Systems-Level Predictions of Electron Flows in TCE-Dechlorinating, Dehalococcoides Containing Microbial Communities Using Modeling and Emerging Molecular Biology Tools

CBET 1336709加州大学伯克利分校的丽莎·阿尔瓦雷斯-科恩在美国和世界各地的数千个地点，氯化溶剂对地下水的污染是一个重要的问题。氯化乙烯污染地下水的就地生物修复涉及对本地脱卤球菌属细菌的生物刺激和/或使用含有脱卤球菌的培养物进行生物增强，以将四氯乙烯和三氯乙烯完全还原为无毒的乙烯。由于这些细菌对底物和辅因子表现出特定的限制性代谢要求，这些底物和辅因子可以由支持微生物通过不同的代谢相互依赖网络提供，因此该项目试图提供对物种间电子和代谢物交换网络的系统级预测，这些网络塑造了含有脱氢球菌的微生物群落的结构和功能的稳健性。利用连续流生物反应器系统中培养物的工程控制、TCE脱氯生物动力学模型和高通量、社区水平的基因组分析，这项研究将在与地下水羽流相关的条件下(即低浓度氯化乙烯的连续流动)开发机械的系统级模型，以优化和主动控制一系列环境情景下的脱氯过程，从而更好地理解和预测生物修复过程。氯化溶剂(例如脱脂液和干洗剂)对地下水的污染在美国和世界各地的数千个地点是一个重要的问题。幸运的是，一种自然产生的细菌在被刺激生长到足够高的种群密度时，能够生物降解这些污染物，这一过程被称为“原位生物修复”。这些细菌生活在复杂的微生物群落中，这些微生物群落提供了细菌生存和生物降解溶剂所需的许多因素。该项目采用系统级别的方法来了解这些微生物群落内的相互作用，以形成复杂的降解群落如何运作和对不同环境应激源做出反应的综合图景。这一理解将被捕捉到预测模型中，这些模型将有助于环境科学家和生物修复从业者评估和优化氯化溶剂的清除策略，并为现场操纵微生物群落的策略提供指导。该项目还将支持多个教育层次的科学推广活动，以通过(联合)课程学习、辅导和培训服务激发人们对科学、技术、工程和数学的兴趣。

CBET 1336709Lisa Alvarez-CohenUniversity of California BerkeleyGroundwater contamination by chlorinated solvents is an important problem at thousands of sites within the United States and worldwide. In situ bioremediation of chlorinated ethene-contaminated groundwater involves the biostimulation of indigenous Dehalococcoides bacteria and/or bioaugmentation using Dehalococcoides-containing cultures to completely reduce perchloroethene and trichloroethene to non-toxic ethene. Because these bacteria exhibit specific restrictive metabolic requirements for substrates and cofactors that can be supplied by supportive microorganisms through diverse networks of metabolic interdependencies, this project seeks to deliver systems-level predictions of interspecies electron and metabolite exchange networks that shape the structural and functional robustness of Dehalococcoides-containing microbial communities. Using a combination of engineered control of cultures in continuous-flow bioreactor systems, TCE dechlorination biokinetic modeling and high-throughput, community-level genomic analysis, this research will develop mechanistic, systems-level models under groundwater plume-relevant conditions (i.e., continuous flow with low concentrations of chlorinated ethenes) to optimize and proactively control dechlorination processes under a range of environmental scenarios, leading to a better understanding and predictive control of bioremediation processes. Groundwater contamination by chlorinated solvents (for example, degreasing fluids and dry-cleaning agents) is an important problem at thousands of sites within the United States and worldwide. Fortunately, a type of naturally-occurring bacteria are capable of biodegrading these contaminants when they are stimulated to grow to high enough population densities, in a process called "in situ bioremediation." These bacteria live in complex microbial communities that provide many of the factors needed by the bacteria to survive and biodegrade the solvents. This project takes a systems-level approach to understanding the interactions within these microbial communities to develop an integrated picture of how complex degrading communities operate and respond to different environmental stressors. This understanding will be captured in predictive models that will be useful for environmental scientists and bioremediation practitioners to evaluate and optimize cleanup strategies for chlorinated solvents, and to provide guidance for strategies to manipulate microbial communities in the field. This project will also support science outreach activities for multiple education levels to stimulate interest in science, technology, engineering, and mathematics through (co-)curricular learning, tutoring and training services.