Detection of Phytophthora nicotianae in Soil with Real-time Quantitative PCR

Phytophthora nicotianae is one of the most important soil-borne plant pathogens. A rapid, specific and sensitive real-time polymerase chain reaction (PCR) detection method for P. nicotianae was established, which used primers targeting the internal transcribed spacer (ITS) regions of rDNA genes of Phytophthora spp. Based on the nucleotide sequences of ITS2 of 15 different species of Phytophthora , the primers and probe were designed specifically to amplify DNA from P. nicotianae. With a series of 10-fold DNA dilutions extracted from P. nicotianae pure cultures, the detection limit was 10 pg/μl in conventional PCR, whereas in SYBR Green I PCR the detection limit was 0.12 fg/μl and in TaqMan PCR 1.2 fg/μl, and real-time PCR was 10⁴–10⁵ times more sensitive than conventional PCR. The simple and rapid procedures maximized the yield and quality of recovered DNA from soil and allowed the processing of many samples in a short time. The direct DNA extractions from soil were utilized to yield DNA suitable for PCR. By combining this protocol with the real-time PCR procedure it has been possible to specifically detect P. nicotianae in soil, and the degree of sensitivity was 1.0 pg/μl. The system was applied to survey soil samples from tobacco field sites in China for the presence of P. nicotianae and the analyses of naturally infested soil showed the reliability of the real-time PCR method.     

Specific and Sensitive Detection of Phytophthora nicotianae by Nested PCR and Loop‐mediated Isothermal Amplification Assays

Phytophthora nicotianae is an important soilborne plant pathogen. It causes black shank in tobacco and other commercially important crop diseases. Early and accurate detection of P. nicotianae is essential for controlling these diseases. In this study, primers based on the Ras‐related protein gene (Ypt1) of P. nicotianae were tested for their specific detection of the pathogen using nested PCR and LAMP assays. For specificity testing, DNA extracts from 47 P. nicotianae isolates, 45 isolates of 16 different oomycetes and 25 isolates of other fungal species were used; no cross‐reaction with other pathogens was observed. The sensitivity assay showed that the nested PCR and LAMP assays had detection limits of 100 fg and 10 fg genomic DNA per 25‐μl reaction, respectively. Furthermore, the nested PCR and LAMP assays were used for the detection of DNA from naturally P. nicotianae‐infected tobacco tissues and soil. Our results suggest that the LAMP assay has the greatest potential for the specific detection of P. nicotianae in regions that are at risk of contracting tobacco black shank disease and that the Ypt1 gene is a novel and effective target of P. nicotianae LAMP visual detection.     

RAPD PCR for Diagnosis of Phytophthora parasitica var. nicotianae Isolates which Cause Black Shank on Tobacco

Phytophthora parasitica var . nicotianae is the fungal pathotype of tobacco black shank (TBS, Disease severity ≥ 2.0). Random amplified polymorphic DNA (RAPD) analysis was used to differentiate isolates which cause TBS from those which do not. Greenhouse assays combined with zoospore inoculation were performed to assess the virulence of the fungal isolates, and the results were compared with the RAPD pattern analysis. The RAPD results exhibited total correlation with the virulence assay results. Amplification patterns generated by RAPD reactions were used to generate a phenogram depicting the genetically distinct nature of the cluster defined by the TBS isolates. This cluster was exclusive and distinct from P. parasitica var . nicotianae isolates which do not cause TBS. Thus, RAPD proved to be a sensitive and highly reliable method for quickly identifying fungal pathotypes which cause TBS.     

