I have been recently experimenting with 3D modeling capabilities in Apophysis 2.08 (3D Hack). As far as I can gather, it is accomplished by deformation of 3D primitives through transform variations such as conic, waves3D, and circlize. In this case of the bioluminescent mushrooms, the stem was generated by deformation of a cylinder using waves3D, and the cap was generated by deformation of a hemisphere using conic and circilize. Xaos settings can be used to further manipulate space (in this case, 3D primitives) by fine-tuning interactions between individual transforms (i.e. adjusting weight modifiers to/from transforms).
This experiment is different from previous work in the respect that the recursive patterns that typically dominate fractal art are absent. Julia sets– a favorite among fractal artists– are still used to generate the base material (soil), lighting effects, and texture of the mushroom cap.