Polymorphism analysis of housekeeping genes for identification and differentiation of <Emphasis Type="Italic">Clavibacter michiganensis</Emphasis> subspecies

The utility of polymorphism analysis was determined for differentiation of the following subspecies of the Gram-positive plant pathogenic bacterium, Clavibacter michiganensis: C. m. subsp. michiganensis, C. m. subsp. sepedonicus, C. m. subsp. insidiosus C. m. subsp. nebraskensis, and C. m. subsp. tessellarius. Specific primers designed for amplification of the housekeeping genes recA, rpoB, and rpoD generated 827-, 1037-, and 862-bp DNA fragments, respectively. PCR products obtained from 40 C. michiganensis strains were analysed using RFLP with four restriction endonucleases, and those PCR products with specific RFLP patterns were sequenced. The genotypes discriminated after PCR–RFLP were specific for each subspecies and also allowed for differentiation of C. m. subsp. michiganensis strains. Sequence analysis of the recA, rpoB, and rpoD gene fragments also distinguished C. michiganensis subspecies and was useful for phylogenetic analysis of all subspecies. For rapid, inexpensive, and effective differentiation of the five subspecies in this research, we recommend the amplification of recA and/or rpoD gene fragments and digestion of the PCR products with the restriction endonuclease FnuDII.     

Rapid phylogenetic identification of members of the Pseudomonas syringae species complex using the rpoD locus

Phylogenies based on four loci confirmed the relatedness of all nine validly published species type strains within the Pseudomonas syringae species complex. To further establish the phylogenetic structure within the complex, all 67 pathovar type strains (with defined host ranges) were sequenced using a 578‐nucleotide rpoD locus. Since this locus encompassed that used in a previous seven‐locus study, it was possible to relate these strains to the existing phylogroup, genomospecies and binomial classifications. All species type strains were distinguished by relatively long branch lengths with all four loci, except for P. savastanoi, P. ficuserectae, P. meliae, P. amygdali and P. tremae, which were attributed to phylogroup 3. The grouping of P. tremae with these genomospecies‐2 species was surprising since this species was previously designated as the sole representative of genomospecies 5. The oat pathogen P. syringae pv. coronafaciens was also distinguished by relatively long branch lengths with all four loci. The rpoD phylogeny grouped all the pathovar type strains into major clades that corresponded to previously defined phylogroups, except for two genomospecies‐7 strains and P. caricapapayae, which were identified as a new phylogroup (6). There was good correlation between phylogroup and genomospecies classifications, except that two genomospecies‐8 strains (P. avellanae and P. syringae pv. theae) were found as a distinct clade within phylogroup 1 along with P. syringae pvs morsprunorum and actinidiae. The rpoD locus will provide a common reference framework to improve monitoring and surveillance of these important pathogens.     

Analysis of sources of oxolinic acid-resistant field strains of <Emphasis Type="Italic">Burkholderia glumae</Emphasis> based on rep-PCR analysis and nucleotide sequences of <Emphasis Type="Italic">gyrB</Emphasis> and <Emphasis Type="Italic">rpoD</Emphasis>

Repetitive sequence-based polymerase chain reaction (rep-PCR) analysis using BOX and ERIC as primers showed a highly divergent phylogeny among field strains of Burkholderia glumae. To elucidate the sources of oxolinic acid (OA) resistance in field strains of B. glumae isolated from rice seedlings cultivated in Mie, Toyama, and Iwate prefectures, Japan, the amino acid at position 83 of GyrA (GyrA83), which is involved in OA resistance, and the DNA patterns from the rep-PCR and the partial nucleotide sequences of gyrB and rpoD from various strains were analyzed. The ten Mie strains, in which GyrA83 was isoleucine (Ile), were divided into two groups based on the band patterns in rep-PCR analysis, although the nucleotide sequences of gyrB and rpoD were identical among the strains. Based on the band patterns in the rep-PCR analysis and the gyrB and rpoD sequences, two highly OA-resistant Toyama strains, Pg-13 and Pg-14, for which GyrA83 was serine (Ser) and Ile, respectively, were in the same lineage. This suggests that the bacteria might acquire OA resistance faster than phylogenic diversity as determined with the repetitive sequences BOX and ERIC and with gyrB and rpoD. Furthermore, three Iwate strains (H95, H101, and H104), isolated from seedlings of different cultivars grown in different years and having Ile at GyrA83, are probably in the same lineage, suggesting that OA-resistant bacteria might be transferred among different cultivars.     

