Genome Characteristics,Phylogeny and Varying Host Specificity of Polish Kra and Ros Isolates of Tomato torrado virus

The genome sequences of two Polish Kra and Ros isolates of Tomato torrado virus (ToTV) were determined and compared with data of previously described ToTV isolates and other Torradovirus members. Whole‐genome sequence comparisons revealed 97.0–99.6% nucleotide sequence identities and close relatedness, with other known ToTV isolates. The high homology between Kra, Ros and Wal'03 ToTVs is likely responsible for the similar symptoms observed on infected plants. However, the symptoms differed in intensity and various host specificity. We report that Kra ToTV caused a milder expression of symptoms on Solanum tuberosum than Wal'03. We hypothesize this may be a result of the significant variability observed within the 3′‐UTR of RNA1 of Kra as well as of Ros ToTV isolates. In the light of this fact, potato may be considered an indicator plant for distinguishing Kra and Wal'03 ToTV isolates.     

Cytopathology of Tomato torrado virus Infection in Tomato and Nicotiana benthamiana

Electron microscopy studies were carried out to investigate the cytopathological changes induced in tomato leaves by Tomato torrado virus (ToTV) that infects tomato plants worldwide causing severe necrotic symptoms. Plants infected with one of the Polish isolates of ToTV were used for cytopathological research. The results revealed severe cellular alterations, especially in Solanum lycopersicum. Moreover, it was shown that crystalline aggregates of virions occurred not only within the phloem cells as it has been previously reported.     

Epidemics of Tomato torrado virus,Pepino mosaic virus and Tomato chlorosis virus in tomato crops: do mixed infections contribute to torrado disease epidemiology?

Torrado disease was first observed in protected tomato crops in the Murcia province of Spain in spring 2001, causing serious concern to regional tomato producers. The disease-causing agent was initially identified as a picorna-like bipartite plant RNA virus, now known as Tomato torrado virus (ToTV), but several additional torradoviruses inducing similar disease symptoms have been described more recently. We studied the incidence of torradoviruses between 2005 and 2008 in two parts of Murcia (Spain) where tomato crops are grown commercially. We also analysed the potential association among ToTV, Pepino mosaic virus (PepMV) and Tomato chlorosis virus (ToCV) in samples showing torrado symptoms of varying severity. ToTV was the only torradovirus found in the samples (predominantly as single infections), but double and triple infections comprising ToTV, PepMV and/or ToCV were also detected. There was no evidence of a specific association among the viruses as the frequencies of mixed infections did not deviate from those expected to occur by chance. Statistical analysis of the potential association between torrado symptoms and the type of infection (single or multiple) was inconclusive. To determine whether co-infections with ToTV and PepMV have any marked influence on the torrado disease, we analysed torrado symptom severity and virus accumulation in tomato plants experimentally infected with ToTV-CE, PepMV-Sp13 and PepMV-PS5 in single and mixed infections. The severity of the torrado symptoms was not affected by the presence of PepMV. In single infections, the ToTV titre remained very low, reaching its maximum in the early stages of infection and declining rapidly thereafter, whereas the disease symptoms became more severe over the same timescale. In mixed infections, the accumulation of both ToTV and PepMV was altered with respect to single infections, and the magnitude of this alteration appeared to be virus and strain specific. Therefore, ToTV and PepMV mixed infections may modulate the epidemiology of both viruses in a complex way by altering virus fitness. The impact of our studies on efforts to track and prevent the spread of torrado disease is discussed.     

