Project 4: Meta-Omics of Microbial Communities Involved in Bioremediation

项目4：参与生物修复的微生物群落的荟萃组学。三氯乙烯(TCE)，a 常见的氯化溶剂和1，4-二氧六环(二恶烷)都是常见的地下水 超级基金网站上的污染物。尽管微生物降解反应可以有效地改变这些 污染物，缺乏对物种间复杂性的整体和生态相关的了解 地下微生物群落阻碍了坚固而有效的原位生物修复的应用 这些化合物。本研究的总体目标是确定和检查社区水平的新陈代谢 影响生物修复群落生物降解能力的相互作用。最基本的 从系统微生物学的角度理解微生物群落将由 在两个不同的模型社区上使用社区规模的工具，这些社区在不同的氧化还原过程中发挥作用 环境，即厌氧和好氧，分别修复三氯乙烯和二恶烷。我们假设 重要的物种间相互作用和调节多种群落行为的基石功能将是 通过应用集成的基于元组学的方法来确定，这反过来将提供对 促进工程高效的生物修复过程。基于DNA的稳定同位素探测将用于 区分和识别功能生物体和内部重要的相互依赖关系 能够生物降解三氯乙烯或二恶烷的社区。然后将进行有针对性的元基因组分析 用来揭示相互依赖的生物降解生物的代谢和功能多样性 他们在社区中的支持或抑制合作伙伴。综合元译本分析 基于信使核糖核酸的靶向微阵列将被用来研究全球基因在 不同环境扰动下的群落，以揭示微生物的响应行为 对于这些变化。为了设计可用于查询环境样本的诊断工具，请访问 TCE和二恶烷污染场地，我们将识别和验证关键代谢的定量生物标志物 以及结合群落使用定量表达分析来交互作用基因 代谢物分析。最后，我们将应用整个研究过程中开发的诊断工具来 检查环境样本以评估这些样本中的微生物行为和相互作用，以便 指导和优化就地生物修复策略。

Project 4: Meta-omics of Microbial Communities Involved in Bioremediation. Trichloroethene (TCE), a common chlorinated solvent, and 1,4-dioxane (dioxane), a solvent stabilizer, both are frequent groundwater contaminants at Superfund sites. Although microbial degradation reactions can effectively transform these contaminants, lack of a holistic and ecologically relevant understanding of the interspecies complexity of subsurface microbial communities impedes the application of robust and effective in situ bioremediation of these compounds. The overall goal of this research is to identify and examine the community-level metabolic interactions that shape the biodegradation capabilities of bioremediating communities. The fundamental understanding of microbial communities from a systems microbiology point of view will be developed by utilizing community-scale tools on two dissimilar model communities that function within different redox environments, i.e. anaerobic and aerobic, to remediate TCE and dioxane, respectively. We hypothesize that important interspecies interactions and keystone functions that regulate multiple community behaviors will be identified by applying an integrated meta-omics based approach, which in turn will provide insights to facilitate engineering efficient bioremediation processes. DNA-based stable isotope probing will be used to distinguish and identify functional organisms and the important interdependent relationships within communities capable of biodegrading TCE or dioxane. Targeted metagenomic analyses will then be employed to reveal the metabolic and functional diversity of interdependent biodegrading organisms and their supporting or inhibiting partners in the communities. Comprehensive metatranscriptomic analyses based on mRNA-targeted microarrays will be employed to investigate the global gene expression in the communities under different environmental perturbations in order to reveal microbial behaviors in response to the changes. In order to design diagnostic tools that can be applied to query environmental samples at TCE and dioxane-contaminated sites, we will identify and validate quantitative biomarkers for key metabolic as well as interacting genes using quantitative expression analyses in conjunction with community metabolite-analyses. Finally, we will apply the diagnostic tools developed throughout the research to examine environmental samples to assess microbial behaviors and interactions in these samples in order to guide and optimize in situ bioremediation strategies.