California Has Provided Incentives for Methane Capture at Dairies, but the Program May Have ‘Unintended Consequences’

The first of a three-part series on California’s program to reduce carbon emissions on dairy farms by subsidizing the construction of digesters to capture methane.

On summer afternoons, thousands of dairy cows at Bar 20 dairy in Kerman, California, seek shelter from the blazing sun under the shade of open-walled barns. After a frenzy of morning activity, the farm is quiet except for an occasional moo, a deep rumble from a tomato truck passing on nearby Highway 180 or the wind whistling through the barn, carrying the acrid manure scent that permeates the air on the farm. The scene is typical in the San Joaquin Valley, an agricultural region that produces more milk than any other part of the country. 

Less typical, though, is the 25 million-gallon pond at the southeast corner of the dairy, covered in a large dusty gray tarp that balloons and shrinks with the day’s fluctuating temperature. Beneath the gray covering, reminiscent of a large inflatable slide and larger than two Olympic swimming pools, sits an enormous amount of manure collected from more than 7,000 dairy cows on the farm. 

The pressure pushing the cover skyward is an accumulation of methane, a powerful greenhouse gas that results from manure decomposition. This methane-trapping contraption is called an anaerobic manure digester, and it’s one of the reasons Bar 20 has won multiple sustainability and innovation awards from industry groups in recent years. 

California, a state proud of its booming dairy industry, has allocated more than $350 million to build digesters like this one on dairy farms in a bid to capture methane and stem climate change. But the technology presents a major paradox: Emerging research suggests that after the digesters process the manure, it emits ammonia, which can travel long distances to contaminate water and soil and threaten ecosystems. Communities nearby also worry that the ammonia emissions will contribute to particulate matter that is seriously dangerous to human health. 

In essence, the digester program could undercut the state’s overarching environmental goals and public health priorities. 

Scientists say that much remains uncertain about how the technology affects agricultural emissions like ammonia. And those who live near sprawling dairies say that California regulators have not adequately evaluated the program’s potentially significant threat to local air quality, even as the state offers the industry millions of dollars in incentives. Neither the state of California nor the federal government directly regulates ammonia emissions from agriculture. 

For years, scientists and community groups have encouraged California and the U.S. Environmental Protection Agency to evaluate air emissions at dairies. In August, federal lawmakers, including Senators Bernie Sanders and Cory Booker, sent letters to the EPA and the U.S. Department of Agriculture expressing concerns about the potential expansion of methane digesters. Research conducted by scientists over the last decade in Wisconsin, Canada, Washington State and Denmark has suggested that digesters may increase ammonia emissions as they process manure. In 2018, a California working group recommended further study of potential air quality impacts related to methane mitigation at dairies. The same year, state regulators began planning to study whether the research from other states applied to California. Four years and more than 50 digester projects later, the state only recently finalized the contracts to begin that research, one in March and another in September. 

Digester companies argue they are providing an essential climate technology that’s ready for deployment today. But scientists told Inside Climate News that a better understanding of the impact of digesters on potentially harmful ammonia emissions is needed as the state centers the technology in its strategy to slash emissions and confront climate change. Today, ammonia mitigation technologies for digesters exist, but the state does not require the digester projects it funds to use them.

Digesters are “one of the most successful ways to mitigate methane emissions,” said Rebecca Larson, an author of the paper published by Wisconsin researchers and an expert in manure management at the University of Wisconsin-Madison. “But sometimes, there’s unintended consequences.” 

Why California Uses Digesters 

Dairy and livestock account for more than half of California’s methane emissions, which makes mitigating that pollutant essential to a state climate mandate to reduce greenhouse gas emissions by 40 percent from 1990 levels by 2030, as well as to a newly codified state commitment to reach carbon neutrality by 2045. But dairy products are a lucrative agricultural commodity in a state with an already massive farm economy: The dairy sector alone generated $7.5 billion in 2020. 

Early on in its plans to draw down emissions, California suggested a way to ensure that the dairy industry could keep humming: reducing heat-trapping methane by encouraging anaerobic digesters at large dairy farms. Those recommended methane reductions were enshrined in law in 2016, when the state passed a bill setting a greenhouse gas emissions reductions target for the dairy and livestock sector. (The law stipulated that enforceable regulations for the industry could not be established until 2024). In the years since, manure digesters have become the primary strategy by which the state plans to cut emissions from the dairy sector. 

Farms with digesters collect a farm’s slurry of manure and urine. In California, the mixture is often separated into liquid and solids, and the liquid goes into a lined and covered lagoon—the digester—to capture the methane that the mixture produces. That methane is then cleaned and processed into natural gas. 

A state program designed to incentivize digester construction has given out nearly $200 million to digester projects since it was established in 2014. The state public utilities commission has authorized another $133 million for the projects, and the state energy commission has approved more than $35 million. The state received applications requesting $35.38 million in funds for digester development this year by a deadline set in May. 

