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.     

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.     

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.     

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.     

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.     

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     

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.     

Mefenoxam sensitivity and fitness analysis of Phytophthora nicotianae isolates from nurseries in Virginia, USA

Mefenoxam is one of the most commonly used fungicides for managing diseases caused by Phytophthora spp. on ornamentals. The objectives of this study were to determine whether Phytophthora nicotianae, a destructive pathogen of numerous herbaceous annual and perennial plant species in nurseries, has developed resistance to mefenoxam, and to evaluate the fitness of mefenoxam‐resistant isolates. Ninety‐five isolates of P. nicotianae were screened for sensitivity to mefenoxam on 20% clarified V8 agar at 100 a.i. µg mL^?1. Twenty‐five isolates were highly resistant to this compound with EC₅₀ values ranging from 235·2 to 466·3 µg mL^?1 and four were intermediately resistant with EC₅₀ values ranging from 1·6 to 2·9 µg mL^?1. Sixty‐six isolates were sensitive with EC₅₀ values less than 0·04 µg mL^?1. Nine resistant and seven sensitive isolates were tested for mefenoxam sensitivity on Pelargonium × hortorum cv. White Orbit. Mefenoxam provided good protection of pelargonium seedlings from colonization by sensitive isolates, but not by any resistant isolates. Four resistant and four sensitive isolates were compared for fitness components and their relative competitive ability on Lupinus Russell Hybrids in the absence of mefenoxam. Resistant isolates outcompeted sensitive ones within 3 to 6 sporulation cycles on lupin seedlings, regardless of their initial proportions in mixed zoospore inoculum. Resistant isolates exhibited greater infection rate and higher sporulation ability than sensitive ones when they were applied separately onto lupins. These results suggest that fungicide resistance may pose a serious challenge to the continued effectiveness of mefenoxam as a control option for nursery growers.     

Development of Specific PCR Primers for Identification and Detection of Rhizopycnis vagum

Rhizopycnis vagum is a recently described coelomycete known to belong to the complex of root rot pathogens contributing to vine decline of cucurbits in several parts of the world. However, the fungus has also been reported to infect tomato, and as an endophytic associate of mycorrhizal roots of wild, asymptomatic Pinus halepensis and Rosmarinus officinalis plants in Italy. To accelerate epidemiological and ecological investigations on this fungus, a PCR primer pair was developed. Primers Rv1-F and Rv1-R were designed, based on alignment of internal transcribed spacer (ITS) sequences (ITS1-5.8S-ITS2), which amplified a 396-bp fragment from all R. vagum isolates tested, including isolates pathogenic to melons and endophytic isolates from mycorrhizae. Specificity of the primer pair was verified both in silico (BLAST searches using each primer string as a query) and in PCR assays, where the primers failed to amplify DNA from any isolate of fungi taxonomically related to R. vagum (e.g. Massarina walkeri and Stagonospora spp.) and other vine decline and common soilborne pathogens (e.g. Monasporascus cannonballus, Acremonium cucurbitacearum, Fusarium spp. and Rhizoctonia solani). Under optimum conditions, detectable amplification of the specific sequence required 0.05 pg of target DNA. Amplification of the expected 369-bp fragment was also obtained from DNA root extracts of nearly asymptomatic Cucumis melo plants inoculated with R. vagum under greenhouse conditions.     

The Use of Molecular Beacons Combined with NASBA for the Sensitive Detection of Sugarcane Yellow Leaf Virus

Sugarcane yellow leaf virus (ScYLV) is widely distributed in Brazil and other sugarcane producing countries causing significant yield losses. Due to the high incidence of the aphid vector, the virus is widespread in the field and in parental clones used in sugarcane breeding programmes. Aiming to present a sensitive and reliable detection of ScYLV, we have adapted an AmpliDet RNA system, compared it with the currently available detection methods and discussed its applicability for routine diagnosis. AmpliDet RNA consists of nucleic acid sequence-based amplification (NASBA) of the target RNA with specific primers and simultaneous real-time detection of the amplification products with molecular beacons. The results showed that the system produced a detection level of at least 100fg of purified virus. Virus was readily detected in plant tissues with low levels of infection (without the need of previous RNA extraction) and in the hemolymph of aphids. The method showed to be virus-specific, testing negative for other species of the Luteoviridae. In conclusion, the system has potential to become a diagnostic method for the detection of sugarcane viruses.     

