Hydrogen rises through soil and grit (5)
I believe the answer is:
heart
'grit' is the definition.
(thesaurus)
I can't explain the remainder of the clue.
Can you help me to learn more?
(Other definitions for heart that I've seen before include "Decorated (cake)" , "See 22" , "the name of a prison in Midlothian!" , "Centre; valour" , "It's in the chest" .)