Ultimately nice and comfortable bit of shrub for biological set-up (9)
I believe the answer is:
ecosystem
'biological set-up' is the definition.
'ultimately nice and comfortable bit of shrub' is the wordplay.
'ultimately' indicates one should take the final letters.
'and' means one lot of letters go next to another.
'comfortable' becomes 'cosy' (similar in meaning).
'bit of shrub' becomes 'stem'.
The final letter of 'nice' is 'e'.
'e'+'cosy'+'stem'='ECOSYSTEM'
'for' is the link.
(Other definitions for ecosystem that I've seen before include "Biological community with its environment" , "integrated community" , "Community of organisms and their environment" , "orderly collection of organisms" , "The interaction of a group of organisms with their physical environment" .)