By Carolyn Beans for the Proceedings of the National Academy of Science.
Broadcast version by Judith Ruiz-Branch for Wisconsin News Connection reporting for the Pulitzer Center-Public News Service Collaboration.
Every year, US dairy producers churn out billions of pounds of cheese—over 14 billion in 2023 alone. As that cheese heads to market, producers must contend with what’s left behind: roughly 6 billion pounds of whey by dry weight, says Declan Roche, chief commercial officer of Foremost Farms USA, a Wisconsin-based dairy cooperative.
Untreated whey can’t be released into waterways. Although it’s about 94% water, the whey’s nutrients would trigger algae blooms, sucking oxygen from water and killing fish. Instead, many cheese producers filter out the protein to sell it as protein powder. But this process leaves behind another by-product, known as whey permeate. Producers might then salvage lactose from the permeate to sell for other uses. Even so, recovering lactose through mechanical processes is expensive. The profits are meager, Roche says. “It’s a least loss option.”
Microbes might offer a better way to manage wastewater. Today, researchers across industries, from food production to textiles to tech, are turning to microbes and their molecules to churn out marketable products as diverse as bioplastics, biofuel, metals, and animal feed (1). The ultimate goal is to transform industries, so waste gets cycled back into production rather than ending up in landfills. It’s a field that’s been “exploding” in the last five years, says environmental engineer Ezequiel Santillan of the Singapore Centre for Environmental Life Sciences Engineering.
Last year, Foremost Farms partnered with a Boston-based biotech company to develop a microbe-powered system that generates new products from the co-op’s waste. And university researchers are moving from the lab to large-scale pilots. “We’re creating a lot more economic value out of what is already there,” says Erica Majumder, a microbiologist at the University of Wisconsin–Madison (UW-Madison), who is studying dairy waste. “[Waste] actually becomes another revenue stream.”
A Circular Bioeconomy
Microbes are already at work digesting nutrients in many industrial waste streams. But these systems don’t typically make desirable products. Once the water is cleaned up and released, the microbes left behind become another type of waste to deal with, Santillan says. At the same time, industries use microbes to generate products through fermentation, including beer, biofuels, and insulin. But these microbes need to be fed. Their meals often consist of crops farmed for this purpose, which leaves less land to grow food for human consumption
Santillan, Majumder, and others want to bring these two processes together: Microbes feeding on the industrial wastewater would be generating the marketable products at the same time. “There are lots and lots of different microorganisms that are very capable of metabolizing the huge variety of chemical compounds that are in waste streams,” Majumder says. These microbes could play a key role in shifting societies toward what’s called a circular bioeconomy.
“The idea of the circular economy is to keep materials in use as much as possible and for as long as possible,” Santillan says. The longer materials stay in circulation, the less waste and the more sustainable the industry is. Metals and plastics, for example, can be recycled through chemical or physical processes.
A fully circular bioeconomy, meanwhile, relies on renewable resources to make products and, often, microbes to do the recycling. Microbes are especially good at recycling resources that are dispersed in liquids, even at low concentrations. “When we have highly complex mixtures, that’s really difficult for chemical or mechanical processes to handle,” Majumder says.
From Dairy Waste to Plastics
When Majumder sees dairy waste, she sees the building blocks for bioplastics. Plastics have traditionally epitomized a linear economy. Fossil fuels extracted from the earth get separated and transformed into petrochemicals. Those chemicals are then formed into plastic products that are often used only briefly before being discarded. An estimated 79% of the 6.3 billion metric tons of plastic discarded globally through 2015 ended up in landfills or the environment (2).
But plastics don’t have to come from fossil fuels. Many bacteria can naturally produce plastic polymers, such as polyhydroxybutyrate (PHB). This easily biodegradable plastic performs much like polypropylene, and it is already being used in some applications, including food packaging and disposable utensils. (PHB does release methane as it biodegrades, but no more so than conventional composting, Majumder says.)
Other bacteria, such as Escherichia coli, can be engineered to make these same plastics. In labs, microbiologists have successfully grown PHB-producing microbes on foods like cornstarch. But it’s dramatically more expensive than producing plastics from fossil fuels.