Genetic diversity of <Emphasis Type="Italic">Rhizobium vitis</Emphasis> strains in Japan based on multilocus sequence analysis of <Emphasis Type="Italic">pyrG</Emphasis>, <Emphasis Type="Italic">recA</Emphasis> and <Emphasis Type="Italic">rpoD</Emphasis>

Forty-one strains of Rhizobium vitis, either tumorigenic (Ti) or nonpathogenic, were characterized using multilocus sequence analysis (MLSA) of the partial nucleotide sequences of pyrG, recA, and rpoD. The strains separated into seven clades. Rhizobium vitis (Ti) strains isolated from Japan were divided into five genetic groups (A to E), and nonpathogenic R. vitis strains were divided into two genetic groups (F and G). This result suggests that there are new genetic groups of R. vitis in Japan. Among these groups, members of A and B groups are widely distributed throughout Japan.     

Biocontrol traits of plant growth suppressive arbuscular mycorrhizal fungi against root rot in tomato caused by <Emphasis Type="Italic">Pythium aphanidermatum</Emphasis>

Arbuscular mycorrhizal (AM) fungi known to cause plant growth depressions in tomato were examined for their biocontrol effects against root rot caused by Pythium aphanidermatum. The main hypothesis was that plant growth suppressive AM fungi would elicit a defence response in the host plant reducing Pythium root rot development. To test this hypothesis a fully factorial experiment was performed with AM fungi (Glomus intraradices, G. mosseae, G. claroideum or nonmycorrhizal), Pythium (± P. aphanidermatum) and harvest (7 and 14 days after pathogen inoculation (dapi)) as the main factors. Two weeks after AM fungi inoculation, roots were challenged with P. aphanidermatum. Variables evaluated at each harvest were root colonization levels of the interacting fungi, plant growth responses, and expression of a plant pathogenesis related protein gene (PR-1). All of the tested AM fungi caused marked growth suppressions, but did not affect PR-1 gene expression or the phosphorous concentration in the host plant. Plants singly inoculated with P. aphanidermatum had an increased PR-1 expression and phosphorous concentration. Among the AM fungi included in the study only G. intraradices reduced the pathogen root infection level, measured both in terms of Pythium ELISA and by recovery on selective media and only at the first harvest. Likewise, P. aphanidermatum root infection reduced colonization levels of G. intraradices, but not that of the two other AM fungi. In conclusion, plant growth suppressive AM fungi may offer plant beneficial traits in terms of biocontrol of root cortical pathogens.     

Colonization of <Emphasis Type="Italic">Arabidopsis</Emphasis> roots by <Emphasis Type="Italic">Trichoderma atroviride</Emphasis> promotes growth and enhances systemic disease resistance through jasmonic acid/ethylene and salicylic acid pathways

Trichoderma spp. are common soil fungi used as biocontrol agents due to their capacity to produce antibiotics, induce systemic resistance in plants and parasitize phytopathogenic fungi of major agricultural importance. The present study investigated whether colonization of Arabidopsis thaliana seedlings by Trichoderma atroviride affected plant growth and development. Here it is shown that T. atroviride promotes growth in Arabidopsis. Moreover, T. atroviride produced indole compounds in liquid cultures. These results suggest that indoleacetic acid-related indoles (IAA-related indoles) produced by T. atroviride may have a stimulatory effect on plant growth. In addition, whether colonization of Arabidopsis roots by T. atroviride can induce systemic protection against foliar pathogens was tested. Arabidopsis roots inoculation with T. atroviride provided systemic protection to the leaves inoculated with bacterial and fungal pathogens. To investigate the possible pathway involved in the systemic resistance induced by T. atroviride, the expression profile of salicylic acid, jasmonic acid/ethylene, oxidative burst and camalexin related genes was assessed in Arabidopsis. T. atroviride induced an overlapped expression of defence-related genes of SA and JA/ET pathways, and of the gene involved in the synthesis of the antimicrobial phytoalexin, camalexin, both locally and systemically. This is the first report where colonization of Arabidopsis roots by T. atroviride induces the expression of SA and JA/ET pathways simultaneously to confer resistance against hemibiotrophic and necrotrophic phytopathogens. The beneficial effects induced by the inoculation of Arabidopsis roots with T. atroviride and the induction of the plant defence system suggest a molecular dialogue between these organisms.     

