> At first, normal wear-and-tear on the surface of a garnet creates divots. Microorganisms, probably fungi, can colonize these hollows. Then, if the stone is the best nearby source for certain nutrients, such as iron, perhaps they use an as-yet mysterious chemical reaction to burrow deeper, harvesting sustenance as they go.

Tunnels like those reported in the article also appear in sand and small rocks in biologically active regions (eg, soil). Some of the theories are the same: The holes are consistent with fungal hyphae ('roots').

I don't think anyone has found a smoking gun yet, and I'm not sure how you can explain finding the same patterns in deep geological formations. But I think they may be trying to answer the same question.