CAREER: Harnessing horizontal gene transfer to engineer environmental microbiomes in situ

微生物群落是在自然和建筑环境中发现的微生物群落。微生物群对我们的生态系统和环境至关重要。它们推动全球生物地球化学循环，并可被利用来推动各种环境和可持续的工程过程，包括废水处理和资源回收、粮食生产和能源生产。这个职业项目将探索利用水平基因转移(HGT)回收废水资源的工程微生物群的开发和验证。这个职业项目的两个关键目标是：1)开发和展示用于工程废水微生物的新型HGT系统，以促进从有机废物中回收资源；2)评估和揭示控制拟议工程微生物的结构、功能和长期稳定性的环境和生态因素。这一项目的成功完成将使社会受益，因为它将产生新的基础知识，以促进环境微生物组工程，目的是开发更有效和可持续的废水处理和资源回收过程。还将通过教育和培训为社会带来更多好处，包括对一名研究生和一名本科生以及莱斯大学的高中STEM教师学员进行指导。水平基因转移(HGT)，即DNA在有机体之间的移动，是微生物群落功能和进化的核心。如果利用得当，HGT可用于设计微生物群，用于环境生物修复、微生物病原体的选择性灭活或从废水中回收有价值的化学品。然而，阻碍通过HGT成功和可重复地进行环境微生物群工程的关键知识差距仍然存在，包括如何最好地传递功能基因，如何以代谢方式改造不可培养的微生物，以及如何确定在HGT后促进基因稳定性和功能的环境条件。这个职业项目的首要目标是开发和验证利用HGT进行环境微生物工程的新颖和安全的策略。这项研究的具体目标是：(1)开发向环境微生物群落运送功能基因的供体和基于质粒的系统；(2)表征在微生物群落中控制HGT转化率、宿主范围和功能基因稳定性的环境和生态因素；以及(3)展示HGT对废水微生物组的原位编辑，以提高酸发酵反应器中有机废物的资源回收，目标是克服木质纤维生物转化的关键瓶颈。通过融合和整合合成生物学和环境工程，首席研究员希望开发和验证新的工具和战略，以促进可持续环境修复、废水处理和资源回收的工程微生物群的设计和控制。拟议的研究活动将与一项教育计划结合起来，该计划的重点是增加对合成生物学和微生物组工程中的伦理问题的认识，并修改环境工程/科学课程的伦理课程。该职业项目的教育和外展目标将通过(1)休斯敦高中STEM教师的教师研究经验(RET)；(2)共同开发高中和本科课程的生物伦理课程模块；以及(3)通过为休斯顿地区高中教师举办的研讨会并在网上公开提供，来传播教师培训模块。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。

Microbiomes are communities of microorganisms found in natural and built environments. Microbiomes are vital to our ecosystems and environment. They drive global biogeochemical cycles and can be harnessed to drive various environmental and sustainable engineering processes including wastewater treatment and resource recovery, food production, and energy generation. This CAREER project will explore the development and validation of engineered microbiomes for wastewater resource recovery using horizontal gene transfer (HGT). Two key goals of this CAREER project are to 1) develop and demonstrate novel HGT systems for engineering wastewater microbiomes to enhance resource recovery from organic wastes and 2) evaluate and unravel the environmental and ecological factors that control the structure, function, and long-term stability of the proposed engineered microbiomes. The successful completion of this project will benefit society through the generation of new fundamental knowledge to advance environmental microbiome engineering with the goal of developing more efficient and sustainable wastewater treatment and resource recovery processes. Additional benefits to society will be achieved through education and training including the mentoring of one graduate and one undergraduate student, and high-school STEM teacher trainees at Rice University.Horizontal gene transfer (HGT), the movement of DNA between organisms, is central to microbial community function and evolution. If harnessed properly, HGT could be used to engineer microbiomes for environmental bioremediation, the selective inactivation of microbial pathogens, or the recovery of valuable chemicals from wastewater. However, critical knowledge gaps remain that hinder the successful and reproducible engineering of environmental microbiomes via HGT, including how to best deliver functional genes, how to metabolically engineer unculturable microbes, and how to identify the environmental conditions that promote the stability and function of a gene after HGT. The overarching goal of this CAREER project is to develop and validate novel and safe strategies for harnessing HGT for environmental microbiome engineering. The specific objectives of the research are to: (1) develop donor and plasmid-based systems for delivering functional genes to environmental microbial communities; (2) characterize environmental and ecological factors that control HGT rates, host range and stability of functional genes delivered via HGT in a microbial community; and (3) demonstrate in situ editing of a wastewater microbiome by HGT to enhance resource recovery from organic wastes in an acid fermentation reactor with the goal of overcoming a critical bottleneck in lignocellulosic bioconversion. By converging and integrating synthetic biology and environmental engineering, the Principal Investigator hopes to develop and validate novel tools and strategies to advance the design and control of engineered microbiomes for sustainable environmental remediation, wastewater treatment, and resource recovery. The proposed research activities will be integrated with an education plan that focuses on increasing knowledge of ethical issues in synthetic biology and microbiome engineering and revamping ethics curriculum for environmental engineering/science courses. The educational and outreach goals of this CAREER project will be implemented through (1) a research experience for teachers (RET) for high school STEM teachers in Houston; (2) the co-development of curricular modules on bioethics for high school and undergraduate courses; and (3) the dissemination of the teacher training modules through a workshop for Houston-area high school teachers and by making them publicly available online.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.