Application of RFLP analysis of recA, gyrA and rpoS gene fragments for rapid differentiation of Erwinia amylovora from Erwinia strains isolated in Korea and Japan

Restriction fragment length polymorphism (RFLP) analysis of the PCR amplified fragments of recA, gyrA and rpoS genes was applied for the characterization of Erwinia amylovora and Erwinia strains, which cause fire blight and Asian pear blight in orchards. Primers, constructed on the basis of the published recA, gyrA and rpoS gene sequences of Erwinia carotovora, allowed us to amplify DNA fragments for RFLP differentiation of E. amylovora and E. pyrifoliae and finally to distinguish strains within these species and relate them to pear pathogens from Japan. Three to seven restriction endonucleases were applied for RFLP analysis of each gene fragment. The electrophoretic patterns generated after PCR–RFLP for each of the tested genes, were characteristic and specific for each species and allowed their differentiation. The data show that PCR–RFLP analysis of the recA, gyrA and rpoS gene fragments may be considered as a useful tool for the identification and differentiation of E. amylovora and E. pyrifoliae. Almost identical restriction patterns of the analyzed gene fragments indicated a high relationship of E. pyrifoliae strains from Korea and pear pathogens from Japan and a divergence to E. amylovora. For quick and effective differentiation of E. amylovora strains from Erwinia strains from Asia without nucleotide sequencing we recommend the amplification of recA and rpoS gene fragments and digestion of each of them with restriction endonuclease Hin6I.     

Taxonomic Position of the Causal Pathogen of Bacterial Shoot Blight of Pear

Bacteriological properties and DNA-DNA homology values were compared among the pathogen causing bacterial shoot blight of pear (BSBP) isolated in 1994–1996, Erwinia amylovora isolated outside of Japan, and other Amylovora group bacteria. Bacteriological properties of BSBP strains were identical to those of E. amylovora in the majority of tests, but differed distinctively in several tests, including hydrolysis of esculin and acid production from salicin, etc. BSBP strains differed from the others in the Amylovora group in many other tests. DNA homology among the strains of BSBP ranged from 85 to 103% and from 83 to 110% among strains of E. amylovora. In contrast, the values between BSBP strains and E. amylovora strains were 55 to 81%, while those between BSBP strains and other Amylovora group strains were 42% or less. We consider, therefore, that the BSBP pathogen may well be included in E. amylovora at the species level. E. amylovora, including BSBP strains, however, can be classified into four biovars based on differences in nine tests such as growth factor requirements and crater formation on high sucrose medium. Namely, there are two biovars from Maloideae sources, one from Rubus idaeus, and one from the source of BSBP in Hokkaido. The presence of these biovars suggests a correlation with geographical, serological, and pathogenic differentiations in the species of E. amylovora. The BSBP pathogen in Hokkaido was identified as E. amylovora bv. 4 which is distinct from E. amylovora bv. 1, 2 and 3 isolated in countries outside of Japan. Received 29 July 1999/ Accepted in revised form 12 October 1999     

Identification of dspEF, hrpW, and hrpN loci and characterization of the hrpN Ep gene in Erwinia pyrifoliae

Erwinia pyrifoliae, the causal pathogen of shoot blight in the Asian pear tree (Pyrus pyrifolia cv. Singo), is host-specific and endemic to Korea. To identify the genes associated with the hypersensitive response (HR) and pathogenicity, a genomic library of E. pyrifoliae WT3 was constructed, and the cosmid clone Escherichia coli (pCEP33) was selected. Sequence analysis of 19.7-kb pCEP33 determined disease-specific (dsp) region homolog and approximately 40% of the hrp genes, which included hrpW, hrpN_Ep, hrpV, hrpT, hrcC, hrpG, hrpF, and partial hrpE homologs, with respect to the cluster of Erwinia amylovora. Additionally, two open reading frames, ORFD and ORFE, were found downstream of the dspEF region. The results of the sequence analysis showed that the pCEP33 did not contain any hrp regulatory genes or most of the genes encoding components of the Hrp protein secretion system. The hrpN_Ep gene of E. pyrifoliae contained five intergenic nucleotide fragment insertions (INFIs) and produced the HR elicitor protein harpin_Ep, with a molecular mass of approximately 44kDa. The purified HrpN_Ep protein elicited faster and stronger HR when infiltrated into tobacco leaves than did HrpN_Ea from E. amylovora. To observe the role of the hrpL gene in the expression of HrpN_Ep, the pEL2 containing hrpL was used to transform E. coli (pCEP33). Expression of HrpN_Ep in E. coli (pCEP33 + pEPL2) was detected with an immunoblot using antiserum raised against HrpN_Ep, indicating a role of hrpL gene in enhancing the expression of HrpN_Ep.     

