土壤中芸薹根肿菌qPCR检测与风险预警体系的建立与应用

 建立了土壤中芸薹根肿菌荧光定量PCR(qPCR)快速检测及风险预警体系。确定了芸薹根肿菌qPCR检测的特异性引物PbF/PbR,对根肿菌质粒DNA的检测灵敏度为1.612×10^-6 ng·μL^-1,比普通PCR高出1 000倍;对土壤和基质中芸薹根肿菌孢子的最低检测下限均为10 个·g^-1,而土壤和基质带菌的发病阈值分别为100和1 000 个·g^-1,高于该浓度时根肿病发生风险大。本研究建立的芸薹根肿菌qPCR技术体系检测下限远低于发病阈值,可以快速、准确、定量地检测出采自四川绵阳、湖北恩施、江苏无锡、山东青岛、辽宁沈阳、山西运城、内蒙古巴彦淖尔和宁夏固原等8个地区的27份田间土壤中芸薹根肿菌的数量,实现对十字花科根肿病的监测预警,为制定产前病害防控方案提供依据。     

树莓根际AM真菌分布和定殖

2004年7~12月在关中盆地西部,每月分别从0~10、10~20、20~30和30~40 cm 4个土层采集树莓根际土样,系统研究树莓根际AM真菌时空分布和土壤因子之间的相关性。结果表明,树莓能与AM真菌形成良好的共生关系。AM真菌的最高定殖率并不伴随有最大孢子密度,最高定殖率发生在9月,达86%,而最大孢子密度出现在11月,平均密度为14个/g土。土壤碱解氮与孢子密度呈极显著负相关,土壤有机质与孢子密度呈显著负相关,土壤pH与菌丝定殖率呈显著负相关,与泡囊定殖率呈极显著负相关。在检测和评估土壤生态状况和植物形成菌根的能力等方面,宿主植物根际AM真菌的孢子密度和AM真菌不同结构的定殖程度是十分有用的指标。     

甜瓜黄斑病毒SYBR Green Ⅰ实时荧光定量PCR方法

为建立检测甜瓜黄斑病毒(melon yellow spot virus, MYSV)的SYBR Green Ⅰ实时荧光定量PCR(qPCR)方法。基于MYSV核衣壳蛋白基因保守序列设计qPCR特异性引物对,针对引物退火温度、引物浓度、特异性和敏感性进行系列优化。结果显示,优化后的qPCR方法最适退火温度为61.3℃,最适引物浓度为0.65μmol·L^-1,特异性强,灵敏度高,比PCR高100倍。以携带目的基因片段的重组质粒为标准品,构建的qPCR标准曲线循环阈值与模板浓度呈良好的线性关系,相关系数为0.999 7。实验样品验证表明建立的qPCR方法可用于MYSV的定量检测。     

棉花黄萎病病原菌大丽轮枝菌的快速分子检测

大丽轮枝菌Verticillium dahliae是引起棉花黄萎病的土传病害病原真菌。快速及时地检测出大丽轮枝菌,对棉花黄萎病的早期预警及后期防治具有重要意义。采用聚合酶链式反应(polymerase chain reaction,PCR)检测技术对已报道大丽轮枝菌的检测引物进行验证、筛选和改进,获得1对改进的特异性PCR引物VDS-F/VDS-R。在优化的反应体系与扩增条件下,能特异性地从大丽轮枝菌基因组扩增出l条约520 bp的产物条带,检测灵敏度达到10~(-2)ng/μL;利用该引物可特异性地从含有大丽轮枝菌的土壤及棉花植株组织中检测出病原菌;采用巢氏PCR法对人工病土的检测灵敏度达到了10个孢子/g土。表明本引物的PCR检测体系可用于棉花黄萎病的早期快速检测。     

