ACQUIRED TASTES

“from 2016: Japanese researchers discovered a microorganism that literally eats plastic. The bacterium, now named Ideonella sakaiensis, has been proven to completely break down polyethylene terephthalate (PET)”

WHAT EATS PLASTIC (cont.)
https://nature.com/articles/s41522-023-00440-1
https://phys.org/plastic-eating-enzymes-pollution-problem
Plastic-eating enzymes could help solve pollution problem
by Brunel University / October 16, 2023

“Two new enzymes can break down one of the most common single-use plastics, according to study “Modulating biofilm can potentiate activity of novel plastic-degrading enzymes” by Brunel University London published in the journal npj Biofilms and Microbiomes. The enzymes could be developed to dissolve plastic bottles faster than current recycling methods and create the raw material to make new ones. Water-polluting plastic waste is a huge problem, with most everyday single-use plastics destined for landfills, where they take hundreds of years to decompose. Bacteria shows potential to help tackle the waste crisis, with scientists pinpointing several new species that encode enzymes that can degrade plastic. But these enzymes degrade plastic too slowly to be useful. “These new findings are really exciting,” said Dr. Ronan McCarthy. “Not only have we identified two new PET (Polyethylene terephthalate) degrading enzymes, but we found a way to improve their degradation abilities by modifying the bacteria as whole, rather than modifying each enzyme individually.”

“Modeling of novel enzymes, and known PET-degrading enzymes”

Biomedical scientists at Brunel are doing extensive research in synthetic biology to find ways to make these useful plastic degrading enzymes work harder. Synthetic biology uses ideas from engineering to design new biological pathways, organisms and devices and to modify ones found in nature. In this new study, the researchers use the techniques to boost bacteria’s abilities to grow in communities called biofilms. Like people, bacteria don’t often like living on their own. Bacteria living together in biofilm communities can share nutrients and communication signals and better withstand extreme temperatures and chemical hazards. The team genetically engineered plastic-degrading bacteria to attach to waste plastic and form biofilms on it. This ramped up the concentration of the enzyme around the plastic, making it much more powerful and better at breaking it down.

“This suggests that modulating biofilm formation may be an effective strategy to increase the efficiency of plastic degrading bacteria,” said Dr. McCarthy. “Using biofilms to enhance plastic-degrading enzyme activity could potentially be applied to all plastic-degrading enzymes currently in development.” Biofilms form on many natural surfaces, such as soil, water and rocks. In health settings, bacterial infections such as MRSA can form biofilms that create a barrier to antibiotics and the immune system. The team now plan to test the two new enzymes in a bioreactor. “We want to see if increasing biofilm formation improves the degradation of plastic in a more industrial-like setting,” added researcher Dr. Sophie Howard. “We also aim to further harness synthetic biology to give even greater control over biofilm formation.”

More information: Sophie A. Howard et al, Modulating biofilm can potentiate activity of novel plastic-degrading enzymes, npj Biofilms and Microbiomes (2023). DOI: 10.1038/s41522-023-00440-1

“An up-close image of microplastics that were collected from a shoreline. Li’s engineered bacteria can degrade macro and micro forms of PET plastic, but the smaller the plastic particles, the faster the break down can occur.”

SEA PLASTIC
https://aiche.onlinelibrary.wiley.com/doi/full/10.1002/aic.18228
https://phys.org/news/2023-09-genetically-bacteria-plastics-saltwater.html
Genetically modified bacteria found to break down plastics in saltwater
by Matt Shipman / September 14, 2023

“Researchers have genetically engineered a marine microorganism to break down plastic in salt water. Specifically, the modified organism can break down polyethylene terephthalate (PET), a plastic used in everything from water bottles to clothing that is a significant contributor to microplastic pollution in oceans. “This is exciting because we need to address plastic pollution in marine environments,” says Nathan Crook, corresponding author of a paper on the work and an assistant professor of chemical and biomolecular engineering at North Carolina State University.

“One option is to pull the plastic out of the water and put it in a landfill, but that poses challenges of its own. It would be better if we could break these plastics down into products that can be re-used. For that to work, you need an inexpensive way to break the plastic down. Our work here is a big step in that direction.” To address this challenge, the researchers worked with two species of bacteria. The first bacterium, Vibrio natriegens, thrives in saltwater and is remarkable—in part—because it reproduces very quickly. The second bacterium, Ideonella sakaiensis, is remarkable because it produces enzymes that allow it to break down PET and eat it. The researchers took the DNA from I. sakaiensis that is responsible for producing the enzymes that break down plastic, and incorporated that genetic sequence into a plasmid.

Plasmids are genetic sequences that can replicate in a cell, independent of the cell’s own chromosome. In other words, you can sneak a plasmid into a foreign cell, and that cell will carry out the instructions in the plasmid’s DNA. And that’s exactly what the researchers did here. By introducing the plasmid containing the I. sakaiensis genes into V. natriegens bacteria, the researchers were able to get V. natriegens to produce the desired enzymes on the surface of their cells. The researchers then demonstrated that V. natriegens was able to break down PET in a saltwater environment at room temperature. “This is scientifically exciting because this is the first time anyone has reported successfully getting V. natriegens to express foreign enzymes on the surface of its cells,” Crook says. “From a practical standpoint, this is also the first genetically engineered organism that we know of that is capable of breaking down PET microplastics in saltwater,” says Tianyu Li, first author of the paper and a Ph.D. student at NC State. “That’s important, because it is not economically feasible to remove plastics from the ocean and rinse high concentration salts off before beginning any processes related to breaking the plastic down.”

