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元组学。三氯乙烯a 常见的氯化溶剂和1，4-二氧六环（二氧六环），一种溶剂稳定剂，都是地下水中常见的 污染物在超级基金网站。虽然微生物降解反应可以有效地将这些 污染物，缺乏对物种间复杂性的整体和生态相关的理解， 地下微生物群落阻碍了应用强大和有效的原位生物修复， 这些化合物。本研究的总体目标是确定和检查社区一级的代谢 形成生物修复群落的生物降解能力的相互作用。根本 从系统微生物学的角度理解微生物群落将通过以下方式发展： 利用社区规模的工具，在两个不同的模型社区，在不同的氧化还原功能， 环境中，即厌氧和好氧，以修复三氯乙烯和二氧六环，分别。我们假设 重要的物种间相互作用和调节多种群落行为的关键功能将是 通过应用基于元组学的综合方法来确定，这反过来又将为以下方面提供见解： 促进设计有效的生物修复过程。基于DNA的稳定同位素探测将用于 区分和识别功能性生物体及其内部重要的相互依存关系 能够生物降解三氯乙烯或二氧六环的社区。目标宏基因组分析将在 用于揭示相互依存的生物降解有机体的代谢和功能多样性， 他们在社区中的支持或抑制伙伴。综合元转录组学分析 基于mRNA靶向的微阵列将被用来调查全球基因表达在 不同环境扰动下的微生物群落，以揭示微生物的响应行为 改变为了设计可应用于查询环境样本的诊断工具， TCE和二氧杂环己烷污染的场地，我们将确定和验证关键代谢的定量生物标志物， 以及使用定量表达分析结合社区 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， 检查环境样品，以评估这些样品中的微生物行为和相互作用， 指导和优化原位生物修复策略。

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.