Today we scrape however many meters deep of soil and haul off to a landfill. I assume you'd scrape it up, run it through something to pull out everything bigger than a pebble. Wash the pebbles, the rinse water goes with the soil through the cleaning process.

Certainly what comes out of the machine will not be living.

I guess it'd be a good time to add some bacteria and life back into the soil that in a controlled manner.