Antagonistic and protective activity of Lactobacillus plantarum strain 17 M against E. amylovora

The subject of the study was to identify the antagonism of the Lactobacillus plantarum strain 17 M against the causative agent of fire blight, the bacterium Erwinia amylovora, and to evaluate its protective capabilities on apple blossoms against this disease. For comparison 9 strains of lactic acid bacteria from the LLP "SPC of Microbiology and Virology" collection were included in the study. Strain 17 M appeared to be superior in limiting the growth of the pathogen on all 3 liquid media tested. Its maximum inhibitory activity was proved on MRS Broth medium. The analysis of the secondary metabolites produced by strain 17 M in liquid medium revealed that it consisted mainly of acetic acid (53.2 ± 4.3%), lactic acid (16.3 ± 2.3%) and 2,3-butanedione (14.84 ± 4.1%). The presence of other organic compounds was also detected but in a smaller amount. Study on influence of those compounds on growth of E. amylovora showed that lactic acid at concentration of 5% showed inhibitory activity but it was not toxic to apple flowers. The effectiveness of strain 17 M culture liquid diluted with sterile water and added to E. amylovora inoculum at 10% or 20% was 76.7 ± 5.8% and 88.3 ± 12.6%, respectively. This study confirms the potential use of strain 17 M as an active microbial agent to combat fire blight of fruit crops in Kazakhstan.

The metastable associations of bacteriophages and Erwinia amylovora

Bacteriophages are often considered as possible agents of biological control of unwanted bacterial populations in medicine, agriculture and food industry. Although the virulent phages can efficiently kill the infected host cells but at the population level phage attack not always leads to the host population collapse but may result in establishment of a more or less stable co-existence. The mechanism of the long-term stabilization of the mixed phage-host cultures is poorly understood. Here we describe bacteriophages VyarbaL and Hena2, the members of the Molineuxvirinae and the Ounavirinae subfamilies, respectively, that are able to form the pseudolysogenic associations (PA) with their host Erwinia amylovora 1/79Sm on solid media. These PAs were stable through multiple passages. The phenomenon of the PA formation between a bacterial culture and bacteriophages decreases the effectiveness of bacteriophage-mediated biological control agents based on lytic bacteriophages.

Broad-host-range lytic Erwinia phage Key with exopolysaccharide degrading activity

In this study, the genome of the lytic broad-host-range phage Key infecting Erwinia amylovora, Erwinia horticola, and Pantoea agglomerans strains was characterized. Key phage has a 115,651 bp long double-stranded DNA genome with the G + C ratio of 39.03%, encoding 182 proteins and 27 tRNA genes. The majority (69%) of predicted coding sequences (CDSs) encode proteins with unknown functions. The protein products of 57 annotated genes were found to have probable functions in nucleotide metabolism, DNA replication, recombination, repair, and packaging, virion morphogenesis, phage-host interaction and lysis. Furthermore, the product of gene 141 shared amino acid sequence similarity and conserved domain architecture with the exopolysaccharide (EPS) degrading proteins of Erwinia and Pantoea infecting phages as well as bacterial EPS biosynthesis proteins. Due to the genome synteny and similarity to the proteins of T5-related phages, phage Key, together with its closest relative, Pantoea phage AAS21, was suggested to represent a novel genus within the Demerecviridae family, for which we tentatively propose the name "Keyvirus".

Variability within a clonal population of Erwinia amylovora disclosed by phenotypic analysis

Background

Fire blight is a destructive disease of pome trees, caused by Erwinia amylovora, leading to high losses of chain-of-values fruits. Major outbreaks were registered between 2010 and 2017 in Portugal, and the first molecular epidemiological characterization of those isolates disclosed a clonal population with different levels of virulence and susceptibility to antimicrobial peptides.

Methods

This work aimed to further disclose the genetic characterization and unveil the phenotypic diversity of this E. amylovora population, resorting to MLSA, growth kinetics, biochemical characterization, and antibiotic susceptibility.

Results

While MLSA further confirmed the genetic clonality of those isolates, several phenotypic differences were recorded regarding their growth, carbon sources preferences, and chemical susceptibility to several antibiotics, disclosing a heterogeneous population. Principal component analysis regarding the phenotypic traits allows to separate the strains Ea 630 and Ea 680 from the remaining.

Discussion

Regardless the genetic clonality of these E. amylovora strains isolated from fire blight outbreaks, the phenotypic characterization evidenced a population diversity beyond the genotype clonality inferred by MLSA and CRISPR, suggesting that distinct sources or environmental adaptations of this pathogen may have occurred.

