Polyphasic characterization of xanthomonas strains from onion

Comparison of three commercial DNA extraction kits for the enhancement of PCR assay sensitivity for Xanthomonas euvesicatoria pv. allii

AIM

The study was carried out to evaluate three commercial DNA extraction kits, Probe GS, FitoSorb and Sorb GMO, thus identifying the most suitable for isolating the phytopathogenic bacteria Xanthomonas euvesicatoria pv. allii.

MATERIALS AND METHODS

Onion seed samples were prepared which were inoculated with bacterial concentrations ranging from 10¹ to 10⁷  CFU per ml. Real-time PCR was performed to determine the efficacy of the isolated DNA in enhancing the sensitivity of the assay. The DNA extracted by Probe GS had the best detectability, having been detected at the lowest concentration used in the study 10¹  × 3 CFU per ml. FitoSorb and Sorb GMO yielded DNA with a higher and similar limit of detection 10³  × 3 CFU per ml. Furthermore, Probe GS had the lowest cycle at every concentration tested as compared to the other methods.

CONCLUSION

Therefore, Probe GS proved to be the most optimized kit for the extraction of X. euvesicatoria pv. allii, hence enhanced degree of sensitivity for the assay.

IMPACT AND SIGNIFICANCE OF THE STUDY

The findings generated in this study can be used by phytosanitary laboratories to develop highly rapid and accurate diagnostic protocols for X. euvesicatoria pv. allii.

Trends in Molecular Diagnosis and Diversity Studies for Phytosanitary Regulated Xanthomonas

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

Draft Genome Sequence of Xanthomonas axonopodis pv. allii Strain CFBP 6369

We report here the draft genome sequence of Xanthomonas axonopodis pv. allii strain CFBP 6369, the causal agent of bacterial blight of onion. The draft genome has a size of 5,425,942 bp and a G+C content of 64.4%.

A Novel Xanthomonas sp. Causes Bacterial Spot of Rose (Rosa spp.)

A bacterial spot of rose (Rosa spp.) caused by a xanthomonad was observed in Florida and Texas. Ten representative strains collected from the two states between 2004 and 2010 were used to determine the taxonomic position of this rose pathogen. Fatty acid methyl ester analysis was performed and a nearly 2-kb 16S-23S rRNA intergenic spacer along with flanking portions of the 16S and 23S rRNA genes were sequenced for selected strains, showing that they were members of the genus Xanthomonas. Multilocus sequence typing and analysis (MLST/MLSA) and pathogenicity tests were conducted to further characterize the Xanthomonas strains. The MLSA, based on six gene fragments-fusA, gapA, gltA, gyrB, lacF, and lepA-showed that the rose strains fell into Xanthomonas axonopodis subgroup 9.2 and shared the highest similarity values (98.8 to 99.7%) with X. alfalfae subsp. citrumelonis of the subgroup. However, principal coordinate analysis grouped the rose strains into a unique cluster distinct from other members of the subgroup according to virulence phenotypes on 11 plant species belonging to five plant families (Araceae, Euphorbiaceae, Rosaceae, Rutaceae, and Solanaceae). Moreover, the rose strains were aggressive on rose and Indian Hawthorn (Rhaphiolepsis indica). On the basis of the MLSA and virulence phenotypes, the pathovar epithet rosa is proposed.

Transmission of Iris yellow spot virus by Frankliniella fusca and Thrips tabaci (Thysanoptera: Thripidae)

Thrips-transmitted Iris yellow spot virus (IYSV) (Family Bunyaviridae, Genus Tospovirus) affects onion production in the United States and worldwide. The presence of IYSV in Georgia was confirmed in 2003. Two important thrips species that transmit tospoviruses, the onion thrips (Thrips tabaci (Lindeman)) and the tobacco thrips (Frankliniella fusca (Hinds)) are known to infest onion in Georgia. However, T. tabaci is the only confirmed vector of IYSV. Experiments were conducted to test the vector status of F. fusca in comparison with T. tabaci. F. fusca and T. tabaci larvae and adults reared on IYSV-infected hosts were tested with antiserum specific to the nonstructural protein of IYSV through an antigen coated plate ELISA. The detection rates for F. fusca larvae and adults were 4.5 and 5.1%, respectively, and for T. tabaci larvae and adults they were 20.0 and 24.0%, respectively, indicating that both F. fusca and T. tabaci can transmit IYSV. Further, transmission efficiencies of F. fusca and T. tabaci were evaluated by using an indicator host, lisianthus (Eustoma russellianum (Salisbury)). Both F. fusca and T. tabaci transmitted IYSV at 18.3 and 76.6%, respectively. Results confirmed that F. fusca also can transmit IYSV but at a lower efficiency than T. tabaci. To attest if low vector competency of our laboratory-reared F. fusca population affected its IYSV transmission capability, a Tomato spotted wilt virus (Family Bunyaviridae, Genus Tospovirus) transmission experiment was conducted. F. fusca transmitted Tomato spotted wilt virus at a competent rate (90%) suggesting that the transmission efficiency of a competent thrips vector can widely vary between two closely related viruses.

