2nd question first...by "cement", do you means brick & mortar type or concrete? I don't think it would be a problem for the rocks or the animals you put in as far as toxicity...but how do you plan to get "cement" to stick to glass? Logistically it creates a few problems. Cement doesn't bond to glass, unless you have holes drilled thru the glass and have a threaded screw, eye bolt, or anchor of some sort the concrete would form around...not to mention the weight of concrete-like cement in a vivarium could make the structure unstable, unmovable, and unsafe. How big exactly were you attempting to build this thing? And how heavy are the rocks you wanted to attach? If you'd like to stick with the rock wall effect in your viv, my suggestion would be to use the Great Stuff foam for cracks, that doesn't expand much...it sticks to everything!! That's if the rocks are less than 20lbs. If you plan on making a Gi-Normous vivarium, and the rocks were going to be heavy...I would say substitue the "real" rock with fiberglass ones. You could also make these if you want to go thru the trouble...or have a ton of time on your hands.
1st question, "aquarium safe" silicone is generally waterproof from the moment you push it out of the tube. It is generally safe for exposure once it's cured so you don't make your "inhabitants" toxic. And it is extremely strong and made to withstand an abundance of pressure and weight. If you are talking about the silicone they sell in the pet store that says "Aquarium Silicone" and they charge $10 for a few ounces...yeah, don't buy that. Use the big tubes you buy from the hardware store. Several posts refer to one made by GE, which comes in black...but any silicone used for building and glazing sealant, weatherproofing type, is fine. The important thing is it doesn't contain latex...this is an ingredient that makes it "Easy to clean up with water"...It will cure and hold, but eventually will degrade because of the latex. The other type (especially if it is a super large enclosure, or one with a lot of water) is a silicone used for Marine purposes...which is made to withstand water exposure/BTW- you can use these type of silicones to attach rocks to glass...lay tank on it's back and let it cure with rocks gravity buried in the silicone.
That being said, if the coco bedding is more decor and not going to have running water dripping from it...the latex brand would probably work.
Does any of that help?? I hope so.
Thx, Teri
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