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Xanthomonas perforans and X. euvesicatoria are the causal agents of bacterial spot disease of tomato and pepper, endemic to the Southeastern United States. Although very closely related, the two bacterial species differ in host specificity, where X. perforans is the dominant pathogen of tomato and X. euvesicatoria that of pepper. This is in part due to the activity of avirulence proteins that are secreted by X. perforans strains and elicit effector-triggered immunity in pepper leaves, thereby restricting pathogen growth. In recent years, the emergence of several pepper-pathogenic X. perforans lineages has revealed variability within the bacterial species to multiply and cause disease in pepper, even in the absence of avirulence gene activity. Here, we investigated the basal evolutionary processes underlying the host range of this species using multiple genome-wide association analyses. Surprisingly, we identified two novel gene candidates that were significantly associated with pepper-pathogenic X. perforans and X. euvesicatoria. Both candidates were predicted to be involved in the transport/acquisition of nutrients common to the plant cell wall or apoplast and included a TonB-dependent receptor, which was disrupted through independent mutations within the X. perforans lineage. The other included a symporter of protons/glutamate, gltP, enriched with pepper-associated mutations near the promoter and start codon of the gene. Functional analysis of these candidates revealed that only the TonB-dependent receptor had a minor effect on the symptom development and growth of X. perforans in pepper leaves, indicating that pathogenicity to this host might have evolved independently within the bacterial species and is likely a complex, multigenic trait.

For most of the 20th century, Xanthomonas euvesicatoria was the only known bacterium associated with bacterial spot of tomato in Florida. X. perforans quickly replaced X. euvesicatoria, mainly because of production of three bacteriocins (BCNs) against X. euvesicatoria; however, X. perforans outcompeted X. euvesicatoria even when the three known BCNs were deleted. Surprisingly, we observed antimicrobial activity against X. euvesicatoria in the BCN triple mutant when the triple mutant was grown in Petri plates containing multiple spots but not in Petri plates containing only one spot. We determined that changes in the headspace composition (i.e., volatiles) rather than a diffusible signal in the agar were required for induction of the antimicrobial activity. Other Xanthomonas species also produced volatile-induced antimicrobial compounds against X. euvesicatoria and elicited antimicrobial activity by X. perforans. A wide range of plant pathogenic bacteria, including Clavibacter michiganensis subsp. michiganensis, Pantoea stewartii, and Pseudomonas cichorii, also elicited antimicrobial activity by X. perforans when multiple spots of the species were present. To identify potential antimicrobial compounds, we performed liquid chromatography with high-resolution mass spectrometry of the agar surrounding the spot in the high cell density Petri plates where the antimicrobial activity was present compared with agar surrounding the spot in Petri plates with one spot where antimicrobial activity was not observed. Among the compounds identified in the zone of inhibition were N-butanoyl-L-homoserine lactone and N-(3-hydroxy-butanoyl)-homoserine lactone, which are known quorum-sensing metabolites in other bacteria.

Although cultivars possessing recessive resistance alleles provide effective control of bacterial spot of pepper (Capsicum annuum), the deployed resistance gene, bs5, is ineffective against Xanthomonas gardneri, one of the pathogenic species. Resistance against X. gardneri was identified in C. annuum accession PI 163192, and this study sought to characterize this novel resistance and to map the resistance gene(s) to the pepper genome. We crossed PI 163192 with the susceptible cultivar Early Calwonder (ECW) to develop resistant near-isogenic lines (NILs) of ECW, designated ECW80R. The novel resistance in ECW80R was determined to be quantitative, recessively inherited, and non-hypersensitive-response causing, and inhibits lesion expansion and chlorosis. Presence of the resistance in NILs decreased the in planta bacterial population by ninefold compared with ECW. Bulked segregant analysis of resistant and susceptible individuals from an F2 population using whole genome single nucleotide polymorphisms identified a major resistance locus within an approximate 6-Mbp interval on the subtelomeric region of chromosome 11. We developed markers spanning this region and used these to genotype backcross F2 populations, which further delimited the resistance locus within a 2.3-Mbp interval. The novel resistance locus has been designated bs8. ECW80R and the linked markers developed in this study should prove useful for breeders seeking to advance this resistance into commercially relevant germplasm and for pyramiding bs8 with other resistance alleles such as bs5 and bs6. The allele bs8 will help prolong the durability of bacterial spot resistance in pepper and improve resistance to multiple species of Xanthomonas.

