Monitoring of functional gene responses to ERD (enhanced reductive dechlorination) from four TCE-contaminated sites

A functional microarray targeting 24 genes involved in chlorinated solvent biodegradation pathways has been developed and used to monitor the gene diversity present in four trichloroethylene (TCE) contaminated sites under ERD (enhanced reductive dechlorination) treatment. The microarray format provided by NimbleGen and used in this study is 12x135K. 2 µg of labelled gDNA from 30 groundwater samples were hybridized on the microarrays. A 30-chip study was performed, each chip corresponding to hybridization with 2 µg of labelled gDNA retrieved from a monitoring well from one of the four contaminated sites. Each probe (760nt) on the microarray was synthesized in eight replicates, and a total of 5,707 random probes was used to determine the background noise. Groundwater samples were collected from four contaminated sites (B, F, G and H), four monitoring wells per site (P1, P2, P3 and P4). P1: well located upstream to the contamination source. P2: well in the contamination source. P3 and P4: wells located downstream to the contamination source. For site B, the monitoring of ERD demonstration was performed through a total of 5 sampling campaigns: C1 (T=0), C2 (T=104 days), C3 (T=231 days), C4 (T=291 days) and C5 (T=378 days). For the three other sites (F, G and H), only one sampling campaign was performed after the treatment.

本研究开发了一款靶向24个参与氯代溶剂生物降解途径的基因的功能微阵列，用于监测4个经强化还原脱氯（Enhanced Reductive Dechlorination, ERD）处理的三氯乙烯（Trichloroethylene, TCE）污染场地中的基因多样性。本研究使用的微阵列由NimbleGen提供，芯片规格为12×135K。将来自30个地下水样品的2微克标记基因组脱氧核糖核酸（genomic DNA, gDNA）与微阵列进行杂交。本研究共开展30张芯片的杂交实验，每张芯片对应从4个污染场地中某一场地的监测井获取的2微克标记gDNA的杂交反应。微阵列上的每条探针（长度为760nt）均设置8次重复合成；同时共使用5707条随机探针以测定背景噪音。地下水样品采自4个污染场地（编号B、F、G、H），每个场地设置4口监测井（编号P1、P2、P3、P4），其中P1位于污染源上游，P2位于污染源区域内，P3与P4位于污染源下游。针对场地B，本研究共开展5次采样批次以实施ERD强化还原脱氯示范工程的监测工作，采样节点分别为C1（T=0）、C2（T=104天）、C3（T=231天）、C4（T=291天）及C5（T=378天）。其余3个场地（F、G、H）仅在处理完成后开展了1次采样。