Modeling gene networks in Dehalococcoides and development of bioindicator assays for bioremediation of chlorinated solvents

该项目将研究Dehalococcoides （DHC）的培养物如何对环境条件做出反应，DHC是一种参与脱氯和降解氯化烃污染物（如TCE（三氯乙烯））的细菌属。在这项工作的基础上，研究人员将开发适用于污染现场的适当的去盐呼吸生物指示剂测定方法。这项工作将把实验室研究与实地生物量取样结合起来。在第一阶段的工作中，将在各种条件下培养两种经过充分研究的含dhc的混合培养物，其中一部分研究将包括化学应激源（O2、pH、氯仿）。将收集异构数据集（基因组学、化学水平、去盐呼吸速率、种群）并将其纳入系统生物学算法以生成基因网络模型。在第二阶段，将在生物增强站点收集现场生物量，以比较现场部署的DHC的基因表达谱与实验室衍生模型预测的基因表达谱。在最后阶段，将选择与脱盐呼吸类型和速率高度相关的基因作为生物指标。将开发两种类型的生物指示剂测定方法用于现场应用。定量反转录PCR （qRTPCR）和试纸式rna生物传感器。将测试这些测定法对其他DHC菌株的稳健性，并最终对野外取样的生物量进行稳健性测试。

CBET-0731169Ruth RichardsonCornell UniversityModeling gene networks in Dehalococcoides and development of bioindicator assays for bioremediation of chlorinated solventsThis project will study how cultures of Dehalococcoides (DHC), the genus of bacteria involved in dechlorinating and degrading chlorinated hydrocarbon contaminants like TCE (trichloroethene) respond to environmental conditions. Based on this work, the investigators will develop appropriate dehalorespiration bioindicator assays that can be applied at contaminated field sites. The work will combine laboratory studies with field biomass sampling. In the first phase of work, two well-studied DHC-containing mixed cultures will be grown under a wide range of conditions and a subset of studies will include chemical stressors (O2, pH, chloroform). Heterogeneous datasets (genomics, chemical levels, dehalorespiration rates, populations) will be collected and incorporated into systems biology algorithms to generate gene network models. In the second phase, field biomass will be collected at bioaugmented sites to compare gene expression profiles of field-deployed DHC with those predicted from lab-derived models. In the final phase, genes highly correlated with dehalorespiration types and rates will be selected as bioindicators. Two types of bioindicator assays will be developed for field application?quantitative reverse transcription PCR (qRTPCR) and dipstick-style RNA-biosensors. The assays will be tested for robustness against other DHC strains and, ultimately, against field-sampled biomass.