Seventeen complete genome assemblies to augment sequencing coverage of bacterial plant pathogens in the UK Plant Health Risk Register

Specific scopeThis Standard describes a diagnostic protocol for Xanthomonas axonopodis pv. allii.This Standard should be used in conjunction with PM 7/76 Use of EPPO diagnostic protocols.Specific approval and amendmentFirst approved in 2016‐09.

The most important thermal properties of typical rocks and fluids encountered in thermal recovery operations and the variation of such properties with temperature, and in the case of rocks, with fluid saturation are discussed. An attempt will be made to cover the available experimental data, and the most acceptable calculation techniques which are suitable for both computer and hand computations. The thermal properties of liquids and gases which may be of interest to petroleum engineers engaged in thermal recovery operations are viscosity, density, thermal conductivity, specific heat, heat of vaporization, and vapor pressure. Some of these properties will be of greater interest in the case of liquids and rocks, than in the case of gases. (27 refs.)

Identification of bacterial isolates from a public hospital in Australia using complexity-reduced genotyping

Xanthomonas axonopodis pv. citrumelo is a citrus pathogen causing citrus bacterial spot disease that is geographically restricted within the state of Florida. Illumina, 454 sequencing, and optical mapping were used to obtain a complete genome sequence of X. axonopodis pv. citrumelo strain F1, 4.9 Mb in size. The strain lacks plasmids, in contrast to other citrus Xanthomonas pathogens. Phylogenetic analysis revealed that this pathogen is very close to the tomato bacterial spot pathogen X. campestris pv. vesicatoria 85-10, with a completely different host range. We also compared X. axonopodis pv. citrumelo to the genome of citrus canker pathogen X. axonopodis pv. citri 306. Comparative genomic analysis showed differences in several gene clusters, like those for type III effectors, the type IV secretion system, lipopolysaccharide synthesis, and others. In addition to pthA, effectors such as xopE3, xopAI, and hrpW were absent from X. axonopodis pv. citrumelo while present in X. axonopodis pv. citri. These effectors might be responsible for survival and the low virulence of this pathogen on citrus compared to that of X. axonopodis pv. citri. We also identified unique effectors in X. axonopodis pv. citrumelo that may be related to the different host range as compared to that of X. axonopodis pv. citri. X. axonopodis pv. citrumelo also lacks various genes, such as syrE1, syrE2, and RTX toxin family genes, which were present in X. axonopodis pv. citri. These may be associated with the distinct virulences of X. axonopodis pv. citrumelo and X. axonopodis pv. citri. Comparison of the complete genome sequence of X. axonopodis pv. citrumelo to those of X. axonopodis pv. citri and X. campestris pv. vesicatoria provides valuable insights into the mechanism of bacterial virulence and host specificity.

The Comprehensive Phytopathogen Genomics Resource (CPGR) provides a web-based portal for plant pathologists and diagnosticians to view the genome and trancriptome sequence status of 806 bacterial, fungal, oomycete, nematode, viral and viroid plant pathogens. Tools are available to search and analyze annotated genome sequences of 74 bacterial, fungal and oomycete pathogens. Oomycete and fungal genomes are obtained directly from GenBank, whereas bacterial genome sequences are downloaded from the A Systematic Annotation Package (ASAP) database that provides curation of genomes using comparative approaches. Curated lists of bacterial genes relevant to pathogenicity and avirulence are also provided. The Plant Pathogen Transcript Assemblies Database provides annotated assemblies of the transcribed regions of 82 eukaryotic genomes from publicly available single pass Expressed Sequence Tags. Data-mining tools are provided along with tools to create candidate diagnostic markers, an emerging use for genomic sequence data in plant pathology. The Plant Pathogen Ribosomal DNA (rDNA) database is a resource for pathogens that lack genome or transcriptome data sets and contains 131 755 rDNA sequences from GenBank for 17 613 species identified as plant pathogens and related genera.Database URL: http://cpgr.plantbiology.msu.edu.