Occurrence of bacterial black shoot disease of European pear in Yamagata Prefecture

Black lesions on shoots of European pear trees observed in an orchard in Yamagata Prefecture in May 2007 were suspected to be caused by a bacterial pathogen. The surface of the colonies isolated on a high sucrose medium did not have the crater morphology that is characteristic of E. amylovora bvs. 1–3, and a specific DNA fragment was amplified from the isolates in the PCR using the EprpoD primer set. The partial sequences of the 16S rRNA gene placed the isolates in the genus Erwinia. The isolates differed serologically from E. amylovora biovars and E. pyrifoliae in an Ouchterlony double-diffusion test although their bacterial properties suggested that they are closely related to E. amylovora biovars and E. pyrifoliae. In a DNA–DNA hybridization test, the relatedness between the isolates and E. amylovora biovars or E. pyrifoliae did not exceed 70% level, indicating that they are independent species. Thus, the isolates belongs to the genus Erwnia but are not E. amylovra or E. pyrifoliae. After succulent pear shoots were injected with bacterial suspensions (10⁹, 10⁸, 10⁷ and 10⁶ cfu/ml) of the isolates, lesions formed with 10⁹ and 10⁸ cfu/ml, but the disease incidence with 10⁸ cfu/ml was much lower than with E. amylovora and E. pyrifoliae. Virulence of the present isolates is thus thought to be very weak. On the basis of these results, we consider that this is a new shoot disease of European pear. In the 2007 season, all affected trees were pulled out after harvest. No symptoms have been observed in field surveys since the fruitlet season in 2007.     

Infection frequency of mature apple fruit with Erwinia amylovora deposited on pedicels and its survival in the fruit stored at low temperature

The infection frequency of mature apple fruit by Erwinia amylovora and the survival of E. amylovora in the fruit stored at low temperature were investigated. The fruit stems (pedicels) of 460 mature apple fruit were inoculated with 10⁵ or 10⁴ cfu of bioluminescent E. amylovora, tagged with lux genes. Nine days after inoculation, 43% and 27% of the fruit inoculated with 10⁵ and 10⁴ cfu, respectively, were infected. All infected fruit looked healthy. After 6 months of storage at 5°C, almost all of the 142 infected fruit had viable E. amylovora. Of the fruit containing E. amylovora internally, 19.5% had latent infections and the rest had blight symptoms. E. amylovora was not uniformly distributed in the fruit flesh, and internal brown lesions were observed where E. amylovora was densely distributed. These findings showed that mature apple fruit may be infected with E. amylovora, especially as latent infections, and act as a source for long-range dissemination.     