Multiplex nested PCR for detection of Xanthomonas axonopodis pv. allii from onion seeds

Bacterial blight of onion (BBO) is an emerging disease that is present in many onion-producing areas. The causal agent, Xanthomonas axonopodis pv. allii, is seed transmitted. A reliable and sensitive diagnostic tool for testing seed health is needed. Detection of X. axonopodis pv. allii was achieved using a multiplex nested PCR assay developed using two randomly amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) sequences corresponding to pilus assembly genes (pilW and pilX) and the avrRxv gene, respectively. The multiplex nested PCR was used with a large collection of X. axonopodis pv. allii strains pathogenic to onion and/or other Allium species isolated in different regions of the world. The internal primers used in the multiplex PCR assay directed amplification for all 86 X. axonopodis pv. allii strains tested, resulting in a 401-bp amplicon, a 444- to 447-bp amplicon, or both amplicons, depending on the strain. No amplification was obtained for 41 unrelated phytopathogenic bacteria and for 14 saprophytic bacteria commonly isolated from onion leaves and seeds. Most Xanthomonas strains also did not produce amplicons, except for nine strains classified in X. axonopodis genetic subgroup 9.1 or 9.2 and not pathogenic to onion. Nevertheless, sequence signatures distinguished most of these strains from X. axonopodis pv. allii. The assay detected X. axonopodis pv. allii in seed lots with contamination levels of 5 x 10(2) CFU g(-1) or higher. The sensitivity threshold of the multiplex nested PCR assay was found to be 1 infected seed in 27,340 seeds. This PCR-based assay should be useful for certifying that commercial seed lots are free of this important seed-borne pathogen.

Polyphasic characterization of Xanthomonas axonopodis pv. allii associated with outbreaks of bacterial blight on three Allium species in the Mascarene archipelago

Based on the number of new reports during the last two decades, bacterial blight of onion (Allium cepa) is considered an emerging disease. The causal agent, Xanthomonas axonopodis pv. allii, is pathogenic to several Allium species after inoculation, but outbreaks worldwide have been primarily reported on onion. We describe a unique epidemiological situation in Réunion Island, France, with concomitant outbreaks on three Allium species, onion, leek (A. porrum), and garlic (A. sativum). There was no host specialization within Allium spp. among strains associated with the three host species. Based on amplified fragment length polymorphism (AFLP) and restriction fragment length polymorphism, strains associated with these outbreaks in Réunion Island were highly related genetically to strains isolated from diseased plant samples and contaminated seed lots in the neighboring island of Mauritius, where the disease has occurred since 1984. All AFLP haplotypes were identified as X. axonopodis pv. allii based on polymerase chain reaction analysis using specific primers, biochemical tests, and/or pathogenicity tests. Two genetically related groups of strains (A and B) that can be distinguished by AFLP, differential utilization of three carbon sources, and xanthomonadin pigment production were detected initially after establishment of the pathogen. In less than 10 years after the establishment of the pathogen there was nearly an extinction of group A strains in Réunion Island, suggesting differences in fitness between strains in the two groups.

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.

Quantitative and molecular epidemiology of bacterial blight of onion in seed production fields

ABSTRACT Onion, a biennial plant species, is threatened by the emerging, seed-borne, and seed-transmitted Xanthomonas axonopodis pv. allii. Bacterial blight epidemics were monitored in seed production fields over two seasons. Temporal disease progress was different between the two seasons, with final incidence ranging from 0.04 to 0.06 in 2003 and from 0.44 to 0.61 in 2004. The number of hours with temperatures above 24 degrees C was the best descriptor for predicting the number of days after inoculation for bacterial blight development on inoculated plants. Fitting the beta-binomial distribution and binary power law analysis indicated aggregated patterns of disease incidence data. The beta-binomial distribution was superior to the binomial distribution for 97% of the examined data sets. Spatial dependency ranged from 5.9 to 15.2 m, as determined by semivariance analysis. Based on amplified fragment length polymorphism (AFLP) analysis, it was concluded that plots predominantly were infected by the inoculated haplotype. A single other haplotype was identified by AFLP in all plots over the 2 years, and its detection in the field always followed wind-driven rains. X. axonopodis pv. allii-contaminated seed were detected by semiselective isolation and a nested polymerase chain reaction assay at levels up to 0.05% when final disease incidence was 0.61. Contaminated seed originated from both diseased and asymptomatic plants.

