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

莉萨·阿尔瓦雷斯-科恩加利福尼亚大学伯克利分校地下水被氯化溶剂污染是一个严重的问题，在美国和世界各地的数千个地点。氯化乙烯污染地下水的原位生物修复包括对本地的去卤球菌进行生物刺激和/或使用含去卤球菌的培养物进行生物强化，以将过氯乙烯和三氯乙烯完全还原为无毒的乙烯。由于这些细菌表现出对底物和辅助因子的特定限制性代谢需求，这些底物和辅助因子可以通过多种代谢相互依赖的网络由支持性微生物提供，因此该项目旨在提供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dehalococcoides的微生物群落的结构和功能稳健性。结合连续流生物反应器系统中培养物的工程控制、TCE脱氯生物动力学建模和高通量、社区水平的基因组分析，本研究将开发地下水羽流相关条件下（即低浓度氯化乙烯连续流动）的机制、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控制生物修复过程。地下水受到氯化溶剂（例如脱脂液和干洗剂）的污染是美国和世界各地数千个地点的一个重要问题。幸运的是，一种自然产生的细菌在刺激它们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许多细菌生存和生物降解溶剂所需的因素。该项目采用系统级方法来理解这些微生物群落之间的相互作用，以形成复杂降解群落如何运作和应对不同环境压力的综合图景。这种理解将被捕获在预测模型中，这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理策略，并为在现场操纵微生物群落的策略提供指导。本项目还将支持不同教育层次的科学推广活动，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.