实时荧光定量PCR法检测十字花科细菌性黑斑病菌

为有效防控我国的检疫性有害生物十字花科细菌性黑斑病菌Pseudomonas syringae pv.maculicola在国内的传播与蔓延,通过设计1对特异性引物3539,利用132株靶标和非靶标菌为模板进行PCR扩增,建立了实时荧光定量PCR法,并进行了模拟种子带菌试验。结果显示,引物3539为只针对十字花科细菌性黑斑病菌扩增出的特异性产物;在模拟种子带菌检测中,常规PCR对菌悬液的检测限为10~5CFU/m L,实时荧光定量PCR的检测限为10~3CFU/m L,其中10~8CFU/m L菌液的Ct值最低,为22.90,10~3CFU/m L菌液的Ct值最高,为35.73,且不同浓度菌液间的Ct值均有显著差异;不同带菌率模拟种子的检测结果表明,常规PCR和实时荧光定量PCR能检测到的带菌率分别为0.5%和0.1%。研究表明,实时荧光定量PCR法不仅可用于病种的检测,也可用于病害的早期诊断。     

马铃薯块茎和土壤样品中粉痂病菌快速检测方法的建立

 马铃薯粉痂菌(Spongospora subterranea f. sp. subterranea)是引起马铃薯粉痂病的病原。本研究根据粉痂菌内部转录间隔区和线粒体DNA的保守区域,分别设计了2对适用于普通PCR的引物A5/A9、C3/C8和1对适用于荧光定量PCR的引物QF/QR,用于检测块茎和土壤样品中的粉痂菌。特异性检测结果表明:引物对A5/A9和C3/C8,以马铃薯粉痂菌DNA为模板,能分别扩增出264和367 bp大小的单一条带,而对其他非靶标DNA无扩增;引物对QF/QR对马铃薯粉痂菌有单一的熔解峰,说明三对引物特异性良好。灵敏性检测结果表明:荧光定量PCR灵敏度为13.8 fg·μL^-1,是普通PCR灵敏度的1 000倍。进一步建立循环域值(Ct)与质粒DNA含量的曲线关系,获得标准曲线y=-3.893 9 x+35.228,R² = 0.9966,呈良好线性关系。通过对不同地区采集的18份带菌种薯和18份带菌土壤进行普通PCR和荧光定量PCR检测,引物A5/A9、C3/C8和QF/QR对带菌种薯检测率均为100%,对带菌土壤的检测率分别为44.44%、66.67%和100%。本研究建立的马铃薯粉痂病菌快速检测方法,能及时、准确地检测带菌种薯和土壤,为马铃薯粉痂病的早期诊断和防治提供依据。     

茄匍柄霉菌实时荧光定量PCR检测方法的建立及应用

 为了准确检测病残体内茄匍柄霉菌(Stemphylium solani)DNA含量在土壤内的动态变化,本研究根据三磷酸甘油醛脱氢酶(GAPDH)基因序列,设计并筛选特异性引物Stem-g7F/Stem-g7R,能从靶标基因组 DNA 中特异性扩增出大小为 150 bp 的目的片段。建立的Stemphylium solani实时荧光定量PCR(Real-time quantitative PCR, qRT-PCR)检测体系的灵敏度比常规 PCR 高 1 000 倍,且特异性良好。标准曲线循环阈值与模板浓度呈良好的线性关系,相关系数为 0.992。利用所建立的qRT-PCR方法对病残体进行检测发现,病残体DNA初始拷贝数为3.69 × 10⁹ 拷贝数/g,经过温度27℃、80%湿度下处理30 d病残体DNA含量下降至1.21 × 10⁶ 拷贝数/g,而在温度27℃、20%湿度下含量为1.29 × 10¹⁰ 拷贝数/g。因此,建立的S. solani的qRT-PCR检测体系具有特异性强、灵敏度高的特点,可以快速准确地定量检测病残体 S. solani 的含量,为番茄匍柄霉叶斑病的早期预防和流行监测提供有效的技术手段。     

