03-24-2011, 11:54 AM
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If I've understood this thread correctly, leave it alone. There is no issue.
The "water" isn't the concern anyway, it's the substrate under the item. Substrate that is "open" at the surface will have a regular flow of water down and back up again. Aerobic bacteria colonize this substrate and interact with organics, plant roots, and water to break down the organics into nutrients for the plants. Oxygen is obtained both from the water and the plant's roots.
Where this water circulation does not occur, due to a chunk of rock or wood on the surface, the substrate under it becomes "dead" or "anaerobic" because little or no direct oxygen gets to this area. This is not at all bad though. These areas will be colonized by anaerobic bacteria that either do not use large amounts of oxygen or they can create their own oxygen. Anaerobic bacteria release toxic gases, especially hydrogen sulphide, which in excess can rot plant roots and become a problem for fish, and encourage algae. But anaerobic areas also allow nutrients to be more readily available and more easily assimilated by plants because it prevents oxygen from binding with the nutrients. Denitrifying bacteria colonize the surface and obtain oxygen from nitrite and nitrate to produce nitrogen gas which usually escapes throuogh the water surface.
The more plants you have, the smaller the anaerobic zones will be. As plant roots spread, they release oxygen, even under rock and wood. Plants like the larger Echinodorus species have very extensive root systems that will work their way throughout the substrate.
I have a lot of chunks of wood and some rock in my tanks, and in 20 years I have never experienced any problems from anaerobic areas. I recently read one botanist's view that anaerobic conditions were actually more beneficial than aerobic conditions for plants. Having a mix as most of us do certainly seems good. I wouldn't disturb these spots under wood and rock; it will significantly alter the conditions and that could really be trouble.