Conclusion

Attending the characteristic clonality of E. amylovora species, the data gathered here emphasizes the importance of phenotypic assessment of E. amylovora isolates to better understand their epidemiological behavior, namely by improving source tracking, make risk assessment analysis, and determine strain-specific environmental adaptations, that might ultimately lead to prevent new outbreaks.

An Erwinia amylovora inducible promoter for improvement of apple fire blight resistance

pPPO16, the first Ea-inducible promoter cloned from apple, can be a useful component of intragenic strategies to create fire blight resistant apple genotypes. Intragenesis is an important alternative to transgenesis to produce modified plants containing native DNA only. A key point to develop such a strategy is the availability of regulatory sequences controlling the expression of the gene of interest. With the aim of finding apple gene promoters either inducible by the fire blight pathogen Erwinia amylovora (Ea) or moderately constitutive, we focused on polyphenoloxidase genes (PPO). These genes encode oxidative enzymes involved in many physiological processes and have been previously shown to be upregulated during the Ea infection process. We found ten PPO and two PPO-like sequences in the apple genome and characterized the promoters of MdPPO16 (pPPO16) and MdKFDV02 PPO-like (pKFDV02) for their potential as Ea-inducible and low-constitutive regulatory sequences, respectively. Expression levels of reporter genes fused to these promoters and transiently or stably expressed in apple were quantified after various treatments. Unlike pKFDV02 which displayed a variable activity, pPPO16 allowed a fast and strong expression of transgenes in apple following Ea infection in a Type 3 Secretion System dependent manner. Altogether our results does not confirmed pKFDV02 as a constitutive and weak promoter whereas pPPO16, the first Ea-inducible promoter cloned from apple, can be a useful component of intragenic strategies to create fire blight resistant apple genotypes.

Selective Quantification of Erwinia amylovora Live Cells in Pome Fruit Tree Cankers by Viability Digital PCR

The accurate assessment of Erwinia amylovora live cell populations in fire blight cankers by classic microbiology methods has major limitations. Some of them are the presence of competitive microbiota in samples that inhibit E. amylovora's growth and the release of toxic compounds by plant material during sample processing, which may hamper the pathogen's ability to form colonies on solid media. Digital PCR (dPCR) combined with the photo-reactive DNA-binding dye propidium monoazide (PMA) allows selective detection and quantification of live E. amylovora cells in woody samples while overcoming the constraints of culture-dependent methods. This work describes a reliable viability dPCR procedure to determine E. amylovora live cell concentrations in fire blight cankers from pome fruit trees. This protocol can be adapted for the analysis of other types of plant material and enables investigation of ecological, epidemiological, and management significance of cankers as a relatively underexplored part of the fire blight disease cycle.

Characterization of the biocontrol activity of three bacterial isolates against the phytopathogen Erwinia amylovora

Antibiotics are sprayed on apple and pear orchards to control, among other pathogens, the bacterium Erwinia amylovora, the causative agent of fire blight. As with many other pathogens, we observe the emergence of antibiotic-resistant strains of E. amylovora. Consequently, growers are looking for alternative solutions to combat fire blight. To find alternatives to antibiotics against this pathogen, we have previously isolated three bacterial strains with antagonistic and extracellular activity against E. amylovora, both in vitro and in planta, corresponding to three different bacterial genera: Here, we identified the inhibitory mode of action of each of the three isolates against E. amylovora. Isolate Bacillus amyloliquefaciens subsp. plantarum (now B. velezensis) FL50S produces several secondary metabolites including surfactins, iturins, and fengycins. Specifically, we identified oxydifficidin as the most active against E. amylovora S435. Pseudomonas poae FL10F produces an active extracellular compound against E. amylovora S435 that can be attributed to white-line-inducing principle (WLIP), a cyclic lipopeptide belonging to the viscosin subfamily (massetolide E, F, L, or viscosin). Pantoea agglomerans NY60 has a direct cell-to-cell antagonistic effect against E. amylovora S435. By screening mutants of this strain generated by random transposon insertion with decreased antagonist activity against strain S435, we identified several defective transposants. Of particular interest was a mutant in a gene coding for a Major Facilitator Superfamily (MFS) transporter corresponding to a transmembrane protein predicted to be involved in the extracytoplasmic localization of griseoluteic acid, an intermediate in the biosynthesis of the broad-spectrum phenazine antibiotic D-alanylgriseoluteic acid.

