柑橘溃疡病菌EMA-PCR快速活体检测技术的建立

传统PCR方法不能诊断柑橘溃疡病菌(Xanthomonas citri subsp.citri Gabriel)的死活状态,往往导致假阳性检测结果.本研究将特异性核酸染料叠氮溴化乙锭(ethidium monoazide bromide,EMA)与PCR技术结合,旨在建立柑橘溃疡病活菌的快速检测技术.根据柑橘溃疡病菌独有的保守蛋白基因设计特异性引物扩增出278 bp的靶带,PCR反应的检测下限为25个细胞/25 μL或2.75 pg/25 μL.EMA-PCR结果表明:当卤钨灯曝光时间1 min,EMA终浓度为1.0 mg/L时,能有效抑制1.0×108 cfu/mL死菌的扩增;当EMA的浓度小于30 mg/L时,EMA对上述相同浓度活菌靶基因的扩增没有明显的抑制.EMA-PCR对死活混合菌的扩增表明,活菌数在6.875×101～6.875×105 cfu/PCR范围时,荧光强度与混合体系中活菌的对数值有线性关系.基于以上建立的EMA-PCR活体检测技术,对疑似带病柑橘材料进行检测,结果发现能降低柑橘溃疡病菌检测过程中的假阳性,有望为柑橘溃疡病的检疫检验提供更科学的技术手段.     

基于致病基因序列的LAMP方法检测番茄种子携带的溃疡病菌

本研究选取番茄溃疡病菌(Clavibacter michiganensis subsp.michiganensis,Cmm)致病岛上的chpC基因的部分序列,作为环介导等温扩增(loop-mediated isothermal amplification,LAMP)靶标片段进行LAMP引物设计。对反应体系优化后进行特异性测定,结果表明供试的89株番茄溃疡病菌中86株检测结果为阳性,3株为阴性,供试的14株非番茄溃疡病菌(其他重要植物病原细菌)均为阴性。检测番茄溃疡病菌菌悬液样品的阈值为4.8×10~5 CFU·mL~(-1),对DNA样品的检测阈值为1.8×10~(-2) ng·μL~(-1),并据此建立了番茄溃疡病菌的LAMP检测方法。将该方法应用于番茄种子携带Cmm的检测,通过提取种子浸提液样品的总DNA,实现了对番茄种子携带Cmm的直接检测。与普通PCR相比,该方法更加快捷简便,不依赖PCR仪等昂贵的仪器设备,可以丰富现有的番茄溃疡病菌分子检测体系,为口岸等检疫部门提供简单易行的检测初筛手段。     

西瓜细菌性果斑病病菌活细胞PMA-PCR检测方法的建立

利用叠氮溴化丙锭与聚合酶链式反应结合(PMA-PCR),建立了西瓜细菌性果斑病病菌(Acidovorax avenae subsp.citrulli)活细胞检测方法。实验结果表明,当PMA浓度为0.5 mg/m L时,对活细胞DNA的PCR扩增无影响,最低检测浓度为1×104cfu/m L。当样品中死亡细胞浓度低于107 cfu/m L时,PMA可抑制死亡细胞DNA的PCR扩增;当死亡细胞浓度为1×107cfu/m L时,PMA失去效果。该方法适用于低浓度西瓜细菌性果斑病病菌活细胞的检测。     

基于锁式探针技术的菜豆晕疫病菌检测技术研究

根据菜豆晕疫病菌的一段特异促旋酶亚组B(gyr B)基因序列,设计锁式探针和扩增引物,优化体系反应条件,建立了基于锁式探针菜豆晕疫病菌滚环扩增特异性检测体系。试验结果表明该检测体系能够从供试菌株中特异性检测出菜豆晕疫病菌。该体系检测DNA的阈值为600 fg/μL,与传统PCR相当;检测菌悬液检测阈值1.3×10~3 cfu/m L,比传统PCR高10倍,在模拟样品检测中也显示了更适合于样品的检测。     

