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

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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.