Scientists are making progress with better plastic-eating bacteria

Molecular biologist Christopher Johnson was schmoozing at a party not long ago, talking with another guest about his research, as scientists often do. Johnson works on breaking down plastics, which tend to be highly resistant to such things.

The woman he was speak­ing with at this particular pre-­wedding soiree replied that she felt overwhelmed—­hopeless—about the whole situation: how we can’t seem to stop using plastics, how they crowd landfills, how their microparticles permeate the oceans.

Overwhelmed, Johnson thought. Hopeless.

“I’m a world away from that perspective,” Johnson says, ­recalling his reaction.

That’s because plastics aren’t just happening to Johnson. He’s happening to them. Johnson is a research scientist at the National Renewable Energy Laboratory, and this past year, he and his colleagues created a biological enzyme that can chew efficiently through throwaway plastics like those that make water bottles and soap containers. The team is optimistic they can engineer a world where humans keep using this overabundant material—without winding up literally or figuratively overwhelmed by it. In that world, as part of a broader, robust recycling system, microorganisms will digest polymers into their chemical components so they can turn a profit as new and better products.

Currently, recycling doesn’t actually turn plastic into anything, chemically speaking: It just grinds the waste into smaller pieces, like shredding paper into strips. Manufacturers then reconstitute those pieces into lower-quality plastic. In bio-based recycling, as those in the field call it, plastic-eating organisms give you back the building blocks to make new materials and, eventually, goods.

Johnson’s group, in particular, captured the public’s imagination because its discovery was accidental and made for a great story. Skeptics feared the effort might backfire—that rogue GMO chompers might start gobbling the wrong polymers. Like the dashboard of your car. As you’re driving. It’s an extremely remote possibility but not completely misguided.

All that plastic trash, after all, is itself an unintended consequence. The synthetic material began, in part, as a substitute for ivory to save ele­phants from slaughter. But that innovation also brought us to where we are today: overwhelmed and hopeless. The amount of plastic that humans produce every year—more than 300 million tons—weighs about five times that of all ­people put together.

We use most of our modern polymers just once: in water bottles, shampoo bottles, milk bottles, chip bags, grocery bags, coffee stirrers. Every year, nearly 9 million tons of the litter ends up offshore. You’ve probably heard of the Great Pacific Garbage Patch: an area in the ocean’s northern half where swirling currents congregate all that refuse. But did you know that by 2050, the high seas could sport more plastic than fish?

Civilization isn’t doing a great job of cleaning up after itself, partly, Johnson and his team believe, because there’s never been a great economic incentive to. But if you can take those plastic building blocks and assemble them into something more valuable than the ­original—such as auto parts, wind turbines, or even surfboards—you can change recycling’s calculus. Companies can do well for themselves by doing good for the world.

———

Much of the accidental enzyme team works at the National Renewable Energy Lab in Golden, Colorado. The campus nudges against the foothills of the Rocky Mountains, which slope up quickly out of nothingness into 14,000-foot peaks. Solar panels occupy the roofs of nearly all of the buildings. Inside the Field Test Laboratory Building, where the group works, a ROYGBIV spectrum of utility pipes runs along ceilings and walls. Labs full of refrigerators, incubators, and high-powered microscopes hum behind card-access entryways. And, in a small meeting room on the ground floor, a matrix of screens backlights four scientists.

They, along with colleagues in Florida, England, and Brazil, form a kind of dream team for this particular bio-based recycling research: Nicholas Rorrer creates polymers. Gregg Beckham tries to figure out how bacterial and fungal chemicals break down compounds such as cellulose, the main ingredient in plant-cell walls and many veggies. Bryon Donohoe studies how ­cells with polymer-eating enzymes work. Johnson engineers new kinds of cells that secrete those enzymes. Those areas of expertise are each key to exploring how bacteria indulge an appetite for plastic—and how to manipulate them into being better snackers.

On one of the screens behind them, an enzyme skates along a close-up of cellulose, chewing off individual strands and spitting them back out as blocks of sugar—the ultimate drive-through eating experience. This simulation, the scientists say, is the same way a polymer meets its match.

The crew first learned of the concept when the March 2016 issue of Science magazine brought news that researchers in Japan had discovered a strange species of bacteria in samples of soil near a bottle recycling plant in the city of Sakai. It could chomp through polyethylene tere­phtha­late, commonly known as PET, which manufacturers widely use to make plastic bottles and containers. A team led by Kenji Miyamoto, a bioscientist at Keio University, found that the organism squirted out an enzyme, which they dubbed PETase, that stripped the polymer into chemical pieces. They called this amazing organism Ideonella sakaiensis, after its home city. Still, not to diss Ideonella, but it didn’t work fast enough: Given six weeks and tropical temps, it could eat through a film of PET. Not exactly the stuff of efficient recycling plants. Plus, getting it to grow required some careful care and feeding.

