Xanthomonas as a model system for studying pathogen emergence and evolution

In this review, we highlight studies where whole genome sequencing, comparative genomics and population genomics have provided unprecedented insights into past and ongoing pathogen evolution. These include new understanding of adaptive evolution of secretion systems and their effectors. We focus on Xanthomonas pathosystems that have seen intensive study and improved our understanding of pathogen emergence and evolution, particularly in the context of host specialization: citrus canker, bacterial blight of rice, and bacterial spot of tomato and pepper. Across pathosystems, pathogens appear to follow a pattern of bursts of evolution and diversification that impact host adaptation. There remains a need for studies on the mechanisms of host range evolution and genetic exchange among closely related but differentially host-specialized species, and to start moving beyond the study of specific strain and host cultivar pairwise interactions to thinking about these pathosystems in a community context.

Effect of Cucurbit Host, Production Region, and Season on the Population Structure of Pseudoperonospora cubensis in Florida

Pseudoperonospora cubensis, the causal agent of Cucurbit downy mildew (CDM), is one of the most important diseases affecting cucurbit production in the United States. This disease is especially damaging to Florida production areas, as the state is a top producer of many cucurbit species. In addition, winter production in central and south Florida likely serves as a likely source of P. cubensis inoculum for spring and summer cucurbit production throughout the eastern United States, where CDM is unable to overwinter in the absence of a living host. Over 2 years (2017 and 2018) and four seasons (spring 2017, spring 2018, fall 2017, and fall 2018), 274 P. cubensis isolates were collected from cucurbit hosts at production sites in south, central, and north Florida. The isolates were analyzed with 10 simple sequence repeat (SSR) markers to establish population structure and genetic diversity and further assigned to a clade based on a qPCR assay. Results of population structure and genetic diversity analyses differentiated isolates based on cucurbit host and clade (1 or 2). Of the isolates assigned to clade by qPCR, butternut squash, watermelon, and zucchini were dominated by clade 1 isolates, whereas cucumber isolates were split 34 and 59% between clades 1 and 2, respectively. Clade assignments agreed with isolate clustering observed within discriminant analysis of principal components (DAPC) based on SSR markers, although watermelon isolates formed a group distinct from the other clade 1 isolates. For seasonal collections from cucumber at each location, isolates were typically skewed to one clade or the other and varied across locations and seasons within each year of the study. This variable population structure of cucumber isolates could have consequences for regional disease management. This is the first study to characterize P. cubensis populations in Florida and evaluate the effect of cucurbit host and clade-type on isolate diversity and population structure, with implications for CDM management in Florida and other United States cucurbit production areas.

Bacterial Mutation During Seasonal Epidemics

Rapidly evolving bacterial pathogens pose a unique challenge for long-term plant disease management. In this study, we investigated the types and rate of mutations in bacterial populations during seasonal disease epidemics. Two phylogenetically distinct strains of the bacterial spot pathogen, Xanthomonas perforans, were marked, released in tomato fields, and recaptured at several time points during the growing season. Genomic variations in recaptured isolates were identified by comparative analysis of their whole-genome sequences. In total, 180 unique variations (116 substitutions, 57 insertions/deletions, and 7 structural variations) were identified from 300 genomes, resulting in the overall host-associated mutation rate of ∼0.3 to 0.9/genome/week. This result serves as a benchmark for bacterial mutation during epidemics in similar pathosystems. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Genome sequencing and de novo assembly of Trichoderma longibrachiatum isolate collected from Florida agricultural soils

We report a draft genome assembly of Trichoderma longibrachiatum isolate GEV 3550, obtained from Florida, United States of America.

Whole-Genome-Sequence-Based Classification of Xanthomonas euvesicatoria pv. eucalypti and Computational Analysis of the Type III Secretion System

Xanthomonas spp. infect a wide range of annual and perennial plants. Bacterial blight in young seedlings of Eucalyptus spp. in Indonesia was originally identified as X. perforans. However, these strains failed to elicit a hypersensitive response (HR) on either tomatoes or peppers. Two of the strains, EPK43 and BCC 972, when infiltrated into tomato and pepper leaves, failed to grow to significant levels in comparison with well-characterized X. euvesicatoria pv. perforans (Xp) strains. Furthermore, spray inoculation of 'Bonny Best' tomato plants with a bacterial suspension of the Eucalyptus strains resulted in no obvious symptoms. We sequenced the whole genomes of eight strains isolated from two Eucalyptus species between 2007 and 2015. The strains had average nucleotide identities (ANIs) of at least 97.8 with Xp and X. euvesicatoria pv. euvesicatoria (Xeu) strains, both of which are causal agents of bacterial spot of tomatoes and peppers. A comparison of the Eucalyptus strains revealed that the ANI values were >99.99% with each other. Core genome phylogeny clustered all Eucalyptus strains with X. euvesicatoria pv. rosa. They formed separate clades, which included X. euvesicatoria pv. alangii, X. euvesicatoria pv. citrumelonis, and X. euvesicatoria pv. alfalfae. Based on ANI, phylogenetic relationships, and pathogenicity, we designated these Eucalyptus strains as X. euvesicatoria pv. eucalypti (Xee). Comparative analysis of sequenced strains provided unique profiles of type III secretion effectors. Core effector XopD, present in all pathogenic Xp and Xeu strains, was absent in the Xee strains. Comparison of the hrp clusters of Xee, Xp, and Xeu genomes revealed that HrpE in Xee strains was very different from that in Xp and Xeu. To determine if it was functional, we deleted the gene and complemented with the Xee hrpE, confirming it was essential for secretion of type III effectors. HrpE has a hypervariable N-terminus in Xanthomonas spp., in which the N-terminus of Xee strains differs significantly from those of Xeu and Xp strains.

Effective Management of Powdery Mildew in Cantaloupe Plants Using Nighttime Applications of UV Light

Ultraviolet light at wavelengths from 254 to 283 nm/has been reported to effectively suppress powdery mildews in several crops, including some cucurbits. Its use to suppress powdery mildew (Podosphaera xanthii) specifically in cantaloupe has not been previously reported. We evaluated the foregoing technology in cantaloupe fields for suppression of powdery mildew and possible effects on plant growth and yield. In a controlled laboratory study, greenhouse-grown cantaloupe plants were exposed to a gradient of UV-C (254 nm) doses during darkness, and the effects upon powdery mildew development and the plant were evaluated. We also evaluated the efficacy of nighttime applications of UV-C at 100 and 200 J/m2 against powdery mildew on adaxial leaf surfaces in greenhouse, high-tunnel, and open-field plantings. UV-C at the foregoing doses reduced sporulation and germination of P. xanthii conidia without damaging plants. On cantaloupe seedlings in the greenhouse, disease severity was equivalently suppressed at all doses and frequencies of applications of the light. In high-tunnel and open-field experiments, the most effective control of powdery mildew was provided by UV-C applied at 200 J/m2 twice every week, where suppression provided by UV-C was generally equal to and sometimes better than the fungicide treatment. The foregoing UV-C dose and frequency of application also provided the highest yield under field conditions, indicating that UV-C treatment is a promising technology for commercially relevant suppression of powdery mildew on cantaloupe in a variety of growing systems.

Potential of Novel Magnesium Nanomaterials to Manage Bacterial Spot Disease of Tomato in Greenhouse and Field Conditions

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.

Strength in Numbers: Density-Dependent Volatile-Induced Antimicrobial Activity by Xanthomonas perforans

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.

Future of Bacterial Disease Management in Crop Production

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.

