yes the microorganisms in the soil are THE KEY! if you study the bioshpere project you will see that the soil bacteria were the critical component in achieving near self sufficiency (though they never actually were fully self sufficient)
in fact the modern day practice of smothering farm fields with industrial nitrogen exists only because the bacteria that fixed the nitrogen naturally has all been destroyed by pesticides. thus the fields are dependant on outside sources of nitrogen becuase the little guys whose job it is to fix the nitrogen directly from the air have all been poisoned to death. healthy soil is teeming with life of all kinds, pesticides create an antiseptic soil that is good for growing antisecptic crops for antiseptic people.
real true living crops come from fields full of bacteria and free of poisons.