Oh, on the subject of trees, and coral reefs--I know the subject of creatures/plants taking up more than one space has been suggested before, but with genetics coming in, how about the possibility of macro-organisms? (Not the true definition, I know, but I can't think of a better one right now.)
This is where the landscape itself (examples include: a big coral reef, the honey mushroom, Poseidnia Oceanica, a creosote bush, or a massive Aspen tree root system) is dominated by not one single huge organism, but an entire structure of them, that usually shares an identical DNA (with coral reefs being one possible exception.).
This wouldn't be a single organizm that just covered severa spaces/z-levels, this would be a single (sortof) organism that was the size of a chasm, or an underground river, or even larger, and had the same level of impact on the environment as other major geological features (as in, whole civilizations of animalmen could live in it, for instance.).
Such a thing would be practically impossible to completely destroy (except possibly with heavy uses of magma, but even that might not be a guarantee of total oblivion), and it would keep on growing, and living, for thousands and thousands of years, having an enormous impact on the surrounding environment, and possibly providing many different benefits and dangers (and different resources, from the same creature).
It could function as a cross between standard geological bands (marble, granite, etc), and plantlife, so that in the place of gems, you might have fruit, or jewellery-quality corals, as well as extracts, wood/mineable coral, food products, etc.
The giant lifeform could also provide shelter for hundreds/thousands of other creatures, ofcourse, and that would also add to both the benefits, and the dangers present.