Duration of Downy Mildew Control Achieved with Fungicides on Cucumber Under Florida Field Conditions

Cucurbit production in Florida is impacted by downy mildew on a yearly basis. Cucurbit downy mildew (CDM), caused by Pseudoperonospora cubensis, is one of the most devastating cucurbit diseases and can lead to complete yield loss. Nearly continuous production of cucurbits occurs temporally throughout Florida, which puts extensive pressure on the pathogen population to select for individuals that are resistant to fungicides in use labeled for CDM. Loss of efficacy as a result of fungicide resistance developing is becoming a major concern for Florida cucurbit growers who rely on these products to manage CDM. This study was established to evaluate the field activity of 11 utilized fungicides by determining their duration of activity when applied at various intervals for the management of CDM in cucumber under Florida field conditions. By comparing levels of percent CDM control and area under the disease progress curve values, the fungicide's duration of field activity was established. Field activities were <1 week for dimethomorph and fluopicolide; 1 week for cymoxanil; 1 to 2 weeks for chlorothalonil and mancozeb; 2 weeks for ethaboxam; 1 to 3 weeks for propamocarb, cyazofamid, and ametoctradin + dimethomorph; and 2 to 4 weeks for oxathiapiprolin and fluazinam. Knowledge of duration of field activity can potentially improve the development of CDM management programs and slow the resistance selection.

Identification of Genes in Xanthomonas euvesicatoria pv. rosa That Are Host Limiting in Tomato

Xanthomonas euvesicatoria pv. rosa strain Xer07 causes a leaf spot on a Rosa sp. and is closely related to X. euvesicatoria pv. euvesicatoria (Xee) and X. perforans (Xp), causal agents of bacterial spot of tomato. However, Xer07 is not pathogenic on tomato and elicits a hypersensitive reaction (HR). We compared the genomes of the three bacterial species to identify the factors that limit Xer07 on tomato. Comparison of pathogenicity associated factors including the type III secretion systems identified two genes, xopA and xer3856, in Xer07 that have lower sequence homology in tomato pathogens. xer3856 is a homolog of genes in X. citri (xac3856) and X. fuscans pv. aurantifolii, both of which have been reported to elicit HRs in tomato. When xer3856 was expressed in X. perforans and infiltrated in tomato leaflets, the transconjugant elicited an HR and significantly reduced bacterial populations compared to the wildtype X. perforans strain. When xer3856 was mutated in Xer07, the mutant strain still triggered an HR in tomato leaflets. The second gene identified codes for type III secreted effector XopA, which contains a harpin domain that is distinct from the xopA homologs in Xee and Xp. The Xer07-xopA, when expressed in X. perforans, did not elicit an HR in tomato leaflets, but significantly reduced bacterial populations. This indicates that xopA and xer3856 genes in combination with an additional factor(s) limit Xer07 in tomato.

Whole genome sequences reveal the Xanthomonas perforans population is shaped by the tomato production system

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.

Supplemental Fumigant Placement Improves Root Knot and Fusarium Wilt Management for Tomatoes Produced on a Raised-Bed Plasticulture System in Florida's Myakka Fine Sand

Fresh-market tomatoes are produced on a raised-bed plasticulture system that relies heavily on soil-applied preplant fumigants for the management of soilborne pathogens, nematodes, and weeds. Since the transition from methyl bromide to alternative fumigants, growers have experienced a resurgence of several soilborne pests and pathogens, including root-knot nematode caused by Meloidogyne spp. and Fusarium wilt caused by Fusarium oxysporum f. sp. lycopersici race 3. This resurgence is attributed to the inability of the alternative fumigants to effectively disperse through the soil in the same manner as methyl bromide. Two supplemental fumigation strategies, the application of chloropicrin (PIC) below bed edges (herein "supplemental PIC") and broadcast deep-shank applications of 1,3-dichloropropene (1,3-D), were evaluated in conjunction with standard raised-bed applications of Pic-Clor 60, Pic-Clor 80, and Pic 100 covered with a virtually impermeable film or a totally impermeable film. Large-plot replicated studies were conducted in two separate commercial tomato fields with a history of production losses caused by root-knot nematode and Fusarium wilt. Deep-shank 1,3-D applications significantly reduced the recovery of root-knot and total parasitic nematodes across field sites before the preparation of raised beds. Both supplemental PIC and deep-shank 1,3-D reduced root-knot galling and Fusarium wilt incidence, but the latter supplemental treatment statistically had the greatest impact. Fumigant applied within raised beds or plastic film had no significant effect on root-knot galling or Fusarium wilt. Although both supplemental fumigation strategies had a significant effect on pest and disease pressure, neither statistically improved tomato yields based on small subplot harvests. Controlled laboratory experiments confirmed the fungicidal activity of 1,3-D against F. oxysporum f. sp. lycopersici, with 75, 90, 95, and 99% lethal doses corresponding to estimated field application rates of 56.1, 93.5, 121.6, and 184.7 liters/ha, respectively. The results demonstrate how fumigant placement can improve pest and disease control activity with current fumigant alternatives to methyl bromide and further support the broader pesticidal activity of some chemical fumigants.

A centenary for bacterial spot of tomato and pepper

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.

Magnesium Oxide Nanomaterial, an Alternative for Commercial Copper Bactericides: Field-Scale Tomato Bacterial Spot Disease Management and Total and Bioavailable Metal Accumulation in Soil

Copper (Cu) is the most extensively used bactericide worldwide in many agricultural production systems. However, intensive application of Cu bactericide have increased the selection pressure toward Cu-tolerant pathogens, including Xanthomonas perforans, the causal agent of tomato bacterial spot. However, alternatives for Cu bactericides are limited and have many drawbacks including plant damage and inconsistent effectiveness under field conditions. Also, potential ecological risk on nontarget organisms exposed to field runoff containing Cu is high. However, due to lack of alternatives for Cu, it is still widely used in tomato and other crops around the world in both conventional and organic production systems. In this study, a Cu-tolerant X. perforans strain GEV485, which can tolerate eight tested commercial Cu bactericides, was used in all the field trials to evaluate the efficacy of MgO nanomaterial. Four field experiments were conducted to evaluate the impact of intensive application of MgO nanomaterial on tomato bacterial spot disease severity, and one field experiment was conducted to study the impact of soil accumulation of total and bioavailable Cu, Mg, Mn, and Zn. In the first two field experiments, twice-weekly applications of 200 μg/mL MgO significantly reduced disease severity by 29-38% less in comparison to a conventional Cu bactericide Kocide 3000 and 19-30% less in comparison to the water control applied at the same frequency (p = 0.05). The disease severity on MgO twice-weekly was 12-32% less than Kocide 3000 + Mancozeb treatment. Single weekly applications of MgO had 13-19% higher disease severity than twice weekly application of MgO. In the second set of two field trials, twice-weekly applications of MgO at 1000 μg/mL significantly reduced disease severity by 32-40% in comparison to water control applied at the same frequency (p = 0.05). There was no negative yield impact in any of the trials. The third field experiment demonstrated that application of MgO did not result in significant accumulation of total and bioavailable Mg, Mn, Cu, or Zn in the root-associated soil and in soil farther away from the production bed compared to the water control. However, Cu bactericide contributed to significantly higher Mn, Cu, and Zn accumulation in the soil compared to water control (p = 0.05). This study demonstrates that MgO nanomaterial could be an alternative for Cu bactericide and have potential in reducing risks associated with development of tolerant strains and for reducing Cu load in the environment.

Need for speed: bacterial effector XopJ2 is associated with increased dispersal velocity of Xanthomonas perforans

Bacterial spot caused by Xanthomonas perforans (Xp) is an economically important disease in tomato. Previous studies have shown that the recently isolated Xp strains have acquired and retained the effector gene, xopJ2, which has been reported to increase fitness of the pathogen in the field. To elucidate the fitness benefit of xopJ2, we quantified the effect of xopJ2 on the dispersal and evolution of Xp populations on tomato. We compared movement of two wild-type Xp strains expressing xopJ2 to their respective xopJ2 mutants when co-inoculated in the field. We developed a binary logistic model to predict the presence of Xp over spatial and temporal dimensions with or without xopJ2. Based on the model, wild-type bacteria were dispersed approximately three times faster than the xopJ2 mutants. In a simulation experiment, the selective advantage due to increased dispersal velocity led to an increase in the frequency of xopJ2 gene in the Xp population and its apparent fixation within 10 to 12 cropping seasons of the tomato crop. Our results show that the presence of a single gene can affect the dispersal of a bacterial pathogen and significantly alter its population dynamics.

