First Report of Leaf Blight of Onion Caused by Xanthomonas campestris in the Continental United States

Isolation and Characterization of Bacteria Associated with Onion and First Report of Onion Diseases Caused by Five Bacterial Pathogens in Texas, U.S.A

Bacterial diseases pose a severe challenge to growers and cause significant loss to the billion-dollar onion industry in the United States. Texas is the sixth largest onion producing state, yet the bacterial communities associated with short-day onion crops grown in Texas have not been studied. This study was conducted to identify, characterize, and understand the diversity of bacteria associated with onion production in Texas. In 2020, 190 foliar and 210 bulb samples were collected from onion crops in the Rio Grande Valley and Winter Garden regions of Texas. Sequencing of the 16s rRNA gene was used to identify each bacterial strains to a genus. The pathogenicity to onion of each bacterial strain was tested using three assays: a red onion scale assay, a yellow onion bulb assay, and a foliar assay. Whole genome sequencing was done to identify the onion-pathogenic strains to species. Collectively, isolates of 24 genera belonging to three phyla were detected, including 19 genera from foliar samples and nine genera from bulb samples. Isolates in the Phylum Proteobacteria, including 15 genera of Gram-negative bacteria, were the most abundant of the taxa, comprising 90.0% of the strains isolated. The diversity of foliar isolates was evenly distributed between Gram-positive and Gram-negative bacteria, while Gram-negative bacteria dominated the isolates from bulb samples. In total, 83.9% of the bacterial isolates were not pathogenic on onion, with only isolates of Pantoea, Pseudomonas, Burkholderia, Erwinia, Enterobacter, and Curtobacterium proving pathogenic. Strains of Burkholderia gladioli, Pseudomonas alliivorans, Pantoea agglomerans, P. ananatis, and P. allii are the first documented cases of these pathogens of onion in Texas. Identifying and characterizing the nature of onion microflora, including pathogens of onion, is vital to developing rapid disease detection techniques via pathogenomics and minimizing losses through the application of effective disease management measures.

OEM--a new medium for rapid isolation of onion-pathogenic and onion-associated bacteria

Onions (Allium cepa L.) are plagued by a number of bacterial pathogens including Pantoea ananatis, P. agglomerans, Burkholderia cepacia, Enterobacter cloacae, Pectobacterium carotovorum subsp. carotovorum, Xanthomonas axonopodis pv. axonopodis and several Pseudomonas spp. We developed a semi-selective medium, termed onion extract medium (OEM), to selectively and rapidly isolate bacteria pathogenic to and associated with onions and onion-related samples including bulbs, seeds, sets, transplant seedlings, soil and water. Most strains of interest grow sufficiently on OEM in 24h at 28°C for tentative identification based on colony morphology, facilitating further characterization by microbiological and/or molecular means.

Management of Xanthomonas Leaf Blight of Onion with Bacteriophages and a Plant Activator

Xanthomonas leaf blight of onion (Allium cepa), caused by Xanthomonas axonopodis pv. allii, continues to be a challenging and yield-threatening disease in Colorado and other regions of onion production worldwide. Studies were conducted to develop management strategies for this disease that are equally effective and more sustainable than the current practices of making multiple applications of copper bactericides. Mixtures of bacteriophages and the plant defense activator, acibenzolar-S-methyl, were evaluated under field and greenhouse conditions for their abilities to reduce Xanthomonas leaf blight severity. Bacteriophage populations in the phyllosphere of onion were monitored over time. Bacteriophage populations persisted on onion leaves for at least 72 to 96 h under field and greenhouse conditions, respectively. Under field conditions at one location, biweekly or weekly applications of bacteriophages reduced disease severity by 26 to 50%, which was equal to or better than weekly applications of copper hydroxide plus mancozeb. Acibenzolar-S-methyl also successfully reduced disease severity by up to 50% when used alone preventatively or followed by biweekly bacteriophage applications. Reductions in disease severity generally were not associated with improvements in onion bulb size or yield. Integration of bacteriophage mixtures with acibenzolar-S-methyl appears to be a promising strategy for managing Xanthomonas leaf blight of onion, and could reduce grower reliance on conventional copper bactericide applied with ethylenebisdithiocarbamate fungicides.

