Validation of a specific PCR screening test for Pantoea stewartii subsp. stewartii in maize (Zea mays) samples

Validation data is presented for a conventional PCR test that specifically detects the quarantine pathogen Pantoea stewartii subsp. stewartii in maize leaf and seed samples and does not cross‐react with the non‐pathogenic P. stewartii subsp. indologenes. The PCR tests currently recommended by the EPPO Diagnostic Protocol PM 7/60 (2) for initial screening bear the risk of false positives as they detect both subspecies of P. stewartii. The test presented here has high analytical sensitivity (10² cells mL^–1 in leaf extracts, at least 10³ cells mL^?1 in seed extracts), high repeatability and high reproducibility and performed well on the two matrices tested: maize seed and leaf extract. Its improved analytical specificity and analytical sensitivity compared to the currently recommended tests lead the authors to suggest that this test should be included as a first screening test in the diagnostic protocol for P. stewartii subsp. stewartii when it is next revised.     

A diagnostic tool for improved detection of Xanthomonas fragariae using a rapid and highly specific LAMP assay designed with comparative genomics

Molecular diagnostics of plant pathogens are crucial to prevent disease spread and to enhance food quality and security. A comparative genomics approach using genomes of different Xanthomonas species and pathovars was applied to identify highly specific targets in the genome of Xanthomonas fragariae, the causal agent of angular leaf spot of strawberry, listed under quarantine regulations in Europe. A reliable and sensitive loop‐mediated isothermal amplification (LAMP) assay was designed using a unique marker, providing a highly specific and rapid detection technique, convenient for on‐site detection. Specificity of the designed assay was tested on 37 strains from a culture collection of X. fragariae, 82 strains of other Xanthomonas species and pathovars and 11 strains of other bacterial genera isolated from strawberry leaves. A detection limit of 10² fg was achieved, approximating to 20 genome copies per reaction. When performing analyses with crude plant material, a consistent lower detection efficiency of 10² CFU mL^?1 was achieved. The LAMP assay designed in this study was adapted to work on crude plant material without any prior extensive extraction steps or incubation period; moreover, it does not require advanced analytical knowledge or a fully equipped laboratory. Results were produced within 7–20 min, depending on the pathogen concentration, thus providing a high‐throughput and user‐friendly method for detection and screening of plant material in support of quarantine regulations.     

Occurrence of azoxystrobin‐resistant isolates in Passalora fulva,the pathogen of tomato leaf mould disease

Since 2007, serious damage to tomato from leaf mould caused by Passalora fulva has frequently been observed in commercial greenhouses in Gifu Prefecture, Japan. One of the factors relating to this damage was suspected to be a decrease in azoxystrobin sensitivity of the pathogen. Biological and molecular studies were conducted to characterize fungicide resistance. In in vitro sensitivity tests using mycelial homogenate placed on fungicide‐amended medium, the minimum inhibitory concentrations (MIC) of azoxystrobin for mycelial growth of the isolates divided into two ranges, 0.031–0.5 mg L^?1 and 8–32 mg L^?1. Isolates with MICs within the two ranges were considered as sensitive and resistant, respectively, to azoxystrobin because, in in vivo tests, the percentage protection conferred by this fungicide (100 mg a.i. L^?1) against these isolates was 89.7–100% and 4.5–31.1%, respectively. Resistant isolates had a replacement of phenylalanine with leucine at codon 129 (F129L) in cytochrome b. Forty‐five percent of the 271 isolates collected from 63 tomato greenhouses from 2007 to 2008 were resistant to azoxystrobin. In many greenhouses where the isolation frequency of resistant isolates was 80% or more, azoxystrobin had been used twice per crop for approximately 6 years. In 2012, 27% of the 405 isolates collected were resistant to azoxystrobin, and there was a marked difference in the frequency of occurrence of resistant isolates in the field populations between the three locations sampled. The occurrence of azoxystrobin‐resistant P. fulva isolates (F129L mutants) inflicted considerable damage on greenhouse tomatoes.     

