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Scientists have made significant strides in engineering bacteria to act as sensors for various environmental molecules, including pollutants and soil nutrients. Traditionally, detecting these signals requires sophisticated lab equipment or microscopy, which limits their practical application in larger settings.
Recently, engineers from MIT introduced a novel technique that enables the bacteria to emit distinct colors in response to specific stimuli. This innovation allows for the detection of bacterial signals from distances of up to 90 meters. The implications of this research are extensive, paving the way for bacterial sensors that could be monitored remotely via drones or satellites.
“This represents a significant advancement in extracting information from cells. While it’s not visible to the naked eye when standing nearby, specialized cameras can capture the information from hundreds of meters away once activated,” explains Christopher Voigt, head of MIT’s Department of Biological Engineering and senior author of the study.
In research published in Nature Biotechnology, the team demonstrated how they engineered two distinct bacterial species to generate molecules that emit specific light wavelengths across both visible and infrared spectra, detectable using hyperspectral cameras. These reporter molecules were embedded in genetic circuits that sense surrounding bacteria, but they could also be merged with existing sensors designed for substances like arsenic and other contaminants, the researchers noted.
“The versatility of this technology is remarkable; any sensor can be integrated with it,” stated Yonatan Chemla, an MIT postdoctoral researcher and co-lead author of the paper. “There is no inherent limitation to compatibility with this approach.”
Itai Levin, a PhD candidate, also contributed as a lead author. Other contributors included former undergraduate students Yueyang Fan and Anna Johnson, along with Connor Coley, an associate professor at MIT.
Hyperspectral Imaging
Multiple techniques exist for modifying bacterial cells to detect specific chemicals. Often, these approaches link the detection of a molecule to the expression of a reporter such as green fluorescent protein (GFP). While effective in laboratory settings, these sensors lack the capacity for long-distance measurement.
To address this challenge, the MIT team proposed a strategy where cells produce hyperspectral reporter molecules that can be captured using hyperspectral imaging technology. Developed in the 1970s, hyperspectral cameras analyze the light spectrum by extracting details on the presence of numerous color wavelengths in each pixel. Rather than appearing simply as red or green, each pixel contains data reflecting hundreds of different light wavelengths.
Currently, applications of hyperspectral cameras include radiation detection. In regions like Chernobyl, these cameras assess subtle color changes in plant chlorophyll associated with radioactive materials. They are similarly utilized to identify signs of nutritional deficiencies or pathogen intrusion in plants.
This existing technology prompted the MIT researchers to investigate whether they could engineer bacteria to create hyperspectral reporters in response to target molecules.
For optimal utility, a hyperspectral reporter is most effective when it exhibits spectral signatures with peaks across multiple light wavelengths, enhancing detection ease. The researchers performed quantum calculations to evaluate the spectral traits of approximately 20,000 naturally occurring cellular molecules, identifying those with the most distinctive light emission patterns. Another important factor was minimizing the number of enzymes necessary for the bacteria to produce the desired reporter, which varies from one bacterial type to another.
“The ideal reporter molecule is unique enough for easy detection while requiring minimal enzymatic involvement for its production in bacteria,” Voigt adds.
In their investigation, the team identified two particularly effective molecules suited for different bacteria. For the soil bacterium Pseudomonas putida, they utilized biliverdin, a pigment formed from heme breakdown. In contrast, for the aquatic bacterium Rubrivivax gelatinosus, they opted for a variant of bacteriochlorophyll. In both instances, the researchers incorporated the necessary enzymes into the bacterial cells and linked them to genetically programmed sensor circuits.
“By integrating one of these reporters into any bacterium or cell with an embedded genetic sensor, it can respond to various stimuli such as metals, toxins, or soil nutrients. The resultant output is a detectable molecule that can be sensed remotely,” Voigt elaborates.
Long-Distance Sensing
In their study, the researchers connected the hyperspectral reporters to circuits that facilitate quorum sensing, enabling cells to identify neighboring bacteria. Additionally, subsequent research has linked these reporters to sensors for diverse chemicals, including arsenic.
During experiments, the team placed the sensors in controlled environments, such as boxes situated in fields or atop buildings. The bacteria produced signals that were detectable by hyperspectral cameras carried by drones. These cameras required roughly 20 to 30 seconds to scan the scene, followed by computer algorithms analyzing the data to confirm the presence of hyperspectral reporters.
The current findings report successful imaging at a distance of up to 90 meters, with ongoing efforts aimed at further increasing this range.
The potential applications for these sensors are vast. They could be effectively employed in agriculture for assessing nitrogen and nutrient levels in soil. Furthermore, there’s potential use for detecting landmines or contaminants.
Before implementation, however, the sensors must gain regulatory approval from the U.S. Environmental Protection Agency and the U.S. Department of Agriculture for agricultural applications. Voigt and Chemla have been actively engaging with these agencies, the scientific community, and various stakeholders to address the pertinent questions necessary for regulatory approval.
“Our focus over the past three years has been on navigating the regulatory landscape and understanding safety concerns, risks, and benefits associated with this technology,” Chemla stated.
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