PMA-PCR方法快速检测VBNC状态青枯菌

青枯菌为应对逆境胁迫,可进入活的但非可培养状态(viable but non-culturable,VBNC)。本文利用叠氮溴化丙锭(PMA)与PCR技术相结合,建立了一种快速有效区分青枯菌死活细胞的分子检测方法。基于hrcS基因序列,设计了一对青枯菌种特异性检测引物hrcSf/hrcSr;利用PMA对青枯菌Po82菌株的细胞悬浮液样品进行预处理,随后进行常规PCR扩增。结果表明,当样品中PMA质量浓度为3μg/mL、曝光时间大于5min时,PMA可有效抑制死亡菌体细胞中的DNA扩增;且对可培养和VBNC状态细胞中的DNA扩增没有影响;本试验建立的PMA-PCR方法能有效对包括VBNC状态在内的青枯菌活菌进行检测,避免了假阳性与假阴性结果的产生。     

番茄细菌性叶斑病菌RPA检测技术研究

青枯菌为应对逆境胁迫,可进入活的但非可培养状态(viable but non-eulturable,VBNC).本文利用叠氮溴化丙锭(PMA)与PCR技术相结合,建立了一种快速有效区分青枯菌死活细胞的分子检测方法.基于hrcS基因序列,设计了一对青枯菌种特异性检测引物hrcSf/hrcSr;利用PMA对青枯菌Po82菌株的细胞悬浮液样品进行预处理,随后进行常规PCR扩增.结果表明,当样品中PMA质量浓度为3 μg/mL、曝光时间大于5 min时,PMA可有效抑制死亡菌体细胞中的DNA扩增;且对可培养和VBNC状态细胞中的DNA扩增没有影响;本试验建立的PMA-PCR方法能有效对包括VBNC状态在内的青枯菌活菌进行检测,避免了假阳性与假阴性结果的产生.     

马铃薯斑纹片病菌IAC-PCR检测方法

马铃薯斑纹片病菌(Candidatus Liberibacter solanacearum)是危害茄科、伞形花科植物的一种重要病原细菌,目前尚不能人工培养,PCR是常用检测方法。为了克服PCR检测中的假阴性,通过复合引物法人工构建扩增内标(internal amplification control,IAC),建立了马铃薯斑纹片病菌含扩增内标的PCR(IAC-PCR)检测体系。测试结果表明,当扩增内标添加量为3.90×10~(-4) ng时,检测灵敏度达2.73×10~(-3) ng,与常规PCR相比,添加扩增内标不影响检测灵敏度。60个样品的检测结果表明,IAC-PCR可克服常规PCR产生的假阴性,进一步提高检测结果的可信度和准确性。     

免疫捕获PCR检测进境苹果果实中梨火疫病菌

利用梨火疫病菌抗体和PCR技术建立了梨火疫病菌免疫捕获PCR方法,检测苹果模拟样品的灵敏度达到了1.5×102cfu/reaction。与直接PCR进行比较,免疫捕获PCR方法检测苹果模拟样品的灵敏度提高了10倍以上,而且省去了DNA提取等步骤。利用该方法成功从进境苹果样品中检测到梨火疫病菌,产物测序结果表明,产物序列和梨火疫病菌的相应序列高度一致。试验结果表明,免疫捕获PCR法能除去样品中的大部分PCR反应抑制物质,可以有效检测进境苹果中梨火疫病菌,在口岸水果检疫中具有一定的应用潜力和推广价值。     

PMA-qPCR定量检测青枯菌活菌方法的建立

本文将叠氮溴化丙锭(PMA)与荧光实时定量PCR技术相结合,建立了一种适于青枯菌不同小种菌株活细胞精准、快速检测的PMA-qPCR方法。通过单因素变化试验对PMA预处理反应体系中的各参数进行优化,确立了PMA终浓度为15 ng/μL,黑暗孵育时间为10 min,曝光时间为5 min的PMA预处理体系。试验结果表明,当活菌比例大于10%,PMA-qPCR的测定结果均在理论活菌数相对应的95%置信区间内。检测灵敏度测试结果显示,该方法适用于活菌数在5.0×10~2～5.0×10~8 cfu/mL范围内菌悬液的检测。本文建立的PMA-qPCR方法可在一定范围内有效去除青枯菌死菌的干扰,定量检测出活菌数量,研究结果可为植物细菌性青枯病的流行规律研究提供新的技术支撑。     