Epidemiology, diversity, and management of bacterial spot of tomato caused by Xanthomonas perforans

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.

Characterization and elimination of linkage-drag associated with Fusarium wilt race 3 resistance genes

Reducing the size of the I-3 introgression resulted in eliminating linkage-drag contributing to increased sensitivity to bacterial spot and reduced fruit size. The I-7 gene was determined to have no effect on bacterial spot or fruit size, and germplasm is now available with both the reduced I-3 introgression and I-7. Tomato (Solanum lycopersicum) production is increasingly threatened by Fusarium wilt race 3 (Fol3) caused by the soilborne fungus, Fusarium oxysporum f. sp. lycopersici. Although host resistance based on the I-3 gene is the most effective management strategy, I-3 is associated with detrimental traits including reduced fruit size and increased bacterial spot sensitivity. Previous research demonstrated the association with bacterial spot is not due to the I-3 gene, itself, and we hypothesize that reducing the size of the I-3 introgression will remedy this association. Cultivars with I-7, an additional Fol3 resistance gene, are available but are not widely used commercially, and it is unclear whether I-7 also has negative horticultural associations. To characterize the effect of I-3 on fruit size, segregating populations were developed and evaluated, revealing that the large I-3 introgression decreased fruit size by approximately 21%. We reduced the I-3 introgression from 5 to 140 kb through successive recombinant screening and crossing efforts. The reduced I-3 introgression and I-7 were then separately backcrossed into elite Florida breeding lines and evaluated for effects on bacterial spot sensitivity and fruit size across multiple seasons. The reduced I-3 introgression resulted in significantly less bacterial spot and larger fruit size than the large introgression, and it had no effect on these horticultural characteristics compared with Fol3 susceptibility. I-7 was also found to have no effect on these traits compared to Fol3 susceptibility. Together, these efforts support the development of superior Fol3-resistant cultivars and more durable resistance against this pathogen.

Phylogenomic Analysis of a 55.1-kb 19-Gene Dataset Resolves a Monophyletic Fusarium that Includes the Fusarium solani Species Complex

Scientific communication is facilitated by a data-driven, scientifically sound taxonomy that considers the end-user's needs and established successful practice. In 2013, the Fusarium community voiced near unanimous support for a concept of Fusarium that represented a clade comprising all agriculturally and clinically important Fusarium species, including the F. solani species complex (FSSC). Subsequently, this concept was challenged in 2015 by one research group who proposed dividing the genus Fusarium into seven genera, including the FSSC described as members of the genus Neocosmospora, with subsequent justification in 2018 based on claims that the 2013 concept of Fusarium is polyphyletic. Here, we test this claim and provide a phylogeny based on exonic nucleotide sequences of 19 orthologous protein-coding genes that strongly support the monophyly of Fusarium including the FSSC. We reassert the practical and scientific argument in support of a genus Fusarium that includes the FSSC and several other basal lineages, consistent with the longstanding use of this name among plant pathologists, medical mycologists, quarantine officials, regulatory agencies, students, and researchers with a stake in its taxonomy. In recognition of this monophyly, 40 species described as genus Neocosmospora were recombined in genus Fusarium, and nine others were renamed Fusarium. Here the global Fusarium community voices strong support for the inclusion of the FSSC in Fusarium, as it remains the best scientific, nomenclatural, and practical taxonomic option available.

Assessing Changes and Associations in the Xanthomonas perforans Population Across Florida Commercial Tomato Fields Via a Statewide Survey

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.

Dynamics and Spread of Bacterial Spot Epidemics in Tomato Transplants Grown for Field Production

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.

First Report of Neopestalotiopsis rosae causing foliar and fruit spots on pomegranate in Florida

Foliar and fruit spots were observed on pomegranate trees (Punica granatum L.) planted in orchards located at Balm and Zolfo Springs, FL, in 2019. Symptoms on leaves and fruits included dark brown to black irregular spots, ranging from 0.2 to 1.5 cm, with gray centers. Visible pycnidia were present in the center of the lesions. Leaves became chlorotic and prematurely dropped from the trees. In a disease survey performed on 24 pomegranate cultivars, all of the trees were infected and the disease severity ranged from 2 to 80%. The cultivars Bhagwa and Mridula were the most susceptible. Symptoms on the fruit were similar to those on the leaves; however incidence on the fruits was less than one percent. To isolate the pathogen, small pieces (5 mm2) of symptomatic leaves and fruits were excised from the area between diseased and healthy tissue. Excised tissue pieces were surface disinfested in 70% ethanol solution for 30 seconds, followed by 10% sodium hypochlorite (NaOCl) solution for 2 minutes, rinsed in sterilized distilled water three times, dried on a paper towel, placed onto potato dextrose agar and incubated at 25°C under 12-hour photoperiod for seven days. Fungal cultures formed white cottony aerial mycelium with undulated edges and abundant black pycnidia. Four-septate conidia were fusiform or clavate, straight or slightly curved measuring on average 29.1 (23.3- 34.4) µm long × 6.3 (5.1- 6.8) µm wide (n = 100). Conidia had three median cells which were dark brown, with a single basal hyaline appendage, 5.9 (4.1- 7.7) µm long, and two or four (usually three) apical hyaline appendages 20.3 (14.8- 24.5) µm long. Morphological features were consistent with those of the genus Neopestalotiopsis (Maharachchikumbura et al., 2014). Single-spore cultures were obtained and genomic DNA was extracted from seven isolates (one from fruit, GEV3523, and six from leaf, GEV3426 - GEV3431). Internal transcribed spacer (ITS) region, partial sequences of elongation factor (TEF), and β-tubulin (TUB2) were amplified with the respective primer pairs ITS4 and ITS5, EF1-1567 and EF1-536, and Bt-2a and Bt-2b (Maharachchikumbura et al., 2014). BLAST analysis of the fruit isolate, GEV3523, showed homology of 100% for ITS, 100% for TEF and 99.8% for TUB2 to fungal pathogen Neopestalotiopsis rosae isolate CBS 101057 obtained from a rose plant in New Zealand (Accession Nos. MT587806, MT605118 and MT597152, respectively), whereas the six leaf isolates were 100% identical, GEV3426- GEV3431, showing homology of 100% for ITS, 99.8% for TEF and 98.4% for TUB2 to the same fungal species. Accession numbers: GEV3423 (MT587806, MT605118, MT597152) and GEV3427 (MT587804, MT605120, MT597150); for ITS, TEF and TUB2, respectively. Maximum likelihood phylogenetic analysis, based on the combined alignment of ITS, TEF, and TUB2, differentiated the leaf isolates from other species, suggesting a new Neopestalotiopsis cryptic species. Three-month-old rooted pomegranate cuttings, cultivars Bhagwa and Mridula, were inoculated with two isolates GEV3523 and GEV3527. Each cutting was treated as two distinct halves; one half was wounded by gently rubbing sterilized sand on the leaves to cause abrasions and the other half remained intact. Four cuttings from each pomegranate cultivar were spray inoculated with a spore suspension (105 conidia mL-1) and four control plants were sprayed with sterilized water. The experiment was performed once on each cultivar. Inoculated cuttings were covered with a transparent plastic bag to maintain 100% humidity and incubated for 36 hours at 26°C under 12-hour photoperiod in a growth chamber. Leaves began to show symptoms of small, irregular, brown spots with a gray center three days after inoculation. The pathogen started to produce pycnidia in the center of the lesions one week after inoculation. Symptoms developed on both wounded and unwounded inoculated leaves with 100% disease incidence on both pomegranate cultivars inoculated separately with GEV3527 and GEV3523. Disease severity on wounded leaves ranged from 10 - 25% for 'Bhagwa' and 30 - 60% for 'Mridula' and on intact leaves from 2 - 5% and 5 - 12%, respectively. Furthermore, the fruit isolate, GEV3523, caused an average disease severity of 8 and 3.5 %, on wounded leaves of 'Bhagwa' and 'Mridula', respectively, whereas the leaf isolate GEV3427 caused 19 and 45% disease severity, respectively. No symptoms were observed on control plants and no fungal growth was observed on the re-isolations performed on the control plants. Neopestalatiopsis spp. were re-isolated from leaves fulfilling Koch's postulates. To our knowledge, this is the first report of Neopestalotiopsis rosae infecting pomegranate in Florida as well as in the United States. This pathogen could represent a threat to pomegranate production in Florida due to its ability to cause premature defoliation.

