This is while Trump attempts to appoint Scott Pruitt to the head of the EPA. He's a noted opponent of the EPA who frequently litigates against it on behalf of the fossil fuel lobby, denies man-made climate change, and would like to dismantle the agency's power altogether.
https://www.nytimes.com/2016/12/07/us/politics/scott-pruitt-...
That's what makes me think this may mean mass defunding/shutting down of departments. Pruitt is a clear offense to the institution of the EPA. You'd put someone like that over a department and tell that department to "shut up" if it were about to get the axe.