Biological Control of Oomycete Soilborne Diseases Caused by Phytophthora capsici,Phytophthora infestans,and Phytophthora nicotianae in Solanaceous Crops

Oomycete pathogens that belong to the genus Phytophthora cause devastating diseases in solanaceous crops such as pepper, potato, and tobacco, resulting in crop production losses worldwide. Although the application of fungicides efficiently controls these diseases, it has been shown to trigger negative side effects such as environmental pollution, phytotoxicity, and fungicide resistance in plant pathogens. Therefore, biological control of Phytophthora-induced diseases was proposed as an environmentally sound alternative to conventional chemical control. In this review, progress on biological control of the soilborne oomycete plant pathogens, Phytophthora capsici, Phytophthora infestans, and Phytophthora nicotianae, infecting pepper, potato, and tobacco is described. Bacterial (e.g., Acinetobacter, Bacillus, Chryseobacterium, Paenibacillus, Pseudomonas, and Streptomyces) and fungal (e.g., Trichoderma and arbuscular mycorrhizal fungi) agents, and yeasts (e.g., Aureobasidium, Curvibasidium, and Metschnikowia) have been reported as successful biocontrol agents of Phytophthora pathogens. These microorganisms antagonize Phytophthora spp. via antimicrobial compounds with inhibitory activities against mycelial growth, sporulation, and zoospore germination. They also trigger plant immunity-inducing systemic resistance via several pathways, resulting in enhanced defense responses in their hosts. Along with plant protection, some of the microorganisms promote plant growth, thereby enhancing their beneficial relations with host plants. Although the beneficial effects of the biocontrol microorganisms are acceptable, single applications of antagonistic microorganisms tend to lack consistent efficacy compared with chemical analogues. Therefore, strategies to improve the biocontrol performance of these prominent antagonists are also discussed in this review.     

龙舌兰麻种质资源抗斑马纹病鉴定研究

通过分离培养斑马纹病病原菌,人工接种鉴定不同龙舌兰麻种质的抗斑马纹病的特性.结果表明,番麻、东368、墨引6、墨引12、墨引7、墨引5、假7、马盖麻、东109、金边孤叶龙舌和兰墨引4号11份种质为高抗种质,病斑扩展速度和病情严重度可作为龙舌兰麻抗病性快速鉴定技术手段.     

Development of a PCR Assay for the Molecular Detection of Phytophthora boehmeriae in Infected Cotton

Cotton blight, caused by the oomycete Phytophthora boehmeriae, is a serious disease of cotton in China. In wet weather conditions, P. boehmeriae is usually the primary pathogen, followed by many saprophytic fungi and pathogens such as Pythium spp., Fusarium spp., Rhizoctonia and others. As P. boehmeriae grows much slower than other pathogens, it is difficult to isolate and identify. A rapid and accurate method for its specific identification is necessary for the detection of blight in infected cotton tissue. The internal transcribed spacer (ITS) regions of ribosomal DNA (rDNA) from three isolates of P. boehmeriae were amplified using the polymerase chain reaction (PCR) with the universal primers DC6 and ITS4. PCR products were cloned and sequenced. The sequences were aligned with those published of 50 other Phytophthora species, and a region specific to P. boehmeriae was used to construct the specific PCR primers PB1 and PB2. Over 106 isolates of 14 Phytophthora species and at least 20 other fungal species were used to check the specificity of the primers. PCR amplification with primers PB1 and PB2 resulted in the amplification of a product of approximately 750 bp only from isolates of P. boehmeriae. Using primers PB1 and PB2, detection sensitivity was approximately 10 fg DNA/μl. In inoculated plant material, P. boehmeriae could be detected in tissue 1 day after inoculation, prior to the appearance of symptoms. The PB primer‐based PCR assay provides an accurate and sensitive method for detecting P. boehmeriae in cotton tissue.     

马铃薯POTHR-1 cDNA的克隆及晚疫病菌和其他非生物因子诱导表达分析

利RACE和重叠延伸相结合的方法,从经晚疫病菌接种诱导的马铃薯水平抗性材料叶片中克隆了一个POTHE 1基因(potato Phytophthora infestans induced hypersensitive response related protein gene)的全长cDNA.序列分析表明,该基因编码225个氨基酸,与烟草harpin诱导蛋白基因hinl有很高的同源性(编码区核苷酸和氨基酸序列分别为83%和81%).Southern杂交结果显示在马铃薯基因组中有2～3个拷贝.对其诱导表达模式研究表明:晚疫病病原菌接种36 h后,该基因表达迅速增加;机械伤害及茉莉酸(JA)处理能够诱导表达;渗透胁迫(NaCl浸泡)能够诱导其微弱表达;但水杨酸(SA)不能诱导表达.该基因可能和病原与寄主互作时寄主产生过敏反应及细胞生理性死亡有关.     