Soybean plants were grown in a greenhouse. In the phase of 4-6 leaves soybeans were artificially infected with strains of pathogens: Xanthomonas axonopodis pv. glycines 9284 and Xanthomonas axonopodis pv. phaseoli 8843. These strains were obtained from the Ukrainian collection of microorganisms of the Zabolotny institute of Microbiology and Virology of National Academy of Sciences of Ukraine. The photochemical activity of soybean leaves was determined by the biophysical method of chlorophyll fluorescence induction in 13 days after plant inoculation with bacterial strains. A portable Florotest fluorometer was use for measurements. A degree of chlorophyll degradation and suppression of photosynthetic activity in soybean leaves at artificial infection with bacterial strains isolated from different plant species of the Fabaceaeae family dependent from its virulence have been shown. The strain X. axonopodis pv. glycines 9284, isolated from soybean plants, have been highly virulent and acted more negatively than the low virulent to soybean strain X. axonopodis pv. phaseoli 8843. In particular, the value of the minimum fluorescence F0 decreased by 37.0 and 15.4 % for inoculation by strains with different virulence degree: X. axonopodis pv. glycines 9284 (from soybeans) and X. axonopodis pv. phaseoli 8843 (from beans) respectively. There was also a significant decrease in the value of Fm in these variants – by 54.9 % (X. axonopodis pv. glycines 9284) and 19.3 % (X. axonopodis pv. phaseoli 8843). At the same time, the value of maximum quantum yield of PSII (Fv / Fm) was decreased by 11.8 % in the variant with inoculation of soybean plants with the highly virulent strain X. axonopodis pv. glycines 9284, that indicates photoinhibition or damage of antenna complexes of the PSII photosynthetic apparatus of soybean plants. At the same time, only the tendency to reduce the maximum quantum yield of PSII was determined under action infection plants with X. axonopodis pv. phaseoli 8843. A parameter chlorophyll fluorescence decrease ratio Rfd, which shows the activity of CO2 assimilation in the Calvin cycle, was inhibition more at the action of artificial infection with a highly virulent strain – X. axonopodis pv. glycines 9284 – 54.5 and less – at infection with a low virulence strain – X. axonopodis pv. phaseoli 8843 – by 10.8 %. With prolonged action of the pathogenic bacterial strains X.axonopodis pv. glycines 9284 and the X. axonopodis pv. phaseoli 8843 (fortnight) showed significant inhibition of the catalase and peroxidase activity of leaf tissues, which is evidence of an increase in the formation of ROS. It was demonstrated that the highly virulent strain X.axonopodis pv. glycines 9284 most of all suppressed the catalase activity of soybean leaf tissues.

In October 2003, a new bacterial disease with symptoms similar to those caused by Xanthomonas axonopodis pv. poinsettiicola was observed on poinsettia leaves at a flower nursery in Zhejiang Province of China. Three Xanthomonas strains were isolated from infected plants and classified as X. axonopodis. They were differentiated from the pathotype strain LMG849 of X. axonopodis pv. poinsettiicola causing bacterial leaf spot of poinsettia by comparison of pathogenicity, substrate utilization and BOX-PCR genomic fingerprints.

A unified approach to naming bacteria ensures accurate communication among scientists, regulators and the public. Rules for nomenclature, set out in the International Code of Nomenclature of Bacteria (ICNB), ensure that proposals for new names and combinations follow a logical and standardized progression that maintains the integrity of the established nomenclature while facilitating changes based on scientific inquiry into relationships among organisms. However, these Rules only apply to ranks at the level of subspecies and above and not to lower taxonomic ranks. The pathovar is one infraspecific rank that is widely used in the classification and nomenclature of plant pathogenic bacteria and is often included in legislation to provide statutory control of bacterial plant pathogens. Thus, phytobacteriologists must rely on two discontinuous but, complimentary systems: the Rules set forth in ICNB for naming down to subspecies level, and the Standards in the International Standards for Naming Pathovars of Plant Pathogenic Bacteria to name pathovars. A framework for determining the priority of names is provided by the Approved Lists of Bacterial Names, which gives genus, species and subspecies names and their corresponding type strains, and subsequent lists of validly published names appearing in the International Journal of Systematic and Evolutionary Microbiology. For pathovar names priority is based on the date of valid publication of legitimate names. A list of pathovar names and pathotype strains is maintained by the Committee on the Taxonomy of Plant Pathogenic Bacteria of the International Society of Plant Pathology. To help researchers avoid common pitfalls encountered when developing nomenclature for novel classification systems, this manuscript clarifies several key Rules and Standards. It aims to promote best practice, in that names developed to conform to the ICNB should also consider precedents set by previous nomenclatural designations as per the International Standards for Naming Pathovars of Plant Pathogenic Bacteria, thus ensuring continuity across the nomenclature of all phytopathogenic bacteria.