Xanthomonas perforans is a seedborne hemibiotrophic pathogen that successfully establishes infection in the phyllosphere of tomato. While most studies investigating mechanistic basis of pathogenesis have focused on successful apoplastic growth, factors important during asymptomatic colonization in the early stages of disease development are not well understood. In this study, we show that tssM gene of the type VI secretion system cluster i3* (T6SS-i3*) plays a significant role during initial asymptomatic epiphytic colonization at different stages during the life cycle of the pathogen. Mutation in a core gene, tssM of T6SS-i3*, imparted higher aggressiveness to the pathogen, as indicated by higher overall disease severity, higher in planta growth, and shorter latent infection period compared with the wild-type upon dip inoculation of 4- to 5-week-old tomato plants. Contribution of tssM toward aggressiveness was evident during vertical transmission from seed to seedling, with wild-type showing reduced disease severity as well as lower in planta populations on seedlings compared with the mutant. Presence of functional TssM offered higher epiphytic fitness as well as higher dissemination potential to the pathogen when tested in an experimental setup mimicking transplant house high-humidity conditions. We showed higher osmotolerance being one mechanism by which TssM offers higher epiphytic fitness. Taken together, these data reveal that functional TssM plays a larger role in offering ecological advantage to the pathogen. TssM prolongs the association of hemibiotrophic pathogen with the host, minimizing overall disease severity yet facilitating successful dissemination.

Bacterial spot is an economically significant disease in tomato and pepper-producing countries globally. We report the whole genome sequence of 11 Xanthomonas strains associated with bacterial spot disease on pepper, tomato, and eggplant in the Southeastern Anatolia Region, Turkey. This genomic information can be used as a reference to study the genetic diversity of these species and contribute to illuminating pathogen evolution with respect to host specificity.

Bacterial spot caused by spp. is a significant disease that challenges pepper growers worldwide and is particularly severe in a hot and humid environment. Understanding the pathogen’s population biology is critical for sustainable disease management. The goal of this study was to characterize the species, race, and bactericide sensitivity of bacterial spot-associated Xanthomonas collected from pepper in Florida. A survey of pepper production fields in Southwest Florida between 2019-2021—covering two counties, eight farms, and two transplant facilities— resulted in the isolation of 542 Xanthomonas euvesicatoria (X. euvesicatoria) and 35 Xanthomonas perforans (X. perforans) strains. Four races were identified on pepper, of which most strains were race P1 (42%), race P6 (26%), race P3 (24%), and less common was race P4 (8%). All X. perforans strains were characterized as race P1 and showed a compatible reaction on tomato. Sixty-two and 96% of strains were sensitive to copper sulfate and streptomycin, respectively. One farm that did not use copper to manage the disease contained only copper-sensitive strains and was the only farm with race P3 strains. Strains were assayed for starch hydrolysis activity of which a third of X. euvesicatoria strains were strongly amylolytic, a characteristic not typically observed in X. euvesicatoria. All X. perforans strains produced bacteriocins against X. euvesicatoria in-vitro. The Xanthomonas population causing bacterial spot-on pepper in Southwest Florida is diverse and dynamic; thus, regular monitoring provides pertinent information to plant breeders and growers for designing disease management strategies. Key words: Bacterial-spot, Xanthomonas, pepper, races, copper, streptomycin, amylase, bacteriocin

Citrus canker (CC) is an economically important bacterial disease caused by Xanthomonas citri subsp. citri (Xcc). There is variability in resistance to CC among Citrus species. Previous transcriptomic studies have shown that Xcc downregulates biosynthesis of secondary metabolites at early stages of infection in susceptible citrus. However, in partially resistant calamondin (Citrus × microcarpa), increased secondary metabolite production has been reported post Xcc inoculation. We analyzed the calamondin transcriptome and discovered 3318 and 7740 differentially expressed (DE) genes between Xcc-inoculated and control samples at 2- and 5-days post inoculation (dpi), respectively. Among the DE genes, the phenylpropanoid biosynthesis (PPB) pathway, a major secondary metabolite synthesis pathway, was upregulated at early stages (2 dpi) of Xcc infection. Furthermore, in contrast to previous studies of susceptible Citrus species, pathways related to a resistance response (such as plant-pathogen interaction and MAPK signaling pathway) were upregulated whereas the pathways related to a susceptible response (such as auxin and gibberellin biosynthesis and cell wall degradation) were not significantly upregulated in calamondin. The transcriptomic regulation of plant hormone biosynthesis in calamondin was also different from the susceptible citrus. Thus, PPB may represent the principal biochemical pathway underlying CC resistance.

Modern agricultural practices increase the potential for plant pathogen spread, while the advent of affordable whole genome sequencing enables in-depth studies of pathogen movement. Population genomic studies may decipher pathogen movement and population structure as a result of complex agricultural production systems. We used whole genome sequences of 281 Xanthomonas perforans strains collected within one tomato production season across Florida and southern Georgia fields to test for population genetic structure associated with tomato production system variables. We identified six clusters of X. perforans from core gene SNPs that corresponded with phylogenetic lineages. Using whole genome SNPs, we found genetic structure among farms, transplant facilities, cultivars, seed producers, grower operations, regions, and counties. Overall, grower operations that produced their own transplants were associated with genetically distinct and less diverse populations of strains compared to grower operations that received transplants from multiple sources. The degree of genetic differentiation among components of Florida’s tomato production system varied between clusters, suggesting differential dispersal of the strains, such as through seed or contaminated transplants versus local movement within farms. Overall, we showed that the genetic variation of a bacterial plant pathogen is shaped by the structure of the plant production system.

