Gardener was a bit upset by a little bird (4)
I believe the answer is:
wren
'a little bird' is the definition.
(I've seen this in another clue)
'gardener was a bit upset' is the wordplay.
'a bit' indicates a hidden word (the answer is formed by a bit of the clue).
'upset' says the letters should be written backwards.
'nerw' is hidden in the letters of 'gardener was'.
'nerw' written backwards gives 'WREN'.
'by' is the link.
(Other definitions for wren that I've seen before include "Bird - former British servicewoman" , "A small garden bird" , "of two wings?" , "Small bird (in the Navy?)" , "flier" .)