Beneath every crop lies a dynamic and invisible ecosystem that plays a vital role in agriculture: the rhizosphere. Microbial communities in this zone drive nutrient cycling, influence greenhouse gas emissions and impact plant productivity. Yet, despite their central role in ecosystem health, we lack the tools to monitor their activity in real time and at scale.
As a FFAR Fellow at the California Institute of Technology, I am developing a sentinel plant platform to serve as a living biosensor to enable aboveground detection of microbial gene activity in the soil. The vision is to create a system that functions like a “molecular window” into the rhizosphere – similar to how Green Fluorescent Protein (GFP) revolutionized cellular biology by allowing scientists to track gene expression and protein activity inside the cell.
The platform integrates two engineered modules. The first module focuses on rhizosphere microbes, specifically Pseudomonas putida which can colonize the plant roots. We are engineering soil microbes to convert internal gene expression events, such as the activation of nitrogen fixation or denitrification pathways, into chemical signals that can be recognized by plants. This work is conducted in collaboration with the Resnick Sustainability Institute. The second module is the sentinel plant itself, designed with synthetic biosensor circuits that detect the microbial signals and report them through visible outputs such as fluorescence or pigmentation. Using a design-build-test-learn framework rooted in synthetic biology, we iteratively optimize these circuits to clearly detect weak signals while minimizing background noise. Together, the microbe and plant work like a biological flare system, sending signals from the soil and lighting up the plant when something important is happening underground. This platform will allow us to probe how microbial activity shapes soil health and nutrient dynamics, with implications for greenhouse gas mitigation and regenerative agriculture.
Incorporating this platform into research and agricultural settings can unlock a new approach for sustainability interventions, where biology itself becomes the tool. For example, farmers could receive early warnings when the sentinel plants sense nutrient deficiencies, inefficient nitrogen cycling or soil degradation. Researchers could use the system to better study how microbiomes respond to changes in climate, fertilizer inputs or plant genotype without disturbing the rhizosphere. Our long-term goal is to make this technology field-deployable, cost-effective and compatible with a wide range of crops and soil types.
What excites me most is the potential of this platform to serve as a diagnostic tool for farmers and scientists, to help make hidden soil processes more quantifiable and actionable. By enabling minimally invasive, field-deployable monitoring, we can begin to build the comprehensive understanding necessary to sustain soil function and improve agricultural resilience.