Pathogenic and Genetic Relatedness Among Xanthomonas axonopodis pv. allii and Other Pathovars of X. axonopodis

ABSTRACT Xanthomonas axonopodis pv. allii is phenotypically and genetically diverse and its relationship to other X. axonopodis pathovars within DNA homology group 9.2 is unknown. In growth chamber experiments, disease symptoms were produced on onion only by inoculation with X. axonopodis pv. allii. Citrus bacterial spot symptoms were induced by X. axonopodis pvs. alfalfae, itrumelo, and allii on Duncan grapefruit and key lime. X. axonopodis pv. allii multiplication and persistence in Duncan grapefruit were equal to those of an aggressive strain of X. axonopodis pv. citrumelo, but populations of X. axonopodis pvs. alfalfae, betlicola, citrumelo, phaseoli, and vesicatoria were 1.3 to 4.0 log units less than X. axonopodis pv. allii in onion. Genomic fingerprinting by repetitive sequence- based polymerase chain reaction demonstrated that X. axonopodis pvs. allii, alfalfae, and citrumelo are distinct from other Xanthomonas species and X. axonopodis pathovars, but these pathovars were indistinguishable from each other. Three genotype groups were apparent among DNA homology group 9.2 strains, and generally correspond to the aggressiveness and genotype groups previously described for X. axonopodis pv. citrumelo. X. axonopodis pvs. allii, alfalfae, and citrumelo appear to have recently diverged from a common ancestral strain.

Epiphytic Survival of Xanthomonas axonopodis pv. allii and X. axonopodis pv. phaseoli on Leguminous Hosts and Onion

Xanthomonas leaf blight of onion (Allium cepa), caused by Xanthomonas axonopodis pv. allii, and common bacterial blight of dry bean (Phaseolus vulgaris), caused by Xanthomonas axonopodis pv. phaseoli, are perennial problems in the Central High Plains of the United States. Onion and dry bean are commonly grown in rotation in Colorado, but it is unknown if X. axonopodis pv. allii and X. axonopodis pv. phaseoli survive epiphytically or pathogenically on dry bean and onion, respectively. Under high humidity growth chamber conditions, epiphytic X. axonopodis pv. allii populations increased on alfalfa, chickpea, dry bean, lentil, and soybean, but the epiphytic populations were at least 10-fold greater on onion. When artificially inoculated under field conditions, epiphytic populations of X. axonopodis pv. allii were recovered from dry bean, lentil, and onion, but the bacterium did not persist on chickpea or soybean. Epiphytic X. axonopodis pv. phaseoli was recovered from symptomless onion plants in fields cropped to dry bean the prior year, but not from fields cropped to a host other than dry bean. Close rotation of onion and dry bean may allow X. axonopodis pv. allii and X. axonopodis pv. phaseoli to persist epiphytically, and crop rotation schemes may need to be altered to reduce survival of these pathogens in onion and dry bean cropping systems.

Polyphasic characterization of xanthomonads isolated from onion, garlic and Welsh onion (Allium spp.) and their relatedness to different Xanthomonas species

Bacterial blight is an emerging disease that affects primarily onion, but also garlic and Welsh onion. The present study was undertaken to characterize the causative xanthomonad(s) by a polyphasic approach using a worldwide collection of 33 bacterial strains. Analysis of 16S rRNA gene sequence similarities indicated that the causal agent belongs to the campestris core in the genus Xanthomonas, which is in agreement with results of phenotypic characterization (analyses of carbon source utilization and fatty acid methyl esters). However, DNA-DNA hybridization, thermal stability of DNA reassociation and fluorescent amplified fragment length polymorphism analysis allowed the causal agent to be identified as a pathovar of Xanthomonas axonopodis.

