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石油是由烷烃、芳香烃以及少量非烃类物质(沥青和树脂等)组成的复杂混合物[1]。在石油的开采、运输、储存以及使用过程中不可避免的存在泄漏和原油落地等问题,对土壤生态环境造成不利影响[2-4]。土壤中蕴含的大量微生物通过产生对石油烃具有降解活性的酶以代谢石油烃,将其矿化为二氧化碳和水[5],对于石油污染环境的修复发挥着重要作用。石油烃降解功能基因是指微生物产生的对于石油烃具有特定降解作用的酶编码基因[6],通过对这些功能基因进行测定,可用于分析污染环境中石油烃降解菌的生物多样性,从而判定石油烃污染环境的生物修复潜势[7]。
在好氧条件下,包括芳香烃在内的许多复杂碳氢化合物较易被生物降解。然而,在非表层的石油污染土壤中,厌氧代谢是石油烃生物降解中的主要方式[8, 9]。在厌氧条件下,烷烃降解途径中琥珀酸合酶基因(masD)催化的富马酸加成反应和琥珀酸烷基代谢物的生成是烷烃降解的关键步骤[10]。而多数芳香族化合物(如甲苯、苯酚、甲酚等)在脱芳构化和裂解环之前,在微生物作用下生成中间体苯甲酰辅酶A,其中6-十六氧环-1-烯-1-羰基CoA水解酶基因(bamA)开环反应是苯甲酰辅酶A厌氧降解途径中的关键步骤[11]。因此,检测石油烃厌氧降解功能基因masD和bamA是研究土壤石油烃厌氧降解菌赋存情况、评价石油烃厌氧生物降解潜势的重要依据。
实时荧光定量聚合酶链式反应(Real-time Quantitative PCR, qPCR)是目前广为采用的基因定量检测技术[12]。在PCR体系中加入荧光探针[13]或荧光染料[14],随着扩增产物不断积累,相应的荧光信号也不断增强,通过监测荧光信号强度变化,结合标准曲线就可以定量分析未知样品中目的基因拷贝数[15-17]。在利用实时荧光定量PCR技术检测功能基因时,设计合适的扩增引物和确定退火温度是保证方法准确度和灵敏度的关键。
宋本如[18]建立了烷烃和芳烃厌氧降解关键基因masD和bamA的实时荧光定量PCR检测方法,方法可较好的用于两种基因的定量检测。但其扩增效率较低,仅为53.0%和63.6%。Aitken等[10]为研究不同条件下烷烃的活化机制,建立了扩增琥珀酸合酶基因(assA)的实时荧光定量PCR检测方法。Martijn等[19]建立了6-十六氧环-1-烯-1-羰基CoA水解酶基因(bamA)的实时荧光定量PCR检测方法,这些方法普遍存在扩增效率较低的问题。
本文通过设计引物及确定合适的退火温度和扩增程序,优化了烷烃和芳烃厌氧降解关键基因masD和bamA的定量检测方法。并利用建立的方法对陕北油井场区土壤中的masD和bamA基因进行了定量检测。研究对于评估污染土壤中石油烃的生物厌氧降解潜势具有重要的理论意义。
石油烃厌氧降解关键基因masD和bamA的实时荧光定量PCR检测方法与应用
Real-time quantitative PCR for determination of petroleum hydrocarbon anaerobic degradation key genes masD and bamA
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摘要: masD和bamA是控制石油烃厌氧降解的关键基因,利用实时荧光定量PCR技术检测masD和bamA基因具有简便快速和易操作等优点。但目前所用方法存在扩增效率低,方法灵敏度较差的问题。本文根据引物设计原则,利用Allele ID6软件重新设计了扩增masD和bamA的实时荧光定量PCR引物,将质粒DNA进行8次10倍梯度稀释后构建实时荧光定量PCR标准曲线。优化后的体系(20 μL)为:FastStart Essential DNA Green Master 10.0 μL,上下游引物各0.4 μL,RNase-Free Water 4.2 μL,5.0 μL DNA 模板。利用新设计的引物扩增masD和bamA基因的最适退火温度分别为61 ℃和57 ℃。优化后的检测方法扩增效率提高至97.5%和71.2%,比文献报道的方法提高了7.6%—44.5%,具有更高的重复性和灵敏度。利用设计的引物对陕北5个地区石油污染土壤中的masD和bamA基因进行定量检测结果表明,石油污染土壤中普遍存在着控制石油烃厌氧降解的关键基因,所测定的土壤中bamA降解基因的拷贝数远高于masD降解基因。Abstract: The masD and bamA are key genes controlling the anaerobic degradation of petroleum hydrocarbons. Real-time quantitative PCR (qPCR) is the common gene detection method which has the advantages of simple, fast and easy operation. In this study, according to the primer design principle, the qPCR primers for amplifying masD and bamA were designed using Allele ID6 software. The obtained primers have uniform base distribution, appropriate amplification length, minor difference of Tm values between forward and reverse primers, as well as single peak in the fusion curve of amplification products, indicating that the primers had good specificity. The plasmid DNA was diluted 8 times with 10 fold gradient to construct the qPCR standard curve. 20 μL of optimized system included 10.0 μL of Faststart essential DNA green master, 4.2 μL RNase-Free Water, 5.0 μL DNA template, 0.4 μL of upstream and downstream primers, respectively. The optimum annealing temperatures for amplification of masD and bamA genes were 61 ℃ and 57 ℃, respectively. Compared with the literatures, the amplification efficiency of this optimized method enhanced by 7.6%—44.5%, indicating the method has higher repeatability and sensitivity. This optimized method can be used to quantitatively detect the masD and bamA genes in the petroleum-contaminated soils collected from five regions in northern of Shaanxi province of China. The results indicated that the anaerobic degradation genes of masD and bamA were ubiquitous in the petroleum-contaminated soils, and the gene copy numbers of bamA was much higher than that of masD in the oil-polluted soils.