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.

Xanthomonas axonopodis pv. glycines에 의해 발병되는 콩 불마름병은 한국에서 콩에 가장 많이 발생하는 중요한 세균성 병해 중 하나이다. 본 연구에서는 Xanthomonas axonopodis pv. glycines를 종자에서 검출하기 위해 PCR기법을 이용하였으며, 한국의 36개 주요 콩 품종의 종자 오염을 조사하였다. 그리고 병원균 검출과 동정을 위한 PCR assay와 dilution plating assay를 비교하였다. PCR assay를 이용하여 인공접종에 의한 이병종자와 자연감염된 이병종자로부터 병원균 검출을 확인하였다. PCR assay를 통한 이런 결과는 dilution plating assay와 비슷한 결과를 보여 주었으며 종자에서 병원균을 검출하는 다른 전통적인 방법보다 더 효과적인 방법으로 증명되었다. 36개 주요 콩 품종의 X. axonopodis pv. glycines에 의한 종자 전염을 확인한 결과 풍산나물콩, 만리콩, 태광콩, 대망콩, 아주까리콩에서 병원균이 검출되었다. 그러므로 PCR assay는 콩 종자에서 신속하고, 민감하게 X. axonopodis pv. glycines 특이적으로 검출할 수 있는 효과적인 방법으로 활용될 수 있을 것이다. Xanthomonas axonopodis pv. glycines is the causal agent of bacterial pustule of soybean(Glycine max. (L.) Merr), which is one of the most prevalent bacterial diseases in Korea. In this study, Polymerase Chain Reaction (PCR) assay was applied to detect Xanthomonas axonopodis pv. glycines and to survey on seed contamination in 36 soybean cultivars of Korea. And we have to compare PCR assay with dilution-plating assay of detection and identification. We confirmed detection of pathogen from artificial infected seeds and natural Infected seeds using PCR assay. This assay gave results similar to a seed-wash dilution plating assay and proved more effective than classical methods. Results of survey on seed contamination by X. axonopodis pv. glycines from 36 cultivar seeds showed that the pathogen was detected from Pungsan-namulkong, Mallikong, Taekwangkong, Daemangkong, Ajukkarikong using PCR assay. Therefore, The PCR assay provides a sensitive, rapid tool for the specific detection of X. axonopodis pv. glycines in soybean seeds.

Xanthan gum were produced from the following Xanthomonas strains; standard strain Xanthomonas campestris NRRL B-1459 and isolated strains Xanthomonas arbicola pv. juglandis, Xanthomonas axonopodis pv. vesicatoria, Xanthomonas axonopodis pv. begonia, Xanthomonas axonopodis pv. dieffenbachia. The viscosity features of the xanthan gums obtained were determined at 25–80°C with different pH values and were compared to commercial xanthan gum. Our results indicate that X. arbicola pv. juglandis showed the highest productivity (8.22±1.52 g/L gum). This was followed by X. axonopodis pv. begonia (7.74±1.30 g/L gum), and the control bacterial strain X. campestris NRRL B-1459 (7.46±0.28 g/L gum). X. axonopodis pv. vesicatoria showed the lowest productivity (6.40±0.55 g/L gum). No xanthan gum could be obtained from X. axonopodis pv. dieffenbachia. Xanthan gum produced by X. axonopodis pv. vesicatoria showed the highest viscosity value (428 mPa·sec at 1% solution) in all Xanthomonas strains isolated from plants.

An Interactive, Online Web Map Resource of Global Fusarium oxysporum ff. spp. Diversity and Distribution.

