Genetic diversity of <Emphasis Type="Italic">Ralstonia solanacearum</Emphasis> strains from Mexico associated with Moko disease

The aim of this study was to develop and validate a standard area diagram set (SADs) to assess the severity of peach rust, caused by Tranzschelia discolor. The proposed SADs includes ten images of leaves with a range of severity (0.1, 0.5, 1.0, 2.0, 5.0, 10, 15, 20, 25 and 30%). The SADs was validated by 14 raters who had no experience in plant disease severity estimation. In the first step of the validation, the raters made severity estimates of 50 leaves with a range of rust severity without using SADs. In the second step, the same raters estimated severity of rust on the same 50 leaves using the SADs to aid estimation. Lin’s concordance correlation analysis showed that both precision and accuracy improved when the raters used the SADs compared to the assessments made without SADs. Accuracy, as measured by the coefficient of bias (C _b ) improved from 0.70 to 0.98, without and with SADs, respectively, and precision measured by the correlation coefficient (r) improved from 0.85 to 0.90, without and with SADs, respectively. Overall agreement, measured by Lin’s concordance correlation coefficient (ρ _c ), improved from 0.59 to 0.88 without and with SADs, respectively. Furthermore, estimates were more reliable when using SADs: the coefficient of determination (R²) was 0.60 without and 0.73 with SADs; and the intra-class correlation coefficient (ρ) was 0.72 without, and 0.86 with SADs. Thus, the use of SADs improved the precision, accuracy and reliability of visual estimates of severity of peach rust.     

Genetic diversity of <Emphasis Type="Italic">Ralstonia solanacearum</Emphasis> strains causing bacterial wilt of solanaceous crops in Myanmar

In 2013 and 2014, an extensive survey of bacterial wilt in Myanmar was performed, and 70 strains of Ralstonia solanacearum (Rs) were collected from wilting plants of tomato, potato, chili and eggplant. Myanmar Rs strains were characterized by traditional and molecular methods. Polymerase chain reaction (PCR) test using Rs-specific primer set amplified one specific band (281-bp) from template DNA of all strains. Pathogenicity tests on the four solanaceous plants differentiated the strains into six pathogenic groups. Biovar determination tests showed that biovar 3 strains predominated (63%) among all Rs strains. Biovar 4 strains (7%) were obtained from both tomato and chili strains, whereas biovar 2 (30%) strains were isolated only from potato. Multiplex-PCR analysis indicated that tomato, eggplant and chili strains belonged to phylotype I, whereas potato strains comprised phylotype I and phylotype II. Strains in phylotype I, which was suggested to have originated from Asia, were the most prevalent in all surveyed areas. Phylogenetic analysis based on the endoglucanase (egl) gene sequences revealed that Myanmar strains partitioned into two major clusters that corresponded to phylotype I and II. Strains in phylotype I were further divided into seven subclusters, each corresponding to a distinct sequevar (15, 17, 46, 47, 48, unknown 1 or unknown 2). All strains in phylotype II belonged to sequevar 1. This is the first comprehensive report of the presence of diverse Rs strains in Myanmar.     

PCR-based specific detection of <Emphasis Type="Italic">Ralstonia solanacearum</Emphasis> race 4 strains

Two primer sets were designed based on the sequence of polymorphic bands that were derived from repetitive sequence-based polymerase chain reaction (rep-PCR) fingerprinting and specifically detected in Ralstonia solanacearum race 4 strains (ginger, mioga, and curcuma isolates). One primer set (AKIF-AKIR) amplified a single band (165bp) from genomic DNA obtained from all mioga and curcuma and some ginger isolates; another set (21F-21R) amplified one band (125bp) from the other ginger isolates. These primer sets did not amplify the bands from genomic DNA of other R. solanacearum strains or of other related bacteria. PCR detection limit for the pathogen was 2 × 10²cfu.The nucleotide sequence data reported are available in the DDBJ/EMBL/GenBank databases under accession numbers AB118756 and AB118757     