不同寄主来源的灰葡萄孢对番茄的致病力分化研究

Eighteen isolates of Botrytis cinerea were obtained from the diseased plant tissue collected in Hefei, Bengbu, Changfeng and Hexian in Anhui province, by means of tissue isolating method. The pathogenicity of the isolates of B. cinerea from different hosts to the fruits and leaves of tomato were investigated by applying wound inoculation with mycelial blocks. The results showed that all of the tested isolates caused grey mould on tomato fruits, but there was significant difference in the average diameters of the lesions caused by different isolates, suggesting that there was significant differentiation in pathogenicity of B. cinerea strains to tomato fruits among isolates. According to the average diameters of the lesions on tomato fruits, the pathogenicity of the all isolates was classified into three categories: strong, intermediate and weak. In general, the isolates from tomato were more strongly pathogenic to tomato fruits than the isolates from strawberry, grape and capsicum. However, there was difference in pathogenicity among the different isolates from the same host, and the pathogenicity difference was not obviously related to the localities of isolates. After inoculating of tomato leaves, all of the tested isolates except CF3 caused grey mould on tomato leaves, but there was significant difference in the average diameters of the lesions caused by different isolates; and the difference in pathogenicity to tomato leaves was not obviously related to the host and locality of isolates.     

Genetic diversity and differentiation of Indian isolates of Phytophthora infestans as revealed by RAPD analysis

Sixty-seven isolates of Phytophthora infestans collected from Himalayan hill regions and subtropical planes of India were characterized by RAPD markers to assess diversity and differentiation based on location of origin. Ten random decamer primers generated 161 polymorphic fragments. Association of P. infestans isolates on the dendrogram and PCO plot revealed two clear grouping based on geographical location of origin-hill isolates and plane isolates. Quantification of diversity by Shannon index of diversity analysis demonstrated that most of the diversity was present with a particular population (hill or plane) of P. infestans isolates, with 85% variation being within and 15% being between hill and plane isolates. Subtropical plane isolates of P. infestans exhibited higher variability compared to hill isolates and they were more dispersed on the PCO plot. No clear differentiation of isolates based on mating type was reflected on the dendrogram and PCO plot.     

不同寄主来源的灰葡萄孢对番茄的致病力分化研究

从安徽合肥、蚌埠、长丰、和县等市、县的番茄、辣椒、草莓、葡萄等发病寄主上分离鉴定获得18个灰葡萄孢Botrytis cinerea菌株,采用菌丝块创伤接种法,分别测定了上述不同寄主来源的灰葡萄孢菌对番茄果实和叶片的致病力.结果表明,所有供试菌株接种番茄果实后均引起发病,但不同菌株所致病斑的平均直径有显著差异,显示灰葡萄孢菌株间对番茄果实的致病力存在明显分化.按照在番茄果实上所致病斑的平均直径大小可将供试菌株致病力划分为较强、中等和较弱3种类型.总体来说,来自番茄的菌株对番茄果实的致病力较强,来自草莓、葡萄和辣椒的菌株对番茄果实的致病力较弱,但来自相同寄主的菌株间致病力也存在差异,菌株致病力差异与菌株地域来源无明显相关.供试灰葡萄孢菌株接种番茄叶片后,除CF1外,均可引起番茄叶片发病,但不同菌株所致番茄叶片病斑的平均直径也有显著差异;供试菌株对番茄叶片的致病力差异与菌株的寄主和地域来源无显著相关.     

Study of the aggressiveness of Rhizoctonia solani isolates

This paper presents an in vitro test to screen the pathogenicity of different Rhizoctonia solani isolates on a host range. The level of aggressivity of the different isolates was different for several host plants tested. There were significant differences between the crops and the isolates tested. In general, the disease level was higher on beans, lettuce and cabbage. In carrot and rye grass the level of infection was lower for the isolates of R. solani tested. The potato isolates of R. solani were less aggressive than the isolates coming from maize, fodder beet and sugar beet. The R. solani isolates were also biochemically characterized by pectic zymograms: the isolates Rs0401 (from maize) and Rs0504 (from sugar beet) belong both to the anastomosis group AG2-2.     

