A seed in the soup? (6)
I believe the answer is:
lentil
This clue is a double definition.
'a seed' is the first definition.
(I know that lentil is a type of bean)
'the soup?' is the second definition.
(lentil soup is a kind of soup)
'in' acts as a link.
(Other definitions for lentil that I've seen before include "Lintel (anag.)" , "Plant - pulse" , "Edible leguminous plant seed" , "Leguminous vegetable" , "Food stuff" .)