Harnessing Phage Therapy to Promote Sustainable Water Reclamation

Wastewater treatment protects public health, ecosystems, and economic prosperity by removing pollutants before water is released back into the environment. At the core of this process are complex microbial communities whose stability strongly affects energy use, treatment reliability, and infrastructure costs. However, engineers currently lack precise tools to control these microbial systems, relying instead on energy intensive operational adjustments such as aeration. This project addresses this challenge by developing new ways to harness bacteriophages or “phages”, which naturally infect and kill bacteria, as precision tools to stabilize wastewater treatment processes. By enabling phage-based control of problematic bacteria that cause sludge bulking or inefficient nitrogen removal, the research supports national priorities in efficient and robust water infrastructure, reduced energy consumption, and protection of waterways from nutrient pollution. The project advances science by transforming naturally occurring microbial diversity into programmable biological tools and contributes to advanced manufacturing by applying those tools to enable the provision of clean water, the recovery of nutrients from waste streams, and the generation of other value-added products. Additional benefits include training undergraduate and graduate students in synthetic biology, environmental engineering, and bioinformatics, thereby strengthening the workforce needed for the growing U.S. bioeconomy. The project will develop synthetic biology methods that allow bacteriophages to be identified, constructed, and activated directly from environmental DNA, bypassing traditional culture-based isolation. The research has three integrated objectives. First, the team will develop and validate methods to genetically manipulate and “reboot” bacteriophages that infect Gordonia, filamentous bacteria responsible for sludge bulking, and demonstrate phage-based control in laboratory-scale bioreactors. Second, the project will characterize phage-enriched metagenomes from wastewater treatment systems using short- and long-read sequencing, proximity ligation, and bioinformatic analyses to establish phage–host relationships, particularly for difficult-to-culture nitrite-oxidizing bacteria. Third, the researchers will assemble fully synthetic phage genomes from metagenomic DNA using advanced synthetic biology techniques, followed by rebooting these synthetic phages in microbial hosts or enrichment cultures. Together, these approaches advance fundamental understanding of phage ecology while introducing a new paradigm for biomanufacturing from environmental sequence data. The resulting methods and phage constructs will provide a scalable platform for precision microbial control in engineered systems, with broad implications for advanced manufacturing of next-generation biological products. 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. NSF Award ID: 2532371 | Program: 01002627DB NSF RESEARCH & RELATED ACTIVIT | Principal Investigator: Erica Hartmann | Institution: Northwestern University at Chicago, EVANSTON, IL | Award Amount: $969,705 View on NSF Award Search: https://www.nsf.gov/awardsearch/show-award/?AWD_ID=2532371 View on Research.gov: https://www.research.gov/awardapi-service/v1/awards/2532371.html