柑橘溃疡病菌的普通LAMP及快速LAMP检测方法的建立

建立柑橘溃疡病菌的普通LAMP和快速LAMP检测方法,使其能应用于基层检验检疫部门对病害的快速检测.利用柑橘溃疡病菌基因组特有的保守区域设计LAMP引物,通过优化反应条件,建立柑橘溃疡病菌的普通LAMP检测体系;在普通LAMP引物的基础上设计一对环引物,建立柑橘溃疡病菌的快速LAMP检测体系,并以多种参比菌DNA以及健康柑橘叶片基因组DNA为模板对普通LAMP和快速LAMP检测体系的特异性进行了验证,利用柑橘溃疡病菌菌液和DNA溶液梯度稀释液对普通LAMP和快速LAMP检测体系的灵敏度进行了验证.普通LAMP检测体系菌体和DNA检测灵敏度分别达到了2.25×104 cfu和2.03×10-1 ng,快速LAMP检测体系菌体和DNA检测灵敏度分别达到了2.25 cfu和2.03×10-5ng.在特异性测试中,普通LAMP检测体系与快速LAMP检测体系均仅对柑橘溃疡病菌进行扩增,对非靶标菌和柑橘叶片基因组DNA不产生扩增,普通LAMP与快速LAMP检测体系特异性测试结果一致.快速LAMP检测体系在0.5h内就可以达到普通LAMP检测体系的扩增量,是普通LAMP检测体系反应时间的一半,大大提高了检测的效率;快速LAMP检测体系菌悬液和DNA检测灵敏度均比普通LAMP检测体系提高了10 000倍.成功地建立了柑橘溃疡病菌的普通LAMP及快速LAMP检测方法,为柑橘溃疡病菌的检测提供了一种新的简便、快速的检测手段.     

Quantification of viable cells of Clavibacter michiganensis subsp. michiganensis using a DNA binding dye and a real-time PCR assay

Viable cells of Clavibacter michiganensis subsp. michiganensis (CMM), the causal agent of bacterial canker of tomato, were discriminated from the dead cells by quantitative real-time polymerase chain reaction (PCR), after the bacterial solution was treated with the DNA binding dye ethidium monoazide (EMA). The primers and TaqMan probe, based on the 16S-23S rDNA spacer sequences, were highly specific for CMM at the subspecies level. The detection limit of the direct real-time PCR was 10³ colony forming units per mL (cfu mL⁻¹) in samples and with an apparent sensitivity of 2 cfu of target cells in PCR reaction solution. Application of this method allows for selective quantification of viable cells of CMM and facilitates monitoring the pathogen in tomato seeds.     

Quantification of viable <Emphasis Type="Italic">Candidatus</Emphasis> Liberibacter asiaticus in hosts using quantitative PCR with the aid of ethidium monoazide (EMA)

Citrus Huanglongbing (HLB) is a devastating disease of citrus known to be associated with a fastidious, phloem-limited Gram-negative, yet to be cultured bacterium in the genus Candidatus Liberibacter. In the present study we have developed a method to quantify viable Candidatus Liberibacter asiaticus (Las) with the aid of ethidium monoazide (EMA) which can differentiate live from dead cells. First, calibration curves were developed with the aid of quantitative real-time PCR (QPCR) by using a plasmid template consisting of a 703 bp DNA fragment of rplKAJL-rpoBC (β-operon) region. Standard equations were then developed to quantify Las genome equivalents in citrus, periwinkle, and Asian citrus psyllid, Diaphorina citri. To overcome the limitation of quantitative PCR in discriminating between live and dead bacterial cells, EMA was used to inhibit the amplification of DNA from the dead cells of Las in plant samples. By using the standard equations and EMA-QPCR methods developed in this study, we found that the proportion of viable cells in citrus and periwinkle ranged from 17–31% and 16–28%, respectively. It was determined that a minimum bacterial concentration is required for HLB symptom development by quantifying the population of Las in symptomatic and asymptomatic leaves. The EMA-QPCR methodology developed in the present study should provide an accurate assessment of viable HLB pathogen, providing a tool to investigate disease epidemiology and thus act as a crucial component for disease assessment and management. The authors P. Trivedi and U. S. Sagaram contributed equally to this work.     

