Shortly after taking office for the second time, President Trump began making deep cuts to agencies and programs that play critical roles in human health, slashing funding for medical research, halting global health aid and firing scores of workers at the Centers for Disease Control and Prevention.

But the campaign to downsize government, which has been led by Mr. Trump and Elon Musk, has also hollowed out agencies and programs devoted to protecting plant and animal health. The recent wave of mass firings hit federal workers responding to the nation’s growing bird flu outbreak, protecting crops from damaging pests and ensuring the safety of pet food and medicine, among other critical duties.

Although the government has since rescinded some of these firings, the terminations — combined with a federal hiring freeze and buyout offers — are depleting the ranks of federal programs that are already short on employees and resources, experts said.

The damage could be long-lasting. Workers whose jobs were spared said that the upheaval had left them eyeing the exits, and graduate students said they were reconsidering careers in the federal government. The shrinking work force could also have far-reaching consequences for trade and food security and leave the nation unequipped to tackle future threats to plant and animal health, experts said.

“These really were indiscriminate firings,” said John Ternest, who lost his job at the U.S. Department of Agriculture, where he was preparing to conduct studies on honeybee health and crop pollination. “We don’t know what we’ve lost until it’s potentially too late.”

Plant and animal inspectors

The most recent wave of firings focused on the roughly 200,000 “probationary” employees across the federal government, who had fewer job protections because they were relatively new to their positions. (For some roles, the probationary period can be as long as three years, and it can also reset when longtime employees are promoted.)