathogenesis may help guide future investigations aiming the development of new drug targets against this important phytopathogen.

Arginine Biosynthesis Modulates Pyoverdine Production and Release in Pseudomonas putida as Part of the Mechanism of Adaptation to Oxidative Stress

Iron is essential for most life forms. Under iron-limiting conditions, many bacteria produce and release siderophores-molecules with high affinity for iron-which are then transported into the cell in their iron-bound form, allowing incorporation of the metal into a wide range of cellular processes. However, free iron can also be a source of reactive oxygen species that cause DNA, protein, and lipid damage. Not surprisingly, iron capture is finely regulated and linked to oxidative-stress responses. Here, we provide evidence indicating that in the plant-beneficial bacterium Pseudomonas putida KT2440, the amino acid l-arginine is a metabolic connector between iron capture and oxidative stress. Mutants defective in arginine biosynthesis show reduced production and release of the siderophore pyoverdine and altered expression of certain pyoverdine-related genes, resulting in higher sensitivity to iron limitation. Although the amino acid is not part of the siderophore side chain, addition of exogenous l-arginine restores pyoverdine release in the mutants, and increased pyoverdine production is observed in the presence of polyamines (agmatine and spermidine), of which arginine is a precursor. Spermidine also has a protective role against hydrogen peroxide in P. putida, whereas defects in arginine and pyoverdine synthesis result in increased production of reactive oxygen species.IMPORTANCE The results of this study show a previously unidentified connection between arginine metabolism, siderophore turnover, and oxidative stress in Pseudomonas putida Although the precise molecular mechanisms involved have yet to be characterized in full detail, our data are consistent with a model in which arginine biosynthesis and the derived pathway leading to polyamine production function as a homeostasis mechanism that helps maintain the balance between iron uptake and oxidative-stress response systems.

Management of Xanthomonas fragariae with Pre- and Postharvest Treatments to Overcome Trade Barriers for California Strawberries

Xanthomonas fragariae, the causal agent of angular leaf spot (ALS) of strawberry, is a quarantine pathogen in some export markets, causing trade restrictions and economic loss to the California fresh-market strawberry industry. Preharvest chemical management options are limited to copper, and there are no postharvest treatments available that reduce populations of the pathogen if ALS is detected at an export destination. Here, we report high preharvest efficacy for the experimental bactericide amino thiadiazole and the commercial product zinc thiadiazole, alone and in mixtures with low rates of copper or the antibiotic kasugamycin, with average disease incidence reduction of up to 92.8% compared with the control. Although effective against quarantine insect pests of strawberry, postharvest methyl bromide fumigation was ineffective against X. fragariae in diseased plant tissue at a standard commercial rate. Postharvest propylene oxide fumigation, used for decades by the California nut industries for insect and microbial disinfestation, significantly reduced X. fragariae populations in infected leaflet tissues by at least 2.5-log compared with controls at a dose of ≥142 µg/ml for 2 h at 15 to 20°C. Fumigated leaflets showed little to no phytotoxicity at effective rates, and fumigated fruit were not significantly affected in appearance or susceptibility to postharvest gray mold or Rhizopus rot following storage at 2°C for 3 days and at 15°C for an additional 5 days. Together, these new treatments offer potential strategies for establishing a systems approach with preharvest treatments significantly reducing the risk of ALS on plants and, in response to quarantine detections, a postharvest fumigation treatment that reduces viable pathogen populations in existing lesions.

Biological control of bacterial plant diseases with Lactobacillus plantarum strains selected for their broad-spectrum activity

The use of lactic acid bacteria (LAB) to control multiple pathogens that affect different crops was studied, namely, Pseudomonas syringae pv. actinidiae in kiwifruit, Xanthomonas arboricola pv. pruni in Prunus and Xanthomonas fragariae in strawberry. A screening procedure based on in vitro and in planta assays of the three bacterial pathogens was successful in selecting potential LAB strains as biological control agents. The antagonistic activity of 55 strains was first tested in vitro and the strains Lactobacillus plantarum CC100, PM411 and TC92, and Leuconostoc mesenteroides CM160 and CM209 were selected because of their broad-spectrum activity. The biocontrol efficacy of the selected strains was assessed using a multiple-pathosystem approach in greenhouse conditions. L. plantarum PM411 and TC92 prevented all three pathogens from infecting their corresponding plant hosts. In addition, the biocontrol performance of PM411 and TC92 was comparable to the reference products (Bacillus amyloliquefaciens D747, Bacillus subtilis QST713, chitosan, acibenzolar-S-methyl, copper and kasugamycin) in semi-field and field experiments. The in vitro inhibitory mechanism of PM411 and TC92 is based, at least in part, on a pH lowering effect and the production of lactic acid. Moreover, both strains showed similar survival rates on leaf surfaces. PM411 and TC92 can easily be distinguished because of their different multilocus sequence typing and random amplified polymorphic DNA profiles.

Ellagitannin HeT obtained from strawberry leaves is oxidized by bacterial membranes and inhibits the respiratory chain

Plant secondary metabolism produces a variety of tannins that have a wide range of biological activities, including activation of plant defenses and antimicrobial, anti‐inflammatory and antitumoral effects. The ellagitannin HeT (1‐O‐galloyl‐2,3;4,6‐bis‐hexahydroxydiphenoyl‐β‐d‐glucopyranose) from strawberry leaves elicits a strong plant defense response, and exhibits antimicrobial activity associated to the inhibition of the oxygen consumption, but its mechanism of action is unknown. In this paper we investigate the influence of HeT on bacterial cell membrane integrity and its effect on respiration. A β‐galactosidase unmasking experiment showed that HeT does not disrupt membrane integrity. Raman spectroscopy analysis revealed that HeT strongly interacts with the cell membrane. Spectrochemical analysis indicated that HeT is oxidized in contact with bacterial cell membranes, and functional studies showed that HeT inhibits oxygen consumption, NADH and MTT reduction. These results provide evidence that HeT inhibits the respiratory chain.