Black deed — river’s picked up germs (8)
I believe the answer is:
bacteria
'germs' is the definition.
(I've seen this in another clue)
'black deed river's picked up' is the wordplay.
'black' becomes 'b' (abbreviation as in pencil classifications).
'deed' becomes 'act' (an action).
'river' becomes 'aire' (River Aire in Yorkshire).
'picked up' says the letters should be written backwards.
'aire' written backwards gives 'eria'.
'b'+'act'+'eria'='BACTERIA'
(Other definitions for bacteria that I've seen before include "Infectious organisms" , "Single-cell organism" , "These single-cell organisms are in bait race" , "Single-celled organisms" , "Care a bit about sources of diseases" .)