That’s my read of this CHE essay on the latest malevolence to emanate from Trump:

Another concern is whether the new rule will affect employers that are currently exempt from the cap on the number of H-1B visas companies can use. Colleges are typically exempt from this cap.

Jeremy Neufeld, director of immigration policy at the Institute for Progress, shared his interpretation on social media that, based on an FAQ page from the White House, the $100,000 fee does apply to cap-exempt organizations.

This is pretty bad news, to put it mildly: it will probably reduce the number of foreign assistant professors being hired at American institutions, and is likely to also depress the number of senior hires. Of course, start-up costs for assistant professors in the natural sciences can run millions of dollars, so perhaps many colleges will simply absorb this additional cost. But in the humanities and social sciences, things are likely to be different.

Of course, this is all consistent with the various efforts of the Trumpistas to destroy American preeminence in research.