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Microbiology Spectrum Aug 2023Genome evolution, and more specifically gene duplication, is a key process shaping host-microorganism interaction. The conserved paralogs usually provide an advantage to...
Genome evolution, and more specifically gene duplication, is a key process shaping host-microorganism interaction. The conserved paralogs usually provide an advantage to the bacterium to thrive. If not, these genes become pseudogenes and disappear. Here, we show that during the emergence of the genus , the gene encoding the porin OmpF was duplicated. Our results show that the expression is deleterious to the virulence of , the agent causing soft rot disease. Interestingly, 2 is regulated while is constitutive but activated by the EnvZ-OmpR two-component system. , acidic pH triggers the system. The pH measured in four eudicotyledons increased from an initial pH of 5.5 to 7 within 8 h post-infection. Then, the pH decreased to 5.5 at 10 h post-infection and until full maceration of the plant tissue. Yet, the production of phenolic acids by the plant's defenses prevents the activation of the EnvZ-OmpR system to avoid the expression even though environmental conditions should trigger this system. We highlight that gene duplication in a pathogen is not automatically an advantage for the infectious process and that, there was a need for our model organism to adapt its genetic regulatory networks to conserve these duplicated genes. IMPORTANCE species cause various diseases in a wide range of crops and ornamental plants. Understanding the molecular program that allows the bacterium to colonize the plant is key to developing new pest control methods. Unlike other enterobacterial pathogens, , the causal agent of soft rot disease, does not require the EnvZ-OmpR system for virulence. Here, we showed that during the emergence of the genus , the gene encoding the porin OmpF was duplicated and that the expression of was deleterious for virulence. We revealed that while the EnvZ-OmpR system was activated by acidic pH and even though the pH was acidic when the plant is colonized, this system was repressed by phenolic acid (generated by the plant's defenses). These results provide a unique- biologically relevant-perspective on the consequence of gene duplication and the adaptive nature of regulatory networks to retain the duplicated gene.
PubMed: 37642428
DOI: 10.1128/spectrum.00833-23 -
Frontiers in Plant Science 2023The genus includes plant pathogenic bacteria attacking a wide range of crops and ornamentals as well as a few environmental isolates from water. Defined on the basis of...
The genus includes plant pathogenic bacteria attacking a wide range of crops and ornamentals as well as a few environmental isolates from water. Defined on the basis of six species in 2005, this genus now includes 12 recognized species. Despite the description of several new species in recent years, the diversity of the genus is not yet fully explored. Many strains have been analyzed for species causing diseases on economically important crops, such as for the potato pathogens and . In contrast, only a few strains have been characterized for species of environmental origin or isolated from plants in understudied countries. To gain insights in the diversity, recent extensive analyzes were performed on environmental isolates and poorly characterized strains from old collections. Phylogenetic and phenotypic analyzes led to the reclassification of (containing strains from tropical or subtropical regions) in the new genus, , the identification of three water species , and , the description of a new species including Australian strains isolated from grasses, and the characterization of the new species and , resulting from the subdivision of the species . Traits distinguishing each new species were identified from genomic and phenotypic comparisons. The high heterogeneity observed in some species, notably for , indicates that additional species still need to be defined. The objective of this study was to clarify the present taxonomy of the genus and to reassign the correct species to several strains isolated before the current classification.
PubMed: 37409305
DOI: 10.3389/fpls.2023.1168480 -
PloS One 2023Average Nucleotide Identity (ANI) is becoming a standard measure for bacterial species delimitation. However, its calculation can take orders of magnitude longer than...
Average Nucleotide Identity (ANI) is becoming a standard measure for bacterial species delimitation. However, its calculation can take orders of magnitude longer than similarity estimates based on sampling of short nucleotides, compiled into so-called sketches. These estimates are widely used. However, their variable correlation with ANI has suggested that they might not be as accurate. For a where-the-rubber-meets-the-road assessment, we compared two sketching programs, mash and dashing, against ANI, in delimiting species among Esterobacterales genomes. Receiver Operating Characteristic (ROC) analysis found Area Under the Curve (AUC) values of 0.99, almost perfect species discrimination for all three measures. Subsampling to avoid over-represented species reduced these AUC values to 0.92, still highly accurate. Focused tests with ten genera, each represented by more than three species, also showed almost identical results for all methods. Shigella showed the lowest AUC values (0.68), followed by Citrobacter (0.80). All other genera, Dickeya, Enterobacter, Escherichia, Klebsiella, Pectobacterium, Proteus, Providencia and Yersinia, produced AUC values above 0.90. The species delimitation thresholds varied, with species distance ranges in a few genera overlapping the genus ranges of other genera. Mash was able to separate the E. coli + Shigella complex into 25 apparent phylogroups, four of them corresponding, roughly, to the four Shigella species represented in the data. Our results suggest that fast estimates of genome similarity are as good as ANI for species delimitation. Therefore, these estimates might suffice for covering the role of genomic similarity in bacterial taxonomy, and should increase confidence in their use for efficient bacterial identification and clustering, from epidemiological to genome-based detection of potential contaminants in farming and industry settings.
