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substrate question

I have a question---I have a 90 gallon well planted tank with an Eheim 
canister providing filtration.  When cleaning/changing water I clean the 
gravel and pull up very dark and nasty smelling compounds from one area of 
the tank.  I have read recently that one should not disturb the substrate of 
a planted tank, and was wondering if I should then leave this smelly dark 
substance in the gravel for the plants?  Thanks,