USS San Francisco (copy)

An environmental "incident take" permit is up for public comment, allowing marine mammals to be killed as the Navy trains with submarines, ships and aircraft offshore South Carolina. Provided/U.S. Navy

Two years ago they locked horns: Oil companies wanted to explore and drill off South Carolina and the rest of the Southeast coast. The Navy wanted to train for warfare.

The Navy won.

Today, the Navy is seeking permits to allow the deaths, or "incidental take," of 48 dolphins or whales for the next five years across 50,000 square miles of its warfare training grounds off the East Coast, starting about 12 miles out.

The training could take place as seismic blast testing for oil and natural gas gets under way.

Conservationists hope to use the reopened prospect of seismic blasts to force more restrictions on the training, to safeguard wildlife against the disturbance from loud sonar and explosions.

They contend the combination of testing and training would be too much for animals, such as the massive right whale now on the edge of extinction, and bottlenose dolphins still recovering from a virus that decimated the population.

Studies have shown the noises disorient and disrupt the animals, which navigate and communicate by sound.

But with the Trump administration pushing to bolster fossil fuel reserves as well as the military, conservationists — like the marine mammals — likely will have to give way for both.

The Navy warfare training includes repeated sonar pinging from an array of submarine, ship and aircraft equipment, as well as ship "shock trials" — detonating loud explosions just off the hull to gauge whether it can handle the strain of bombardment.

In seismic testing, powerfully loud air guns are fired underwater every 16 seconds or so to read “echoes” from the bottom geology.

In 2016, Navy concerns were a big reason why the leases were denied by the Obama administration. An official with the federal Bureau of Ocean Energy Management cited the impact of the oil work on Navy training as a critically important factor in the decision that eventually denied the oil and natural gas leases.

This go-round, though, a Navy spokesman said the service has no problem with working alongside the companies. It is actively working with BOEM to handle problems that could come up, said spokesman Ted Brown.

"The Navy recognizes the inextricable link between national security and energy security and supports the development of national domestic energy resources, to include oil and gas development on the outer continental shelf, in a manner compatible with military operations," Brown said.

The disruption to marine life could be in the millions of animals across the span the Navy plans to train in the Southeast, said Michael Jasny, the marine animal protection director of the National Resources Defense Council. The mitigations agreed to by the Navy aren't sufficient, he said.

"The Navy assumes these animals will just move away (from training noises and vessels). They assume they can spot the animals," Jasny said.

Based on studies of the ability to sight the animals by the Fisheries Service itself, "that's completely unrealistic," he said.

The Navy request is a renewal, the third time it has sought this permit from the Fisheries Service. It comes after a federal judge in 2013 ruled that a Fisheries Service permit failed to make sure whales, dolphins and other marine mammals were protected from underwater blasts caused by Navy training in the Pacific Ocean.

The new permit application doesn't substantively change what the Navy asked for in the Atlantic in 2013.

"Because we have been working with the Navy for years, we have worked through and laid out fairly detailed procedures and timelines for dealing with the complex administrative facets of ensuring environmental compliance," said Jennie Lyons, a Fisheries Service spokeswoman for the Southeast region.

Denying a permit for the military doesn't get very far, a legal analyst said.

"Federal environmental law cases don't go to court often because the Department of Justice's position is the United States can't sue itself," said Rena Steinzor, a University of Maryland law professor affiliated with the Center for Progressive Reform.

If a federal agency objects to a military environmental practice, its staff usually must convince the service to sign a Memorandum of Understanding agreeing to address the concerns. But the agreement isn't enforceable, she said.

Incidental take requests usually involve a small risk to the animals, said marine biologist Lauren Rust, of the Charleston-based Lowcountry Marine Mammal Network, a private forensics company working with stranded dolphins and whales.

"With large projects like the Navy's request, the potential for incidental takes is much higher than they're asking for," she said. The bigger concern is for the long-term harm to hearing, foraging, as well as other sense behaviors the animals rely on to survive, she said.

Public comments on the proposed National Marine Fisheries Service "incidental take" environmental permit can be made until April 26.

The environmental groups will comment on the proposal, but it's too earlier to say if they will go court.

Reach Bo Petersen Reporter at Facebook, @bopete on Twitter or 1-843-937-5744.

Science and environment reporter. Author of Washing Our Hands in the Clouds.