Publications by authors named "Sujan Timilsina"

27 Publications

  • Page 1 of 1

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

ISME J 2021 Sep 6. Epub 2021 Sep 6.

Department of Plant Pathology, IFAS, University of Florida, Gainesville, FL, USA.

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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41396-021-01104-8DOI Listing
September 2021

A centenary for bacterial spot of tomato and pepper.

Mol Plant Pathol 2021 Sep 2. Epub 2021 Sep 2.

Gulf Coast Research and Education Center, University of Florida, Wimauma, Florida, USA.

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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/mpp.13125DOI Listing
September 2021

Adrenal Leiomyoma: A case report.

Int J Surg Case Rep 2021 Aug 29;85:106249. Epub 2021 Jul 29.

Department of Pathology, Tribhuvan University Teaching Hospital, Institute of Medicine, Kathmandu, Nepal.

Introduction And Importance: Adrenal Leiomyomas are infrequent tumors with only a few cases reported to date. They are difficult to differentiate from malignant adrenal tumors due to non-specific findings on clinical examination and imaging studies.

Case Presentation: We discuss the case of a 49-year old male who had been experiencing generalized abdominal pain for 14 months and was found to have a mass on ultrasonography. Further evaluation with Contrast-enhanced Computerized Tomography (CECT) revealed an uneven soft tissue density mass in the retroperitoneal region of the left side. The histopathological examination of the excised mass was suggestive of a mesenchymal tumor, which was further confirmed as leiomyoma by immunohistochemistry.

Clinical Discussion: Adrenal Leiomyomas are rare smooth muscle tumors that present with heterogeneously enhancing mass on radiologic imaging. On histopathological examination, spindle cells arranged in lobules and fascicles can be appreciated. Positive staining for desmin and smooth muscle actin in immunohistochemistry confirms the diagnosis.

Conclusion: Identification of the type of tumor in any adrenal mass is challenging pertaining to the non-specific findings on imaging studies. So, prompt surgical resection is the mainstay of the treatment.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ijscr.2021.106249DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8347817PMC
August 2021

Adrenal schwannoma: A case report of an unusual incidentaloma.

Int J Surg Case Rep 2021 Jun 26;83:106018. Epub 2021 May 26.

Department of Urology and Kidney Transplant Surgery, Tribhuvan University Teaching Hospital, Kathmandu, Nepal. Electronic address:

Introduction And Importance: Adrenal schwannomas are extremely rare tumors often misdiagnosed. The patients are usually asymptomatic while some present with non-specific abdominal pain. Only a few cases are reported to date.

Case Presentation: We here present a case of a 55-year-old Nepalese man presented with nonspecific abdominal pain at our Outpatient Department (OPD) found to have mass on ultrasonography of abdomen. On further investigation with Contrast Enhanced Computerized Tomography (CECT) of the abdomen and pelvis, a well-defined heterogeneous adrenal mass of size (7.8 ∗ 8.3 ∗ 6) cm with foci of calcification was seen in the left retroperitoneum. The intraoperative finding of adrenal mass and histopathology of resected mass was suggestive of schwannoma arising from the adrenal gland which was further confirmed by immunohistochemistry.

Clinical Discussion: Adrenal schwannoma can mimic tumors like pheochromocytoma, adrenal adenoma, cortical carcinoma, neuroblastoma, and other masses. Only 1-3% of schwannomas are retroperitoneal. Radiological findings of this tumor are non-suggestive. The histological section shows spindle cells with Antoni A and Antoni B regions while positive staining of S-100 protein in Immunohistochemistry.

Conclusion: The diagnosis of adrenal schwannoma in the retroperitoneum is often challenging. The treatment of choice is surgical resection with a good prognosis.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ijscr.2021.106018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8175416PMC
June 2021

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

Environ Microbiol 2021 Apr 23. Epub 2021 Apr 23.

Department of Plant Pathology, University of Florida, Gainesville, Florida, USA.

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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/1462-2920.15541DOI Listing
April 2021

Draft Genome Sequences of Pseudomonas syringae pv. tomato Strains J4 and J6, Isolated in Florida.

Microbiol Resour Announc 2021 Apr 15;10(15). Epub 2021 Apr 15.

Plant Pathology Department, University of Florida, Gainesville, Florida, USA

pv. tomato causes bacterial speck in tomato. We report the genome sequences of two pv. tomato strains, J4 and J6, that are genetically closely related, with >99.9 average nucleotide identity (ANI), but vary in the presence of coronatine-associated genes.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/MRA.00127-21DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8050965PMC
April 2021

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

Phytopathology 2021 Apr 8:PHYTO09200402R. Epub 2021 Apr 8.