基于MaxEnt模型预测梨火疫病菌的潜在地理分布

为探究梨火疫病菌解淀粉欧文氏菌Erwinia amylovora在全球的潜在地理分布,基于其全球分布数据和筛选得到的环境变量,利用MaxEnt模型对其在当前气候和未来气候条件下的潜在地理分布进行预测,并利用刀切法和皮尔逊相关性分析法筛选对梨火疫病菌分布有重要影响的环境变量。结果显示,对梨火疫病菌分布有重要影响的环境变量包括2月平均最高温度、1月平均降水量、7月平均最低温度、温度变化方差、昼夜温差月均值和7月平均降水量,表明春季和夏季的温度和降水对梨火疫病菌的分布有较大影响。在当前气候条件下,梨火疫病菌在全球的适生区分布较广,适生区总面积达到5.58×10⁷ km²,且高适生区主要分布在北美洲沿海地区、地中海沿岸和亚洲中部及东部的部分地区;梨火疫病菌在我国的适生区总面积为7.36×10⁶ km²,占全国陆地总面积的76.70%;在未来气候SSP126和SSP585情景下,梨火疫病菌在全球的适生区总面积分别为5.52×10⁷ km²和5.24×10⁷ km²。表明梨火疫病菌对我国大部分地区有潜在威胁,应加强监测与防控。     

Phylogenetic study of Japanese Dickeya spp. and development of new rapid identification methods using PCR–RFLP

Forty-one representative Japanese Dickeya spp. (Erwinia chrysanthemi) strains isolated from 24 plants in Japan were investigated using multilocus sequence analysis of recA, dnaX, rpoD, gyrB and 16S rDNA; PCR–RFLP (restriction fragment length polymorphism) of recA, rpoD and gyrB genes; PCR genomic fingerprinting; and biochemical tests. Based on the recA, dnaX, rpoD, gyrB and 16S rDNA sequences and PCR genomic fingerprinting, the strains were essentially divided into six groups (I–VI). Group I corresponded to D. chrysanthemi, group II corresponded to D. dadantii, group III to D. dianthicola and group IV to D. zeae. Meanwhile, group V and group VI could not be assigned to any existing Dickeya species, and they were deduced to be two putative new species. The PCR–RFLP analysis of gyrB, rpoD and recA clearly differentiated the six groups of Dickeya strains. From the results of the biochemical tests, the strains were assigned to biovars 1, 3, 5, 8 and 9; only one strain (SUPP 2525) was not assignable to the existing biovars. We also showed that the PCR–RFLP analysis of rpoD, gyrB and recA can be used as a rapid technique to identify Japanese Dickeya strains.     

Serological Differences among Erwinia amylovora Biovars

Serological properties were compared among four biovars of Erwinia amylovora. Two biovars (bvs. 1 and 2) from Maloideae sources outside of Japan, one (bv. 3) from Rubus idaeus and one causing bacterial shoot blight of pear (bv. 4) had different reactions in Ouchterlony double diffusion tests using living cells and lipopolysaccharides (LPS) as antigens. These findings indicate that E. amylovora can be classified into three serotypes; i.e., bvs. 1 and 2, bv. 3 and bv. 4. From results of Ouchterlony double diffusion tests and immunoblots, the specific antigen of the three serotypes may each exist in the LPS of E. amylovora strains. Received 27 March 2002/ Accepted in revised form 2 July 2002     

An oligonucleotide probe for the detection of Erwinia herbicola and Erwinia ananas

An oligonucleotide probe targeting the rRNA of Erwinia herbicola and Erwinia ananas was designed to detect their cells using fluorescence in situ hybridization. The Cy3-labeled probe hybridized strongly with these species but very weakly with nontarget species such as Erwinia mallotivora, Erwinia nigrifluens, Erwinia cypripedii, Erwinia chrysanthemi, Erwinia carotovora subsp. carotovora, E. carotovora subsp. atroseptica, and Escherichia coli. This technique visualized E. herbicola cells after inoculation of kumquat fruits. The probe is promising as a tool for studying population dynamics of E. herbicola and E. ananas.     

