Beyond the Wall: Exopolysaccharides in the Biofilm Lifestyle of Pathogenic and Beneficial Plant-Associated Pseudomonas

PelD is required downstream of c-di-GMP for host specialization of Pseudomonas lurida

BACKGROUND

The bacterial second messenger c-di-GMP is known to influence the formation of biofilms and thereby persistence of pathogenic and beneficial bacteria in hosts. A previous evolution experiment with Pseudomonas lurida MYb11, occasional symbiont of the nematode Caenorhabditis elegans, led to the emergence of host-specialized variants with elevated intracellular c-di-GMP. Thus far, the molecular underpinnings of c-di-GMP-mediated host specialization were unknown in this symbiosis. Therefore, the current study aimed at identifying candidate molecular processes by combining transcriptomic and functional genetic analyses.

RESULTS

We found that MYb11 host specialists differentially expressed genes related to attachment, motility and biofilm production, including pelD from the pel gene cluster. pelD deletion resulted in reduced intra-host competitive fitness, lower bacterial numbers in C. elegans and loss of biofilm biomass.

CONCLUSION

Our results identify pelD as a previously unknown key modulator of beneficial symbiont-host associations that acts downstream of c-di-GMP.

Effect of Pseudomonas protegens EMM-1 Against Rhizopus oryzae in Interactions with Mexican Autochthonous Red Maize

In the present study, the strain Rhizopus oryzae EMM was isolated from germinated autochthonous red maize seeds, which were harvested in a region of San Diego-Buenavista, Papalotla, Tlaxcala, Mexico, where cobs with fungal infections have been observed. This fungal strain caused wilting in the maize seedlings. Pseudomonas protegens EMM-1 was tested for its ability to inhibit R. oryzae EMM, both in culture media and in association with maize plantlets. P. protegens EMM-1 inhibited the growth of R. oryzae EMM under all culture media conditions explored. The ability of P. protegens EMM-1 to inhibit the growth of R. oryzae EMM associated with plants was evaluated in both a hydroponic system and in vermiculite. In both systems, P. protegens EMM-1 strongly inhibited the growth of R. oryzae EMM. The dry weight of root plants infected with R. oryzae EMM and inoculated with P. protegens EMM-1 increased to 0.43 g, while that of plants infected only with R. oryzae EMM reached just 0.19 g under hydroponic conditions. However, no differences were observed under vermiculite conditions. The dry weight of the aerial region of plants infected with R. oryzae EMM and inoculated with P. protegens EMM-1 was greater than that of plants infected only with R. oryzae EMM, both under hydroponic and vermiculite conditions. These results indicate that P. protegens EMM-1 inhibits the infection caused by R. oryzae EMM, thereby improving plant growth. Moreover, the genome analysis of P. protegens EMM-1 revealed the presence of several genes that potentially encode for antimicrobial compounds, which could strengthen the potential use of P. protegens EMM-1 as a biocontrol agent in maize plants.

Synthesis of antibiofilm (1R,4S)-(-)-fenchone derivatives to control Pseudomonas syringae pv. tomato

BACKGROUND

Biofilm plays a crucial role in Pseudomonas syringae pv. tomato (Pst) infection. We identified (1R,4S)-(-)-fenchone (FCH) as the most potent antibiofilm agent against Pst among 39 essential oil compounds. Subsequently, we synthesized a series of FCH oxime ester and acylhydrazine derivatives to explore more potent derivatives.

RESULTS

II3 was screened out as the most potent derivative, exhibiting a minimal biofilm inhibitory concentration of 60 μg mL-1 and a lowest concentration with maximal biofilm inhibition (LCMBI) of 200 μg mL-1, lower than those of FCH (80 and 500 μg mL-1, respectively). II3 and FCH showed minimum inhibitory concentration values >1000 μg mL-1 and similar maximal biofilm inhibition extents of 48.7% and 49.5% at their respective LCMBIs, respectively. Meanwhile, neither of them influenced cell viability or the activity of metabolic enzymes at their respective LCMBIs. II3 at its LCMBI significantly reduced biofilm thickness, extracellular polysaccharide content, and pectinase and cellulase production indices. In vivo assay results indicated that II3 could preventatively reduce the bacterial contents in tomato leaves at its LCMBI, and when combined with kasugamycin (KSG) (10 μg mL-1), II3 achieved the same level of bacterial reduction as the sole application of KSG (70 μg mL-1), thereby reducing the required dosage of KSG. Mechanistic studies demonstrated that II3 can down-regulate biofilm-related genes and inhibit PsyR/PsyI quorum sensing system, which differs from the bactericidal mechanisms.

CONCLUSION

These results underscore the potential of II3 as an antibiofilm agent for the control of Pst or FCH as a promising natural candidate for future in-depth optimization. © 2024 Society of Chemical Industry.

