Great thread! I had an idea for a kind of underground tree quite a while ago, might as well repost it here. The original idea was to give us true underground forests complete with "trees".
Sorry about the wall of text yet again, but there is too much detail for cliffs notes.
To start with, the system we use for wood is almost certainly going to change. It just doesn't make sense to get only one log from each tree, and to make only 1 or a handful of items for each log. So eventually the yield of wood we get from trees and tower caps will be changed to reflect their size. Tower caps are mushrooms, so when you cut down the mushroom the only part you could probably use as wood is the stalk. The stalk is very thick but not very long compared to surface trees. This means you wouldn't be able to use them to make something like a trebuchet arm which must be one piece.
So what I thought of was a mushroom that takes the shape of a tree but it works far different. The more I thought about it the more complicated it got and it became more than just a source of wood. For simplicity I'll just refer to it as a "pillar mushroom". At the start of their life the mushroom looks much like other mushrooms with a cap and a stem, one thing that sets them apart is that the stem is long and thin and always grows perfectly upright. The mushroom will continue to grow taller and thicker until its cap reaches the ceiling.
At this point the mushroom enters the second stage of its lifecycle. The cap splits and releases pods of seed. Technically these are spores but they are of such size that it makes more sense to call them seeds. Anyway, the seeds are held in place by a mesh of plant material which is sort of like orange pith. (the white stuff that holds the insides together) Not all of the seed pods are mature and only mature pods separate from the pith. So when the the cap first splits some of the immature pods hang down from the top on strands of pith. It ends up looking a lot like a coconut tree.
Most of the pods fall to the ground and burst. These seeds grow into a symbiotic form of fungi that hangs around with the pillar mushrooms. The takes the form of these large barbed nets of plant material. They spread around in a massive carpet around the base of the pillar. While this happens the pillar grows until it touches the ceiling and starts to grow "branches" and "roots". Think of a double ended tree growing roots into the ceiling and ground. The branches drill up through the rock and fragment it. The roots below spread out and widen the base of the pillar to anchor it. The rock that drops to the ground is slowly constricted and pulverized into sand by the net shaped fungi. After many years what you end up with is a massive underground tree boring its way into the ceiling, creating a pile of gravel around its roots and a large dome shaped cavern that grows ever higher.
Sometime around this point the tree enters its third stage. Those immature seeds pods mentioned before have changed into much larger pods that contain smaller spores. Eventually these pods will burst and spread massive clouds of spores over the surrounding area. Since there are few immature pods per pillar to begin with and few of those pods have survived the rock shower over the years, pillar mushrooms spread very slowly and forests rarely reach large numbers. At this point the seeds can be harvested and planted in an organized manner by dwarf farmers thereby increasing the yield.
When the third stage begins, the stalk of the mushroom which has previously only grown thicker will begin to grow taller again. This pushes the branches ever higher and excavates ever more rock. Eventually a single mushroom will bore a mini chasm into the rock above it. In the rare cases where multiple pillars grow close together, the tallest and oldest of the pillars will slow their growth to allow the younger trees to catch up.
Much much later, and only if a forest of mushrooms has sprung up will the fourth stage begin. All of the mature pillar mushrooms in the forest will begin to slow their growth. While new mushrooms will spring up all the time, none of them will ever exceed a certain size. At this point there will usually be a hundred or so mature and immature mushrooms of various sizes, especially around the edges of the growing cavern. The cavern itself is going to quite big at this point, supported by ten or so of the massive mature pillars. These pillars enter into a final race with each other. Each one begins to slowly petrify from the inside out. While this happens these pillars continues to grow until they fully turn to stone.
The pillar that grows the tallest invariably digs a dome into the ceiling of the cavern that is higher than any other point. This one pillar will eventually be surrounded by a crown of stalactites and stalagmites that form around the edges of the dome.
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So imagine, if you can, a giant underground cavern bigger than most sports stadiums. A cavern of this size is a very rare find, and within it is a forest of pillar mushrooms of all sizes. About 10 or so titanic pillars of petrified wood hold up the ceiling high above. Giant cave spiders spin colossal webs between them. To one side a pillar has broken through into an underground river and a waterfall splashes down from the ceiling in a ring shape. The base of that pillar rises from a lake which empties into multiple rivers that disappear through tunnels in all directions.
At this point we could introduce all of the things you guys have been talking about. Imagine an underground civ making its home in one of these forests. Or a rock titan eating the petrified trees. Sound like fun?