A species of fig (Ficus, family Moraceae) from the Transvaal of South Africa was determined to have roots reaching at least 122 meters - source, google fu
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I think the phrase down the rabbit hole is actually referring to Alice in Wonderland. But.
I would say the organism that tends to burrow the deepest into the Earth is humans. Average oil well depth appears to be around 5,964 feet (1818 meters), that's pretty deep. The deepest hole we ever drilled is supposedly the Kola Superdeep Borehole dug by the Soviets, it was 40,230 feet (12.2km) deep.
Perhaps not answer your looking for though.
Oh, that's a fair point on both counts, I should have specified non-human organisms. Still, we're apparently really good at digging deep holes, so that's fun!
This is still a fun question and I am learning!
I agree. When I hear the phrase, I automatically think of Alice and the White Rabbit.
I only know of earthworm that they have been found up to 7 meters deep. But the rabbit hole thing is definitely not about the depth but about Alice in wonderland and the strange things you might find down there.
That sounds like some pretty dedicated earthworms! Also, as noted in another comment about the Alice reference, that's a good point, albeit I guess one could say it's about more of a figurative depth than literal given the curious places they go!