An In Vitro Evaluation of Industrial Hemp Extracts Against the Phytopathogenic Bacteria Erwinia carotovora, Pseudomonas syringae pv. tomato, and Pseudomonas syringae pv. tabaci

Pests and diseases have caused significant problems since the domestication of crops, resulting in economic loss and hunger. To overcome these problems, synthetic pesticides were developed to control pests; however, there are significant detrimental side effects of synthetic pesticides on the environment and human health. There is an urgent need to develop safer and more sustainable pesticides. Industrial hemp is a reservoir of compounds that could potentially replace some synthetic bactericides, fungicides, and insecticides. We determined the efficacy of industrial hemp extracts against Pseudomonas syringae pv. tabaci (PSTA), Pseudomonas syringae pv. tomato (PSTO), and Erwinia carotovora (EC). The study revealed a minimum inhibitory concentration (MIC) of 2.05 mg/mL and a non-inhibitory concentration (NIC) of 1.2 mg/mL for PSTA, an MIC of 5.7 mg/mL and NIC of 0.66 mg/mL for PSTO, and an MIC of 12.04 mg/mL and NIC of 5.4 mg/mL for EC. Time-kill assays indicated the regrowth of E. carotovora at 4 × MIC after 15 h and P. syringae pv. tomato at 2 × MIC after 20 h; however, P. syringae pv. tabaci had no regrowth. The susceptibility of test bacteria to hemp extract can be ordered from the most susceptible to the least susceptible, as follows: P. syringae pv. tabaci > P. syringae pv. tomato > E. carotovora. Overall, the data indicate hemp extract is a potential source of sustainable and safe biopesticides against these major plant pathogens.

Stimulation of Arabidopsis thaliana Seed Germination at Suboptimal Temperatures through Biopriming with Biofilm-Forming PGPR Pseudomonas putida KT2440

This study investigated the germination response to temperature of seeds of nine Arabidopsis thaliana ecotypes. They are characterized by a similar temperature dependency of seed germination, and 10 °C and 29 °C were found to be suboptimal low and high temperatures for all nine ecotypes, even though they originated from regions with diverse climates. We tested the potential of four PGPR strains from the genera Pseudomonas and Bacillus to stimulate seed germination in the two ecotypes under these suboptimal conditions. Biopriming of seeds with only the biofilm-forming strain Pseudomonas putida KT2440 significantly increased the germination of Cape Verde Islands (Cvi-0) seeds at 10 °C. However, biopriming did not significantly improve the germination of seeds of the widely utilized ecotype Columbia 0 (Col-0) at any of the two tested temperatures. To functionally investigate the role of KT2440's biofilm formation in the stimulation of seed germination, we used mutants with compromised biofilm-forming abilities. These bacterial mutants had a reduced ability to stimulate the germination of Cvi-0 seeds compared to wild-type KT2440, highlighting the importance of biofilm formation in promoting germination. These findings highlight the potential of PGPR-based biopriming for enhancing seed germination at low temperatures.

In vitro, in planta, and comparative genomic analyses of Pseudomonas syringae pv. syringae strains of pepper (Capsicum annuum var. annuum)

Pseudomonas syringae pv. syringae (Pss) is an emerging phytopathogen that causes Pseudomonas leaf spot (PLS) disease in pepper plants. Pss can cause serious economic damage to pepper production, yet very little is known about the virulence factors carried by Pss that cause disease in pepper seedlings. In this study, Pss strains isolated from pepper plants showing PLS symptoms in Ohio between 2013 and 2021 (n = 16) showed varying degrees of virulence (Pss populations and disease symptoms on leaves) on 6-week-old pepper seedlings. In vitro studies assessing growth in nutrient-limited conditions, biofilm production, and motility also showed varying degrees of virulence, but in vitro and in planta variation in virulence between Pss strains did not correlate. Comparative whole-genome sequencing studies identified notable virulence genes including 30 biofilm genes, 87 motility genes, and 106 secretion system genes. Additionally, a total of 27 antimicrobial resistance genes were found. A multivariate correlation analysis and Scoary analysis based on variation in gene content (n = 812 variable genes) and single nucleotide polymorphisms within virulence genes identified no significant correlations with disease severity, likely due to our limited sample size. In summary, our study explored the virulence and antimicrobial gene content of Pss in pepper seedlings as a first step toward understanding the virulence and pathogenicity of Pss in pepper seedlings. Further studies with additional pepper Pss strains will facilitate defining genes in Pss that correlate with its virulence in pepper seedlings, which can facilitate the development of effective measures to control Pss in pepper and other related P. syringae pathovars.

IMPORTANCE

Pseudomonas leaf spot (PLS) caused by Pseudomonas syringae pv. syringae (Pss) causes significant losses to the pepper industry. Highly virulent Pss strains under optimal environmental conditions (cool-moderate temperatures, high moisture) can cause severe necrotic lesions on pepper leaves that consequently can decrease pepper yield if the disease persists. Hence, it is important to understand the virulence mechanisms of Pss to be able to effectively control PLS in peppers. In our study, in vitro, in planta, and whole-genome sequence analyses were conducted to better understand the virulence and pathogenicity characteristics of Pss strains in peppers. Our findings fill a knowledge gap regarding potential virulence and pathogenicity characteristics of Pss in peppers, including virulence and antimicrobial gene content. Our study helps pave a path to further identify the role of specific virulence genes in causing disease in peppers, which can have implications in developing strategies to effectively control PLS in peppers.