Department of Plant Pathology, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611.

Before 1991, was the causal agent of bacterial spot of tomato in Florida but was quickly replaced by . The population has changed in genotype and phenotype despite lack of a clear selection pressure. To determine the current population in Florida, we collected 585 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 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 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 . Effector profiles were highly variable among strains, which could impact the strains' host range. The effector , which was previously thought to be conserved in 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 population is diverse and complex.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1094/PHYTO-09-20-0402-RDOI Listing
April 2021

Draft Genome Sequences of Plant-Pathogenic Klebsiella variicola Strains Isolated from Plantain in Haiti.

Microbiol Resour Announc 2020 Jul 16;9(29). Epub 2020 Jul 16.

Department of Plant Pathology, University of Florida, Gainesville, Florida, USA

The genus includes pathogenic and nonpathogenic species. We report the 5.57-Mb genome sequences of two strains, G18-1365 and G18-1376, isolated from symptomatic plantain plants in Haiti. These strains are genetically closely related (average nucleotide identity [ANI] > 99%) to the previously described type strain of , DSM 15968.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/MRA.00336-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7365790PMC
July 2020

Characterization of three novel genetic loci encoding bacteriocins associated with Xanthomonas perforans.

PLoS One 2020 29;15(5):e0233301. Epub 2020 May 29.

Department of Plant Pathology, University of Florida, Gainesville, Florida, United States of America.

Bacterial spot is a destructive disease of tomato in Florida that prior to the early 1990s was caused by Xanthomonas euvesicatoria. X. perforans was first identified in Florida in 1991 and by 2006 was the only xanthomonad associated with bacterial spot disease in tomato. The ability of an X. perforans strain to outcompete X. euvesicatoria both in vitro and in vivo was at least in part associated with the production of three bacteriocins designated Bcn-A, Bcn-B, and Bcn-C. The objective of this study was to characterize the genetic determinants of these bacteriocins. Bcn-A activity was confined to one locus consisting of five ORFs of which three (ORFA, ORF2 and ORF4) were required for bacteriocin activity. The fifth ORF is predicted to encode an immunity protein to Bcn-A based on in vitro and in vivo assays. The first ORF encodes Bcn-A, a 1,398 amino acid protein, which bioinformatic analysis predicts to be a member of the RHS family of toxins. Based on results of homology modeling, we hypothesize that the amino terminus of Bcn-A interacts with a protein in the outer membrane of X. euvesicatoria. The carboxy terminus of the protein may interact with an as yet unknown protein(s) and puncture the X. euvesicatoria membrane, thereby delivering the accessory proteins into the target and causing cell death. Bcn-A appears to be activated upon secretion based on cell fractionation assays. The other two loci were each shown to be single ORFs encoding Bcn-B and Bcn-C. Both gene products possess homology toward known proteases. Proteinase activity for both Bcn-B and Bcn-C was confirmed using a milk agar assay. Bcn-B is predicted to be an ArgC-like serine protease, which was confirmed by PMSF inhibition of proteolytic activity, whereas Bcn-C has greater than 50% amino acid sequence identity to two zinc metalloproteases.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0233301PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7259588PMC
August 2020

Xanthomonas diversity, virulence and plant-pathogen interactions.

Nat Rev Microbiol 2020 08 28;18(8):415-427. Epub 2020 Apr 28.

Plant Pathology Department, University of Florida, Gainesville, FL, USA.

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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41579-020-0361-8DOI Listing
August 2020

Widespread QoI Fungicide Resistance Revealed Among Tomato Isolates in Florida.

Plant Dis 2020 Mar 30;104(3):893-903. Epub 2019 Dec 30.

University of Florida, Gulf Coast Research and Education Center, Wimauma, FL 33598.

Target spot of tomato caused by 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 (). Cleavage of by restriction enzyme (4HI) 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 isolates from tomato is widespread in Florida and validates rapid screening methods using MGI or molecular assays to identify resistant isolates in future studies.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1094/PDIS-03-19-0460-REDOI Listing
March 2020

Molecular Epidemiology of Outbreaks in Tomato Plants from Transplant to Field as Determined by Single-Nucleotide Polymorphism Analysis.

Appl Environ Microbiol 2019 09 29;85(18). Epub 2019 Aug 29.