芹菜APX基因家族鉴定及其表达分析

抗坏血酸过氧化物酶（Ascorbate peroxidase, APX）是植物活性氧代谢中重要的抗氧化酶之一，在植物抵抗氧化胁迫方面发挥重要作用。利用生物信息学方法对芹菜基因组中的APX基因家族成员进行鉴定和分析，并通过实时荧光定量PCR（quantitative real\|time PCR, qRT-PCR）验证分析AgAPXs在高温胁迫下的表达情况，为开展芹菜APX基因参与高温胁迫调控机制提供依据。结果表明：芹菜基因组中共有9个APX基因，随机分布在5个染色体上，并出现了基因片段复制现象；大多数基因被定位在细胞质中。系统发育分析表明，AgAPX基因家族可分为3个亚族，同一亚族中的成员具有相似的基因结构和基序。启动子顺式元件分析表明，大多数AgAPX基因含有多种与生长发育、植物激素和逆境胁迫相关的顺式元件。高温胁迫下，芹菜APX活性提高。qRT-PCR分析表明，AgAPXs在不同时间的高温处理下表达具有显著差异，并与转录组表达丰度相一致，AgAPX2、AgAPX3、AgAPX4、AgAPX5、AgAPX7的表达量和APX活性具有显著相关性，推测AgAPXs可能参与了芹菜抵御高温的调控过程。本研究初步鉴定并提供了芹菜APX基因家族成员信息，为今后进一步探索芹菜APX基因功能提供了重要的研究基础。     

Climatic Zoning and Plant Disease Potential – Examples from the Near and Middle East1

Actual plant disease and pest occurrence depends on many genetic and environmental factors, and frequently obscures the basic suitability of a given location to support or prevent epidemic development. In order to allow the demarcation of climatic zones related to the potential of disease or pest occurrence, we have used long-term average climatic data, especially monthly average temperatures and monthly average rainfall. If applied to sugar beet leaf pathogens such as Cercospora beticola and Erysiphe betae in the Near and Middle Eastern region, some interesting zoning became possible, which could be verified by extended field studies. Other examples that have been analysed in the region are apple scab, Venturia inaequalis, and downy mildew of grapes, Plasmopara viticola. A recent and ongoing analysis of the factors controlling chickpea anthracnose caused by Ascochyta rabiei indicates that the same principle may be applied for very different pathogens. Large-scale planning and control strategies as tried by the International Agricultural Research Centers should therefore be based on careful climatic zoning for plant pest and disease potential, to avoid waste of the limited genetic and financial resources available.     

Erwinia isolates from the bacterial shoot blight of pear in Japan are closely related to Erwinia pyrifoliae based on phylogenetic analyses of gyrB and rpoD genes

The phylogenetic relationships among Erwinia amylovora biovar 4 (the pathogen of bacterial shoot blight of pear in Japan), other biovars of E. amylovora, and Erwinia pyrifoliae were investigated using the sequences of 16S rRNA, gyrB, and rpoD genes. The tested isolates formed two distinct monophyletic groups in the phylogenetic trees constructed based on the gyrB gene, rpoD gene, or a combination of the three genes: group 1 contained E. amylovora biovars 1, 2, and 3; group 2 contained E. amylovora bv. 4 and E. pyrifoliae. This phylogenetic analysis showed that E. amylovora bv. 4 was more closely related to E. pyrifoliae than to other biovars of E. amylovora. The nucleotide sequence data reported are available in the DDBJ/EMBL/GenBank databases under the accession numbers AB242876 to AB242925.     

