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Deploying bacteria as environmental sensors

In recent years, numerous strains of engineered bacteria have been developed. These strains can be used as sensors to detect environmental contaminants such as heavy metals.

Using these strains in the natural environment could help scientists track how pollutant levels change overtime over a wide geographic area.

Thanks to a new study, this deployment process now becomes easier. MIT Scientists have developed a new way that includes encasing bacterial sensors in a tough hydrogel shell that prevents them from escaping into the environment and potentially spreading modified genes to other organisms.

MIT graduate student Tzu-Chieh Tang, one of the lead authors of the new study, said, “Right now there are a lot of whole-cell biosensors being developed, but applying them in the real world is a challenge because we don’t want any genetically modified organisms to be able to exchange genetic material with wild-type microbes.”

Using their method, scientists were able to embed E. coli into hydrogel spheres. Doing so enabled the detection of the contaminants they’re looking for while remaining isolated from other organisms.

By designing bacteria to communicate genetic circuits that they don’t ordinarily have, analysts can empower them to recognize a wide range of particles. Regularly, the circuits are designed to discover the creation of the objective trigger of green fluorescent protein or bioluminescence. In different circuits, cell’s DNA stores the memory of the occasion.

The genes for antibiotic resistance in these genetic circuits ensured scientists that their genetic circuit had been correctly inserted into the bacterial cells. Sometimes, these genes are hazardous if releasing they into the environment.

Many bacteria and other microbes can exchange genes, even between different species, using horizontal gene transfer.

Using a method called chemical containment, scientists prevented gene exchange. The method involves designing the bacterial sensors to require an artificial molecule that they can’t get in the wild.

Another option is physical containment that includes encapsulating bacteria within a device that prevents them from escaping. Here, the problem lies within the materials such as plastic and glass. These materials do not offer efficiency as they form diffusion barriers preventing bacteria from interacting with the molecules they are designed to detect.

In this study, scientists tried encapsulating bacterial sensors in hydrogels made from a combination of alginate and polyacrylamide. Unlike naturally occurring hydrogels, this newly developed hydrogel is very tough and stretchy.

Scientists made the protective spheres by embedding bacteria and some essential nutrients in alginate. They then coated the spheres with hydrogels. This external layer has pores that range from 5 to 50 nanometers in diameter, allowing molecules such as sugars or heavy metals to pass through. However, DNA and larger proteins cannot go through.

Using spheres, scientists encapsulated E. coli bacteria that were designed to detect cadmium. For testing, the sensors were placed into the water samples.

To determine whether the sensors could detect pollutants from inside their spheres, scientists added cadmium to the samples and found that the bacteria could accurately see it. Scientists also showed that the bacteria did not escape from the sphere or leak any genetic material.

Scientists found that their encapsulation technique worked so well with a different strain of E. coli as well. This additional strain was designed o be dependent on an artificial molecule.

Tang said, “We are trying to come up with a solution to see if we can combine chemical and physical containment. That way, if either one of them failed, the other one can keep things in check.”

Scientists are looking forward to testing their sensors in a model environment that would simulate real-world conditions.

Journal Reference:
  1. Tang, TC., Tham, E., Liu, X. et al. Hydrogel-based biocontainment of bacteria for continuous sensing and computation. Nat Chem Biol (2021). DOI: 10.1038/s41589-021-00779-6

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