Why worms (and microbes) are catching on as a manure pollution solution

Anthony Agueda, a third-generation California dairy farmer, pulls a rake through a bed of dark, wet wood chips on his family’s land in Hickman, a tiny town in the state’s agricultural heartland.

He reaches down with both hands and pulls up a clump of muck, turning it over to reveal a half-dozen squirming red earthworms. There are likely hundreds of thousands more wriggling just under the surface of the three-foot mound of wood and crushed river rock before us, which stretches across the equivalent of six football fields. These natural materials form a biofilter that may dramatically cut the methane, nitrous oxide, and water pollution generated by the massive amounts of manure that hundreds of Holstein cows produce each day.

Agueda’s family business, the Alberto Dairy, was one of the first cattle operations in California to adopt this approach to manure treatment, developed and patented by the Chilean company BioFiltro. Eight more of these so-called vermifiltration systems are already operating on US dairies, according to the company, while another 16 are under construction or set to be next year, nearly all of them in California. 

Vermifiltration is just one of a variety of methods that farmers, companies, and scientists are employing to drive down manure pollution as the livestock industry faces growing pressure to address the environmental harms from one of the smelliest parts of the business. California, easily the nation’s largest milk producer, has established a handful of programs to promote their adoption, including one initiative that has funneled more than a billion dollars to farms.

Researchers stress that much more work needs to be done to determine the most effective approaches, the trade-offs between them, and their success over the long term, under actual farm conditions.

Agueda says that he and his family recognized the need to adopt new practices as environmental rules tightened. They were drawn to vermifiltration because it’s simple and relatively cheap compared with other, higher-tech options.

“California daily farmers are constantly facing more and more regulation,” says Agueda, standing alongside one of the farm’s free-stall barns. “This makes me excited, because it shows how we are part of the solution.”

The growing manure problem

Manure is responsible for a significant portion of the climate pollution from livestock operations. The World Resources Institute estimates that manure management on dairy and swine farms accounts for 1.6% of the US’s greenhouse-gas emissions. Globally, manure storage and processing makes up about 10% of the livestock industry’s contributions to climate change. 

“Farms have become larger in the past two decades or so, so there’s much more manure—and that has to be stored somewhere,” says Swati Hegde, the organization’s global manager of agricultural methane.

Typically, cattle and swine farms spray manure into lagoons or tanks, creating a foul-smelling, low-oxygen slurry in which microorganisms known as methanogens thrive. They gobble up hydrogen, carbon dioxide, and other compounds and produce methane as a by-product. Other microbes in the mix produce smaller amounts of nitrous oxide.

Both are particularly potent greenhouse gases, with as much as 30 to nearly 275 times the warming power of carbon dioxide, respectively, over a century.

The slurry is often spread onto fields to add nutrients to the soil. When it’s done excessively or improperly, this part of the practice can pollute soil or groundwater with drug residues, pathogens like salmonella and E. coli, and nitrates. Nitrates that leach into drinking water have been linked to a variety of human health risks. And those that flow into rivers, lakes, and coastal waters can spawn algae blooms that poison fish, block sunlight, suck up oxygen, or form large coastal dead zones devoid of marine life.

Policy drivers

A number of regions, nations, and states have passed regulations or offered subsidies designed to limit the pollution from livestock manure, but so far, most of the major initiatives have focused on water contamination rather than greenhouse-gas emissions.

The European Union, for instance, restricts the amount of manure that farmers can apply to fields and requires member nations to monitor nitrate levels in ground and surface water. The US’s Clean Water Act requires large livestock operations to obtain permits and develop manure management plans that limit pollution. 

But California has arguably done the most to use government policy specifically to drive down the methane emissions from livestock. The dairy industry accounts for about 45% of the state’s pollution from the potent greenhouse gas, and more than half of that comes from manure, according to the government’s estimates. 