Evaluation of the grapevine nursery propagation process as a source of <Emphasis Type="Italic">Phaeoacremonium</Emphasis> spp. and <Emphasis Type="Italic">Phaeomoniella chlamydospora</Emphasis> and occurrence of trunk disease pathogens in rootstock mother vines in Spain

Five commercial nurseries were sampled in 2007 to evaluate the grapevine nursery propagation process as a source of Petri disease pathogens (Phaeoacremonium spp. and Phaeomoniella chlamydospora). Samples were taken at four stages of the propagation process: pre-grafting hydration tanks, scissors used for cutting buds, grafting machines and peat used to promote root development. All samples were analysed using two different techniques: nested PCR using specific primers for Phaeoacremonium spp. (Pm1/Pm2) and Pa. chlamydospora (Pch1/Pch2); and fungal isolation by culturing on semi-selective medium. Either Phaeoacremonium spp. or Pa. chlamydospora were detected at any of these stages, and more importantly they were viable since they were detected by isolating on culturing medium. Additionally, the importance of grapevine rootstock mother fields as sources of inoculum in the nurseries was studied. Fourteen grapevine rootstock mother fields were surveyed in 2006 and 2007 for the occurrence of fungal trunk pathogens. A total of 16.4% and 30% of the plants sampled in 2006 and 2007, respectively were infected. Petri disease pathogens (Pa. chlamydospora, Phaeoacremonium aleophilum, Pm. parasiticum) and several Botryosphaeriaceae species (Neofusicoccum parvum, Botryosphaeria dothidea, Lasiodiplodia theobromae, N. australe, N. mediterraneum and N. vitifusiforme) and Phomopsis viticola were isolated. This is the first time N. mediterraneum has been isolated from grapevines and the first report of N. australe, N. mediterraneum and N. vitifusiforme in Spain. This work shows that grapevine rootstock mother plants and the propagation process of grapevine plants should be considered as important sources of inoculum for fungal trunk pathogens, and especially of Petri disease pathogens.     

Host range expansion in a powdery mildew fungus (<Emphasis Type="Italic">Golovinomyces</Emphasis> sp.) infecting <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis>: <Emphasis Type="Italic">Torenia fournieri</Emphasis> as a new host

Since 2003, Torenia fournieri plants grown for experimental purposes were repeatedly infected by powdery mildew in a laboratory in Hungary. Based on morphological characteristics, the pathogen belonged to the mitosporic genus Oidium subgen. Reticuloidium, the anamorph stage of Golovinomyces. The rDNA ITS sequence was identical to that of two other powdery mildew fungi, infecting Arabidopsis and Veronica, respectively, in different parts of the world. According to a previous phylogenetic analysis of ITS and 28S rDNA sequences, those two powdery mildews belong to a recently evolved group of Golovinomyces characterized by multiple host range expansions during their evolution. Both the ITS sequence and the morphological data indicate that the powdery mildew anamorph infecting Torenia also belongs to this group. It is likely that the powdery mildew infections of the experimental T. fournieri plants, native to south-east Asia, were the result of a very recent host range expansion of a polyphagous Golovinomyces because (i) T. fournieri is absent from our region, except as an experimental plant grown in the laboratory, (ii) the powdery mildew fungus infecting this exotic plant belongs to a group of Golovinomyces where host range expansion is a frequent evolutionary scenario, (iii) cross-inoculation tests showed that this pathogen is also able to infect other plant species, notably A. thaliana and tobacco, and (iv) no Golovinomyces species are known to infect T. fournieri anywhere in the world. Although host range expansion has often been proposed as a common evolutionary process in the Erysiphales, and also in other biotrophic plant pathogens, this has not been clearly demonstrated in any case studies so far. To our knowledge, this is the first convincing case of a host range expansion event in the Erysiphales.     

Composting to sanitize plant‐based waste infected with organisms of plant health importance

The potential for using the composting process to sanitize plant waste infected with one of three plant pathogens was investigated using bench‐scale composting equipment. Two of these pathogens, the potato wart disease fungus Synchytrium endobioticum and Potato spindle tuber viroid (PSTVd) are currently subject to European quarantine regulations. The third, Polymyxa betae, a parasite of sugar beet, is regulated in some European countries when in association with Beet necrotic yellow vein virus (BNYVV), the causal organism of rhizomania disease of sugar beet. Survival of test organisms following various combinations of compost temperature, exposure time and moisture was determined using RNA‐based detection methodology and/or plant‐based bioassays. Mathematically definable relationships between compost treatment (temperature/time) and organism viability were identified for P. betae and S. endobioticum; these give some indication of the practicality of using composting for dealing with infected wastes. However, for PSTVd, the considerable variability in measured susceptibility of the viroid to the composting process meant that no such definable relationship could be determined and further work would be needed to extrapolate to practical situations.     