Soon after the journal article appeared, Beckham found himself in England, having a beer with University of Portsmouth’s John McGeehan, a colleague in cellulose research and an expert at mapping the structures of tiny enzymes. They began to brainstorm how to combine forces to better understand how PETase digests PET. After all, their work already looked at how the natural degrades the natural—for example, how bacteria and fungi use enzymes to digest cellulose. Maybe that work could help them understand how the natural breaks down the synthetic.

After their brainstorming pint, the two recruited Johnson, Donohoe, and Rorrer, as well as another colleague in Florida, Lee Woodcock, whose sophisticated computer models simulate how cellular chemicals work. Then, they got started.

First, the team needed to understand how PETase breaks down its chosen plastic. The molecules in a polymer are like connected Lego bricks that can just pull apart. For PET, PETase is the puller. But to understand how PETase could grab onto and torque the plastic’s molecules, the team needed enough of the enzyme to be able to map it.

That’s where Johnson’s cellular expertise came in. Working with an outside ­company, they synthesized the gene that produces PETase so it could later be slipped into E. coli, a single-celled organism that is quick and easy to grow in a lab. He sent the genetic code across the pond to McGeehan’s lab. There, the mutant food-poisoner had some grub and began pumping out PETase.

McGeehan schlepped the PETase enzyme to a facility with a super-powerful X-ray microscope that uses light 10 billion times stronger than the sun to probe samples and create ­atomic-​scale pictures. Inside the exotic microscope, supercooled magnets guided the X-rays until the scientists could see PETase itself—and not just its goo-​­making effects.

The enzyme, to the untrained eye, resembles the love child of a sea sponge and a human brain. Or, if you are a very lucky biologist, it looks almost exactly like cutinase, the puller for cutin, a waxy polymer that coats many plants. Cutinase has a narrow U-shaped pit that notches into cutin just so. PETase has the same U, just wider, kind of like a cutinase in a fun-house mirror. The PETase U notches into PET, like the two sides of a BFF necklace.

This is a no-brainer, Beckham thought at the time: The enzyme, he reasoned, initially evolved to eat cutin, and clearly had adapted in the presence of so much trash to have a new favorite food.

The form, function, and evolutionary idea in hand, the team submitted their paper for publication in October 2017. But the origin story—their most beloved part—was problematic. “One of our reviewers said, ‘No, you have to show that,’” Beckham recalls.

This is going to be a crap activity, he imagined. It seemed so obvious that cutinase had Darwined its way into PETase. But to show how that had happened, they would have to wind back the evolutionary clock, shrinking the wide PETase U back to a wee cutinase U, and in the process, they thought, making it unable, or at least less able, to chew plastic. Then they would reverse course, turning the cutinase back into PETase, showing how one became the other.

Beckham would have to eat (and digest) those words.

———

The team began the first half of the experiment, turning PETase back into cutinase, in late 2017. First, they tweaked the DNA that makes the enzyme PETase. Specifically, they mutated two amino acids so their replacements pinched into a U, creating an enzyme that was closer to cutinase. For his part, ­Rorrer—the polymer guy—began to harvest bottles from colleagues, including staff favorites such as Diet Pepsi and Diet Dr Pepper. (Today, the refuse still lines the top of his cubicle.) He used a standard office hole puncher to snip out circles. He then placed those in close quarters with versions of the modified enzyme, expecting he’d come back to find it making minimal progress, if any.

But that’s not what happened. When Rorrer returned four days later, he found the hacked enzyme was not only working, but it was eating about 30 percent more than the PETase from the Sakai recycling plant. The team members began to doubt themselves. Maybe I mislabeled the samples, Rorrer thought. Donohoe, the cell-breakdown specialist, suspected they’d mixed up the samples. They repeated the experiment two more times but kept getting the same outcome: The new enzyme had a good appetite. Donohoe recalls, “I’m like, ‘I guess we have to believe it, even though I don’t know how to.'”

The result still left open whether PETase had morphed from cutinase in the “oh, of course” way the team had surmised. But the unexpected outcome is still good news: It means they can improve what evolution hath already wrought. “Nature hasn’t necessarily found the ultimate solution,” Beckham, the chemical engineer, says.

When they announced the discovery in April 2018, people latched on to its oopsiness. John McGeehan got a Goop award from Gwyneth Paltrow’s pseudoscience wellness brand. He tried to reject it, but there is no rejecting Gwyneth Paltrow. But for this group, being famous wasn’t enough. And improving PETase a little wasn’t either. “There’s probably room here to make it a heck of a lot better,” Beckham says.

