Bird initially near atomic plant (5)
I believe the answer is:
henna
'plant' is the definition.
(plant which henna dye is made from)
'bird initially near atomic' is the wordplay.
'bird' becomes 'hen' (hen is a kind of bird).
'initially' indicates taking the first letters.
The first letters of 'near atomic' is 'na'.
'hen'+'na'='HENNA'
(Other definitions for henna that I've seen before include "Beauty aid" , "Red-brown dye used for body decorations" , "Hair/skin dye" , "Red-brown plant dye" , "Natural hair dye" .)