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GB depth is one of many great debates in this hobby. The 12" or 300mm guidelines are just that, sort of a guideline.
Take into consideration what you want to plant - tomatoes or other large plants need support (a good anchor) and do well in a deeper environment. Many of the leafy plants could get by in just a few inches.
You ask an important question as to micro organisms...a shallow GB offers less surface area for bacteria to reside. That said, it's all about total volume. More shallow GB's can equal fewer deep GB's, etc. Calculate total GB volume in relationship to your total system volume.
My GB's have about 9" deep media, but I use heavy river rock for good holding power on the larger plants. I also use external filtration as I don't have enough GB area to support my FT size and stocking density.
One thing to consider - if you are limited in space, deeper GB's allow more bacteria surface area in the same footprint as shallower GB's.
As to your GB's, you can always go an inch or so deeper on the water - you don't need a full two inches below the surface to avoid algae. Actually, a half inch is enough in a level, balanced GB.
Hope that helps
Absolutely Chip ...
this is awesome information since I only plan to plant leafy veggies, such as lettuce, spinach, herbs and things of that nature and not corn or tomatoes that would require deep anchoring in my aquaponic system.
I will raise the level of water a bit since I have well over 2" of dry bed.
I have about 8 inches of media in a flood/drain micro system. I haven't had any luck getting plants started up to now. The flood/drain cycle time was 2-3 min. This is partly due to the small GB and partly to the plumbing. Plants would grow to about an inch tall and stall out. I reworked the plumbing and increased the cycle time to 11 min. So far I'm seeing positive results. Seedlings are looking good and growing fast. My guess is that the roots were too wet.
As far as fish heath, the small GB did just fine supporting the necessary microorganisms. Water quality always remained good. I had no additional filtration.
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