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bioRxiv · 10.64898/2026.03.18.712767

Sentinel plants enable quantitative monitoring of bioavailable nitrate in soils and microbial environments

Li, E.·Berruto, C.·Oz, T.·Grillo, E.·Griffin, C.·Wang, Y.·Jones, J.·Demirer, G. S.
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Abstract

Microbial transformations of nitrogen in soils strongly influence plant nutrition and ecosystem function, yet these processes remain difficult to monitor. Existing approaches rely largely on destructive soil sampling and laboratory analysis, limiting the ability to track nitrate dynamics in situ. Here, we engineer "sentinel plants," genetically encoded plant biosensors that convert nitrate perception into a quantitative signal reporting plant-accessible nitrate. The sensor uses a synthetic nitrate-responsive promoter coupled to a ratiometric luciferase reporter, enabling high-dynamic-range measurements. Sentinel plants exhibit a dose-dependent, reversible nitrate response with high specificity over alternative nitrogen sources. In agricultural soils from multiple California field sites, sensor output closely tracked analytically measured nitrate concentrations and resolved nitrate amendments without destructive extraction. Beyond environmental sensing, sentinel plants enabled screening of nitrogen-fixing microbial communities and the detection of microbially generated nitrate in both liquid culture and soil systems. Using this platform, we identified a minimal three-member microbial consortium capable of converting atmospheric nitrogen into nitrate via sequential nitrogen fixation and nitrification. This consortium increased tissue nitrate accumulation and plant fresh weight, demonstrating that sentinel plants can both monitor nitrate availability and identify microbial communities that enhance plant growth. Significance StatementNitrogen availability in soils fluctuates across space and time, yet most measurements rely on extracting soil samples and analyzing them in the laboratory. Such measurements provide only snapshots of nitrogen status and do not necessarily reflect the nitrogen that plants themselves experience. Here, we engineer plants that act as living nitrate sensors by converting nitrate perception into a measurable optical signal. Because these sensors operate within intact plants, they report nitrate availability as integrated through plant uptake and physiology rather than through chemical extraction alone. Using this platform, we tracked nitrate levels in agricultural soils and identified a minimal microbial consortium capable of converting atmospheric nitrogen into plant-available nitrate. This plant-based sensing strategy enables direct monitoring of nitrogen dynamics in soils and microbial environments, providing a platform for identifying microbial communities that enhance nitrogen availability for crops.

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Li, E., Berruto, C., Oz, T., Grillo, E., Griffin, C., Wang, Y., Jones, J., Demirer, G. S.. 2026-03-23. Sentinel plants enable quantitative monitoring of bioavailable nitrate in soils and microbial environments. https://doi.org/10.64898/2026.03.18.712767

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