Topics: Animals; Escherichia coli; Gammaproteobacteria; Dickeya; Genomics; Agriculture
PubMed: 37708115
DOI: 10.1371/journal.pone.0291492 -
International Journal of Molecular... Dec 2023Bacterial diversity analyses often suffer from a bias due to sampling only from a limited number of hosts or narrow geographic locations. This was the case for the...
Bacterial diversity analyses often suffer from a bias due to sampling only from a limited number of hosts or narrow geographic locations. This was the case for the phytopathogenic species , whose members were mainly isolated from a few hosts-potato and ornamentals-and from the same geographical area-Europe and Israel, which are connected by seed trade. Most members were clonal with the notable exception of the potato isolate RNS05.1.2A and two related strains that are clearly distinct from other genomes. To investigate if genomic diversity might be broadened by analysis of strains isolated from other environments, we analysed new strains isolated from ornamentals and from river water as well as strain CFBP 5647 isolated from tomato in the Caribbean island Guadeloupe. While water strains were clonal to RNS05.1.2A, the Caribbean tomato strain formed a third clade. The genomes of the three clades are highly syntenic; they shared almost 3900 protein families, and clade-specific genes were mainly included in genomic islands of extrachromosomal origin. Our study thus revealed both broader diversity with the characterisation of a third clade isolated in Latin America and a very high genomic conservation between clade members.
Topics: Enterobacteriaceae; Dickeya; Genomics; Water
PubMed: 38139383
DOI: 10.3390/ijms242417553 -
Systematic and Applied Microbiology Jan 2024Outbreaks of potato blackleg and soft rot caused by Pectobacterium species and more recently Dickeya species across the U.S. mid-Atlantic region have caused yield loss...
Multilocus sequence and phenotypic analysis of Pectobacterium and Dickeya type strains for identification of soft rot Pectobacteriaceae from symptomatic potato stems and tubers in Pennsylvania.
Outbreaks of potato blackleg and soft rot caused by Pectobacterium species and more recently Dickeya species across the U.S. mid-Atlantic region have caused yield loss due to poor emergence as well as losses from stem and tuber rot. To develop management strategies for soft rot diseases, we must first identify which members of the soft rot Pectobacteriaceae are present in regional potato plantings. However, the rapidly expanding number of soft rot Pectobacteriaceae species and the lack of readily available comparative data for type strains of Pectobacterium and Dickeya hinder quick identification. This manuscript provides a comparative analysis of soft rot Pectobacteriaceae and a comprehensive comparison of type strains from this group using rep-PCR, MLSA and 16S sequence analysis, as well as phenotypic and physiological analyses using Biolog GEN III plates. These data were used to identify isolates cultured from symptomatic potato stems collected between 2016 and 2018. The isolates were characterized for phenotypic traits and by sequence analysis to identify the bacteria from potatoes with blackleg and soft rot symptoms in Pennsylvania potato fields. In this survey, P. actinidiae, P. brasiliense, P. polonicum, P. polaris, P. punjabense, P. parmentieri, and P. versatile were identified from Pennsylvania for the first time. Importantly, the presence of P. actinidiae in Pennsylvania represents the first report of this organism in the U.S. As expected, P. carotorvorum and D. dianthicola were also isolated. In addition to a resource for future work studying the Dickeya and Pectobacterium associated with potato blackleg and soft rot, we provide recommendations for future surveys to monitor for quarantine or emerging soft rot Pectobacteriace regionally.
Topics: Dickeya; Solanum tuberosum; Pennsylvania; Plant Diseases; Phylogeny; RNA, Ribosomal, 16S; Pectobacterium; Gammaproteobacteria
PubMed: 38113702
DOI: 10.1016/j.syapm.2023.126476 -
Frontiers in Microbiology 2023Coumarin-3-carboxylic acid (3-CCA), previously screened from natural coumarins, was found to possess strong antibacterial activity against (). In order to further...