泰国榴莲上棕榈疫霉的分离和鉴定

在对来自泰国的榴莲检验中分离到1株引起榴莲果皮和果肉变色、软腐的病原真菌。通过形态鉴定和核糖体ITS区DNA序列测定以及系统发育分析,最终将该病菌鉴定为棕榈疫霉(Phytophthora palmivora)。     

Molecular and Pathogenicity Characteristics of Phytophthora nicotianae Responsible for Root Necrosis and Wilting of Pepper (Capsicum annuum L.) in Tunisia

Isolates of Phytophthora from pepper, produced in Tunisia, were characterised according to molecular and pathogenicity criteria. Polymerase chain reaction amplification of the ITS1 region in the ribosomal DNA resulted in different sized fragments. The pepper isolates and P. nicotianae yielded a fragment of 310bp that distinguished it from P. capsici with a fragment of 270bp. The ribosomal RNA gene amplicons of both internal transcribed spacers and the 5.8 S of the pepper Phytophthora and P. nicotianae were digested with 8 endonucleases. The patterns generated, with the 2 enzymes that cut, were identical for both taxa. This molecular analysis corroborated the morphological and biological characteristics and suggests strongly that the isolates of Phytophthora from pepper belong to the species P. nicotianae. Inoculation of pepper, tomato, eggplant and tobacco plants with the isolates of P. nicotianae from pepper showed they were highly pathogenic on pepper but not on tobacco, while their pathogenicity was weak on tomato and eggplant and was associated with atypical symptoms not observed in the field. These pathogenicity tests suggest that pepper isolates of P. nicotianae are particularly adapted to their host and may thus constitute a forma specialis of P. nicotianae.     

马铃薯晚疫病菌拮抗粘细菌YR–35的分离鉴定及其代谢产物稳定性

从乌拉山镇的农田土壤中分离获得致病疫霉的高效拮抗菌株YR-35,通过形态特征、生理生化特征以及16S rDNA序列分析将其鉴定为变绿色粘球菌Myxococcus virescens。菌株YR-35对马铃薯晚疫病致病菌菌丝生长抑制率高达96.67%。抗菌活性物质在30~80℃处理1 h后菌丝生长抑制率可达21.70%,高于80℃时活性逐渐下降,90℃处理后菌丝生长抑制率仍然可达15.38%。活性物质在pH 5.0~9.0条件下菌丝生长抑制率保持在25.27%以上,当pH5.0或pH9.0时,抗菌活性显著降低。活性物质不能被蛋白酶降解,不受紫外线、自然光照射的影响。对马铃薯离体叶片的生防效果检测表明,菌株YR-35的发酵无菌液处理组叶片相对病斑面积仅为0.57%,对照组的相对病斑面积高达87.72%。菌株YR-35的发酵无菌液可以有效抑制致病疫霉侵染马铃薯叶片。本研究首次发现变绿色粘球菌对致病疫霉有显著拮抗活性,为研发有效防治马铃薯晚疫病的生物农药奠定了基础。     

French isolates of Phytophthora infestans from potato and tomato differ in phenotype and genotype

Prior to 1996, the A2 mating type of Phytophthora infestans was not detected on potato in France, but was found at one site on tomato in 1995. This finding lead to the question of the extent of differences and relationships existing between the populations of P. infestans present on each host. A collection of 76 isolates collected in France, mainly in 1996, from potato and tomato was characterised for mating type, allozyme genotype at the Gpi and Pep loci, and mitochondrial DNA haplotype; 74 of these isolates were also characterised for multilocus RFLP fingerprint, and 62 for virulence. All isolates except four showed allozyme genotypes (Gpi 90/100 or 100/100, Pep 83/100 or 100/100) and mtDNA haplotypes (Ia or IIa) characteristic of the populations introduced into Europe in the late 1970s. The four exceptions were isolates collected from tomato in Southern France in 1988-1991, which showed some characteristics of the former European populations (Gpi 86/100, Pep 92/100, mtDNA Ib). Both mating types were present among the collections from both hosts, but isolates with the A2 mating type were found on potato only in one garden crop, adjacent to tomato. Nine different RG57 fingerprints were observed, with a greater diversity among tomato isolates. Furthermore, tomato and potato collections differed markedly in the frequencies of genotypes present. Finally, tomato isolates generally had a lower virulence complexity than potato isolates. These data suggest that P. infestans populations on tomato and potato are largely separated, despite the occurrence of limited gene flow.     

Comparison of Chinese and Japanese A1 isolates of <Emphasis Type="Italic">Phytophthora infestans</Emphasis>

The mating type, glucose-6-phosphate isomerase (Gpi) and peptidase (Pep) genotypes, RG57 fingerprint, and mitochondrial DNA (mtDNA) haplotype of Chinese isolates of Phytophthora infestans collected in Hebei and Gansu in 1996 were compared with those of Japanese isolates collected during 1997–2000. The Chinese isolates were divided into four genotypes, one of which was identical to the dominant Japanese genotype, A1-A (mating type A1; Gpi 100/100; Pep 100/100; RG57 100010001100110100011001110: 1–25, 14a, and 24a; and mtDNA haplotype IIa). Comparison of the genotypes with reported data revealed that some completely and partially identical genotypes occur in Russia and parts of Europe. The other two A1 genotypes and one A2 genotype were also detected in Gansu (Gpi 100/100, Pep 100/100, and mtDNA haplotype Ia), which were regarded as unique to this region.