Detection of Phytophthora nicotianae and P. citrophthora in Citrus Roots and Soils by Nested PCR

The polymerase chain reaction (PCR) was used for the specific detection of Phytophthora nicotianae and P. citrophthora in citrus roots and soils. Primers were based on the nucleotide sequences of the internal transcribed space regions (ITS1 and ITS2) of 16 different species of Phytophthora. Two primer pairs, Pn5B–Pn6 and Pc2B–Pc7, were designed specifically to amplify DNA from P. nicotianae and P. citrophthora, respectively. Another primer pair (Ph2–ITS4) was designed to amplify DNA from many Phytophthora species. All primer pairs were assessed for specificity and absence of cross-reactivity, using DNA from 118 isolates of Phytophthora and 82 of other common soil fungi. In conventional PCR, with a 10-fold dilution series of template DNA, the limit of detection was of 1pgl^–1 DNA for all the primer pairs (Ph2–ITS4, Pn5B–Pn6, and Pc2B–Pc7). In nested PCR, with primers Ph2–ITS4 in the first round, the detection limit was of 1fgl^–1 for both the primer sets (Pn5B–Pn6 and Pc2B–Pc7). Simple, inexpensive and rapid procedures for direct extraction of DNA from soil and roots were developed. The method yielded DNA of a purity and quality suitable for PCR within 2–3h. DNA extracted from soil and roots was amplified by nested PCR utilizing primers Ph2–ITS4 in the first round. In the second round the primer pairs Pn5B–Pn6 and Pc2B–Pc7 were utilized to detect P. nicotianae and P. citrophthora, respectively. Comparison between the molecular method and pathogen isolation by means of a selective medium did not show any significant differences in sensitivity.     

Specific detection of Phytophthora nicotianae using the polymerase chain reaction and primers based on the DNA sequence of its elictin gene ParA1

Six primers based on the sequence of the flanking and coding regions of the elicitin gene ParA1 of Phytophthora nicotianae were tested for specific detection of the fungus by the polymerase chain reaction (PCR). One combination, IL7/IL8, with IL7 in a flanking region and IL8 in a coding region of the gene, gave an intense 378 bp signal with a diverse collection of isolates of P. nicotianae, that included some from black shank disease of tobacco and others from a variety of hosts. The sequence of the amplification product obtained with an isolate that produces elicitin and one that does not, was homologous with the known sequence of the ParA1 gene. The same primer combination gave no signal with sixteen other Phytophthora species tested except for two isolates P. palmivora with which it gave a weak 800 bp signal. It gave no signal with DNA from healthy tobacco and tomato plants but P. nicotianae was detected in inoculated tobacco and tomato plants. Small numbers of zoospores (>100) trapped onto a nitrocellulose membrane after filtration from suspension were also detected after two successive rounds of PCR.     

安徽省烟草黑胫病菌的交配型及其地理分布研究

 Total 69 isolates of Phytophthora nicotianae var. nicotianae were isolated and identified from tobacco black shank samples collected from different areas of Anhui province, and mating types of the oomycete were investigated by the method of partnership culture in vitro on L-tryptophan medium with β-sitosterol. The results showed that A2 mating type was the predominant in isolates of P. nicotianae var. nicotianae, next was A₀ mating type, A₁ and other mating types were not observed. It was suggested that sexual reproduction of P. nicotianae var. nicotianae might not take place frequently, and Anhui province might not be the original center of P. nicotianae var. nicotianae. The results indicated further that mating type geographical distribution of P. nicotianae var. nicotianae in Anhui province was in line with that in China. In addition, the significance of the test results and the possible reason for A₁ mating type being absent were discussed.     

