The flow of water is essential to life on Earth. It distributes nutrients, creates and maintains ecosystem biodiversity, enables agriculture through irrigation, removes waste products, regulates temperature, supports the planet’s water cycle, and provides a source of clean energy. However, water flow can have profound negative consequences, which are often exacerbated by human interaction (Plessis, 2022). The same flow that can replenish a drying lake or provide running water to a household can also contaminate an ecosystem with pollutants, shuttle pathogenic bacteria through a showerhead, erode shorelines, and degrade habitats.
Existing mitigation strategies for problems associated with water flow often rely on harmful chemicals or cause unintended damage to surrounding ecosystems (Kumar, 2022). While synthetic biology holds great promise for addressing these challenges—and has shown success in controlled laboratory settings—its efficacy in dynamic, real-world environments, particularly those involving flowing water, remains limited.
We aim to make a foundational advance by enabling synthetic biology solutions to function reliably in dynamic, flowing-water environments—the very settings where these interventions are most urgently needed. Currently, there is a significant lack in our understanding of how engineered chassis function in natural aquatic ecosystems in which they are continually subjected to an array of physical forces as well as ever-changing environmental conditions due to the complex fluid dynamics of water flow.
We plan to address this gap in knowledge through a combination of mathematical modeling and genomic and transcriptomic analyses, specifically by (1) identifying factors that adversely affect the performance of circuits under these conditions and (2) potentially engineering solutions that mitigate these adverse effects. To do so we plan to construct microcosms that mimic and serve as accurate proxies for real-world environments.
We will focus on four different examples of both local and global problems caused by adverse effects of runoff and water flow, spanning the various water systems.
Beginning with the largest water system, oceans face persistent issues with metal corrosion which has become a critical global concern. Chemical-based anti-corrosion treatments often harm marine ecosystems, and corrosion-related infrastructure failures lead to substantial economic losses (Furdek et al., 2012). To address this, we propose promoting the formation of thicker and denser single-species biofilms to protect metal surface (Gao et al., 2021) by overexpressing two regulatory pathways in Bacillus subtilis, comparing their effect on biofilm growth and persistence, and testing their ability to resist corrosion on metal. We are testing the SinI/SinR regulatory pathway, including downstream components as TasA protein and the TapA-SipW-TasA operon, as well as the expression of BslA protein to determine their effects on biofilm thickness and strength.
In freshwater systems, cyanobacterial harmful algal blooms (cyanoHABs), exacerbated by nutrient runoff, threaten biodiversity and release toxins hazardous to wildlife and humans (Bhatt et al., 2023). We aim to develop engineered cyanophages as a sustainable strategy for CyanoHAB mitigation by using Microcystis aeruginosa to screen for novel cyanophages that could be engineered to treat HABs after formation. We plan to engineer these phages to have broader host ranges, shorter incubation periods, increased lytic efficiency, and higher environmental resilience. In addition to treatment, we are addressing prevention by designing a toehold riboswitch-based biosensor capable of detecting mcyE mRNA, a marker associated with microcystin-producing Microcystis strains (Eldridge & Wood, 2019). This biosensor will be integrated into a freeze-dried, cell-free system for potential field-deployable early detection.
At the household level, water distribution introduces new challenges—namely, biofilm formation in plumbing systems Mycobacterium smegmatis, in particular, forms robust, disinfectant-resistant biofilms that contribute to pulmonary infections (Dowdell et al., 2019). To mitigate this, we propose engineering bacteriophages to deliver a gene encoding a functional cellulase into M. smegmatis after the formation of a biofilm. The enzyme will degrade the cellulose-rich extracellular matrix, enhancing phage access, lysing the bacteria in the process for more efficient biofilm disruption (Zhang et al., 2024).
Hydraulic erosion, prevalent in Virginia, contributes to sediment buildup and nutrient runoff, which harm aquatic ecosystems and stimulate further HABs. This is especially problematic in sloped areas subject to heavy runoff (Feng et al., 2024). To combat this, we plan to engineer Nostoc, a filamentous heterocyst cyanobacterium, to overexpress its endogenous ExoD gene, which encodes an integral membrane protein involved in exopolysaccharide secretion (Raghavan et al., 2023). Enhanced polysaccharide production will aid soil stabilization and help prevent erosion.
We will use differential equation-based modeling to simulate interactions under dynamic, non-laboratory conditions to predict the feasibility of our constructs. Additionally, we plan to develop a machine learning model to assist future researchers in selecting suitable microbial hosts for specific aquatic environments. This model will predict host compatibility based on environmental factors such as pH, temperature, and nutrient availability, streamlining the application of synthetic biology to bioremediation efforts.
Our project is inspired by local problems that affect our university and geographic region. The surrounding Virginia coastal systems—which include the eastern shore, various wetlands, tidal marshes, and the Chesapeake Bay—equip us with first hand experience of the need for advancement in the methods and tools used to handle contaminated water flow due to recurrent issues. For example, there are water quality crises in Richmond and the Hampton Roads area, frequent algal blooms across Virginia, and excessive coastline erosion in the broader Chesapeake Bay Watershed.
William & Mary has officially declared 2025 to be the Year of the Environment and plans to begin sustainability initiatives both locally and outside of the William & Mary community. Furthermore, William & Mary has chosen water as a key area of focus—finding ways to improve and ensure the resilience of water systems–an endeavour that shaped the trajectory of our project.