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I would not be too concerned if your fish and plants are both doing fine. My aquarium is not densely populated with rooted plants so I have similar concerns. What I did was use a small chop stick ones you get from a Chinese restaurants when dining and used a knife to make a point at one end(optional). Then I just poke into the dirt a dozen spots every few weeks to aerate the soil and release the bubbles. With a pointed chop stick I just rotate as I go down the substrate. Having a point helps to not push the substrate into the soil, at least that's my logic.
 

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Also try smell the water when the bubbles are released, if they smell bad then the soil may be bad so try my previous step more frequent and all will be ok;) Don't poke too much at one time(if soil is bad) or you might release too much toxin into the water and harm the fish.
 

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Rusalka, enjoy your comments and enthusiasm. I hope you can provide more pictures! I love pictures. I bought topsoil form home depot. Never have this yellow water ppl mention here. I take a little effort to remove most of the larger wood chips. I do notice that my trumpet snails will push out the rest of the larger chips later after I setup the tank. One thing I am definitely going to do for my next tank setup is mineralized soil substrate. This should help greatly reduce the new tank syndrome. The concept is basically soak the soil in water for a day. Pour out the water and spread thin the wet soil on a plastic sheet and let it dry a day or longer. Repeat a few more times. This drying process oxygenates the soil, gets the microbes going and ultimately mineralized the nutrients in the soil. Sounds like a fun idea to try and have a proven record so they say.
 
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