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(CNN) —  

As the clash between Justice Department leaders and career prosecutors in the case of President Donald Trump’s longtime friend Roger Stone spilled into public earlier this week, the leaders of the public-corruption unit in the Manhattan US attorney’s office sat on a courtroom bench, watching with unease as the news flashed across their cell phone screens.

Those prosecutors, who had put Trump’s former personal attorney Michael Cohen in prison, were in court Tuesday to oversee the trial of another politically tinged defendant, Michael Avenatti, the celebrity lawyer who has claimed Trump as his nemesis. For them, the prospect of interference in sensitive cases carries particularly high stakes.

And beyond New York, the Stone situation has reverberated across the country in the past few days, with prosecutors incensed over the apparent intervention by Attorney General William Barr to lighten the sentencing recommendation for Trump’s ally, along with fear of what some perceive as a growing political directive coming from Washington.

On the West Coast, one federal prosecutor said there was an overwhelming sense of “outrage” felt in his office.

A prosecutor on the East Coast voiced concern about the potential impact of political interference on juries and judges, who could perceive that cases aren’t being brought objectively.

And a former prosecutor said his clients have expressed concern about cooperating with investigations out of fear that the Justice Department could interfere improperly in a case, putting them in jeopardy.

Some concerns arose even before the Stone situation. In the past two weeks, the Justice Department has twice ordered US attorney’s offices around the country to participate in what some of them perceive as politically charged actions, according to people familiar with the matter.

First, the department ordered prosecutors to hold news conferences, make statements and use social media to promote Barr’s initiative to crack down on “sanctuary cities,” according to a person with direct knowledge of the matter. The Justice Department later retracted the demand, the person said. Still, at least two US attorneys wrote op-eds.

The department also instructed federal prosecutors to write op-eds to push for passage of pending legislation on fentanyl. More than a dozen US attorneys complied with publishing op-eds or written statements. The person said that historically prosecutors have been instructed to avoid commenting on pending legislation. 

Elsewhere, in Connecticut, Pittsburgh and St. Louis, the US attorney’s offices have picked up investigations that are in line with what the President has wanted, looking into the origins of the investigation into the 2016 election, examining the Ukraine dealings of the son of Trump’s political rival Joe Biden and reviewing the Michael Flynn prosecution.

A career prosecutor in the rural Northwest said she has faith in Barr and wishes Trump would get out of his way. “He’s not a rookie. He knows what he’s doing,” she said of the attorney general. “Let him do his job.”

New York is ground zero

The fears over potential political interference are particularly acute in New York, where prosecutors with the US attorney’s office in Manhattan handle high-profile cases with a broad range of geopolitical implications, including terrorism prosecutions as well as investigations involving foreign governments and financial institutions, all of which can intersect with White House interests.

Manhattan prosecutors have also generated cases that are of concern to Trump personally, including the prosecution of Cohen and an investigation of the Trump Organization that ended without charges.

And for the past few months, prosecutors there have been investigating Rudy Giuliani, Trump’s personal attorney, as well as Trump’s inaugural committee.

Still, despite the alarm sounded in recent days, Southern District of New York prosecutors believe that their leader, Geoffrey Berman, has defended the office’s relative autonomy, particularly since Barr’s arrival, according to people familiar with the matter.

Barr, these people said, has attempted to micromanage certain cases, asking more questions and for more frequent updates than his predecessors on matters from Berman. 

Berman has bristled at those demands, according to these people, and has repeatedly pushed for actions on certain politically sensitive cases in opposition to Justice Department leadership, most notably the indictment in October of the state-owned Turkish bank, Halkbank.

According to a person familiar with the discussions, Barr personally spearheaded an effort last year to negotiate a settlement with the bank that would have allowed it to sidestep an indictment after Turkey’s President, Recep Tayyip Erdogan, pressed Trump in a bid to avoid charges. Berman, however, insisted on criminal prosecution, according to the people familiar with the matter.

A spokesman for the Manhattan US attorney’s office declined to comment for this story.

Those types of actions have pacified Berman’s staff in New York, who recall a message that Berman, a Trump appointee, delivered soon after taking his oath of office in 2018: “I want to be clear: Politics is not going to have a role in what we do. We’re going to keep doing business as we always have.” 

(It hasn’t hurt that Berman has developed a rapport through personal touches. At a barbecue for interns, he wore an apron and manned the grill, one former prosecutor recalled. On another occasion, he distributed blue flannel pajama pants with “SDNY” emblazoned across the butts.)

Tensions with Washington  

Even so, New York federal prosecutors’ independence – so staunch, they joke, that their version of notifying Justice Department leadership about a consequential decision is to leave an after-hours voicemail on someone’s desk phone the evening before they’re about to take a significant action – has been tested under the Trump administration.

When the US Commerce Department was sued in 2018 by multiple state attorneys general over adding a citizenship question to the 2020 census, lawyers from the SDNY’s civil division initially took the standard approach of representing the federal agencies in court.

But four months into the case, the SDNY attorney removed herself, telling the judge the matter would be handled “exclusively by attorneys from the Department of Justice.” No additional detail was provided, but, according to people familiar with the matter, there was disagreement between the offices, prompting SDNY’s exit. 

The move drew attention from the judge overseeing the case, US District Judge Jesse Furman.

“There are dozens of highly qualified lawyers and professional staff in the Civil Division of the United States Attorney’s Office for the Southern District of New York – the office that normally represents the Government in this District,” Furman wrote. “The Court can only speculate why the lawyers from that Office withdrew from their representation of Defendants in these cases.”

More recently, the Justice Department made a filing in support of Trump’s lawsuit to block a New York state grand jury subpoena to his accounting firm. Attorneys with SDNY’s civil division were involved in the initial court filing but their names are not signed on to the Justice Department’s appeals court filings.  

Already in New York, in just the past several months during Barr’s tenure, several politically connected defendants have attempted to use perceived political influence to their advantage in court.

In December, Cohen claimed in court papers that prosecutors have retaliated against him, saying the Justice Department pursued him to “protect” Trump. 

Avenatti sought to argue to a jury that he was being prosecuted for taking on Trump and asked a judge to dismiss an indictment against him, claiming he was the subject of “vindictive and selective prosecution” for going up against the President. He was convicted Friday.

A lawyer for an indicted Giuliani associate, Lev Parnas, has formally requested that Barr recuse himself from the case “in an effort to preserve the public trust in the rule of law.”

Judges typically disavow those claims – Avenatti’s request was denied and Cohen’s hasn’t received a ruling – but attorneys are concerned that could change.

One veteran federal prosecutor in Southern California said she was “extremely concerned” by the President interjecting himself into a pending criminal case with a tweet, and by the notion that it had prompted Barr to undermine line prosecutors.

She said she was encouraged, however, by the attorney general’s comments Thursday, when he told ABC News that he had acted before Trump tweeted his displeasure with the Stone sentencing recommendation, and that the President’s tweets make it “impossible” for Barr to do his job.

“It’s about time,” she said.

CNN’s Scott Glover contributed to this story.