Majumder has been working with Deepak Kumar, a bioprocess scientist at the State University of New York College of Environmental Science and Forestry in Syracuse, to identify industry waste streams that could feed plastic-producing microbes at a lower cost. One of the team’s most promising waste targets is another dairy by-product: acid whey. Unlike the whey left over from cheese making, acid whey—from Greek yogurt and cottage cheese production—is highly acidic. That makes acid whey even more challenging to safely discard. But it’s also chock-full of lactose and lactic acid, which many microbes will happily digest.
Majumder and Kumar grew a strain of E. coli engineered to produce PHB on acid whey collected from a local creamery. Untreated, acid whey is so acidic that it would quickly kill off E. coli and destroy any plastics that the microbes managed to produce. But by raising the pH and adding some additional ingredients, such as minerals and salts, the team created an environment where the microbes thrived.
The microbes fed on the lactose and lactic acid, recycling the nutrients’ carbon molecules into the backbone of PHB, which accumulated inside their cells. Ultimately, when the team harvested and dried the E. coli, 70% of the microbes’ dry weight was made up of this bioplastic (3). A dairy producer could extract the PHB and ship it to a plastics company just like any raw polymer derived from fossil fuels, Majumder says. What’s more, in producing PHB, the microbes digested 96% of the whey’s lactose and over 61% of the lactic acid (3).
This team has shown from start to finish how microbes can transform waste that’s available on many dairy plants right now, says Stephanie Lansing, a bioenergy and biotechnology expert at the University of Maryland in College Park, who was not involved in the research. Lansing studies how microbes can generate bioplastics when fed on food waste (4). The environment benefits, she says. “You’re taking something that you might have to treat—and use energy to treat—and you’re turning it into a beneficial product.”
Foraging for Metal
Other researchers have their sights on wastewater from the tech industry. Producing microchips, films, and many other high-tech components relies on expensive metals, including gallium, germanium, and indium. These metals are considered critical elements because they are in high demand, but their supply is not assured, says biochemical and environmental engineer Rohan Jain. Small fragments of these metals end up in wastewater at multiple steps of the production process, including during etching and polishing. The metal concentrations in wastewater are high enough to make the water toxic and expensive to treat, yet low enough to make retrieving the metals difficult.
But Jain is using iron-loving molecules naturally produced by bacteria to capture these metals. Many bacteria send out these molecules, known as siderophores, to bind to iron and retrieve it from the environment, Jain explains. Because gallium, germanium, and indium are structurally similar to iron, siderophores can find and bind to these metals too, even in liquids with metal concentrations as low as 300 parts per million (5).
Jain’s team at the Helmholtz Institute Freiberg for Resource Technology, Helmholtz-Zentrum Dresden-Rossendorf, in Germany, began developing siderophores into a technology for recovering metals from wastewater in 2016. The researchers first targeted gallium. “Will [the siderophores] survive the wastewater conditions? Can you regenerate them? Concentrate them?” Jain recalls asking. “All those environmental engineering problems were unknown.”
In 2019, the team reported that it had extracted gallium from wastewater collected from a factory after the production of silicon wafers (6). Siderophores found and stuck to 100% of the gallium. The team then added an acid that separated most of the gallium from the siderophores. In an industrial setting, that gallium could then be cycled back into production and the siderophores put to work again, Jain says.
The team is now operating a pilot-scale system that processes 1,000 liters of wastewater daily. The system relies on the only two commercially available siderophores—one synthetic and the other harnessed from bacteria. Neither is currently used by companies for drawing metals from industrial waste streams.
Jain is also screening siderophores to identify the most effective foragers for specific metals. “We know that there are more than 500 types of siderophores with different structures,” he says. He uses computer modeling to predict which siderophores will work best and then grows the bacteria to harness the siderophores and test his predictions (5).
Interest in recycling metals from wastewater is growing, he says, especially after China began limiting exports of gallium and germanium last year (7). While his system might prove economical for extracting a large percentage of many different metals in water, he notes that it can’t recover everything. “That last 5%,” Jain says, “would cost you an enormous amount of energy, time, and money.”
