Hyperspectral reporters for long-distance and wide-area detection of gene expression in living bacteria

Abstract

Genetically encoded reporters are suitable for short-distance imaging in the laboratory but not for scanning wide outdoor areas from a distance. Here we introduce hyperspectral reporters (HSRs) designed for hyperspectral imaging cameras that are commonly mounted on unmanned aerial vehicles and satellites. HSR genes encode enzymes that produce a molecule with a unique absorption signature that can be reliably distinguished in hyperspectral images. Quantum mechanical simulations of 20,170 metabolites identified candidate HSRs, leading to the selection of biliverdin IXα and bacteriochlorophyll a for their distinct absorption spectra and biosynthetic feasibility. These genes were integrated into chemical sensor circuits in soil (Pseudomonas putida) and aquatic (Rubrivivax gelatinosus) bacteria. The bacteria were detectable outdoors under ambient light from up to 90 m in a single 4,000-m² hyperspectral image taken using fixed and unmanned aerial vehicle-mounted cameras. The dose–response functions of the chemical sensors were measured remotely. HSRs enable large-scale studies and applications in ecology, agriculture, environmental monitoring, forensics and defense.