烟草环斑病毒和番茄环斑病毒的半巢式RT-PCR检测

烟草环斑病毒(Tobacco ringspot virus,TRSV)和番茄环斑病毒(Tomato ringspot virus,ToRSV)是我国禁止入境的检疫性有害生物。采用半巢式RT-PCR方法对这两种病毒进行了检测,用Trizol快速提取病毒总RNA,并根据TRSV和ToRSV的外壳蛋白基因设计特异性引物,经过第一轮RT- PCR和第二轮半巢式PCR扩增,TRSV样本分别得到359 bp和206 bp特异性片段,ToRSV样本分别得到340 bp和219 bp特异性片段。半巢式RT-PCR扩增产物的测序表明,TRSV产物序列与GenBank中登录的外壳蛋白基因存在88%～97%的同源性,ToRSV产物序列与GenBank中登录的外壳蛋白基因存在96%～100%的同源性。研究显示,DAS-ELISA与RT-PCR的检测灵敏度相近,而半巢式RT-PCR的检测灵敏度比这两种方法高出10~3倍以上。     

利用实时荧光RT-PCR方法检测番茄环斑病毒和烟草环斑病毒

根据番茄环斑病毒和烟草环斑病毒各分离物CP基因的保守序列分别设计并合成1对引物和1条TaqMan荧光探针,分别建立了ToRSV和TRSV的实时荧光RT-PCR检测方法。该方法具有更加灵敏、特异、快速和简便的特点,在口岸病害检疫中具有广泛的应用前景。     

Genomics‐informed design of loop‐mediated isothermal amplification for detection of phytopathogenic Xanthomonas arboricola pv. pruni at the intraspecific level

The objective of this study was to develop a rapid, sensitive detection assay for the quarantine pathogen Xanthomonas arboricola pv. pruni, causal agent of stone fruit bacterial spot, an economically important disease of Prunus spp. Unique targets were identified from X. arboricola pv. pruni genomes using a comparative genomics pipeline of other Xanthomonas species, subspecies and pathovars, and used to identify specific diagnostic markers. Loop‐mediated isothermal amplification (LAMP) was then applied to these markers to provide rapid, sensitive and specific detection. The method developed showed unrivalled specificity with the 79 tested strains and, in contrast to previously established techniques, distinguished between phylogenetically close subspecies such as X. arboricola pv. corylina. The sensitivity of this test is comparable to that of a previously reported TaqMan^? assay at 10³ CFU mL^?1, while the unrivalled speed of LAMP technology enables a positive result to be obtained in <15 min. The developed assay can be used with real‐time fluorescent detectors for quantitative results as well as with DNA‐staining dyes to function as a simplified strategy for on‐site pathogen detection.     

Evaluation of the biocontrol potential of various Metarhizium isolates against green peach aphid Myzus persicae (Homoptera: Aphididae)

BACKGROUND: Twenty‐three isolates of Metarhizium anisopliae (Metschnikof) Sorokin and M. acridum (Driver & Milner) JF Bischoff, Rehner & Humber from non‐aphid host insects around the globe were evaluated for their aphid biocontrol potential, which is not well known. RESULTS: The apterous adults of green peach aphid Myzus persicae (Sulzer) were exposed to the fungal sprays of 11.5, 99 and 1179 conidia mm^?2 and blank control in three leaf‐dish bioassays. All the tested isolates except one were proven to be infective to the aphid species at 21 ± 1 °C and 14:10 h light:dark photoperiod, causing corrected mortalities of 10.1–95.3% at the high spore concentration. The data from ten isolates causing > 50% mortality at the high concentration were found to fit a time–concentration–mortality model well, yielding parameters for the estimates of their LC₅₀ and LT₅₀ that vary with post‐spray time and spore concentration respectively. Four isolates of M. anisopliae (ARSEF 759, 4132, 2080 and 576) had LC₅₀ values of 44–80 conidia mm^?2 on day 8 and LT₅₀ values of 4.9–6.8 days at 100 conidia mm^?2, with 91–98% of the killed aphids being well mycotised after death. CONCLUSION: The Metarhizium infectivity to M. persicae differs greatly among the tested isolates. The four mentioned isolates with desired virulence and sporulation potential are excellent candidates for microbial control of aphids. Copyright © 2010 Society of Chemical Industry     