Activation of metabolic and stress responses during subtoxic expression of the type I toxin hok in Erwinia amylovora

Background

Toxin-antitoxin (TA) systems, abundant in prokaryotes, are composed of a toxin gene and its cognate antitoxin. Several toxins are implied to affect the physiological state and stress tolerance of bacteria in a population. We previously identified a chromosomally encoded hok-sok type I TA system in Erwinia amylovora, the causative agent of fire blight disease on pome fruit trees. A high-level induction of the hok gene was lethal to E. amylovora cells through unknown mechanisms. The molecular targets or regulatory roles of Hok were unknown.

Results

Here, we examined the physiological and transcriptomic changes of Erwinia amylovora cells expressing hok at subtoxic levels that were confirmed to confer no cell death, and at toxic levels that resulted in killing of cells. In both conditions, hok caused membrane rupture and collapse of the proton motive force in a subpopulation of E. amylovora cells. We demonstrated that induction of hok resulted in upregulation of ATP biosynthesis genes, and caused leakage of ATP from cells only at toxic levels. We showed that overexpression of the phage shock protein gene pspA largely reversed the cell death phenotype caused by high levels of hok induction. We also showed that induction of hok at a subtoxic level rendered a greater proportion of stationary phase E. amylovora cells tolerant to the antibiotic streptomycin.

Conclusions

We characterized the molecular mechanism of toxicity by high-level of hok induction and demonstrated that low-level expression of hok primes the stress responses of E. amylovora against further membrane and antibiotic stressors.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07376-w.

Development of a novel biological control agent targeting the phytopathogen Erwinia amylovora

Antibiotics are used extensively to control animal, plant, and human pathogens. They are sprayed on apple and pear orchards to control the bacterium Erwinia amylovora, the causative agent of fire blight. This phytopathogen is developing antibiotic resistance and alternatives either have less efficacy, are phytotoxic, or more management intensive. The objective of our study was to develop an effective biological control agent colonizing the host plant and competing with Erwinia amylovora. It must not be phytotoxic, have a wide spectrum of activity, and be unlikely to induce resistance in the pathogen. To this end, several bacterial isolates from various environmental samples were screened to identify suitable candidates that are antagonistic to E. amylovora. We sampled bacteria from the flowers, leaves, and soil from apple and pear orchards from the springtime bloom period until the summer. The most effective bacteria, including isolates of Pseudomonas poae, Paenibacillus polymyxa, Bacillus amyloliquefaciens and Pantoea agglomerans, were tested in vitro and in vivo and formulated into products containing both the live strains and their metabolites that were stable for at least 9 months. Trees treated with the product based on P. agglomerans NY60 had significantly less fire blight than the untreated control and were statistically not different from streptomycin-treated control trees. With P. agglomerans NY60, fire blight never extended beyond the central vein of the inoculated leaf. The fire blight median disease severity score, 10 days after inoculation, was up to 70% less severe on trees treated with P. agglomerans NY60 as compared to untreated controls.

First Report of Fire Blight of Apricot (Prunus armeniaca) Caused by Erwinia amylovora in Korea

