Germ gets in badly preserved root (4,6)
I believe the answer is:
stem ginger
'preserved root' is the definition.
(preserved root of a ginger plant)
'germ gets in badly' is the wordplay.
'badly' is an anagram indicator.
'germ'+'gets'+'in'='germgetsin'
'germgetsin' with letters rearranged gives 'STEM GINGER'.
(Other definitions for stem ginger that I've seen before include "It's tasty" , "sort of ice cream" , "Plant root of a pungent spice" , "As food" , "spicy ingredient" .)