Selection of global Metarhizium isolates for the control of the rice pest Nilaparvata lugens (Homoptera: Delphacidae)

BACKGROUND: This study was initiated to search for fungal candidates for microbial control of brown planthopper (BPH) Nilaparvata lugens Stål, to which little attention has been paid in the past two decades. RESULTS: Thirty‐five isolates of Metarhizium anisopliae (Metschnikoff) Sorokin and M. flavoviride Gams & Rozsypal from different host insects worldwide were bioassayed for their lethal effects against third‐instar BPH nymphs at 25 °C and a 14:10 h light:dark photoperiod at ca 1000 conidia mm^?2. On day 9 post‐treatment, mortality attributable to mycosis ranged from 6.5 to 64.2% and differed significantly among the tested isolates with no apparent relationship to their host origin. Only two BPH‐derived M. anisopliae isolates from the Philippines (ARSEF456) and Indonesia (ARSEF576) killed > 50% of the nymphs. Both isolates were further bioassayed for time–concentration–mortality responses of the nymphs to the sprays of 19–29, 118–164 and 978–1088 conidia mm^?2 in repeated bioassays. The resultant data fitted a time–concentration–mortality model very well. Their LC₅₀ values were estimated as 731 and 1124 conidia mm^?2 on day 7 and fell to 284 and 306 conidia mm^?2, respectively, on day 10. CONCLUSION: The two M. anisopliae isolates are potential biocontrol agents of BPH for further research. This is the first report of the lethal effects of global Metarhizium isolates on the rice pest. Copyright © 2008 Society of Chemical Industry     

Distribution and molecular characterization of Corynespora cassiicola isolates resistant to boscalid

A total of 618 isolates of corynespora leaf spot fungus (Corynespora cassiicola) collected from 24 commercial cucumber greenhouses in 12 cities in Ibaraki Prefecture, Japan, were tested for their sensitivity to boscalid. Boscalid‐resistant isolates were detected in 17 out of 19 greenhouses with a history of use of this fungicide and detection frequencies of the resistant isolates exceeded 47% in nine greenhouses. Frequencies of very highly resistant (VHR) isolates with 50% effective concentration (EC₅₀) values of boscalid exceeding 30 μg mL^?1 were higher than those of moderately resistant (MR) isolates with EC₅₀ ranging from 2·0 to 5·9 μg mL^?1 in 11 greenhouses. Additionally, highly resistant (HR) isolates with EC₅₀ from 8·9 to 10·7 μg mL^?1 were first detected. Furthermore, molecular characterization of genes encoding succinate dehydrogenase (SDH) subunits (SdhA, SdhB, SdhC and SdhD) was carried out to elucidate the amino acid substitution responsible for the resistance to boscalid. All 23 VHR isolates had the same mutation from CAC to TAC in the SdhB gene leading to the substitution of histidine with tyrosine at amino acid position 278 (B‐H278Y). At the same position, the substitution to arginine conferred by a mutation to CGC (B‐H278R) was detected in all four HR isolates. Some MR isolates showed a substitution from serine to proline at position 73 in SdhC (C‐S73P), from serine to proline or from glycine to valine at position 89 (D‐S89P) and 109 (D‐G109V), respectively, in SdhD. There was no common mutation in SDH genes of all MR isolates.     

