"There have been too many ethical lapses under Administrator Pruitt's watch and this decision is in the best interests of the agency and our country", she said in a statement.
Wheeler has worked in Washington for more than 20 years.
By the end, Pruitt had few defenders in the West Wing.
The Adirondack Council, an environmental advocacy group based in Elizabethtown, has been outspoken in its criticism of Pruitt and also celebrated his resignation.
"I'm concerned that the Trump administration's assault on human health and the environment will continue long past Pruitt's departure from EPA", Pallone said.
Pruitt was critical of the EPA in his career as Oklahoma Attorney General, suing the agency 13 times to try and stop emissions rules and block regulations that impeded coal-fired power plants and calling for the EPA to be eliminated entirely. Wheeler also represented Underwriters Laboratories, which does testing and certification for the EPA among other organizations; Xcel Energy; and Insurance Auto Auctions, a salvaged vehicle company, according to his financial disclosure form.
Wheeler is not someone who has sought the spotlight.
"[Wheeler] has the relationships on Capitol Hill", Dempsey said.
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Last month, while praising Pruitt's "fantastic job" at the EPA, the president admitted, "I'm not happy about certain things, I'll be honest".
Political observers are expecting Wheeler to be in his new role as acting EPA administrator for an extended period.
"When you feel like you are being thrown out of the pot and into the frying pan, it's not cause for enthusiasm", Natural Resources Defense Council spokesperson Bob Deans told the NewsHour.
And environmentalists have seized on Wheeler's record as a former energy lobbyist and coal lover to herald the acting administrator as the environment's biggest enemy. He then left to work as an advisor to Republican Senator Jim Inhofe, a notorious climate change denier who published a book calling global warming a "conspiracy" and "the greatest hoax".
Prior to being confirmed by the Senate as deputy EPA administrator, Wheeler previously worked in the agency's office of pollution prevention during the administration of the first President George Bush. As The Intercept reported in February, he made campaign contributions and hosted fundraisers in May 2017 for two Republican senators, Inhofe and John Barrasso, R-Wyo., both of whom are members of the Committee on Environment and Public Works.
During the hearings, Sen.
"I believe man has an impact on the climate, but what is not completely understood is what the impact is", Wheeler responded.
Now, in Wheeler, Murray not only has one of his former lobbyists inside the EPA, he has them running it. Joe Donnelly, D-Indiana, Sen. Three moderate Democrats - Heidi Heitkamp of North Dakota, Joe Donnelly of IN and Joe Manchin of West Virginia - joined with Republicans to support Wheeler IN April.