Anaerobic consortia and enzymes for biotransformation of aromatic compounds

这是基础和应用环境微生物学和生物技术领域非常令人振奋的时期，这是因为最近在审问复杂微生物生态系统的分析工具和技术方面取得的进展。这些工具包括定量DNA和RNA提取和放大工具、负担得起的大规模DNA测序以及适用于环境样本的蛋白质和蛋白质组学分析。这些技术使新的方法能够探索和理解微生物种群在具有全球重要性的复杂的“难以研究”的生态系统中生长和相互作用的多种方式，例如土壤、废水处理系统和人类肠道中循环营养的微生物群落。尤其是，这项研究侧重于沼泽、沉积物、深层地下、温泉和大多数生物肠道内的厌氧环境中发生的过程。这种厌氧微生物生态系统在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中也是关键。有机物的分解和矿物在厌氧环境中的循环依赖于复杂的微生物群落，这些微生物群落挑战了传统的还原方法。这项提议的重点是苯的厌氧生物转化，因为苯在地球上丰富。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，占原油中化石碳的30%。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仪来最终弄清楚酶是如何在没有氧气的情况下打破苯环的。这是一个多年来一直在探索的问题，但新工具的出现让我们比以往任何时候都更接近这个目标。苯和相关化合物是我们最严重的环境违规者之一。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来改进生物修复，并扩大处理受污染地点的战略武器库。

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.********