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TINY ORGANISMS, TRANSFORMATIVE OUTCOMES
USING GENETICALLY ENGINEERED MARINE MICROORGANISMS
TO BREAK DOWN PLASTIC IN SALT WATER.
Dr. Nathan Crook is an Assistant Professor of Chemical and Biomolecular Engineering at North Carolina State University. He received a B.S. in Chemical Engineering from the California Institute of Technology and a Ph.D. in Chemical Engineering from the University of Texas at Austin. He pursued postdoctoral studies in Pathology and Immunology at Washington University in the Saint Louis School of Medicine and came to NCSU in 2018. In 2023, he received an NSF Career Award and a NIH New Innovator Award. Today, we talk to Dr. Crook and several of the graduate students and postdocs he continues to mentor.
INTERVIEWER INTRODUCTION
THIS SPACE RESERVED FOR INTERVIEWER'S OPENING REMARKS
But before we go further, we know that you came to the University as part of its Chancellor’s Faculty Excellence Program. Can you please tell us what this means?
I think you will find this interesting.
Normally, academic departments foot the bills for bringing in new faculty, including paying their salary for their first few years of research. Later, the new faculty members will apply and compete for their own external research funding.
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But with the Faculty Excellence Program, the initial expenses are paid from a central fund rather than from a department’s budget.
Why is this important?
Because it allows departments to recruit individuals that have expertise in new or emerging research fields that are important to the departments, but for which they may not have the necessary funds to pursue on their own. This program funds these initial new faculty startup costs before they apply for external research funding.
In my case, the University’s Chemical Engineering department may not have been able to have me perform research in the area of microbiomes without the Chancellor’s Program.
You have spent much of your career working with single-celled organisms. Generally speaking, why did you decide on this particular career path and what is it that you hoped to understand and accomplish?
As very young students, we were encouraged to perform “engineering” challenges, like building bridges out of popsicle sticks or spaghetti. These were cool challenges that forced us to make tradeoffs and be clever in design approaches. Unfortunately, I was never very good at these.
But when I learned about biological evolution in high school, I was fascinated! I remember reading a paper in Scientific American about engineers who used an evolutionary algorithm to design better electronic circuits.
They found that these innovative designs performed better than the existing circuits at that time, and I found this to be most interesting.
Was there anything in that paper that particularly impressed you and may have inspired you to the path you are on today?
Yes there was!
One thing that really impressed me was that these designs included some very strange features like loops of wire that were disconnected from the rest of the circuit. Even though these were disconnected, these same loops of wire were still essential to the function of the device. Evolution had found a superior, yet very non-intuitive design!
Nathan, that is very interesting and it must have really surprised you to learn that the disconnected wires were still essential. Let’s move on to your experiences in your college years.
In college, I was fortunate to have worked in the lab of Professor Frances Arnold at Caltech, who was using evolutionary methods to design enzymes that can perform chemical reactions that natural ones cannot. I worked in her lab for 3 years.
You should know that she won the Nobel Prize in Chemistry in 2018 for using evolutionary methods to design enzymes. And since January 2021, she served as an external co-chair of President Joe Biden's Council of Advisors on Science and Technology.
What an honor and privilege it must have been to be able to work under someone as prestigious as Professor Arnold!
I think that this would be a good time to talk about your research to see if some bacteria could be paired and used to break down microplastics in the ocean. We know that non-biodegradable plastics are in our oceans and that some aquatic life is affected by these materials.
Not only was she an amazing mentor, but the postdocs who supervised me in the lab really took me under their wing. Rudi Fasan, Andrea Rentmeister, and Eric Brustad taught me the lab skills and how to think like a scientist. The Arnold lab was truly a unique place to be.
Today, it is difficult to find products that do not contain some type of plastics. The use of plastic is so wide-spread today because it is so cheap and easy to work with. It also has favorable properties that are difficult to find in materials like wood, metal, and stone.
But what about things like recycling? Why is this not taking care of much of the problem?
