The Dawn of a Biodegradable Future: Students Engineer Bacteria to Devour Plastic Waste
The pervasive problem of plastic pollution, a crisis that chokes our oceans, landfills, and even our bodies, is facing a potential game-changer. Microplastics, insidious particles less than 0.20 of an inch in size, infiltrate ecosystems and human physiology, often originating from the breakdown of larger plastic debris. Traditionally, plastic has been regarded as an indestructible substance, a testament to its durability but a curse for environmental sustainability. However, a growing body of scientific inquiry is revealing that certain bacteria possess the remarkable capability to metabolize plastics, offering a glimmer of hope in the fight against this global menace.
The Genesis of Plastic-Eating Microbes
The journey towards harnessing bacterial power against plastic began with dedicated researchers and students delving into the intricate world of microbiology. At Wesleyan University, Chloe De Palo ’22, Rachel Hsu ’23, Claudia Kunney ’24, and biology PhD candidate Fatai Olabemiwo, under the guidance of Professor Fred Cohan, embarked on an ambitious project. Their exploration led them to the soil of Wesleyan's Long Lane Farm, where they collected samples on March 7, 2020. These samples, combined with plastic strips, were introduced into a modified Winogradsky column, a sophisticated tool designed to cultivate a diverse array of microorganisms. Olabemiwo elaborated on their innovative approach: "We modified this wonderful device to yield a range of plastic degrades by placing plastic strips at four different zones inside the column." The experiment yielded promising results, with the team meticulously removing the plastic strips after 496 days in the soil-broth mixture. The next crucial phase involved isolating individual bacteria and, in the fall, systematically confirming their plastic-degrading potential by feeding them minute plastic discs in a petri dish.
Parallel to this endeavor, a team of 13 bachelor's and master's students, driven by a profound concern over the alarming discovery of microplastics in human blood, dedicated their summer to an intensive research effort. Jasper Smits, a member of this group, expressed their motivation: "We wanted to do something about it." Their research highlighted how agricultural practices, such as the use of plastic foils to aid plant growth and plastic coatings on fertilizer pellets, contribute to microplastic contamination, as these plastics often fail to decompose effectively, entering our food chain and the environment. These students are actively participating in the International Genetically Engineered Machine (iGEM) competition, a global platform where student teams leverage synthetic biology to address pressing world issues. With 400 teams entering this year's competition, the winners are set to be announced at the Grand Jamboree in Paris in early November.
The PHAse Out Project: Engineering Biodegradable Plastics
The iGEM team's project, named "PHAse Out," focuses on developing a biodegradable plastic suitable for agricultural applications. Their initial months were dedicated to extensive literature research and consultations with experts, transitioning to intensive laboratory work in July. Their primary objective is to engineer the production of polyhydroxyalkanoate (PHA), a type of biodegradable plastic that bacteria can naturally break down within approximately three months. The current high cost of PHA production presents a significant barrier to its widespread adoption by industries. To overcome this, the students are genetically modifying the Methylobacterium extorquens bacterium, a naturally occurring PHA producer.
"We are causing overexpression of the gene that produces PHA," Smits explained. "This makes the bacterium produce more PHA than it normally would." Furthermore, they are refining the extraction process, which represents a substantial expense. Their aim is to engineer genetic modifications that induce the bacteria to lyse-that is, for their cell membranes to break down, releasing the PHA-of their own accord. The choice of M. extorquens is not solely based on its PHA production; Smits notes its unique characteristic of metabolizing methanol instead of sugars. This is a significant advantage, as methanol does not compete with human food sources and can be produced in a carbon-neutral manner through the reaction of green hydrogen and CO2, paving the way for climate-neutral plastic production. The students face a time constraint, needing to vacate their lab in September, but will continue their experiments in other facilities. The inherent stress of completing their work within the given timeframe is compounded by the need for self-funding through crowdfunding, with a goal of raising 9,800 euros for lab materials. The amount raised will directly influence the scope of their experiments, with donors offered rewards such as biology comic strips or personalized VR lab tours.
Read also: Mastering Research: A Student's Handbook
Unearthing Nature's Plastic-Eating Arsenal
The quest to find natural solutions to plastic pollution has led scientists to explore microbial life for organisms capable of degrading various plastics. Morgan Vague, a biology student at Reed College in Oregon, has been instrumental in identifying bacteria that can break down polyethylene terephthalate (PET), a prevalent plastic used in countless consumer products, from clothing to beverage bottles. PET, notorious for its centuries-long decomposition time, poses a significant threat to the environment. Vague's research, if accelerated, could become a crucial component in mitigating the millions of tonnes of plastic waste that accumulate annually in landfills and oceans, with only a fraction being recycled.