Gulf Coast Research and Education Center, University of Florida, Wimauma, Florida, USA

Outbreaks of bacterial spot on tomato (BST) caused by are a major concern for sustainable crop production. BST is a common occurrence in tomato transplants grown for field production. We hypothesized that BST outbreaks in commercial fields originate from strains inadvertently introduced from commercial transplant facilities. To test this hypothesis, we used a genome-wide single-nucleotide polymorphism (SNP) analysis to characterize strains recovered from tomato transplant facilities and fields in commercial production areas. strains were isolated from symptomatic transplants prior to roguing at two commercial transplant growers. Then, the same groups of transplants were tracked to commercial fields to recover strains from diseased plants prior to harvest. Whole-genome sequencing was carried out on 84 strains isolated from transplant and field plants from Florida and South Carolina. SNPs were called using three reference strains that represented the genetic variation of the sampled strains. Field strains showing genetic similarity to transplant strains had a difference of 2 to 210 SNPs. Transplant and field strains clustered together by grower within each phylogenomic group, consistent with expectations. The range of genetic divergence among strains isolated from field plants was similar to the range obtained from strains on transplants. Using the range of genetic variation observed in transplants, we estimate that 60% to 100% of field strains were an extension of the transplant strain population. Our results stress the importance of BST management to reduce movement from transplant to field and to minimize subsequent disease outbreaks. Current management of on tomato plants mainly relies on the frequent application of pesticides. However, the lack of effective pesticides and the development of strain tolerance to certain bactericides limit the ability to control outbreaks in production fields. Better knowledge of probable sources of inoculum during tomato production is required to refine management strategies. Tomato plants are typically established in the field using transplants. This study aimed to determine if strains from field epidemics were coming from transplant facilities or resulted from local field outbreaks. The overall goal was to identify potential sources of inoculum and subsequently develop strategies to reduce carryover from transplant production to the field. Our results indicate that tomato producers should shift disease management efforts to transplant facilities to reduce disease in the field. Improved transplant health should reduce the likelihood of bacterial spot outbreaks and subsequently reduce pesticide usage in the field.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/AEM.01220-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6715834PMC
September 2019

Corrigendum: Inference of Convergent Gene Acquisition Among Strains Isolated From Watermelon, Cantaloupe, and Squash.

Front Microbiol 2019 3;10:963. Epub 2019 May 3.

Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, United States.

[This corrects the article DOI: 10.3389/fmicb.2019.00270.].
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fmicb.2019.00963DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6510182PMC
May 2019

Phenotypic and Genetic Diversity of Populations from Tomato in North Carolina.

Phytopathology 2019 Sep 5;109(9):1533-1543. Epub 2019 Aug 5.

Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695.

Bacterial spot caused by spp. is one of the most devastating diseases of tomato in North Carolina (NC). In total, 290 strains of spp. from tomato in NC collected over 2 years (2015 and 2016) were analyzed for phenotypic and genetic diversity. In vitro copper and streptomycin sensitivity assays revealed that >95% ( = 290) of the strains were copper tolerant in both years, whereas 25% ( = 127) and 46% ( = 163) were streptomycin tolerant in 2016 and 2015, respectively. Using BOX repetitive element PCR assay, fingerprint patterns showed four haplotypes (H1, H2, H3, and H4) among the strains analyzed. The multiplex real-time quantitative PCR on a subset of representative strains ( = 45) targeting the highly conserved gene identified strains from tomato in NC that belonged to . Race profiling of the representative strains ( = 45) on tomato and pepper differentials confirmed that ∼9 and 91% of strains are tomato races T3 and T4, respectively. Additionally, PCR assays and sequence alignments confirmed that the , , ( copper tolerance gene cluster), and genes are present in the strains analyzed. Phylogenetic and comparative sequence analyses of six genomic regions (elongation factor G [], glyceraldehyde-3-phosphate dehydrogenase A [], citrate synthase [], gyrase subunit B [], ABC transporter sugar permease [], and GTP binding protein []) suggested that 13 and 74% of strains from NC were genetically similar to races T3 and T4 from Florida, respectively. Our results provide insights that bacterial spot management practices in tomato should focus on deploying resistance genes to combat emerging pathogenic races of and overcome the challenges currently posed by intense use of copper-based bactericides.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1094/PHYTO-01-19-0019-RDOI Listing
September 2019

Multiple Recombination Events Drive the Current Genetic Structure of in Florida.

Front Microbiol 2019 13;10:448. Epub 2019 Mar 13.

Department of Plant Pathology, University of Florida, Gainesville, FL, United States.

Prior to the identification of associated with bacterial spot of tomato in 1991, was the only known species in Florida. Currently, is the sp. associated with tomato in Florida. Changes in pathogenic race and sequence alleles over time signify shifts in the dominant genotype in Florida. We previously reported recombination of strains with closely related species as a potential driving factor for evolution. However, the extent of recombination across the 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 . A total of 1,356 genes were determined to be "core" genes conserved among the 58 genomes used in the study. Our approach identified three genetic groups of 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 , 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 in Florida.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fmicb.2019.00448DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6425879PMC
March 2019

Inference of Convergent Gene Acquisition Among Strains Isolated From Watermelon, Cantaloupe, and Squash.