Nanocomposites against Pseudomonas aeruginosa biofilms: Recent advances, challenges, and future prospects

Pseudomonas aeruginosa is an opportunistic bacterial pathogen that causes life-threatening and persistent infections in immunocompromised patients. It is the culprit behind a variety of hospital-acquired infections owing to its multiple tolerance mechanisms against antibiotics and disinfectants. Biofilms are sessile microbial aggregates that are formed as a result of the cooperation and competition between microbial cells encased in a self-produced matrix comprised of extracellular polymeric constituents that trigger surface adhesion and microbial aggregation. Bacteria in biofilms exhibit unique features that are quite different from planktonic bacteria, such as high resistance to antibacterial agents and host immunity. Biofilms of P. aeruginosa are difficult to eradicate due to intrinsic, acquired, and adaptive resistance mechanisms. Consequently, innovative approaches to combat biofilms are the focus of the current research. Nanocomposites, composed of two or more different types of nanoparticles, have diverse therapeutic applications owing to their unique physicochemical properties. They are emerging multifunctional nanoformulations that combine the desired features of the different elements to obtain the highest functionality. This review assesses the recent advances of nanocomposites, including metal-, metal oxide-, polymer-, carbon-, hydrogel/cryogel-, and metal organic framework-based nanocomposites for the eradication of P. aeruginosa biofilms. The characteristics and virulence mechanisms of P. aeruginosa biofilms, as well as their devastating impact and economic burden are discussed. Future research addressing the potential use of nanocomposites as innovative anti-biofilm agents is emphasized. Utilization of nanocomposites safely and effectively should be further strengthened to confirm the safety aspects of their application.

Exploring Pseudomonas syringae pv. tomato biofilm-like aggregate formation in susceptible and PTI-responding Arabidopsis thaliana

Bacterial biofilm-like aggregates have been observed in plants, but their role in pathogenicity is underinvestigated. In the present study, we observed that extracellular DNA and polysaccharides colocalized with green fluorescent protein (GFP)-expressing Pseudomonas syringae pv. tomato (Pst) aggregates in Arabidopsis leaves, suggesting that Pst aggregates are biofilms. GFP-expressing Pst, Pst ΔalgU ΔmucAB (Pst algU mutant), and Pst ΔalgD ΔalgU ΔmucAB (Pst algU algD mutant) were examined to explore the roles of (1) alginate, a potential biofilm component; (2) Pst AlgU, thought to regulate alginate biosynthesis and some type III secretion system effector genes; and (3) intercellular salicylic acid (SA) accumulation during pathogen-associated molecular pattern-triggered immunity (PTI). Pst formed extensive aggregates in susceptible plants, whereas aggregate numbers and size were reduced in Pst algU and Pst algD algU mutants, and both multiplied poorly in planta, suggesting that aggregate formation contributes to Pst success in planta. However, in SA-deficient sid2-2 plants, Pst algD algU mutant multiplication and aggregate formation were partially restored, suggesting plant-produced SA contributes to suppression of Pst aggregate formation. Pst algD algU mutants formed fewer and smaller aggregates than Pst algU mutants, suggesting both AlgU and AlgD contribute to Pst aggregate formation. Col-0 plants accumulated low levels of SA in response to Pst and both mutants (Pst algU and Pst algD algU), suggesting the regulatory functions of AlgU are not involved in suppressing SA-mediated plant defence. Plant PTI was associated with highly reduced Pst aggregate formation and accumulation of intercellular SA in flg22-induced PTI-responding wild-type Col-0, but not in PTI-incompetent fls2, suggesting intercellular SA accumulation by Arabidopsis contributes to suppression of Pst biofilm-like aggregate formation during PTI.

Polyhydroxyalkanoate production by the plant beneficial rhizobacterium Pseudomonas chlororaphis PCL1606 influences survival and rhizospheric performance

Pseudomonas chlororaphis PCL1606 (PcPCL1606) is a model rhizobacterium used to study beneficial bacterial interactions with the plant rhizosphere. Many of its beneficial phenotypes depend on the production of the antifungal compound 2-hexyl, 5-propyl resorcinol (HPR). Transcriptomic analysis of PcPCL1606 and the deletional mutant in HPR production ΔdarB strain, assigned an additional regulatory role to HPR, and allowed the detection of differentially expressed genes during the bacterial interaction with the avocado rhizosphere. Interestingly, the putative genes phaG (PCL1606_46820) and phaI (PCL1606_56560), with a predicted role in polyhydroxyalkanoate biosynthesis, were detected to be under HPR control. Both putative genes were expressed in the HPR-producing wild-type strain, but strongly repressed in the derivative mutant ΔdarB, impaired in HPR production. Thus, a derivative mutant impaired in the phaG gene was constructed, characterized and compared with the wild-type strain PcPCL1606 and with the derivative mutant ΔdarB. The phaG mutant had strongly reduced PHA production by PcPCL1606, and displayed altered phenotypes involved in bacterial survival on the plant roots, such as tolerance to high temperature and hydrogen peroxide, and decreased root survival, in a similar way that the ΔdarB mutant. On the other hand, the phaG mutant does not have altered resistance to desiccation, motility, biofilm formation or adhesion phenotypes, as displayed by the HPR-defective ΔdarB mutant have. Interestingly, the mutant defective in PHA production also lacked a biocontrol phenotype against the soilborne pathogenic fungus Rosellinia necatrix, even when the derivative mutant still produced the antifungal HPR compound, demonstrating that the final biocontrol phenotype of PcPCL1606 first requires bacterial survival and adaptation traits to the soil and rhizosphere environment.