Disease symptoms Symptoms include water‐soaked areas surrounded by chlorosis turning into necrotic spots on all aerial parts of plants. On tomato fruits, small, water‐soaked, or slightly raised pale‐green spots with greenish‐white halos are formed, ultimately becoming dark brown and slightly sunken with a scabby or wart‐like surface. Host range Main and economically important hosts include different types of tomatoes and peppers. Alternative solanaceous and nonsolanaceous hosts include Datura spp., Hyoscyamus spp., Lycium spp., Nicotiana rustica, Physalis spp., Solanum spp., Amaranthus lividus, Emilia fosbergii, Euphorbia heterophylla, Nicandra physaloides, Physalis pubescens, Sida glomerata, and Solanum americanum. Taxonomic status of the pathogen Domain, Bacteria; phylum, Proteobacteria; class, Gammaproteobacteria; order, Xanthomonadales; family, Xanthomonadaceae; genus, Xanthomonas; species, X. euvesicatoria, X. hortorum, X. vesicatoria. Synonyms (nonpreferred scientific names) Bacterium exitiosum, Bacterium vesicatorium, Phytomonas exitiosa, Phytomonas vesicatoria, Pseudomonas exitiosa, Pseudomonas gardneri, Pseudomonas vesicatoria, Xanthomonas axonopodis pv. vesicatoria, Xanthomonas campestris pv. vesicatoria, Xanthomonas cynarae pv. gardneri, Xanthomonas gardneri, Xanthomonas perforans. Microbiological properties Colonies are gram‐negative, oxidase‐negative, and catalase‐positive and have oxidative metabolism. Pale‐yellow domed circular colonies of 1–2 mm in diameter grow on general culture media. Distribution The bacteria are widespread in Africa, Brazil, Canada and the USA, Australia, eastern Europe, and south‐east Asia. Occurrence in western Europe is restricted. Phytosanitary categorization A2 no. 157, EU Annex designation II/A2. EPPO codes XANTEU, XANTGA, XANTPF, XANTVE., In this review we provide a historical perspective as well as an updated overview on the aetiology, epidemiology, and management strategies of bacterial spot of tomato and pepper.

Five bacterial strains were isolated from symptomatic leaves of Achillea millefolium, Delphinium sp. and Hydrangea sp. in California. Colonies isolated on King’s medium B (KMB) appeared white, mucoid and round, similar to Pseudomonas species. Phylogenetic analyses based on 16S rRNA, rpoB, rpoD and gyrB genes placed the bacteria into three distinct groups within Pseudomonas that were most closely related to Pseudomonas viridiflava , Pseudomonas cichorii or Pseudomonas caspiana . To further characterize the strains, phenotypic analyses and the following tests were performed: fatty acid methyl ester composition, LOPAT, fluorescence on KMB, Biolog assay, and transmission electron microscopy. Finally, whole genome sequencing of the strains was conducted, and the sequences were compared with reference genomes of Pseudomonas species based on average nucleotide identity (ANI). The first group, which consists of three strains isolated from delphinium, hydrangea and achillea, had 95.6–96.9 % pairwise ANI between each other; the second group consists of two strains isolated from delphinium that had 100 % pairwise ANI. Although comparisons of the two groups with publicly available genomes revealed closest relationships with P. viridiflava (91.6 %), P. caspiana (88.3 %) and P. asturiensis (86.7 %), ANI values were less than 95 % compared to all validly published pseudomonads. Combining genomic and phenotypic data, we conclude that these strains represent two new species and the names proposed are Pseudomonas quasicaspiana sp. nov. (type strain DSMZ 11 30 42T=LMG 32 434T) for the strains isolated from delphinium, achillea and hydrangea and Pseudomonas californiensis sp. nov. (DSMZ 11 30 43T=LMG 32 432T) for the two strains isolated from delphinium. The specific epithets quasicaspiana and californiensis were selected based on the close phylogenetic relationship of strains with P. caspiana and on the geographic location of isolation, respectively.

Bacterial spot of tomato continues to pose a significant problem to tomato production worldwide. In Florida, bacterial spot of tomato caused by

Bacterial spot caused by Xanthomonas euvesicatoria is a major disease of pepper (Capsicum annuum L.) in warm and humid production environments. Use of genetically resistant cultivars is an effective approach to manage bacterial spot. Two recessive resistance genes, bs5 and bs6, confer non-race-specific resistance against bacterial spot. The objective of our study was to map these two loci in the pepper genome. We used a genotyping-by-sequencing approach to initially map the position of the two resistances. Segregant populations for bs5 and bs6 were developed by crossing susceptible Early CalWonder (ECW) with near-isogenic lines ECW50R (bs5 introgression) or ECW60R (bs6 introgression). Following fine-mapping, bs5 was delimited to a ~535 Kbp interval on chromosome 3, and bs6 to a ~666 Kbp interval in chromosome 6 of pepper. We also identified 14 and 8 candidate resistance genes for bs5 and bs6, respectively, based on predicted protein coding polymorphisms between ECW and the corresponding resistant parent. Mapping of bs5 and bs6 will facilitate their use in breeding programs through marker-assisted selection and is also a crucial step towards understanding the mechanisms of resistance.Key messageTwo recessive bacterial spot resistance genes were mapped in the pepper genome, which will facilitate their advancement in commercial pepper for management of all races of Xanthomonas euvesicatoria.

