MIT Bacteria Could Help Monitor Soil Health From the Air

Genetically engineered bacteria could monitor soil health

Assessing soil health may soon be as straightforward as consulting local bacteria. In response to prompts such as nutrients or contaminants, they could provide answers through differently coloured glows that drones or satellites can detect.

Bacteria are already commonly used as sensors because they can be readily modified to create molecules under particular conditions. However, observing their response generally takes both a microscope and time.

Researchers at MIT may have found a faster approach. They have developed a sensing system in which bacteria emit light at specific wavelengths after identifying a target, potentially allowing results to be gathered by drone photography in 30 seconds.

The system appears adaptable enough to identify almost any molecule, chemical or bacterium, whether beneficial or harmful. With two distinct bacterial types included, it could theoretically cause fields to glow red when pollution is present and green where nutrient levels are high.

"So, it might respond to metals or radiation or toxins in the soil, or nutrients in the soil, or whatever it is you want it to respond to," says Christopher Voigt, biological engineer at MIT.

"Then the output of that would be the production of this molecule that can then be sensed from far away."

Hyperspectral cameras detect bacterial signals

Using specialised cameras fitted to drones or buildings, the researchers scanned soil samples inhabited by genetically engineered bacteria. Samples containing the target stood out clearly, producing a signal up to 12 times stronger than control samples at distances of up to 90 metres.

The resulting glow would not be apparent to the unaided eye, as the system relies on hyperspectral cameras. Such devices identify hundreds of visible and infrared wavelengths, then measure the amount of each wavelength in every image pixel. This lets them spot very small changes in colour that other instruments-and certainly human vision-would be unable to perceive.

The researchers modified bacteria to make ‘reporter’ molecules detectable with hyperspectral cameras. First, they carried out quantum-mechanical simulations involving 20,170 metabolites to identify the most appropriate options.

"The best hyperspectral reporters (HSRs) are those whose spectra are the most unique and require the smallest number of enzymes to produce," the authors write in their paper describing the work.

They ultimately selected two encouraging candidates: biliverdin, a pigment that can give bruises a greenish hue, and a bacteriochlorophyll used by microbes in photosynthesis. The team engineered the enzymes needed to make biliverdin into the soil bacterium Pseudomonas putida. Meanwhile, the aquatic microbe Rubrivivax gelatinosus was modified to produce bacteriochlorophyll.

Soil monitoring with microbial sentinels

These outputs were connected to sensor circuits within the bacteria’s genomes, which in this experiment were designed to identify other nearby bacteria. In principle, though, the activating trigger could be nearly anything, including chemicals found in contaminated soil.

"The nice thing about this technology is that you can plug and play whichever sensor you want," says Yonatan Chemla, environmental microbiome engineer at MIT. "There is no reason that any sensor would not be compatible with this technology."

To evaluate the concept, the team put soil or sand samples into boxes exposed to the air, with some boxes containing buried discs of the target. Hyperspectral cameras positioned on drones or rooftops captured images across hundreds or thousands of square metres in less than 30 seconds.

As expected, the boxes holding the targets glowed intensely, creating a clear contrast with the control samples.

The researchers report funding from the US Department of Defense and Israel’s Ministry of Defense.

"We've been very busy in the past three years working to understand what are the regulatory landscapes and what are the safety concerns, what are the risks, what are the benefits of this kind of technology?" Chemla says.

Although the safety issues and regulations surrounding these systems remain to be resolved, the researchers believe the technique has potential for continuous environmental monitoring.

"Microbial sentinels have advantages as in-field sensors. They can be spread over wide areas and respond to unique signals and are persistent without the need for electrical power," the authors write.

"Further, HSRs can be imaged during the daytime under ambient conditions and identified in spectrally complex environments, including open ground, greenery, and urban structures."

The research was published in the journal Nature Biotechnology.