In 2016, the state enacted a law that requires dairies, landfills, and other businesses to cut methane emissions 40% below 2013 levels by 2030, as part of a broader effort to reduce pollution from powerful but short-lived greenhouse gases. The measure directed the California Air Resources Board, the state’s main climate regulatory agency, to set up various incentive programs to encourage these industries to shift to cleaner practices. 

“In terms of bang for your buck, short-term benefits, methane can go a long way toward reaching climate goals,” says Tawny Mata, director of California’s Office of Agricultural Resilience and Sustainability. 

Between these various programs—and falling livestock numbers in the state—the dairy sector is on track to reduce annual methane emissions by the equivalent of 5 million metric tons of carbon dioxide by 2030, the state estimates. That would still fall about 4 million tons short of the target under the 2016 law.

The downsides of dairy digesters

Excluding the decline in herd populations—which has been driven by growing international competition and rising costs—the vast majority of California’s estimated methane reductions come from the use of what are known as anaerobic digesters. This technology entails covering the slurry lagoons to prevent methane from leaking into the air and then piping the biogas into separate vessels, where it’s cleaned and converted into natural gas. 

Under California’s Low Carbon Fuel Standard program, dairies that use digesters to produce gas delivered into pipelines can earn credits and sell them to petroleum refineries and other major polluters, as a means of helping those companies meet their own emissions reduction requirements. 

The gas can then fuel power plants, produce hydrogen, or power natural-gas vehicles. These uses still release carbon dioxide, but the state considers it a climate win because it avoids the release of methane, which traps even more heat. 

The rich revenue stream from California’s program has spurred hundreds of US farms to install anaerobic digesters over the last decade. Since 2020, it has produced more than $1 billion for farms, Cal Poly researchers noted in a paper last year.

But there are a variety of concerns about this approach.

The first is that it’s viable only for farms with about 2,000 cattle or more, because the equipment is very expensive to install, says Frank Mitloehner, a professor and chair of the Department of Animal Science at the University of California, Davis.

“For the lion’s share of dairies, digesters will not be a solution,” he says. 

Since the manure is often still spread across fields, digesters also do little to address the water pollution problems—and can even exacerbate them because of some of the chemistry that occurs during that process. 

Yet the huge subsidies flowing to digesters have steered money, energy, and attention away from other solutions that may offer better overall environmental outcomes, says Danny Cullenward, a senior fellow with the Kleinman Center for Energy Policy at the University of Pennsylvania, who has closely studied the California program.

“That is really not a solution at scale, and it’s diverting a huge fraction of precious resources to what I think is mostly not the right answer,” he says. 

Alternatives

The high up-front costs and limitations of digesters have spawned growing interest in alternative solutions—many of which work by reducing the formation of methane in the first place instead of turning that methane into a sellable fuel.

One of the cheapest, easiest, and most popular approaches, known as solid separation, uses simple machinery like a screw press to squeeze much of the water out of the manure slurry. The remaining solids are dry and exposed to open air, shifting away from the oxygen-free conditions in which methane is readily produced.

Other methods include increasing acidity in lagoons, bubbling air through them, or adding methane-eating microbes to the slurry, all of which alter the chemistry in ways that promise to reduce the amount of methane released. One company, Sedron Technologies of Sedro-Woolley, Washington, has also developed a sort of high-tech solid separation approach that extracts several marketable products from the animal waste, including a liquid organic fertilizer.  

The state of California set up a pair of additional programs to help smaller farmers adopt some of these other approaches, dubbed the Alternative Manure Management Program and the Dairy Plus Program.

The bulk of the funds have gone to solid separation systems. But the state has provided more than $18 million to support 15 vermifiltration projects. The Alberto Dairy has received nearly $2 million between the two programs.

Oreo cows

As I drove down a dusty road bordering the dairy, black-and-white bovines, affectionately known as Oreo cows, stretched their heads through the rails of an open barn, nibbling on golden silage scattered along the structure. Agueda’s grandfather Antonio Alberto founded the dairy 45 years ago in nearby Atwater, California, but eventually settled in Hickman, population 604, in 1989. 