“NC State PhD candidate Tianyu Li led the project that developed a genetically modified organism to eat PET in salt water. She has spent more than two years working in the Crook Lab bioengineering marine bacteria”

“However, while this is an important first step, there are still three significant hurdles,” Crook says. “First, we’d like to incorporate the DNA from I. sakaiensis directly into the genome of V. natriegens, which would make the production of plastic-degrading enzymes a more stable feature of the modified organisms. Second, we need to further modify V. natriegens so that it is capable of feeding on the byproducts it produces when it breaks down the PET. Lastly, we need to modify the V. natriegens to produce a desirable end product from the PET—such as a molecule that is a useful feedstock for the chemical industry. Honestly, that third challenge is the easiest of the three,” says Crook.

“Proposed PET complete hydrolysis pathway by Is29”

“Breaking down the PET in saltwater was the most challenging part. We are also open to talking with industry groups to learn more about which molecules would be most desirable for us to engineer the V. natriegens into producing,” Crook says. “Given the range of molecules we can induce the bacteria to produce, and the potentially vast scale of production, which molecules could industry provide a market for?”

More information: Tianyu Li et al, Breakdown of polyethylene therepthalate microplastics under saltwater conditions using engineered Vibrio natriegens, AlChE Journal (2023). DOI: 10.1002/aic.18228

After an oil spill, humans rush to the scene to minimize impacts. But if the oil sticks around long enough, nature’s responders—bacteria such as Alcanivorax borkumensis—start to roll in.

New observations show exactly how this bacterium breaks oil down: https://t.co/BliCsBmL6S pic.twitter.com/VHvBor8qQ8

— Science Magazine (@ScienceMagazine) September 15, 2023

BIODEGRADABLE PLASTIC
https://ami-journals.onlinelibrary.wiley.com/doi/10.1111/1462-2920.16512
https://phys.org/enzyme-molecule-marine-bacteria-degrades
Enzyme molecule in marine bacteria degrades plastic polymer
by Hokkaido University / October 16, 2023

“A bacterium that can degrade the common polymer polybutylene succinate (PBS), which naturally biodegrades only to a limited extent in marine environments, could lead to improved ways to recycle this polymer. The bacterium’s potential, and its enzyme molecule that breaks down PBS, were discovered by researchers at Hokkaido University, working with colleagues at the Mitsubishi Chemical Group in Japan. The team published their results in the journal Environmental Microbiology. PBS is generally regarded as an eco-friendly polymer due to its biodegradability when discarded on land and exposed to the atmosphere. This has led to its increased use since the early 1990s in industrial plastics, including mulching films, compostable bags, and catering packaging. But many discarded plastics eventually find their way into the sea, and unfortunately, PBS does not biodegrade well in that environment.

“Plastic pollution in the ocean is a global problem and we need to tackle it by gaining new understanding of plastic behavior in that environment, and new technologies to deal with the pollution,” says Tomoo Sawabe, leader of the research team at Hokkaido University’s Faculty of Fisheries Sciences. As only a small number of marine microorganisms able to biodegrade PBS had been discovered previously, Sawabe and his colleagues set out to try to find others, especially those with better activity. They examined the effect on PBS of microbes gathered from natural seawater off Japan, allowing them to identify several types of marine bacteria that could degrade it. They also identified the enzyme responsible for degrading PBS in a specific strain of bacteria called Vibrio ruber. They named the enzyme PBSase.

“Vibrio ruber (bottom left) was shown to degrade PBS”

They then took things further by using molecular biological techniques to insert the gene for PBSase into the common bacterium Escherichia coli, which they cultured to produce highly purified samples of the enzyme for further study. “Elucidating the degradation mechanism in seawater at the molecular level may lead to the development of new marine biodegradable polymers,” says Yasuhito Yamamoto, Sawabe’s collaborator at Mitsubishi Chemical Corporation of the Mitsubishi Chemical Group. “This enzyme could be used as a decomposition accelerator or catalyst for chemical recycling of collected waste plastics.” The availability of the purified enzyme also allowed the researchers to examine its structure, with simulations suggesting it was closely related to a different enzyme known to degrade another common polymer: polyethylene terephthalate (PET).

“Protein structure comparison between PBSase (pink gold backbone) and PET degrading enzyme PET6 (cobalt backbone). Catalytic centers indicated by magenta and green. PET binding residues of PET6 are shown in yellow”

“By exploring the enzyme’s activity in degrading other polymers, such as PET, we hope that our work will contribute more widely to advances in plastic recycling technologies,” Sawabe concludes. This research is part of wider efforts to address the complexity of biodegradable polymer technologies caused by their differing biodegradability on land and in the sea. By learning more about what controls biodegradability in different environments, scientists will hopefully develop polymers that are best suited to the environments they are used in, and those that they may end up in after use.”

More information: Yutaro Kimura et al, A lesson from polybutylene succinate plastisphere to the discovery of novel plastic degrading enzyme genes in marine vibrios, Environmental Microbiology (2023). DOI: 10.1111/1462-2920.16512

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