Pan-metagenome reveals the abiotic stress resistome of cigar tobacco phyllosphere microbiome

The important role of microbial associations in mediating plant protection and responses to abiotic stresses has been widely recognized. However, there have been limited studies on the functional profile of the phyllosphere microbiota from tobacco (Nicotiana tabacum), hindering our understanding of the mechanisms underlying stress resilience in this representative and easy-to-cultivate model species from the solanaceous family. To address this knowledge gap, our study employed shotgun metagenomic sequencing for the first time to analyze the genetic catalog and identify putative plant growth promoting bacteria (PGPB) candidates that confer abiotic stress resilience throughout the growth period of cigar tobacco in the phyllosphere. We identified abundant genes from specific bacterial lineages, particularly Pseudomonas, within the cigar tobacco phyllospheric microbiome. These genes were found to confer resilience against a wide range of stressors, including osmotic and drought stress, heavy metal toxicity, temperature perturbation, organic pollutants, oxidative stress, and UV light damage. In addition, we conducted a virome mining analysis on the metagenome to explore the potential roles of viruses in driving microbial adaptation to environmental stresses. Our results identified a total of 3,320 scaffolds predicted to be viral from the cigar tobacco phyllosphere metagenome, with various phages infecting Pseudomonas, Burkholderia, Enterobacteria, Ralstonia, and related viruses. Within the virome, we also annotated genes associated with abiotic stress resilience, such as alkaline phosphatase D (phoD) for nutrient solubilization and glutamate-5-semialdehyde dehydrogenase (proA) for osmolyte synthesis. These findings shed light on the unexplored roles of viruses in facilitating and transferring abiotic stress resilience in the phyllospheric microbiome through beneficial interactions with their hosts. The findings from this study have important implications for agricultural practices, as they offer potential strategies for harnessing the capabilities of the phyllosphere microbiome to enhance stress tolerance in crop plants.

Carbohydrate flow through agricultural ecosystems: Implications for synthesis and microbial conversion of carbohydrates

Carbohydrates are chemically and structurally diverse biomolecules, serving numerous and varied roles in agricultural ecosystems. Crops and horticulture products are inherent sources of carbohydrates that are consumed by humans and non-human animals alike; however carbohydrates are also present in other agricultural materials, such as soil and compost, human and animal tissues, milk and dairy products, and honey. The biosynthesis, modification, and flow of carbohydrates within and between agricultural ecosystems is intimately related with microbial communities that colonize and thrive within these environments. Recent advances in -omics techniques have ushered in a new era for microbial ecology by illuminating the functional potential for carbohydrate metabolism encoded within microbial genomes, while agricultural glycomics is providing fresh perspective on carbohydrate-microbe interactions and how they influence the flow of functionalized carbon. Indeed, carbohydrates and carbohydrate-active enzymes are interventions with unrealized potential for improving carbon sequestration, soil fertility and stability, developing alternatives to antimicrobials, and circular production systems. In this manner, glycomics represents a new frontier for carbohydrate-based biotechnological solutions for agricultural systems facing escalating challenges, such as the changing climate.

Selective Antagonism of Lactiplantibacillus plantarum and Pediococcus acidilactici against Vibrio and Aeromonas in the Bacterial Community of Artemia nauplii

Empiric probiotics are commonly consumed by healthy individuals as a means of disease prevention, pathogen control, etc. However, controversy has existed for a long time regarding the safety and benefits of probiotics. Here, two candidate probiotics, Lactiplantibacillus plantarum and Pediococcus acidilactici, which are antagonistic to Vibrio and Aeromonas species in vitro, were tested on Artemia under in vivo conditions. In the bacterial community of Artemia nauplii, L. plantarum reduced the abundance of the genera Vibrio and Aeromonas and P. acidilactici significantly increased the abundance of Vibrio species in a positive dosage-dependent manner, while higher and lower dosages of P. acidilactici increased and decreased the abundance of the genus Aeromonas, respectively. Based on the liquid chromatography-mass spectrometry (LC-MS) and gas chromatography-mass spectrometry (GC-MS) analyses of the metabolite of L. plantarum and P. acidilactici, pyruvic acid was used in an in vitro test to explain such selective antagonism; the results showed that pyruvic acid was conducive or suppressive to V. parahaemolyticus and beneficial to A. hydrophila. Collectively, the results of this study demonstrate the selective antagonism of probiotics on the bacterial community composition of aquatic organisms and the associated pathogens. IMPORTANCE Over the last decade, the common preventive method for controlling potential pathogens in aquaculture has been the use of probiotics. However, the mechanisms of probiotics are complicated and mostly undefined. At present, less attention has been paid to the potential risks of probiotic use in aquaculture. Here, we investigated the effects of two candidate probiotics, L. plantarum and P. acidilactici, on the bacterial community of Artemia nauplii and the in vitro interactions between these two candidate probiotics and two pathogens, Vibrio and Aeromonas species. The results demonstrated the selective antagonism of probiotics on the bacterial community composition of an aquatic organism and its associated pathogens. This research contributes to providing a basis and reference for the long-term rational use of probiotics and to reducing the inappropriate use of probiotics in aquaculture.