It was mid-March but already above 80 °F in the Central Valley, which is walled off from the cool Pacific air by the coastal mountain range. Knee-high oat stalks swayed in fields that stretched to a line of almond trees in the distance.

Agueda, who graduated from Fresno State last year and now helps lead the operations on the farm, met me and UC Davis’s Mitloehner, who has studied the effects of vermifiltration, along the side of the barn. (UC Davis has no affiliation with the farm, but the university helped facilitate the meeting.)

He led us along dirt lanes as he explained the workings of the vermifiltration system, which they began using in October 2024.  

As before, a flush system washes manure from the floors of the barns into a large collection pit. But now a set of pumps funnels it through a series of large V-shaped metal contraptions standing on a nearby concrete pad, where mechanical screens separate most of the solids from the water.

A conveyor belt takes away the solids, which the farm composts for cow bedding or fertilizer. The remaining liquid moves through a system of pipes, first to settling ponds and then on to an irrigation system suspended above the vermifiltration beds. The long, tubular structure runs over the mounds on wheels set in gravel tracks, wetting the wood chips as it goes. The worms and various microbes residing in the biofilter then set to work consuming much of the remaining solid material, according to BioFiltro.

“Once the water is sprinkled on top, it takes about four hours from beginning to end for it to percolate through and drain to the end,” Agueda says.

He then defers to Mitloehner to explain the science of what happens as it does, adding, “I’m just the dairyman.”

The science

Mitloehner says he was skeptical of BioFiltro’s claims when he first heard them, particularly the assertion that the system could nearly eliminate nitrogen and, with it, the various forms of pollution it can produce, including ammonia and nitrates. 

So he decided to study a similar setup at the Fanelli Dairy, an operation in Hilmar, California, about 20 miles to the south. He and colleagues monitored the emissions from wastewater samples that were taken from the system before and after the liquid moved through the filter. In a paper published in 2018, the researchers concluded that vermifiltration reduced ammonia emissions from the resulting water by about 90%.

BioFiltro, whose tagline is “worm-powered solutions,” states that its technology “catalyzes the digestive power of worms and microbes to remove up to 99% of wastewater contaminants.”

But Mitloehner questions how big a role the invertebrates play in the process, calling it “kind of a catchy narrative.”

His take is simpler: The rocks and wood chips form a porous filter that replaces the anaerobic environment of a manure lagoon with an aerobic one. And in that oxygen-rich environment, different types of microbes thrive. 

His study suggests that these microbes are highly effective at converting nitrogen compounds in manure into nitrogen gas—a benign gas that makes up 78% of Earth’s atmosphere—instead of ammonia. That’s notable because while ammonia in manure acts as a fertilizer when it’s applied to fields, it also converts into the nitrates that can leach into groundwater.

Several more recent studies, which were partially or fully funded by BioFiltro and one of its regional distribution partners, Organix, produced similarly promising results. For instance, a 2022 study in Bioresource Technology Reports, also conducted at the Fanelli Dairy, concluded that the filter removed nearly 85% of the nitrogen in the operation’s wastewater. 

But a befuddling wrinkle is that when it came to methane, those studies and Mitloehner’s independent one found nearly opposite results.

While both the company- and partner-supported studies concluded that the filter eliminated the vast majority of methane pollution, Mitloehner’s study found that methane emissions were nearly 85% higher than those from the lagoon. 

In a follow-up email exchange, Mitloehner stressed that it’s not appropriate to compare his results with those that emerged from the other study at the same dairy, because the teams used very different methods, instruments, and measurement periods. Moreover, the focus of his research was the effect on nitrogen.

He said it’s “entirely reasonable” and “biologically plausible” that vermifiltration could substantially reduce methane emissions, simply by creating that aerobic environment.

