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

Eighty stone fruit nurseries located in different regions of Poland were examined for the presence of crown gall affected plants. The disease was observed in 39 nurseries, and galls were sampled for bacterial isolation. Out of 1213 isolates, 409 were pre-identified as Agrobacterium/Rhizobium spp. with 23S rDNA-based multiplex PCR, and out of these, 315 were pathogenic when tested on sunflowers. Sequence analysis of three housekeeping genes (fusA, recA, rpoD) revealed that 366 strains belonged to Rhizobium rhizogenes, 23 to Agrobacterium tumefaciens species complex, and the rest of the strains were allocated to new phylogenetic lineages. Of these, the most numerous was the lineage allocated in the Pararhizobium genus. Positive results obtained from pathogenicity tests were generally in agreement with results obtained by PCR with primers complementary to T-DNA except for two strains, which were positive for PCR but negative for the pathogenicity test. All detected Ti plasmids were nopaline-type. Independent of their pathogenicity, 59% of tested strains were not sensitive to agrocin 84 in in vitro tests. Analysis of biochemical and physiological features distinguished 50 groups with different phenotypic profiles, but the tested traits were not consistent for strains classified to one taxon. This finding shows limited value of biochemical tests in identification procedures. The bacteria causing tumours were heterogeneous and strains classified to different taxa were found even in a single tumour.

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The possibility of inducing resistance to the two-spotted spider mite, Tetranychus urticae Koch, in 'Gala' apple trees growing under optimal fertilization or nitrogen-deficiency conditions was investigated. The effects of jasmonic acid (JA) at 1.5 and 2.5 mM, and acibenzolar-S-methyl (benzothiadiazole, BTH) at 0.5 and 1.5 mM, applied separately or together, on the fecundity of T. urticae females in a laboratory test as well as on the population growth of the pest in a greenhouse experiment were determined. The influence of both elicitors on the induction of LOX and PAL gene expression was assessed in a parallel experiment using real-time PCR. Jasmonic acid showed significantly higher effectiveness in inducing apple tree resistance to T. urticae, as compared to BTH. This was particularly evident in the reduction in pest numbers that was observed in the greenhouse experiment and was also confirmed by increased LOX gene expression after treatment with JA. BTH induced the expression of the PAL gene more strongly than jasmonic acid; however, this was not reflected in the performance of the two-spotted spider mite in the laboratory and greenhouse experiments. It was also found that the antagonistic effect of BTH on JA might lead to decreased effectiveness of the jasmonic acid used to induce apple tree resistance to the two-spotted spider mite. Although nitrogen fertilization stimulated the development of spider mite populations, the resistance induction mechanism was more effective in N-fertilized plants, which was especially evident at the higher jasmonic acid concentration.

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The cabbage whitefly (CW), Aleyrodes proletella (L.) (Hemiptera: Aleyrodidae), is an important pest in Brassica oleracea L. crops. Little is known about the mechanisms of resistance to CW of savoy cabbage and kale cultivars. Light microscopy (LM) and scanning electron microscopy (SEM) analysis were used to determine the relationship between the morphological and anatomical features of savoy cabbage (Brassica oleracea L. convar. capitata (L.) Alef. var. sabauda L.) and kale (Brassica oleracea L. convar. acephala (DC.) Alef. var. sabellica L.) leaves and host suitability to colonization by CW. Two kale cultivars, “Redbor” and “Starbor”, and two savoy cabbage cultivars, “Gloriosa” and “Alcosa”, that differed in the degree of infestation by A. proletella were taken for histological analysis. The lowest infestation by all forms of A. proletella was observed on savoy cabbage cultivar “Alcosa” and kale cultivar “Starbor”. The reduced colonization by cabbage whitefly may be related to the structure of the epidermis and the anatomical features of the leaf. The leaves of “Starbor” and “Alcosa” had more folds in the epidermis, less numerous but larger stomata, and a more compact mesophyll structure compared to “Redbor” and “Gloriosa”. In both analysed species, there was no clear relationship between the thickness of the abaxial epidermal layer, thickness of the lamina, number of vascular bundles, and degree of infestation by the cabbage whitefly. This study identified promising sources of resistance to A. proletella among cultivars of savoy cabbage and kale. Varying infestation by CW was associated with morphological and anatomical characteristics of leaves. Further study is needed to confirm the relationship between insect resistance and leaf surface and morphological characteristics of leaves in a broader range of Brassica spp.

Xanthomonas fragariae is a quarantine bacterial pathogen that causes angular leaf spot on strawberry. The aim of our study was to analyse the mechanism of interaction of this bacterium with its host plant at the transcriptome level. For this purpose, mRNAs of X. fragariae growing in Wilbrink’s medium and from infected strawberry cv. Elsanta plants were isolated and sequenced using the Illumina MiSeq platform. The expression profiles of the bacteria in Wilbrink’s medium and in planta were very diverse. Of the 3939 CDSs recorded, 1995 had significantly different expression in planta (966 and 1029 genes were down- and upregulated, respectively). Among the genes showing increased expression in planta, those with eggNOG/COG (evolutionary genealogy of genes: Non-supervised Orthologous Groups/Cluster of Orthologous Groups) categories associated with bacterial cell motility, signal transduction, transport and metabolism of inorganic ions and carbohydrates and transcription were overrepresented. Among the genes with the most increased expression in planta, genes primarily associated with flagella synthesis and chemotaxis were found. It is also interesting to note that out of the 31 genes localized on a plasmid, 16 were expressed differently in planta, which may indicate their potential role in plant–pathogen interactions. Many genes with differentiated expression that were localized on chromosome and plasmid encode proteins of unknown function.

Treating apple trees and strawberry plants with methyl jasmonate (JA-Me) was investigated to see how the treatment affects the population size of the two-spotted spider mite (Tetranychus urticae Koch.). Both apple and strawberry were represented by two cultivars: Jester, Close and Aga, Kent, respectively. Each plant was infested with mites one day after being treated with a methyl jasmonate (JA-Me) solution. The negative influence of the JA-Me plant treatment on the growth of the subsequently colonized population of the two-spotted spider mite was observed both for strawberry plants and apple trees. A significant interaction (plant treatment x cultivar), however, was observed in the experiment conducted on apple trees. The population of mites feeding on the cv. Jester was not influenced by the JA-Me treatment. This lack of influence by JA-Me treatment was in contrast to what was found with the cultivar Close.