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By sealing bacteria in tough yet porous, outer casings, environmental scientists could use these organisms as safe and effective detectors of environmental contaminants like heavy metals.
Developing a strain of engineered bacteria that can effectively be used as a sensor to detect contaminants in environments has been a hot scientific topic for years. Bacteria created this way could help researchers in the vital task of tracking changes in pollution levels over wide geographical areas.
Yet, whilst genetically modified microorganisms (GMMs) are great for a wide range of essential applications, including environmental sensing, containing them and preventing them from growing in the environment has been a major stumbling block to their wider use.
Now, new research from a team of scientists at the Massachusetts Institute of Technology (MIT) could help simplify the deployment of this bacteria and make it safer. The researchers have developed a method of sealing these natural sensors in a shell made of hydrogel — a 3D network of hydrophilic polymers capable of holding large amounts of water without losing structural integrity.
This hydrogel shell prevents the bacteria from leaking into the wider environment, thus protecting organisms that exist there from picking up their modified genes — a potential environmental contaminant itself.
Right now there are a lot of whole-cell biosensors being developed, but applying them in the real world is a challenge. We don’t want any genetically modified organisms to be able to exchange genetic material with wild-type microbes.
Tzu-Chieh Tang, Graduate Student, MIT
Alongside professors Timothy Lu and Xuanhe Zhao, Tang is one of the authors of a paper documenting the development of what the team terms a deployable physical containment strategy (DEPCOS) published in the latest edition of the journal Nature Chemical Biology¹.
How Bacteria Become Sensors
For some time, researchers have been able to engineer genetic traits in bacteria that they normally don’t possess. These traits can be specially tailored to detect a range of molecules and react to the presence of these molecules with a bioluminescence glow. Bioluminescence is the emission of light by a living organism that is fairly common in marine animals, fungi and perhaps most familiarly, fireflies.
Remarkably, in some cases, biological engineers have even been able to create organisms that can hold a record of encounters with certain materials in their DNA.
The downside is, these specially engineered genes are often programmed with resistance to antibiotics. This is included to help the scientists determine if the genes have been properly inserted into the bacteria, but it has the knock-on effect of making these genes dangerous should they be released into an ecosystem.
This risk is compounded by the fact that bacteria and other microorganisms can exchange genetic material — even between different species — in a phenomenon known as horizontal gene transfer.
Scientists have been working on containment methods for these bacteria sensors for some time. One of these avenues of study has been the possibility of engineering the bacteria with a dependence on a molecule that doesn’t exist in the wild. That means that if they move from a certain area, they die.
The risk inherent in this method is if some of the bacteria evolve a mechanism that helps them survive this artificially introduced dependence. The question is, how do you trap bacteria and still have them interact enough with the environment enough to act as a sensor?
Hydrogel Shielding for Bacterial Sensors
Many materials have thus far been tried as containment measures for bacterial sensors. The problem is, materials like plastic and glass form such effective barriers that the sensors can’t actually interact with their environment enough to detect the contaminants they are engineered to trace.
The team embedded e.coli in hydrogel spheres made from tough and stretchy hydrogels made from a combination of alginate and polyacrylamide, previously developed in the lab of Zhao, a professor of mechanical, civil and environmental engineering.
Sealed within each sphere — 5 mm in diameter — is up 1 billion bacterial cells wrapped in a naturally occurring hydrogel also made from algae-derived alginate. Packed alongside the bacteria — specially engineered to trace the heavy metal cadmium — are essential nutrients to feed the bacteria.
The outer layer of this system is punctuated with pores, ranging in size from 5 to 50 nm. These pores allow molecules like sugars and heavy metals to pass through while blocking DNA and larger proteins. Thus, it still permitted the bacterial sensors to detect contaminants that they were engineered to seek, without the risk of exposing natural organisms to their engineered genes.
But, the protection offered by the hydrogel shell worked both ways. As it protected the ecosystem and its inhabitants around the bacterial sensor, the shield was also protecting its bacterial load from potentially harmful pH levels and antibiotics.
Putting the Hydrogel Sheild to the Test
To test their DEPCOS system, the team collected water samples from the Charles River, which flows for 80 miles from Hopkinton, Massachusetts, to Boston Harbor. To these samples, to put the sensors to the test, the team added cadmium.
The tests showed that not only did the sensor bacteria detect cadmium while wrapped in hydrogel shells, but the leakage of genetic material was also prevented.
The researchers then retested the hydrogel shells with an alternative e.coli strain, this time developed to depend on an artificial amino acid not available naturally.
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.
Tzu-Chieh Tang, Graduate Student, MIT
The next step for the researchers is to test the DEPCOS hydrogel shell system in a lab-based simulation of real-world conditions. They will also investigate if the system they have developed could be used in alternative fields. This could include medical applications such as detecting internal bleeding, particularly in the gut.
References
1. Tang. T-C., Zhao. X., Lu. T. K., [2021], ‘Hydrogel-based biocontainment of bacteria for continuous sensing and computation,’ Nature Chemical Biology, [https://doi.org/10.1038/s41589-021-00779-6]
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