Resistance of Phytophthora capsici to metalaxyl in plastic‐house capsicum crops in southern Italy*

In Calabria (southern Italy), control of crown and root rot of capsicum caused by Phytophthora capsici has relied primarily on soil drenches of metalaxyl. However, severe outbreaks occur every year in glasshouse crops, in which the practice of using plastic mulch and furrow irrigation favours the disease. Single‐hypha isolates of P. capsici collected in Calabria in 1992/1998 were tested in vitro for their level of sensitivity to metalaxyl. Isolates of other species of Phytophthora were used as reference. Fungicide sensitivity was determined by plating mycelial plugs onto potato dextrose agar amended with metalaxyl, at final concentrations ranging from 0.1 to 1000μg mL^?1 a.s. Inhibition of radial growth (%) was determined when colonies on unamended medium had covered approximately two‐thirds of the plate. The ED₅₀ values for inhibition of mycelial growth of P. capsici isolates ranged from 1.41 to44.6μg mL^?1 a.s. More than 80% of the P. capsici isolates from commercial plastic‐house crops in Calabria showed a moderate level of resistance as they were inhibited less than 60% at 5 μg mL^?1 but more than 60% at 100μg mL^?1     

Test validation for the detection of Tilletia indica Mitra by multiplex real‐time PCR

Tilletia indica Mitra is a fungal pathogen causing Karnal bunt of wheat. Tilletia indica is a quarantine pest in many countries worldwide. In the European Union, imported wheat grain from countries where the fungus is present must be checked for the presence of T. indica teliospores. The inspection services at the borders need rapid, sensitive and reliable detection tests to identify T. indica spores on wheat grain. In this work, validation was carried out according to EPPO Standard PM 7/98 to evaluate the multiplex real‐time PCR test described in ISPM 27 Diagnostic Protocol for regulated pests (Annex 4 Tilletia indica Mitra) by means of a test performance study with nine participating laboratories, and the performance characteristics of the test were established. The original protocol was modified with regard to the extraction of DNA from the pellet obtained from the ‘washing test’ and the enrichment PCR step in order to increase the amount of template DNA for the real‐time PCR. The optimized test still has five teliospores as the limit of detection for the contaminated pellet but has an increased analytical sensitivity and had positive results with three teliospores in 93% of cases instead of 43% for the original test. The two closest Tilletia species, Tilletia horrida and Tilletia walkeri, were used to evaluate analytical specificity (exclusivity) and no cross‐reactions were obtained. Diagnostic sensitivity, diagnostic specificity, accordance and concordance were also evaluated.     

Development of a real‐time PCR assay for Pseudomonas cichorii,the causal agent of midrib rot in greenhouse‐grown lettuce,and its detection in irrigating water

Midrib rot is an emerging disease in greenhouse production of lettuce caused by Pseudomonas cichorii, and probably introduced through contaminated irrigation water. Concentrations of 100 CFU mL^?1 are enough to induce the typical midrib rot symptoms. A sensitive real‐time PCR assay was developed, based on a 90‐bp amplicon from the pathogenicity gene cluster hrcRST and a Taqman Minor Groove Binding probe. Specificity of the assay was tested with 39 P. cichorii strains, including the type strain, and 89 strains from 83 other Pseudomonas species. The relationship between detection signals and P. cichorii DNA concentrations was linear over 6‐logs. Detection threshold with excellent reproducibility was 500 fg of DNA or about 70 genome copies. Sample preparation and DNA isolation were optimized to allow detection in 1 L water samples. The assay was first evaluated with greenhouse irrigation water spiked with serial dilutions of P. cichorii. The calculated cell numbers obtained with real‐time PCR were 10‐fold lower than plate counts of actual spiked cells. However, the assay consistently detected 100 CFU per reaction, corresponding to the detection of 1 CFU mL^?1 of irrigation water, which is well below the concentration needed for midrib rot infection. Finally, the assay proved to be valuable for detecting infective P. cichorii concentrations in the irrigation water of a commercial lettuce production greenhouse.     

