(CNN) The US ambassador to Estonia is resigning in frustration with President Donald Trump's comments about, and treatment of, European allies.

James D. Melville Jr.'s resignation, first reported by Foreign Policy magazine, makes him the third ambassador in the last year to leave the State Department early. He is among many senior State Department officials who have headed for the exits or been pushed toward them since Trump assumed office.

In a statement, a State Department spokesperson confirmed Melville's departure.

"Earlier today, the United States' Ambassador to Estonia, Jim Melville, announced his intent to retire from the Foreign Service effective July 29 after 33 years of public service," the statement read in its entirety.

Melville's resignation comes at a time of acutely heightened tension in an alliance that, before Trump's election, had been one of the most solid, reliable and interconnected US relationships.

But Trump's attacks on NATO members, his trade tariffs against EU nations, his rejection of the Iran nuclear deal and the Paris climate agreement and his attacks on leaders such as German Chancellor Angela Merkel have cast a pall over US ties to Europe.

Many European officials are wary about Trump's mid-July visit to the NATO summit in Belgium. Those officials there fear that Trump's meeting with Russian President Vladimir Putin after NATO will look like the friendlier encounter in comparison.

"The transatlantic relationship, which all around the table we consider a given, is not a given," a European diplomat told CNN. "We now have a major crisis."

'It's time to go'

Foreign Policy quoted from a private post on Melville's Facebook page in which the seasoned diplomat referred to the President's comments about Europe in explaining his decision to retire early.

"A Foreign Service Officer's DNA is programmed to support policy and we're schooled right from the start, that if there ever comes a point where one can no longer do so, particularly if one is in a position of leadership, the honorable course is to resign," the magazine quotes Melville's post as saying. "Having served under six presidents and 11 secretaries of state, I never really thought it would reach that point for me."

"For the President to say the EU was 'set up to take advantage of the United States, to attack our piggy bank,' or that 'NATO is as bad as NAFTA' is not only factually wrong, but proves to me that it's time to go," Melville said in the post.

The announcement of Melville's departure was followed by that of Susan Thornton, Trump's choice to be the nominee to be assistant secretary for East Asian affairs, later on Friday.

Two State Department officials said Thornton notified staff in an email today that she is retiring in July.

The officials said Thornton, a well-respected career diplomat who has been doing the job in an acting capacity since Trump took office, was notified she will in fact not be the nominee and she decided to retire.

Former Secretary of State Rex Tillerson pushed very hard for Thornton's nomination amid intense pushback from conservatives on Capitol Hill and hardliners in the administration.

Secretary of State Pompeo tipped his hand on Thornton about a month ago during testimony on Capitol Hill, in which he said he would be making announcements on personnel, including a top diplomat for East Asia, signaling Thornton was no longer going to be considered for the post.

State Department spokesperson Heather Nauert said the administration was grateful for Thornton's two-and-a-half decades of service.

"We particularly appreciate her dedication to Department and interagency colleagues, her extraordinary leadership, especially as Acting Assistant Secretary over the past year and a half, and the personal example she set as an embodiment of the best qualities of a Senior Foreign Service Officer," Nauert said in a statement. She added that Pompeo is moving forward with efforts to nominate someone for the key position.

The duo is only the latest foreign service officer to leave in a department where the senior ranks have been deeply depleted and even rising stars have resigned rather than serve the President.

In November, an award-winning US diplomat based in Nairobi wrote then Tillerson a blistering letter saying that the Trump administration had diminished the influence of State Department with its preference for military solutions.

Elizabeth Shackelford wrote that "despite the stinging disrespect this Administration has shown our profession," the State Department's diplomats "continue the struggle to keep our foreign policy on the positive trajectory necessary to avert global disaster in increasingly dangerous times."

'Traditional values ... betrayed'

In her resignation letter, Shackelford told Tillerson that she "would humbly request that you follow me out the door."

In January, then-US Ambassador to Panama John Feeley resigned over differences with the Trump administration, saying in his resignation letter that "as a junior foreign service officer, I signed an oath to serve faithfully the President and his administration in an apolitical fashion, even when I might not agree with certain policies."

"My instructors made clear that if I believed I could not do that, I would be honor bound to resign. That time has come," wrote Feeley.

Once he had left office, Feeley was less circumspect in a scathing oped in the Washington Post, saying that he had "resigned because the traditional core values of the United States, as manifested in the President's National Security Strategy and his foreign policies, have been warped and betrayed."

In March, another career diplomat, then-US Ambassador to Mexico Roberta Jacobson, announced her decision to step down amid increased tensions between the US and Mexico that's due in large part to Trump's incendiary rhetoric about the country, its citizens and its trade relationship with the US.

A few days after her announcement, the White House delivered the equivalent of a slap, excluding Jacobson -- who served as ambassador until May -- from a meeting in Mexico City between Trump son-in-law and senior adviser Jared Kushner and President Enrique Pena Nieto.