Rapid detection and quantification of viable potato cyst nematodes using qPCR in combination with propidium monoazide

Potato cyst nematodes (PCN), Globodera pallida and Globodera rostochiensis, are obligate parasites of solanaceous plants, causing severe losses in several potato growing areas throughout the world. To date, management of PCN is related to nematode population densities estimated as eggs per gram of soil, without considering the actual number of viable juveniles within the cysts. In classical nematology, the standard method to determine PCN viability is based on a staining assay, using Meldola's blue dye (MB) followed by microscopic visualization of MB‐treated nematodes. Although MB is considered to be reliable in staining embryonated juveniles within eggs and cysts, it is a time‐ and labour‐consuming assay. In the present work, a real‐time PCR (qPCR)‐based method combined with propidium monoazide (PMA), a photoreactive DNA‐intercalating dye, was developed for the quantification of viable PCN. This dye renders exposed DNA of dead cells unable to be amplified by PCR, and thus only DNA from viable/intact PCN juveniles is amplified and detected. The novelty of the present method lies in the simultaneous quantitative and qualitative estimation of viable PCN inocula using species‐specific primers and TaqMan probes. The PMA–qPCR viability method (v‐PCR) developed for the two Globodera species successfully discriminated dead from living specimens in heat‐treated samples and eggs in old and newly formed cysts. Interestingly, the detection of DNA from 34‐year‐old nematode cysts stored at room temperature was observed. In conclusion, the proposed v‐PCR method should prove to be very useful for the routine determination of PCN viability from field samples.     

应用微滴数字PCR同时检测瓜类种子携带果斑病菌和角斑病菌

细菌性果斑病和角斑病是葫芦科作物两大重要细菌病害,病原菌分别为西瓜嗜酸菌Acidovorax citrulli和丁香假单胞菌黄瓜致病变种Pseudomonas syringae pv.lachrymans。两种菌均可通过种子、种苗带菌进行远距离传播。种子检测是预防和控制这两种病害发生的首要环节。本研究应用微滴数字PCR技术(droplet digital PCR,ddPCR)建立了同时检测种子携带西瓜嗜酸菌和丁香假单胞菌的方法。结果显示:两种细菌菌悬液和DNA样品等浓度混合时,ddPCR能同时检测到两种靶标菌的最低混合菌悬液浓度和最低DNA浓度分别为10³ cfu/mL和10^-3 ng/μL,其检测灵敏度是平行测试的real-time PCR方法的10倍;对于非等浓度混合的菌悬液和DNA样品,两种靶标菌菌悬液按浓度比1∶1000(10³∶10⁶ cfu/mL)混合或其DNA浓度比为1∶10000(2.28×10^-3 ng/μL∶22.8 ng/μL)条件下,ddPCR可检测到低浓度的靶标菌,检测灵敏度同样是real-time PCR的10倍。此外,在人工接菌种子测试中,西瓜、甜瓜单粒种子平均带菌量10⁵~10⁶ cfu/粒时,ddPCR方法可检测到带菌率0.2%(n=500)的西瓜、甜瓜种子样品。将分别携带两种菌的种子按比例1∶10混合时ddPCR方法可以准确检出浓度相对低的靶标菌;而使用相同检测引物的real-time PCR检测方法则只能检出西瓜嗜酸菌和丁香假单胞菌带菌率分别为0.2%和2%(n=500)的甜瓜种子混合样品中的西瓜嗜酸菌,未能稳定检出丁香假单胞菌。综上所述,本研究基于ddPCR技术建立了可同时检测两种重要葫芦科种传细菌的方法,检测结果稳定可靠,丰富了当前种传病原细菌的检测技术体系。     

