Under most circumstances, you as the end user need to do nothing. The root certificate store is maintained by the operating system provider (Apple, in this case) and there's a revocation system that handles certificates that need to specifically not be trusted.
If you are getting a certificate error, contact the provider (email, web, etc.) and let them know the error so they can fix it on their end.
As an end user there's very little cause for overriding a certificate the operating system is rejecting or warning about.
If you explicitly trusted a certificate, it would show up where
@DeltaMac directed you
or in
Settings > General > Profiles (which is near the bottom of the general screen); you can remove trust from these locations by toggling the switch or removing the profile.
On a side note: The list of trusted root certificates provided by the oprerating system vendor it pretty extensive and to my knowledge there's no way to list it all in iOS. On macOS you can see it in the Keychain app.
