Metagenomic-enabled rapid development of multiple biomarkers for trace organic contaminant biodegradation through Functional gene Amplicon Sequencing tests (FASt)

微量有机污染物(Torc)在美国的水系统中广泛存在。其中最常见的是个人护理产品、抗生素、阻燃剂、杀虫剂和除草剂。毒理学研究表明，长期接触许多Torcts可能会导致癌症，并对人类胎儿发育产生负面影响。在传统的污水处理厂中，TORCs很难去除，导致在接收水中广泛扩散。生物处理使用降解Torcts的细菌，是一项很有前途的技术，可以在现有的处理厂内实施，以去除Torcts并防止其释放。然而，目前还没有工具可以监测这些能够降解Torcs的特定细菌。该项目的目标是满足对下一代监测工具的迫切需求，以验证和优化生物废水处理系统的性能。为了实现这一目标，研究人员将开发FAST(功能基因扩增序列测试)，这是一种下一代基因测序技术，用于识别仅在Torc降解菌中发现的特定“功能基因”。该项目的成功完成将通过开发新的知识和工具来监测和优化废水处理系统中Torcs的去除效率，从而造福社会。将通过教育、研究培训以及通过面向未来教师的研究体验计划向教师推广，进一步造福社会。全国几乎所有的废水、雨水和地表水系统都含有一定水平的微量有机污染物，如个人护理产品、抗生素、杀虫剂和除草剂。解决Torc污染的一个有希望的解决方案是通过改造传统的市政污水处理设施，采用生物处理系统来去除Torc。然而，采用这项技术的进展缓慢，因为目前的方法通常使用“黑箱”方法来建立和管理TORC处理反应器微生物群。这是由于缺乏能够直接探测TORC生物降解的遗传潜力和活性的生物标记物造成的瓶颈。这个项目的目标是通过开发一套生物标志物来解决这一瓶颈，该生物标记物使用基于功能基因扩增序列测试(FAST)的新方法来对Torc进行好氧生物降解。该项目的一个关键新特点是实现了一种名为rhAmp聚合酶链式反应(RhAmp PCR)的功能性基因扩增片段生成方法，该方法可以同时扩增数百个潜在的生物标志物基因。实现这一目标的具体研究目标是：1)使用FAST识别用于Torc生物降解的功能基因生物标记物；2)利用新陈代谢组学验证新的生物标记物；3)将项目结果转化为现场可部署的分析。该项目的成功完成将改变我们通过开发基于生物标记物的新工具来快速监测和优化废水处理系统中TORC降解微生物性能的能力。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

Trace organic contaminants (TOrCs) are widespread in US water systems. Among the most prevalent TOrCs are personal care products, antibiotics, flame-retardants, pesticides, and herbicides. Toxicological studies suggest that chronic exposure to many TOrCs may cause cancer and negatively affect human fetal development. TOrCs are difficult to remove in conventional wastewater treatment plants, resulting in widespread dispersal in receiving waters. Biological treatment, which uses bacteria that degrade TOrCs, is a promising technology that could be implemented within existing treatment plants to remove TOrCs and prevent their release. However, no tools are currently available to monitor these specific bacteria capable of degrading TOrCs. The goal of this project is to address the critical need for next-generation monitoring tools to validate and optimize the performance of biological wastewater treatment systems. To achieve this goal, researchers will develop FASt (Functional gene Amplicon Sequencing tests), a next-generation gene sequencing technology to identify specific “functional genes” found only in TOrC degrading bacteria. Successful completion of this project will benefit society through the development of new knowledge and tools to monitor and optimize the removal efficiency of TOrCs in wastewater treatment systems. Further benefits to society will be achieved through education, research training, and outreach to teachers through a Research Experience for Future Teachers program.Nearly all wastewater, storm water, and surface water systems in the Nation have some levels of trace organic contaminants (TOrCs) like personal care products, antibiotics, pesticides, and herbicides. One promising solution for tackling TOrC pollution is through modification of conventional municipal wastewater treatment facilities to employ biological treatment systems to remove TOrCs. However, progress towards employing this technology has been slow as current approaches often use a “black box” approach to establish and manage TOrC treatment reactor microbiomes. This is due to the bottleneck created by the lack of biomarkers that can directly probe genetic potential and activity for TOrC biodegradation. The goal of this project is to address this bottleneck by developing a suite of biomarkers for aerobic TOrC biodegradation using a new approach based on Functional gene Amplicon Sequencing tests (FASt). A key novel feature of this project is the implementation of a functional gene amplicon generation method known as rhAmp polymerase chain reaction (rhAmp PCR), which can amplify hundreds of potential biomarker genes simultaneously. Specific research objectives to achieve this goal are to 1) identify functional gene biomarkers for TOrC biodegradation using FASt; 2) validate the new biomarkers using metabolomics; and 3) translate project findings into field-deployable assays. Successful completion of this project will transform our ability to rapidly monitor and optimize the performance of TOrC-degrading microorganisms in wastewater treatment systems through the development of new biomarker-based tools.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.