Colonization of roots of cultivated Solanum lycopersicum by dark septate and other ascomycetous endophytes

Tomato (Solanum lycopersicum L.) roots from four different crop sites in Colombia were surface sterilized and 51 fungal isolates were obtained and conserved for further analysis. Based on microscopical observations and growth characteristics, 20 fungal isolates corresponded to genus Fusarium, six presented asexual conidia different from Fusarium, eight were sterile mycelia, seven of which had dark septate hyphae and 17 did not continue to grow on plates after being recovered from conservation. Growth on different media, detailed morphological characterization and ITS region sequencing of the six sporulating and eight sterile isolates revealed that they belonged to different orders of Ascomycota and that the sterile dark septate endophytes did not correspond to the well known Phialocephala group. Interactions of nine isolates with tomato plantlets were assessed in vitro. No effect on shoot development was revealed, but three isolates caused brown spots in roots. Colonization patterns as analyzed by confocal microscopy differed among the isolates and ranged from epidermal to cortical penetration. Altogether 11 new isolates from root endophytic fungi were obtained, seven of which showed features of dark septate endophytes. Four known morphotypes were represented by five isolates, while six isolates belonged to five morphotypes of putative new unknown species.     

Characterization of actinomycetes isolated from the indoor air of the church of Saint Katherine Monastery, Egypt

Actinomycetes were isolated from the indoor air of the church of Saint Katherin Monastery during different visiting hours. Fifty air samples collected over one year by using automated air sampler were plated on four different media. The low nutrient-content medium 1/10 SC was significantly effective in recovery of actinomycetes compared to the other formula of rich media. Average counts of bacteria, actinomycetes and fungi were 487, 65 and 90 cfu/m³, respectively. Fifty-six morphologically different actinomycetes isolates were recovered during this study assigned into five different genera, in addition to three unidentified isolates. Tentative identification of the isolates indicated predominance of genus Streptomyces, representing 59% of the isolates. Isolates were screened for resistance to 11 antibiotics, antimicrobial activities towards seven microbial strains, Growth on 12 different carbon source, acid production and pigmentation. About 77% of actinomycete isolates were resistant to the antibiotics with different resistance patterns. 12.5% of the airborne actinomycetes exhibited antinmicrobial activities. The isolates showed wide variation in carbon source usage. Forty percent of the isolates were able to utilize all tested carbon sources while 80% were acid producers. Melanin production was produced by 34% of the isolates. While 45% of the isolates were able to produce other diffusible pigments, the majority of the pigments were brown in color however; yellow, orange and green pigments were produced by a number of isolates. The impact of these activities on the historical objects of the church and the tourist’s health is discussed.     

Pathogenicity of Race-1 and Race-2 Tomato Wilt Isolates of Verticillium dabliae to Four Solanaceous and Two Non-Solanaceous Hosts

The pathogenicity of four race-1 and three race-2 tomato with isolates of Verticallium dahliae to tomato, eggplant, tobacco, pepper, French bean and cabbage was investigated. Plants were inoculated without wounding and the symptoms assessed 6, weeks later. Both race-1 and race-2 isolates caused foliar symptoms on the race-1 susceptible tomato cultivar GCR-26 ( Ve/Ve ) although these were generally more severe with race-1. All race-2 isolates were significantly more pathogenic than race-1, on the race-1 resistant tomato cultivar GCR-218 (ve/ve), although two of the race-1 isolates caused mild foliar symptoms. None of the race-2 isolates caused stunting of GCR-26 whereas they all caused significant stunting of GCR-218. All isolates reduceddry weight on GCR-26 whereas only race-2 affected GCR-218. All isolates induced significant foliar symptoms, stunting and reduction in dry weight on eggplant. Only one isolates (race-1) caused foliar symptoms on tobacco but this was not accompanied by areduction in either plant height or dry weight. All isolates were able to cause foliar symptoms on pepper, and two caused moderate to severe symptoms. Four isolates caused a significant reduction in plant height and one of these reduced dry weight. One isolates which caused mild foliar symptoms on papper increased host dry weight. No disease symptoms were observed on the non-solanaceous host French bean. All isolates were capable of inducing mild foliar symptoms on cabbage but none caused reductions ineither plant height or dry weight. Race-1 and race-2 isolates could only be distinguished on the near-isogenic pair of tomato cultivars. Verticallium was re-isolated for each fungal isolate/host cultivar combination for tomato, eggplant and tobacco but was sporadic for the other hosts.     