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%。     

枯草芽胞杆菌R31影响巴西蕉根系活性氧产生及对枯萎病的防治效果

研究枯草芽胞杆菌R31接种浓度对香蕉根系活性氧产生、R31自身根系定殖和枯萎病防治效果的影响。首先检测了不同浓度R31接种对巴西蕉根系Mn-SOD活性和过氧化氢含量的影响,并研究了过氧化氢对不同细胞浓度R31生物被膜形成的影响,然后利用R31-gfp观察了不同浓度R31接种在香蕉根表定殖的差异,最后利用大田试验验证了不同浓度R31可湿性粉剂的枯萎病防效。研究结果显示,1.0×10~6和1.0×10~7 cfu/mL R31菌体灌根使巴西蕉根系Mn-SOD活性分别在0.76~5.99和0.81~6.55 U/g显著波动,根系过氧化氢含量显著增加,而1.0×10~8 cfu/mL R31菌体接种的根系Mn-SOD活性在4~5 U/g波动,不激发根系过氧化氢爆发。80和120μmol/mL以上过氧化氢分别抑制1.0×10~5和1.0×10~6 cfu/mL R31在24 h内形成薄皮,但分别显著促进2种浓度R31在72 h形成薄皮。40~240μmol/mL过氧化氢对1.0×10~7和1.0×10~8 cfu/mL R31 24 h的薄皮形成无影响,但显著促进2种浓度R31 72 h的薄皮形成。1.0×10~6 cfu/mL R31-gfp接种巴西蕉后第5 d才可以观察到根表产生荧光,而1.0×10~7和1.0×10~8 cfu/mL R31-gfp接种处理在第3 d即可观察到根表产生明显荧光。利用R31可湿性粉剂进行田间试验,以2.0×10~6和2.0×10~7 cfu/mL2000 mL灌根处理新植巴西蕉,施用4次后,枯萎病防效分别为35.41%和72.96%。R31低浓度接种能够激发香蕉根系免疫反应和活性氧产生,并延缓低浓度R31在根表定殖,最终影响其对枯萎病的防效。     

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。     

针茅属植物RAPD条件优化

本试验以针茅属 ( Stipa L.)植物为材料 ,使用 CTAB法提取其基因组 DNA,通过对 RAPD( Random amplified polymorphic NDA,随机扩增的多态性 )条件优化分析 ,初步确定了针茅属植物 RAPD的最佳方案 ,即在 PCR扩增程序为 94℃预变性 3min,94℃变性 1 min,37℃复性 1 min,72℃延伸 1 .5 min,设 45个循环 ,最后 72℃保温 5 min时 ,2 5μL反应体系中包括 :0 .2 μL( 1 0 mmol/L) d NTPs,2 .0 μL( 1 0 mmol/L) Mg2 + ,0 .5 μL( 1 0 0 pmol/μL)引物 ,模板DNA80 ng,Taq酶 ( Sangon) 1 .0 U,2 .5 μL1 0×buffer缓冲液 ,其余部分用无菌三蒸水补平可以得到较好的扩增结果。     

Assessment of viable conidia of Monilinia fructicola in flower and stone fruit combining propidium monoazide (PMA) and qPCR

Brown rot is the most economically important fungal disease of stone fruits and is primarily caused by Monilinia laxa and M. fructicola. Conventional methods used to identify M. fructicola are mainly based on phenotypic characteristics and pathogen quantification is not always accurate. In contrast, methodologies based on molecular tools improve pathogen characterization and identification but are not able to differentiate between live and dead conidia. In this study the PMA‐qPCR methodology was optimized, validated and applied to quantify viable cells of M. fructicola in artificially and naturally infected samples. qPCR methodology showed good primer efficiency and sensitivity with quantification limits lower than obtained using a plate count method. The conditions of propidium monoazide (PMA) pretreatment were 60 μm PMA for 20 min incubation and 30 min of light‐emitting diode (LED) exposure that, combined with qPCR, measured live cells accurately without overestimation of dead cells. Using this methodology in naturally infected samples, M. fructicola live cells were quantified specifically, in contrast to other traditional methodologies that cannot distinguish among Monilinia spp. The developed methodology based on combined PMA‐qPCR will be a new tool to quantify viable M. fructicola in further epidemiological and ecological studies of this fungus.