A comprehensive species to strain taxonomic framework for xanthomonas

ABSTRACT A comprehensive classification framework was developed that refines the current Xanthomonas classification scheme and provides a detailed assessment of Xanthomonas diversity at the species, subspecies, pathovar, and subpathovar levels. Polymerase chain reaction (PCR) using primers targeting the conserved repetitive sequences BOX, enterobacterial repetitive intergenic consensus (ERIC), and repetitive extragenic palindromic (REP) (rep-PCR) was used to generate genomic fingerprints of 339 Xanthomonas strains comprising 80 pathovars, 20 DNA homology groups, and a Stenotrophomonas maltophilia reference strain. Computer-assisted pattern analysis of the rep-PCR profiles permitted the clustering of strains into distinct groups, which correspond directly to the 20 DNA-DNA homology groups(genospecies) previously identified. Group 9 strains (X. axonopodis) were an exception and did not cluster together into a coherent group but comprised six subgroups. Over 160 strains not previously characterized by DNA-DNA hybridization analysis, or not previously classified, were assigned to specific genospecies based on the classification framework developed. The rep-PCR delineated subspecific groups within X. hortorum, X. arboricola, X. axonopodis, X. oryzae, X. campestris, and X. translucens. Numerous taxonomic issues with regard to the diversity, similarity, redundancy, or misnaming were resolved. This classification framework will enable the rapid identification and classification of new, novel, or unknown Xanthomonas strains that are pathogenic or are otherwise associated with plants.

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.

Management of Xanthomonas Leaf Blight of Onion with a Plant Activator, Biological Control Agents, and Copper Bactericides

Xanthomonas leaf blight (Xanthomonas axonopodis pv. allii) is a yield-limiting disease of onion (Allium cepa) in the western United States. Frequent applications of copper-based bactericides amended with an ethylenebisdithiocarbamate fungicide (e.g., maneb or mancozeb, class B2 carcinogens) provide some disease suppression, but strategies to reduce conventional bactericide use are needed to minimize grower costs, environmental impact, and public exposure to class B2 pesticides. Applications of acibenzolar-S-methyl reduced in planta and epiphytic populations of X. axonopodis pv. allii as effectively as applications of copper hydroxide-mancozeb in growth chamber studies. Under field conditions, four weekly applications of acibenzolar-S-methyl reduced severity of Xanthomonas leaf blight as or more effectively than 9 to 12 weekly applications of copper hydroxide or copper hydroxide-mancozeb. Acibenzolar-S-methyl applications did not increase bulb yield or grade compared with copper bactericide treatments. However, bulb yield was reduced 22 to 27% when 10 weekly applications of acibenzolar-S-methyl were made in the absence of disease. Application of a commercial formulation of both Pantoea agglomerans strain C9-1 and Pseudomonas fluorescens strain A506 reduced severity of Xanthomonas leaf blight in field experiments. Weekly copper hydroxide applications starting 1 to 2 weeks before bulb initiation were as effective as weekly applications started 3 to 4 weeks before bulb initiation, irrespective of the maneb rate used. Integration of acibenzolar-S-methyl and biological control agents with copper hydroxide in a carefully timed spray program may eliminate the use of the class B2 carcinogens maneb and mancozeb on onion without compromising efficacy for management of Xanthomonas leaf blight.

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.

Inoculum Sources and Survival of Xanthomonas axonopodis pv. allii in Colorado

Xanthomonas leaf blight, caused by the bacterium Xanthomonas axonopodis pv. allii, is an emerging disease of onion in the western United States and worldwide, but few management strategies have been developed because little is known about disease epidemiology and pathogen survival. Therefore, we sought to identify and quantify primary inoculum sources of the pathogen in Colorado. Growth chamber and field studies evaluated survival and dissemination of X. axonopodis pv. allii in association with weed, alternate host, and volunteer onion plants, irrigation water, and crop debris. Epiphytic X. axonopodis pv. allii was recovered from the foliage of nine asymptomatic weed species and Medicago sativa, but the bacterium was not recovered from plants in locations where an epidemic of Xanthomonas leaf blight did not occur the prior year. The bacterium also was isolated from volunteer onion with characteristic Xanthomonas leaf blight symptoms. A rifampicin mutant of X. axonopodis pv. allii strain O177 was recovered consistently from the irrigation tail water of onion fields inoculated with the bacterium; populations as large as 3.02 × 10⁴ CFU/ml were recovered. X. axonopodis pv. allii was recovered from infested onion leaves 9 months after they were placed on the soil surface or buried to a depth of 25 cm, but culturable populations of the pathogen decreased 10⁴ to 10⁶ more in buried leaves. Cultural practices that avoid or eliminate X. axonopodis pv. allii inoculum sources should reduce Xanthomonas leaf blight losses to onion.