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There is alot to that question. There has been some great discussion recently on the APD about the benefits. I think, it allows plants to take up nutrients that would otherwise be used by algae. The more plants, the more oxygen that gets released, and the more balanced the tank is. The more plant roots running through the substrate, the more nutrients get sucked into the substrate and out of the water column (away from algae).
 

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Also it gives the fish a place to hide if they feel stressed/threaten and gives a shaded area for those fish that like darker areas.
 
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