基于Ypt1基因为靶标的木香疫病病组织及病田土壤分子检测技术

A species-specific PCR assay was established for rapid and accurate detection of the oomycete pathogen Phytophthora tentaculata in diseased plant tissues and infected soil.A pair of species-specific primers Pt1/Pt2 were designed on the basis of Ras-related protein(Ypt1) gene sequences of the Phytophthora species.PCR amplification with the Pt primers resulted in a 386 bp product only from isolates of P.tentaculata.The detection threshold with Pt primers was 100 pg of genomic DNA.A nested PCR procedure was developed using Ypt1F/Ypt1R as the first-round amplification primers and Pt1/Pt2 as the second-round primers,which increased the detection sensitivity 100-fold to 1 pg.PCR using these Pt primers can also be used to detect P.tentaculata in naturally infected plant tissues and soil.The PCR-based method developed in this study provides a rapid and sensitive tool for detection of P.tentaculata.     

雪松疫霉根腐病菌

雪松疫霉根腐病菌(Phytophthora lateralis Tucker et Milbrath)是我国进境植物检疫性有害生物,可引起寄主植物严重的根腐病。鉴于该病原菌潜在的危险性,本文就其分布、寄主范围、传播方式、危害症状、形态特征以及检疫鉴定方法等进行了综述,供检疫鉴定参考。     

Phytophthora diversity and the population structure of Phytophthora ramorum in Swiss ornamental nurseries

Invasive oomycete pathogens have been causing significant damage to native ecosystems worldwide for over a century. A recent well‐known example is Phytophthora ramorum, the causal agent of sudden oak death, which emerged in the 1990s in Europe and North America. In Europe, this pathogen is mainly restricted to woody ornamentals in nurseries and public greens, while severe outbreaks in the wild have only been reported in the UK. This study presents the results of the P. ramorum survey conducted in Swiss nurseries between 2003 and 2011. In all 120 nurseries subjected to the plant passport system, the main P. ramorum hosts were visually checked for above ground infections. Phytophthora species were isolated from tissue showing symptoms and identified on the basis of the morphological features of the cultures and sequencing of the ribosomal ITS region. Phytophthora was detected on 125 plants (66 Viburnum, 58 Rhododendron and one Pieris). Phytophthora ramorum was the most frequent species (59·2% of the plants), followed by P. plurivora, P. cactorum, P. citrophthora, P. cinnamomi, P. cactorum/P. hedraiandra, P. multivora and P. taxon PgChlamydo. The highest incidence of P. ramorum was observed on Viburnum × bodnantense. Microsatellite genotyping showed that the Swiss P. ramorum population is highly clonal and consists of seven genotypes (five previously reported in Europe, two new), all belonging to the European EU1 clonal lineage. It can therefore be assumed that P. ramorum entered Switzerland through nursery trade. Despite sanitation measures, repeated P. ramorum infections have been recorded in seven nurseries, suggesting either reintroduction or unsuccessful eradication efforts.     

Molecular detection of Phytophthora capsici in infected plant tissues, soil and water

A species-specific PCR assay was developed for rapid and accurate detection of the pathogenic oomycete Phytophthora capsici in diseased plant tissues, soil and artificially infested irrigation water. Based on differences in internal transcribed spacer (ITS) sequences of Phytophthora spp. and other oomycetes, one pair of species-specific primers, PC-1/PC-2, was synthesized. After screening 15 isolates of P. capsici and 77 isolates from the Ascomycota, Basidiomycota, Deuteromycota and Oomycota, the PC-1/PC-2 primers amplified only a single PCR band of c . 560 bp from P. capsici . The detection sensitivity with primers PC-1/PC-2 was 1 pg genomic DNA (equivalent to half the genomic DNA of a single zoospore) per 25- µ L PCR reaction volume; traditional PCR could detect P. capsici in naturally infected plant tissues, diseased field soil and artificially inoculated irrigation water. Using ITS1/ITS4 as the first-round primers and PC-1/PC-2 in the second round, nested PCR procedures were developed, increasing detection sensitivity to 1 fg per 25- µ L reaction volume. The results suggested that the assay detected the pathogen more rapidly and accurately than standard isolation methods. The PCR-based methods developed here could simplify both plant disease diagnosis and pathogen monitoring, as well as guiding plant disease management.     