Use of a diagnostic medium for<Emphasis Type="Italic">in situ</Emphasis> determination of the response of<Emphasis Type="Italic">Erwinia amylovora</Emphasis> strains to bactericides

Erwinia amylovora, the causal agent of fire blight, is managed by application of bactericides to protect fruit tree blossoms from infection. Monitoring the response ofE. amylovora strains to bactericides is crucial for adequate disease management. The coliform agar medium produced by Merck was recently reported as an effective tool for rapid diagnosis ofE. amylovora (RD-medium). The objective of the present study was to examine the possibility of using the RD-medium forin situ determination of the response ofE. amylovora strains to oxolinic acid and streptomycin. The phenotypic response of 48E. amylovora strains isolated in 2002 to both bactericides was determined with the RD-medium and, for comparison, by a routine laboratory test. The results of 45 samples (93.7%) were in agreement with the findings of the routine laboratory test. Aχ ² test rejected the null hypothesis that the phenotypic characteristics as determined by the two respective methods differed significantly (P=0.389). Thein situ test was implemented on a national scale in 2003 and the results were in agreement with those obtained in laboratory tests, which suggests that this medium can be usedin situ for monitoring the appearance of resistance inE. amylovora populations. http://www.phytoparasitica.org posting Feb. 11, 2004.     

Erwinia amylovora can pass through the abscission layer of fruit-bearing twigs and invade apple fruit during fruit maturation

Invasion of apple fruit by Erwinia amylovora from fruit-bearing twigs through the abscission layer at fruit maturation was examined. Erwinia amylovora (ca. 10⁵ cfu) tagged with bioluminescence genes from Vibrio fischeri was deposited in artificial wounds on fruit-bearing twigs of apple trees grown in a containment greenhouse on September 22, 27, or October 5, 2004. On October 22, 176 apples were harvested and cut horizontally in half. The upper halves were stamped on plates of selective medium, and the lower halves were flooded with iodine solution to assess maturity. All fruit were symptomless and fully mature. The pathogen was recovered from 19 (10.8%) apples. The result showed that if at least ca. 10⁵ cfu of E. amylovora are present in fruit-bearing twigs at the time of fruit maturation, the bacteria can pass through the abscission layer into the fruit, even though the mature fruit lack symptoms.     

Distribution of streptomycin-resistant strainsof Erwinia amylovora in Israel and occurrence of blossom blight in the autumn

Following failure in control of fire blight with streptomycin, the distribution of streptomycin-resistant strains ofErwinia amylovora in Israel was surveyed. During 1994–1997 109 pear, apple, loquat and quince orchards were monitored. Streptomycin-resistant strains ofE. amylovora were recovered from flowers and from infected branches collected at 18 locations in the Sharon, Galilee and Golan Heights regions. In the Sharon region all the isolated strains ofE. amylovora were streptomycin-resistant, whereas in the Galilee and Golan Heights, resistant as well as sensitiveE. amylovora strains were recovered at different locations. In the southern coastal plain no resistance could be detected. Streptomycin-resistant strains ofE. amylovora did not hybridize with the DNA probe SMP3, and resistance could not be transferred by mating to a sensitive strain, suggesting that streptomycin resistance in Israel is not plasmid-mediated. Fire blight symptoms were observed, for the first time, on pear blossoms during the autumn of 1994. A high population of 2x 10⁶-6x 10⁷ CFU/flower in the autumn of 1995 and of 1996 was correlated with the appearance of blossom blight symptoms.     

Phylogenetic relationships of Ralstonia solanacearum species complex strains from Asia and other continents based on 16S rDNA, endoglucanase, and hrpB gene sequences

The 16S rDNA, endoglucanase, and hrpB genes were partially sequenced for Asian strains of Ralstonia solanacearum spp. complex, including 31 strains of R. solanacearum and two strains each of the blood disease bacterium (BDB) and Pseudomonas syzygii. Additional sequences homologous to these DNA regions, deposited at DDBJ/EMBL/GenBank databases were included in the analysis. Various levels of polymorphisms were observed in each of these DNA regions. The highest polymorphism (approximately 25%) was found in the endoglucanase gene sequence. The hrpB sequence had about 22% poly-morphism. The phylogenetic analysis consistently divided the strains into four clusters, as distinctly shown on the phylogenetic trees of 16S rDNA, hrpB gene, and endo-glucanase gene sequences. Cluster 1 contained all strains from Asia, which belong to biovars 3, 4, 5, and N2. Cluster 2 comprised the Asian strains of R. solanacearum (as biovars N2 and 1) isolated from potato and clove, as well as BDB and P. syzygii. Cluster 3 contained race 3 biovar 2 strains from potato, race 2 biovar 1 strains from banana, and race 1 biovar 1 strains isolated from America, Asia, and other parts of the world. Cluster 4 was exclusively composed of African strains. The results of the study showed the distribution and diversity of the Asian strains, which are present in three of the four clusters. The similarity of Asian strains to those in the other regions was also observed.The nucleotide sequence data reported are available in the DDBJ/EMBL/GenBank databases under accession numbers AY464950 to AY465050     

