Photo credit: phys.org
Bacteria can be modified to detect various substances, including pollutants and nutrients in the soil. Traditionally, the detection of these signals has required the use of microscopes or advanced laboratory tools, which restricts their practical application on a larger scale.
Researchers from MIT have pioneered a novel technique that enables bacterial cells to produce molecules resulting in distinct color patterns, allowing these signals to be discerned from distances of up to 90 meters. This advancement could pave the way for the creation of bacterial sensors that monitor environmental conditions, which could be particularly useful in agriculture and can be accessed via drones or satellites.
According to Christopher Voigt, head of MIT’s Department of Biological Engineering and senior author of the study, “It’s a new way of getting information out of the cell. If you’re standing next to it, you can’t see anything by eye, but from hundreds of meters away, using specific cameras, you can get the information when it turns on.“
The research, detailed in a paper published in Nature Biotechnology, illustrates that the team successfully engineered two types of bacteria to emit unique wavelengths of light across visible and infrared spectrums, making them detectable by hyperspectral cameras.
The genetically engineered reporting molecules are linked to circuits that can sense nearby bacteria. However, the researchers emphasize that this approach is versatile; it can easily integrate with existing sensors used for detecting substances like arsenic or other environmental contaminants. Lead author Yonatan Chemla stated, “The nice thing about this technology is that you can plug and play whichever sensor you want.“
The study’s lead authors also included Itai Levin, Ph.D., alongside former undergraduate students Yueyang Fan and Anna Johnson, as well as Connor Coley, an associate professor at MIT.
Hyperspectral Imaging
Current methods for engineering bacterial cells to sense specific chemicals typically involve connecting the molecular detection to outputs like green fluorescent protein (GFP). While effective in laboratory settings, these conventional sensors are not capable of long-distance measurements.
To enable remote sensing, the MIT team focused on engineering cells that produce hyperspectral reporter molecules, detectable by hyperspectral cameras. These specialized cameras, developed in the 1970s, analyze the quantity of various light wavelengths in each pixel, thereby providing detailed information beyond simple color representation.
Presently, hyperspectral cameras are employed in several applications, such as identifying radiation presence. They have been instrumental in post-Chernobyl studies to observe subtle color changes in plant chlorophyll caused by radioactive metals. Additionally, these cameras are used to detect signs of malnutrition or pathogen invasion in plants.
This inspired the MIT researchers to investigate whether they could program bacterial cells to generate hyperspectral reporters when exposed to target molecules.
For these reporters to be effective, they should exhibit a diverse spectral signature across multiple light wavelengths, which simplifies the detection process.
The researchers conducted quantum calculations to forecast the hyperspectral signatures of approximately 20,000 naturally occurring cellular molecules, which helped them identify those with the most distinctive light emission patterns. A crucial consideration in their development involved the number of enzymes required to synthesize the reporter molecules— a variable that differs between bacterial types.
Voigt noted, “The ideal molecule is one that’s really different from everything else, making it detectable, and requires the fewest number of enzymes to produce it in the cell.” In their study, they identified two optimally suited molecules for two distinct bacteria. For a soil bacterium, Pseudomonas putida, they utilized biliverdin—a pigment formed from heme breakdown. For the aquatic bacterium Rubrivivax gelatinosus, they selected a type of bacteriochlorophyll.
After this identification, the researchers added the necessary enzymes for these reporters into the bacterial cells and connected them to genetically engineered sensor circuits.
Long-Distance Sensing
The study linked the hyperspectral reporters to circuits capable of quorum sensing, which helps cells identify other nearby bacteria. They have since demonstrated that these reporting molecules can also connect to sensors detecting various chemicals, including arsenic.
In their experimental setups, the researchers contained the sensors in boxes placed in diverse environments such as fields and rooftops. The cells emitted signals detectable by drones equipped with hyperspectral cameras. These cameras take approximately 20 to 30 seconds to survey their field of view, with algorithms subsequently analyzing the captured signals to ascertain the presence of hyperspectral reporters.
While initial tests reported imaging distances of up to 90 meters, the team is actively working to expand these capabilities.
The researchers foresee applications of this technology in agricultural settings, specifically for monitoring nitrogen and nutrient concentrations in soil. They also envision its potential use in detecting landmines. However, before any deployment, the sensors must gain approval from regulatory bodies like the U.S. Environmental Protection Agency and the U.S. Department of Agriculture for agricultural applications. Voigt and Chemla have been collaborating closely with these agencies and various stakeholders to address necessary regulatory questions regarding the technology’s safety and efficacy.
Chemla commented on the ongoing efforts, stating, “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?“
More information: Hyperspectral reporters for long-distance and wide-area detection of gene expression in living bacteria, Nature Biotechnology (2025). DOI: 10.1038/s41587-025-02622-y
Source
phys.org