A Simple PCR-based Method for the Detection of the Chickpea-wilt Pathogen Fusarium oxysporum f.sp. ciceris in Artificial and Natural Soils

A fast and simple polymerase chain reaction method has been developed for the detection of Fusarium oxysporum f.sp. ciceris, the causal agent of Fusarium wilt of chickpea, in natural and artificial soils. The method involves the disruption of fungal biomass by grinding dry soil, using its abrasive properties, in the presence of skimmed milk powder. The latter prevents loss of DNA by adsorption to soil particles or by degradation and reduces the co-extraction of PCR inhibitors with the DNA. After phenol/chloroform extraction, the DNA is suitable for direct PCR amplification without a precipitation step. For the efficient detection of small amounts of DNA extracted from soil, a two step amplification with nested primers was used. The dilution step reduced the effect of Taq-polymerase inhibitors. The specificity of the amplification, and consequently the yield of specific product, was increased by the use of a modified touch down process during the annealing step. The method has been applied to the specific detection of wilt-inducing isolates of the pathogen in a variety of natural and artificial soils. The amplification was improved by the use of increased concentrations of skimmed milk powder in soils with high organic or clay contents.     

Genome-based PCR Primers for Specific and Sensitive Detection and Quantification of Xylella fastidiosa

Xylella fastidiosa is an important pathogen of many commercial crops. Detection of X. fastidiosa is difficult due to low concentrations of the bacteria in insects and asymptomatic plant tissue, and non-uniform distribution in infected plants. A dual purpose conventional PCR and quantitative PCR (TaqMan™) system was developed for the generic detection of X. fastidiosa strains. Primers HL5 and HL6, designed to amplify a unique region common to the sequenced genomes of four Xylella strains, amplified a 221 bp fragment from strains associated with Pierce’s disease of grapes, almond leaf scorch, and oleander leaf scorch disease and from DNA from an Xf strain associated with citrus variegated chlorosis. Standard curves were obtained using concentrations of Xylella ranging from 5 to 10⁵ cells per reaction in water and grape extracts and 10–10⁵ cells in insect DNA. Regression curves were similar, with correlation coefficients of r ² > 0.97. In quantitative PCR, C_t values ranged between 20 and 36 cycles for 5–10⁵ bacterial cells per reaction. No amplicons were obtained with several non-Xf bacterial strains tested including related plant pathogenic, grape endophytic bacteria and endosymbiotic bacteria isolated from glassy-winged sharpshooters. The method was evaluated for clinical diagnosis of Xf in grapes, almonds and insect vectors. The procedure described is reliable for detection of the pathogen with a high degree of sensitivity and specificity.     

Dieback and mortality of Nothofagus in Britain: ecology,pathogenicity and sporulation potential of the causal agent Phytophthora pseudosyringae

Since 2009 extensive dieback and mortality of Nothofagus obliqua, associated with bleeding cankers on stems and branches, has been observed in the UK. The causal agent was identified as Phytophthora pseudosyringae, based on morphological and analysis of the internal transcribed spacer (ITS) sequences. Between 2011 and 2013, a survey assessed the frequency and nature of these P. pseudosyringae infections. Mature trees of Nothofagus with stem lesions caused by P. pseudosyringae were found across England, Scotland and Wales. Additional symptoms such as twig blight and leaf necrosis indicated that aerial infection was occurring. Besides N. obliqua, other hosts regularly encountered included Nothofagus alpina, Fagus sylvatica and Vaccinium myrtillus. In pathogenicity tests involving inoculation of logs, P. pseudosyringae was shown to be an aggressive bark pathogen of N. obliqua and F. sylvatica, but significantly less aggressive on N. alpina. Foliage susceptibility and sporulation tests showed marked differences between the six host species tested. Leaves of N. obliqua and V. myrtillus were highly susceptible. Leaves of N. alpina were moderately susceptible, those of Rhododendron ponticum slightly susceptible and those of F. sylvatica not susceptible at all. High levels of sporulation were observed only on inoculated N. obliqua and V. myrtillus leaves. This suggests that P. pseudosyringae may sporulate heavily on N. obliqua foliage in the field and that this inoculum initiates the aerial lesions observed on the shoots, branches and stems. The results also suggest that P. pseudosyringae has the potential to pose a serious threat to N. obliqua and other Nothofagus species in their Southern Hemisphere native ranges.     

