Working without fanfare, federal scientists at 22 U.S. sites maintain the nation's agricultural plant species collected since 1898, including crops native to New Mexico. But the Trump administration's DOGE agency has fired them. The move creates uncertainly for hundreds of crop species that undergird the country's food system. The U.S. National Plant Germplasm System safeguards the genetic diversity of agriculturally important plants.

Iago Hale, associate professor of specialty crop improvement at the University of New Hampshire, said the potential loss of these "seed bunkers" should alarm every American.

"If you subsist totally on chicken nuggets and KFC, that's fine - understand that that comes back to plants grown in the field. The breading on your fried chicken, the French fries that you're eating - these are all products of crops, and this is how it works," he said.

A court order has temporarily reinstated some of the 300 NPGS scientists, but it's unclear when their work will resume - putting 600,000 genetic lines of some 200 crop species in jeopardy. New Mexico's pinto beans, jujube and ornamental species are included in the crop research and improvement dataset historically housed through the NPGS.

Hale said the NPGS is central to the nation's preparedness, because the food system is only as safe as our ability to respond to the next plant disease. Unless dormant seeds are continually cared for and periodically replanted, Hale noted the lines will die, along with their evolutionary history. Hale said potatoes, the fourth-largest crop, require even more care than wheat or corn.

"They're not maintained as seed, they're maintained as potatoes - it's a clonally propagated crop, and there is no long-term storage for those things. So, the nation's entire potato collection has to be grown out every year - has to be regenerated every year, without fail, or it will die. And the potato season has been disrupted," he explained.

Hale said apples also must be maintained as living plants in the open field and scientists follow strict requirements to sustain genetic purity. In the 1980s, he notes, scientists at a gene bank in New York helped identify genetic traits that made apples resistant to several destructive diseases, including deadly fire blight.


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CLARIFICATION: In the initial release of this story, the photo caption included a typo that resulted in an unintentional racial slur. In discussions with every staff member involved in the story, it was clearly a typing error, with no intention of including an offensive term. We deeply apologize for the error. (9:35 a.m. CST, June 23, 2025

From poultry to beer, Minnesota has an avid interest in producing food with ingredients and practices mindful of the state's water resources and the latest recipients of specialized grants are taking charge.

The grants were awarded by the "Continuous Living Cover" program under the Minnesota Department of Agriculture. Food manufacturers and others in the supply chain use the funds to develop larger markets for crops that help stabilize the soil in which they are planted.

Sandy Boss Febbo, co-owner of Bang Brewing in St. Paul, said their grant allows them to use more "Kernza," a sustainable alternative to wheat. She called it a "beautiful grain."

"Once we tried it and saw how well it performs in beer and what it lends to beer flavor profiles, we were hooked," Boss Febbo explained.

Boss Febbo pointed out crops like Kernza have root systems that keep nitrates from flowing into waterways, preventing algae blooms and providing other environmental benefits. One catch is Kernza is more expensive than traditional beer ingredients. This legislative session, Minnesota lawmakers approved $450,000 for future grants under the cover crop program.

Boss Febbo noted the state aid is not just for the processing of Kernza at her brewery. Marketing is a key strategy as well. Bang Brewing plans to retrofit a van with a mobile tap setup so they can travel to licensed events around Minnesota and spread the word about this largely unknown crop.

"Agricultural practices have a massive impact on the health of our land and water," Boss Febbo emphasized. "To bring that message, to get more people involved and more people supporting, that is really our goal."

According to program backer Friends of the Mississippi River, other grantees include a hazelnut company, as well as a farm raising chickens on forested pastures. The farm will also use its grant money to help market its product to schools, retailers and restaurants across Minnesota.

With more than 95,000 farms, Missouri ranks among the top farming states in the nation. Now, a national agriculture group is warning that bills moving through Congress could hurt rural communities.
According to the National Sustainable Agriculture Coalition, the Senate's reconciliation bill, sometimes called "The Big Beautiful Bill Act," would deepen hunger and hinder small farmers. At the same time, the group contends the House's 2026 spending plan slashes funding for conservation, research and local food programs.

Mike Lavender, the coalition's policy director, said the consequences of these cuts will be felt directly by those working the land.

"These cuts, even to relatively small programs, are going to mean that fewer farmers have access to resources and information that help them have a successful livelihood, help their business work and help them be successful in providing for their family," he said.

Supporters have said the bills promote responsible budgeting by cutting spending and boosting efficiency. The Senate's agriculture bill awaits full debate, while the House's 2026 funding bill has cleared committee.

Nearly 90% of Missouri's farms are family-owned. Lavender said his organization has been working closely with members of the Senate and the Appropriations Committee to make sure they understand the importance of these programs for farmers across the country.

"Don't do what the House did. Don't undercut farmers, don't undercut rural communities by reducing funding for these programs," he said, "but rather they deliver funding for these programs based on demand, and we know there's a high demand and a high need for these programs across the country."

