These two substrates are chemically very different. The amount of recalcitrant organic matter in cow dung is much larger than in green algae. What kind of differences are you looking for?
I want to find the effect of nanoparticles on increase of biogas and methane using waste. People have used nanoparticles for cow dung and got some increase in biogas and methane. I want to use same nanoparticles with alage and want to see if methane production increases or not. For this i want to know the difference between two which will help me to decide which type of nanoparticle i should use.
This is beyond my field of experience. I suppose nanoparticles serve as a catalyst in cow dung. Cow dung contains a lot of lignin, which may be influenced by a catalyst. I don't expect so much effect in the much more digestible algae.