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Chitin amendment of peat substrate has been proven effective in promoting lettuce growth and increasing phenolic compounds in lettuce seedlings. However, the effect of chitin soil amendment on lettuce growth in mineral soil remains unexplored. The effect of chitin amendment of mineral soil on lettuce growth and metabolite changes was investigated for the first time in the present study in comparison to chitin amended peat substrate. Our findings showed that chitin addition in peat substrate increased lettuce head weight by approximately 50% at harvest, whereas this increase was 30% when added to mineral soil. Targeted metabolomics analysis indicated that chitin addition affected the phenolic compounds in lettuce seedlings, but this effect varied between soil types. Moreover, untargeted metabolomics analysis suggested that using peat substrate or mineral soil had a greater influence on produced lettuce metabolites than chitin addition. Rhizobiome analysis showed that specifically Mortierellaceae family members, known for chitin degradation and plant growth promotion, significantly increased in peat substrate upon chitin treatment. In mineral soil, three bacterial genera and five fungi, including known plant growth promoting genera, were significantly more abundant upon chitin treatment but not Mortierellaceae. We assume that the observed effects primarily stem from soil physiochemical characteristics and from chitin induced alterations in rhizobiome composition, particularly the presence of Mortierellaceae members, leading to promoted lettuce growth. Despite the variability, chitin remains an environmentally friendly alternative to synthetic fertilizers in lettuce production, but its beneficial effects are dependent on rhizobiome composition, which should be considered before chitin application.

Xanthomonads, including Xanthomonas and Xylella species, constitute a large and significant group of economically and ecologically important plant pathogens. Up-to-date knowledge of these pathogens and their hosts is essential for the development of suitable control measures. Traditional review articles or book chapters have inherent limitations, including static content and rapid obsolescence. To address these challenges, we have developed a web-based knowledge platform dedicated to xanthomonads, inspired by the concept of living systematic reviews. This platform offers a dynamic resource that encompasses bacterial virulence factors, plant resistance genes, and tools for diagnostics and genetic diversity studies. Our goal is to facilitate access for newcomers to the field, provide continuing education opportunities for students, assist plant protection services with diagnostics, provide valuable information to breeders on sources of resistance and breeding targets, and offer comprehensive expert knowledge to other stakeholders interested in plant-pathogenic xanthomonads. This resource is available for queries and updates at https://euroxanth.ipn.pt.

Technologien zur frühzeitigen Erkennung neu auftretender Pflanzenkrankheiten sind ein wichtiges Instrument im Kampf gegen hohe Produktionsverluste durch Pflanzenkrankheiten in der Landwirtschaft. Mit der Entwicklung und Kombination innovativer Methoden trägt das Projekt «ToViPoRe» zur Prävention und Kontrolle viraler Pathogene bei, welche die Tomatenproduktion in der Schweiz bedrohen. Verläuft der Machbarkeitsnachweis der Methoden erfolgreich, wird die zukünftige Diagnostik stark von diesem Forschungsprojekt profitieren.

Xanthomonas arboricola pv. corylina is the causal agent of bacterial blight of hazelnut. The bacterium has been listed as an A2 quarantine pathogen in Europe since 1978 and on the regulated non-quarantine pest list since 2019. Three isolates from various geographic regions and isolated at different times were sequenced using a hybrid approach with short- and long-read technologies to generate closed genome and plasmid sequences in order to better understand the biology of this pathogen.

[No abstract available]

Xanthomonas arboricola pv. corylina (Xac; formerly Xanthomonas campestris pv. corylina) is the causal agent of the bacterial blight of hazelnuts, a devastating disease of trees in plant nurseries and young orchards. Currently, there are no PCR assays to distinguish Xac from all other pathovars of X. arboricola. A comparative genomics approach with publicly available genomes of Xac was used to identify unique sequences, conserved across the genomes of the pathogen. We identified a 2,440 bp genomic region that was unique to Xac and designed identification and detection systems for conventional PCR, qPCR (SYBR® Green and TaqMan™), and loop-mediated isothermal amplification (LAMP). All PCR assays performed on genomic DNA isolated from eight X. arboricola pathovars and closely related bacterial species confirmed the specificity of designed primers. These new multi-platform molecular diagnostic tools may be used by plant clinics and researchers to detect and identify Xac in pure cultures and hazelnut tissues rapidly and accurately.