Improved deferred antagonism technique for detecting antibiosis

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.

Fungicide Application Timing Essential for the Management of Leaf Spot and Fruit Rot on Pomegranate (Punica granatum L.) in Florida

Pomegranate (Punica granatum L.) has emerged as an alternative fruit crop for growers dealing with devastating threats to citrus and avocado in the southeastern United States. However, foliar and fruit diseases are major constraints to commercial pomegranate production. Replicated field trials were performed in 2015 at three separate sites in Florida (Dover, Plant City, and Parrish) to evaluate Merivon (pyraclostrobin and fluxapyroxad), Luna Experience (fluopyram + tebuconazole), and a rotational program consisting of these two fungicides as well as Penncozeb 75DF (mancozeb) for the management of leaf spot and fruit rot of pomegranate. The fungicide programs were evaluated on the varieties Vietnam in Dover, FL; Angel Red in Plant City, FL; as well as Christina, Azadi, Vikusnyi, Alsirinnar, Sakerdze, and Wonderful in Parrish, FL. Mean leaf spot severity varied across sites at the end of each trial in August, with values ranging from 4.5 to 62.5% in Plant City, 7.5 to 45.8% in Dover, and 4.5 to 54.2% in Parrish. Based on area under the disease progress curve, all treatments that included at least one at bloom application significantly reduced disease levels compared with postbloom treatments and the nontreated control across all trial sites. Based on fruit rot incidence, Luna Experience and Merivon, when applied twice at bloom in the beginning of the season, reduced disease by 66.6 and 88.4%, respectively, in comparison with the nontreated control in Plant City. A rotational program further reduced disease by at least 97% at the end of the season in Parrish. The proper timing of fungicide application and rotation with different modes of action provided a feasible disease management option for pomegranate growers in the Southeast United States.

Pest control with drip-applied dimethyl disulfide and chloropicrin in plastic-mulched tomato (Solanum lycopersicum L.)

BACKGROUND

Dimethyl disulfide (DMDS) is used as a preplant soil fumigant for weed and soilborne pathogen control in plasticulture vegetable crops. The objective of this research was to determine the control efficacy of emulsifiable concentrate (EC) formulation of DMDS or DMDS + chloropicrin (Pic) on weed and Fusarium wilt in tomato (Solanum lycopersicum L.) plasticulture.

RESULTS

The effective DMDS rates required to provide 50% (ER₅₀ ) control of purple nutsedge (Cyperus rotundus L.) were 210 and 340 kg ha^-1 at 4 weeks after fumigation (WAF) in fall 2017 and fall 2018, respectively, while these values increased to 348 and >467 kg ha^-1 , respectively, at 12 WAF. The ER₅₀ values of DMDS + Pic were 150 and 240 kg ha^-1 at 4 WAF in fall 2017 and fall 2018, respectively, while these values increased to 255 and 450 kg ha^-1 , respectively, at 12 WAF. DMDS + Pic was generally more effective than DMDS for C. rotundus control. The high rates of DMDS or DMDS + Pic provided adequate C. rotundus control in early season but failed to provide effective control by season end. In addition, DMDS + Pic injections through drip tape effectively reduced Fusarium oxysporum f. sp. lycopersici (FOL) inoculum while DMDS alone was generally ineffective.

CONCLUSION

Injection of the EC formulation of DMDS or DMDS + Pic through drip tape should have been provided a viable option for C. rotundus and Fusarium wilt control in plastic-mulched tomato. However, supplemental weed management actions, such as herbicide applications, may be required to achieve season-long control. © 2019 Society of Chemical Industry.

Widespread QoI Fungicide Resistance Revealed Among Corynespora cassiicola Tomato Isolates in Florida

Target spot of tomato caused by Corynespora cassiicola is one of the most economically destructive diseases of tomato in Florida. A collection of 123 isolates from eight counties in Florida were evaluated for sensitivity to azoxystrobin and fenamidone based on mycelial growth inhibition (MGI), spore germination (SG), detached leaflet assays (DLAs), and sequence-based analysis of the cytochrome b gene (cytb). Cleavage of cytb by restriction enzyme (Fnu4HI) revealed the presence of a mutation conferring a glycine (G) to alanine (A) mutation at amino acid position 143 (G143A) in approximately 90% of the population, correlating with quinone outside inhibitor (QoI) resistance based on MGI (<40% at 5 μg/ml), SG (<50% at 1 and 10 μg/ml), and DLA (<10% severity reduction). The mutation conferring a phenylalanine (F) to leucine (L) substitution at position 129 (F129L) was confirmed in moderately resistant isolates (#9, #19, and #74) based on MGI (40 to 50% at 5 μg/ml), SG (<50% at 1 μg/ml and >50% at 10 μg/ml), and DLA (>10% and <43% severity reduction) for both QoI fungicides, whereas sensitive isolates (#1, #4, #7, #28, #29, #46, #61, #74, #75, #76, #91, #95, and #118) based on MGI (>50% at 5 μg/ml), SG (>50% at 1 μg/ml and 10 μg/ml), and DLA (>50% severity reduction) correlated to non-mutation-containing isolates or those with a silent mutation. This study indicates that QoI resistance among C. cassiicola isolates from tomato is widespread in Florida and validates rapid screening methods using MGI or molecular assays to identify resistant isolates in future studies.

Characterization of Colletotrichum Species Causing Anthracnose of Pomegranate in the Southeastern United States

Anthracnose fruit rot and leaf blight caused by Colletotrichum species are important diseases of pomegranate in the southeastern United States. In this study, 26 isolates from pomegranate were identified based on pathological and molecular characterization. Isolates were identified to species based on multilocus sequence analysis with the internal transcribed spacer region, glyceraldehyde-3-phosphate dehydrogenase, β-tubulin, and chitin synthase genomic genes. Pomegranate isolates grouped within the C. acutatum and C. gloeosporioides species complexes, with more than 73% belonging to the latter group. Three species were identified within the C. acutatum species complex (C. nymphaeae [n = 5], C. fioriniae [n = 1], and C. simmondsii [n = 1]), and three other species were identified within the C. gloeosporioides species complex (C. theobromicola [n = 11], C. siamense [n = 6], and C. gloeosporioides [n = 2]). Inoculations of pomegranate fruit showed that isolates from the C. acutatum species complex were more aggressive than isolates from the C. gloeosporioides species complex. Interestingly, opposite results were observed when leaves of rooted pomegranate cuttings were inoculated. In addition, Colletotrichum isolates from pomegranate, strawberry, blueberry, mango, and citrus were cross-pathogenic when inoculated to fruit. This is the first study identifying six different species of Colletotrichum causing pomegranate leaf blight and fruit anthracnose in the southeastern United States and the potential cross-pathogenic capability of pomegranate isolates to other commercially important crops.

