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Anaerobic substrate is, as the name implies, an oxygen free zone in the
substrate. There are microbes that can create hydrogen sulfide, which, I
guess, is toxic. Some old books call this "blackening" of the substrate,
so, I guess it looks black. If poked the substrate will bubble and the
bubbles will smell bad. My substrate regularly bubbles but it is oxygen (O2)
from the vascular transport of gas into the plant roots.
In healthy planted aquaria this isn't a problem. Even though I run an
almost 6 inch deep substrate the roots penetrate deeply and pump oxygen down
there so the substrate is never going to go that low in O2 levels. There is
some evidence that low O2 levels may contribute to denitrification, the
conversion of Nitrite into nitrous oxide and nitrogen gas, which freely
escapes the aquarium a la the Jalbert reef system. If the plants in your
tank are actually growing this isn't something you have to worry about. I
think you would basically have to have a ton of organics and a really dead
substrate to cause this to happen. I can imagine this occurring with the
Walstad method (lots of garden soil) even so I am trying an experiment with
it in a smaller tank and I haven't seen it even there.
Don't worry about it.