Federal health officials have reversed the decision to fire a few dozen scientists at the Food and Drug Administration’s food-safety labs, and say they are conducting a review to determine if other critical posts were cut.

A spokesman for the Department of Health and Human Services confirmed the rehirings and said that several employees would also be restored to the offices that deal with Freedom of Information requests, an area that was nearly wiped out.

In the last few months, roughly 3,500 F.D.A. jobs, about 20 percent, were eliminated, representing one of the largest work force reductions among all government agencies targeted by the Trump administration.

The H.H.S. spokesman said those employees called back had been inadvertently fired because of inaccurate job classification codes.

The decision to rehire specialists on outbreaks of food-related illnesses and those who study the safety of products like infant formula follows contradictory assertions made by Dr. Marty Makary, the F.D.A. commissioner, in media interviews this week.

“I can tell you there were no cuts to scientists or inspectors,” Dr. Makary said Wednesday on CNN.

In fact, scientists had been fired from several food and drug safety labs across the country, including in Puerto Rico, and from the veterinary division where bird flu safety work was underway. Scientists in the tobacco division who were dismissed in February — including some who studied the health effects of e-cigarettes — remain on paid leave and have not been tapped to return, according to employees who were put on leave.

How many fired employees will be permitted to return remained unclear.

About 40 employees at the Moffett Lab in Chicago and at a San Francisco-area lab are being offered their jobs back, the department spokesman said. Scientists in those labs studied a variety of aspects of food safety, from how chemicals and germs pass through food packaging to methods for keeping bacteria out of infant formula. Some scientists in Chicago reviewed the work and results of other labs to ensure that milk and seafood were safe.

Dr. Robert Califf, the F.D.A. commissioner under President Joseph R. Biden, said the terms “decapitated and eviscerated” seemed fitting to describe the steep loss of expertise at the agency. He said the F.D.A. was already falling behind on meetings meant to help companies develop safe products — and to design studies that give clear answers about their effectiveness.

“Most of it is really at this level of fundamental, day-to-day work that has a huge impact overall, but it’s not very controversial,” he said. “It’s just that it takes work, and they have to have people to do the work.”

Dr. Makary has also said the layoffs did not target product reviewers or inspectors. But their work has been hampered by voluntary departures, the elimination of support staff and the broader disruption at an agency where many are fleeing for the exits, according to former staff members.

Hundreds of drug and medical device reviewers, who make up about one-fourth of the agency work force, have recused themselves from key projects, Dr. Scott Gottlieb, a former agency commissioner, said on CNBC. Under F.D.A. ethics rules, staff members who are interviewing for jobs cannot do agency review work on products by companies where they are seeking employment — or for a competitor.

Dr. Gottlieb also said cuts to the office of generic drug policy wiped out employees with expertise in determining which brand-name drugs are eligible to be made as lower-cost generics, calling those job eliminations “profound.” Approving generic drugs can save consumers billions of dollars.

Support staff for inspectors investigating food and drug plants overseas were also cut, raising security concerns. Dozens of workers who lost their jobs attended to security monitoring to ensure that inspectors were safe, especially in hostile nations.

Life at the bottom of the Pacific Ocean is slow, dark and quiet. Strange creatures glitter and glow. Oxygen seeps mysteriously from lumpy, metallic rocks. There is little to disturb these deep-ocean denizens.

“There’s weird life down here,” said Bethany Orcutt, a geomicrobiologist at Bigelow Laboratory for Ocean Sciences.

Research in the deep sea is incredibly difficult given the extreme conditions, and rare given the price tag.

On Thursday, President Trump signed an executive order that aims to permit, for the first time, industrial mining of the seabed for minerals. Scientists have expressed deep reservations that mining could irreversibly harm these deep-sea ecosystems before their value and workings are fully understood.

What’s down there, anyway?

Seafloor mining could target three kinds of metal-rich deposits: nodules, crusts and mounds. But right now, it’s all about the nodules. Nodules are of particular value because they contain metals used in the making of electronics, sophisticated weaponry, electric-vehicle batteries and other technologies needed for human development. Nodules are also the easiest seafloor mineral deposit to collect.

Economically viable nodules take millions of years to form, sitting on the seafloor the whole time. A nodule is born when a resilient bit of matter, such as a shark tooth, winds up on the ocean floor. Minerals with iron, manganese and other metals slowly accumulate like a snowball. The largest are the size of a grapefruit.

Life accumulates on the nodules, too. Microbial organisms, invertebrates, corals and sponges all live on the nodules, and sea stars, crustaceans, worms and other life-forms scuttle around them.