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.     

Phylogenetic analyses of plant-growth-promoting rhizobacteria isolated from tomato,lettuce, and Japanese pepper plants in Hyogo Prefecture,Japan

Approximately 30,000 fluorescent bacterial strains isolated from tomato, lettuce, eggplant, Chinese cabbage, and Japanese pepper plants at seven different locations in Hyogo Prefecture, were screened for plant-growth-promoting (PGP) activity to induce disease resistance against bacterial wilt in tomato. The 37 strains that had higher PGP activity were subjected to molecular phylogenetic analyses using the sequences of the 16S rRNA, gyrB and rpoD genes. Most of the strains were identified as Pseudomonas fluorescens or its close relative, P. putida, while a few strains were grouped with more distantly related bacterial species such as Enterobacter and Stenotrophomonas. The phylogenetic relationships among tomato and lettuce isolates mostly coincided with the source locality and host plants, with a few exceptions. In contrast, isolates from Japanese pepper plants did not form their own cluster but represented several different bacterial species.     

Invasion and colonization of mature apple fruit by Erwinia amylovora tagged with bioluminescence genes

Invasion and colonization of mature apple fruit by a transformant of Erwinia amylovora tagged with bioluminescence genes from Vibrio fischeri was examined. The transformant was deposited on cut surfaces of fruit stems, wounds on the shoulders and calyces, injured fruit-bearing twigs of harvested apple fruit, and cut fruit flesh. After incubation in closed stainless steel or plastic boxes at 25°C, fruit were periodically observed with a two-dimensional luminometer. The presence of the transformant in luminous areas was confirmed by isolating it on selective media. E. amylovora, when deposited in fruit stems: (1) can invade mature as well as immature apple fruit; (2) vertically and horizontally spreads and colonizes along vascular bundles, increasing its population; (3) reaches the calyx end and the flesh just under the exocarp within 3–4 days after inoculation; (4) when deposited on cut fruit flesh, irrespective of its maturity, can easily increase its population and survive 2–4 weeks or more at 25°C; and (5) even at the time of fruit maturation, can migrate within twigs rapidly and reaches the abscission layers between fruit-bearing twigs and fruit stems.     

Identification and Characterisation of Bacteria Causing Soft-rot in Agave tequilana

Agave tequilana is the raw material for the production of the alcoholic beverage tequila. A bacterial disease has affected the A. tequilana crop in recent years. Previous reports based on colony and cell morphology, Gram stain and potato rot indicated that Erwinia sp. is the main pathogen. We isolated a several bacterial isolates capable of producing soft-rot symptoms in greenhouse pathogenicity assays. An extensive characterisation involving pathogenicity tests, fatty acid profile, metabolic and physiological properties, ribosomal DNA sequence and intergenic transcribed spacer amplification (ITS-PCR) and restriction banding pattern (ITS-RFLP) was made of each isolate. Three different species: Erwinia cacticida, Pantoea agglomerans and Pseudomonas sp. were identified. Fatty acid and metabolic profiles gave low similarity values of identification but 16S rDNA sequence, ITS-PCR and ITS-RFLP confirmed the identification of E. cacticida. In the phylogenetic tree, E. cacticida from blue agave was grouped neither with E. cacticida type strains nor with Erwinia carotovora. This is the first report that associates E. cacticida with A. tequilana soft-rot symptoms.     