马铃薯POTHR-1 cDNA的克隆及晚疫病菌和其他非生物因子诱导表达分析

利用RACE和重叠延伸相结合的方法,从经晚疫病菌接种诱导的马铃薯水平抗性材料叶片中克隆了一个POTHR-I基因(potato Phytophthora infestans-induced hypersensitive response related protein gene)的全长cDNA。序列分析表明,该基因编码225个氨基酸,与烟草harpin诱导蛋白基因hinI有很高的同源性(编码区核苷酸和氨基酸序列分别为83％和81％)。Southern杂交结果显示在马铃薯基因组中有2、3个拷贝。对其诱导表达模式研究表明：晚疫病病原菌接种36h后,该基因表达迅速增加;机械伤害及茉莉酸(JA)处理能够诱导表达;渗透胁迫(NaCI浸泡)能够诱导其微弱表达;但水杨酸(SA)不能诱导表达。该基因可能和病原与寄主互作时寄主产生过敏反应及细胞生理性死亡有关。     

寄生疫霉parA1基因的克隆及在大肠杆菌中的表达

根据已报道的寄生疫霉(Phytophthora parasitica)parA1基因的序列设计引物,从4株寄生疫霉中国菌株(3株来自烟草,1株来自刺槐)中克隆到此基因并进行了重组表达。序列分析表明4株寄生疫霉parA1基因序列高度保守。对表达载体pET30a(+)双酶切,构建表达Parasiticein蛋白的表达载体pETeli,用CaCl\-2法转化大肠杆菌(Escherichia coli)BL21,通过诱导在大肠杆菌中进行非融合表达,表达产物在烟草上引起过敏性反应。性质测定表明,表达产物有一定的耐热性,并对蛋白酶K敏感。     

三种猕猴桃根腐病致病菌多重实时定量PCR检测技术的建立及应用

[背景]近年来,随着猕猴桃种植面积的不断扩大,病害的频繁发生已逐渐影响猕猴桃的产量和品质。恶疫霉(Phytophthora cactorum)、樟疫霉(P.cinnamomi)和雪松疫霉(P.lateralis)是一类可以引起猕猴桃根腐病的致病疫霉菌。[目的]建立并优化可以同时检测3种致病疫霉的多重实时定量检测技术,并调查猕猴桃主要产区的致病菌分布情况。[方法]基于Ypt1 (ras-related protein gene)基因设计恶疫霉、樟疫霉和雪松疫霉的特异性TaqMan探针和引物,建立并优化多重实时荧光定量PCR检测体系。利用近缘种检验检测体系特异性并进行灵敏度测试,应用该检测体系分析猕猴桃主要产区根际土壤中3种致病疫霉的Yt1基因含量。[结果]供测试的11个恶疫霉近缘种、11个樟疫霉近缘种、13个雪松疫霉近缘种及非目标菌种DNA样品中均无荧光信号,反应结果为阴性,而在恶疫霉、樟疫霉和雪松疫霉DNA样品中分别检测出HEX、FAM和ROX荧光信号,反应结果为阳性。三种疫霉的检测灵敏度均达到100fg。此外,通过对猕猴桃主产区陕西省周至县和眉县果园共166份土壤样品的检测发现,恶疫霉的分布最广泛且Ypt1基因含量最高,樟疫霉和雪松疫霉则相对较少。[结论]建立的猕猴桃根腐病致病疫霉多重实时定量检测体系特异性强、灵敏度高,适合于恶疫霉、樟疫霉和雪松疫霉的检测及定量分析。该技术可为猕猴桃疫霉病害的早期诊断、监测及预防提供指导。     

Genetic and Pathogenic Variation Among Tobacco Black Shank Strains of Phytophthora parasitica var. nicotianae from the Main Tobacco Growing in China