“That said, I would be cautious about calling the magnitude of the reduction a fully settled issue,” he added. “While the available studies, including those you mentioned, point in the same general direction, the number of independent studies remains relatively limited, and results can vary.”

Patrick Beckett, BioFiltro’s vice president of quality and R&D, also stressed that there were crucial differences in the methodology of Mitloehner’s study that could have affected his methane findings.

In addition, he said the Organix funding came by way of a Washington state grant and described that study and the one BioFiltro supported as “high quality, peer reviewed” research that “has been submitted to other technical third parties for review and acceptance.”

Beckett says he agrees that additional independent reviews of BioFiltro’s systems is “fair and necessary” and notes that other studies have occurred or are underway.  

“That said,” Beckett wrote in an emailed response to questions from MIT Technology Review, “it seems unreasonable that BioFiltro would be held to a standard of not being allowed to invest in technical research by qualified third parties to learn more about the capabilities of our technology, and use the results of that research to enter new markets and to understand the value we can bring to projects or entire industries beyond water treatment.”

Milk money

BioFiltro is already building a business model around the available findings.

The company, founded in 2009, has been selling its vermifiltration systems or services to other industries around the world for years. It says there are around 225 operating in nine countries, at sites including municipal wastewater facilities, wineries, fruit processors, and other industrial operations.

But BioFiltro, whose US headquarters are in Davis, California, is seeing increasing demand among dairies as the industry faces growing pressure to address manure pollution. Late last year, it raised $35 million that the business says it will use, in large part, to accelerate its growth across the sector.

In an interview, Sarah Ploss, the company’s senior vice president of agriculture, explains the basic financial template for how it works with dairies: BioFiltro pays for, owns, installs, and operates the system. The farm, in turn, covers a share of the additional electricity, operations, and maintenance costs. 

Ploss says the dairy gets back clean water and the ability to focus on what it does best: producing milk. For its part, BioFiltro can generate carbon credits from the reduction in greenhouse gases, which it can then sell to makers of consumer packaged goods that are looking for ways to address the emissions throughout their supply chains, she says.

BioFiltro says that Verra, which sets standards for and assesses greenhouse-gas crediting projects, has registered two of its projects: the Royal Dairy and Moxee Dairy, both in Washington.

The Swiss confectionary giant Nestlé has bought more than 150,000 credits generated by the Royal Dairy’s vermifiltration system, according to an offsets database managed by CarbonPlan, which assesses the scientific integrity of climate action programs. Ploss said that BioFiltro has sold more than 200,000 credits from the project so far, and adds that it secured a different buyer for a project in California, which she said she couldn’t name. 

Three additional projects involving BioFiltro systems took the initial steps to become registered through Verra but didn’t move forward and weren’t built, Ploss said in an email. The request for registration for the Alberto Dairy estimates that the system there will reduce emissions by the equivalent of more than 30,000 metric tons of carbon dioxide per year. 

BioFiltro could take advantage of another revenue source as well: selling what it calls vermicompost, a rich soil additive composed of the leftover materials in the biofilter, including worm castings—a combination of cocoons, excrement, and remains. At retail, worm castings can run more than $500 per ton.

Beckett says the company is still developing that market but notes that it could help the industry offset rising fertilizer costs. 

“I think we’re going to enable a larger-scale use and adoption of it that could be meaningful to agriculture,” he says, adding: “These will become basically soil production facilities.” 

Concerns

Determining how well vermifiltration and other manure management approaches work will require more time and more research, experts say. 

Katharine Dickson, an agricultural emissions scientist who recently finished a postdoctoral program at UC Davis, says there should be in-the-field accounting to ensure that any of these methods are working as well as hoped—or to the degree government policy programs assume. All of which is tricky to achieve given the dynamic biological processes playing out in live animals and microbial communities on open farms, she adds.

