It may be anaerobic pockets of bacteria. How thick is your substrate?
It is strange that it is occurring around the roots of your plants, as they should help aerate the substrate.
Also, with a planted aquarium, why are you vacuuming the substrate? All you really need to do is to vacuum lightly over the surface of the substrate to suck up any loose detritus/mulm.
I have 100 lbs in a 75G tank, I think it works out to be about 1.5-2" in depth.
I'm vacuuming it because I noticed while I was gently going around the surface that little pockets of air were bubbling out... this is when I went deeper and found the black gravel. Anaerobic bacteria does make a lot of sense.
If the bacteria die and something else eats the gravel clean it will turn back...
How big is the gravel? If its pretty fine, then 2" of it might be your problem.
It's pretty coarse... I've read that's a problem with sand where gasses get trapped though... does sound like a similar problem. I guess I'll have to make sure to vacuum the gravel better.
If I turn the gravel, the next day, the black color disappears.
As long as it's not harmful to the fish... (?)
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