Lavender added that the 2026 spending bill has "one bright spot" in its support for direct purchases from local producers, but he said that's overshadowed by cuts that hurt those very farmers.


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By Seth Millstein for Sentient.
Broadcast version by Chrystal Blair for Missouri News Service reporting for the Sentient-Public News Service Collaboration

An estimated 99 percent of farm animals in the U.S. live in what the government calls Concentrated Animal Feeding Operations, or CAFOs. But what exactly makes something a CAFO, and are they the same as factory farms? Generally speaking, CAFOs are large industrial facilities where hundreds, thousands or hundreds of thousands of farmed animals are densely packed in sheds or feed yards. They're an example of what's also called intensive farming, in which the goal is to produce the maximum amount of product using the least amount of physical space.maximum amount of product using the least amount of physical space.

"They work like an industry," John Ikerd, professor emeritus of agricultural economics at the University of Missouri, tells Sentient. "The basic characteristics of an industrial operation is to specialize. You specialize in just doing one thing, so you can do it more effectively. And once you specialize, then you can routinize the process. And once you routinize, you can mechanize, and once you mechanize, then you simplify the whole production process, so that you can consolidate into larger and larger operations."

The argument for farming more like an industrialized factory came from agriculture researchers in the mid-20th century, according to agricultural economist Jayson Lusk, and it wasn't seen as a bad thing. Getting bigger was a way for farms to become more efficient and, therefore, more economically sustainable. Unfortunately, that efficiency comes with a multitude of tradeoffs, for animals, workers and the environment.

What Is a CAFO?

The term "CAFO" was created by the U.S. government in the 1970s as part of a federal effort to reduce water pollution. It began in 1972, when Congress passed the Clean Water Act. This law authorized the EPA to regulate point source pollution, or water pollution that comes from a single identifiable source; while the law didn't include the acronym "CAFO," it did mention "concentrated animal feeding operations" as an example of point source pollution.

Ikerd says the amount of water pollution a farm emits is directly tied to how densely concentrated the animals on the farm are.

"If you have the animals dispersed out across the land, as they were before we had CAFOs, then you're not concentrating the waste in one place," Ikerd says. "When you concentrate the animals, then you concentrate the manure, and the urine and all the waste from the animals."

In 1974, the EPA formalized and expanded upon this designation, issuing a rule that defined CAFOs as a subset of AFOs, or (non-concentrated) animal feeding operations.

The difference between an AFO and a CAFO is important, as CAFOs are subject to more stringent regulations.

AFOs vs. CAFOs

The size designation of any given AFO depends on a number of factors, the primary one being the number of animals in the facility and the species of animal in question. For instance, a dairy AFO is considered large (and therefore a CAFO) if it has over 700 dairy cows; a turkey AFO, meanwhile, needs 55,000 or more turkeys to qualify as a CAFO.

There are a few other factors that determine whether a facility qualifies as a CAFO. With pig farms, the weight of the animal is taken into consideration. On chicken farms, the size designation depends on whether the birds are being farmed for meat or eggs.

Manure Processing

There's another important factor in determining whether or not a farm qualifies as a CAFO, and that's the manner in which it processes and stores manure. This is because manure storage plays a big role in determining how much water pollution a CAFO creates, and managing water pollution was the government's impetus for coining the term "CAFO" in the first place.

Each year, industrial livestock operations create a staggering amount of manure and other farm animal waste; 941 billion pounds, according to a Food and Water Watch report from 2024.

For poultry farms, the threshold to qualify as medium- or large-sized is lower if the facility uses liquid manure handling systems, as these systems are more prone to leakage, and thus polluting nearby waterways, than dry systems.

Finally, the director of the EPA has the authority to designate individual facilities as CAFOs on a case-by-case basis, should they determine that the facility in question is a significant contributor to water pollution.

Are CAFOs the Same as Factory Farms?

Unlike "CAFO," the term "factory farm" isn't a legal term with a statutory definition. It's more of a general concept that's used colloquially to describe CAFO-like facilities.

Merriam-Webster defines a factory farm as one in which "large numbers of livestock are raised indoors in conditions intended to maximize production at minimal cost." That's a simpler, less specific and potentially more expansive definition than the government's definition of a CAFO; depending on how one interprets the word "large," it's easy to imagine a facility that meets the dictionary definition of factory farm but doesn't technically qualify as a CAFO.

Ikerd, however, defines "factory farm" a bit differently. He says that it's a "farming operation that basically functions like a factory."

"You put [the animals] into this factory-like setting, and then you apply certain routine procedures to them that are specified by the people that are contracting with them," Ikerd says. "And then you come out with a finished product on the other end, whether that's meat, or milk or eggs."

CAFOs, by the Numbers

According to the EPA's latest numbers, there are 21,179 CAFOs in the United States.