For most of the 20th century

The pathogen that causes stem gall in Loropetalum chinense was first identified in Florida and Alabama in 2018 and named Pseudomonas amygdali pv. loropetali. We report the genome sequence of the pathotype strain of this pathogen, Pseudomonas amygdali pv. loropetali DSM105780 PT.

Phytophthora parasitica is a devastating plant pathogen that has a wide host range. As a new approach, silver nanoparticles (AgNPs) were assessed to control it. Previously AgNPs were shown to inhibit mycelial growth, zoospore production and germination, and germ tube elongation. However, the mechanism(s) of bioactivity of AgNPs on changes in metabolic patterns in P. parasitica has not been completely resolved. P. parasitica was exposed to AgNPs at several time points, RNA-Sequences were extracted, and then selected key genes in several of the pathways were verified for the level of expression using qRT-PCR. For RNA-Seq, the reads were mapped to the P. parasitica genome INRA 310.3. Principle component analysis illustrated low variation among biological replicates and emphasized the reproducibility of results. In this paper, seven candidate genes identified by RNA-Seq were evaluated for their expression using qRT-PCR. Interestingly, qRT-PCR confirmed that the genes that were significantly altered were found to be involved in major cellular pathways such as glutathione metabolism and ribosome biogenesis. qRT-PCR also revealed heat shock protein, ABC transporter, and Glutathione-S-Transferase (GST) genes were significantly affected. These genes are related to oxidative stress. Expression of GST and heat-shock protein significantly increased at 1 hr post-exposure to AgNPs, indicating a rapid response. The analysis based on qRT-PCR makes it evident that key genes involved in many major pathways were significantly altered on exposure to AgNPs.

Tomato is an important crop grown worldwide. Various plant diseases cause massive losses in tomato plants due to diverse biotic agents. Bacterial spot of tomato (BST) is a worldwide disease that results in high losses in processed and fresh tomato. Xanthomonas perforans, an aerobic, single-flagellated, rod-shaped, Gram-negative plant pathogenic bacterium, is one of the leading causes of BST. Over the past three decades, X. perforans has increasingly been reported from tomato-growing regions and became a major bacterial disease. X. perforans thrives under high humidity and high temperature, which is commonplace in tropical and subtropical climates. Distinguishing symptoms of BST are necrotic lesions that can coalesce and cause a shot-hole appearance. X. perforans can occasionally cause fruit symptoms depending on disease pressure during fruit development. Short-distance movement in the field is mainly dependent on wind-driven rain, whereas long distance movement occurs through contaminated seed or plant material. X. perforans harbors a suite of effectors that increase pathogen virulence, fitness, and dissemination. BST management mainly relies on copper-based compounds; however, resistance is widespread. Alternative compounds, such as nanomaterials, are currently being evaluated and show high potential for BST management. Resistance breeding remains difficult to attain due to limited resistant germplasm. While the increased genetic diversity and gain and loss of effectors in X. perforans limits the success of single-gene resistance, the adoption of effector-specific transgenes and quantitative resistance may lead to durable host resistance. However, further research that aims to more effectively implement novel management tools is required to curb disease spread. KEY POINTS: • Xanthomonas perforans causes bacterial spot on tomato epidemics through infected seedlings and movement of plant material. • Genetic diversity plays a major role in shaping populations which is evident in loss and gain of effectors. • Management relies on copper sprays, but nanoparticles are a promising alternative to reduce copper toxicity.

Before 1991, Xanthomonas euvesicatoria was the causal agent of bacterial spot of tomato in Florida but was quickly replaced by X. perforans. The X. perforans population has changed in genotype and phenotype despite lack of a clear selection pressure. To determine the current Xanthomonas population in Florida, we collected 585 Xanthomonas strains from 70 tomato fields, representing 22 farms across eight counties, in the Florida tomato production region. Strains were isolated from 23 cultivars across eight seed producers and were associated with eight transplant facilities during the fall 2017 season. Our collection was phenotypically and genotypically characterized. Only X. perforans was identified, and all strains except one (99.8%) were tolerant to copper sulfate and 25% of strains were resistant to streptomycin sulfate. Most of the strains (99.3%) that were resistant to streptomycin sulfate were sequence type 1. The X. perforans population consisted of tomato races 3 (8%) and 4 (92%) and all three previously reported sequence types, ranging from 22 to 46% frequency. Approximately half of all strains, none of which were sequence type 2, produced bacteriocins against X. euvesicatoria. Effector profiles were highly variable among strains, which could impact the strains’ host range. The effector xopJ4, which was previously thought to be conserved in X. perforans tomato pathogens, was absent in 19 strains. Nonmetric multidimensional scaling and network analyses show how strains and strain traits were associated with production system variables, including anonymized farms and transplant facilities. These analyses show that the composition of the Florida X. perforans population is diverse and complex.

