It cannot fly in the murky gloom (3)
I believe the answer is:
emu
'it cannot fly' is the definition.
(emus are flightless birds)
'in the murky gloom' is the wordplay.
'in' says the answer is hidden in the clue.
'EMU' is hidden within 'the murky gloom'.
(Other definitions for emu that I've seen before include "Large Australian flightless bird" , "Aussie runner" , "Parky's nemesis" , "Flightless Aus. bird" , "one offering challenge to Hull?" .)