Note: Evaluation of antibacterial activity of essential oil of<Emphasis Type="Italic">Rosa damascena</Emphasis> on<Emphasis Type="Italic">Erwinia amylovora</Emphasis>

Significant antibacterial activity was observed in the essential oil (E.O.) ofRosa damascena Mill. and the Minimum Bactericidal Concentration (MBC) of the E.O. was determined as 1386.5 μg ml⁻¹ forErwinia amylovora, the causal agent of fire blight disease. Ooze formation on immature pears and lesion formation in artificially inoculated shoots were completely (100%) prevented by the essential oil ofR. damascena (1500 μg ml⁻¹), essential oil ofThymbra spicata var.spicata (500 μg ml⁻¹) and streptomycin (100 μg ml⁻¹). Copper oxychloride plus maneb significantly reduced ooze formation and lesion formation, but the control was less than that obtained with the essential oils or streptomycin. The essential oil ofR. damascena may be a useful natural bactericide for the control of the fire blight pathogen,E. amylovora. http://www.phytoparasitica.org posting July 14, 2004.     

Extract of Hedera helix induces resistance on apple rootstock M26 similar to Acibenzolar-S-methyl against Fire Blight (Erwinia amylovora)

The potential of acibenzolar-S-methyl (Benzo [1,2,3]thiadiazole-7-carbothioic acid-S-methyl ester, ASM; Bion 50 WG) and of an extract of Hedera helix, to protect M26 apple rootstocks against fire blight was determined under controlled conditions. Marked differences were observed in the rate and extent of multiplication as well as in pathogen cell viability between control and ASM and H. helix-treated rootstocks. Although the pathogen multiplied abundantly in the plant tissue of water-treated rootstocks and showed severe damage, ASM and the plant extract of H. helix applied prior to inoculation with the causal agent of fire blight, E. amylovora (strain 7/74), suppressed disease development and bacterial multiplication. Physiological observations of ASM and plant extract-treated rootstocks indicated that restriction of pathogen colonization in plant tissue was correlated with a pronounced increase of peroxidase (POX) and chitinase activity. Furthermore, physiological changes caused by these treatments in host cells were characterized by POX labeling methods with SDS-Page electrophoresis. Differences in expression of the POX and protein bands were observed in tissues of plants treated with different inducers. POX activity was determined by the presence of three strong bands in plant extract-treated leaves, two strong bands and one very weak band of about 20.1 and 43 kDa were visible in ASM-treated leaves. Evidence is provided that ASM, as well as extract of H. helix are equally capable of inducing of resistance responses in M26 apple rootstock, which result in an increased resistance to E. amylovora—the fire blight pathogen. These findings demonstrate that both treatments have the ability to induce the activation of defense genes leading to the accumulation of structural and biochemical activities at strategic sites, and these can be associated with induction of resistance against fire-blight.     

Influence of Stigmatic Morphology on Flower Colonization by <Emphasis Type="Italic">Erwinia amylovora</Emphasis> and <Emphasis Type="Italic">Pantoea agglomerans</Emphasis>

The morphology of apple and pear stigma was investigated with confocal laser scanning microscopy and scanning electron microscopy. The floral colonization process by Erwinia amylovora was studied with gfp-labelled bacteria and confocal laser scanning microscopy to allow the in vivo observation of the pathogen colonization on intact, viable plant tissues without any kind of staining of the specimens. The interaction on the stigma between Erwinia amylovora and Pantoea agglomerans, both labelled with genes encoding for fluorescent proteins (DsRed-GFP), was also investigated. A stylar groove, covered by papillae and dwelling from the stigma along the style, was visualized. In laboratory conditions, this groove was shown to be an important way for E. amylovora migration towards the nectarthodes. Due to its anatomical structure the groove can sustain bacterial multiplication and thus may play an important role on the interactions between the pathogen and the bacterial antagonist P. agglomerans.