Pathogenic and genetic variability among seven populations of Phytophthora parasitica var. nicotianae from individual tobacco fields (Yunnan, Shandong, Henan, Heilongjiang, Shanxi, Fujian and Sichuan provinces) were investigated using pathogenicity and randomly amplified polymorphic DNA (RAPD) analyses; 63 strains were isolated from different fields of seven tobacco growing regions, using tobacco cv. Hongda as a baiting host. Pathogenic variability was evaluated in greenhouse studies using five tobacco cultivars that have different levels of resistance to tobacco black shank; 75 and 73% of the strains were pathogenic on M3 and M4, 29 and 33% on M1 and M2, and 94% were pathogenic on M5, respectively. Disease severity incited by different strains varied significantly on individual tobacco cultivars. The percentage of strains pathogenic on different cultivars varied among locations. Genotypic variation among 63 strains was evaluated by RAPD analysis. Ten primers detected 89 polymorphic bands. Cluster and principal coordinates analysed cluster groups. the minor group contained 26 strains, and major group contained 37 strains. Estimates of genetic diversity based on RAPD analysis ranged from 0.24 to 0.34 within populations to 0.36 among all strains from all populations. Phytophthora parasitica var. nicotianae populations were genotypically and phenotypically variable, but no distinct genotypic differences were identified among populations from the seven locations.     

In vitro and in vivo antimicrobial efficacy of essential oils and individual compounds against Phytophthora parasitica var. nicotianae

Aim

To evaluate the antimicrobial effects of essential oils (EOs) from cassia, basil, geranium, lemongrass, cumin and thyme, as well as their major components, against Phytophthora parasitica var. nicotianae; to investigate morphological changes in hyphae and sporangia in response to treatment with cinnamaldehyde; and to further evaluate potential biocontrol capacities against tobacco black shank under greenhouse conditions.

Methods and Results

The results revealed that the extent of mycelial growth inhibition was primarily dependent on the composition and concentration of the EOs and the structure of individual compounds. Cinnamaldehyde had a significantly higher inhibitory effect on mycelial growth, formation of sporangia, and production and germination of zoospores in P. parasitica var. nicotianae in vitro, achieving complete inhibition of these phenotypes at 72, 36, 36 and 18 mg l^?1, respectively. Scanning electron microscopic observations revealed that cinnamaldehyde can cause considerable morphological degenerations of hyphae and sporangia such as cytoplasmic coagulation, shrivelled mycelia and sporangia aggregates and swelling and lysis of mycelia and sporangia walls. In vivo assays with cinnamaldehyde demonstrated that this compound afforded protective effect against tobacco black shank under greenhouse conditions in susceptible tobacco plants.

Conclusions

The results of in vitro and in vivo bioassays, together with SEM imaging of the microstructure of P. parasitica var. nicotianae supported the possibility of using cinnamaldehyde as a potent natural biofungicide in the greenhouse.

Significance and Impact of the Study

This study provides a theoretical basis for the potential use of cinnamaldehyde as commercial agents or lead compounds that can be exploited as commercial biofungicides in the protection of tobacco plants from P. parasitica var. nicotianae infection.     

Rapid detection of Phytophthora nicotianae by simple DNA extraction and real‐time loop‐mediated isothermal amplification assay

Phytophthora nicotianae is a phytopathogenic oomycete with a wide host range and worldwide distribution. Rapid detection and diagnosis at the early stages of disease development are important for the effective control of P. nicotianae. In this study, we designed a simple and rapid loop‐mediated isothermal amplification (LAMP)‐based detection method for P. nicotianae. We tested three DNA extraction methods and selected the Kaneka Easy DNA Extraction Kit version 2, which is rapid and robust for LAMP‐based detection. The designed primers were tested using mycelial DNA from 35 species (81 isolates) of Phytophthora, 12 species (12 isolates) of Pythium, one isolate of Phytopythium and one isolate each from seven other soil‐borne pathogens. All of the 42 P. nicotianae isolates were detected by these primers, and no other isolates gave positive results. Three isolates were tested for the sensitivity of the reaction, and the lowest amounts of template DNA that could be detected were 10 fg for two isolates and 1 fg for the third. The target was detected within 25 min in all tested samples, including DNA extracted from both inoculated and naturally infected plants. In contrast, PCR assays with P. nicotianae‐specific primers failed or showed weakened detection in several samples. Thus, we found that the rapid DNA extraction and LAMP assay methods developed in this study can be used to detect P. nicotianae with high sensitivity, specificity and stability.     