Pseudomonas syringae pv. tomato is the causal agent of bacterial speck of tomato, an important disease that results in severe crop production losses worldwide. Currently, two races within phylogroup 01a (PG01a) are described for this pathogen. Race 0 strains have avirulence genes for the expression of type III system-associated effectors AvrPto1 and AvrPtoB, that are recognized and targeted by the effector-triggered immunity in tomato cultivars having the pto race-specific resistance gene. Race 1 strains instead lack the avrPto1 and avrPtoB genes and are therefore capable to aggressively attack all tomato cultivars. Here, we have performed the complete genome sequencing and the analysis of P. syringae pv. tomato strain DAPP-PG 215, which was described as a race 0 strain in 1996. Our analysis revealed that its genome comprises a 6.2 Mb circular chromosome and two plasmids (107 kb and 81 kb). The results indicate that the strain is phylogenetically closely related to strains Max13, K40, T1 and NYS-T1, all known race 1 strains. The chromosome of DAPP-PG 215 encodes race 1-associated genes like avrA and hopW1 and lacks race 0-associated genes like hopN1, giving it a race 1 genetic background. However, the genome harbors a complete ortholog of avrPto1, which allows the strain to display a race 0 phenotype. Comparative genomics with several PG01a genomes revealed that mobile DNA elements are rather involved in the evolution of the two different races.

Here, we report the high-quality draft genome sequence of the actinomycete Streptomyces albidoflavus CCOS 2040, isolated from a Swiss soil sample. The genome contains 7,136,301 bp with 73.35% GC content. In total, 22 biosynthetic gene clusters, including polyketides and terpenes, were predicted within the sequenced genome.

This Standard describes a diagnostic protocol for Pseudomonas syringae pv. actinidiae. It should be used in conjunction with PM 7/76 Use of EPPO Diagnostic Protocols.

Bacteria in the genus Xanthomonas infect a wide range of crops and wild plants, with most species responsible for plant diseases that have a global economic and environmental impact on the seed, plant, and food trade. Infections by Xanthomonas spp. cause a wide variety of non-specific symptoms, making their identification difficult. The coexistence of phylogenetically close strains, but drastically different in their phenotype, poses an added challenge to diagnosis. Data on future climate change scenarios predict an increase in the severity of epidemics and a geographical expansion of pathogens, increasing pressure on plant health services. In this context, the effectiveness of integrated disease management strategies strongly depends on the availability of rapid, sensitive, and specific diagnostic methods. The accumulation of genomic information in recent years has facilitated the identification of new DNA markers, a cornerstone for the development of more sensitive and specific methods. Nevertheless, the challenges that the taxonomic complexity of this genus represents in terms of diagnosis together with the fact that within the same bacterial species, groups of strains may interact with distinct host species demonstrate that there is still a long way to go. In this review, we describe and discuss the current molecular-based methods for the diagnosis and detection of regulated Xanthomonas, taxonomic and diversity studies in Xanthomonas and genomic approaches for molecular diagnosis.

We report here the complete genome sequences of two Xanthomonas arboricola strains isolated in 2013 from blueberry plants displaying bacterial leaf blight in Poland. These two strains – the new blueberry pathogens – were sequenced using a hybrid approach with short- and long-read technologies. The genomes will be used for further analysis of evolution within the species X. arboricola for determining if the strains constitute a new pathovar within the species and improving the molecular diagnostics of this relevant pathogen of blueberry.

Taxonomy: Bacteria; Phylum Proteobacteria; Class Gammaproteobacteria; Order Lysobacterales (earlier synonym of Xanthomonadales); Family Lysobacteraceae (earlier synonym of Xanthomonadaceae); Genus Xanthomonas; Species X. hortorum; Pathovars: pv. carotae, pv. vitians, pv. hederae, pv. pelargonii, pv. taraxaci, pv. cynarae, and pv. gardneri. Host range: Xanthomonas hortorum affects agricultural crops, and horticultural and wild plants. Tomato, carrot, artichoke, lettuce, pelargonium, ivy, and dandelion were originally described as the main natural hosts of the seven separate pathovars. Artificial inoculation experiments also revealed other hosts. The natural and experimental host ranges are expected to be broader than initially assumed. Additionally, several strains, yet to be assigned to a pathovar within X. hortorum, cause diseases on several other plant species such as peony, sweet wormwood, lavender, and oak-leaf hydrangea. Epidemiology and control: X. hortorum pathovars are mainly disseminated by infected seeds (e.g., X. hortorum pvs carotae and vitians) or cuttings (e.g., X. hortorum pv. pelargonii) and can be further dispersed by wind and rain, or mechanically transferred during planting and cultivation. Global trade of plants, seeds, and other propagating material constitutes a major pathway for their introduction and spread into new geographical areas. The propagules of some pathovars (e.g., X. horturum pv. pelargonii) are spread by insect vectors, while those of others can survive in crop residues and soils, and overwinter until the following growing season (e.g., X. hortorum pvs vitians and carotae). Control measures against X. hortorum pathovars are varied and include exclusion strategies (i.e., by using certification programmes and quarantine regulations) to multiple agricultural practices such as the application of phytosanitary products. Copper-based compounds against X. hortorum are used, but the emergence of copper-tolerant strains represents a major