During a survey in May 2020, symptoms of blight were observed on apricot (Prunus armeniaca cv. undetermined) in an orchard (37°06´01.5″N 127°57´44.9″E) in Chungju, South Korea, where fire blight of apple occurred. Three apricot trees in the apple orchard were heavily diseased and showed severe shoot blight and stem canker symptoms. Bacterial isolates were recovered on King's medium B from leaves and twigs that were surface-sterilized with 70% alcohol. Colonies with uniform mucoid, smooth surfaces were collected. DNA from nine isolates did not yield an amplicon in a PCR assay for detection of Erwinia pyrifoliae using primer set CPS1/CPS2c (Kim et al. 2001). Each isolate was positive in PCR assays for E. amylovora using primer sets A/B (Bereswill et al. 1992) and AJ75/76 (Llop et al. 2000) that target pEA29. Sequencing of the PCR products resulted in 99.9% (929 bp out of 930 bp) and 100% (747 bp out of 747 bp) identity with sequences of E. amylovora FB20 (GeneBank: CP050240), respectively. Amplifications of the partial 16S rRNA (GeneBank: LC557153) and hrpN (GeneBank: LC575997) genes were performed, and the products were sequenced. The primers used to amplify 16S rRNA were 518F: 5'-CCAGCAGCCGCGGTAATACG-3' and 800R: 5'-TACCAGGGTATCTAATCC-3', and those for the hrpN genes were HRPN1: 5'-ATGAGTCTGAATACAAG-3' and HRPN3c: 5'-GCTTGCCAAGTGCCATA-3'. BLAST analyses showed 99.8% (1439 bp out of 1442 bp) and 100% (1136 bp out of 1136 bp) identities, respectively, to the sequences of E. amylovora FB20. The ability of the isolates to induce a hypersensitive reaction on tobacco (Nicotiana tabacum cv. Xanthi) leaves was also evaluated. Bacterial suspensions (1.5 ⅹ 108 CFU) of 2 isolates were injected into tobacco leaves, and after 48 h, both isolates caused a hypersensitive response. To confirm pathogenicity of isolates, 3-mm-deep holes in five immature apricot (cv. Goldcot) and five immature apple (cv. Fuji) fruits were inoculated with 10 µl bacterial suspension (1.5 ⅹ 108 CFU/ml). The inoculated fruits were placed in a humid plastic box. After 7 days at 27℃, severe necrosis and bacterial ooze were present at the inoculated sites in three repeated tests. No symptoms were observed on fruits inoculated with sterile water. To complete Koch's postulates, bacteria were reisolated from the inoculated apricot and apple fruits. PCR using the specific primer sets stated above confirmed the identity as E. amylovora. Thus, based on disease symptoms, sequences, and pathogenicity, the bacterium causing blight of apricot was identified as E. amylovora. Natural infections of E. amylovora on apricot trees have been reported in the Czech Republic and Hungary (Korba and Sillerova 2011; Vegh and Palkovics 2013). Fire blight was observed in the Czech Republic on apricot trees near pear seedlings, which are highly susceptible to E. amylovora (Korba and Sillerova 2011). Natural infections of E. amylovora on Japanese plum planted adjacent to an apple orchard with severe fire blight has been reported in the United States (Mohan and Thomson 1996). Moreover, susceptibility to fire blight has been reported for apricot and Japanese plum cultivars (Mohan and Bijman 1999). To our knowledge, this the first report of fire blight of apricot caused by E. amylovora in Korea. This report is important because it provides evidence that apricot may be an overlooked reservoir for E. amylovora, in addition to apple, pear, and other rosaceous plants, in Korea. An intensive survey for additional host plants for the fire blight pathogen will be continued in Korea. This work was supported by a grant from the Agenda program (PJ01530202) of Rural Development Administration, Republic of Korea.

An Erwinia amylovora uracil transporter mutant retains virulence on immature apple and pear fruit

Erwinia amylovora is the causal agent of fire blight, a devastating disease of apples and pears. A previous study revealed that an E. amylovora uracil auxotroph was still virulent and can cause disease, suggesting that uracil can be obtained from the host environment. The E. amylovora genome contains a locus encoding for a uracil transporter belonging to the nucleobase cation symporter 2 family, displaying a high level of amino acid sequence similarity to the Escherichia coli UraA. Expression of E. amylovora UraA in nucleobase transporter-deficient E. coli strains, coupled with radiolabeled uptake studies reveal that E. amylovora UraA is a high affinity uracil transporter with a K_m of 0.57 μM. Both E. coli and E. amylovora carrying extra copies of E. amylovora UraA are sensitive to growth on the toxic analog 5-fluorouracil. An E. amylovora ΔuraA::Cam^r mutant is still able to grow and cause disease symptoms on immature pears and apples.

Comparative genomic analysis of Erwinia amylovora reveals novel insights in phylogenetic arrangement, plasmid diversity, and streptomycin resistance

Erwinia amylovora is a destructive pathogen of Rosaceous plants and an economic concern worldwide. Herein, we report 93 new E. amylovora genomes from North America, Europe, the Mediterranean, and New Zealand. This new genomic information demonstrates the existence of three primary clades of Amygdaloideae (apple and pear) infecting E. amylovora and suggests all three independently originate from North America. The comprehensive sequencing also identified and confirmed the presence of 7 novel plasmids ranging in size from 2.9 to 34.7 kbp. While the function of the novel plasmids is unknown, the plasmids pEAR27, pEAR28, and pEAR35 encoded for type IV secretion systems. The strA-strB gene pair and the K43R point mutation at codon 43 of the rpsL gene have been previously documented to confer streptomycin resistance. Of the sequenced isolates, rpsL-based streptomycin resistance was more common and was found with the highest frequency in the Western North American clade.

Comparison of the Levansucrase from the epiphyte Erwinia tasmaniensis vs its homologue from the phytopathogen Erwinia amylovora

Erwinia tasmaniensis is an epiphytic bacterium related to the plant pathogen Erwinia amylovora, the etiological agent of fire blight. In this study the levansucrase from E. tasmaniensis (EtLsc) has been compared with the homologous enzyme from E. amylovora (EaLsc). We characterized the enzymatic activity and compared the products profile of both enzymes by High Performance Anion Exchange Chromatography coupled with Pulsed Amperometric Detector (HPAEC-PAD). Moreover we determined the crystal structure of EtLsc to understand the structural peculiarity causing the different product profiles of the two homologues. EtLsc exhibits increased efficiency in the production of FOS, resulting in a better catalyst for biotechnological synthesis than EaLsc. Based on our results, we propose that the role of this enzyme in the life cycle of the two bacteria is most likely related to survival, rather than linked to pathogenicity in E. amylovora.