Microbes to Feed the Masses
Instead of generating some useful product, microbes feeding on wastewater streams can instead be the product. In 2020, Santillan’s team began analyzing the contents of wastewater collected from Mr Bean, a soybean processing company in Singapore (8). The water contained nutrients including salts and sugars, as well as a community of microbes that colonized this rich food source on their own. The team placed the wastewater into bioreactors in the lab. “As the microbes grow, they generate protein through their biological metabolism, so you make protein out of simple, or even more complex, carbon compounds,” Santillan says. The result: a protein-rich mass of microbes, plus water clean enough to be discharged or cycled back into production.
In January 2024, the team reported on what happened when they added these microbes into an aquaculture feed for Asian sea bass (9). Today, sea bass and other carnivorous fish raised in aquaculture are often fed fishmeal and oil from wild-caught fish, such as sardines and anchovies (10). But as aquaculture expands, there’s a growing need for alternatives that won’t deplete natural fish populations.
After swapping out half of the fishmeal in sea bass feed with the protein-rich microbes, Santillan’s team found that young fish survived and gained just as much weight as those raised on conventional feed (9).
Turning to microbes for feed could reduce the environmental impact of aquaculture. It could also aid the Singapore government’s mission to increase its food security by producing 30% of its own food by 2030, Santillan says. Currently, the country generates only about 10% of the food it consumes. “In Singapore, the only reasonable animal protein industry that has the space to grow is aquaculture,” he says. “But all the fish feed that they use is imported.” Meanwhile, wastewater from soybean processing is local, abundant, and costly to treat. “The goal is to connect these two needs,” Santillan says.
Based on the success of his soybean wastewater study, Santillan says that he and his team are now collaborating with Mr Bean and other partners to try to develop an industrial-scale demonstration facility adjacent to a soybean processing plant. He’s hoping it will prove the economic feasibility of his system. “We need to have a demonstration plant where we can produce, instead of kilograms of microbial protein, tons of microbial protein,” he says. But pulling it off will require buy-in from companies across the soybean, fish feed, and aquaculture industries, as well as investors.
From Lab to Factory
For any of these processes to work at an industrial scale, companies will have to build bioreactors to treat the waste where it is produced. “If you have to drive tankers full of this waste long distances, that negates a lot of the sustainability gains,” Majumder says.
At the UW-Madison Center for Dairy Research, a 400-liter bioreactor now sits alongside the dairy production facilities. There, Majumder is exploring how her team’s technology could work on a larger scale. Other UW-Madison researchers interested in turning waste into other products will also have access to the bioreactor.
For now, it’s hard for emerging microbe-driven, wastewater-repurposing technologies to compete with decades-old practices, says Piergiuseppe Morone, an economist at The University of Rome Unitelma Sapienza and a co-author of the 2023 book The Circular Bioeconomy: Theories and Tools for Economists and Sustainability Scientists. His research suggests that bio-based certification labels could help tip the balance. Some consumers, he says, are willing to pay more for products derived from bio-based materials and produced in a socially and environmentally responsible way (11).
But moving toward an economy that is environmentally sustainable requires not only the willingness to pay a small green premium, but also radical changes in production practices and consumer mindset, Morone says. “The idea of associating well-being with the accumulation of more and more goods is something that is no longer feasible,” he says. Consumers should instead measure well-being based on their access to goods and services they truly need, he says, such as access to transportation, rather than ownership of a car.
As for Roche of Foremost Farms, he hopes that turning dairy waste into new products will ultimately increase the value of milk—a pressing need for dairy producers who have struggled to cover the cost of production in recent years. What product exactly his team’s new microbe-powered system will generate isn’t yet public. But he says the possibilities extend far beyond food and extend into the chemical and energy industries. “We’re the largest cheese maker in Wisconsin,” Roche says. “But for the co-op to prosper and grow, value-added products need to be generated from every component of the milk.” Microbes, he hopes, will help make that happen.
Carolyn Beans wrote this article for the Proceedings of the National Academy of Science.
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