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表 1 文献报道的masD和bamA降解基因引物
Table 1. Primers of masD and bamA degradation genes reported in literature
表 2 本文设计的扩增masD和bamA降解基因的荧光定量PCR引物
Table 2. Self-designed fluorescent quantitative PCR primers for masD and bamA degradation genes
引物
Primers引物序列
Sequence (5’-3’)扩增尺寸/ bp
Amplicon size退火温度/℃
Annealing temperaturemasD-f2 GCTGAAGAAAGGCTGCGTTA 98 61 masD-r2 TGATACTTACGGGCAGACCA bamA-f2 TGATATGGTGAAGGCGGTGA 195 57 bamA-r2 GCCGAAACCATGTCGTTGAA 表 3 引物浓度优化数据
Table 3. Primer concentration optimization data
引物终浓度/(µmol·L−1)
Final primer concentrationmasD bamA Ct平均值
Ct MeanCt标准偏差
Ct SDCt平均值
Ct MeanCt标准偏差
Ct SD0.1 18.47 0.104 28.95 0.799 0.2 13.79 0.069 23.09 0.044 0.4 14.93 0.357 24.45 0.103 表 4 退火温度优化数据
Table 4. Annealing temperature optimization data
退火温度/℃
Annealing temperaturemasD bamA Ct平均值
Ct MeanCt标准偏差
Ct SDCt平均值
Ct MeanCt标准偏差
Ct SD52 18.95 0.079 27.98 0.619 57 19.42 0.133 25.11 0.105 61 18.91 0.036 26.10 0.153 表 5 实时荧光定量PCR检测masD和bamA基因的组内重复性试验结果
Table 5. Intra- repeatability of masD and bamA genes detected by real-time fluorescence quantitative PCR
质粒标准品浓度/(copy·μL−1)
Plasmid standard concentrationmasD bamA 组内变异系数
Coefficient of variation within groups组内变异系数
Coefficient of variation within groupsCt`x±SD 变异系数/%
Coefficient of variationCt`x±SD 变异系数/%
Coefficient of variation1010 4.44 ±0.29 6.49% 109 8.52 ±0.02 0.19% 108 10.88 ±0.10 0.90% 14.36 ±0.06 0.45% 107 14.43 ±0.04 0.29% 17.21 ±0.11 0.64% 106 17.59 ±0.06 0.35% 21.07 ±0.05 0.26% 105 21.06 ±0.01 0.06% 26.32 ±0.15 0.56% 104 24.48 ±0.05 0.21% 表 6 陕北油田区污染土壤中masD和bamA降解基因定量结果
Table 6. Quantitative results of masD and bamA degradation genes in five polluted soils in the northern of Shaanxi province
地区
Regions石油烃浓度/(mg·kg−1 土)
Petroleum hydrocarbon concentrationsmasD 拷贝数/(copy·g−1土)
masD copy numbersbamA 拷贝数/(copy·g−1土)
bamA copy numbers安塞Ansai 50200 7.52×103 1.00×104 志丹Zhidan 26633 4.40×103 3.05×104 延安Yanan 6661 4.65×102 5.05×104 绥德Suide 5533 2.69×102 3.60×105 定边Dingbian 146500 4.43×102 1.43×105 -
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