Pantocin A, a peptide-derived antibiotic involved in biological control by plant-associated Pantoea species

The genus Pantoea contains a broad range of plant-associated bacteria, including some economically important plant pathogens as well as some beneficial members effective as biological control agents of plant pathogens. The most well-characterized representatives of biological control agents from this genus generally produce one or more antimicrobial compounds adding to biocontrol efficacy. Some Pantoea species evaluated as biocontrol agents for fire blight disease of apple and pear produce a histidine-reversible antibiotic. Three commonly studied histidine-reversible antibiotics produced by Pantoea spp. are herbicolin O, MccEh252, and pantocin A. Pantocin A is a novel ribosomally encoded and post-translationally modified peptide natural product. Here, we review the current knowledge on the chemistry, genetics, biosynthesis, and incidence and environmental relevance of pantocin A and related histidine-reversible antibiotics produced by Pantoea.

The Apple Fruitlet Model System for Fire Blight Disease

Fire blight is a perennial disease affecting apple and pear production worldwide. Development of resistant cultivars and disease control measures are crucial aspects of managing fire blight. Furthermore, the study of the causal agent, the Gram-negative bacterium Erwinia amylovora, has led to important insights into molecular plant-microbe interactions. However, fire blight does not have a suitable model host, since its host range is limited to plants with complex genetics and relatively limited resources for genetic analysis. Here, we present a rationale for using apple fruitlets as a potential fire blight model host system, and describe a protocol for quantitative fruit inoculation, bacterial growth measurement, and symptom assessment. The use of apple fruitlets is applicable to the molecular genetic analysis of E. amylovora, including high-throughput genetic screens for E. amylovora virulence-defective mutants, and is potentially useful to study host resistance and responses to E. amylovora as well.

Structural and functional analysis of Erwinia amylovora SrlD. The first crystal structure of a sorbitol-6-phosphate 2-dehydrogenase

Sorbitol-6-phosphate 2-dehydrogenases (S6PDH) catalyze the interconversion of d-sorbitol 6-phosphate to d-fructose 6-phosphate. In the plant pathogen Erwinia amylovora the S6PDH SrlD is used by the bacterium to utilize sorbitol, which is used for carbohydrate transport in the host plants belonging to the Amygdaloideae subfamily (e.g., apple, pear, and quince). We have determined the crystal structure of S6PDH SrlD at 1.84 Å resolution, which is the first structure of an EC 1.1.1.140 enzyme. Kinetic data show that SrlD is much faster at oxidizing d-sorbitol 6-phosphate than in reducing d-fructose 6-phosphate, however, equilibrium analysis revealed that only part of the d-sorbitol 6-phosphate present in the in vitro environment is converted into d-fructose 6-phosphate. The comparison of the structures of SrlD and Rhodobacter sphaeroides sorbitol dehydrogenase showed that the tetrameric quaternary structure, the catalytic residues and a conserved aspartate residue that confers specificity for NAD⁺ over NADP⁺ are preserved. Analysis of the SrlD cofactor and substrate binding sites identified residues important for the formation of the complex with cofactor and substrate and in particular the role of Lys42 in selectivity towards the phospho-substrate. The comparison of SrlD backbone with the backbone of 302 short-chain dehydrogenases/reductases showed the conservation of the protein core and identified the variable parts. The SrlD sequence was compared with 500 S6PDH sequences selected by homology revealing that the C-terminal part is more conserved than the N-terminal, the consensus of the catalytic tetrad (Y[SN]AGXA) and a not previously described consensus for the NAD(H) binding.

New potential bacterial antagonists for the biocontrol of fire blight disease (Erwinia amylovora) in Morocco

