Anaerobic consortia and enzymes for biotransformation of aromatic compounds

由于研究复杂微生物生态系统的分析工具和技术的最新进展，这是基础和应用环境微生物学和生物技术的非常激动人心的时期。这些工具包括定量DNA和RNA提取和扩增工具，经济实惠的大规模DNA测序，以及适用于环境样品的蛋白质和蛋白质组学分析。这些技术使探索和理解微生物种群在复杂的“难以研究的”全球重要生态系统中生长和相互作用的许多方式成为可能，例如微生物群落在土壤、废水处理系统和人体肠道中循环养分。******特别地，这项研究集中在厌氧环境中发生的过程，这些环境存在于沼泽、沉积物、地下深处、温泉和大多数生物的肠道内。这种厌氧微生物生态系统也是厌氧消化器和人工湿地等工程废物处理系统以及工业或食品发酵和生物能源过程的关键。有机物的分解和厌氧环境中矿物质的循环依赖于复杂的微生物群落，这违背了传统的还原论方法。***本提案的重点是苯的厌氧生物转化，因为它在地球上丰富。事实上，苯环结构存在于包括木质素、蛋白质和植物代谢物在内的常见分子中，并且构成了原油中高达30%的化石碳。苯也是一种有价值的工业化学品和有毒的地下水污染物。在这个项目中，我们建议使用灵敏质谱法来最终弄清楚酶是如何在缺氧的情况下破坏苯环的。这是多年来的一个追求，但新工具的出现使我们比以往任何时候都更接近这个目标。苯及其相关化合物是最严重的环境破坏者。这项工作的主要目标是消除主要的降解瓶颈，开发有用的工具和知识，以改善生物修复和扩大处理污染地点的策略库。********

These are very exciting times in fundamental and applied environmental microbiology and biotechnology owing to recent advances in analytical tools and techniques to interrogate complex microbial ecosystems. These tools include quantitative DNA and RNA extraction and amplification tools, affordable large-scale DNA sequencing, and protein and proteomics analyses applicable to environmental samples. These techniques are enabling novel approaches to explore and understand the many ways microbial populations grow and interact in complex "difficult-to-study" ecosystems of global importance, such as microbial communities cycling nutrients in soils, in wastewater treatment systems, and in the human gut.******In particular, this research focuses on processes that occur in anaerobic environments that exist in swamps, sediments, the deep subsurface, hot springs, and inside the guts of most creatures. Such anaerobic microbial ecosystems are also key in engineered waste treatment systems like anaerobic digestors and constructed wetlands and in industrial or food fermentation and bioenergy processes. The decomposition of organic matter and the cycling of minerals in anaerobic environments rely on complex microbial communities that have defied traditional reductionist approaches.  ***The focus of this proposal is on the anaerobic biotransformation of benzene, because of its abundance on the planet. Indeed the benzene ring structure is found in common molecules including lignin, proteins, and plant metabolites, and makes up to 30% of the fossil carbon in crude oil. Benzene is also a valuable industrial chemical and a toxic groundwater contaminant.  In this project, we propose to use sensitive mass spectrometry to finally figure out how enzymes break the benzene ring in the absence of oxygen.  This has been a quest for many years, but the advent of new tools brings us closer to this goal than ever before.   Benzene and related compounds are some of our worst environmental offenders.  The major goal of this work is to unblock major degradation bottlenecks and to develop useful tools and knowledge to improve bioremediation and expand the arsenal of strategies to deal with contaminated sites.********