"When I started learning about the statistics about all the plastic waste we have, essentially that told me we have a really serious problem here and we need some way to address it," Ms. Vague stated. Her investigation into bacterial metabolism and its "crazy things bacteria can do" led her to explore the possibility of microbes degrading "straight-from-the-store" plastic. Her search focused on the soil and water surrounding refineries in her hometown of Houston, where she collected samples. Back at college in Portland, Oregon, Vague tested approximately 300 bacterial strains for lipase, a fat-digesting enzyme that showed potential for breaking down plastic. She identified 20 strains producing lipase, with three exhibiting high levels of the enzyme. Subsequently, she placed these three microbes, one of which may be a new discovery, on a diet of PET derived from water bottle strips. She was astonished to observe the bacteria actively digesting the plastic. The process appears to break down PET into harmless by-products, with the bacteria utilizing the hydrocarbons within the plastic as a source of food and energy. "So essentially it’s using that to live. It’s essentially turning plastic into food," Vague explained. However, she cautioned that significant further development is needed before these microbes can be effectively deployed for large-scale plastic waste management. Professor Jay Mellies, a microbiologist who supervised Vague's thesis, emphasized the need to accelerate the degradation rate, enhance pre-treatment methods for PET to improve its digestibility, and expand the bacteria's capability to break down a wider range of plastics. He acknowledged that while this research is not a panacea, it represents a vital part of the multifaceted solution to the plastic crisis.
The Evolution of Plastic Degradation: From Discovery to Engineering
The scientific community's understanding of plastic-degrading capabilities has evolved significantly. In 2001, Japanese scientists, led by Professor Kohei Oda of the Kyoto Institute of Technology, made a groundbreaking discovery at a landfill. They identified a bacterial film that was actively consuming plastic bottles and toys, deriving energy from the carbon within the plastic. Oda, a microbiologist, believed that nature often held solutions to human-made problems. His team was initially searching for substances that could soften synthetic fabrics like polyester, a component of most beverage bottles. The bacteria they found were not merely attacking the plastic's surface; they appeared to be fully breaking it down into essential nutrients. At the time, this discovery, predating the widespread use of the term "microplastic," was not considered a topic of major interest, and the preliminary research papers were not published.
However, as plastic pollution escalated over the following two decades-with an estimated 2.5 billion tonnes of plastic waste generated and an annual production of around 380 million tonnes, projected to triple by 2060-the significance of Oda's findings became undeniable. Vast plastic gyres, like the one in the Pacific Ocean seven times the size of Great Britain, and plastic-choked coastlines worldwide underscore the urgency of the situation. At a microscopic level, microplastics and nanoplastics have infiltrated fruits and vegetables and have been found in nearly every human organ, with the potential to transfer from mother to child via breast milk. Current plastic recycling methods are largely inadequate. Most recycling processes involve crushing and grinding, which degrades the plastic's quality, rendering it suitable for fewer applications compared to materials like glass or aluminum that can be infinitely recycled. The reality is that only about 9% of plastic ever enters a recycling plant. Incineration, the primary method for disposing of nearly 70 million tonnes of plastic annually, contributes to the climate crisis by releasing carbon and noxious chemicals into the atmosphere.
Oda and his student Kazumi Hiraga continued their research, publishing their work in the prestigious journal Science in 2016. Their discovery of Ideonella sakaiensis, named after the city where it was found, and its specific enzyme, PETase, capable of breaking down PET plastic, emerged at a time when the world was desperately seeking solutions to the plastic crisis. This publication garnered widespread media attention and has since accumulated over 1,000 scientific citations. The ultimate hope extends beyond a single species capable of degrading one type of plastic. Microbiology, over the past half-century, has witnessed a revolution, revealing a vast and intricate microbial world with astonishing capabilities. Many scientists now share Oda's conviction that microbes may already hold the keys to solving seemingly intractable problems, provided we diligently explore their potential.
Read also: Enrollment at Notre Dame
Accelerating Nature's Processes: Enzyme Engineering and Bioprospecting
While discoveries like Oda's provide a crucial starting point, the scale of the plastic pollution crisis necessitates faster and more efficient degradation processes. In initial laboratory tests, Ideonella sakaiensis broke down a small piece of plastic film in about seven weeks at room temperature-a rate far too slow for impactful waste management. Fortunately, over the past four decades, scientists have become adept at engineering and manipulating enzymes. Professor Andy Pickford from the University of Portsmouth notes that the PETase enzyme is "actually very early in its evolutionary development," suggesting that human intervention can significantly enhance its capabilities.
Enzymes, the molecular machines within cells responsible for breaking down complex compounds, work by facilitating chemical reactions. To improve enzyme performance, scientists employ various strategies. While chemical reactions often benefit from higher temperatures, most enzymes are most stable at ambient temperatures. By rewriting the DNA that codes for an enzyme, scientists can alter its structure and function, increasing its stability at higher temperatures and thus accelerating its activity. However, this process is complex and often involves trade-offs. Elizabeth Bell, a researcher at the National Renewable Energy Laboratory (NREL), describes the process as "two steps forward, one step back," acknowledging the difficulty in predicting the precise genetic tweaks that will yield optimal results. Her own research on PETase involves a brute-force approach of subjecting the enzyme's active regions to every possible mutation. This allows for the testing of hundreds or thousands of potentially beneficial mutants, with any showing even marginal improvement undergoing further rounds of mutation. Gregg Beckham, head of the NREL research group, likens this method to "evolving the crap out of an enzyme." Bell's recent findings demonstrate a PETase enzyme engineered to degrade PET significantly faster than the original.