The effectiveness of antagonistic bacteria to control Erwinia amylovora was evaluated under in vitro and field conditions. Among 61 bacteria isolated from soil and flowers of fire blight host plants of different Moroccan areas, 20 bacterial isolates showed higher antagonistic activity against the pathogen during agar-diffusion-test, attached blossoms assay and in a bioassay on immature pear fruits. Effective isolates were identified by using biochemical tests and 16 S rRNA genes sequencing. These isolates were grouped into the following genera: Alcaligenes (ACBC1), Pantoea (ACBC2, ACBP1, and ACBP2), Serratia (HC4), Brevibacterium (SF3, SF4, SF7, and SF15), Pseudomonas (SP9), and Bacillus (CPa12, CPa2, HF6, JB2, LMR2, SF14, SF16, SP10, SP13, and SP18). Furthermore, isolates were reported in the NCBI nucleotide sequence database (Genbank) under the accession numbers from KY357285 to KY357304. A 2-year field trials consisted of spray treatments with different bacterial antagonists was conducted on the susceptible apple cultivars 'Gala', 'Golden Parsi' and 'Golden Smoothee'. Their efficacies were evaluated 15 days post-inoculation on detached blossoms and were ranged from 54.6 to 95.0% for 11 strains, most of them were slightly better or better than that obtained with commercial bacterial strains P10c (66%) and QST713 (63%). In field trials, the most effective were P. agglomerans ACBP2, B. amyloliquefaciens LMR2, B. halotolerans (SF3 and SF4), and B. mojarvensis SF16. In addition, effective bacterial isolates did not show the pathogenicity signs towards plant tissue and are, therefore, considered as potential candidates to be integrated in actives ingredients of microbial formulation for the effective control of Fire Blight.

Conservation of Erwinia amylovora pathogenicity-relevant genes among Erwinia genomes

The Erwinia genus comprises species that are plant pathogens, non-pathogen, epiphytes, and opportunistic human pathogens. Within the genus, Erwinia amylovora ranks among the top 10 plant pathogenic bacteria. It causes the fire blight disease and is a global threat to commercial apple and pear production. We analyzed the presence/absence of the E. amylovora genes reported to be important for pathogenicity towards Rosaceae within various Erwinia strains genomes. This simple bottom-up approach, allowed us to correlate the analyzed genes to pathogenicity, host specificity, and make useful considerations to drive targeted studies.

Modelling the effects of cutting off infected branches and replanting on fire-blight transmission using Filippov systems

Fire blight is one of the most devastating plant diseases in the world. This paper proposes a Filippov fire-blight model incorporating cutting off infected branches and replanting susceptible trees. The Filippov-type model is formulated by considering that no control strategy is taken if the number of infected trees is less than an infected threshold level I_c; further, we cut off infected branches once the number of infected trees exceeds I_c; meanwhile, we replant trees if the number of susceptible trees is less than a susceptible threshold level S_c. The global dynamical behaviour of the Filippov system is investigated. It is shown that model solutions ultimately converge to the positive equilibrium that lies in the region above I_c, or below I_c, or on I=I_c, as we vary the susceptible and infected threshold values S_c and I_c. Our results indicate that proper combinations of the susceptible and infected threshold values based on the threshold policy can lead the number of infected trees to an acceptable level, when complete eradication is not economically desirable.

Comparative transcriptome analysis of a lowly virulent strain of Erwinia amylovora in shoots of two apple cultivars - susceptible and resistant to fire blight

Background

Erwinia amylovora is generally considered to be a homogeneous species in terms of phenotypic and genetic features. However, strains show variation in their virulence, particularly on hosts with different susceptibility to fire blight. We applied the RNA-seq technique to elucidate transcriptome-level changes of the lowly virulent E. amylovora 650 strain during infection of shoots of susceptible (Idared) and resistant (Free Redstar) apple cultivars.

Results

The highest number of differentially expressed E. amylovora genes between the two apple genotypes was observed at 24 h after inoculation. Six days after inoculation, only a few bacterial genes were differentially expressed in the susceptible and resistant apple cultivars. The analysis of differentially expressed gene functions showed that generally, higher expression of genes related to stress response and defence against toxic compounds was observed in Free Redstar. Also in this cultivar, higher expression of flagellar genes (FlaI), which are recognized as PAMP (pathogen-associated molecular pattern) by the innate immune systems of plants, was noted. Additionally, several genes that have not yet been proven to play a role in the pathogenic abilities of E. amylovora were found to be differentially expressed in the two apple cultivars.

Conclusions

This RNA-seq analysis generated a novel dataset describing the transcriptional response of the lowly virulent strain of E. amylovora in susceptible and resistant apple cultivar. Most genes were regulated in the same way in both apple cultivars, but there were also some cultivar-specific responses suggesting that the environment in Free Redstar is more stressful for bacteria what can be the reason of their inability to infect of this cultivar. Among genes with the highest fold change in expression between experimental combinations or with the highest transcript abundance, there are many genes without ascribed functions, which have never been tested for their role in pathogenicity. Overall, this study provides the first transcriptional profile by RNA-seq of E. amylovora during infection of a host plant and insights into the transcriptional response of this pathogen in the environments of susceptible and resistant apple plants.

Electronic supplementary material

The online version of this article (10.1186/s12864-017-4251-z) contains supplementary material, which is available to authorized users.