Evaluation of Allyl Isothiocyanate as a Soil Fumigant for Tomato (Lycopersicon esculentum Mill.) Production

Fusarium wilt (Fusarium oxysporum f. sp. lycopersici), root-knot nematodes (Meloidogyne spp.), and purple nutsedge (Cyperus rotundus L.) are among the most damaging soilborne pests for tomato (Lycopersicon esculentum Mill.) production in the southeastern United States. Allyl isothiocyanate (allyl ITC) was evaluated as a potential fumigant alternative for control of soilborne pathogens, nematodes, and weeds. Shank- or drip-injected allyl ITC at rates ranging from 221 to 367 kg ha^-1 exhibited excellent performance, reducing the recovery of total F. oxysporum from treated soils. Shank- or drip-injected allyl ITC at 367 kg ha^-1 provided equivalent control of C. rotundus compared with 1,3-dichloropropene + chloropicrin and metam potassium, respectively. Totally impermeable film (TIF) did not further reduce the recovery of F. oxysporum and various nematodes from soil treated with allyl ITC compared with virtually impermeable film (VIF). However, TIF mulch significantly improved C. rotundus control versus shank- or drip-injected allyl ITC treatments under VIF mulch. Overall, allyl ITC is an effective methyl bromide alternative against F. oxysporum, C. rotundus, and plant-parasitic nematodes Criconemella spp. and Hoplolaimus spp. in plasticulture tomato production.

Tomato tolerance and pest control following fumigation with different ratios of dimethyl disulfide and chloropicrin

BACKGROUND

The phaseout of methyl bromide (MeBr) continues to stimulate research into the use of other soil fumigants for controlling soil-borne diseases and weeds. This research evaluated tomato (Solanum lycopersicum L.) tolerance, weed emergence and the recovery of Fusarium oxysporum f.sp. lycopersici (FOL) inoculum following fumigation with various combination ratios of dimethyl disulfide plus chloropicrin (DMDS + Pic).

RESULTS

On its own, DMDS did not effectively control purple nutsedge (Cyperus rotundus L.) compared with DMDS + Pic. Control of C. rotundus and fusarium wilt increased with Pic based on weed emergence throughout the growing season and FOL inoculum recovery from soil. In all three growing seasons, 159 kg ha^-1 DMDS + 379 kg ha^-1 Pic provided season-long control of C. rotundus.

CONCLUSION

This research confirms that formulating DMDS + Pic containing a high percentage of Pic offers an effective alternative to MeBr for tomato production. © 2018 Society of Chemical Industry.

Harvest of Lettuce from Verticillium-Infested Fields Has Little Impact on Postharvest Quality

Verticillium wilt of lettuce, caused by the soilborne pathogen Verticillium dahliae, poses a serious threat to the California lettuce industry. Knowledge of disease development and its impact on postharvest marketability would facilitate better management of the affected fields. This study investigated postharvest marketability of 22 lettuce varieties harvested from two Verticillium-infested commercial lettuce fields in Salinas and Watsonville, CA, in 2005 using a randomized complete block design. Periodic sampling to monitor disease in several crisphead varieties in the field demonstrated that root symptoms developed quickly at later stages of heading, followed by the onset of foliar symptoms as the crop reached harvest maturity. Harvested marketable heads were vacuum cooled soon after harvest to about 4°C and maintained at this temperature in commercial coolers. The impact of V. dahliae on postharvest marketability was assessed based on the percentage of heads per case deemed marketable following 1, 2, and 3 weeks of refrigerated storage. Across both field experiments, the average disease incidence and postharvest marketability ranged from 4.2 to 87.5% and from 69.4 to 100.0%, respectively, among lettuce types and varieties. The Pearson correlation analysis detected no significant relationship between disease incidence and postharvest marketability across all varieties tested (r = 0.041, P = 0.727), or within lettuce types, even though V. dahliae was recovered from 34% of the plants harvested, and recovery ranged from 0 to 73.3% for V. dahliae and from 10 to 91.7% for non-V. dahliae (V. isaacii or V. klebahnii) species. These findings demonstrate that growers can harvest lettuce from an infested field before foliar symptoms develop with negligible impact by Verticillium spp. on postharvest marketability or quality.

Multiple Recombination Events Drive the Current Genetic Structure of Xanthomonas perforans in Florida

Prior to the identification of Xanthomonas perforans associated with bacterial spot of tomato in 1991, X. euvesicatoria was the only known species in Florida. Currently, X. perforans is the Xanthomonas sp. associated with tomato in Florida. Changes in pathogenic race and sequence alleles over time signify shifts in the dominant X. perforans genotype in Florida. We previously reported recombination of X. perforans strains with closely related Xanthomonas species as a potential driving factor for X. perforans evolution. However, the extent of recombination across the X. perforans genomes was unknown. We used a core genome multilocus sequence analysis approach to identify conserved genes and evaluated recombination-associated evolution of these genes in X. perforans. A total of 1,356 genes were determined to be "core" genes conserved among the 58 X. perforans genomes used in the study. Our approach identified three genetic groups of X. perforans in Florida based on the principal component analysis (PCA) using core genes. Nucleotide variation in 241 genes defined these groups, that are referred as Phylogenetic-group Defining (PgD) genes. Furthermore, alleles of many of these PgD genes showed 100% sequence identity with X. euvesicatoria, suggesting that variation likely has been introduced by recombination at multiple locations throughout the bacterial chromosome. Site-specific recombinase genes along with plasmid mobilization and phage associated genes were observed at different frequencies in the three phylogenetic groups and were associated with clusters of recombinant genes. Our analysis of core genes revealed the extent, source, and mechanisms of recombination events that shaped the current population and genomic structure of X. perforans in Florida.

Comparing Host Plant Resistance, Repellent Mulches, and At-Plant Insecticides for Management of Bemisia tabaci MEAM1 (Hemiptera: Aleyrodidae) and Tomato Yellow Leaf Curl Virus

Bemisia tabaci MEAM1 (Gennadius), the sweetpotato whitefly, transmits Tomato yellow leaf curl virus (TYLCV), which causes significant yield losses annually in Florida and other tomato-producing regions. Field trials were carried out at the University of Florida's Gulf Coast Research and Education Center to evaluate integration of plastic mulch type, at-plant insecticide, and tomato variety for management of the sweetpotato whitefly and TYLCV. The tomato varieties Charger, Rally, and Tygress had significantly lower season-long densities of whitefly eggs and nymphs than Florida-47 in one or more trials. Aggressive chemical control measures failed to reduce virus incidence in two of the three trials and did not improve yield. In 2013, when virus pressure was extremely high, yield in the susceptible variety was decimated, but virus-tolerant varieties produced a crop. Egg and nymph densities tended to be lowest on TYLCV-tolerant varieties and on tomato grown on metalized mulch. Differences in yield were primarily due to tomato variety and TYLCV incidence. Intensive insecticide use common in Florida tomato production may reduce losses when viral pressure is moderate, but not when migration of viruliferous whiteflies into the field is constant. Without significant winter freezes or a coordinated host-free period to reduce whitefly populations, insecticidal control and repellent-metalized mulches will offer limited protection compared with genetic tolerance to the virus, which may also be overcome under high virus pressure.

