Discovery at Depth: A Whole Cell Bioreporter for Subterranean Detection of Chemical Agents

Despite advances in synthetic biology, a robust bioreporter system for subterranean detection (≥ 1 meter) of buried weapons signatures or natural resources has not been produced or deployed at scale in a soil-based matrix. To meet these challenges, we developed the Spore Amplified Detection (SPADe) system as part of a DARPA-funded study. This living reporter system utilizes engineered Bacillus subtilis, a native soil bacterium capable of sporulating, in combination with modular chemical agent sensing of subsurface signatures to produce volatile organic compounds (VOCs) that are compatible with standoff detection. Key aspects were characterized, including chassis dissemination in soil up to a meter deep, chemical signature detection and VOC production in a variety of matrices, and standoff detection by hyperspectral imaging. Utilizing vegetative and spore forms, we demonstrated chassis dissemination through a soil column at 0.5- and 1.0-meter depths. IPTG was initially leveraged as a chemical surrogate, due to the robust nature of induction. The engineered chassis produced VOCs ethylene and methyl bromide in response to IPTG in liquid culture, detected by GC/MS, and within a soil profile, producing detectable ethylene out to 10 days. Focusing on more realistic chemical weapon signatures, the chassis was engineered for reactive chlorine species detection. Similar testing in liquid medium and soil was performed, with successful signature detection and ethylene production. To validate standoff detection compatibility, bacterially produced ethylene, from both liquid and soil matrices, was collected in a meter-long chamber and measured at a 10-meter distance using the Telops Hyper-Cam LW hyperspectral camera. Ethylene was detectable from both scenarios, down to ~15 ppmv. This works supports SPADe as a modular system for detection of chemical targets within complicated environments and highlights the potential for this system to be tailored to a range of soil-based and subterranean applications, such as for defense, remediation, or prospecting.