Erwinia amylovora psychrotrophic adaptations: evidence of pathogenic potential and survival at temperate and low environmental temperatures

The fire blight pathogen Erwinia amylovora can be considered a psychrotrophic bacterial species since it can grow at temperatures ranging from 4 °C to 37 °C, with an optimum of 28 °C. In many plant pathogens the expression of virulence determinants is restricted to a certain range of temperatures. In the case of E. amylovora, temperatures above 18 °C are required for blossom blight epidemics under field conditions. Moreover, this bacterium is able to infect a variety of host tissues/organs apart from flowers, but it is still unknown how environmental temperatures, especially those below 18 °C, affect the pathogen ability to cause fire blight disease symptoms in such tissues/organs. There is also scarce information on how temperatures below 18 °C affect the E. amylovora starvation-survival responses, which might determine its persistence in the environment and probably contribute to the seasonal development of fire blight disease, as occurs in other pathogens. To characterize the virulence and survival of E. amylovora at temperate and low temperatures, we evaluated the effect of three temperatures (4 °C, 14 °C, 28 °C) on symptom development, and on different parameters linked to starvation and virulence. E. amylovora was pathogenic at the three assayed temperatures, with a slow-down of symptom development correlating with colder temperatures and slower growth rates. Siderophore secretion and motility also decreased in parallel to incubation temperatures. However, production of the exopolysaccharides amylovoran and levan was enhanced at 4 °C and 14 °C, respectively. Similarly, biofilm formation, and oxidative stress resistance were improved at 14 °C, with this temperature also favoring the maintenance of culturability, together with a reduction in cell size and the acquisition of rounded shapes in E. amylovora cells subjected to long-term starvation. However, starvation at 28 °C and 4 °C induced an enhanced viable but nonculturable (VBNC) response (to a lesser extent at 4 °C). This work reveals E. amylovora as a highly adaptable pathogen that retains its pathogenic potential even at the minimal growth temperatures, with an improved exopolysaccharide synthesis, biofilm formation or oxidative stress resistance at 14 °C, with respect to the optimal growth temperature (28 °C). Finally, our results also demonstrate the thermal modulation of starvation responses in E. amylovora, suggesting that the starvation-survival and the VBNC states are part of its life cycle. These results confirm the particular psychrotrophic adaptations of E. amylovora, revealing its pathogenic potential and survival at temperate and low environmental temperatures, which have probably contributed to its successful spread to countries with different climates. This knowledge might improve integrated control measures against fire blight.

Role of the type VI secretion systems during disease interactions of Erwinia amylovora with its plant host

Background

Type VI secretion systems (T6SS) are widespread among Gram-negative bacteria and have a potential role as essential virulence factors or to maintain symbiotic interactions. Three T6SS gene clusters were identified in the genome of E. amylovora CFBP 1430, of which T6SS-1 and T6SS-3 represent complete T6SS machineries, while T6SS-2 is reduced in its gene content.

Results

To assess the contribution of T6SSs to virulence and potential transcriptomic changes of E. amylovora CFBP 1430, single and double mutants in two structural genes were generated for T6SS-1 and T6SS-3. Plant assays showed that mutants in T6SS-3 were slightly more virulent in apple shoots while inducing less disease symptoms on apple flowers, indicating that T6SSs have only a minor effect on virulence of E. amylovora CFBP 1430. The mutations led under in vitro conditions to the differential expression of type III secretion systems, iron acquisition, chemotaxis, flagellar, and fimbrial genes. Comparison of the in planta and in vitro transcriptome data sets revealed a common differential expression of three processes and a set of chemotaxis and motility genes. Additional experiments proved that T6SS mutants are impaired in their motility.

Conclusion

These results suggest that the deletion of T6SSs alters metabolic and motility processes. Nevertheless, the difference in lesion development in apple shoots and flower necrosis of T6SS mutants was indicative that T6SSs influences the disease progression and the establishment of the pathogen on host plants.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-4010-1) contains supplementary material, which is available to authorized users.

Lysozyme enhances the bactericidal effect of BP100 peptide against Erwinia amylovora, the causal agent of fire blight of rosaceous plants

Background

Fire blight is an important disease affecting rosaceous plants. The causal agent is the bacteria Erwinia amylovora which is poorly controlled with the use of conventional bactericides and biopesticides. Antimicrobial peptides (AMPs) have been proposed as a new compounds suitable for plant disease control. BP100, a synthetic linear undecapeptide (KKLFKKILKYL-NH₂), has been reported to be effective against E. amylovora infections. Moreover, BP100 showed bacteriolytic activity, moderate susceptibility to protease degradation and low toxicity. However, the peptide concentration required for an effective control of infections in planta is too high due to some inactivation by tissue components. This is a limitation beause of the high cost of synthesis of this compound. We expected that the combination of BP100 with lysozyme may produce a synergistic effect, enhancing its activity and reducing the effective concentration needed for fire blight control.