Coumarin-3-carboxylic acid (3-CCA), previously screened from natural coumarins, was found to possess strong antibacterial activity against (). In order to further evaluate the activity of this compound against plant bacterial pathogens and explore its potential value as a bactericidal lead compound, the activity of 3-CCA against 14 plant pathogenic bacteria and was tested. Results showed that 3-CCA exhibited strong activities against pv. pv. , and with EC values ranging from 26.64 μg/mL to 40.73 μg/mL. showed that 3-CCA had powerful protective and curative effects against . In addition, the protective efficiency of 3-CCA was almost equivalent to that of thiodiazole copper at the same concentration. The results of SEM and TEM observation and conductivity tests showed that 3-CCA disrupted the integrity of the cell membrane and inhibited polar flagella growth. Furthermore, 3-CCA resulted in reductions in motility and extracellular exopolysaccharide (EPS) production of while inhibiting the biofilm formation of . These findings indicate that 3-CCA could be a promising natural lead compound against plant bacterial pathogens to explore novel antibacterial agents.
PubMed: 37799610
DOI: 10.3389/fmicb.2023.1207125 -
Microbial Biotechnology Nov 2023Virulence factor modulating (VFM) is a quorum sensing (QS) signal shared by and specific to Dickeya bacteria, regulating the production of plant cell wall degrading...
Virulence factor modulating (VFM) is a quorum sensing (QS) signal shared by and specific to Dickeya bacteria, regulating the production of plant cell wall degrading enzymes (PCWDEs) and virulence of Dickeya. High polarity and trace of VFM signal increase the difficulty of signal separation and structure identification, and thus limit the development of quorum quenching strategy to biocontrol bacterial soft rot diseases caused by Dickeya. In order to high-throughput screen VFM quenching bacteria, a vfmE-gfp biosensor VR2 (VFM Reporter) sensitive to VFM signal was first constructed. Subsequently, two bacterial strains with high quenching efficiency were screened out by fluorescence intensity measurement and identified as Pseudomonas chlororaphis L5 and Enterobacter asburiae L95 using multilocus sequence analysis (MLSA). L5 and L95 supernatants reduced the expression of vfm genes, and both strains also decreased the production of PCWDEs of D. zeae MS2 and significantly reduced the virulence of D. oryzae EC1 on rice seedlings, D. zeae MS2 on banana seedlings, D. dadantii 3937 on potato and D. fangzhongdai CL3 on taro. Findings in this study provide a method to high-throughput screen VFM quenching bacteria and characterize novel functions of P. chlororaphis and E. asburiae in biocontrolling plant diseases through quenching VFM QS signal.
Topics: Virulence Factors; Dickeya; Quorum Sensing; Pseudomonas chlororaphis; Enterobacteriaceae; Plant Diseases
PubMed: 37815509
DOI: 10.1111/1751-7915.14351 -
Plants (Basel, Switzerland) Jun 2023The application of compost and metallic nanoparticles has a significant impact on the productivity and chemical composition of horticulture plants. In two subsequent...
The application of compost and metallic nanoparticles has a significant impact on the productivity and chemical composition of horticulture plants. In two subsequent growing seasons, 2020 and 2021, the productivity of L. plants treated with various concentrations of silver nanoparticles (AgNPs) and compost was assessed. In the pot experiments, the soil was amended with 25% or 50% compost, and the plants were sprayed with 10, 20, and 30 mg/L of AgNPs. Scanning electron microscopy (SEM), transmission electron microscopy (TEM), X-ray diffraction analysis (XRD), and dynamic light scattering (DLS) were used to characterize AgNPs. The TEM measurements of AgNPs showed that the particles had spherical forms and ranged in size from roughly 5 to 16 nm. Leaf methanol extracts (LMEs) were prepared from the treated plants and assayed against the growth of two soft rot bacteria, and . The maximum plant height, diameter, number of branches/plant, total fresh weight (g), total dry weight (g), and leaf area (cm) was recorded when levels of 25% compost + AgNPs 20 mg/L, 25% compost, or 50% + AgNPs 20 mg/L, 25% compost + AgNPs 30 mg/L or 50% compost + AgNPs 20 mg/L, 50% compost + AgNPs 20 mg/L, 50% compost + AgNPs 30 or 20 mg/L, and 25% compost + AgNPs 30 mg/L, respectively, were applied. The plants treated with 25% or 50% compost + 30 mg/L AgNPs showed a high chlorophyll content, while the plants treated with 50% compost + AgNPs 30 mg/L or 20 mg/L showed the highest extract percentages. The highest inhibition zones (IZs), 2.43 and 2.2 cm, against the growth of were observed in the LMEs (4000 mg/L) extracted from the plants treated with compost (/) + AgNPs (mg/L) at the levels of 50% + 30 and 25% + 30, respectively. The highest IZs, 2.76 and 2.73 cm, against the growth of were observed in the LMEs (4000 mg/L) extracted from the plants treated at the levels of 50% + 30 and 25% + 30, respectively. Several phenolic compounds such as syringic acid, p-coumaric acid, chlorogenic acid, cinnamic acid, ellagic acid, caffeic acid, benzoic acid, gallic acid, ferulic acid, salicylic acid, pyrogallol, and catechol, as well as flavonoid compounds such as 7-hydroxyflavone, naringin, rutin, apigenin, quercetin, kaempferol, luteolin, hesperidin, catechin, and chrysoeriol, were identified in the LMEs as analyzed by HPLC with different concentrations according to the treatment of compost + AgNPs used for the plants. In conclusion, the specific criteria that were utilized to measure the growth of revealed the novelty of compost and AgNPs combination treatments, particularly at a concentration of 50% compost + AgNPs 30 mg/L or 20 mg/L, which is better for the growth and phytochemical production of in the field.