The state’s Low Carbon Fuel Standard, which incentivizes the use of renewable fuel sources, gives digester owners carbon credits for the biogas that the digester produces, which they can sell or trade. 

In the years since California started supporting the technology, it has funded 117 digesters, including the one at Bar 20. Each year, the digester projects installed in the state achieve greenhouse gas reductions comparable to more than 2 million metric tons of carbon dioxide, according to the state. That’s equivalent to taking more than 400,000 gas-powered cars off the road for a year. To reach the methane reductions that California law requires by 2030, the state expects it will need to install more than 200 more digesters.

Unintended Consequences?

At Bar 20, another lagoon sits next to the pond covered with the huge gray tarp. This one is larger than seven football fields and filled to the brim with a bubbling reddish-brown liquid. The smell is particularly pungent on this side of the farm and carries a distinctly strong chemical odor along with the familiar rotten-eggs scent of manure. 

On farms with digesters like Bar 20, the digestion process results in two products: biogas and the leftover digestate. While the biogas is captured and piped elsewhere for processing and then sold as fuel, the digestate often sits in an uncovered secondary storage pond until a farmer collects it to spread its valuable nutrients on crops. 

At dairies like Bar 20, the length of time that the digestate sits in the pond depends on which crops need to be irrigated, a process that varies by season. When the fertile sludge, sitting in a secondary pond or spread on a crop field, is open to the air, it continues to release trace amounts of leftover methane as well as other pollutants like nitrous oxides and ammonia. 

The nitrogen cycle on farms, and how it contributes to emissions, is complex. And substances like ammonia, or NH3, often do not get the attention they deserve, scientists say. “Ammonia is a story that’s not often told,” said Joe Rudek, an agricultural emissions scientist at the Environmental Defense Fund, an advocacy organization that helped sponsor California’s keystone emissions reduction legislation in 2006. “Ammonia loss to the atmosphere has both public health risk issues and environmental issues.”

At least four studies published between 2011 and 2018 conclude that the digestion process can result in multiplied ammonia emissions from digestate. In a 2017 study conducted in Wisconsin, researchers collected digested and undigested manure from two dairies and measured the greenhouse gases, nitrous oxide and ammonia it emitted as it sat in storage in 55-gallon drums, simulating what usually happens on farms once digestate leaves the digester. After six months of storage, the manure was applied to a crop field, where researchers also measured emissions.

Over the entire study period, the digested manure emitted 81 percent more ammonia than undigested manure. Most of those emissions came from the storage period, when digested manure sat exposed to the open air, simulating what happens in the period before it would be applied to crops.

Authors of the 2017 study acknowledge its limitations: The research was done on a small scale and in a controlled setting. The digester used in the study was different from the type installed in California. Wisconsin also has a different climate, and dairy farmers in each state have slightly different manure management practices, all of which could influence results at individual dairies. Representatives of California’s digester industry have held up these differences as evidence that these results are not applicable to operations in their state.

The paper’s authors, however, said the overall trend—higher ammonia emissions from digested manure in open storage—would hold true across the country, although the magnitude of the emissions might vary. “If anybody’s telling you that a digester doesn’t mineralize and produce more ammonia that could be lost to the atmosphere, well, they’re not using data,” Larson said. “It’s important to tell the story that it is possible to curb that unintended consequence, and there are people out there doing it.”

Scientists not associated with the paper say that further study is needed to fully understand how digesters impact ammonia production. “We need to have a better handle on ammonia emissions, and we need to develop better strategies to mitigate them, because we know it’s an important contributor to PM2.5,” said Francesca Hopkins, an emissions researcher and assistant professor of climate change and sustainability at the University of California, Riverside. (PM2.5 refers to fine, inhalable particulates with diameters of 2.5 micrometers or less.) “And we know agriculture is a major source.” 

Hopkins said that more data is needed to establish whether digesters increase or reduce ammonia emissions. Rudek of the EDF agrees. “The digester gives you methane reduction, which is a big climate benefit,” he said. “EDF is very, very much focused on the importance of that benefit. But the ammonia is a local impact. And if you just take the digestate out and put it into an open system, you don’t decrease the local impact of the ammonia.” 

Ammonia emissions are already at unacceptable levels, and any increase could have serious consequences, but it’s important to determine whether the digesters are contributing to the damage, Rudek added. 

Mark Zondlo, a professor at Princeton University who heads its atmospheric chemistry and composition group, said that it was not “terribly well understood” how digesters affect ammonia emissions. He praised the Wisconsin study and said it raised important questions worthy of further research. 

He is now in discussions with the state air resources board about a three-year study that would examine how different manure management techniques at California dairies affect nitrous oxide and ammonia emissions. The contract for that work was recently finalized.

