I hope I can give you a little guidance here, being that I have a heavily planted tank, and have had reefs in the past.
A quick rundown on the major chemisty differences between a
SW reef and a planted
FW tank, aside from the salinity:
In the
FW planted tank,
NO3 becomes a natural fertilizer. It is the waste byproduct of the completed breakdown of ammonia in the nitrogen cycle.
NH3 ----> consumed by nitrogenizing bacteria A which produces ------>
NO2 as waste, consumbed by nitrogenizing bacteria B which producee ------>
NO3. end waste product.
The
NO3 is then consumed by plants, as a fertilizer.
The level of
NO3 in a
FW tank is cosiderably higher as an acceptable level in a
SW tank, as the
SW species have a much, much lower tolerance for
NO3 poisoning, and there are no plants to fertilize (except algaes, in which case macro algaes can help keep the level of
NO3 down in
SW tanks).
The nitrogenizing bacterias in
FW AND
SW will live on any surface they can attach to. Because
FW fish are often accompanied by plants that can utilize the
NO3, and are more tolerant to
NO3 levels, often, water changes can keep them acceptable, and further breakdown of
NO3 is not needed.
However, the
SW side is a bit different.
In
SW keeping, live rock provides ENORMOUS anaerobic surface area for a possible third bacteria to live, nitrogenizing bacteria C for the purpose of this discussion. Bacteria C is an anaerobic organism, requiring a lack of oxygen to thrive. It will take the
NO3 waste product and further break it down to N- gas, which is then released in the water column.
Much of that is, however, theory. Most
SW keepers avoid high levels of nitrogen byproducts and ammonia via protien skimming, which removes large and minute waste particles from the water column via frationization before they even break down into ammonia. Also, due to the increased presence of proteins in
SW tanks, live rock surfaces provide large amounts of surface to break down these nitrogens.
Bioballs, in the
SW tank, do not provide the same porous surface in
SW as they do in
FW. Likewise, the bacters that work the nitro cycle in
SW are not the same as
FW. They often work better directly in the water column. Bioballs tend to work almost "too well", creating a
NO3 "nitrate factory" which spills into the water column, and increases the levels in the tank. A
FW tank and it's inhabitants can handle levels of
NO3 upwards of 50ppm, while
SW inhabitants, especially inverts/corals cannot tolerate more than 10, preferrably less than 5
ppm.
Therefore, many
SW keepers introduce
LR rubble to replace the bioballs to avoid the "nitrate factory". Also,
SW husbandry habits tend to differ from
FW husbandry in that 1.) corals and inverts are in abundance and are animal lifeforms, not plants, with increased value $wise, and higher sensitivity to poisoning (see articles about the difference between animal cellular structure and plant cellular structure), and 2.) often,
SW keepers do many more smaller water changes than
FW keepers. Usually in the neighborhood of 10-20% 2-3x weekly, to further assist in reducing
NO3. and 3.) plants can and do utilizes
NO3 as fertilizer and food, and having a consistantly increased level of
NO3 is actually beneficial to their wellbeing, while in
SW tanks, there is nothing to utilize the
NO3 end waste product.
hope this helps explain some of what you are asking.
Just because I am working at Petco does not mean I am a sell out, they are still an evil empire, that I am trying to make better. 
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