Unfortunately, recycling often yields inferior plastics when compared to new or “virgin” plastics, so it has limited alternatives for reuse. Recycling plastics must be separated by type – something that is very difficult and expensive because of the different types of plastic in use today.
For example, soda cans and chip bags have layers of different plastic to keep the food inside safe from spoiling and these and other waste plastic often ends up in landfills or in the environment, and nature is very bad at biodegrading them.
Courtesy of The Ocean Cleanup
What about landfills? Are our waste plastics safe there?
Not necessarily.
Plastics in our landfills degrade very slowly. Sunlight can oxidize the bonds within the plastic, and then forces like waves or wind can fragment the plastic into ever smaller pieces.
But why is that an issue?
Tiny pieces of plastic are very mobile – they can be carried by the wind to remote places, and they can spread worldwide in the oceans. Microplastics have been found in nearly every place scientists have looked for them.
What then?
These plastics contain chemicals that we should be concerned about, such as monomers, additives and the chemicals incorporated into them.
These are released into the environment when plastics begin to degrade.
And of course, plastics harm marine life by entrapping them or by ingestion.
Courtesy of The Ocean Cleanup
Very good points!
I think we should also touch on your research on how we might use certain combinations of bacteria to break down microplastics in the ocean. This seems so very important and exciting. Where do you want to begin?
From the outset, we need to talk about where and how we might actually use this technology. One could visualize ships or planes spreading chemicals that will break down plastics in our oceans and waterways, but this is hardly the case.
We need to conduct the actual plastic degradation process in a well-controlled, physically contained environment.
Nathan, I had not realized that. Why is that necessary?
Another good question.
In our oceans, there are many plastics that are actually supposed to be there – things like coatings on marine structures, fishing nets, ropes, just to name a few. Obviously, we do not want these to be degraded by bacteria while they are still in use.
So what do we do about the “bad” plastics in our oceans?
We need to collect them, and there are groups world-wide already doing this, such as The Ocean Cleanup Project. The collected waste would be placed in reaction vessels, where modified bacteria can convert them into biomass, or into beneficial things like plastic monomers, biofuels, or specialty chemicals.
We think that this approach of collection is currently safer than the alternative where plastic-eating bacteria would be dispersed in the environment.
Courtesy of The Ocean Cleanup
What are some of the issues you are currently working on?
In the short term, we are focusing on improving the rate at which our microbes can break down PET (Polyethylene terephthalate), a widely used plastic in commercial application, since this rate is currently too slow to be commercially viable.
It’s important to note that we are not alone in our research – there are other groups working on these same issues. They are also working on related issues such as designing a microbe that is safe to release into the environment.
Nathan, I think this might be a good time to talk to Tianyu Li about her research in your lab.
Tianyu, you were part of a team that created an engineered strain of bacteria that displays plastic-degrading enzymes on its surface. Will this help with the plastics problem in the oceans, and if so, how?
Thank you for asking, glad to help.
We do think that this organism is a step in the right direction. The organism we chose is very fast-growing, even by bacterial standards, and it can live in salty water. It is also easy to genetically engineer, which makes it a great candidate for this application.
We were able to successfully engineer this microbe to allow us to put plastic-degrading enzymes on its surface, which in turn were able to depolymerize PET plastics in salt-containing media.
This was the first time that engineered PET breakdown has been reported under these conditions, which was very exciting for us.
What might be next here?
We plan to further engineer this microbe to “eat” the breakdown products of PET and actually gain energy from them. Because the PET-degrading enzyme is the slowest step of this process, we think that faster-growing microbes will arise due to mutations in the PET gene that make it more efficient.
It's very important to note that our goal is not to release this microbe into the environment – as previously noted. Some plastics are very important to us! This microbe could
Courtesy of the Ocean Cleanup
be used to break down “point sources” of plastic, like unrecyclable, dirty, or mixed plastic coming from a recycling center - even laundry fibers coming from a wastewater treatment plant.
However, if we do find PETases that work well, those could be purified and actually be spread on plastic-contaminated areas to help breakdown the contaminants.