Occurrence of virulence factors among human intestinal enterococcal isolates

AIMS: The aim of this study was to investigate the frequency of enterococcal virulence factors among human intestinal Enterococcus faecalis strains and to find out whether the pattern differs from that seen in published reports on food and clinical isolates. METHODS AND RESULTS: The E. faecalis isolates were cultured from human faecal samples obtained from five ulcerative colitis patients in remission phase. The species identification was based on API120 strips and species-specific PCR primers. The isolates were further characterized using the pulsed-field gel electrophoresis. The presence of seven different known enterococcal virulence factors among the confirmed E. faecalis isolates were screened using PCR techniques and published primers. CONCLUSIONS: Among the 35 isolates representing nine different pulsotypes the most frequent virulence factors were cpd (33 isolates), agg (25 isolates), gelE (22 isolates) and esp (15 isolates). No complete sets of genes associated for the production of functional cytolysin were encountered indicating that intestinal enterococci may differ in this respect from clinical strains. SIGNIFICANCE AND IMPACT OF THE STUDY: According to the results, the commensal enterococcal strains appear to differ from clinical isolates in their complement of presumed virulence factors.     

Screening of New Zealand Native White-Rot Isolates for PCP Degradation

From a pool of 367 white-rot fungi native to New Zealand (over 77 genera), isolates were screened for their bioremediation potential of pentachlorophenol (PCP). Fungi were tested for their ligninolytic activity (Poly R-478, 367 isolates; wood decay, 235 isolates), tolerance to temperature (261 isolates), resistance to PCP (253 isolates), and PCP degradation potential plus laccase expression (20 isolates). Of the isolates tested, 26% showed a discolouration in the polymeric dye assay, but all caused wood decay (5 to 169 mm) on willow cuttings. In the temperature tolerance tests, all isolates survived incubation from 0 to 30°C, however, 18% and 40% did not survive incubation at 35 and 40°C, respectively. In the PCP resistance tests, 23 isolates (9%) were able to grow on 200 mg/L PCP amended agar, of which 20 isolates were further studied for laccase expression and PCP degradation in vitro. All 20 isolates reduced (P < 0.05) PCP in the liquid fraction in the absence or presence of laccase and five of the isolates produced no detectable levels of PCP. None of the screening tests were predictive for PCP degradation in vitro. The requirements to build a database to select a superior white-rot fungal isolates for bioremediation is discussed.     

Characterization of Isolates of Meloidogyne from Rice-Wheat Production Fields in Nepal

Thirty-three isolates of root-knot nematode were recovered from soil samples from rice-wheat fields in Nepal and maintained on rice cv. BR 11. The isolates were characterized using morphology, host range and DNA sequence analyses in order to ascertain their identity. Results indicated phenotypic similarity (juvenile measurements, perennial pattern, host range and gall shape) of the Nepalese isolates with Meloidogyne graminicola, with minor variations. The rice varieties LA 110 and Labelle were susceptible to all of the Nepalese isolates, but differences in the aggressiveness of the isolates were observed. Phylogenetic analyses based on the sequences of partial internal transcribed spacer (ITS) of the rRNA genes indicated that all Nepalese isolates formed a distinct clade with known isolates of M. graminicola with high bootstrap support. Furthermore, two groups were identified within the M. graminicola clade. No correlation between ITS haplotype and aggressiveness or host range was found among the tested isolates.     