About half of the known life in flat, vast expanses of seafloor called the abyssal plain live on these nodules, said Lisa Levin, an oceanographer at the Scripps Institution of Oceanography. But “we don’t know how widespread species are, or whether if you mine one area, there would be individuals that could recolonize another place,” she said. “That’s a big unknown.”

How do you mine the sea?

Two main approaches to nodule mining are being developed. One is basically a claw, scraping along the seabed and collecting nodules as it goes. Another is essentially an industrial vacuum for the sea.

In both, the nodules would be brought up to ships on the surface, miles above the ocean floor. Leftover water, rock and other debris would be dropped back into the ocean.

Both dredging and vacuuming would greatly disturb, if not destroy, the seafloor habitat itself. Removing the nodules also means removing what scientists think is the main habitat for organisms on the abyssal plain.

Mining activities would also introduce light and noise pollution not only to the seafloor, but also to the ocean surface where the ship would be.

Of central concern are the plumes of sediment that mining would create, both at the seafloor and at depths around 1,000 meters, which have “some of the clearest ocean waters,” said Jeffrey Drazen, an oceanographer at the University of Hawaii at Manoa. Sediment plumes, which could travel vast distances, could throw life off in unpredictable ways.

Sediment could choke fish and smother filter-feeders like shrimp and sponges. It could block what little light gets transmitted in the ocean, preventing lanternfish from finding mates and anglerfish from luring prey. And laden with discarded metals, there’s also a chance it could pollute the seafood that people eat.

“How likely is it that we would contaminate our food supply?” Dr. Drazen said. Before mining begins, “I really would like an answer to that question. And we don’t have one now.”

What do mining companies say?

Mining companies say that they are developing sustainable, environmentally friendly deep-sea mining approaches through research and engagement with the scientific community.

Their research has included basic studies of seafloor geology, biology and chemistry, documenting thousands of species and providing valuable deep-sea photos and video. Interest in seafloor mining has supported research that might have been challenging to fund otherwise, Dr. Drazen said.

Preliminary tests of recovery equipment have provided some insights into foreseeable effects of their practices like sediment plumes, although modeling can only go so far in predicting what would happen once mining reached a commercial scale.

Impossible Metals, a seafloor mining company based in California, is developing an underwater robot the size of a shipping container that uses artificial intelligence to hand pick nodules without larger organisms, an approach it claims minimizes sediment plumes and biological disturbance. The Metals Company, a Canadian deep-sea mining company, in 2022 successfully recovered roughly 3,000 tons of nodules from the seafloor, collecting data on the plume and other effects in the process.

The Metals Company in March announced that it would seek a permit for seafloor mining through NOAA, circumventing the International Seabed Authority, the United Nations-affiliated organization set up to regulate seafloor mining.

Gerard Barron, the company’s chief executive, said in an interview on Thursday that the executive order was “not a shortcut” past environmental reviews and that the company had “completed more than a decade of environmental research.”

Anna Kelly, a White House spokeswoman, said the United States would abide by two American laws that govern deep-sea exploration and commercial activities in U.S. waters and beyond. “Both of these laws require comprehensive environmental impact assessments and compliance with strong environmental protection standards,” she said.

What are the long-term risks?

Many scientists remain skeptical that enough is known about seafloor mining’s environmental effects to move forward. They can only hypothesize about the long-term consequences.

Disrupting the bottom of the food chain could have ripple effects throughout the ocean environment. An extreme example, Dr. Drazen said, would be if sediment diluted the food supply of plankton. In that case they could starve, unable to scavenge enough organic matter from a cloud of sea dust.

Tiny plankton are a fundamental food source, directly or indirectly, for almost every creature in the ocean, up to and including whales.

Part of the challenge in understanding potential effects is that the pace of life is slow on the seafloor. Deep-sea fish can live hundreds of years. Corals can live thousands.

“It’s a different time scale of life,” Dr. Levin said. “That underpins some of the unknowns about responses to disturbances.” It’s hard for humans to do 500-year-long experiments to understand if or when ecosystems like these can bounce back or adapt.

And there are no guarantees of restoring destroyed habitats or mitigating damage on the seafloor. Unlike mining on land, “we don’t have those strategies for the deep sea,” Dr. Orcutt said. “There’s not currently scientific evidence that we can restore the ecosystem after we’ve damaged it.”

Some scientists question the need for seafloor mining at all, saying that mines on land could meet growing demand for metals.

Proponents of deep-sea mining have claimed that its environmental or carbon footprint would be smaller than traditional mining for those same minerals.

“There has been no actual recovery of minerals to date,” said Amy Gartman, an ocean researcher who leads the United States Geological Survey seabed minerals team, referring to commercial-scale mining. “We’re comparing theoretical versus actual, land-based mining practices. If and when someone actually breaks ground on one of these projects, we’ll get a better idea.”

Eric Lipton contributed reporting.