Nano-Magnesium Oxide: A Novel Bactericide Against Copper-Tolerant Xanthomonas perforans Causing Tomato Bacterial Spot

Bacterial spot caused by Xanthomonas perforans causes significant damage on tomato in Florida. Due to the presence of copper (Cu)-tolerant X. perforans strains, Cu bactericides are not effective in disease management. Hence, there is a critical need to find alternatives for Cu. Antibacterial activity of magnesium oxide (Nano-MgO), and other metal oxide nanoparticles, were evaluated against a Cu-tolerant and -sensitive X. perforans strain. In vitro experiments demonstrated high antibacterial activity of Nano-MgO against both strains compared with the commercial Cu. The minimum inhibitory concentration of Nano-MgO is 25 µg/ml and the minimum bactericidal concentration is 100 µg/ml against a Cu-tolerant X. perforans strain after 4 h of exposure. Structural changes in the bacterial membrane following exposure to Nano-MgO treatments compared with the controls were observed using transmission electron microscopy. In two greenhouse experiments with a Cu-tolerant strain, bacterial spot severity was significantly reduced by Nano-MgO at 200 µg/ml compared with Cu-ethylene bis-dithiocarbamate (grower standard), and the untreated control (P = 0.05). In three field experiments, Nano-MgO at 200 µg/ml significantly reduced disease severity with no negative impact on yield compared with the untreated control. Inductively coupled plasma mass spectrometric analysis of the fruit confirmed that Nano-MgO application did not lead to the accumulation of Mg, Cu, Ca, K, Mn, P, and S. This study is the first to demonstrate the potential of Nano-MgO against bacterial spot of tomato.

Transgenic Expression of EFR and Bs2 Genes for Field Management of Bacterial Wilt and Bacterial Spot of Tomato

Field trials were conducted at two locations in Florida to evaluate transgenic tomato expressing the ELONGATION FACTOR TU RECEPTOR (EFR) gene from Arabidopsis thaliana, the Bs2 gene from pepper, or both Bs2 and EFR (Bs2/EFR) for managing bacterial wilt caused by Ralstonia solanacearum and bacterial spot caused by Xanthomonas perforans. Expression of EFR or Bs2/EFR in the susceptible genotype Fla. 8000 significantly reduced bacterial wilt incidence (50 to 100%) and increased total yield (57 to 114%) relative to lines expressing only Bs2 or the nontransformed Fla. 8000 control, although the marketable yield was not significantly affected. Following harvest, surviving symptomatic and nonsymptomatic plants were assessed for colonization by R. solanacearum. There were no significant differences in the population at the lower stem. Interestingly, in the middle stem, no bacteria could be recovered from EFR or Bs2/EFR lines but viable bacterial populations were recovered from Bs2 and nontransformed control lines at 10² to 10⁵ CFU/g of stem tissue. In growth-chamber experiments, the EFR transgenic tomato lines were found to be effective against seven different R. solanacearum strains isolated from the southeastern United States, indicating utility across the southeastern United States. In all of the bacterial spot trials, EFR and Bs2/EFR lines had significantly reduced disease severity (22 to 98%) compared with the Fla. 8000 control. The marketable and total yield of Bs2/EFR were significantly higher (43 to 170%) than Fla. 8000 control in three of four field trials. These results demonstrate for the first time the potential of using the EFR gene for field management of bacterial wilt and bacterial spot diseases of tomato.

The Type III Effector AvrBsT Enhances Xanthomonas perforans Fitness in Field-Grown Tomato

Type III secretion system effectors contribute to pathogenicity through various mechanisms. Recent surveys showed an increasing prevalence of the type III secretion effector avrBsT among Xanthomonas perforans strains. We hypothesized that the acquisition of avrBsT has a fitness advantage for the pathogen. The contribution of avrBsT to fitness on tomato was evaluated based on disease severity, in planta growth, competition, and recovery rates of wild-type (WT) and avrBsT mutant strains in greenhouse and field plants. GEV872 and GEV1001, representative strains of two phylogenomic groups of X. perforans, were selected for generating avrBsT mutants. Disease severity was higher for WT strains compared with the avrBsT mutant strains. X. perforans WT and avrBsT mutant strains did not differ following leaf infiltration of greenhouse plants in direct competition and in planta growth assays. The effect of avrBsT on pathogen fitness was noticeable under field conditions. Differences in strain recovery were significant, with WT being recovered two to eight times more than avrBsT mutant strains in the case of both strains GEV872 and GEV1001. WT strains were capable of spreading longer distances across field plots compared with avrBsT mutant strains. Findings suggest that the functional AvrBsT affects the fitness of X. perforans under field conditions, making it an ideal candidate for bacterial spot resistance breeding efforts in tomato.

Reclassification of Xanthomonas gardneri (ex Šutič 1957) Jones et al. 2006 as a later heterotypic synonym of Xanthomonas cynarae Trébaol et al. 2000 and description of X. cynarae pv. cynarae and X. cynarae pv. gardneri based on whole genome analyses

Multilocus sequence analysis of Xanthomonas species revealed a very close relationship between Xanthomonas cynarae, an artichoke pathogen and Xanthomonas gardneri, a tomato and pepper pathogen. Results of whole genome sequence comparisons using average nucleotide identity between representative strains of X. gardneri and X. cynarae were well above the threshold of 95-96 %. Inoculations of X. gardneri strains in artichoke leaves caused mild disease symptoms, but only weak symptoms were observed in the bracts. Both X. cynarae and X. gardneri grew equally and caused typical bacterial spot symptoms in pepper after artificial inoculation. However, X. cynarae induced a hypersensitive reaction in tomato, while X. gardneri strains were virulent. Pathogenicity-associated gene clusters, including the protein secretion systems, type III effector profiles, and lipopolysaccharide cluster were nearly identical between the two species. Based on our results from whole genome sequence comparison, X. gardneri and X. cynarae belong to the same species. The name X. cynarae has priority and X. gardneri should be considered as a later heterotypic synonym. An emended description of X. cynarae (type strain=CFBP 4188^T, =DSM 16794^T) is given. However, due to the host specificity in artichoke and tomato, two pathovars, X. cynarae pv. cynarae and X. cynarae pv. gardneri, are proposed.

Effect of Formulations of Allyl Isothiocyanate on Survival of Macrophomina phaseolina from Strawberry

Management of Macrophomina phaseolina, causal agent of charcoal rot in many crops worldwide, including strawberry, has become more challenging since the phase out of methyl bromide (MeBr). The search for a fumigant equally effective as MeBr to control soilborne pathogens has been extensive. Allyl isothiocyanate (AITC), a biofumigant recently registered in the United States, was evaluated at different rates, formulations, fumigant combinations, and application methods in the fall of 2014 and 2015 at two research facilities in Balm and Dover, FL. The efficacy of treatments was determined by evaluating the survival of M. phaseolina inoculum on infested corn-cob litter buried in bags 7.6 and 20.3 cm deep in the center, and 7.6 cm deep in the side, of plastic mulched raised beds. The biofumigant was shown to be more or as effective in reducing populations of M. phaseolina in the soil compared with standard fumigants, such as chloropicrin and 1,3-dichloropropene with chloropicrin. Thus, AITC is a promising biofumigant alternative for managing charcoal rot of strawberry, particularly in organic production systems, and should be evaluated for the management of other soilborne pathogens.

Genomic Inference of Recombination-Mediated Evolution in Xanthomonas euvesicatoria and X. perforans

Recombination is a major driver of evolution in bacterial populations, because it can spread and combine independently evolved beneficial mutations. Recombinant lineages of bacterial pathogens of plants are typically associated with the colonization of novel hosts and the emergence of new diseases. Here we show that recombination between evolutionarily and phenotypically distinct plant-pathogenic lineages generated recombinant lineages with unique combinations of pathogenicity and virulence factors. Xanthomonas euvesicatoria and Xanthomonas perforans are two closely related lineages causing bacterial spot disease on tomato and pepper worldwide. We sequenced the genomes of atypical strains collected from tomato in Nigeria and observed recombination in the type III secretion system and effector genes, which showed alleles from both X. euvesicatoria and X. perforans Wider horizontal gene transfer was indicated by the fact that the lipopolysaccharide cluster of one strain was most similar to that of a distantly related Xanthomonas pathogen of barley. This strain and others have experienced extensive genomewide homologous recombination, and both species exhibited dynamic open pangenomes. Variation in effector gene repertoires within and between species must be taken into consideration when one is breeding tomatoes for disease resistance. Resistance breeding strategies that target specific effectors must consider possibly dramatic variation in bacterial spot populations across global production regions, as illustrated by the recombinant strains observed here.IMPORTANCE The pathogens that cause bacterial spot of tomato and pepper are extensively studied models of plant-microbe interactions and cause problematic disease worldwide. Atypical bacterial spot strains collected from tomato in Nigeria, and other strains from Italy, India, and Florida, showed evidence of genomewide recombination that generated genetically distinct pathogenic lineages. The strains from Nigeria and Italy were found to have a mix of type III secretion system genes from X. perforans and X. euvesicatoria, as well as effectors from Xanthomonas gardneri These genes and effectors are important in the establishment of disease, and effectors are common targets of resistance breeding. Our findings point to global diversity in the genomes of bacterial spot pathogens, which is likely to affect the host-pathogen interaction and influence management decisions.

