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6 year oldPresident Donald Trump said Mr Pruitt had done "an outstanding job, and I will always be thankful to him".
But Mr Pruitt has been embroiled in allegations of ethics violations for months.
His deputy Andrew Wheeler will take over as acting head of the agency, Mr Trump said.
The long list of Scott Pruitt controversiesNewer articles
<p>They have been blasted from car stereos on the streets of New York City, played by DJs at nightclubs across the US, dubbed into Chinese on TikTok and inspired merengue songs...