Diversity of Phytophthora Clandestina Isolated From Subterranean Clover in Southern Australia: Analysis of Virulence and RAPD Profiles

The virulence spectrum of 112 isolates of Phytophthora clandestina collected from 56 sites in four subterranean clover-growing states in southern Australia was determined using differential cultivars of subterranean clover. Five races were detected, with race 0 in all states except New South Wales, race 1 in all states, race 2 only in Victoria, race 3 only in New South Wales, and race 4 in Victoria and Western Australia. The level of genotypic diversity among the different P. clandestina populations was investigated using five RAPD primers. Among 30 bands amplified, only two were polymorphic. This enabled identification of four multilocus RAPD genotypes. Three of the four genotypes occurred in all four states. Races 2 and 3 occurred with RAPD genotypes 1 and 2 only whereas races 0 and 1 occurred in all four multilocus RAPD genotypes. These results indicate that the pathogenicity spectrum of P. clandestina can change rapidly.     

Characterization of accessions and species of Macadamia to stem infection by Phytophthora cinnamomi

Phytophthora cinnamomi is a major pathogen in most macadamia plantations worldwide. Due to stem lesions, stem cankers and leaf defoliation, it results in loss of productivity and tree death. This study examined accessions of the four Macadamia species and their hybrids, produced via rooted stem cuttings or germinated seeds, for susceptibility to stem canker and necrotic lesions caused by P. cinnamomi. Plants were wound‐inoculated with agar containing P. cinnamomi. The symptoms produced in inoculated plants were used to characterize host susceptibility variation within and among the population. Lesion length and severity of stem canker were recorded. The four species and hybrids differed significantly in stem canker severity (P < 0.001) and lesion length (P = 0.04). Macadamia integrifolia and M. tetraphylla hybrids were the most susceptible. Macadamia integrifolia had the greatest stem canker severity and the most extensive lesions above and below the site of inoculation. Restricted lesion sizes were observed in M. ternifolia and M.  jansenii. The effects of basal stem diameter and the method of propagation either from cuttings or from seed were not significant. The genetic variation in the reaction of macadamia accessions to stem infection by P. cinnamomi is discussed.     

Detection and identification of Phytophthora fragariae Hickman by the polymerase chain reaction

Phytophthora fragariae Hickman, which causes strawberry red stele and raspberry root rot, is a quarantine organism for which specific and sensitive detection methods are required to test the health of planting material. Sequences of the internal transcribed spacer regions of the ribosomal gene repeat (rDNA) were used to develop primers for P. fragariae in a nested Polymerase Chain Reaction (PCR). The fungus was readily detected in infected but symptomless roots by nested, but not single-round, PCR. It was also detected in infested water samples obtained from the Dutch General Inspection Service by nested PCR. Detection of PCR products was at least 10-fold more sensitive by PCR-ELISA than by conventional visualisation on agarose gels.     

The Effect of Soil Moisture and Cabbage Amendment on the Thermoinactivation of Phytophthora nicotianae

The analysis of the effect of soil water matric potential and temperature regimes on the inactivation of chlamydospores of Phytophthora nicotianae in cabbage amended soils was evaluated using three matric potentials (0, -10, and -30kPa), temperature regimes of 1.5h at 44°C, 5h at 41°C and 8h at 35°C, or 3h at 47°C, 5h at 44°C and 8h at 35°C, with a baseline temperature of 25°C during the rest of the day. The results indicated that survival of P. nicotianae was lowest in saturated soil; and as temperature increased, survival of the pathogen decreased at all soil water matric potentials evaluated. Cabbage amendments can enhance the effect of the heat treatment, further decreasing the pathogen population. The soil water matric potentials evaluated represent optimum levels for the study of thermal inactivation. However, under field conditions lower potentials may be found. Extending the range of soil water matric potentials and the treatment time would allow better comparisons with the field data. There is a clear indication that one irrigation period prior to solarization would provide enough moisture to inactivate the primary inoculum of P. nicotianae in the top soil under field conditions; however, other factors may affect the effectiveness of solarization, reducing or enhancing its potential.     