Molecular subtype analyses of Campylobacter spp. from Arkansas and California poultry operations

Campylobacter isolates from diverse samples within broiler production and processing environments were typed by using flaA short variable region DNA sequence analysis. Sixteen flocks from four different farms representing two broiler producers in Arkansas and California were analyzed. Fourteen of the flocks (87.5%) were Campylobacter-positive; two remained negative throughout the 6-week rearing period. In general, multiple clones were present within a flock. Additionally, clones found within a flock were also present on the final product, although the diversity of Campylobacter spp. on the final product appeared to be reduced relative to that observed within the flock. Comparison of clones between flocks on the same farm revealed that some clones of Campylobacter persisted in multiple flocks. Furthermore, some clones were identified across the two farms that were under the same management. In two sampling periods, environmental isolates were positive for Campylobacter prior to flock shedding. Environmental samples associated with five additional flocks were positive for Campylobacter concomitantly with recovery of Campylobacter from the birds. Analysis of the environmental isolates that were positive prior to flock shedding demonstrated that in some instances the environmental isolates possessed genotypes identical to those of isolates originating from the flock, while in other cases the environmental isolates possessed genotypes that were distantly related to isolates obtained from the flock. Analyses of environmental isolates that tested positive concurrently with the positive isolates from the flocks demonstrated varied results; in some instances the environmental isolates possessed genotypes identical to those of isolates originating from the flock, while in other cases the environmental isolates possessed genotypes that were distantly related to isolates obtained from the flock. These data suggest that the external environment may contribute to Campylobacter contamination during poultry production and processing. However, environmental contamination with Campylobacter does not appear to be the sole contributing factor.     

Effect of dsRNA-containing and dsRNA-free hypovirulent isolates of Fusarium oxysporum on severity of Fusarium seedling disease of soybean in naturally infested soil

In the sandy soils of eastern Virginia, soybean seedlings are colonized by hypovirulent and virulent isolates of Fusarium oxysporum and F. solani. Our objectives were to determine if prior inoculation of soybean seeds with hypovirulent F. oxysporum isolates reduced severity of seedling disease in naturally infested soil, and to determine if there was an association between the presence of dsRNA mycovirus and hypovirulence in isolates of F. oxysporum and F. solani from soybean plants. The presence of dsRNA was not associated with hypovirulence in F. oxysporum since some hypovirulent isolates contained dsRNA while other hypovirulent isolates did not. Furthermore, of six dsRNA-containing F. oxysporum isolates, three were hypovirulent and three were virulent. Four segments of dsRNA, with sizes of 4.0, 3.1, 2.7 and 2.2 kb were detected in extracts of all six F. oxysporum isolates. No hypovirulent or dsRNA-containing of F. solani isolates were found. Prior inoculation of cv. Essex soybean seeds with conidia of dsRNA-free hypovirulent F. oxysporum isolates significantly (P < 0.05) reduced disease severity on cotyledons and hypocotyls, and increased the rate of seedling emergence in field soil, compared to control plants. No significant (P > 0.05) differences were found between dsRNA-containing and dsRNA-free hypovirulent F. oxysporum isolates in their effects on reducing disease severity. Hypovirulent isolates that colonize soybean tissues may play a role in reducing Fusarium seedling disease of soybean in natural soils.     

Identification and Characterization of the Causal Agent of Gummy Stem Blight from Muskmelon and Watermelon in East China

Gummy stem blight (GSB) is one of the most destructive foliar diseases of cucurbits, worldwide. To identify and characterize the pathogen which causes GSB on watermelon and muskmelon in East China, morphological characteristics, pathogenicity assays as well as sequence characterization of the rDNA internal transcribed spacer (ITS) were performed on 41 isolates collected from Jiangsu, Zhejiang, Anhui and Jiangxi provinces. The mycelia of all the isolates were white on top and olivaceous green to black with concentric circles at the bottom on potato‐dextrose agar medium. The isolates differed significantly on aggressiveness based on pathogenicity assays. rDNA‐ITS sequences and phylogenetic analysis confirmed the isolates as Didymella bryoniae. The isolates were found to be highly identical with the exception of 13 isolates, which had a guanine substitution instead of adenine at position 131 of the ITS.     