Related publications: https://doi.org/10.1099/ijsem.0.004386, https://doi.org/10.3390/microorganisms9030624, Xanthomonas euroxanthea is a bacterial species encompassing both pathogenic and non-pathogenic strains and is frequently found colonizing the same host plants as X. arboricola. This presents the need to develop a detection and genotyping assay able to track these bacteria in microbial consortia with other xanthomonads. Eight X. euroxanthea-specific DNA markers (XEA1-XEA8) were selected by comparative genomics and validated in silico regarding their specificity and consistency using BLASTn, synteny analysis, CG content, codon usage (CAI/eCAI values) and genomic proximity to plasticity determinants. In silico, the selected eight DNA markers were found to be specific and conserved across the genomes of 11 X. euroxanthea strains, and in particular, five DNA markers (XEA4, XEA5, XEA6, XEA7 and XEA8) were unfailingly found in these genomes. A multiplex of PCR targeting markers XEA1 (819 bp), XEA8 (648 bp) and XEA5 (295 bp) was shown to successfully detect X. euroxanthea down to 1 ng of DNA (per PCR reaction). The topology of trees generated with the concatenated sequences of three markers (XEA5, XEA6 and XEA8) and four housekeeping genes (gyrB, rpoD, fyuA and acnB) underlined the equal discriminatory power of these features and thus the suitability of the DNA markers to discriminate X. euroxanthea lineages. Overall, this study displays a DNA-marker-based method for the detection and genotyping of X. euroxanthea strains, contributing to monitoring for its presence in X. arboricola-colonizing habitats. The present study proposes a workflow for the selection of species-specific detection markers. Prospectively, this assay could contribute to unveil alternative host species of Xanthomonas euroxanthea; and improve the control of phytopathogenic strains.

Related publications: https://doi.org/10.1099/ijsem.0.005163, https://doi.org/10.1002/ndr2.12008, The seven pathovars of Xanthomonas hortorum and Xanthomonas hydrangeae, referred to as the X. hortorum – X. hydrangeae species complex, cause disease on a multitude of plants, including crops, ornamental and wild plants. Cross-pathogenicity was proven for some of the strains within this species complex. It is thus important to have highly specific and fast diagnostics methods for members of the X. hortorum – X. hydrangeae species complex. A comparative genomic analysis was conducted for representative members within the complex to identify singletons for use as genomic targets for the assays. Seven loop-mediated isothermal amplification (LAMP) diagnostics assays were developed for the detection of six clades within the X. hortorum – X. hydrangeae species complex, in addition to one assay specific for the entire species complex. Primer sets were tested on a set of 62 reference strains. The primer sets amplified their respective targets within 15 minutes. Based on the reference set, all assays had a sensitivity, specificity, and efficiency of 100%. The assays were used on a validation set of 60 strains. According to the LAMP results, out of the 60 strains, 39 strains were assigned to one of the clades within the complex, 9 were assigned to the complex but to yet undefined clades within the complex, and 12 strains were previously misclassified as X. hortorum since their genomic DNA did not yield amplification with any of the assays. The seven genome-based assays are promising for use as diagnostic tools for various members within the X. hortorum – X. hydrangeae species complex, and for assigning new and historical isolates to this complex.

Xanthomonas arboricola comprises a number of economically important fruit tree pathogens classified within different pathovars. Dozens of nonpathogenic and taxonomically unvalidated strains are also designated as X. arboricola, leading to a complicated taxonomic status in the species. In this study, we have evaluated the whole-genome resources of all available Xanthomonas spp. strains designated as X. arboricola in the public databases to refine the members of the species based on DNA similarity indexes and core genome-based phylogeny. Our results show that, of the nine validly described pathovars within X. arboricola, pathotype strains of seven pathovars are taxonomically genuine, belonging to the core clade of the species regardless of their pathogenicity on the host of isolation (thus the validity of pathovar status). However, strains of X. arboricola pv. guizotiae and X. arboricola pv. populi do not belong to X. arboricola because of the low DNA similarities between the type strain of the species and the pathotype strains of these two pathovars. Thus, we propose to elevate the two pathovars to the rank of a species as X. guizotiae sp. nov. with the type strain CFBP 7408T and X. populina sp. nov. with the type strain CFBP 3123T. In addition, other mislabeled strains of X. arboricola were scattered within Xanthomonas spp. that belong to previously described species or represent novel species that await formal description.