Tomato transplants are the primary means of establishing commercial tomato production fields in the eastern United States. Transplants are often suspected as the source of inoculum for major outbreaks in production fields of bacterial spot of tomato (BST) caused by Xanthomonas perforans (Xp). A combination of high plant densities with overhead irrigation, high humidity, and high temperatures are conducive to BST outbreaks during transplant production. In addition to chemical control, transplant growers use roguing to remove diseased transplants, as a primary way to manage BST during transplant production. The value of roguing is often questioned, because information about the rate of pathogen spread and the incubation period between infection and symptom development is limited. In this study, we evaluated the extent of X. perforans spread on tomato transplants relative to symptom development by using a rifampicin-resistant X. perforans strain and conducting experiments in an environmentally controlled greenhouse simulating grower practices and also at a commercial transplant facility in Florida. BST symptom development typically lagged behind X. perforans dispersal by at least 5 to 7 days depending on environmental conditions. Furthermore, X. perforans was capable of aerosolization, which resulted in long-distance dispersal of ≤2 m under highly favorable conditions. Growers should rogue diseased plants and surrounding nonsymptomatic plants by >1 and ≤3 m, depending on outbreak severity, to limit disease spread. As a result, proper disease management should reduce introduction of nonsymptomatic transplants into the field and subsequently reduce pesticide applications.

International audience; Plant pathogenic bacteria are among the major challenges in crop production, amplified by their continuous and rapid evolution and resulting in the emergence of virulent, competitive, and elusive plant pathogens. To further understand these bacteria, their interactions with host plants, and their responses to disease management, comprehensive methods are necessary. In recent years, phytobacteriology research has used population and comparative studies to quantify the diversity of plant pathogenic bacteria and their virulence mechanisms, including the effectors secreted from different protein secretion systems, phytohormones, or toxins that mediate their interactions with the hosts and/or competing microbes in the phyllosphere. Studies comparing strains over time, within and among geographic regions, and across phylogenetic trees has provided insights into scales of variation and changes in pathogens over time and in response to selection pressures. In this series of articles, population and comparative genomics were used to investigate plant pathogens representing diverse bacterial genera including Gram-negative bacteria composed of facultative anaerobes (i.e., Dickeya, Pantoea, and Pectobacterium) as well as obligate aerobes (i.e., Pseudomonas, Xanthomonas, and Xylella) as well as the Gram-positive genus, Clavibacter.

Bacterial diseases are a constant threat to crop production globally. Current management strategies rely on an array of tactics, including improved cultural practices; application of bactericides, plant activators, and biocontrol agents; and use of resistant varieties when available. However, effective management remains a challenge, as the longevity of deployed tactics is threatened by constantly changing bacterial populations. Increased scrutiny of the impact of pesticides on human and environmental health underscores the need for alternative solutions that are durable, sustainable, accessible to farmers, and environmentally friendly. In this review, we discuss the strengths and shortcomings of existing practices and dissect recent advances that may shape the future of bacterial disease management. We conclude that disease resistance through genome modification may be the most effective arsenal against bacterial diseases. Nonetheless, more research is necessary for developing novel bacterial disease management tactics to meet the food demand of a growing global population.

The National Plant Diagnostic Network (NPDN), comprising diagnostic professionals from more than 70 pathology, entomology, and nematology laboratories, safeguards U.S. plant systems through accurate diagnosis and effective communications with clients, partners, and stakeholders. As a USDA-NIFA extension program built on the land-grant university system, the network has dual responsibilities to extension clientele such as farmers and the green industry, as well as state and federal regulatory agencies. Following strategic planning in 2019, the network emerged with a concise plan and strong committees of network participants to enhance and sustain service to NPDN clientele and partners, even through significant disruptions like the 2020 coronavirus pandemic. The commitment to building diagnostic capacity and expertise across the country allows these plant clinics to assist during a response to detections of high-consequence plant pathogens by clearing healthy plants for commerce while identifying potential positives for regulators to quarantine and/or eradicate, similar to the test and trace efforts for human diseases such as COVID-19. In this review, we describe the network’s recent activities to protect U.S. plant agriculture and natural ecosystems and its plans to improve and expand capacity for national plant biosecurity.

The deferred antagonism technique has been utilized for several decades for detecting antibiosis activity. Most protocols require the elimination of antibiotic-producing cells by exposing them to chloroform vapour, UV radiation or filter sterilizing the filtrate steps that require additional time and expense to complete. We provide a modified approach to current soft agar overlay practices, which involves addition of antibiotics to the soft agar overlay to inhibit growth of the producer but not the indicator strain. This technique can be used to reproducibly and efficiently screen for antibiotic production with ease. We demonstrate the effectiveness of this technique with three bacterial systems: inhibition of the bacterial spot of tomato pathogen, Xanthomonas euvesicatoria, by its pathogenic competitor Xanthomonas perforans; and inhibition of the fire blight pathogen, Erwinia amylovora, by Pantoea vagans C9-1 or Pseudomonas fluorescens A506. Significance and Impact of the Study Deferred antagonism assays are used commonly to observe antibiotic production by micro-organisms. Killing or removing the producer cells prior to introduction of the indicator strain is a standard practice but requires additional time and special handling procedures. We evaluated a modification of the assay, where the overlay medium is amended with an antibiotic to which the indicator strain is resistant and the producer strain is sensitive. This modification obviates extra steps to kill the producer strain prior to overlaying with the indicator strain and provides a rapid, consistent and cost-effective method to detect antibiosis.

