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Republican Rep. Elise Stefanik, of NY, said it's "time for new leadership at the EPA" after the resignation.
In recent weeks, Pruitt has come under increasing scrutiny for numerous scandals that include spending behaviors, allegations that he rented a Capitol Hill condominium linked to an energy lobbyist and a CNN report released this week that accuses the chief of using "secret" calendars and schedules to hide controversial meetings with industry players.
Sen. John Barrasso, the Republican chairman of the Senate Committee on Environment and Public Works and until Thursday a strong defender of Pruitt, said Trump made the right decision to accept the resignation. "Pruitt created a culture of corruption at EPA that has never been seen before in a federal agency, and for months President Trump idly stood by and allowed him to do further harm".
Pruitt's former deputy Andrew Wheeler has been put in temporary charge of the agency. "I applaud President Trump for placing him in this position".
Under Pruitt, the EPA "rolled back punishing regulations that were hurting American workers and stifling our economy", Barrasso said.
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".
Barrasso will manage the confirmation hearing for Pruitt's successor, as long as Trump nominates a replacement before the end of the year. And later: "I count it a blessing to be serving you in any capacity". No stranger to the EPA, where he worked for almost two decades, Wheeler has also served as an advisor to Senator James Inhofe (R-Okla.), a fierce critic of climate protection policy.
"We now face the stark reality of a coal lobbyist, Andrew Wheeler, running the agency that is supposed to protect our air, water and climate", he said, in a statement.
Brandon Hurlbut, former chief of staff at the Department of Energy, said the ethics complaints are one thing that is likely to change with Wheeler.
Senator Kamala Harris, Democrat from California:"Just because Scott Pruitt resigned doesn't mean we've forgotten about the taxpayer funds he's misused or the damage he's done to our environment".
Wheeler was only marginally approved as EPA deputy in April. Documents later showed Pruitt's chief of staff had signed off on the pay hikes, indicating he had the administrator's consent.