First of all we must consider what the substrate is at 30 meters and deeper, either clay, anaerobic, impermeable or permeable substrates, everywhere that you find liquid water between 0-100 degrees you find life (Geogemma barossii reproduces at 120'C 250'F), even if the peak of everest is mostly under zero and has 270kph winds, algae grows there.
Plant life requires light, so you will only find roots underground, the deepest roots are an african fig that has a record of 120m 400ft. Most plants have roots that can go as deep as the tree is high in permeable ground while clay soil is very low on oxygen and voids for anything to infiltrate. Underground mining will rarely affect tree roots, or any other notable biotope, unless it encounters a rare cave system with fish and so on.
In very deep caves 200 meters deep there can be all kinds of insects and fish, although that doesnt qualify as ground.Krubera cave georgia has insects at 1.5 kilometers depth.
The solution of the question is that of matabolism, anaerobic versus aerobic, and it's effects on biotope richness. Funghi breathe and bacteria can be anaerobic, so they are the deepest, you can find some in oil wells and 1.6km under the sea floor.
The major concerns for drilling and damaging deep biotopes are from mining isolated aquifers with endemic animals, for example the deep lakes of antarctica that have been set apart from the rest of the world for 10's and 100's of thousands of years.
The ecosystem richness of zones without light and oxygen and flowing water is generally too low to foster much attention from any environmentalists and conservation organisations, it's also not a rare biotope.