콩 불마름병을 일으키는 Xanthomonas axonopodis pv. glycines를 종자에서 DNA 추출없이 바로 검출하는 방법에 대하여 연구하였다. 콩 종자에서 X. axonopodis pv. glycines를 특이적으로 검출하기 위해 특이적인 유전자로 알려져 있는 glycinecin A로부터 증폭 size가 401 bp인 primer Xag F1 & Xag R1을 고안하였다. Xag Fl과 Xag R1 primer는 콩 종자와 잎에서 분리한 균주와 KACC에서 분양받은 X. axonopoids pv. glycines 균주를 증폭시켰으나 근연종인 X. axonopodis pv. citri, X. axonopodis pv. vesicatoria 등은 증폭되지 않았다. 콩 종자에 존재하는 것으로 알려진 다른 세균들 역시 증폭되지 않았다. 고안된 Xag F1 & Xag R1 primer를 이용한 X. axonopodis pv. glycines의 검출 한계 농도 측정은 genomic DNA와 세포 현탁액을 이용하였다. X. axonopodis pv. glycines의 genomic DNA는 200 fg까지 증폭이 되었으며, 세포현탁액은 <TEX>$OD_{600nm}$</TEX> 0.1로 농도를 조정한 뒤, <TEX>$10^{-8}$</TEX>까지 희석하여 측정한 결과 <TEX>$10^{-6}$</TEX>인 <TEX>$1.8{\times}10^3$</TEX> cfu/ml까지 증폭이 확인되었다. 자연 감염된 종자에서 병원균을 검출하기 위해 종자를 육안상 건전종자와 불건전한 종자(변색립, 피해립)로 구분하여 direct PCR 방법으로 실험 한 결과 육안상 건전종자에서는 병원균이 검출되지 않았으나 불건전한 종자에서는 병원균의 검출이 확인되었다. 또한 진탕 배양 시간에 따른 병원균의 검출여부를 조사한 결과 진탕 배양 2시간부터 병원균의 검출이 확인되었으며 시간이 지날수록 증폭 밴드가 더욱 선명해 지는 것을 확인할 수 있었다. 그러므로 고안된 Xag Fl & Xag R1 primer를 이용한 direct PCR 방법은 다른 많은 미생물들로 오염되어진 콩종자에 있는 X. axonopodis pv. glycines를 신속하고 민감하게 검정할 수 있는 효과적인 방법으로 활용될 수 있을 것이다. Direct Polymerase Chain Reaction (PCR) method that combines biological and enzymatic amplification of PCR targets was developed for the detection of Xanthomonas axonopodis pv. glycines on soybeen seeds without DNA isolation. Primers Xag F1 and Xag R1 were designed to specifically amplify a 401 bp fragment of the glycinecin A gene of X axonopodis pv. glycines. Xag F1 and Xag R1 were used to carry out the PCR analysis with genomic DNA from 45 different bacterial strains including phylogenetically related bacteria with X axonopodis pv. glycines, and other bacterial strains of different genus and species. The PCR assay using this set of primers were able to detect X axonopodis pv. glycines with DNA concentration as low as 200 fg and <TEX>$1.8{\times}10^3$</TEX> cfu/ml. The Xag was detected from the seed samples incubated for 2 hrs with shaking and the intensity of the band was increase with the incubation time of seeds. The Direct PCR assay method without DNA isolation makes detection of X. axonopodis pv. glycines on soybean seeds easier and more sensitive than other conventional methods. The developed seed assay using direct PCR method will be useful for the specific detection of X. axonopodis pv. glycines in soybean seed samples.