利用EMAqPCR建立快速检测猕猴桃溃疡病菌活菌的方法

利用叠氮溴乙锭(ethidium monoazide bromide,EMA)与实时荧光定量PCR技术相结合(EMA-qPCR),建立了一种有效快速检测猕猴桃溃疡病菌活菌的方法。以猕猴桃溃疡病菌ITS序列为检测靶标,菌体经EMA渗透处理,再进行qPCR特异性扩增。结果显示,qPCR检测灵敏度为2cfu;当EMA的浓度为2.0μg/mL时,能有效抑制1.0×10~7 cfu/mL经高温灭活的死菌的扩增,对活菌的扩增没有影响。当活菌数在1.0×10~1~1.0×10~5 cfu范围内,每个qPCR反应体系中活菌数与Ct值呈线性相关(R~2=0.988)。不同温度处理活菌菌悬液后用EMA-qPCR检测猕猴桃溃疡病菌的存活情况并与平板计数法进行比较,结果表明待检样品可在4℃和20℃短期保存。对疑似带病猕猴桃材料进行EMA-qPCR检测,结果表明能减少猕猴桃溃疡病菌PCR的假阳性结果。本研究建立的EMAqPCR方法是一种有效检测猕猴桃溃疡病菌活菌的方法,能有效避免PCR检测实际样品可能造成的假阳性结果。     

实时荧光定量PCR技术在湖南油菜根肿病菌检测中的应用

为完善湖南油菜根肿病的监测预警体系, 分析油菜根肿病的发生与芸薹根肿菌休眠孢子量的关系, 防止湖南油菜根肿病进一步蔓延?本研究依据芸薹根肿菌ITS序列设计了一对特异性引物, 通过制备标准质粒构建了快速?精准的实时荧光定量PCR检测方法?其检测灵敏度为3×10-10 μg/μL, 比常规PCR 高100 倍; 利用建立的方法检测了来自湖南各地土壤样品中芸薹根肿菌的休眠孢子数量, 64份土样中的休眠孢子含量基本大于104个/g, 所检测的土样中孢子含量最高为2.22×107个/g?据实地调查, 当土壤中休眠孢子数量大于 104个/g 时, 油菜发生根肿病的风险较大, 休眠孢子含量较高的田块其发病程度也较为严重?结果表明, 建立的实时荧光定量PCR检测方法能对油菜根肿病进行早期诊断, 为湖南油菜根肿病发生的监测预警提供有效技术参考?     

甜菜黄萎病病原菌（Gibellulopsis nigrescens）的快速分子检测

甜菜黄萎病是由变黑轮枝菌(Gibellulopsis nigrescens)引起的一种土传真菌病害。快速、准确地检测出变黑轮枝菌(G. nigrescens),对该病害的监测以及防治十分必要。根据变黑轮枝菌(G. nigrescens)的内转录间隔区,设计了一对引物GNS-F/GNS-R并验证该对引物的特异性和灵敏度。结果表明,该对引物仅能从变黑轮枝菌(G. nigrescens)的DNA中扩增出唯一条带,而其他供试菌株的DNA及阴性对照中未扩增出任何条带,片段长度为502 bp;引物的检测灵敏度为1×10~(-3) ng/μL。该病原菌也可在人工接种的发病组织及土壤中被检测到,且土壤中分生孢子的检测阈值为1×10~4cfu/g。基于该引物建立的常规PCR检测体系适用于甜菜黄萎病的快速检测,可为该病害早期诊断及药剂防治提供参考依据。     

Detection and quantification of Fusarium commune in host tissue and infested soil using real‐time PCR