Cold adapted Pseudomonas: ecology to biotechnology

The cold adapted microorganisms, psychrophiles/psychrotolerants, go through several modifications at cellular and biochemical levels to alleviate the influence of low temperature stress conditions. The low temperature environments depend on these cold adapted microorganisms for various ecological processes. The ability of the microorganisms to function in cold environments depends on the strategies directly associated with cell metabolism, physicochemical constrains, and stress factors. Pseudomonas is one among such group of microorganisms which is predominant in cold environments with a wide range of ecological and biotechnological applications. Bioformulations of Pseudomonas spp., possessing plant growth promotion and biocontrol abilities for application under low temperature environments, are well documented. Further, recent advances in high throughput sequencing provide essential information regarding the prevalence of Pseudomonas in rhizospheres and their role in plant health. Cold adapted species of Pseudomonas are also getting recognition for their potential in biodegradation and bioremediation of environmental contaminants. Production of enzymes and bioactive compounds (primarily as an adaptation mechanism) gives way to their applications in various industries. Exopolysaccharides and various biotechnologically important enzymes, produced by cold adapted species of Pseudomonas, are making their way in food, textiles, and pharmaceuticals. The present review, therefore, aims to summarize the functional versatility of Pseudomonas with particular reference to its peculiarities along with the ecological and biotechnological applications.

Effect of Arsenic on EPS Synthesis, Biofilm Formation, and Plant Growth-Promoting Abilities of the Endophytes Pseudomonas PD9R and Rahnella laticis PD12R

Phytoremediation, a cost-effective, eco-friendly alternative to conventional remediation, could expand efforts to remediate arsenic-contaminated soils. As with other pollutants, the plant microbiome may improve phytoremediation outcomes for arsenic-contaminated sites. We used in vitro and in silico methods to compare the arsenic resistance mechanisms, synthesis of extracellular polymeric substances (EPS), biofilm formation, and plant growth-promoting abilities of the endophytes Pseudomonas sp. PD9R and Rahnella laticis PD12R. PD12R, which tolerates arsenate (As(V)) and arsenite (As(III)) to concentrations fivefold greater than PD9R, synthesizes high volumes of EPS in response to arsenic, and sequesters arsenic in the capsular EPS and cells. While arsenic exposure induced EPS synthesis in both strains, only PD12R continued to form biofilms at high As(III) and As(V) concentrations. The effects of endophyte inoculation on Arabidopsis growth varied by strain and As(V) concentration, and PD9R had positive effect on plants exposed to low levels of arsenic. Comparative genomic analyses exploring the EPS synthesis and arsenic resistance mechanisms against other Pseudomonas and Rahnella strains suggest that both strains possess atypical arsenic resistance mechanisms from other plant-associated strains, while the configuration of the EPS synthesis systems appeared to be more broadly distributed among plant- and non-plant-associated strains.

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.

Genome Analysis of Two Pseudomonas syringae pv. aptata Strains with Different Virulence Capacity Isolated from Sugar Beet: Features of Successful Pathogenicity in the Phyllosphere Microbiome

Members of the Pseudomonas syringae species complex are heterogeneous bacteria that are the most abundant bacterial plant pathogens in the plant phyllosphere, with strong abilities to exist on and infect different plant hosts and survive in/outside agroecosystems. In this study, the draft genome sequences of two pathogenic P. syringae pv. aptata strains with different in planta virulence capacities isolated from the phyllosphere of infected sugar beet were analyzed to evaluate putative features of survival strategies and to determine the pathogenic potential of the strains. The draft genomes of P. syringae pv. aptata strains P16 and P21 are 5,974,057 bp and 6,353,752 bp in size, have GC contents of 59.03% and 58.77%, respectively, and contain 3,439 and 3,536 protein-coding sequences, respectively. For both average nucleotide identity and pangenome analysis, P16 and P21 largely clustered with other pv. aptata strains from the same isolation source. We found differences in the repertoire of effectors of the type III secretion system among all 102 selected strains, suggesting that the type III secretion system is a critical factor in the different virulent phenotypes of P. syringae pv. aptata. During genome analysis of the highly virulent strain P21, we discovered genes for T3SS effectors (AvrRpm1, HopAW1, and HopAU1) that were not previously found in genomes of P. syringae pv. aptata. We also identified coding sequences for pantothenate kinase, VapC endonuclease, phospholipase, and pectate lyase in both genomes, which may represent novel effectors of the type III secretion system. IMPORTANCE Genome analysis has an enormous effect on understanding the life strategies of plant pathogens. Comparing similarities with pathogens involved in other epidemics could elucidate the pathogen life cycle when a new outbreak happens. This study represents the first in-depth genome analysis of Pseudomonas syringae pv. aptata, the causative agent of leaf spot disease of sugar beet. Despite the increasing number of disease reports in recent years worldwide, there is still a lack of information about the genomic features, epidemiology, and pathogenic life strategies of this particular pathogen. Our findings provide advances in disease etiology (especially T3SS effector repertoire) and elucidate the role of environmental adaptations required for prevalence in the pathobiome of the sugar beet. From the perspective of the very heterogeneous P. syringae species complex, this type of analysis has specific importance in reporting the characteristics of individual strains.

