A safe way to use bacteria as environmental sensors

In recent years, scientists have developed many strains of bacteria that can be used as sensors to detect environmental pollutants such as heavy metals. When used in the natural environment, these sensors can help scientists track how pollutant concentrations change over time over a wide geographic area.

MIT engineers have now found a way to make this type of delivery safer by encasing bacterial sensors in a sturdy hydrogel shell that prevents them from entering the environment and potentially transferring modified genes to other organisms.

MIT engineers have found a way to encapsulate bacteria sensors in a tough hydrogel ball that prevents them from interacting with other microbes in the environment.
Photo credit: Christine Daniloff, MIT

"A lot of whole-cell biosensors are currently being developed, but their application in the real world is challenging because we don't want genetically modified organisms to be able to exchange genetic material with wild-type microbes," says MIT graduate student Tzu-Chieh Tang, one of them of the lead authors of the new study.

Tang and his colleagues showed that they could embed E. coli in hydrogel spheres so that they can identify the contaminants they are looking for while remaining isolated from other organisms. The shells also help protect the sensors from environmental damage.

Timothy Lu, Associate Professor of Electrical and Computer Science at MIT and Biotechnology at MIT, and Xuanhe Zhao, Professor of Mechanical and Civil and Environmental Engineering at MIT, are the lead authors of the study, which appears in Natural chemical biology. In addition to Tang, Eleonore Tham PhD '18 and MIT doctoral student Xinyue Liu are also the main authors of the paper.

Physical containment

By developing bacteria to express genetic circuits that they normally don't have, researchers can enable them to detect a wide variety of different molecules. Often times, the circuitry is designed so that detection of the target triggers the production of green fluorescent protein or bioluminescence. In other circuits there is a reminder of the event recorded in the DNA of the cells.

The genetic circuitry that gets into these bacteria often contains genes for antibiotic resistance, which allows researchers to ensure that their genetic circuitry has been properly inserted into the bacterial cells. However, these genes could be harmful if released into the environment. Many bacteria and other microbes are able to exchange genes, even between species, using a process called horizontal gene transfer.

To prevent this type of gene exchange, researchers have used a strategy called "chemical containment," where the bacteria sensors are engineered to require an artificial molecule that they cannot get in the wild. However, with a very large population of bacteria, there is a chance that a small number will acquire mutations that will allow them to survive without this molecule.

Another option is physical containment, which is achieved by encapsulating bacteria in a device that prevents bacteria from escaping. However, the materials tested so far, such as plastic and glass, don't work well because they create diffusion barriers that prevent bacteria from interacting with the molecules they are supposed to detect.

In this study, the researchers decided to encapsulate bacterial sensors in hydrogels. These are stretchy materials that can be made from a wide variety of different building blocks. Many naturally occurring hydrogels, such as alginate, which is derived from algae, are too fragile to protect cells in an outdoor environment. However, Zhao's lab previously developed some very tough, ductile ones Hydrogelsthat the researchers believed could be useful for encapsulating bacteria.

To produce the protective spheres, the researchers first embedded bacteria along with some essential nutrients in alginate. These spheres were then coated with one of Zhao's tough hydrogels, which is made from a combination of alginate and polyacrylamide. This outer layer has pores with a diameter of 5 to 50 nanometers through which molecules such as sugar or heavy metals can pass. However, DNA and larger proteins cannot be traversed.

Detect pollution

The spheres that the researchers constructed for this study are around 5 millimeters in diameter and can hold up to 1 billion bacterial cells. The researchers used the spheres for encapsulation E. coli Bacteria designed to detect cadmium, a heavy metal.

To test the sensors, the researchers placed them in water samples taken from the Charles River. To see if the sensors could detect pollutants from inside their spheres, the researchers added cadmium to the samples and found that the bacteria could detect it accurately. The researchers also showed that the bacteria did not escape from the sphere or leak genetic material.

The researchers showed that their encapsulation technique worked with a different strain of as well E. coli that was designed to be dependent on an artificial molecule – an amino acid that does not occur in nature.

“We're trying to find a solution to see if we can combine chemical and physical containment. That way, the other can keep things in check if one of them fails, ”says Tang.

In future studies, the researchers hope to test the sensors in a model environment that would simulate real-world conditions. In addition to detecting environmental pollution, this type of sensor could potentially be used for medical applications like detecting bleeding in the digestive tract, the researchers say.

Written by Anne Trafton

Source: Massachusetts Institute of Technology

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