———

Ideonella sakaiensis, turns out, is far from the only organism that can use plastic waste as fuel. “Bacteria probably do just evolve to eat things all around them,” says genetic engineer Johnson. Biologists have known for decades that existing enzymes, such as the so-​called esterases that microbes and fungi spit out, can break down PET and nylon.

Plastics floating in Lake Zurich carry four organisms primed to eat polyurethane. In the ocean, investigators in India have discovered bacterial species that can degrade polyvinyl alcohol, which water­proofs paper. Another group found a fungus whose cutinase also munches PET. None of these, though, can feast fast enough at scale to be useful to industry—yet. With more than 300 million tons of plastic produced every year, organisms would need to churn through around 906,000 tons on all days ending in “y” to get the job done. Taking four days to dissolve the surface of a Diet Dr Pepper bottle isn’t fast enough.

In its own search for better polymer eaters, the dream team recently recruited new players from Montana State University who study extremophiles boiling in the brightly colored pools of Yellowstone. ­Selfie-​­snapping tourists throw a lot of trash into those hot springs. At temperatures like these—­sometimes more than 400 ­degrees—​­plastic melts.

To a bacterium, munching overheated junk is like taking speed: Everything happens a lot faster. If the scientists can find an extremophile, or engineer one, that likes it hot and eats PET, then they’re one step closer to a process that works fast enough to be useful in the real world.

In that scenario, a future recycling plant would heat or dice up the plastic, then throw it in a big pot of hot water and sprinkle in some PETase (or other hungry enzyme). That would produce a soup of polysyllabic ingredients: terephthalic acid and ethylene glycol, the stuff that companies can spin into stronger, higher-value polymers.

First, though, they need a better enzyme. “Life will find a way,” Beckham says, smiling as he paraphrases Jurassic Park. Still, nature could use an assist. So the team starts by exploiting evolution’s secret: random mutation. Sometimes new genetic code makes the organism better suited for its environment, and the microbe lives to pass that wonkiness to its offspring. In the lab, though, we can accelerate evolution by, say, feeding the would-be plastic-eaters only PET. If they don’t sit down to dinner, they starve.

The team is also trying to create new life by injecting the PETase gene into bacteria that is less picky than Ideonella. Beckham pulls up an unpublished paper and scrolls to before-and-after pictures. After four days in a test tube with a new mutant, a bit of hole-punched plastic is what he calls “a soupy mix of crap.” “Crap,” here, is ­chewed-​up plastic parts.

The effort, in other words, is working. As Beckham looks at his pictures, he laughs and recalls a link people sent him when the team’s first paper came out. It pointed to a 1971 book called Mutant 59: The Plastic-Eaters. In the tale, a ­polymer-​­dissolving virus takes over—killing spacecraft, crashing planes, sinking submarines, and generally causing uncontrollable chaos as it destroys seemingly all the plastic in the world.

Nonfictional researchers plan for their engineered organisms to stay in the lab, in tubes, and, eventually, in industrial processes. Such organisms might even already exist on the outside, having evolved the old-fashioned way. Remember, the world has bacteria that eat lots of other things we love: metal, bread, cheese, our own skin. And we’re all still here, nibbling bread and cheese, sitting on metal chairs. Given an eons-long head start, the microbes have not yet managed to take over. So, unless nature gets remarkably better remarkably fast (it took something like 50 years to make the inefficient version of PETase), or a rogue actor stages a coup, no bitsy beasts will be gutting your Walmart kayak anytime soon.

Beckham does give more credence to a concern that carbon, spit out during digestion, eventually becomes carbon dioxide, a greenhouse gas that contributes to climate change. But any addition would be dwarfed by gases from other industries. His group wants neither a bio-warmed world nor one without plastics.

Instead, they aim to create a real economic incentive for reclaiming most polymers. Right now, what comes out the recycling end is just PET with weaker bonds: It’s challenging to make another bottle out of it, and it’s worth about 75 percent of what the original plastic was. It goes into textiles or carpets. Those usually wind up in landfills.

Biologically breaking down plastic, though, produces components that can become the precursors to pricey materials like Kevlar, which sells for two or three times as much as recycled PET and goes into stress-​­resistant products like snowboards. These materials give companies a cash-​based reason to reclaim plastic. Innovators might even use them to build flightier aircraft, more-­efficient cars, and hardy, lightweight stuff we ­haven’t thought of yet. Stuff that maybe does its part to reduce ­greenhouse-​gas emissions.

This world won’t exist tomorrow, or next year. But it’s a foreseeable future, synthesized through the dream team’s microbes, or others’, and whatever nature brings to the polymer picnic table. If they succeed, we’ll be able coexist with plastics, not atop of a heap of them.

This article was originally published in the Summer 2019 Make It Last issue of Popular Science.