Bacterial Gall of Loropetalum chinense caused by Pseudomonas amygdali pv. loropetali pv. nov

In 2012, stem gall samples on Loropetalum chinense were sent to Florida diagnostic labs from Alabama and Florida nurseries. A fluorescent pseudomonad was consistently isolated from the galls. The organism was originally identified in Alabama based on 16S rRNA sequencing as Pseudomonas savastanoi, which causes a production-limiting disease of olive. The loropetalum strains and reference strains were compared using LOPAT, Biolog, fatty acid analysis, multilocus sequence analysis (MLSA), and pathogenicity tests. The LOPAT tests placed the loropetalum strains within Pseudomonas syringae. Biolog and fatty acid analysis placed the strains in various pathovars of P. syringae and P. savastanoi, respectively. MLSA of a set of housekeeping genes separated the loropetalum strains from the olive knot-inducing strains. Our work indicates there is a need to use more tests than 16S rRNA to accurately diagnose new bacterial diseases. In pathogenicity tests, the loropetalum strains produced galls only on loropetalum, but not on olive, mandevilla, or almond, indicating this strain is not a threat to the olive industry. Based on the pathogenicity assays and molecular tests, loropetalum strains represent a distinct and new pathovar, P. amygdali pv. loropetali pv. nov., for which the strain PDC13-208 (= DSMZ 105780^PT) has been designated as the pathotype strain.

Advanced Copper Composites Against Copper-Tolerant Xanthomonas perforans and Tomato Bacterial Spot

Bacterial spot, caused by Xanthomonas spp., is a widespread and damaging bacterial disease of tomato (Solanum lycopersicum). For disease management, growers rely on copper bactericides, which are often ineffective due to the presence of copper-tolerant Xanthomonas strains. This study evaluated the antibacterial activity of the new copper composites core-shell copper (CS-Cu), multivalent copper (MV-Cu), and fixed quaternary ammonium copper (FQ-Cu) as potential alternatives to commercially available micron-sized copper bactericides for controlling copper-tolerant Xanthomonas perforans. In vitro, metallic copper from CS-Cu and FQ-Cu at 100 μg/ml killed the copper-tolerant X. perforans strain within 1 h of exposure. In contrast, none of the micron-sized copper rates (100 to 1,000 μg/ml) from Kocide 3000 significantly reduced copper-tolerant X. perforans populations after 48 h of exposure compared with the water control (P < 0.05). All copper-based treatments killed the copper-sensitive X. perforans strain within 1 h. Greenhouse studies demonstrated that all copper composites significantly reduced bacterial spot disease severity when compared with copper-mancozeb and water controls (P < 0.05). Although there was no significant impact on yield, copper composites significantly reduced disease severity when compared with water controls, using 80% less metallic copper in comparison with copper-mancozeb in field studies (P < 0.05). This study highlights the discovery that copper composites have the potential to manage copper-tolerant X. perforans and tomato bacterial spot.

Pseudomonas floridensis sp. nov., a bacterial pathogen isolated from tomato

An unusual fluorescent pseudomonad was isolated from tomato exhibiting leaf spot symptoms similar to bacterial speck. Strains were fluorescent, oxidase- and arginine-dihydrolase-negative, elicited a hypersensitive reaction on tobacco and produced a soft rot on potato slices. However, the strains produced an unusual yellow, mucoid growth on media containing 5 % sucrose that is not typical of levan. Based on multilocus sequence analysis using 16S rRNA, gap1, gltA, gyrB and rpoD, these strains formed a distinct phylogenetic group in the genus Pseudomonas and were most closely related to Pseudomonas viridiflava within the Pseudomonassyringae complex. Whole-genome comparisons, using average nucleotide identity based on blast, of representative strain GEV388T and publicly available genomes representing the genus Pseudomonas revealed phylogroup 7 P. viridiflava strain UASW0038 and P. viridiflava type strain ICMP 2848T as the closest relatives with 86.59 and 86.56 % nucleotide identity, respectively. In silico DNA-DNA hybridization using the genome-to-genome distance calculation method estimated 31.1 % DNA relatedness between GEV388T and P. viridiflava ATCC 13223T, strongly suggesting the strains are representatives of different species. These results together with Biolog GEN III tests, fatty acid methyl ester profiles and phylogenetic analysis using 16S rRNA and multiple housekeeping gene sequences demonstrated that this group represents a novel species member of the genus Pseudomonas. The name Pseudomonas floridensis sp. nov. is proposed with GEV388T (=LMG 30013T=ATCC TSD-90T) as the type strain.

A Novel Phylogroup of Pseudomonas cichorii Identified Following an Unusual Disease Outbreak on Tomato

Recently, in Central Florida tomato production fields, tomato foliage and fruit were observed with symptoms similar to bacterial speck. Fluorescent pseudomonads were consistently isolated and the strains were characterized by standard LOPAT tests, pathogenicity tests, and genetic characterization using 16S ribosomal RNA (rRNA) sequences and multilocus sequence analysis (MLSA) of conserved housekeeping genes. LOPAT test results indicated that the strains were likely Pseudomonas cichorii. These strains were pathogenic on tomato and were also pathogenic on lettuce, the host for the type strain of P. cichorii. Likewise, strains of P. cichorii isolated in Florida since the early 1980s from hosts other than tomato, along with the type strain, were also pathogenic on tomato. Genetic characterization using 16S rRNA and MLSA confirmed that the strains were most closely related to P. cichorii but varied significantly from the type strain. The Florida P. cichorii strains formed a separate phylogenetic group along with P. cichorii strains isolated from tomato in Tanzania. These strains were different from the previously described morphotypes and genomovars of P. cichorii. Our results indicate the presence of a genetically distinct group of multihost pathogenic P. cichorii strains that have been present in Florida since at least the early 1980s.

Whole-Genome Sequences of Xanthomonas euvesicatoria Strains Clarify Taxonomy and Reveal a Stepwise Erosion of Type 3 Effectors

Multiple species of Xanthomonas cause bacterial spot of tomato (BST) and pepper. We sequenced five Xanthomonas euvesicatoria strains isolated from three continents (Africa, Asia, and South America) to provide a set of representative genomes with temporal and geographic diversity. LMG strains 667, 905, 909, and 933 were pathogenic on tomato and pepper, except LMG 918 elicited a hypersensitive reaction (HR) on tomato. Furthermore, LMG 667, 909, and 918 elicited a HR on Early Cal Wonder 30R containing Bs3. We examined pectolytic activity and starch hydrolysis, two tests which are useful in differentiating X. euvesicatoria from X. perforans, both causal agents of BST. LMG strains 905, 909, 918, and 933 were nonpectolytic while only LMG 918 was amylolytic. These results suggest that LMG 918 is atypical of X. euvesicatoria. Sequence analysis of all the publicly available X. euvesicatoria and X. perforans strains comparing seven housekeeping genes identified seven haplotypes with few polymorphisms. Whole genome comparison by average nucleotide identity (ANI) resulted in values of >99% among the LMG strains 667, 905, 909, 918, and 933 and X. euvesicatoria strains and >99.6% among the LMG strains and a subset of X. perforans strains. These results suggest that X. euvesicatoria and X. perforans should be considered a single species. ANI values between strains of X. euvesicatoria, X. perforans, X. allii, X. alfalfa subsp. citrumelonis, X. dieffenbachiae, and a recently described pathogen of rose were >97.8% suggesting these pathogens should be a single species and recognized as X. euvesicatoria. Analysis of the newly sequenced X. euvesicatoria strains revealed interesting findings among the type 3 (T3) effectors, relatively ancient stepwise erosion of some T3 effectors, additional X. euvesicatoria-specific T3 effectors among the causal agents of BST, orthologs of avrBs3 and avrBs4, and T3 effectors shared among xanthomonads pathogenic against various hosts. The results from this study supports the finding that T3 effector repertoire and host range are fundamental for the study of host-microbe interaction but of little relevance to bacterial speciation.

