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I've collected my own substrate. I've collected them from two creek beds on some family property. One of them was very fine particle size, and this worked okay, after I capped it with Quikrete brand play sand. I've not had any real algae issues, and the tank is all native N.A. plants and collected substrate/wood (other than the play sand).

The other tank is no longer set up, but I mixed fluorite with small gravel and sand mix pulled from the creek bed. I had some minor hair algae growth in that tank, but it was not to crazy levels by any means.
In both cases, I washed the substrate with boiling water poured into a 5 gal bucket. I did several boiling water baths to kill potential bacteria/algae/critters.

I also did this to the wood I collected, after I stripped any rotted wood off it. I let it sit in the water for a few days to remove tannins and let the wood absorb water so it would be less buoyant. I skinned any remaining bark off of it as well. I've had some minor fungal growth on it, but nothing time didn't take care of. The wood (It's Oak) I put in the tank I adhered with silicone to a piece of slate tile, and then put the substrate in the tank to bury the tile. It hasn't caused any problems, and I use slate tiles as a background regularly. I just cut them to fit with a tile wet saw and diamond blade and silicone them to the back glass inside the tank.

I've tried to be careful to avoid limestone, which is common here. I have not seen any big pH fluctuations, and the plants are all doing fine. There are no fish in that tank. It's really a grow out tank for plants to be added to the 150 gal tank I'm setting up for native fish.
 
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