Most U.S. states have at least one CAFO, but they're not evenly distributed across the country. Iowa is home to the most CAFOs (around 4,025), and another five states have over 1,000 CAFOs in their borders. The majority of states (28) have between 100 and 1,000 CAFOs, while a small handful have under 10.

How CAFOs Pollute the Water

CAFOs generate an estimated 941 billion pounds of manure each year, and dealing with that manure is a major challenge for farm operators. Typically, it's either stored on-site in a lagoon or similar structure until it can be sprayed onto nearby crops for use as untreated fertilizer.

Nutrient Runoff

Manure lagoons can be prone to leaks and malfunctions, especially during storms, and even a light rain can wash the fertilizer on cropland into nearby rivers, lakes and streams. This is what's known as nutrient runoff, and it's especially common when manure is overapplied as fertilizer, which Ikerd says is common on CAFOs.

Algal Blooms

The impacts of CAFO-sourced water pollution has severe consequences for humans, animals and the environment. Along with other pollution, it leads to harmful algal blooms, an overgrowth of algae that can cause mass fish die-offs and extensive damage to aquatic ecosystems. Harmful algal blooms can also contaminate drinking and recreational water, and have been linked to at least one fatal case of paralytic shellfish poisoning in a human.

Disease Risk & Antibiotic Resistance

Livestock manure can also contain infectious bacteria, such as E.coli and salmonella, that can end up in the air and water nearby CAFOs, and even nearby fruit and vegetable farms.

The antibiotics that farmers administer to animals on CAFOs are also fueling the world's antibiotic resistance problem, a public health threat that kills over one million people every year.

How Are CAFOs Regulated?

Facilities that meet the government's definition of a CAFO have to abide by a few modest requirements relating to its manure and waste management.

First, any CAFO that discharges pollutants into waters of the United States - a legal term that we'll discuss in a moment - is required to obtain a National Pollutant Discharge Elimination System (NPDES) permit. These permits place limits on the amount and type of pollutants that the CAFO in question is allowed to discharge. The EPA defines a pollutant as "any industrial, municipal and agricultural waste."

Second, any CAFOs with a NPDES permit - and all large CAFOs, regardless of whether they have a permit - must present the EPA with a nutrient management plan. This is simply a description of the procedures the CAFO will use to manage the manure, animal parts, wastewater and other potential pollutants it produces, and ensure that they don't contaminate nearby water in excess of the limits imposed by the NPDES.

Environmental Loopholes to CAFO Regulation

There are some loopholes in this system. The first concerns which types of waterways a CAFO isn't allowed to discharge pollutants into without a permit. EPA rules use the phrase "waters of the United States" (WOTUS), a legal designation created by the Clean Water Act that's been subject to significant litigation and modification over the decades, most recently in 2023.

The nuances of WOTUS designations are incredibly complex and technical, but broadly speaking, the term covers most major and permanent waterways while excluding some smaller, unofficial and impermanent ones.

As a result, there are some CAFOs that don't need to obtain an NPDES permit, or abide by any limits that such a permit would impose. CAFOs that discharge their waste into non-WOTUS designated waterways are exempt from permitting, and so are those whose waste indirectly ends up in waterways. This latter category includes farms that store their manure in lagoons or apply it as untreated fertilizer to crops.

This might sound like a small loophole, but it has enormous implications. According to the EPA's own data, less than one-third of all CAFOs in the U.S. have an NPDES permit. In Iowa, the state with the most CAFOs, less than four percent are NPDES-permitted.

If CAFOs violate the terms of their NPDES permit - and they often do - the EPA can fine them. But this brings us to another problem with the regulatory framework around CAFOs: When the water is polluted, it's tough to figure out exactly where that pollution came from.

"It's very difficult to prove a violation, and link a violation to a particular CAFO," Ikerd explains. "If you've got pollution in a stream, it's very hard to bring that back to one particular operation. So you've got to go through the process of saying, 'it came from this particular operation rather than another,' and that's really made it difficult to enforce."

Some states have created their own permitting regimes for CAFOs that go above and beyond the EPA's requirements. Oregon, for instance, allows its state environmental agency to require NPDES permits for all enclosed animal farms, regardless of their size. As a result, the state has issued more than twice as many NPDES permits as there are CAFOs within its borders.

Some Community Groups Are Pushing Back on New CAFOs

The rising number of CAFOs in the United States are driven by a growing global population with a massive appetite for cheap meat. But a relatively new phenomenon is emerging in communities across the United States: small groups of residents who oppose the construction of new CAFOs are working together to block factory farm expansion. And some of them, like one that formed in Linn County, Oregon, are even finding success. Of course, it's highly unlikely that the CAFO industry will be put out of business anytime soon, but still, the nascent anti-factory farm movement is one to watch.


Seth Millstein wrote this article for Sentient.


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