Strawberry is economically important and widely grown but susceptible to a large variety of phytopathogenic organisms. Among them, Xanthomonas fragariae is a quarantine bacterial pathogen threatening strawberry productions by causing angular leaf spots. Using whole transcriptome sequencing, gene expression of both plant and bacteria in planta was analyzed at two time points, 12- and 29-days post inoculation, in order to compare pathogen and host response between the stages of early visible and of well-developed symptoms. Among 28’588 known genes in strawberry and 4’046 known genes in X. fragariae expressed at both time points, a total of 361 plant and 144 bacterial genes were significantly differentially expressed, respectively. The identified higher expressed genes in the plants were pathogen-associated molecular pattern receptors and pathogenesis related thaumatin encoding genes, whereas the more expressed early genes were related to chloroplast metabolism as well as photosynthesis related coding genes. Most of X. fragariae genes involved in host interactions, recognitions and pathogenesis, were lower expressed at late-phase infection. This study gives a first insight on the interaction of X. fragariae with its host. The strawberry plant changed its metabolism consistently with the progression of infection.

Xanthomonas arboricola pv. juglandis is one of the most serious and widespread threats of walnut orchards, associated with severe production losses having a large negative economic impact. We report here high-quality draft genome sequences of Xanthomonas arboricola and Xanthomonas sp. isolates from one walnut tree located in Loures (Portugal) showing typical symptoms of walnut bacterial blight.

We report the genome sequences of six Xanthomonas hortorum species level clade members: complete genomes of X. hortorum pv. taraxaci, pv. pelargonii, pv. cynarae and pv. gardneri, in addition to high-quality draft genomes of X. hortorum pv. carotae and pv. vitians. Both short- and long-read sequencing technologies were utilized.

We report the genome sequences of four strains isolated from a hydrangea plants that belong to the Xanthomonas hortorum species level clade but forms a new species.

Xanthomonas fragariae is a quarantine organism in Europe, causing angular leaf spots on strawberry. It is spreading worldwide in strawberry-producing regions due to import of plant material through trade and human activities. In order to resolve the population structure at the strain level, we have employed high-resolution molecular typing tools on a comprehensive strain collection representing global and temporal distribution of the pathogen. Clustered regularly interspaced short palindromic repeat regions (CRISPRs) and variable number of tandem repeats (VNTRs) were identified within the reference genome of X. fragariae LMG 25863 as a potential source of variation. Strains from our collection were whole-genome sequenced and used in order to identify variable spacers and repeats for discriminative purpose. CRISPR spacer analysis and Multiple-Locus VNTR analysis (MLVA) displayed a congruent population structure, in which two major groups and a total of four subgroups were revealed. The two main groups were genetically separated before the first X. fragariae isolate was described, and are potentially responsible for the worldwide expansion of the bacterial disease. Three primer sets were designed on discriminating CRISPR-associated markers in order to streamline group determination of novel isolates. Overall, this study delivers typing methods to discriminate strains and monitor the pathogen population structure, more especially in the view of a new outbreak of the pathogen.

The seed-borne bacterium Xanthomonas campestris pv. campestris (Xcc) as a causal organism of black rot disease remains the most serious bacterial problem of agricultural production of cruciferous plants worldwide. The eradication of a primary inoculum originating in seeds is available, but no treatment is totally effective. With the threat of developing chemical resistance and increasing pressure for sustainable disease management, biocontrol methods represent one of the main strategies currently applied in agriculture. Natural antimicrobials, including essential oils, are promising tools in disease management with low risks of environmental pollution and impact on human health. Thyme and clove essential oils were demonstrated to be highly effective in Xanthomonas studies in vitro; therefore, their application in black rot control was evaluated in this study. From five phenolic substances originating from thyme and clove essential oils (carvacrol, eugenol, linalool, p-cymene and thymol), the most promising in vitro results were observed with carvacrol, for which 0.0195% led to the death of all Xcc cells in 30 min. Moreover, a synergistic antibacterial effect of carvacrol and thymol solutions decreased the minimal inhibition concentration to 0.0049% and 0.0195% for carvacrol and thymol, respectively. Using the quadruple bactericidal values, the complete elimination of Xcc from the surface of infested cabbage seeds was obtained for both carvacrol and thymol solutions and their combined mixture at 2 MIC value. The elimination of bacterial infection from germinated cabbage plants was observed for both plate counting and quantitative real-time PCR methods. We also evaluated the effect of the application of phenolic treatment on the seed germination and germinated plants. Our results suggest a high potential of the application of carvacrol and thymol in vegetable seed production, specifically for cabbage, thus representing a suitable alternative to cupric derivatives.