Distribution of avirulence genes <Emphasis Type="Italic">avrA</Emphasis> and <Emphasis Type="Italic">popP1</Emphasis> in 22 Japanese phylotype I strains of <Emphasis Type="Italic">Ralstonia solanacearum</Emphasis>

Sequence analysis of hrp loci and effector genes in the flanking regions showed significantly high similarities between two phylotype I strains of Ralstonia solanacearum, GMI1000 and Japanese strain OE1-1. Further sequence analysis of the distribution of avrA and popP1, known as determinants of a hypersensitive response (HR) induction on Nicotiana tabacum (tobacco), in 22 Japanese phylotype I strains revealed that all strains had one of the two distinct avrA alleles and that 10 strains had an identical popP1 but the other 12 did not. After infiltration of tobacco leaves, more than half of these 22 strains elicited HR. In combination with the ability to induce HR, avrA and popP1 are thus not likely to be the sole determinants of HR in Japanese phylotype I strains.     

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.     

Analysis of genetic and biological characters of Japanese potato strains of <Emphasis Type="Italic">Ralstonia solanacearum</Emphasis>

We assessed the geographic distribution, biovar, phylotype, DNA fingerprints (rep-PCR), and/or endoglucanase sequence of potato bacterial wilt pathogen, Ralstonia solanacearum (Rs), in Japan. Rs has been isolated from potato fields in southwestern, warm, temperate regions. Of the 188 isolates, 74 belonged to biovar N2 (39%), 44 to biovar 3 (24%), and 70 to biovar 4 (37%). Biovars N2 and 4 strains were widely distributed, from northern (Hokkaido) to southern (Okinawa) Japan. Based on the results of multiplex-PCR analysis, every potato strains belonged to either phylotype I or IV. Phylotype I comprised both biovars 3 and 4 strains. On the other hand, phylotype IV included biovar N2 strains. None of the strains belonged to phylotype II or III or biovar 1 or 2. Phylogenetic analysis based on DNA fingerprints and endoglucanase gene sequences clarified the genetic diversity of the Japanese potato strains and the close genetic relationship between the Japanese strains and the Asian strains in phylotypes I and IV.     

Contribution of the type II secretion system in systemic infectivity of <Emphasis Type="Italic">Ralstonia </Emphasis><Emphasis Type="Italic">solanacearum</Emphasis> through xylem vessels

Ralstonia solanacearum strain OE1-1 (OE1-1) systemically invades tobacco plants and causes bacterial wilt. A type II secretion system (T2SS)-deficient mutant of OE1-1, derived from EZ::TN<KAN-2>transposon-insertion, retained the ability of the parent strain to produce exopolysaccharide in vitro and grow in intercellular spaces immediately after invasion of host plants, but lost the ability to systemically infect the host. With transmission electron microscopy, the mutant was not observed in xylem vessels. These findings suggest that the T2SS contributes to systemic infection by enabling the bacteria to invade xylem vessels.     

Extracts from <Emphasis Type="Italic">Ralstonia solanacearum</Emphasis> induce effective resistance to the pathogen in both <Emphasis Type="Italic">Arabidopsis</Emphasis> and solanaceous plants

Plants defend themselves against microbial invasions by detecting conserved molecules, collectively called pathogen-associated molecular patterns (PAMPs). PAMPs-triggered basal resistance is the first inducible layer of plant defense. Here we found that Ralstonia solanacearum strain RS1002 can efficiently grow and cause disease in ecotype Columbia-0 of the model plant Arabidopsis thaliana in a manner dependent on the Hrp type III secretion system (T3SS). The extent of disease symptoms caused by R. solanacearum was reduced in plants pretreated with ΔhrpY mutant deficient in the functional Hrp T3SS. Pretreatment with a boiled extract (BE) from R. solanacearum had a similar inhibitory effect on disease development or bacterial multiplication in both Arabidopsis and several solanaceous plants. Simultaneous inoculations with BE and R. solanacearum did not induce BE-mediated resistance, nor did a BE treatment with proteinases. These results indicate that host plants recognize an unknown proteinaceous PAMP in the BE to induce disease resistance and that the Hrp T3SS of R. solanacearum can suppress it. From an analysis using Arabidopsis mutants lacking PAMP receptors, the elongation factor Tu of R. solanacearum was shown to partially contribute to BE-mediated basal resistance in Arabidopsis plants.     

