Hi all,
I don't like bare bottom tanks, it is certainly true you can go down the ultra clean route, and try to limit any bacteria other than those in the filter, but I think it makes it much more difficult to maintain stable water conditions, and you are very dependent upon your filter, and large water changes, with no back-up in emergency.
I know it sounds silly but a complex "dirty" tank with mulm, plants, substrate and biofilm will often have much better water parameters than an ultra clean one.
The other thing I'd say is that CUP likes a substrate, good enough for him, good enough for me, and I'd also refer people to Brett the "Skeptical Aquarist", as he is a lot more eloquent at explaining the reasons for having a substrate than I am.
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http://www.skepticalaquarist.com/docs/nutrient/nitcyc.shtml>
Particularly this bit:
"All surfaces in the aquarium offer a potential home to the community of aerobic bacterial that metabolize ammonia finally to nitrate. The uppermost surfaces of the substrate are a prime location for these populations, as you know. The nitrification process demands a lot of oxygen, more than familiar cellular respiration. Only a few centimeters below the substrate's surface, the diffusion of oxygen can't keep up with demand. As oxygen levels drop, facultative anaerobic bacteria find their niche. "Facultative" in this sense merely means "opportunistic." Many ordinary bacteria are facultative anaerobes; when oxygen is in short supply, these kinds of bacteria are able to switch to a metabolism that doesn't require oxygen. Instead, they use nitrate. The familiar nitrating bacteria provide the nitrate, and their high oxygen demands also tend to exhaust the limited supply. So besides providing the nitrate, a thriving microzone of aerobic nitrifiers provide the low-oxygen conditions too. You can visualize a mutually beneficial exchange between the two types of bacteria across a fluctuating boundary lying not far beneath the surface of the substrate. If there were no other reason not to disturb the substrate in an aquarium, this would be enough for me."
cheers Darrel