Pathogenicity and toxicity of Fusarium tucumaniae and Fusarium crassistipitatum to soybean and Arabidopsis thaliana

Sudden death syndrome (SDS) of soybean is a fungal disease caused by at least four distinct Fusarium species: F. tucumaniae, F. virguliforme, F. brasiliense, and F. crassistipitatum. All four species are present in Argentina. These fungi are soilborne pathogens that only colonize roots and cause root necrosis. However, damage also reaches the aboveground part of the plant, and foliar chlorosis and necrosis, followed by premature defoliation, can be observed. Although the pathogenicity and phytotoxicity of F. virguliforme has been well characterized, knowledge regarding disease development by other fungal species is scarce. In this study, two plant species, soybean (Glycine max) and Arabidopsis thaliana, and isolates from two fungal species, F. tucumaniae and F. crassistipitatum, were used to comparatively analyse the fungal pathogenicity and the phytotoxicity of volatile organic compounds (VOCs) and cell-free culture filtrates. Fungal inoculation had a significant effect on plant growth, regardless of the plant species. In addition, infected soybean plants showed disease incidence and foliar and root symptoms. Inhibition of A. thaliana growth was not due to VOCs emitted by fungi. Instead, both pathogens were shown to produce toxins that caused typical SDS foliar symptoms in soybean and root length reduction in A. thaliana. As far as we know, this is the first report that demonstrates that F. tucumaniae and F. crassistipitatum affect A. thaliana growth and emit VOCs, and that F. crassistipitatum produces toxins.     

A Survey of Trunk Disease Pathogens within Rootstocks of Grapevines in Spain

Grapevine trunk disease pathogens, and specifically Petri disease pathogens, can be spread by planting infected plants. Due to the increasing incidence of Petri disease and other young grapevine declines reported lately in Spain, a sampling of plants used before for new vineyards were carried out in 2002 and 2004. A total number of 208 plants (grafted and non grafted) were collected, of which 94 plants (45.2%) were infected with at least one of the following pathogens: Phaeomoniella chlamydospora, and species of Phaeoacremonium, Botryosphaeria, Cylindrocarpon, and Phomopsis. Species of the genera Phaeoacremonium and Botryosphaeria isolated in 2004 were identified using morphological and molecular characters. Species of Phaeoacremonium identified were P. aleophilum and P. parasiticum; and those of Botryosphaeria were B. obtusa, B. dothidea and B. parva. This is the first report of P. parasiticum and B. parva occurring on grapevines in Spain. Distribution of pathogens within the plants was studied in 2004. Phaeomoniella chlamydospora was not detected in the graft union of any plant; however, species of Botryosphaeria and Phomopsis were detected along the plant, but mainly in the graft union; Phaeoacremonium aleophilum was detected along the grafted plants, but not in rooted rootstocks. The results suggest that infected plants used for new plantings in Spain are an important source of primary inoculum of the pathogens associated with grapevine trunk diseases in the field.     

Occurrence and diversity of fungal pathogens associated with water hyacinth and their potential as biocontrol agents in the Rift Valley of Ethiopia

Water hyacinth poses serious socio-economic and environmental problems in Ethiopia. To integrate fungal pathogens into water hyacinth management, a survey was conducted in the Rift Valley of Ethiopia. Based on morphological characterization and DNA sequencing, 25 fungal species were identified that belong to nine genera. Alternaria tenuissima, A. alternata, Aspergillus niger, Phoma sp., Curvularia trifolii, Mucor fragilis, M. racemosus, A. fumigatus, Fusarium oxysporum, and F. equiseti were the most common fungi detected. However, their occurrence was influenced by water wave action, temperature, season, and altitude. Among the fungal pathogens, A. alternata, A. tenuissima, F. oxysporum, F. equiseti, and Neofisicoccum parvum were highly pathogenic to water hyacinth. Alternaria alternata and A. tenuissima did not cause disease symptoms on ecologically important plant species (e.g. Noug, Tef, and Coffee). Application of the fungal pathogens on water hyacinth plants also showed 11%–67%, 22%–72%, 15%–55%, and 12%–50% reduction in fresh weight, dry weight, plant height, and root length of water hyacinth, respectively. This study suggests that fungal species have the potential to control water hyacinth biologically and provides baseline data for biological control efforts in the future.     