泛耐药细菌NDM-1基困Taqman PCR快速检测方法的建立

产NDM-1(New Delhi Metallo-β-lactamase 1,Ⅰ型新德里金属β-内酰胺酶)细菌是新近报道的一种泛耐药细菌,由于对绝大多数常用抗生素均耐药,又被称为超级细菌.目的:建立一种可快速检测泛耐药细菌NDM-1基因的Taqman探针实时荧光定量PCR法.方法:根据NDM-1基因序列,设计引物和Ta...     

toxR基因作为荧光定量PCR靶基因设计TaqMan探针快速检测副溶血弧菌

以toxR基因为靶基因,通过优化反应条件建立了快速检测副溶血弧茵的TaqMan实时荧光PCR方法.特异性试验表明,该方法能选择性检测副溶血弧茵,而与金黄色葡萄球菌、沙门氏菌、单增李斯特杆菌等多种常见的食源性病原茵没有交叉反应:灵敏度试验表明,该方法最少可检测到25个拷贝的toxR基因重组质粒,对纯培养物和模拟食品样品直接检测的灵敏度分别为21 cfu/mL和210 cfu/g;重复性试验表明,同一样品于试验内及试验间的变异系数分别为0.9%和1.3%:所制作的标准曲线在2.5 × 101～2.5 × 106拷贝数之间有较好的线性关系,能对副溶血孤菌进行准确的定量分析.结果表明,本研究所建立的副溶血弧菌实时荧光PCR检测方法具有特异性好,灵敏度高、重复性好的特点,能进行定量检测,而且检测时间从核酸抽提到出实验结果仅需要3 h.是快速检测副溶血弧菌的有效手段.     

Molecular Distinctions Between Phytophthora capsici and Ph. tropicalis Based on ITS Sequences of Ribosomal DNA

Among four species of Phytophthora tested, only Ph. capsici and Ph. tropicalis showed the same length for DNA sequence for both internal transcribed spacer (ITS)1 and ITS2 of ribosomal DNA. Phytophthora palmivora and P. nicotianae have lengths different from each other, and from the other two species. Although A1 and A2 types of Ph. capsici differ from each other by only one nucleotide, there are 10 different nucleotides between A1 and A2 types of Ph. tropicalis. Phylogenetic analysis of combined ITS sequences identified four clades each consisting A1 and A2 mating types of same species. The neighbor‐joining and maximum parsimony trees show that Ph. tropicalis (A2) is clustered with the clade of two isolates of Ph. capsici before joining the clade of A1 and two other isolates of Ph. tropicalis from GenBank. Our results support the separation of Ph. tropicalis and demonstrate the need to sequence more than a single isolate of a species in the study of molecular phylogeny of Phytophthora. The phylogenetic trees also suggest that Ph. tropicalis (A2) may represent a transitional isolate in the process of species evolution.     

Yeast dynamin and Ypt6 function in parallel for the endosome‐to‐Golgi retrieval of Snc1

Protein recycling is an important cellular process required for cell homeostasis. Results from prior studies have shown that vacuolar sorting protein‐1 (Vps1), a dynamin homolog in yeast, is implicated in protein recycling from the endosome to the trans‐Golgi Network (TGN). However, the function of Vps1 in relation to Ypt6, a master GTPase in the recycling pathway, remains unknown. The present study reveals that Vps1 physically interacts with Ypt6 if at least one of them is full‐length. We found that overexpression of full‐length Vps1, but not GTP hydrolysis‐defective Vps1 mutants, is sufficient to rescue abnormal phenotypes of Snc1 distribution provoked by the loss of Ypt6, and vice versa. This suggests that Vps1 and Ypt6 function in parallel pathways instead of in a sequential pathway and that GTP binding/hydrolysis of Vps1 is required for proper traffic of Snc1 toward the TGN. Additionally, we identified two novel Vps1‐binding partners, Vti1 and Snc2, which function for the endosome‐derived vesicle fusion at the TGN. Taken together, the present study demonstrates that Vps1 plays a role in later stages of the endosome‐to‐TGN traffic.