烟草疫霉拮抗菌株P 72 10的鉴定及其拮抗代谢 产物 初步分析

 为探讨烟草根际生防细菌的生防机制,从重庆地区连作烟田健康烟株根际土壤中分离筛选到1株对烟草疫霉具有较强拮抗作用和对黑胫病具有良好防效的细菌菌株P-72-10。根据培养性状、形态特征、生理生化特性、基因组DNA的(G+C)mol%含量测定以及16S rDNA基因序列分析确定该菌株的分类地位。该菌株菌落乳白色,能产生水溶性荧光色素,革兰氏染色反应阴性,菌体杆状、大小(8.1~16.2)μm×(1.8~4.8)μm,单端生鞭毛,不形成芽孢。The BIOLOG GN2 结果显示该菌株属于假单胞菌属Pseudomonas。该菌株基因组DNA的(G+C)mol%含量为 60.72 mol%。16S rDNA基因序列分析显示该菌株与假单胞菌属荧光假单胞杆菌多个菌株的序列同源性达到99%,GenBank上的登录号为：HQ888871。结合其形态特征和生理生化特性,将菌株P-72-10鉴定为荧光假单胞杆菌P. fluorescens。平板检测拮抗代谢产物结果表明：该菌株具有分解纤维素、蛋白质和结合Fe ³⁺的能力,但不能分解几丁质。     

泸州烟草黑胫病病原生理小种组成及对甲霜灵和烯酰吗啉的敏感性

烟草黑胫病(Phytophthora nicotianae)是四川省泸州烟区最为严重的病害之一,为明确泸州烟草黑胫病生理小种组成及其对甲霜灵和烯酰吗啉的敏感性,从泸州主产烟区采集样品,分离得到24株烟草黑胫病菌株;通过鉴别寄主法结合TTZ生化反应,发现24株菌株中,0号生理小种15株,占62.50%,1号生理小种9株,占37.50%。对24株菌株进行甲霜灵和烯酰吗啉的药剂敏感性检测,发现甲霜灵对24株菌株的EC50范围在0.052~0.513μg/mL之间,敏感菌株和中抗菌株分别占41.67%和58.33%,未发现高抗菌株;烯酰吗啉对24株菌株的EC50范围在0.110~1.615μg/mL之间,敏感菌株和中抗菌株分别占37.50%和62.50%,未发现高抗菌株。上述结果表明,泸州烟区烟草黑胫病菌同时存在0号生理小种和1号小种,而且该烟区的黑胫病菌已对甲霜灵和烯酰吗啉产生不同程度的抗性。     

Rapid and Sensitive Detection of Phytophthora sojae in Soil and Infected Soybeans by Species-Specific Polymerase Chain Reaction Assays

ABSTRACT Root and stem rot caused by Phytophthora sojae is one of the most destructive diseases of soybean (Glycine max) worldwide. P. sojae can survive as oospores in soil for many years. In order to develop a rapid and accurate method for the specific detection of P. sojae in soil, the internal transcribed spacer (ITS) regions of eight P. sojae isolates were amplified using polymerase chain reaction (PCR) with the universal primers DC6 and ITS4. The sequences of PCR products were aligned with published sequences of 50 other Phytophthora species, and a region specific to P. sojae was used to design the specific PCR primers, PS1 and PS2. More than 245 isolates representing 25 species of Phytophthora and at least 35 other species of pathogens were used to test the specificity of the primers. PCR amplification with PS primers resulted in the amplification of a product of approximately 330 bp, exclusively from isolates of P. sojae. Tests with P. sojae genomic DNA determined that the sensitivity of the PS primer set is approximately 1 fg. This PCR assay, combined with a simple soil screening method developed in this work, allowed the detection of P. sojae from soil within 6 h, with a detection sensitivity of two oospores in 20 g of soil. PCR with the PS primers could also be used to detect P. sojae from diseased soybean tissue and residues. Real-time fluorescent quantitative PCR assays were also developed to detect the pathogen directly in soil samples. The PS primer-based PCR assay provides a rapid and sensitive tool for the detection of P. sojae in soil and infected soybean tissue.     

