Molecular Insight into Polyaromatic Toxicant Degradation by Microbial Communities

微生物群落对多环芳烃有毒物质降解的分子洞察

基本信息

批准号：
8055596
负责人：
JAMES M TIEDJE
金额：
$ 43.56万
依托单位：
MICHIGAN STATE UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2010
资助国家：
美国
起止时间：
2010-04-01 至 2013-03-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/8055596
关键词：
Academy Address Aerobic American Aromatic Hydrocarbons Aromatic Polycyclic Hydrocarbons Biochemical Pathway Biodegradation Bioremediations Burkholderia Cataloging Catalogs Categories Characteristics Chemicals Cloning Communities Complement DNA Dependence Diagnostic Dioxins Drug Metabolic Detoxication Ecology Environment Environmental Microbiology Enzymes Equipment and supply inventories Evolution Fingerprint Gene Family Genes Genetic Variation Genomics Goals Intervention Knowledge Libraries Measures Metabolic Metagenomics Methods Michigan Microarray Analysis Microbiology Modeling Molecular Molecular Analysis Molecular Biology Monitor Nature Operon Organism Oxygenases Pathway interactions Physiology Polychlorinated Biphenyls Population Recovery Reporting Sampling Scientist Screening procedure Site Soil Stress Superfund System Systems Biology Techniques Technology Time Toxicogenomics Universities Ursidae Family base dechlorination dibenzofuran genome sequencing high throughput screening insight interest knowledge base metabolic abnormality assessment microbial microbial community molecular marker pollutant remediation research study stable isotope superfund chemical tool toxicant

项目摘要

The microbial world is diverse owing to its 3.7 billion years of evolution, which provides for both the opportunity of undiscovered metabolic capacity, including that for pollutant degradation, and the challenge of detecting and recovering this activity. It is well known that more than 99% of the microbial world has not been cultured and hence remains undiscovered. We propose to explore and recover genes for two key biodegradative steps in the detoxification of chlorinated polyaromatic compounds from the DNA of this uncultured microbial diversity, and then to use the molecular markers from this study to aid in site assessment and quantitative predictions of biodegradation at contaminated sites. We are targeting the reductive dehalogenases and the aromatic oxygenases as the key functions to recover since they are most often the rate limiting steps in the degradation of the polychlorinated dioxins and dibenzofurans, PCBs and polynuclear aromatic hydrocarbons (PAHs), the Superfund chemicals of focus in our study. Our specific aims are to: (1) explore and recover nature's catalytic diversity with the goal of developing a comprehensive profile of microbial metabolic capabilities for these polyaromatic compounds, (2) use the genome sequence information of Burkholderia xenovorans LB400, the most effective PCB degrader, to study the metabolic features important to the degradation of these chemicals and (3), develop quantitative diagnostic tools based on Bayesian probabilistic networks to predict biodegradation at contaminated sites. We propose to use enrichments to help identify the functionally active populations and hence genes, to use stable isotope probing to recover DNA from the active degrading populations, to use metagenomic libraries to recover the full genes and operons, and to use high throughput PCR screening for identifying clones with the targeted gene families. This project combines the expertise of the Rutgers University scientists in aromatic oxygenases and high throughput screening and metagenomics with the expertise at Michigan State University in reductive dechlorination and genomics and microarray technology.

微生物世界经过 37 亿年的进化而呈现多样性，这为微生物世界提供了多样性未被发现的代谢能力的机会，包括污染物降解的能力，以及检测并恢复此活动。众所周知，99%以上的微生物世界还没有已被培养，因此仍未被发现。我们建议探索和恢复两个关键基因从 DNA 中解毒氯化多芳香族化合物的生物降解步骤这种未培养的微生物多样性，然后使用本研究中的分子标记来帮助污染场地生物降解的现场评估和定量预测。我们是将还原性脱卤酶和芳香加氧酶作为恢复的关键功能它们通常是多氯二恶英降解的限速步骤，二苯并呋喃、多氯联苯和多环芳烃 (PAH) 是超级基金重点关注的化学品我们的研究。我们的具体目标是：（1）探索和恢复自然的催化多样性，目标是开发这些多芳香族化合物的微生物代谢能力的综合概况， (2)利用异源伯克霍尔德氏菌LB400的基因组序列信息，最有效的PCB 降解器，研究对这些化学物质降解很重要的代谢特征，并且（3）开发基于贝叶斯概率网络的定量诊断工具，用于预测生物降解受污染的地点。我们建议使用富集来帮助识别功能活跃的人群和因此基因，使用稳定同位素探测从活跃的降解群体中回收 DNA，使用宏基因组文库可恢复完整的基因和操纵子，并使用高通量 PCR 筛选识别具有目标基因家族的克隆。该项目结合了罗格斯大学的专业知识芳香加氧酶、高通量筛选和宏基因组学方面的大学科学家密歇根州立大学在还原脱氯、基因组学和微阵列技术方面拥有专业知识。