“Vermifiltration, for example, depends on a live earthworm population whose performance is sensitive to temperature, moisture, and toxicity, and can shift with seasonal conditions or changes in herd size and manure characteristics on a given farm,” Dickson said in an email. 

The use of carbon credits to earn money from vermifiltration projects raises a different set of potential concerns. Most notably, if the methane decreases aren’t as significant as assumed, the projects could receive more credits than they deserve. 

There are more complicated issues as well. For the carbon credit system to make any real difference in the net amount of greenhouse gas in the atmosphere, it must produce emissions reductions that wouldn’t have occurred without that financial incentive. If it was going to happen anyway—as a result, say, of rich grants, legal pressures, or looming policies—the buyer of the credits can’t legitimately claim to have made any progress on its own climate emissions, says Grayson Badgley, a research scientist at CarbonPlan.

On that point, if California agriculture doesn’t meet its looming methane reduction targets, the carrots the state offers could be replaced by sticks: The California Air Resources Board recently began discussing rules that would force, rather than nudge, the sector to meet the 40% reduction required under the 2016 law.

“If lots of dairies are cleaning up their act ahead of pending regulation, it really does seem like the regulation, not offsets, is driving that action,” Badgley wrote in an email. “Trying to collect as many offsets prior to that deadline might adhere to the rules of the market, while still raising questions about whether those rules have enabled real climate action.”

Investing in sustainability 

Beckett disagreed that the possibility of forthcoming regulations undermines the case for generating carbon credits from current projects. 

“It’s true the state has net reduction targets that it hopes to meet, but it’s clear the state of California has favored market-based solutions and tried to provide some support via grant programs,” he wrote. “I’m on the science side of our business, not the business development side, but still think I can tell you with complete transparency that we would not have systems installed on [California] dairies without the sale of voluntary carbon credits.”

Ploss also stressed that the company goes through a careful “validation and verification process” on the farms to understand how much vermifiltration reduces greenhouse gases.

“We’ve got sensors and cameras and all sorts of stuff so that we can look into any of our systems, 24-7,” Ploss says. “We know through sampling. We know through what’s going through the system, what came out of the system. We know by all the measurements on any given month: What did that system do in terms of generating carbon credits?”

Agueda also disputes the critique. 

“The installation of the vermifiltration system would not have occurred without the ability to generate carbon credits,” he said in an email. “The project required a substantial capital investment, and the anticipated carbon credit revenue was a key factor in making the investment financially feasible.”

California decided to incentivize vermifiltration, along with other approaches, because it can offer multiple benefits, including cleaner water, less nitrogen, and lower greenhouse-gas emissions, while also creating economic value from manure, wrote Roberta Franco, a senior environmental scientist at the California Department of Food and Agriculture, in an emailed response to questions from MIT Technology Review.

She added that the decision was based on a number of studies as well as the 2022 recommendations from a task force composed of scientists, technical experts, and others. 

Even if California has made missteps, most notably in funneling too much money to anaerobic digesters at the expense of other methods, it’s created a test lab that’s achieved real progress and provided lessons that other regions can learn from.

One way or another, more parts of the world will need to set up similar programs, offering greater support or creating stricter rules, if we hope to really drive down the emissions from manure, says Maria Bowman, who leads the Agricultural Nitrogen Transformation Program at Spark Climate, a San Francisco nonprofit.

For his part, Agueda says that the vermifiltration system has offered a number of benefits to his family’s farm, at little additional cost to them. By cleaning up the water that cycles back through their flush and irrigation systems, the biofilter has reduced clogging, decreased odors, and improved the health of the herd.  

He says that each generation modernizes dairy farming in its own way. His father and uncle, for instance, incorporated computers and data management systems into the daily operations of the Alberto Dairy. He believes it’s the responsibility of his generation to make a similar effort to reduce the pollution that’s long plagued the sector.

“We knew that in the next generation we have to invest in environmental sustainability,” he says. “We didn’t know if it was gonna work or not, but we’re very happy with how it’s turned out.”