Genetic diversity among <Emphasis Type="Italic">Brenneria nigrifluens</Emphasis> strains in Iran

To investigate the variability of Brenneria nigrifluens, the casual agent of shallow bark canker of Persian walnut (Juglans regia L.), a collection of 24 strains isolated from five geographic regions, was analyzed by means of three marker systems, repetitive polymerase chain reaction (rep-PCR), insertion sequence (IS50)-PCR and random amplified polymorphic DNA (RAPD). Cluster analysis was performed using UPGMA. Strains were differentiated into 6 groups at about 80% similarity according to geographic regions. This is possibly due to cultivation of Persian walnut being mainly based on the ecotype and/or local seedlings that have become adapted to particular environments and so have allowed selection of different B. nigrifluens populations. The results of this study showed that the four rep-PCR primers produced 75 products of which 73.3% were polymorphic, eight RAPD primers produced 146 fragments of which 74.6% were polymorphic and IS50 produced 32 fragments of which 93.75% were polymorphic. The usefulness of each system was examined in terms of polymorphism information content (PIC) and marker index (MI). The highest MI was observed for IS50-PCR (21.11) followed by RAPD (7.85), and rep-PCR (6.92). The Mantel test identified significant correlation between the similarity coefficients calculated from them. Among the molecular markers tested, IS50-PCR appears to be a more suitable marker for fingerprinting and assessing genetic relationships among B. nigrifluens strains. This is the first study on genetic diversity of B. nigrifluens. The results can have a bearing on the choice of disease management strategies.     

Visualization of <Emphasis Type="Italic">Ralstonia solanacearum</Emphasis> cells during biocontrol of bacterial wilt disease in tomato with <Emphasis Type="Italic">Pythium oligandrum</Emphasis>

The biocontrol agent Pythium oligandrum (PO) can suppress bacterial wilt caused by Ralstonia solanacearum (RS) in tomato. To understand the primary biocontrol mechanisms of bacterial wilt by PO, we pretreated tomato plants with sterile distilled water or preinoculated them with PO, followed by inoculation with RS, then observed PO and RS in fixed sections of tomato tissues using a confocal laser-scanning microscope and fluorescence labeling until 14 days after the inoculation with RS. Horizontal and vertical movement of RS bacteria was frequently observed in the xylem vessels of roots and stems of tomato plants (cv. Micro-Tom) that had not been inoculated with PO. In plants that were preinoculated with PO, the movement of RS was suppressed, and bacteria appeared to be restricted to the pit of vessels, a reaction similar to that observed in resistant rootstocks. PO colonization was mainly observed at the surfaces of taproots, the junctions between taproots and lateral roots, and the middle sections of the lateral roots. PO was not observed near wound sites or root tips where RS tended to colonize. However, RS colonization was significantly repressed at these sites in PO preinoculated plants. These observations suggest that the induction of plant defense reactions is the main mechanism for the control of tomato bacterial wilt by PO, not direct competition for infection sites.     

Application of matrix-assisted laser desorption ionization time-of-flight mass spectrometry for rapid and accurate identification of <Emphasis Type="Italic">Ralstonia solanacearum</Emphasis> and <Emphasis Type="Italic">Ralstonia pseudosolanacearum</Emphasis>