HomePlant DiseaseVol. 99, No. 4First Report of Cassava Bacterial Blight Caused by Xanthomonas axonopodis pv. manihotis in Burkina Faso PreviousNext DISEASE NOTES OPENOpen Access licenseFirst Report of Cassava Bacterial Blight Caused by Xanthomonas axonopodis pv. manihotis in Burkina FasoI. Wonni, L. Ouedraogo, S. Dao, C. Tekete, O. Koita, G. Taghouti, P. Portier, B. Szurek, and V. VerdierI. WonniSearch for more papers by this author, L. OuedraogoSearch for more papers by this author, S. DaoSearch for more papers by this author, C. TeketeSearch for more papers by this author, O. KoitaSearch for more papers by this author, G. TaghoutiSearch for more papers by this author, P. PortierSearch for more papers by this author, B. SzurekSearch for more papers by this author, and V. VerdierSearch for more papers by this authorAffiliationsAuthors and Affiliations I. Wonni L. Ouedraogo , INERA Farako-Ba, Bobo-Dioulasso, Burkina-Faso S. Dao C. Tekete O. Koita , Université des Sciences Techniques et Technologiques, Faculté des Sciences et Techniques, LBMA, Bamako, Mali G. Taghouti P. Portier , CIRM-CFBP, UMR 1345 IRHS INRA, ACO, UA, 49070 Beaucouzé Cedex, France B. Szurek V. Verdier , UMR186, Interactions Plantes Microorganismes Environnement (IPME), IRD-Cirad-UM, 34394 Montpellier Cedex 5, France. Published Online:1 Apr 2015https://doi.org/10.1094/PDIS-03-14-0302-PDNAboutSectionsSupplemental ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InRedditEmailWechat Xanthomonas axonopodis pv. manihotis is the causal agent of cassava bacterial blight (CBB), a major disease of cassava in tropical and subtropical areas. CBB is a foliar and vascular disease characterized by angular leaf lesions, blight, wilting, stem exudates, and stem cankers. Since cassava is propagated clonally from stem cuttings, CBB plays a major role in limiting productivity, with losses between 12 and 100% affecting both yield and planting material. In August of 2011 and October of 2012, CBB symptoms were observed on 10-month-old field cassava grown in Bonfeba and in Takeledougou, Burkina-Faso (Cascades region). Symptoms consisted of angular, water-soaked leaf lesions, wilt, and visible exudates on the stem. White Xanthomonas-like strains were isolated from leaf tissues on LPGA medium (yeast, 5 g; peptone, 5 g; glucose, 5 g; bacto agar, 15 g; and distilled water, 1,000 ml). A PCR assay developed for the identification of X. axonopodis pv. manihotis (2) was used to determine the identity of Xanthomonas-like strains. X. axonopodis pv. manihotis strain CFBP7661 was used as a positive control. The expected DNA fragment (898 bp) was obtained from all the strains. No fragment was observed for negative controls (distilled water as the template). Three X. axoponodis pv. manihotis strains were further analyzed by sequence analysis using the gyrB and rpoD housekeeping genes. Comparison of rpoD and gyrB sequences showed that strains were 99 to 100% identical to 65 different strains of X. axonopodis pv. manihotis. Pathogenicity tests were performed on greenhouse-grown 4-week-old cassava plants, cv. MCOL 1522. Cultures were grown overnight in LPGA medium, adjusted in sterile water to 1 × 108 CFU/ml, and inoculated into cassava leaves and stems as previously described (1). Control plants were inoculated with sterile water. X. axonopodis pv. manihotis strain CFBP7661 was used as a positive control. After 7 days of incubation in the greenhouse at 28 ± 1°C with a 12-h photoperiod, inoculated leaves developed water-soaked lesions. Wilted leaves and stem exudates were visible at 30 days after stem inoculation. Symptoms were identical to those seen in the field. Control plants remained symptomless. Koch’s postulates were fulfilled after re-isolation of Xanthomonas-like white strains from leaf symptoms on inoculated cassava and confirmation as X. axonopodis pv. manihotis by PCR assay as described above. Three strains (CFBP7945, CFBP7946, CFBP7947) were deposited in the French Collection for Plant-Associated Bacteria (CIRM-CFBP). Information on Xam strains as well as gyrB and rpoD sequences are available through CIRM-CFBP http://www6.inra.fr/cirm_eng/CFBP-Plant-Associated-Bacteria. To our knowledge, this is the first report of CBB in Burkina Faso. Since cassava is becoming a crop of importance for human consumption in Burkina-Faso, CBB may limit productivity. Further surveys will be necessary to evaluate the geographic distribution and prevalence of CBB in Burkina-Faso and neighboring countries.

Twenty-five strains of Xanthomonas axonopodis pv. citri and 14 strains of Xanthomonas spp. were tested for bacteriocin production. X. axonopodis pv. passiflorae strains were sensitive to the bacteriocins produced by the 25 X. axonopodis pv. citri strains evaluated in this study while strains of X. axonopodis pv. manihotis and X. campestris pv. campestris showed variable sensitivity. Only five of the 25 X. axonopodis pv. citri strains were not inhibited by the bacteriocins produced by the two X. axonopodis pv. passiflorae strains. The bacteriocins produced by the Xanthomonas axonopodis pv. citri (FDC-806) and X. axonopodis pv. passiflorae (Mar-2850 A) strains were thermolabile, resistant to lysozyme and sensitive to DNAse. The bacteriocin produced by X. axonopodis pv. passiflorae was resistant to the action of proteinase K, trypsin and RNAse while the bacteriocin produced by X. axonopodis pv. citri was sensitive to these enzymes. The bacteriocins produced by X. axonopodis pv. passiflorae and X. axonopodis pv. citri were called passifloricin and citricin, respectively.