Fusarium wilt caused by Fusarium commune is a major limiting factor for Chinese water chestnut (Eleocharis dulcis) production in China. A SYBR Green I real‐time quantitative polymerase chain reaction (qPCR) assay was developed based on the mitochondrial small subunit rDNA of F. commune. Assay specificity of the FO1/FO2 primer set was tested on 41 fungal isolates, and only a single PCR band of c. 178 bp from F. commune was amplified. The detection limits of the assay were 1 fg μL^?1 pure F. commune genomic DNA, 1 pg μL^?1 F. commune genomic DNA mixed with host plant genomic DNA (0·5 ng μL^?1), and 1000 conidia/g soil (artificially inoculated). The amount of F. commune DNA in stem tissues detected by qPCR was significantly correlated with the disease severity (DS) ratings; however, the qPCR assay showed no significant positive correlation between spore densities in soil of different fusarium wilt DS groupings and the DS ratings. The qPCR assay was further applied to 76 soil samples collected from commercial fields of E. dulcis during the 2011 and 2012 growing seasons. The spore density of F. commune detected was positively correlated with disease index in the 2012 growing season but not in 2011. The qPCR method can be used for rapid and specific detection of F. commune in plant and soil samples, which will facilitate monitoring of the pathogen and improvement of disease management.     

Disease risk assessment of sugar beet root rot using quantitative real-time PCR analysis of <Emphasis Type="Italic">Aphanomyces cochlioides</Emphasis> in naturally infested soil samples

Sugar beet root rot, caused by the oomycete Aphanomyces cochlioides, is a serious and economically important disease of sugar beets world-wide. Today, disease risk assessment consists of a time-consuming greenhouse bioassay using bait plants. In the present study, a real-time quantitative PCR (qPCR) assay for determination of A. cochlioides DNA in field-infested soil samples was developed and validated using the standard bioassay. The qPCR assay proved to be species-specific and was optimized to give high amplification efficiency suitable for target copy quantification. A high correlation (R² > 0.98, p < 0.001) with pathogen inoculum density was shown, demonstrating the suitability for monitoring soil samples. The limit of detection (LOD) was evaluated in several different soil types and varied between 1 and 50 oospores/g soil, depending on clay content. Soils with a high LOD were characterised as having a low clay content and high content of sand. Varying levels of the A. cochlioides target sequence were detected in 20 of the 61 naturally infested soil samples. Discrepancies between the bioassay and the qPCR assay were found in soils from low- and medium-risk fields. However, the qPCR diagnostic assay provides a potentially valuable new tool in disease risk assessment, enabling sugar beet growers to identify high-risk fields.     

尖镰孢菌(Fusarium oxysporum)的快速分子检测

 由尖镰孢菌(Fusarium oxysporum Schlecht.)引起的大豆枯萎病是危害大豆生产的主要土传病害^［1］。该菌在土壤和病残体上均可长期生存造成危害。快速准确地在发病初期植株和带病土壤中进行鉴定和检测对防治该病害至关重要。     

Detection and quantification of Fusarium oxysporum f. sp. cucumerinum in environmental samples using a specific quantitative PCR assay

The rapid and reliable identification and quantification of pathogens is essential for the management of economically important plant diseases. Fusarium oxysporum f. sp. cucumerinum is the soil borne fungus responsible for Fusarium vascular wilt of cucumber. In this study, we report the development of a specific and reliable real-time quantitative PCR assay and the development of an ultra-sensitive diagnostic pseudo-nested PCR assay. The capacity of the PCR assays to accurately identify and quantify Fusarium oxysporum f. sp. cucumerinum was experimentally tested by the development of standard curves from serial dilutions of copy numbers in a range of complex environmental DNA samples. The amplification efficiency, sensitivity and reproducibility of the qPCR assays were not significantly affected by the presence of any of the non-target background DNA tested. In quantitative real-time PCR, as few as 100 copies could be reliably quantified, and in simple and pseudo-nested PCR as little as 10 pg and 10 fg, respectively, could be detected. This rapid and sensitive qPCR method can be used to facilitate investigations into plant–pathogen interactions, epidemiology, and disease management practices.     