People living near dairies have long voiced concerns to regulators about the smell and emissions from farm operations. In 2001, Tom Vilsack, then Iowa’s governor and now the U.S. secretary of agriculture, asked two Iowa universities to look into emissions associated with concentrated animal-feeding operations in the state. A peer-reviewed study created by a group of researchers a year later recommended ambient air-quality limits for certain emissions including ammonia.

Emissions of ammonia and other pollutants have been “factors of interest” in California’s digester development program since its inception, according to the state Department of Food and Agriculture, which manages the initiative. In 2018, a unit of a working group assembled by the state to evaluate potential methods to reduce greenhouse gas emissions from dairies and livestock recommended that California investigate localized pollution impacts associated with methane mitigation at dairies. “The implementation of various dairy methane emissions mitigation strategies may alter the emissions of other air pollutants such as ammonia,” the subgroup wrote. 

The California Air Resources Board, or CARB, which sets standards for air pollution and greenhouse gas emissions in the state, says it is still somewhat uncertain about the impacts of digesters on air quality. Qian Mitloehner, an air pollution specialist for the agency, told Inside Climate News that the agency doesn’t “quite understand the downstream emissions at this point.” 

Before joining the agency, Mitloehner studied methane emissions from livestock as a doctoral student at the University of California, Davis. She is now married to her former graduate school adviser, Frank Mitloehner, an animal scientist with deep ties to the livestock industry who has downplayed the role of methane emissions from livestock in climate change.

In emailed comments to Inside Climate News, a CARB spokesperson said that after speaking with the lead author of the Wisconsin study, the agency believed that further study was needed and decided to pursue its own research on potential downstream ammonia emissions from digesters. “The agency finalized the contracts to begin that research this year, in March and September. The state said in its emailed comments that those contracts were nearly final in early 2020 but were upended by the Covid-19 pandemic and the uncertainty it spawned about California’s “anticipated budget position.”

Community Concerns

While scientists have raised questions about how digesters may contribute to ammonia emissions, environmental justice advocates and some residents in the San Joaquin Valley have raised direct concerns. 

Some community groups express frustration that the state hasn’t done more to align climate strategies with air quality and public health priorities. If those strategies lined up, says Genevieve Amsalem, research and policy director at the Central California Environmental Justice Network, “then we would have been talking about ammonia when we started talking about dairy digesters seven years ago.”

Community members and activists in the state like Amsalem have argued for years that the push for digesters would support an industrial agricultural system that contributes to air pollution. Ammonia is one of the most significant precursors to speck-like PM2.5 particles, which hang in a haze in the San Joaquin Valley and can lodge in the lungs and the bloodstreams of the people who live there. The fine particles are known to increase the severity of asthma and can boost the risk of heart and lung disease and even premature death. 

PM2.5 is a leading killer worldwide, but it especially threatens the San Joaquin Valley. Many of the most polluted counties in the United States are there, and asthma diagnoses in the valley are higher than in the state as a whole, according to a 2016 assessment.

The air in the valley is so bad that last year a group of local and national environmental organizations represented by the environmental organization Earthjustice filed a suit against the EPA, arguing that the federal government is required to step in to ensure that the state has a plan to improve its air quality. The valley has still not attained the PM2.5 standards established by the EPA more than two decades ago.

Each year, California calculates how much of its cap-and-trade money goes to projects that benefit “priority communities,” which the state defines as low-income populations or those most likely to experience disproportionate impacts from pollution. At least 35 percent of the state’s climate investments must benefit these populations overall. Over the past five years, the state has asserted that at least 60 percent of the digester projects it has funded benefited low-income and disadvantaged groups. 

But communities near digesters dispute that categorization. Maria Arevalo, a resident of the San Joaquin Valley town of Pixley, said that a digester installed north of the community had actually made the dairy smell worse. “It has a burning odor—it smells bad, of burning cow waste,” Arevalo said. “They think they’re making it better, but the industry has the same [number of] cows and they keep buying more, and more, and more. And the digesters still release gas, chemicals and emissions into the community.”

Arevalo, who has lived in Pixley for decades and suffers from sleep apnea, has had to sleep with a CPAP, or continuous positive airway pressure machine, to aid her breathing for about 15 years. She wants the state to impose more regulations on dairy emissions. 

This year, a group of environmental organizations including the Central California Environmental Justice Network and the Central California Asthma Collaborative argued in comments to the federal EPA that both CARB and the local air district “have repeatedly avoided regulating agricultural sources of pollution even though the impacts of those decisions disproportionately fall on surrounding communities of color.” 

