President Trump is unhappy about a report in The Atlantic which says a member of EPA Administrator Scott Pruitt's press team has been shopping negative stories about Interior Secretary Ryan Zinke to multiple outlets. A source who spoke to Trump told me the president raised the issue in conversation and said, "That's not good." Trump has been souring on Pruitt as the negative press about him piles up.

Why this matters: Pruitt — who is under siege from federal investigators, the White House, Capitol Hill, and the media — survives because the one guy who matters in the White House won't fire him. Trump's draining supply of goodwill towards Pruitt is the EPA administrator's lifeline. Most everyone else in the building wants him gone.

Pruitt's spokesman Jahan Wilcox has denied that his team pushed negative stories about Zinke: "This did not happen and it's categorically false."

Behind the scenes: On Friday afternoon, Pruitt had lunch with four members of his team at Ambar restaurant on Capitol Hill. The gathering came as a surprise to just about the entire senior staff of the EPA; they found out about the meeting from a picture a lobbyist tweeted.

Over the last few months, Pruitt has walled himself off from all but five EPA political appointees: ​Millan Hupp, Sarah Greenwalt, Hayley Ford, Lincoln Ferguson, and Wilcox. Of those five, only Wilcox is over 30. Hupp, Greenwalt and Ferguson came with Pruitt from Oklahoma. Wilcox is the only press aide Pruitt appears to trust.

Pruitt’s chief of staff, Ryan Jackson, runs the agency’s operations but rarely knows where his boss is. Pruitt has frozen Jackson out of his inner circle — a disaster for a chief of staff. Pruitt and Jackson don’t trust each other, multiple sources told me.

"All of us have been frozen out over time," one EPA political appointee told me. "It's absolutely unreal working here. Everyone's miserable. Nobody talks. It's a dry wall prison."

Pruitt never trusted the EPA's career staff. But for the first 10 months of his tenure as EPA administrator, he kept most political appointees at least partially in the loop. Now, he's frozen out almost all of them.

In his early days as administrator, Pruitt helmed daily morning meetings with dozens of political appointees. Those larger meetings stopped in the fall, and he reduced the meetings to a group of about 10, including his chief.

Even those smaller meetings grew rare over the winter.

The pushback: Wilcox told me Pruitt ended the all-hands meetings because they had grown unwieldy and unproductive. "There were 98 individuals that were invited to the morning meeting with Administrator Pruitt and it’s been pared down to make it more efficient."

Now, senior political appointees tell me they have no idea where and how Pruitt spends his time. They scan Twitter and the news to try to keep tabs on him.

Pruitt used to share his travel schedule with political appointees. Then, over the winter, he sent out a redacted schedule simply saying "travel." After that, he stopped sharing it altogether. Since his April 26 congressional testimony, senior staff outside his inner circle have had virtually no idea of his whereabouts.

The leadership in Pruitt's congressional affairs shop have complained to associates that they can't do their jobs. They've griped about complaints from members of Congress when the members find out after the fact that Pruitt has visited their state or congressional district. The embarrassing reality for Pruitt's legislative affairs team is they had no idea either.

Wilcox pushed back on that complaint, noting that Pruitt has appeared with members in their districts at least twice in the last few months.

Two sources told me that Pruitt's hardly been in the office this past week. He's been planning to set up an external legal defense fund — a development first reported by the New York Times.

The bottom line: Pruitt has grown paranoid and isolated, and he only trusts a small handful of people at the agency. Senior White House staff darkly joke among themselves every time a fresh bad story comes out about Pruitt. Numerous senior EPA staff have already resigned or plan to quit.

At the same time: Despite Pruitt's problems, my colleague Amy Harder reports that the EPA's policy trains appear to be running mostly on track, largely due to key leadership positions being filled.