Thank you Tianyu, and your point about not releasing your microbe into the environment is very important. I want to get back to Nathan and ask him about possible commercial applications from this research. But before I do, I want to ask Ethan Gates for his comments, as he has also done research on this issue.
Thank you.
I focused on screening for environmental microbes and enzymes capable of degrading polyethylene and polystyrene. Polyethylene is by far the most widely used plastic, and polystyrene, according to some sources, accounts for some 10-20% of the weight in landfills.
In my research we found some very interesting microbes in and around the Raleigh area, but we need to do more work on them before we can definitively say whether or not they can degrade plastic.
Nathan, what about potential commercial applications? What might we see down the road?
Well, we hope that the insights we uncover can eventually fit into a process that is commercially viable.
Initially, there might be a capture of plastics before they are released into the environment at factories where microplastics are currently a waste stream or are in wastewater treatment plants. The plan might be to convert these into plastic monomers, and sell them back to plastic manufacturers for the creation of recycled plastics that have the same properties as virgin plastics.
What about existing plastic-contaminated sites? What can be done here with the results of your research?
Once we have a proven and safe process, the owners of plastic-contaminated sites might pay to have plastic treated on-site with plastic-eating microbes that will have built-in “kill switches” so that the process can be stopped when necessary.
On-site plastic treatment might be one of the only options for sites where recovery of waste plastic is too difficult, for example where the plastics are mixed in the soil.
Anything else here before we move on?
Eventually, our goal is for plastic waste to have a treatment process that provides value to the organizations who are able to treat it. At the same time, we all need to do a better job about making sure that waste plastic makes its way into these treatment streams, rather than into environmental ones.
Nathan, it is obvious that student participation in your research programs is an important ingredient to your success. In your mind, what makes a good student for your curriculums and research programs?
I look for students who did some type of undergraduate research during college, ideally with microbes and involving cloning of recombinant DNA.
Equally important are students who are intensely motivated – the type who get obsessed about things and are willing to tinker or experiment in order to figure out the right approach.
What would you say are the qualifications?
Students who have graduated from a bachelor’s program and are pursuing their PhD make up the majority of my group. Many started their PhD program right after graduating college, but several have spent a couple of years working in the industry before doing their PhDs.
My students pursue PhDs in Chemical Engineering, Genetics, and Microbiology, and in all cases, their ability to graduate depends upon a body of independent research work.
Are financial assistance and grants available to them?
What’s nice about a PhD program, and what most people don’t realize, is that you actually get paid to be a PhD student, at least for the students I supervise.
Each student is provided a living stipend to support their studies. This year, the Chemical Engineering PhD stipend is $36,000 per year after tuition, fees and health insurance are deducted.
And who typically provides this financial assistance?
What might be their later career paths?
In my case, it comes out of the research grants that I compete for (like the NSF and NIH grants mentioned earlier). That said, students who are US citizens are eligible for a wide range of government fellowships, including those from the NSF and NIH. These types of fellowships essentially allow the student to work on projects for which I don’t currently have funding.
After graduation with a PhD, essentially any role in STEM (science, technology, engineering, and math) is available to them. Prior students of mine have led their own startup companies, become university professors, and became scientists at both large and small companies.
Getting a PhD is a great way to have an impact!
What about industry collaborations?
I understand that you regularly collaborate with industry, and you have performed research for several companies to help bring beneficial therapies to market. Can you give us a few examples of your collaborative efforts?
We previously worked with Novozymes (now Novonesis) on a project to help genetically engineer a microbe with which they were working. The Novozymes project started with an event that NC State University hosted, where companies are invited to attend, and our professors talk about some of their research projects.
We also collaborated with company called Synlogic. In this instance, Synlogic knew of our research on this subject through our publications and reached out to us directly
In both cases, these companies provided funds to support research in our lab. It was a great opportunity for us to see science from their perspective and hear their company’s goals and values. While these projects may not seem interesting on the surface, from a business perspective all the industry scientists involved were excited to take part.
THIS SPACE RESERVED FOR INTERVIEWER'S CLOSING REMARKS
ENTER ARTICLE ABOUT INTERVIEWER'S ORGANIZATION HERE