Ralstonia solanacearum “species complex” (RSSC) represents soil-borne plant pathogenic bacteria, consisting of diverse and widespread strains that cause bacterial wilt on a wide range of host plants. A recent polyphasic taxonomic study has divided the RSSC into three bacterial species; Ralstonia pseudosolanacearum (phylotypes I and III), Ralstonia solanacearum (phylotype II) and Ralstonia syzygii (phylotype IV). Currently, standard identification of RSSC in plant health laboratories mainly relies on performance of two tests that are based on a different principle. However, these tests are inadequate to precisely discriminate among the three bacterial species in the RSSC. The accurate identification of each of the three bacterial species in the RSSC requires additional molecular tests, including a phylotype determination. These methodologies are labor-intensive, time consuming and rather impractical for routine identification purposes in a plant health laboratory. We explored the potential for an accurate identification of R. pseudosolanacearum (phylotypes I and III) and R. solanacearum (phylotype II) in RSSC, upon implementation of the MALDI-TOF MS tool, and after the creation and validation of an in-house database supplementing the commercial database and covering the entire known genetic diversity in RSSC. MALDI-TOF MS is an emerging approach for identification of bacterial plant pathogens and has been shown to be robust and reproducible. Additionally, when compared to the conventional microbial identification methods it is shown to be less laborious and less expensive. Validation data demonstrated that our in-house database (Mass Spectra Profiles, MSPs) was very specific resulting in the rapid and accurate identification of Ralstonia solanacearum (phylotype II), and Ralstonia pseudosolanacearum (phylotypes I and III). Additionally, no false positive results were obtained with our in-house database for other related Ralstonia sp., such as the R. picketii isolate PD 3286, or for the Pseudomonas syringae and Pseudomonas spp. isolates.     

Bacterial wilt of sweet potato caused by <Emphasis Type="Italic">Ralstonia solanacearum</Emphasis> in Taiwan

During the last decade, a new bacterial disease has impaired the yield of vegetable sweet potato (30–80%) in Taiwan. Infected plants developed stunting, root and stem rot, vascular discoloration and wilting. Ten bacterial isolates that caused the same symptoms in sweet potatoes after inoculation were reisolated and classified as Ralstonia solanacearum phylotype I biovar 4 based on physical and molecular analyses. Moreover, these isolates also caused wilting in convolvulaceous, solanaceaous and cruciferous plants. This report is the first of bacterial wilt of sweet potato caused by R. solanacearum in Taiwan.     

Genetic structure of <Emphasis Type="Italic">Pyrenophora teres</Emphasis> f. <Emphasis Type="Italic">teres</Emphasis> and <Emphasis Type="Italic">P. teres</Emphasis> f. <Emphasis Type="Italic">maculata</Emphasis> populations from western Canada

Infection by Pyrenophora teres f. teres (Ptt) or P. teres f. maculata (Ptm), the causal agents of the net and spot forms of net blotch of barley, respectively, can result in significant yield losses. The genetic structure of a collection of 128 Ptt and 92 Ptm isolates from the western Canadian provinces of Alberta (55 Ptt, 27 Ptm), Saskatchewan (58 Ptt, 46 Ptm) and Manitoba (15 Ptt, 19 Ptm) were analyzed by simple sequence repeat (SSR) marker analysis. Thirteen SSR loci were examined and found to be polymorphic within both Ptt and Ptm populations. In total, 110 distinct alleles were identified, with 19 of these shared between Ptt and Ptm, 75 specific to Ptt, and 16 specific to Ptm. Genotypic diversity was relatively high, with a clonal fraction of approximately 10 % within Ptt and Ptm populations. Significant genetic differentiation (PhiPT = 0.230, P = 0.001) was found among all populations; 77 % of genetic variation occurred within populations and 23 % between populations. Lower, but still significant genetic differentiation (PhiPT = 0.038, P = 0.001) was detected in Ptt, with 96 % of genetic variation occurring within populations. No significant genetic differentiation (PhiPT = 0.010, P = 0.177) was observed among Ptm populations. Isolates clustered in two distinct groups conforming to Ptt or Ptm, with no intermediate cluster. The high number of haplotypes observed, combined with an equal mating type ratio for both forms of the fungus, suggests that P. teres goes through regular cycles of sexual recombination in western Canada.     