Front Microbiol 2019 19;10:270. Epub 2019 Feb 19.

Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, United States.

(phylogroup 2; referred to as ) consists of an environmentally ubiquitous bacterial population associated with diseases of numerous plant species. Recent studies using multilocus sequence analysis have indicated the clonal expansion of several lineages, located in phylogroups 2a and 2b, in association with outbreaks of bacterial spot disease of watermelon, cantaloupe, and squash in the United States. To investigate the evolutionary processes that led to the emergence of these epidemic lineages, we sequenced the genomes of six strains that were isolated from cucurbits grown in the United States, Europe, and China over a period of more than a decade, as well as eight strains that were isolated from watermelon and squash grown in six different Florida counties during the 2013 and 2014 seasons. These data were subjected to comparative analyses along with 42 previously sequenced genomes of stains collected from diverse plant species and environments available from GenBank. Maximum likelihood reconstruction of the core genome revealed the presence of a hybrid phylogenetic group, comprised of cucurbit strains collected in Florida, Italy, Serbia, and France, which emerged through genome-wide homologous recombination between phylogroups 2a and 2b. Functional analysis of the recombinant core genome showed that pathways involved in the ATP-dependent transport and metabolism of amino acids, bacterial motility, and secretion systems were enriched for recombination. A survey of described virulence factors indicated the convergent acquisition of several accessory type 3 secreted effectors (T3SEs) among phylogenetically distinct lineages through integrative and conjugative element and plasmid loci. Finally, pathogenicity assays on watermelon and squash showed qualitative differences in virulence between strains of the same clonal lineage, which correlated with T3SEs acquired through various mechanisms of horizontal gene transfer (HGT). This study provides novel insights into the interplay of homologous recombination and HGT toward pathogen emergence and highlights the dynamic nature of genomes.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fmicb.2019.00270DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6390507PMC
February 2019

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

Plant Dis 2018 Apr 2;102(4):799-806. Epub 2018 Feb 2.

University of Florida Department of Plant Pathology, Gainesville, FL.

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) has been designated as the pathotype strain.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1094/PDIS-04-17-0505-REDOI Listing
April 2018

A bacterial epidemic in wild plants.

Nat Ecol Evol 2018 10;2(10):1529-1530

Department of Plant Pathology, University of Florida, Gainesville, FL, USA.

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41559-018-0692-2DOI Listing
October 2018

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

Phytopathology 2018 Dec 15;108(12):1355-1362. Epub 2018 Oct 15.

First, second, fourth, and seventh authors; Gulf Coast and Research Education Center, Wimauma, FL; first, second, third, fifth, sixth, and seventh authors: Department of Plant Pathology, University of Florida, Gainesville; and fifth author: Emerging Pathogens Institute, University of Florida, Gainesville.

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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1094/PHYTO-02-18-0052-RDOI Listing
December 2018

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

Appl Environ Microbiol 2018 07 18;84(13). Epub 2018 Jun 18.

Department of Plant Pathology, University of Florida, Gainesville, Florida, USA

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. and 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 and 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 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. 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 and , as well as effectors from 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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/AEM.00136-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6007113PMC
July 2018

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

Int J Syst Evol Microbiol 2018 Jan 17;68(1):64-70. Epub 2017 Nov 17.

Gulf Coast Research and Education Center, University of Florida, Gainesville, FL 32611, USA.

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 GEV388 and publicly available genomes representing the genus Pseudomonas revealed phylogroup 7 P. viridiflava strain UASW0038 and P. viridiflava type strain ICMP 2848 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 GEV388 and P. viridiflava ATCC 13223, 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 GEV388 (=LMG 30013=ATCC TSD-90) as the type strain.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1099/ijsem.0.002445DOI Listing
January 2018

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

Phytopathology 2017 Nov 15;107(11):1298-1304. Epub 2017 Aug 15.

First, fourth, seventh, eighth, and ninth authors: Department of Plant Pathology, University of Florida, Gainesville 32611; first, second, and tenth authors: Gulf Coast Research and Education Center, University of Florida, Balm 33598; third and fifth authors: Department of Plant Pathology, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster 44691; fourth and sixth authors: North Florida Research and Education Center, Quincy 32251; and eighth author: Emerging Pathogens Institute, University of Florida, Gainesville 32610.

