Permaculture is not just limited to crops either. I do recall seeing something about a farmer spending thirty years to research away to permaculture cattle. He used a blend of grasses to create a solid mat of roots, this means that the cattle could stay out all year with no risk of them curning the ground to slurry in winter. He also planted hedges to use as fodder. In all seriousness the only fuel he used was the quad bikes he used to heard them.

From what I understand of 3D the idea is to create a mix of crops rather than rows and rows of just one plant. This creates a vertical column of a biosphere with harvests at multiple levels. I would not call it "natural" but high yield, low energy and environmentally sustainable? Thats the Idea.