Results

The combination of a synhetic multifunctional undecapeptide (BP100) with lysozyme produces a synergistic effect. We showed a significant increase of the antimicrobial activity against E. amylovora that was associated to the increase of cell membrane damage and to the reduction of cell metabolism. Combination of BP100 with lysozyme reduced the time required to achieve cell death and the minimal inhibitory concentration (MIC), and increased the activity of BP100 in the presence of leaf extracts even when the peptide was applied at low doses. The results obtained in vitro were confirmed in leaf infection bioassays.

Conclusions

The combination of BP100 with lysozyme showed synergism on the bactericidal activity against E. amylovora and provide the basis for developing better formulations of antibacterial peptides for plant protection.

Virulence of Erwinia amylovora, a prevalent apple pathogen: Outer membrane proteins and type III secreted effectors increase fitness and compromise plant defenses

Until now, no data are available on the outer membrane (OM) proteome of Erwinia amylovora, a Gram-negative plant pathogen, causing fire blight in most of the members of the Rosaceae family. Since the OM forms the interface between the bacterial cell and its environment it is in direct contact with the host. Additionally, the type III secretion system, embedded in the OM, is a pathogenicity factor of E. amylovora. To assess the influence of the OM composition and the secretion behavior on virulence, a 2D-DIGE analysis and gene expression profiling were performed on a high and lower virulent strain, both in vitro and in planta. Proteome data showed an increase in flagellin for the lower virulent strain in vitro, whereas, in planta several interesting proteins were identified as being differently expressed between both the strains. Further, gene expression of nearly all type III secreted effectors was elevated for the higher virulent strain, both in vitro and in planta. As a first, we report that several characteristics of virulence can be assigned to the OM proteome. Moreover, we demonstrate that secreted proteins prove to be the important factors determining differences in virulence between the strains, otherwise regarded as homogeneous on a genome level.

Same ammo, different weapons: enzymatic extracts from two apple genotypes with contrasted susceptibilities to fire blight (Erwinia amylovora) differentially convert phloridzin and phloretin in vitro

The necrogenic bacterium Erwinia amylovora responsible for the fire blight disease causes cell death in apple tissues to enrich intercellular spaces with nutrients. Apple leaves contain large amounts of dihydrochalcones (DHCs), including phloridzin and its aglycone phloretin. Previous work showed an important decrease in the constitutive DHCs stock in infected leaves, probably caused by transformation reactions during the infection process. At least two flavonoid transformation pathways have been described so far: deglucosylation and oxidation. The aim of the present study was to determine whether DHCs are differentially converted in two apple genotypes displaying contrasted susceptibilities to the disease. Different analyses were performed: i) enzymatic activity assays in infected leaves, ii) identification/quantification of end-products obtained after in vitro enzymatic reactions with DHCs, iii) evaluation of the bactericidal activity of end-products. The results of the enzymatic assays showed that deglucosylation was dominant over oxidation in the susceptible genotype MM106 while the opposite was observed in the resistant genotype Evereste. These data were confirmed by LC-UV/Vis-MS analysis of in vitro reaction mixtures, especially because higher levels of o-quinoid oxidation products of phloretin were measured by using the enzymatic extracts of Evereste infected leaves. Their presence correlated well with a strong bactericidal activity of the reaction mixtures. Thus, our results suggest that a differential transformation of DHCs occur in apple genotypes with a potential involvement in the establishment of the susceptibility or the resistance to fire blight, through the release of glucose or of highly bactericidal compounds respectively.

Deep sequencing revealed genome-wide single-nucleotide polymorphism and plasmid content of Erwinia amylovora strains isolated in Middle Atlas, Morocco

Erwinia amylovora causes economic losses that affect pear and apple production in Morocco. Here, we report comparative genomics of four Moroccan E. amylovora strains with the European strain CFBP1430 and North-American strain ATCC49946. Analysis of single nucleotide polymorphisms (SNPs) revealed genetic homogeneity of Moroccan's strains and their proximity to the European strain CFBP1430. Moreover, the collected sequences allowed the assembly of a 65 kpb plasmid, which is highly similar to the plasmid pEI70 harbored by several European E. amylovora isolates. This plasmid was found in 33% of the 40 E. amylovora strains collected from several host plants in 2009 and 2010 in Morocco.