Molecular cloning and expression analysis of genes related to phosphatidic acid synthesis in Japanese pear leaves inoculated with <Emphasis Type="Italic">Venturia nashicola</Emphasis>

Phosphatidic acid, which can be generated by the action of phospholipase D (PLD) and by the combined action of phospholipase C (PLC) and diacylglycerol kinase (DGK), is a plant defense signal. To identify the role of the PLD, PLC, and DGK genes encoding these enzymes in pear resistance to the scab fungus Venturia nashicola, we report the cloning of these genes and analysis of their expression in inoculated pear leaves. The results showed that PLD mRNA increased in the leaves of the susceptible pear cv. Kousui 1 day after inoculation (dai), then decreased to the basal level. In resistant pear cv. Kinchaku, PLD mRNA did not change significantly except for a small increase at 2 and 3 dai. However, the level of PLD mRNA in Kinchaku was higher than in Kousui 2 dai. The level of PLC mRNA significantly increased in cvs. Kousui and Kinchaku by 1 dai, peaked at day 2, then decreased to the basal level. Thus, the gene expression pattern did not differ between the two cultivars. PLC gene expression was also induced by environmental stress. The DGK gene seemed to be constitutively expressed and was not induced by inoculation in either the susceptible or resistant cultivars. Together, this data showed that both PLD and PLC are possibly involved in a defense response to V. nashicola in Japanese pear leaves, and the PLD gene seems to play a more important role than does the PLC gene.     

Differential effects of phytotoxic metabolites from <Emphasis Type="Italic">Alternaria tagetica</Emphasis> on <Emphasis Type="Italic">Tagetes erecta</Emphasis> cell cultures

Alternaria tagetica, a fungus that causes early blight in marigold (Tagetes erecta), produces two groups of phytotoxic metabolites: one hydrophilic and the other lipophilic that show phytotoxic activity when tested by the leaf-spot assay in T. erecta. We evaluated the cellular effects of the phytotoxic culture filtrate of A. tagetica and the hydrophilic and lipophilic fractions, then determined whether the filtrate or the fractions differentially induced pathogenesis-related mechanisms in the plant. The culture filtrate and the phytotoxic fractions had adverse effects on cell viability, fresh mass, and the number of cells, and induced ROS accumulation, lipid peroxidation and DNA damage on T. erecta cell suspension cultures, and these effects are related to pathogenic mechanisms attributed to phytotoxins. However, although exposure of marigold cells to the phytotoxic culture filtrate of A. tagetica triggered programmed cell death, the hydrophilic and the lipophilic phytotoxic fractions induced death that was more related to a toxic effect leading to necrosis. This study presents a complementary perspective in the search for the roles of metabolites, including phytotoxins, produced by phytopathogenic fungi during plant infection.     

<Emphasis Type="Italic">N</Emphasis>,<Emphasis Type="Italic">N</Emphasis>-dimethylsphingosine,an inhibitor of sphingosine kinase,induces phytoalexin production and hypersensitive cell death of Solanaceae plants without generation of reactive oxygen species

Plant recognition of elicitors derived from pathogens induces various resistant reactions, including production of reactive oxygen species, hypersensitive cell death and accumulation of phytoalexins. Previously, we isolated a ceramide elicitor from Phytophthora infestans, which activates O₂ ⁻ production of potato suspension-cultured cells. In this study, we employed nine ceramide-related chemicals to test their elicitor activity. Although, none of the tested chemicals induced O₂ ⁻ production, N,N-dimethylsphingosine (DMS) induced accumulation of phytoalexin in potato tubers. In potato, tobacco and Nicotiana benthamiana, DMS also induced rapid cell death. DMS-treated potato cells stained with 4′,6-diamidino-2-phenylindole (DAPI) showed chromatin condensation, and isolated DNA from DMS-treated cells had ladder pattern, confirming that DMS-induced plant cell death is a hypersensitive reaction-like programmed cell death. Involvement of ceramide signaling in induction of plant defense reactions is discussed. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.