Diversity of isolates of Rhodococcus equi from Australian Thoroughbred horse farms

Pulsed field gel electrophoresis of restriction endonuclease digested genomic DNA from a collection of clinical isolates of Rhodococcus equi was used to compare strain diversity on different Thoroughbred horse farms over time. Restricted diversity was found among the isolates tested, as the same strains were detected on multiple farms and in multiple years. Marked variation occurred in strain prevalence with some strains being represented by single isolates, and the most prevalent by 26 isolates. There were dominant strains on some farms and the prevalence of some strains differed between farms. Infection with multiple strains was noted in some cases where multiple isolates from a single foal were examined.     

申克孢子丝菌菌丝相至酵母相转化的实验研究

目的观察申克孢子丝菌菌丝相向酵母相转化的形态学变化并初步研究连续传代后菌株转化为酵母相的百分率。方法将95株申克孢子丝菌临床株于脑心浸液琼脂培养基上连续传代至酵母相,利用显微镜及血细胞计数板计数菌丝和孢子比例并记录显微镜下形态。结果 95株申克孢子丝菌中,经1次传代即成功转化有23株,经2次传代有14株,经3次传代有10株,经4次传代有6株,4次传代后总计55.8%实验菌株转化为酵母相。结论部分申克孢子丝菌由菌丝相向酵母相转化需经过连续多次传代,连续传代增加了菌丝相至酵母相的转化率。     

Biological control of Tiarosporella phaseolina the causal agent of charcoal rot of soybean

Charcoal rot caused by Tiarosporella phaseolina (Tassi) Van der Aa is an important disease of soybean in Gorgan province of Iran. Experiments were carried out with 95 bactenal isolates that were collected from the rhizosphere of soybean plant. Among these bacteria only 50 isolates showed antagonistic effect on Tiarosporella phaseolina using dual culture test. Six highly effective bacteria were selected for subsequent studies. Based on biochemical physiological and morphological tests, isolates Pf-12 and Pf-63 were identified as Pseudomonas fluorescens, isolates B-13, B-42,B-126 and B-84 as Bacillus subtilis. The isolates of P. fluorescens produced antibiotics as well as volatile metabolites that inhibited mycelial growth of fungus. Bacillus subtilis isolates inhibited the fungal growth through volatile and non-volatile metabolites production. Only P. fluorescens isolates produced hydrogen cyanide. In greenhouse studies, the isolates B-13 and B-126 reduced 59% and 66% the intensity of charcoal rot of soybean respectively. The combinations of isolates B-13 and B-126 were also effective on reducing the intensity of disease.     

Phenotypic characteristics of root-nodulating bacteria isolated from Acacia spp. grown in Libya

Thirty isolates of root-nodulating bacteria obtained from Acacia cyanophylla, A. karroo, A. cyclops, A. tortilis (subsp.raddiana), Faidherbia albida and Acacia sp., grown in different regions of Libya, were studied by performing numerical analysis of 104 characteristics. Three fast- and one slow-growing reference strains from herbaceous and woody legumes were included. Five distinct clusters were formed. The fast-growing reference strains were separated from the isolates whereas the slow-growing was included in cluster 4. With the exception of one cluster, the majority of clusters were formed regardless of the host plant or site of origin. Based on plant tests, generation times, acid production and carbon utilization the isolates were diverse (fast and slow-growing isolates). Like slow-growing isolates, most of the fast-growing isolates appeared to be non-specific, nodulated many species from the same genus notably F. albida, known to nodulate only with slow-growing strains. Most clusters grew at temperatures 35 °C and 37 °C; some grew at temperatures above 40 °C. The majority of isolates grew at acid and alkaline pH and only one isolate grew below pH 4. Most isolates were able to utilize many amino acids as nitrogen sources and to reduce nitrate. Urea was hydrolysed by all clusters. Monosaccharides and polyols were used by slow and fast-growing isolates as the only carbon sources whereas assimilation of disaccharides varied: Some isolates, like slow-growing isolates, failed to utilize these carbon sources. Most isolates were unable to utilize polysaccharides. Regarding tolerance to NaCl on agar medium, the majority of isolates were unable to grow at a concentration of 2% NaCl, but some were highly resistant and there was one isolate which grew at 8% NaCl. Most isolates were resistant to heavy metals and to antibiotics.