Pyruvate-amended modified SMSA medium: improved sensitivity for detection of <Emphasis Type="Italic">Ralstonia solanacearum</Emphasis>

The viable but nonculturable (VBNC) state is induced in the bacterial wilt pathogen Ralstonia solanacearum under prolonged environmental stress. These VBNC cells lose their ability to grow on standard media such as CPG agar, but some of the cells can recover this ability on media supplemented with sodium pyruvate (SP), that degrades hydrogen peroxide. Recently, we suggested that some of the cells in the low-temperature-induced SP-recoverable VBNC state regained their ability to grow on CPG agar after exposure to moderate temperature. These revived cells also retained their virulence on tomato. Although R. solanacearum is detectable on semiselective media, VBNC cells are not detectable on any known semiselective media for the pathogen. To create a suitable medium to detect VBNC cells, we therefore added various compounds that can either degrade hydrogen peroxide or serve an antioxidant function in a semiselective medium, modified SMSA. SP at 5 g/l most improved the sensitivity of R. solanacearum detection. Furthermore, counts on modified SMSA plates for R. solanacearum that had been added to field soil also increased after the addition of 5 g/l SP. SP thus improved the medium’s sensitivity for the detection of R. solanacearum by rescuing a portion of the VBNC cells.     

Effect of simultaneous and sequential inoculations of <Emphasis Type="Italic">Meloidogyne incognita</Emphasis>, <Emphasis Type="Italic">Ralstonia solanacearum</Emphasis> and <Emphasis Type="Italic">Phomopsis vexans</Emphasis> on eggplant in sand mix and fly ash mix soil

Effects simultaneous and sequential inoculations of Meloidogyne incognita, Ralstonia solanacearum and Phomopsis vexans were studied on the growth, chlorophyll and carotenoid contents of eggplants grown in 25% fly ash and 25% sand mix soil. Plants grown in 25% fly ash mix soil had lesser plant growth than grown in 25% sand ash mix soil. Inoculation of M. incognita / R. solanacearum or P. vexans caused reduction in plant growth, chlorophyll and carotenoid contents in both types of soils but these pathogens in combination caused a greater reduction in than individual inoculation. Inoculation of M. incognita 20 days prior to R. solanacearum caused a greater reduction in plant growth than inoculation of M. incognita prior to P. vexans. Inoculation of P. vexans prior to R. solanacearum caused a lesser reduction in plant growth, chlorophyll and carotenoid contents than inoculation of P. vexans prior to M. incognita. Inoculation of R. solanacearum 20 days prior to M. incognita caused a greater reduction in plant growth, chlorophyll and carotenoid contents than inoculation of R. solanacearum prior to P. vexans. Galling and multiplication of M. incognita was higher in plants grown in 25% sand amended soil than with 25% fly ash soil. R. solanacearum and P. vexans had adverse effects on galling and nematode multiplication. Wilt and blight indices caused by R. solanacearum and P. vexans were 3 respectively. Wilt and blight indices were 4 when two pathogens were inoculated together.     

Genetic diversity and pathogenicity of cucurbit-associated <Emphasis Type="Italic">Acidovorax</Emphasis>

Bacterial fruit blotch of cucurbits is a destructive disease caused by Acidovorax avenae subsp. citrulli, which is a typical seedborne pathogen. In seed health testing for this disease, we have detected many strains of Acidovorax with some differences from A. avenae subsp. citrulli. Their 16S rRNA sequences were divided into six types. The most common sequence was completely consistent with that of A. avenae subsp. avenae originally isolated from rice. The other sequences were over 99% similar but not identical to those of A. avenae subsp. avenae and A. avenae subsp. citrulli. Some commercialized antibodies against A. avenae subsp. citrulli reacted with several of these strains. Some of these strains incited yellow spots or brownish water-soaked lesions mainly on young true leaves of cucumber and squash after spray inoculation. Histological observations showed that these strains entered the leaf tissues of cucurbit plants through stomata and multiplied in the intercellular spaces of parenchymatous tissues as well as in the vascular tissues. The amount of bacterial multiplication and spread in the tissues differed among the strains, presumably reflecting their ability to induce symptoms. These isolated strains are therefore different from A. avenae subsp. citrulli, and their potential threat to the cultivation of cucurbits is lower than that of A. avenae subsp. citrulli.     