Management of Powdery Mildew in Squash by Plant and Alga Extract Biopesticides

Although many fungicides are registered for use to control powdery mildew on cucurbits, management of resistance to fungicides in pathogen populations still remains a major challenge. Two biopesticides Regalia SC and HMO 736 were evaluated in the greenhouse and field for their efficacy against powdery mildew in squash. In greenhouses, Regalia SC alone significantly (P < 0.05) reduced powdery mildew compared to the nontreated control, and was as effective as the chemical standard Procure 480SC (triflumizole). In alternation with Procure 480SC, Regalia SC demonstrated greater or equivalent effects on reducing the disease. HMO 736 alone showed varying levels of disease control, but alternating with Procure 480SC significantly improved control efficacy. In addition, application of Regalia SC or HMO 736 each in alternation with Procure 480SC significantly increased the chlorophyll content in leaves and the total fresh weight of squash plants, when compared with the water control, Regalia SC and HMO 736 alone. In field trials, application of Regalia SC and HMO 736 each alone significantly reduced disease severity in one of two field trials during the early stage of disease development, but not during later stages when disease pressure became high. Both Regalia SC and HMO 736 each applied in alternation with Procure 480SC significantly improved the control efficacy compared to Procure 480SC alone. Results from this study demonstrated that an integrated management program can be developed for powdery mildew in squash by integrating the biopesticides Regalia SC, HMO 736 with the chemical fungicide Procure 480SC.

Analysis of Sequenced Genomes of Xanthomonas perforans Identifies Candidate Targets for Resistance Breeding in Tomato

Bacterial disease management is a challenge for modern agriculture due to rapid changes in pathogen populations. Genome sequences for hosts and pathogens provide detailed information that facilitates effector-based breeding strategies. Tomato genotypes have gene-for-gene resistance to the bacterial spot pathogen Xanthomonas perforans. The bacterial spot populations in Florida shifted from tomato race 3 to 4, such that the corresponding tomato resistance gene no longer recognizes the effector protein AvrXv3. Genome sequencing showed variation in effector profiles among race 4 strains collected in 2006 and 2012 and compared with a race 3 strain collected in 1991. We examined variation in putative targets of resistance among Florida strains of X. perforans collected from 1991 to 2006. Consistent with race change, avrXv3 was present in race 3 strains but nonfunctional in race 4 strains due to multiple independent mutations. Effectors xopJ4 and avrBs2 were unchanged in all strains. The effector avrBsT was absent in race 3 strains collected in the 1990s but present in race 3 strains collected in 2006 and nearly all race 4 strains. These changes in effector profiles suggest that xopJ4 and avrBsT are currently the best targets for resistance breeding against bacterial spot in tomato.

A Multiplex Real-Time PCR Assay Differentiates Four Xanthomonas Species Associated with Bacterial Spot of Tomato

Bacterial spot of tomato, a major problem in many tomato production areas, is caused by Xanthomonas euvesicatoria, X. vesicatoria, X. perforans, and X. gardneri. In order to detect and identify the bacterial spot pathogens, we evaluated a region of hrpB operon as a source for primers and probes for real-time polymerase chain reaction (PCR). A 420-bp fragment of the hrpB7 gene was amplified by PCR from 75 strains representing the four species. The PCR products were sequenced and phylogenetic analysis revealed that hrpB7 is highly conserved within each species, with a single-nucleotide polymorphism (SNP) among the X. vesicatoria strains. X. euvesicatoria and X. perforans varied by two SNP. Four probes and two primer sets were designed to target the four bacterial spot pathogens based on their hrpB7 gene sequences. In order to simultaneously detect the four bacterial spot pathogens, the four probes and two primer sets were optimized for a multiplex real-time TaqMan PCR assay. The optimized multiplex assay was determined to be highly specific to the four bacterial spot pathogens. Because the optimized multiplex assay facilitated the identification of each bacterial spot pathogen from pure cultures and infected plant tissue, it holds great potential as a diagnostic tool.

Bacterial spot of tomato and pepper: diverse Xanthomonas species with a wide variety of virulence factors posing a worldwide challenge

TAXONOMIC STATUS

Bacteria; Phylum Proteobacteria; Class Gammaproteobacteria; Order Xanthomonadales; Family Xanthomonadaceae; Genus Xanthomonas; Species Xanthomonas euvesicatoria, Xanthomonas vesicatoria, Xanthomonas perforans and Xanthomonas gardneri.

MICROBIOLOGICAL PROPERTIES

Gram-negative, rod-shaped bacterium, aerobic, motile, single polar flagellum.

HOST RANGE

Causes bacterial spot disease on plants belonging to the Solanaceae family, primarily tomato (Solanum lycopersicum), pepper (Capsicum annuum) and chilli peppers (Capsicum frutescens).

DISEASE SYMPTOMS

Necrotic lesions on all above-ground plant parts.

DISTRIBUTION

Worldwide distribution of X. euvesicatoria and X. vesicatoria on tomato and pepper; X. perforans and X. gardneri increasingly being isolated from the USA, Canada, South America, Africa and Europe. A wide diversity within the bacterial spot disease complex, with an ability to cause disease at different temperatures, makes this pathogen group a worldwide threat to tomato and pepper production. Recent advances in genome analyses have revealed the evolution of the pathogen with a plethora of novel virulence factors. Current management strategies rely on the use of various chemical control strategies and sanitary measures to minimize pathogen spread through contaminated seed. Chemical control strategies have been a challenge because of resistance by the pathogen. Breeding programmes have been successful in developing commercial lines with hypersensitive and quantitative resistance. However, durability of resistance has been elusive. Recently, a transgenic approach has resulted in the development of tomato genotypes with significant levels of resistance and improved yield that hold promise. In this article, we discuss the current taxonomic status, distribution of the four species, knowledge of virulence factors, detection methods and strategies for disease control with possible directions for future research.

Evaluating Weeds as Hosts of Tomato yellow leaf curl virus

Bemisia tabaci (Gennadius) biotype B transmits Tomato yellow leaf curl virus (TYLCV), which affects tomato production globally. Prompt destruction of virus reservoirs is a key component of virus management. Identification of weed hosts of TYLCV will be useful for reducing such reservoirs. The status of weeds as alternate hosts of TYLCV in Florida remains unclear. In greenhouse studies, B. tabaci adults from a colony reared on TYLCV-infected tomato were established in cages containing one of four weeds common to horticultural fields in central and south Florida. Cages containing tomato and cotton were also infested with viruliferous whiteflies as a positive control and negative control, respectively. Whitefly adults and plant tissue were tested periodically over 10 wk for the presence of TYLCV using PCR. After 10 wk, virus-susceptible tomato plants were placed in each cage to determine if whiteflies descended from the original adults were still infective. Results indicate that Bidens alba, Emilia fosbergii, and Raphanus raphanistrum are not hosts of TYLCV, and that Amaranthus retroflexus is a host.