Efficacy of Trichoderma longibrachiatum Trichogin GA IV Peptaibol analogs against the Black Rot Pathogen Xanthomonas campestris pv. campestris and other Phytopathogenic Bacteria

Black rot caused by the Gram-negative bacterial pathogen Xanthomonas campestris pv. campestris (Xcc) is considered one of the most destructive diseases affecting crucifers. Xcc is a seedborne pathogen able to infect the host at any growth stage. The management of the pathogen mainly relies on the use of copper-based products with possible negative effects on human health and the environment. Searching for protection alternatives is crucial for achieving a sustainable management of Xcc. Trichoderma spp. has been largely used as a biocontrol agent against several phytopathogens. Among Trichoderma species, Trichoderma longibrachiatum produces the peptaibol trichogin GA IV, a secondary metabolite with antimicrobial activity against Gram-positive bacteria, as well as filamentous and yeast-like fungi. In this work, we tested, at micromolar concentrations, 25 synthetic analogs of the peptaibol trichogin GA IV for their bacteriostatic and bactericidal activity toward the bacterium Xcc. One of the most effective peptides (4r) was also tested against the Gram-negative bacteria Xanthomonas arboricola, Pseudomonas corrugata, Pseudomonas savastanoi pv. savastanoi, Agrobacterium tumefaciens, Ralstonia solanacearum, and Erwinia carotovora subsp. carotovora, as well as the Gram-positive bacterium Bacillus subtilis. The peptide 4r reduced black rot symptoms on cauliflower plants when administered both before and 24 h after inoculation with Xcc. The cytotoxic activity of the peptide 4r was also evaluated towards suspensions of tobacco cells by Evans Blue assay.

Brevibacillus DesertYSK and Rhizobium MAP7 stimulate the growth and pigmentation of Lactuca sativa L

BACKGROUND

Applying microbial biostimulants during crop cultivation allows for higher sustainability levels. It reduces the need for fertilizers and environmental contaminants while enhancing plant quality. This study assessed 13 endophytic bacteria, 4 newly isolated, and 9 donated, for plant growth-promoting capabilities. Quantitative assessments of indole acetic acid (IAA), gibberellic acid (GA₃), siderophores, ammonia, exopolysaccharides, volatile HCN, and phosphate solubilization, along with Bray-Curtis cluster analyses were performed.

RESULTS

Upon the results  we selected RhizobiumMAP7, Brevibacillus DesertYSK, Pseudomonas MAP8, BacillusMAP3, Brevibacillus MAP, and Bacillus DeltaYSK to evaluate their effects on Lactuca sativa growth and pigmentation in a 30-day greenhouse pot experiment. Both Brevibacillus DesertYSK and Rhizobium MAP7surpassed other strains in growth promotional effects. They doubled shoot length (12 and 12.3 cm, respectively, when compared with 7 cm for control after 30 days), and fresh weight (0.079 and 0.084 g, respectively, when compared with 0.045 g for control after 30 days), and increased root length by at least 3-fold when compared with control (4.5 and 3.5 cm, respectively, when compared with 1.2 cm for control after 30 days). Chlorophyll content also exhibited at least a 2-fold significant increase in response to bacterization compared with control.

CONCLUSIONS

This strain superiority was consistent with the in vitro assays data that showed strains capability as IAA and GA₃producers. Also, strains were highly capable ammonia and siderophore producers and phosphate solubilizers, providing considerable hormone and nutrient levels for L. sativa plantsleading to improved growth parameters and appearance. These data support the notion that nodule-based bacteria are potential plant growth-promoting bacteria (PGPB) that may be used on a wider scale rather than just for legumes.

A New Face of the Old Gene: Deletion of the PssA, Encoding Monotopic Inner Membrane Phosphoglycosyl Transferase in Rhizobium leguminosarum, Leads to Diverse Phenotypes That Could Be Attributable to Downstream Effects of the Lack of Exopolysaccharide

The biosynthesis of subunits of rhizobial exopolysaccharides is dependent on glycosyltransferases, which are usually encoded by large gene clusters. PssA is a member of a large family of phosphoglycosyl transferases catalyzing the transfer of a phosphosugar moiety to polyprenol phosphate; thus, it can be considered as priming glycosyltransferase commencing synthesis of the EPS repeating units in Rhizobium leguminosarum. The comprehensive analysis of PssA protein features performed in this work confirmed its specificity for UDP-glucose and provided evidence that PssA is a monotopic inner membrane protein with a reentrant membrane helix rather than a transmembrane segment. The bacterial two-hybrid system screening revealed interactions of PssA with some GTs involved in the EPS octasaccharide synthesis. The distribution of differentially expressed genes in the transcriptome of the ΔpssA mutant into various functional categories indicated complexity of cell response to the deletion, which can mostly be attributed to the lack of exopolysaccharide and downstream effects caused by such deficiency. The block in the EPS biosynthesis at the pssA step, potentially leading to an increased pool of UDP-glucose, is likely to be filtered through to other pathways, and thus the absence of EPS may indirectly affect the expression of proteins involved in these pathways.