Monilinia species identified on peach and nectarine in Croatia,with the first record of Monilinia fructicola

During 2012, an official survey was conducted for Monilinia species present on peach and nectarine in Croatia. In total, 169 Monilinia spp. isolates were collected from 24 commercial orchards and identified according to morphology in culture and PCR. Eighty of the isolates were identified as Monilinia laxa, 70 as M. fructigena and 19 as M. fructicola. M. fructicola was found only at one location in the Mediterranean part of the country, and this is the first record of this quarantine fungus in Croatia. PCR diagnostic tests using M. fructicola‐specific primer pair MO368‐5/MO368‐10R repeatedly gave false negatives for some isolates. PCR tests using primer pair ITS1‐Mfc1/ITS4‐Mfc1 amplified M. fructicola‐specific product in all isolates and was therefore shown to be more suitable for diagnostic purposes.     

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.     

Failure to detect highly resistant strains in dicarboximide resistant field populations of Botrytis cinerea1

Field isolates of Botrytis cinerea with moderate levels of resistance to dicarboximide fungicides (ED50 1.0–4.9 μg ml^?1) and to dicloran were obtained from glasshouses where vinclozolin and iprodione failed to control grey mould. From sensitive and moderatcly-resistant cultures, laboratory isolates were selected on dicarboximide-amended medium, which were highly resistant to these fungicides (ED50 125->3000 μg ml^?1). Conidia of all the resistant isolates germinated well on media amended with 100 μg ml^?1 of the dicarboximides vinclozolin, iprodione, procymidone and myclozolin and with 5 μg ml^?1 of metomeclan. However, the spores of the moderately resistant isolates did not germinate on 100 μg ml^?1 metomeclan while the spores of the highly resistant isolates germinated well. Using media with 100 μg ml^?1 of metomeclan to distinguish between the two phenotypes, no highly resistant strain was detected among 312 resistant samples from five cucumber glasshouses with a high frequency of moderately resistant strains. From air-borne inoculum of five glasshouses with 100% resistant populations, 1604 colonies were recovered on vinclozolin-amended (100 μg ml^?1) medium and none on metomeclan-amended (100 μg ml^?1) medium. It is concluded that strains of B. cinerea highly resistant to dicarboximides are absent from field populations.     

A monoclonal antibody‐based ELISA for the analysis of the insecticide flucythrinate in environmental and crop samples

A competitive enzyme‐linked immunosorbent assay (ELISA) has been developed for the detection of the insecticide flucythrinate in environmental and food samples. Two types of haptens, the acid moiety that is the hydrolyzed product of flucythrinate, and the carboxylated propyl derivative of the alcohol moiety, were used to prepare monoclonal antibodies (MAbs). Five MAbs, which raised against the former hapten, were reactive with flucythrinate. Among them, MAb F1A27‐4 showed the highest activity toward flucythrinate, and did not cross‐react with other pyrethroids such as cycloprothrin, fenvalerate, fluvalinate, etofenprox and silafluofen. The assay conditions of indirect competitive ELISA with MAb F1A27‐4 were studied to optimize the detection of flucythrinate in environmental and food samples. Incubation at 4 °C in the assay buffer, pH 8, with 300 mM sodium chloride improved the sensitivity. The addition of rabbit serum albumin or rabbit antiserum and the presence of 50 ml litre^?1 of methanol reduced matrix effects of the samples. Under optimized conditions, the ELISA detected flucythrinate spiked in water, soil, and extracts of apple and tea samples down to 10 mg litre^?1, 0.2 mg litre^?1, 0.3 mg litre^?1 and 0.3 mg litre^?1, respectively. The mean recovery and CV ranged from 91% to 120% and from 5% to 12%, respectively. The ELISA results in apple samples correlated well with those from LC–MS analysis (r² = 0.99, n = 12). © 2001 Society of Chemical Industry     

