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Newbie Questions - Long

I am a very new aquatic gardener. I recently read a lot of information on a
page written by Don Quackenbush? and being the newbie that I am, I ran out
and bought kitty litter. I redid my 30 gal. aquarium with kitty litter on
the bottom, and a layer of coarse sand on top. I then pitched all of my
plastic plants, and ordered a slew of plants from Arizona Gardens. The
plants arrived in beautiful condition - even though the more expensive next
day service took 3 days to get to me (in Texas 100 deg. weather).  I buy RO
water from a large Aquarium suppy store in Houston, but order almost
everything else from Pet Warehouse (at huge savings compared to the supply
store in Houston). I have tried the DIY CO2 unit described on the krib site,
but it fizzles after a couple of days, and I'm getting tired of re-doing the
mixture all of the time. I have 2 30W flourescent bulbs in a hood that sits
on top of a glass cover for the aquarium. Except for the holes we cut in the
hard plastic extension for the inlet/outlet tubes of the Magnum 350, the
aquarium is completely closed. We do have the two biowheels functioning even
though D. Quackenbush says no water surface disturbance is the key to saving
CO2. I also fertilize the substrate with fertilizer sticks that I purchased
from Arizona Gardens. 

I have quite a few fish (I've had them for quite some time), and they've
been very accepting of all the new changes in their environment! :)

Now for my questions:

The plants still look healthy after about 2 weeks in the aquarium. The
foxtail has grown so tall that it is starting to grow on top of the water
surface. So- this weekend, I went in to prune the foxtail. When I uprooted
it, the roots were BLACK and they smelled terribly. Why are they growing so
well when the roots are rotting, and why are the roots rotting? 

The temple is losing it's leaves, but the very top leaves are very pretty
and pink.  Why? 
The Bacopa is also losing all it's leaves. It has a nice green stem, but no
leaves. :)

One thing I should note: after we filled the aquarium with water, we did
notice a lot of air gaps in the kitty litter. We still see bubbles streaming
to the top every once in a while presumably from the air that is still stuck
in the kitty litter. Can this be contributing to the root rot?

Any suggestions would be greatly appreciated as I would really like to be
successful at my new endeavor!

I think I have remembered all of the important info, if not I will gladly
provide more!  

slangner at kleinisd_net