Polyphasic characterization of xanthomonas strains from onion

ABSTRACT Xanthomonas leaf blight has become an increasingly important disease of onion, but the diversity among Xanthomonas strains isolated from onion is unknown, as is their relationship to other species and pathovars of Xanthomonas. Forty-nine Xanthomonas strains isolated from onion over 27 years from 10 diverse geographic regions were characterized by pathogenicity to onion and dry bean, fatty acid profiles, substrate utilization patterns (Biolog), bactericide resistance, repetitive sequence-based polymerase chain reaction fingerprinting, rDNA internally transcribed spacer (ITS) region, and hrp b6 gene sequencing. Multiplication of onion Xanthomonas strain R-O177 was not different from X. axonopodis pv. phaseoli in dry bean, but typical common bacterial blight disease symptoms were absent in dry bean. Populations from each geographical region were uniformly sensitive to 100 mug of CuSO(4), 100 mug of ZnSO(4), and 100 mug of streptomycin sulfate per ml. Biolog substrate utilization and fatty acid profiles revealed close phenoltypic relatedness between onion strains of Xanthomonas and X. axonopodis pv. dieffenbachiae (57% of strains) and X. arboricola pv. poinsettiicola (37% of strains), respectively. A logistic regression model based on fatty acid composition and substrate utilization classified 69% of strains into their geographical region of origin. Sequencing of a portion of the hrp B6 gene from 24 strains and ITS region from 25 strains revealed greater than 97% sequence similarity among strains. DNA fingerprinting revealed five genotype groups within onion strains of Xanthomonas and a high degree of genetic diversity among geographical regions of origin. Based on pathogenicity to onion, carbon substrate utilization, fatty acid profiles, rDNA genetic diversity, and genomic fingerprints, we conclude that the strains examined in this study are pathovar X. axonopodis pv. allii. Implications of genetic and phenotypic diversity within X. axonopodis pv. allii are discussed in relation to an integrated pest management program.

Spatial and Temporal Analyses of Bacterial Blight of Onion Caused by Xanthomonas axonopodis pv. allii

ABSTRACT Bacterial blight of onion is a severe disease, which emerged over the past decade in several onion-producing areas. This disease currently is observed in both the Old and New Worlds. Although the causative agent, Xanthomonas axonopodis pv. allii, is potentially seedborne, seed transmission and significance of seedborne initial inoculum for the development of bacterial blight of onion previously has not been assessed. This article describes experimental work designed to evaluate the biological importance of seedborne X. axonopodis pv. allii as an initial inoculum source, and examine the temporal and spatial dynamics of the disease. Over 3 years, outbreaks of bacterial blight of onion always were induced in experimental plots sown with naturally contaminated seed lots, with a contamination rate determined as 0.04%. Analyses of disease patterns indicated a likely seedborne origin for the inoculum associated with the early stages of epidemics. Spatial analyses performed with several statistical methods indicated aggregated patterns of disease incidence data. Primary foci enlarged over time, and a few distinct secondary foci sometimes were established after occurrence of wind-driven rains (with gusts up to 15 m s(-1)). Distances between primary and secondary foci ranged from less than 1 m (satellite foci) to 25 m. It remains possible that longdistance dispersal of inoculum was at least partly involved in the later stages of epidemics.

Relation of Temperature and Rainfall to Development of Xanthomonas and Pantoea Leaf Blights of Onion in Colorado

During the 1996 to 1999 growing seasons, some areas of Colorado's onion-growing regions experienced a complex of bacterial diseases including leaf blights caused by Xanthomonas campestris and Pantoea ananatis. Crop losses varied depending on adverse weather (associated with rain, storm, and temperature patterns) and stage of onion plant development. Environmental conditions during vegetative development had no significant association with the initial appearance or subsequent intensity of disease. Both pathogens were active at average high temperatures that ranged from 28 to 35°C during bulbing. Multiple regression models were developed to predict the initial appearance (growing degree day [GDD]) and subsequent Xanthomonas leaf blight intensity (final proportion of disease [FPD]) using macroclimatic meteorological conditions, including July average daily high temperature (T_jmax), August cumulative rainfall (P_a), and cumulative rainfall in July and August (P_ja). Initial disease appearance and disease intensity were described by GDD₁₀ = -6,153.43 + 215.50T_jmax - 0.92P_a and FPD = 222.79 - 6.92T_jmax + 0.52P_ja, respectively. Pantoea leaf blight initial appearance was strongly associated with July average daily temperatures (T_j) and was described by GDD₁₀ = -5,930.43 + 289.07T_j. Results are discussed in relation to an integrated pest management strategy in Colorado.