The development of tailored enzymes is not solely reliant on laboratory tinkering. The discovery of plastic-eating bacteria like Ideonella sakaiensis is a testament to the vast, largely unexplored microbial world. Scientists grapple with the question of whether to continue searching for naturally occurring, potentially superior microbes or to focus on enhancing the capabilities of those already discovered. This dilemma has fueled a surge in bioprospecting, the search for novel microorganisms with valuable properties. Teams at Chonnam National University in South Korea have explored deep landfill sites, discovering a variety of Bacillus thuringiensis that appears to metabolize polyethylene bags. Similarly, microbiologist Simon Cragg from the University of Portsmouth is investigating microbes in Vietnamese and Thai mangrove swamps, hypothesizing that bacteria adapted to degrade the waterproof coatings on mangrove roots might also be capable of breaking down plastic.
The Evolving Landscape of Microbial Research
For much of their history, microbes were primarily viewed as pathogens or simple agents for industrial processes like fermentation. However, advancements in DNA sequencing, particularly since the 1970s and becoming widely available in the mid-1980s, have revolutionized the field. These techniques allow for the cataloging and identification of microbes based on their DNA, offering insights into their functions and diversity. The genetic diversity observed has been immense, revealing that seemingly similar microorganisms are, in fact, profoundly different. This has opened up a new understanding of the sheer scale of microbial life on Earth, with estimates of species ranging from millions to potentially a trillion, the vast majority remaining undiscovered.
Historically, a significant challenge in microbiology was the "great plate count anomaly," where the number of microorganisms observed under a microscope far exceeded the number that could be cultured in a laboratory petri dish. This suggested that most microbes had specific, often unfulfilled, environmental requirements for growth. The discovery of penicillin by Alexander Fleming and the work of Selman Waksman in identifying antibiotic-producing bacteria from soil highlighted the importance of exploring natural environments for microbial solutions. Waksman's tireless efforts to cultivate wild bacteria led to the discovery of streptomycin and several other crucial antibiotics, underscoring the principle that searching the environment, rather than waiting for microbes to appear in the lab, is often more fruitful.
Read also: Movies for Student Success
Harnessing Marine Microbes and "Self-Digesting" Plastics
The imperative to address plastic pollution in marine environments has spurred the genetic engineering of marine microorganisms. Researchers have successfully modified Vibrio natriegens, a marine bacterium known for its rapid reproduction, to break down PET in saltwater. By incorporating genes from Ideonella sakaiensis, which produces PET-degrading enzymes, into V. natriegens, the modified organism can now produce these enzymes on its cell surfaces. This breakthrough, published in the AIChE Journal, marks the first instance of V. natriegens expressing foreign enzymes externally. Nathan Crook, a lead author of the study, highlighted the significance of this achievement.
Further research has focused on the bacterium Rhodococcus ruber, which has demonstrated the ability to consume and digest plastic. PhD student Maaike Goudriaan at the Royal Netherlands Institute for Sea Research (NIOZ) conducted laboratory experiments using specially manufactured plastic with a distinct carbon isotope (13C). After pre-treating the plastic with UV light, she observed the appearance of this labeled carbon as CO2, providing direct proof that bacteria can indeed metabolize plastic into CO2 and other harmless substances. Goudriaan estimates that Rhodococcus ruber can break down approximately one percent of available plastic per year, though she stresses this is likely an underestimate as not all breakdown products were measured. While excited by the discovery, Goudriaan emphasizes that microbial digestion is not a singular solution to the vast plastic soup in our oceans, viewing it as one piece of a larger puzzle. Pilot experiments with natural seawater and sediment suggest that plastic degradation may occur even in natural environments, necessitating further research to quantify this process.
In a novel approach to mitigate plastic pollution, researchers have developed a "self-digesting plastic" by incorporating spores of plastic-eating bacteria into polyurethane, a material commonly used in products like phone cases and trainers, which is difficult to recycle. These spores remain dormant during the plastic's useful life, activating and beginning to digest the material when exposed to nutrients in compost. Han Sol Kim, a researcher at the University of California San Diego, expressed hope that this innovation could "mitigate plastic pollution in nature." An added benefit is that the spores can enhance the plastic's toughness, extending its lifespan. Jon Pokorski, a co-researcher, noted, "Our process makes the materials more rugged, so it extends its useful lifetime. And then, when it's done, we're able to eliminate it from the environment, regardless of how it's disposed." While currently at the laboratory stage, this technology could potentially be implemented in a few years with industry partnership. The bacteria used, Bacillus subtilis, is a common food additive and probiotic, but it has been genetically engineered to withstand the high temperatures required for plastic manufacturing.
However, not all scientists endorse the development of biodegradable alternatives as the primary solution. Some argue that reducing plastic production and consumption in the first place is a more effective strategy. Professor Steve Fletcher of the Revolution Plastics Institute at the University of Portsmouth advocates for legally binding global cuts in plastic production, cautioning that potential solutions like self-digesting plastics might create a false sense of complacency regarding plastic pollution.
tags: #students #invent #bacteria #that #eats #plastic
