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Even in the real world we're starting to discover a staggering amount of subterranean organisms which by some estimates may, pound for pound, actually outweigh our above-ground biosphere. It's not so hard to imagine that, with the preponderance of vast subterranean caverns and tunnels in most fantasy worlds, that much more elaborate and sustainable ecosystems may develop. Giant mushroom forests, subterranean rivers teaming with blind fish and fungus-scrounging herbivores aren't really all that outlandish. All of it together could form a tightly efficient and sustainable food chain.
As for dwarves, they serves as a bridge between the realms below and those above. Dwarves are often depicted as mining and smithing the deep earth's riches and then trading them to surface dwellers. Although dwarven merchants love money, what they're more likely to trade for is what their kinsman are in short supply of underground; grains (especially barley & hops!), vegetables, meat, leather, wood, etc. So their diet is likely a mix of what they can farm & fish below and what their traders bring down from above.