Back in early March, Massachusetts Agriculture Commissioner Ashley Randle sent a letter to the new U.S. Agriculture Secretary Brooke Rollins, voicing congratulations — and a number of concerns.

Randle, a fifth-generation dairy farmer, shared that USDA's freeze on grants — imposed before Rollins was sworn in — had left Massachusetts farmers in limbo, wondering if they'd ever be reimbursed for investments they'd made based on those grants.

She also sounded the alarm on positions that had been cut.

"The loss of USDA staff has also left Massachusetts farmers without essential resources that have long been an important part of their success," Randle wrote, pointing to diminished staffing at the local Farm Service Agency office, which helps with loans, insurance and disaster relief.

Outside groups sued; a court order later required USDA to reinstate fired employees. But since then, the Trump administration has moved swiftly to "reorient the department to be more effective and efficient at serving the American people," according to a USDA spokesperson. 

As part of the overhaul, USDA allowed more than 15,000 employees — close to 15% of its workforce — to resign with pay and benefits through September.

Those departures have led to new concerns for Randle, including whether the federal government will be able to respond quickly in a crisis. She's been told that many of USDA's Area Veterinarians in Charge, who get the first call whenever a pest or disease is detected on a farm, have resigned, including the one assigned to New England.

With avian flu likely to return with the fall bird migration, and other diseases including New World screwworm and African swine fever creeping ever closer to the U.S., Randle knows U.S. farmers and ranchers, along with the U.S. food supply, could be at risk.

"Being able to be nimble and respond as quickly as possible in these types of incidents is incredibly important," she told NPR. "It could be challenging."

Growing fears of damage already done

Even as lawsuits challenge President Trump's dismantling of the federal government, there are growing fears among those who work in agriculture that the exodus of thousands of employees from USDA, including more than 1,300 from the agency's Animal and Plant Health Inspection Service (APHIS), has left American agriculture vulnerable.

"There's no way APHIS can do its job with 1,300 fewer people," says Kevin Shea, a 45-year veteran of USDA who led APHIS for 11 of those years. He retired in January after helping with the presidential transition.

Shea notes that over the years, APHIS employees have worked to successfully eradicate or keep at bay pests such as the boll weevil, a beetle that feeds on cotton buds, and New World screwworm, a parasite that burrows into the open wounds of animals. It's recently resurfaced in Mexico.

He fears that progress could now be lost, with animal health technicians, epidemiologists, entomologists, wildlife biologists and many who supported them gone.

"It'll be very hard to ever rebuild the animal health workforce and the plant health workforce because they've taken away so much of what made government service attractive to those people — stability, security and a sense of public mission," Shea says.

He points to disparaging comments made by the Trump administration, including Office of Management and Budget Director Russell Vought, who once said he wanted government bureaucrats to be "traumatically affected," to the point where they wouldn't want to go to work.

"When they use rhetoric like that, why would you work for the government if you had another choice?" says Shea.

Helping U.S. farms maintain a competitive advantage 

Given the depletion of key staff at APHIS, Shea presumes there was a lack of understanding among the new political leadership of what the agency does. He also presumes the Trump administration outsourced the reduction of the workforce to Elon Musk's Department of Government Efficiency, "who I'm sure have no idea," he says.

What he would want them to know is that American agriculture has been relatively free of pests and disease in recent decades thanks in large part to the work of APHIS. And that, in turn, has given the U.S. two important things: a trade advantage in relation to the rest of the world and an abundant, cheap supply of food.