‘A Huge Question That Needs to be Answered‘

In reports to the EPA, the state air resources board has argued that it is not required to regulate ammonia because the formation of particulate matter in the San Joaquin air basin is primarily influenced not by that gas, but by another: nitrous oxide. Several scientists told Inside Climate News that CARB’s reasoning appears sound. But some suggested that regulatory agencies are missing out on an opportunity to deal with ammonia emissions anyway.

Regardless of the balance of nitrous oxide and ammonia in the air, “removing ammonia, if you remove enough of it, could make a big impact” on the spread of small particulates that endanger human health, said Daven Henze, an air pollution expert and associate professor of mechanical engineering at the University of Colorado Boulder. But doing so would require stringent controls and regulating ammonia emissions from agriculture and livestock, something that the federal government hasn’t historically done. 

Henze argues that ammonia on its own has worrisome environmental impacts. Emissions from the San Joaquin Valley can travel as far as Colorado, he said, settling into and disrupting ecosystems. 

Zondlo, the Princeton atmospheric chemistry expert, whose grandparents were dairy farmers in Wisconsin, says that managing the nitrogen cycle is as complex as managing the carbon cycle. “We’re just decimating natural ecosystems with human-influenced nitrogen,” of which a major portion comes from agriculture, he said. “Where does it go? And what are the downstream effects? I think that’s a huge question that needs to be answered.”

Neither California Bioenergy nor Maas Energy Works, the companies responsible for more than 90 percent of the 117 state-funded digester projects funded by the California state government, mitigate ammonia emissions from storage of digested manure. 

Neil Black, California Bioenergy’s president, said the issue “needs to be looked at carefully from a California perspective.” “We got into this business because we wanted to decrease greenhouse gases, but we sure didn’t want to add to any local pollution,” he said. 

Daryl Maas of Maas Energy said in an email that the results observed in the Wisconsin study do not seem applicable to how digesters function in California. Michael Boccadoro, a lobbyist for the dairy industry, also argued in an email that the findings did not apply to California because of differences in how the states’ digesters process manure. On California farms, manure liquids and solids are separated before digestion. In the Wisconsin study, researchers separated the solids after digestion and composted them, which Boccadoro said caused the excess ammonia emissions. 

But that explanation isn’t based in science, said Michael Holly, the lead author of the 2017 Wisconsin paper and an assistant professor in environmental engineering at the University of Wisconsin-Green Bay. “They’re just throwing stuff at the wall now and seeing what will stick,” said Holly, who added that it doesn’t matter when separation happens. “If you store digested manure, you’re going to have ammonia emissions higher than undigested manure.” 

Looking for Mitigation

Manure management strategies that mitigate ammonia emissions do exist, though it is unclear how many farms with digesters use them. According to the 2017 study, covering the secondary storage lagoon with covers or with organic charcoal-like materials or straw prevents the ammonium in digestate from being released into the air. Adopting more precise crop irrigation that keeps digestate from interacting with air can help, too. Ammonia-capture technology, like separating ammonia from the manure slurry using a stripper and sending it into a tower where it can be processed and used as fertilizer, also exists. 

Such strategies appear rare, says Rudek of the EDF: He estimates that “less than 1 percent” of dairies are using them. California does not currently require farmers or developers to use such mitigation when pursuing new digester projects.

Both scientists and environmental advocates warn that the state should consider the potential local impacts of digesters along with climate solutions.“It’s a good idea for us to consider these air pollution and climate change problems together because there may be cases where one mitigation strategy for methane could lessen the air pollution problem or, conversely, make it worse,” said Hopkins. 

California does offer financial incentives for farmers to adopt manure management strategies aside from digesters that limit both methane and ammonia emissions through its Alternative Manure Management Program. Although that initiative has funded around the same number of projects as the digester program, it has received less than a third of the government funding available to digester projects. California has said those projects are less economically efficient per metric ton of greenhouse gas reduction than digesters.

More study could help dispel uncertainty about the potential side effects of digesters. Communities near dairies and the agricultural emissions that accelerate climate change are hanging in the balance.

“Good research raises questions,” said Zondlo. “We need to look at this.”

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                Emma Foehringer Merchant is a journalist who has covered environmental issues ranging from disasters to wonky energy regulations to air pollution. She’s reported on the environment and energy for publications including The Boston Globe Magazine, The New Republic, Vice News, and Grist. Most recently, Emma covered clean energy as a staff writer for Greentech Media and helped alums of that organization form a new publication called Canary Media. She’s attending MIT’s Graduate Program in Science Writing and holds a bachelor’s degree in environmental analysis from Pomona College, where she lived through a California drought while studying how climate change is impacting the state’s environment and people.






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                Grace is a journalist who writes about climate change, science, agriculture and food systems. She’s a graduate student in MIT’s Science Writing Program, and holds bachelor’s degrees in biology and anthropology from Tufts University. She previously worked as a researcher, studying coffee farming in Costa Rica and honey bee survival in southern Wisconsin, where she grew up. 






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