Regulation of hierarchical carbon substrate utilization, nitrogen fixation, and root colonization by the Hfq/Crc/CrcZY genes in Pseudomonas stutzeri

Bacteria of the genus Pseudomonas consume preferred carbon substrates in nearly reverse order to that of enterobacteria, and this process is controlled by RNA-binding translational repressors and regulatory ncRNA antagonists. However, their roles in microbe-plant interactions and the underlying mechanisms remain uncertain. Here we show that root-associated diazotrophic Pseudomonas stutzeri A1501 preferentially catabolizes succinate, followed by the less favorable substrate citrate, and ultimately glucose. Furthermore, the Hfq/Crc/CrcZY regulatory system orchestrates this preference and contributes to optimal nitrogenase activity and efficient root colonization. Hfq has a central role in this regulatory network through different mechanisms of action, including repressing the translation of substrate-specific catabolic genes, activating the nitrogenase gene nifH posttranscriptionally, and exerting a positive effect on the transcription of an exopolysaccharide gene cluster. Our results illustrate an Hfq-mediated mechanism linking carbon metabolism to nitrogen fixation and root colonization, which may confer rhizobacteria competitive advantages in rhizosphere environments.

Microbially-derived cocktail of carbohydrases as an anti-biofouling agents: a 'green approach'

Enzymes, also known as biocatalysts, display vital properties like high substrate specificity, an eco-friendly nature, low energy inputs, and cost-effectiveness. Among their numerous known applications, enzymes that can target biofilms or their components are increasingly being investigated for their anti-biofouling action, particularly in healthcare, food manufacturing units and environmental applications. Enzymes can target biofilms at different levels like during the attachment of microorganisms, formation of exopolymeric substances (EPS), and their disruption thereafter. In this regard, a consortium of carbohydrases that can target heterogeneous polysaccharides present in the EPS matrix may provide an effective alternative to conventional chemical anti-biofouling methods. Further, for complete annihilation of biofilms, enzymes can be used alone or in conjunction with other antimicrobial agents. Enzymes hold the promise to replace the conventional methods with greener, more economical, and more efficient alternatives. The present article explores the potential and future perspectives of using carbohydrases as effective anti-biofilm agents.

Multiomics Reveals the Effect of Root Rot on Polygonati Rhizome and Identifies Pathogens and Biocontrol Strain

Root (rhizome) rot of Polygonatum plants has received substantial attention because it threatens yield and sustainable utilization in the polygonati rhizome industry. However, the potential pathogens that cause rhizome rot as well as the direct and indirect (via root-associated microbes) strategies by which Polygonatum defends against pathogens remain largely unknown. Herein, we used integrated multiomics of plant-targeted metabolomics and transcriptomics, microbiome, and culture-based methods to systematically investigate the interactions between the Polygonatum cyrtonema Hua root-associated microbiota and pathogens. We found that root rot inhibited P. cyrtonema rhizome growth and that the fresh weight significantly decreased (P < 0.001). The transcriptomic and metabonomic results showed that the expression of differentially expressed genes (DEGs) related to specialized metabolic and systemic resistance pathways, such as glycolysis/gluconeogenesis and flavonoid biosynthesis, cycloartenol synthase activity (related to saponin synthesis), mitogen-activated protein kinase (MAPK) signaling, and plant hormone signal transduction, was particularly increased in diseased rhizomes. Consistently, the contents of lactose, d-fructose, sarsasapogenin, asperulosidic acid, botulin, myricadoil, and other saponins, which are functional medicinal compounds present in P. cyrtonema rhizomes, were also increased in diseased plants infected with rhizome rot. The microbiome sequencing and culture results showed that root rot disrupted the P. cyrtonema bacterial and fungal communities and reduced the microbial diversity in the rhizomes and rhizosphere soil. We further found that a clear enrichment of Streptomyces violascens XTBG45 (HJB-XTBG45) in the healthy rhizosphere could control the root rot caused by Fusarium oxysporum and Colletotrichum spaethianum. Taken together, our results indicate that P. cyrtonema can modulate the plant immune system and metabolic processes and enrich beneficial root microbiota to defend against pathogens. IMPORTANCE Root (rhizome or tuber) reproduction is the main method for the agricultural cultivation of many important cash crops, and infected crop plants rot, exhibit retarded growth, and experience yield losses. While many studies have investigated medicinal plants and their functional medicinal compounds, the occurrence of root (rhizome) rot of plant and soil microbiota has received little attention. Therefore, we used integrated multiomics and culture-based methods to systematically study rhizome rot on the famous Chinese medicine Polygonatum cyrtonema and identify pathogens and beneficial microbiota of rhizome rot. Rhizome rot disrupted the Polygonatum-associated microbiota and reduced microbial diversity, and rhizome transcription and metabolic processes significantly changed. Our work provides evidence that rhizome rot not only changes rhizome transcription and functional metabolite contents but also impacts the microbial community diversity, assembly, and function of the rhizome and rhizosphere. This study provides a new friendly strategy for medicinal plant breeding and agricultural utilization.

