We may not notice it in our everyday lives, but bacteria and other microorganisms are responsible for recycling a lot of our trash. They turn our organic waste into compost, take part in the decomposition of dead plants in the forest, and some of them can even help us with nuclear waste! This is possible because many bacteria have evolved to eat the waste that lies around them, convert it into useful nutrients for other organisms, closing the circle of an ecosystem. In the last 200 hundred years, the bacteria that populate our planet have met a challenge: we generate a lot more trash than before and some of it, like plastics or industrial waste, has never existed before. What happens when this new kind of waste appears? With no specialised bacteria around to take care of it, it can stay in the environment for a long time. Luckily, the latest biotechnological advances can help us tune bacteria to get rid of this new waste. To know more about this, we talked with Drs. Jiří Damborský and Zbyněk Prokop, of Loschmidt Laboratories from the Faculty of Science of the Masaryk University and the International Centre for Clinical Research.
“Industrial processes sometimes generate anthropogenic compounds: substances that are not found in nature, but are a result of human activity”, explains Dr. Damborský. “A lot of the new materials and products we enjoy today depend on the so-called commodity chemicals”. These chemicals are useful substances in many industrial processes, so they are produced in bulk in chemical plants. However, these industrial procedures are not always clean. They generate residues. The perfect example of this are epoxy resins, a group of compounds that is widely used: from binder in cement and mortars, to composite materials in bicycle frames and aerospace components. Sadly, the chemical reactions that produce these resins, also create the pollutant TCP —or 1,2,3-Trichloropropane for the chemists out there. This pollutant has shown carcinogenic effects in animals, and the effects in humans are still being studied, although we know that long-term exposure to TCP can cause us liver and kidney damage.
“Currently, the solution for TCP is to store it, since we cannot degrade it into less harmful compounds”, stresses Dr. Damborský, “And although the people in the chemical industry are making the industrial processes more efficient, to reduce the amount of TCP they generate, we still face the problem of what to do with the TCP we already have.” In addition, there have been cases of TCP leaking into groundwater reserves. And once it reaches the underground water levels, it gets harder to remove. In these cases, the only viable solution is bioremediation, a process that uses bacteria and other microorganisms to degrade the pollutant.
“Because TCP is man-made, we cannot find in nature bacteria that efficiently remove this substance, so the TCP can stay in the environment for more than 100 years.”, explains Dr. Damborský. However, we no longer need to wait for bacteria to evolve to get rid of TCP. Thanks to synthetic biology, we can tailor these microorganisms to get rid of the pollutant. To do this, Drs. Damborský’s and Prokop’s teams have designed a sort of “robot scientist”, that allows them to optimize the metabolic pathways that bacteria can use to degrade TCP into less harmful compounds. “We use a microfluidic chip that we have developed in a collaboration with Drs. Andrew deMello and Stavros Stavrakis at ETH Zurich. The chip with microchannels allows us to conduct multiple experiments within a very short period.”, clarifies Dr. Prokop, “The experiments are done in tiny droplets of liquid, that then flow through the channels, and the results of the experiments are read out by a laser beam. We have automated the system, so it can be done over and over, to find the most optimal pathways. We have already engineered bacteria that produce the enzymes in the ratios necessary to degrade TCP into CO2 and water.”
For this system to work, one key factor is optimisation. The bacteria have to munch the pollutant fast and efficiently enough. And that’s where the team is facing a second challenge. “Currently, the bacteria create the enzymes that degrade the TCP inside their cytoplasm. But TCP is toxic to the bacteria and kills a lot of them, making the process inefficient.”, declares Dr. Prokop, “To avoid this, in Rafts4Biotech we are using the lipid rafts in the membrane of the bacteria to produce these enzymes. The whole process will be done in the outskirts of the organism, so it is less toxic for the bacteria.”
This approach of using bacteria to get rid of man-made pollutants is a novel approach that has shown some promising results (like in the case of plastics). But Dr. Prokop has it clear: “Our hope is that both the microfluidic chip and the Rafts4Biotech technology can be adapted to many more pollutants in the future, helping us clean the waste we generate.”