We present an amended description of the bacterial species Xanthomonas vasicola to include the causative agent of banana Xanthomonas wilt, as well as strains that cause disease on Areca palm, Tripsacum grass, sugarcane, and maize. Genome-sequence data reveal that these strains all share more than 98% average nucleotide with each other and with the type strain. Our analyses and proposals should help to resolve the taxonomic confusion that surrounds some of these pathogens and help to prevent future use of invalid names. [Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .

This review summarizes the current status of citrus canker in the United States. The disease is present in Florida, Louisiana, and Texas. In Florida, the eradication program ended in 2006 and now citrus canker is endemic to many citrus-growing areas, although it is still possible to find canker-free groves. In endemic areas, the disease is controlled using windbreaks, applying copper-based bactericides, controlling the citrus leafminer, and applying systemic plant activators. In Louisiana, citrus canker was identified in 2013, the first time since the 1940s, and has since been identified in 10 of the parishes where plant material and fruit are not allowed to leave the quarantine areas. There are no eradication efforts in Louisiana and removal of trees is voluntary. Finally, citrus canker resurfaced in Texas in 2015 and has been detected in several locations. Currently only the type AW strain is present in Texas and quarantine efforts are being taken to mitigate the risk of introduction of the type A strain into the state.

Xanthomonas spp. encompass a wide range of plant pathogens that use numerous virulence factors for pathogenicity and fitness in plant hosts. In this Review, we examine recent insights into host-pathogen co-evolution, diversity in Xanthomonas populations and host specificity of Xanthomonas spp. that have substantially improved our fundamental understanding of pathogen biology. We emphasize the virulence factors in xanthomonads, such as type III secreted effectors including transcription activator-like effectors, type II secretion systems, diversity resulting in host specificity, evolution of emerging strains, activation of susceptibility genes and strategies of host evasion. We summarize the genomic diversity in several Xanthomonas spp. and implications for disease outbreaks, management strategies and breeding for disease resistance.

Since citrus canker was first described in the early 1900’s, four major types and three species of pathogenic xanthomonads associated to citrus were identified based on the characteristic symptoms and host range. Type A, caused by X. citri subsp. citri, develops typical raised cankered lesions and is pathogenic on most commercial citrus species and cultivars. Types B and C are caused by X. citri pv. aurantifolii which elicits canker lesions. Besides the typical type A, the more aggressive and most widely spread type, other subtypes have been described, such as type A*, type Aw, type A-Manatee, type A-Miami, type A-minus pthA, and type-A etrog. The type B strains are found only in Argentina and are more pathogenic on lemon and less aggressive on sweet orange, tangerines and grapefruit. The type C strains are found only in Brazil and are pathogenic only on Key lime. X. alfalfae subsp. citrumelonis, formerly known as type E, causes citrus bacterial spot and is more aggressive on trifoliate citrus and its hybrids. Lesions caused by citrus bacterial spot are flat or sunken and not raised. Several subtypes of X. citri subsp. citri have also been identified. Besides the differences in pathogenicity, xanthomonads may also vary in their sensitivity to copper. Copper resistance has been reported for strains of X. citri subsp. citri and X. alfalfae subsp. citrumelonis and is conferred by the gene clusters copLAB or copABCD. Resistance to copper has serious implications for the use of copper-based bactericides, which are the most important chemicals for the control of diseases caused by Xanthomonas on citrus.

Changes in Xanthomonas race and species composition causing bacterial spot of tomato have occurred throughout the world and are often associated with epidemics. Knowledge of bacterial population structure is key for resistance discovery and deployment. We surveyed Xanthomonas spp. composition from processing tomato fields in the Midwestern United States over a 4-year period between 2017 and 2020, compared these to strains collected previously, and found that X. perforans is currently the most prevalent species. We characterized 564 X. perforans isolates for sequence variation in avrXv3 to distinguish between race T3 and T4 and validated race designation using hypersensitive response (HR) assays for 106 isolates. Race T4 accounted for over 95% of X. perforans isolates collected in the Midwest between 2017 and 2020. Whole genome sequencing, Average Nucleotide Identity (ANI) analysis, core genome alignment and single nucleotide polymorphism (SNP) detection relative to a reference strain, and phylogenomic analysis suggest that the majority of Midwestern X. perforans strains collected between 2017 and 2020 were nearly identical, with greater than 99.99% ANI to X. perforans isolates collected from Collier County, Florida in 2012. These isolates shared a common SNP variant resulting an a premature stop codon in avrXv3. One sequenced isolate was identified with a deletion of avrXv3 and shared 99.99% ANI with a strain collected in Collier Co., Florida in 2006. A population shift to X. perforans T4 occurred in the absence of widely deployed resistance, with only 7% of tomato varieties tested having the resistant allele at the Xv3/Rx-4 locus. The persistence of nearly identical strains over multiple years suggests that migration led to the establishment of an endemic population. Our findings validate a genomics-based framework to track shifts in X. perforans populations due to migration, mutation, drift, or selection based on comparisons to 146 genomes.