Gene and Genotypic Diversity of Phytophthora cinnamomi in South Africa and Australia Revealed by DNA Polymorphisms

Phytophthora cinnamomi isolates from South Africa and Australia were compared to assess genetic differentiation between the two populations. These two populations were analysed for levels of phenotypic diversity using random amplified polymorphic DNAs (RAPDs) and gene and genotypic diversity using restriction fragment length polymorphisms (RFLPs). Sixteen RAPD markers from four decanucleotide Operon primers and 34 RFLP alleles from 15 putative loci were used. A few isolates from Papua New Guinea known to posses alleles different from Australian isolates were also included for comparative purposes. South African and Australian P. cinnamomi populations were almost identical with an extremely low level of genetic distance between them (D_m=0.003). Common features for the two populations include shared alleles, low levels of phenotypic/genotypic diversity, high clonality, and low observed and expected levels of heterozygosity. Furthermore, relatively high levels of genetic differentiation between mating type populations (D_m South Africa=0.020 and D_m Australia=0.025 respectively), negative fixation indices, and significant deviations from Hardy–Weinberg equilibrium, all provided evidence for the lack of frequent sexual reproduction in both populations. The data strongly suggest that both the South African and Australian P. cinnamomi populations are introduced.     

Sensitivity of Phytophthora infestans to mandipropamid and the effect of enforced selection pressure in the field

Sensitivity to the new carboxylic acid amide (CAA) fungicide mandipropamid (MPD) in Phytophthora infestans was measured for isolates collected between 1989 and 2002 in Israel prior to the commercial use of MPD (baseline sensitivity, 44 isolates), and from MPD-treated (25 isolates) and untreated fields (215 isolates) in nine European countries and Israel between 2001 and 2005. All isolates were sensitive to MPD, with EC₅₀ values ranging between 0·02 and 2·98  µ g mL⁻¹. Plastic-tunnel (UK), shade-house (Israel) and field experiments (Israel) conducted during 2001–05 showed that enforced selection pressure, applied preventively or curatively, imposed by repeated sublethal (5  µ g mL⁻¹) or excessive (500–1000  µ g mL⁻¹) doses of MPD on mixed isolates of P. infestans produced no isolates resistant to the compound. The results of this study indicate that the probability of a buildup of resistant sub-populations of P. infestans to mandipropamid in the field is low.     

Effects of hydrostatic pressure,agitation and CO2 stress on Phytophthora nicotianae zoospore survival

BACKGROUND: Phytophthora nicotianae Breda de Haan is a common pathogen of ornamental plants in recycled irrigation systems. In a previous study, annual vinca (Catharanthus roseus Don) inoculated with zoospore suspensions using a CO₂‐pressurized sprayer had less foliage blight than plants inoculated using a hand sprayer. Here, the impact of hydrostatic pressure, agitation and aeration with CO₂ on the survival of P. nicotianae zoospores was examined. RESULTS: Exposure of zoospores to 840 kPa hydrostatic pressure for 8 min or agitation at a mixing intensity (G) of 6483 s^?1 for 4 min at 22–23 °C did not kill zoospores, but resulted in viable cysts. Motile and forcefully encysted zoospores of P. nicotianae were equally infectious on vinca or lupine (Lupinus polyphylus Lindl.). Bubbling CO₂ into zoospore‐infested water at 110.4 mL (0.2 g) min^?1 for 5 min caused 81% reduction in the number of germinated zoospores. Pressure at 630 kPa (16.3 g CO₂) or 70 kPa (3.85 g CO₂) facilitated CO₂ injection and shortened the zoospore inactivation time to 30 s. When air was bubbled through the suspension, germination was similar to the control. CONCLUSIONS: Exposure to CO₂ killed P. nicotianae zoospores in water. Neither pressure nor agitation had an effect on zoospore viability or infectivity. Based on results of this study, the authors designed a recycling CO₂ water treatment system that is currently under evaluation. Copyright © 2010 Society of Chemical Industry