Survival of <Emphasis Type="Italic">Ralstonia solanacearum</Emphasis> in infected tissues of <Emphasis Type="Italic">Capsicum annuum</Emphasis> and in soils of the state of Pernambuco,Brazil

The survival of Ralstonia solanacearum A1-9^Rif race 1 phylotype I was studied in ten different soil types in the absence of the host plant as well as in infected tissues of the stem and root of bell peppers buried in the soil at 0, 5, and 15 cm. The survival time of R. solanacearum A1-9^Rif in the ten soil types ranged from 42 up to 77 days. Among the chemical and physical characteristics of the soil, clay content, residual moisture, and available water were positively correlated, and pH was negatively correlated, with survival time, population size at 42 days, and area under the population curve. The pathogen survival differed significantly in relation to the plant tissues, but not with respect to the incorporation depth of the infected tissues. The root tissue of bell pepper supported a larger bacterial population at 7 and 21 days (5 × 10⁴ and 3.1 × 10⁴ CFU g⁻¹ tissue, respectively) compared with the stem tissue (0.35 × 10⁴ and 0.48 × 10⁴ CFU g⁻¹ tissue, respectively) and also had a larger area under the population curve. On the other hand, the stem tissues presented a greater decomposition rate and pH compared with the roots. In conclusion, the different types of studied soils as well as the infected bell pepper tissues were considered potential primary sources of R. solanacearum inocula, but only for a short period.     

The sequevar distribution of <Emphasis Type="Italic">Ralstonia solanacearum</Emphasis> in tobacco-growing zones of China is structured by elevation

Bacterial wilt, caused by Ralstonia solanacearum, is a devastating disease resulting in tremendous losses of economic crops such as plants in the Solanaceae. Recent studies showed that R. solanacearum is spreading from the lowlands to the highlands in China. We studied 97 Chinese R. solanacearum strains that were isolated from four tobacco-growing zones over a wide range of elevations using phylotype specific multiplex polymerase chain reaction (Pmx-PCR) and phylogenetic relationships (egl and mutS). The results showed that all isolates belonged to phylotype I, which were further clustered into eight egl-sequence type groups (egl-group, sequevar): sequevars 13, 14, 15, 17, 34, 44, 54, and 55. In addition, Sequevar 55, found from the highlands, was a new/unknown one. Southeast China (Z3) had the largest number of egl-groups, containing six sequevars. The basin of the Yangzi River (Z1) and southwestern China (Z2) contained five egl-groups. The basin of the Huai River (Z4), near the north of China, where slight bacterial wilt occurred recently, contained a single group, sequevar 15. The distribution of sequevars was associated with elevation. Sequevar 15 was over-represented in lowland elevations, while sequevar 54 and the new/unknown one were only found in areas of moderate to high elevations. This finding suggested that the phylotype I strains infecting tobacco were diverse in China and regional integrated control strategies should be considered.     

First report of blueberry red ringspot disease caused by <Emphasis Type="Italic">Blueberry</Emphasis><Emphasis Type="Italic">red</Emphasis><Emphasis Type="Italic">ringspot</Emphasis><Emphasis Type="Italic">virus</Emphasis> in Japan

Virus-like symptoms—red ringspots on stems and leaves, circular blotches or pale spots on fruit—were found on commercial highbush blueberry (Vaccinium corymbosum) cultivars Blueray, Weymouth, Duke and Sierra in Japan. In PCR testing, single DNA fragments were amplified from total nucleic acid samples of the diseased blueberry bushes using primers specific to Blueberry red ringspot virus (BRRV). Sequencing analysis of the amplified products revealed 95.7–97.7% nucleotide sequence identity with the BRRV genome. This paper is the first report of blueberry red ringspot disease caused by BRRV in Japan. The nucleotide sequence data reported in this paper are available in the GenBank/EMBL/DDBJ database as accessions AB469884 to AB469893 for BRRV isolates from Japan.