Bacterial spot of tomato is among the most economically relevant diseases affecting tomato plants globally. In previous studies, non-formulated magnesium oxide nanoparticles (nano-MgOs) significantly reduced the disease severity in greenhouse and field conditions. However, the aggregation of nano-MgO in liquid suspension makes it challenging to use in field applications. Therefore, we formulated two novel MgO nanomaterials (SgMg #3 and SgMg #2.5) and one MgOH2 nanomaterial (SgMc) and evaluated their physical characteristics, antibacterial properties, and disease reduction abilities. Among the three Mg nanomaterials, SgMc showed the highest efficacy against copper-tolerant strains of Xanthomonas perforans in vitro, and provided disease reduction in the greenhouse experiments compared with commercial Cu bactericide and an untreated control. However, SgMc was not consistently effective in field conditions. To determine the cause of its inconsistent efficacy in different environments, we monitored particle size, zeta potential, morphology, and crystallinity for all three formulated materials and nano-MgOs. The MgO particle size was determined by the scanning electron microscopy (SEM) and dynamic light scattering (DLS) techniques. An X-ray diffraction (XRD) study confirmed a change in the crystallinity of MgO from a periclase to an Mg(OH)2 brucite crystal structure. As a result, the bactericidal activity correlated with the high crystallinity present in nano-MgOs and SgMc, while the inconsistent antimicrobial potency of SgMg #3 and SgMg #2.5 might have been related to loss of crystallinity. Future studies are needed to determine which specific variables impair the performance of these nanomaterials in the field compared to under greenhouse conditions. Although SgMc did not lead to significant disease severity reduction in the field, it still has the potential to act as an alternative to Cu against bacterial spot disease in tomato transplant production.

Bacterial spot disease was first reported from South Africa by Ethel M. Doidge in 1920. In the ensuing century after the initial discovery, the pathogen has gained global attention in plant pathology research, providing insights into host–pathogen interactions, pathogen evolution, and effector discovery, such as the first discovery of transcription activation-like effectors, among many others. Four distinct genetic groups, includingXanthomonas euvesicatoria(proposed name:X. euvesicatoriapv.euvesicatoria),Xanthomonas perforans(proposed name:X. euvesicatoriapv.perforans),Xanthomonas gardneri(proposed name:Xanthomonas hortorumpv.gardneri), andXanthomonas vesicatoria, are known to cause bacterial spot disease. Recently, a new race of a bacterial spot pathogen, race T5, which is a product of recombination between at least twoXanthomonasspecies, was reported in Nigeria. In this review, our focus is on the progress made on the African continent,vis-à-visprogress made in the global bacterial spot research community to provide a body of information useful for researchers in understanding the diversity, evolutionary changes, and management of the disease in Africa.

Contains minor updates to the 2009 revision, Previous version:Zhang, Shouan, Aaron J. Palmateer, Ken Pernezny, and Jeffrey B. Jones. 2009. “Common Bacterial Blight of Snap Bean in Florida”. EDIS 2009 (2). https://journals.flvc.org/edis/article/view/117842.

Microbes are natural chemical factories and their metabolome comprise diverse arrays of chemicals. The genus Xanthomonas comprises some of the most important plant pathogens causing devastating yield losses globally and previous studies suggested that species in the genus are untapped chemical minefields. In this study, we applied an untargeted metabolomics approach to study the metabolome of a globally spread important xanthomonad, X. perforans. The pathogen is difficult to manage, but recent studies suggest that the small molecule carvacrol was efficient in disease control. Bacterial strains were treated with carvacrol, and samples were taken at time intervals (1 and 6 h). An untreated control was also included. There were five replicates for each sample and samples were prepared for metabolomics profiling using the standard procedure. Metabolomics profiling was carried out using a thermo Q-Exactive orbitrap mass spectrometer with Dionex ultra high-performance liquid chromatography (UHPLC) and an autosampler. Annotation of significant metabolites using the Metabolomics Standards Initiative level 2 identified an array of novel metabolites that were previously not reported in Xanthomonas perforans. These metabolites include methoxybrassinin and cyclobrassinone, which are known metabolites of brassicas; sarmentosin, a metabolite of the Passiflora-heliconiine butterfly system; and monatin, a naturally occurring sweetener found in Sclerochiton ilicifolius. To our knowledge, this is the first report of these metabolites in a microbial system. Other significant metabolites previously identified in non-Xanthomonas systems but reported in this study include maculosin; piperidine; β-carboline alkaloids, such as harman and derivatives; and several important medically relevant metabolites, such as valsartan, metharbital, pirbuterol, and ozagrel. This finding is consistent with convergent evolution found in reported biological systems. Analyses of the effect of carvacrol in time-series and associated pathways suggest that carvacrol has a global effect on the metabolome of X. perforans, showing marked changes in metabolites that are critical in energy biosynthesis and degradation pathways, amino acid pathways, nucleic acid pathways, as well as the newly identified metabolites whose pathways are unknown. This study provides the first insight into the X. perforans metabolome and additionally lays a metabolomics-guided foundation for characterization of novel metabolites and pathways in xanthomonad systems.