Multiple resistance of Botrytis cinerea from kiwifruit to SDHIs,QoIs and fungicides of other chemical groups

BACKGROUND: Botrytis cinerea Pers.: Fr. is a high‐risk pathogen for fungicide resistance development that has caused resistance problems on many crops throughout the world. This study investigated the fungicide sensitivity profile of isolates from kiwifruits originating from three Greek locations with different fungicide use histories. Sensitivity was measured by in vitro fungitoxicity tests on artificial nutrient media. RESULTS: Seventy‐six single‐spore isolates were tested for sensitivity to the SDHI fungicide boscalid, the QoI pyraclostrobin, the anilinopyrimidine cyprodinil, the hydroxyanilide fenhexamid, the phenylpyrrole fludioxonil, the dicarboxamide iprodione and the benzimidazole carbendazim. All isolates from Thessaloniki showed resistance to both boscalid and pyraclostrobin, while in the other two locations the fungal population was sensitive to these two fungicides. Sensitive isolates showed EC₅₀ values to boscalid and pyraclostrobin ranging from 0.9 to 5.2 and from 0.04 to 0.14 mg L^?1 respectively, while the resistant isolates showed EC₅₀ values higher than 50 mg L^?1 for boscalid and from 16 to > 50 mg L^?1 for pyraclostrobin. All QoI‐resistant isolates carried the G143A mutation in cytb. Sensitivity determinations to the remaining fungicides revealed in total eight resistance phenotypes. No isolates were resistant to the fungicides fenhexamid and fludioxonil. CONCLUSION: This is the first report of B. cinerea field isolates with resistance to both boscalid and pyraclostrobin, and it strongly suggests that there may be a major problem in controlling this important pathogen on kiwifruit. Copyright © 2010 Society of Chemical Industry     

烟草环斑病毒RT-Realtime PCR检测方法

烟草环斑病毒(Tobacco ringspotvirus,TRSV)是我国公布的二类检疫危险性有害生物,对农业生产危害较大。受该病毒侵染的一些寄主植物出现隐症,并伴随病毒浓度降低,给检测工作造成困难。根据TRSV外壳蛋白基因序列设计合成了一对引物及一条MGB探针,优化了反应条件,建立了TRSV实时荧光RT-PCR检测方法。该方法与常规的DAS-ELISA方法和RT-PCR方法相比,灵敏度分别提高了200倍和4倍,并且对不同寄主上的TRSV均有较好的检测效果。     

A real‐time (TaqMan) PCR assay to differentiate Monilinia fructicola from other brown rot fungi of fruit crops

To prevent the entry and spread of the brown rot fungus Monilinia fructicola in Europe, a fast and reliable method for detection of this organism is essential. In this study, an automated DNA extraction method combined with a multiplex real‐time PCR based on TaqMan chemistry was developed for fast, convenient and reliable detection of both the EU quarantine organism Monilinia fructicola and the three other brown rot fungi M. fructigena, M. laxa and Monilia polystroma. Using the internal transcribed spacer (ITS) region of the nuclear ribosomal RNA gene repeat, a Monilinia genus‐specific primer pair and two differently labelled fluorogenic probes specific for M. fructicola and the group M. fructigena/M. laxa/Monilia polystroma were developed. The analytical specificity of the assay was assessed by testing 33 isolates of the four brown rot fungi and 13 isolates of related fungal species or other fungal species that can be present on stone and pome fruit. No cross‐reactions were observed. The assay was found to have a detection limit of 0·6 pg of DNA, corresponding to 27 haploid genomes or four conidia. Comparison of a manual DNA isolation followed by a conventional PCR with an automated DNA isolation combined with the presently developed real‐time PCR showed that the latter method gave improved results when tested with 72 naturally infected stone fruit samples. The detection rate increased from 65 to 97%.