A Cross-Kingdom View on the Immunomodulatory Role of MIF/D-DT Proteins in Mammalian and Plant Pseudomonas Infections

Gram-negative Pseudomonas bacteria are largely harmless saprotrophs, but some species can be potent pathogens of both plants and mammals. Macrophage migration inhibitory factor (MIF) and its homolog D-dopachrome tautomerase (D-DT, also referred to as MIF-2) are multifunctional proteins that in addition to their intracellular functions also serve as extracellular signaling molecules (cytokines) in orchestrating mammalian immune responses. It recently emerged that plants also possess MIF-like proteins, termed MIF/D-DT-like (MDL) proteins. We here provide a comparative cross-kingdom view on the immunomodulatory role of MIF and MDL proteins during Pseudomonas infections in mammals and plants. Although in both kingdoms the lack of MIF/MDL proteins is associated with a reduction in bacterial load and disease symptoms, the underlying molecular principles seem to be different. We provide a perspective for future research activities to unravel additional commonalities and differences in the MIF/MDL-mediated adjustment of antibacterial immune activities.

Mycobacterial Adhesion: From Hydrophobic to Receptor-Ligand Interactions

Adhesion is crucial for the infective lifestyles of bacterial pathogens. Adhesion to non-living surfaces, other microbial cells, and components of the biofilm extracellular matrix are crucial for biofilm formation and integrity, plus adherence to host factors constitutes a first step leading to an infection. Adhesion is, therefore, at the core of pathogens’ ability to contaminate, transmit, establish residency within a host, and cause an infection. Several mycobacterial species cause diseases in humans and animals with diverse clinical manifestations. Mycobacterium tuberculosis, which enters through the respiratory tract, first adheres to alveolar macrophages and epithelial cells leading up to transmigration across the alveolar epithelium and containment within granulomas. Later, when dissemination occurs, the bacilli need to adhere to extracellular matrix components to infect extrapulmonary sites. Mycobacteria causing zoonotic infections and emerging nontuberculous mycobacterial pathogens follow divergent routes of infection that probably require adapted adhesion mechanisms. New evidence also points to the occurrence of mycobacterial biofilms during infection, emphasizing a need to better understand the adhesive factors required for their formation. Herein, we review the literature on tuberculous and nontuberculous mycobacterial adhesion to living and non-living surfaces, to themselves, to host cells, and to components of the extracellular matrix.

Identification of Aerotaxis Receptor Proteins Involved in Host Plant Infection by Pseudomonas syringae pv. tabaci 6605

Pseudomonas syringae pv. tabaci 6605 (Pta6605) is a foliar plant pathogen that causes wildfire disease on tobacco plants. It requires chemotaxis to enter plants and establish infection. While chemotactic signals appear to be the main mechanism by which Pta6605 performs directional movement, the involvement of aerotaxis or energy taxis by this foliar pathogen is currently unknown. Based on domain structures and similarity with more than 50 previously identified putative methyl-accepting chemotaxis proteins (MCPs), the genome of Pta6605 encodes three potential aerotaxis transducers. We identified AerA as the main aerotaxis transducer and found that it possesses a taxis-to-serine-and-repellent (Tsr)-like domain structure that supports a periplasmic 4HB-type ligand-binding domain (LBD). The secondary aerotaxis transducer, AerB, possesses a cytosolic PAS-type LBD, similar to the Aer of Escherichia coli and Pseudomonas aeruginosa. Aerotaxis ability by single and double mutant strains of aerA and aerB was weaker than that by wild-type Pta6605. On the other hand, another cytosolic PAS-type LBD containing MCP did not make a major contribution to Pta6605 aerotaxis in our assay system. Furthermore, mutations in aerotaxis transducer genes did not affect surface motility or chemotactic attraction to yeast extract. Single and double mutant strains of aerA and aerB showed less colonization in the early stage of host plant infection and lower biofilm production than wild-type Pta6605. These results demonstrate the presence of aerotaxis transducers and their contribution to host plant infection by Pta6605.

A regulatory network involving Rpo, Gac and Rsm for nitrogen-fixing biofilm formation by Pseudomonas stutzeri

Biofilm and nitrogen fixation are two competitive strategies used by many plant-associated bacteria; however, the mechanisms underlying the formation of nitrogen-fixing biofilms remain largely unknown. Here, we examined the roles of multiple signalling systems in the regulation of biofilm formation by root-associated diazotrophic P. stutzeri A1501. Physiological analysis, construction of mutant strains and microscale thermophoresis experiments showed that RpoN is a regulatory hub coupling nitrogen fixation and biofilm formation by directly activating the transcription of pslA, a major gene involved in the synthesis of the Psl exopolysaccharide component of the biofilm matrix and nifA, the transcriptional activator of nif gene expression. Genetic complementation studies and determination of the copy number of transcripts by droplet digital PCR confirmed that the regulatory ncRNA RsmZ serves as a signal amplifier to trigger biofilm formation by sequestering the translational repressor protein RsmA away from pslA and sadC mRNAs, the latter of which encodes a diguanylate cyclase that synthesises c-di-GMP. Moreover, RpoS exerts a braking effect on biofilm formation by transcriptionally downregulating RsmZ expression, while RpoS expression is repressed posttranscriptionally by RsmA. These findings provide mechanistic insights into how the Rpo/Gac/Rsm regulatory networks fine-tune nitrogen-fixing biofilm formation in response to the availability of nutrients.