PubMed: 37375900
DOI: 10.3390/plants12122274 -
Microbial Biotechnology Jul 2023Soft rot pectobacteria (SRP) are phytopathogens of the genera Pectobacterium and Dickeya that cause soft rots on a wide range of crops and ornamental plants. SRP produce...
Soft rot pectobacteria (SRP) are phytopathogens of the genera Pectobacterium and Dickeya that cause soft rots on a wide range of crops and ornamental plants. SRP produce plant cell wall degrading enzymes (PCWDEs), including pectinases. Bdellovibrio and like organisms are bacterial predators that can prey on a variety of Gram-negative species, including SRP. In this research, a low methoxyl pectin (LMP)-based immobilization system for B. bacteriovorus is established. It takes advantage that pectin residues induce PCWDE secretion by the pathogens, bringing upon the release of the encapsulated predators. Three commercial LMPs differing in the degree of esterification (DE) and amidation (DA) were tested as potential carriers, by examining their effect on SRP growth, enzymes secretion and substrate breakdown. A clear advantage was observed for pectin 5 CS with the lowest DE and DA content. The degradation of 5 CS pectin-based carriers was further optimized by reducing cross-linker and pectin concentration, by adding gelatin and by dehydration. This resulted in SRP-induced disintegration of the carrier within 72 h. The released encapsulated predator caused a large decrease in SRP population while its own significantly increased, demonstrating the efficiency of this system in which the pathogen brings about its own demise.
Topics: Pectins; Bacteria
PubMed: 37209364
DOI: 10.1111/1751-7915.14271 -
Haematologica Oct 2023For several decades, asparaginase has been considered world-wide as an essential component of combination chemotherapy for the treatment of childhood acute lymphoblastic...
For several decades, asparaginase has been considered world-wide as an essential component of combination chemotherapy for the treatment of childhood acute lymphoblastic leukemia (ALL). Discovered over 60 years ago, two main unmanipulated asparaginase products originated from primary bacteria sources, namely Escherichia coli and Erwinia chrysanthemi, have been available for clinical use. A pegylated product of the Escherichia coli asparaginase was subsequently developed and is now the main product used by several international co-operative groups. The various asparaginase products all display the same mechanism of action (hydrolysis of circulating asparagine) and are associated with similar efficacy and toxicity patterns. However, their different pharmacokinetics, pharmacodynamics and immunological properties require distinctive modalities of application and monitoring. Erwinia chrysanthemi asparaginase was initially used as a first-line product, but subsequently became a preferred second-line product for children who experienced immunological reactions to the Escherichia coli asparaginase products. An asparaginase product displaying the same characteristics of the Erwinia chrysanthemi asparaginase has recently been produced by use of recombinant technology, thus securing a preparation available for use as an alternative, or as a back-up in case of shortages, for the non-recombinant product. The long journey of the Erwinia chrysanthemi asparaginase product as it has developed throughout the last several decades has made it possible for almost every child and adult with ALL to complete the asparaginase-based protocol treatment when an immunological reaction has occurred to any Escherichia coli asparaginase product.
Topics: Child; Adult; Humans; Asparaginase; Dickeya chrysanthemi; Drug Hypersensitivity; Precursor Cell Lymphoblastic Leukemia-Lymphoma; Escherichia coli; Antineoplastic Agents
PubMed: 37470157
DOI: 10.3324/haematol.2022.282324