Crop yield loss due to bacterial plant pathogens need to be reduced to increase global food production demand. Currently available disease management strategies involving copper-based bactericides and antibiotics are losing efficacy due to development of resistance in bacteria. There is long familiar demand of environmentally friendly and sustainable strategies to control bacterial diseases. Bacteriophages are virus that kill target bacteria without affecting another microorganism and environment. Bacteriophage efficiency on phyllosphere is mainly affected by ultraviolet (UV) light. Use of combination of phage, mixture with phage carrier bacteria and optimizing time of application helps in persistence of bacteriophage. There are several bacteriophage products already available in the market to control destructive bacterial diseases. Unlike chemical based traditional control measure, bacteriophage mixture can be easily amended to reduce resistance development in bacteria. In this chapter, the authors discuss from phage isolation to interaction with bacteria and control mechanism of plant diseases.

Blueberry (Vaccinium spp.) plants are exposed to existing and emerging viruses as a result of expanding acreage of blueberry plantations across the world, primarily in North America. Since blueberry is cultivated in areas where there are wild Vaccinium spp., there is increasing risk of virus movement between wild and cultivated blueberries. This is theoretically possible because viruses can spread from commercial cultivars to native species and vice versa causing the spread of existing and new viruses. The occurrence of these viruses in blueberry can be devastating to the industry considering the cost for cultivation and production of this perennial crop. However, the advent of high-throughput sequencing and bioinformatic sequence analysis have allowed for rapid identification of known and novel viruses in any crop including blueberry, thus facilitating proper intervention in response to serious viral diseases. In this paper, we aim to focus on the current status of known and novel viruses emerging in blueberry worldwide, which may impact the blueberry industry.

Citrus canker (CC), caused by the bacterial pathogen Xanthomonas citri subsp. citri, impacts citrus production in many areas of the world by reducing yields, degrading tree health, and severely blemishing the outer peels of fresh fruit. The relative susceptibility to CC among different species of Citrus varies from the highly susceptible lime (Citrus × aurantifolia), sweet orange (C. × sinensis), and grapefruit (C. × paradisi) to the much less susceptible calamondin (C. × microcarpa) and kumquat (C. japonica). This investigation compares the responses to infection with X. citri subsp. citri of these five genotypes with respect to phenylpropanoid compound profiles and relative increases or decreases of specific compounds postinoculation. In response to X. citri subsp. citri infection, all hosts possessed increased concentrations of phenylpropanoids in leaf tissue, whereas the similarly treated nonhost orange jessamine (Murraya paniculata) did not. Several of the tested genotypes exhibited notably increased production of fluorescent phenylpropanoids, including umbelliferone, herniarin, auraptene, scoparone, and others. The profiles of these compounds and their levels of production varied among the tested species yet all investigated Citrus genotypes exhibited increased concentrations of phenylpropanoids regardless of their degree of susceptibility to X. citri subsp. citri. Kumquat and calamondin, the tested genotypes least susceptible to X. citri subsp. citri, also exhibited the highest levels of the dihydrochalcone 3′,5′-di-C-glucosyl phloretin, the aglycone portion of which, phloretin, is a known antibiotic, although levels of this compound were not affected by inoculation with X. citri subsp. citri.

The relative susceptibility of six Rutaceae family genotypes to bacterial citrus canker (CC) caused by Xanthomonas citri subsp. citri (Xcc) was assessed by measuring and comparing in planta bacterial populations over time following inoculation using a minimally destructive inoculation. These genotypes included lime (Citrus aurantifolia), grapefruit (C. paradisi), sweet orange (C. sinensis), calamondin (C. reticulata X C. japonica), kumquat (C. japonica), and orange jessamine (Murraya paniculata). Internal Xcc populations in orange jessamine plateaued early and remained significantly lower than other genotypes. Xcc populations increased rapidly in all other genotypes, decreasing precipitously and significantly over time in kumquat and calamondin as compared to the more susceptible genotypes sweet orange, grapefruit, and lime. Xcc populations in calamondin peaked by 7 DPI then began to fall significantly relative to the more susceptible genotypes sweet orange, grapefruit, and lime. Given the steep decline in populations in calamondin and kumquat, we compared water-soluble extracts from healthy leaf tissue from all previously investigated Citrus genotypes to determine if the extracts had any inhibitory effect on Xcc, implicating them in this abrupt population decline late in the infection process. Only extracts from calamondin leaf tissue significantly inhibited Xcc growth within 24 h. Potentially, constitutively produced inhibitory compounds in calamondin may result in less severe CC symptoms as a result of the rapid decline in Xcc populations.