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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1094/PHYTO-05-17-0178-RDOI Listing
November 2017

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

Front Plant Sci 2016 9;7:1805. Epub 2016 Dec 9.

UMR Interactions - Plantes - Microorganismes - Environnement, IRD-Cirad-Université Montpellier Montpellier, France.

Multiple species of cause bacterial spot of tomato (BST) and pepper. We sequenced five 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 . We examined pectolytic activity and starch hydrolysis, two tests which are useful in differentiating from , 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 . Sequence analysis of all the publicly available and 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 strains and >99.6% among the LMG strains and a subset of strains. These results suggest that and should be considered a single species. ANI values between strains of subsp. citrumelonis, , and a recently described pathogen of rose were >97.8% suggesting these pathogens should be a single species and recognized as . Analysis of the newly sequenced strains revealed interesting findings among the type 3 (T3) effectors, relatively ancient stepwise erosion of some T3 effectors, additional -specific T3 effectors among the causal agents of BST, orthologs of and , 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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fpls.2016.01805DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5146329PMC
December 2016

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

Phytopathology 2016 10 11;106(10):1097-1104. Epub 2016 Aug 11.

First, fourth, fifth, seventh, and ninth authors: Department of Plant Pathology, University of Florida, Gainesville; first, second and eighth authors: Gulf Coast Research and Education Center, University of Florida, Wimauma; third author: U.S. Vegetable Laboratory, 2700 Savannah Highway, USDA, Charleston, SC; sixth author: Department of Plant and Microbial Biology, University of California, Berkeley; and ninth author: Emerging Pathogens Institute, University of Florida, Gainesville.

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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1094/PHYTO-03-16-0119-FIDOI Listing
October 2016

Phylogenomics of Xanthomonas field strains infecting pepper and tomato reveals diversity in effector repertoires and identifies determinants of host specificity.

Front Microbiol 2015 3;6:535. Epub 2015 Jun 3.

Department of Plant and Microbial Biology, University of California, Berkeley Berkeley, CA, USA.

Bacterial spot disease of pepper and tomato is caused by four distinct Xanthomonas species and is a severely limiting factor on fruit yield in these crops. The genetic diversity and the type III effector repertoires of a large sampling of field strains for this disease have yet to be explored on a genomic scale, limiting our understanding of pathogen evolution in an agricultural setting. Genomes of 67 Xanthomonas euvesicatoria (Xe), Xanthomonas perforans (Xp), and Xanthomonas gardneri (Xg) strains isolated from diseased pepper and tomato fields in the southeastern and midwestern United States were sequenced in order to determine the genetic diversity in field strains. Type III effector repertoires were computationally predicted for each strain, and multiple methods of constructing phylogenies were employed to understand better the genetic relationship of strains in the collection. A division in the Xp population was detected based on core genome phylogeny, supporting a model whereby the host-range expansion of Xp field strains on pepper is due, in part, to a loss of the effector AvrBsT. Xp-host compatibility was further studied with the observation that a double deletion of AvrBsT and XopQ allows a host range expansion for Nicotiana benthamiana. Extensive sampling of field strains and an improved understanding of effector content will aid in efforts to design disease resistance strategies targeted against highly conserved core effectors.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fmicb.2015.00535DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4452888PMC
June 2015

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

Mol Plant Pathol 2015 Dec 29;16(9):907-20. Epub 2015 Apr 29.

Department of Plant Pathology, Fifield Hall, University of Florida, Gainesville, FL, 32611, USA.

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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/mpp.12244DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6638463PMC
December 2015

Multilocus sequence analysis of xanthomonads causing bacterial spot of tomato and pepper plants reveals strains generated by recombination among species and recent global spread of Xanthomonas gardneri.

Appl Environ Microbiol 2015 Feb;81(4):1520-9

Four Xanthomonas species are known to cause bacterial spot of tomato and pepper, but the global distribution and genetic diversity of these species are not well understood. A collection of bacterial spot-causing strains from the Americas, Africa, Southeast Asia, and New Zealand were characterized for genetic diversity and phylogenetic relationships using multilocus sequence analysis of six housekeeping genes. By examining strains from different continents, we found unexpected phylogeographic patterns, including the global distribution of a single multilocus haplotype of X. gardneri, possible regional differentiation in X. vesicatoria, and high species diversity on tomato in Africa. In addition, we found evidence of multiple recombination events between X. euvesicatoria and X. perforans. Our results indicate that there have been shifts in the species composition of bacterial spot pathogen populations due to the global spread of dominant genotypes and that recombination between species has generated genetic diversity in these populations.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/AEM.03000-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4309686PMC
February 2015
-->