Using the TxtAB operon to quantify pathogenic Streptomyces in potato tubers and soil

The phytotoxin thaxtomin, produced by plant pathogenic Streptomyces species, is the only known pathogenicity determinant for common scab diseases of potato and other root and tuber crops. Genes encoding thaxtomin synthetase (txtAB) are found on a pathogenicity island characteristic of genetically diverse plant pathogenic Streptomyces species. In this study, an SYBR Green quantitative real-time polymerase chain reaction (PCR) assay using primers designed to anneal to the txtAB operon of Streptomyces was developed to quantify pathogenic bacterial populations in potatoes and soil. The real-time PCR assay was specific for pathogenic Streptomyces strains. The detection limit of the assay was 10 fg of the target DNA, or one genome equivalent. Cycle threshold (Ct) values were linearly correlated with the concentration of the target DNA (correlation coefficient R(2) = 0.99) and were not affected by the presence of plant DNA extracts, indicating the usefulness of the assay for quantitative analyses of the pathogenic bacteria in plant tissues. The amount of pathogenic Streptomyces DNA in total DNA extracts from 1 g asymptomatic and symptomatic tubers was quantified using the assay and ranged from 10(1) to 10(6) pg. A standard curve was established to quantify pathogenic Streptomyces in soil. Using the standard curve, numbers of pathogenic Streptomyces colony forming units were extrapolated to range from 10(3) to 10(6) per gram of soil from potato fields where common scab was found. This real-time PCR assay using primers designed from the txtAB operon allows rapid, accurate, and cost effective quantification of pathogenic Streptomyces strains in potato tubers and in soil.     

马铃薯疮痂病菌在植株和田间的分布与动态分析

为探明马铃薯疮痂病菌在植株和土壤中的分布情况及种群动态变化特点,利用常规PCR和定量PCR(qPCR)技术对不同环境的马铃薯疮痂病株和田间植株不同生育期的土壤样品进行病原菌的定性定量检测.结果 表明,病田、温室盆栽和微型薯苗床中马铃薯疮痂病重度发病植株的根、匍匐茎、块茎、地上茎、叶片等组织样品均可检测到184 bp的疮...     

超高效液相色谱-串联质谱法分析氟虫双酰胺在稻田生态系统中的消解动态

应用超高效液相色谱-串联质谱(UPLC-MS/MS)建立了氟虫双酰胺(NNI-0001)及其代谢产物(NNI-des)在土壤和田水中的残留检测方法。样品采用乙腈提取,乙二胺-N-丙基硅烷吸附剂(PSA)净化,UPLC-MS/MS检测。氟虫双酰胺及其代谢产物NNI-des在土壤和田水中的最低检测浓度分别为0.002 mg/kg和0.001 mg/L,最小检出量分别为1.2×10-13和3.1×10-14 g。在土壤和田水中的添加水平为0.001~1 mg/kg(mg/L)条件下,氟虫双酰胺及其代谢产物NNI-des的平均回收率在78.2%~108.2%之间,相对标准偏差在8.2%~15.3%之间。消解动态试验结果表明,氟虫双酰胺在土壤和田水中的半衰期分别为1.0和 5.4 d。施药21 d后,消解率均在85%以上,属易降解农药。     

枯草芽胞杆菌HMB19198在番茄叶片上定殖能力的分子检测

枯草芽胞杆菌HMB19198能有效防治番茄灰霉病,为快速、准确检测HMB19198在叶面的定殖能力,本研究通过对HMB19198全基因组序列比对分析,获得该菌株102 bp功能未知的独有基因序列,设计出针对HMB19198的特异性引物和探针。荧光定量PCR结果表明,该引物和探针对HMB19198具有较高的特异性,在有番茄叶片DNA干扰下,体系检测阈值为10²拷贝/μL。利用荧光定量PCR技术和菌落计数法检测了HMB19198在叶片上定殖动态。叶片喷施1×10⁸ cfu/mL的菌体悬浮液,0 d后菌体数量分别为1.7×10⁸拷贝/g叶片和8.9×10⁷ cfu/g叶片,2、4、6和8 d后菌株HMB19198在叶面的定殖数量逐渐降低,8 d后定殖数量分别为1.0×10⁷拷贝/g叶片和1.2×10⁷cfu/g叶片。防效试验结果表明,喷施菌株HMB19198悬浮液2 d后防效在80%以上,8 d后防效降为37.9%。