There are billions of soil microorganisms in a mere handful of a healthy soil. That single handful might well contain thousands of different species of bacteria (most of whom have yet to be classified), hundreds of different species of fungi and protozoa, dozens of different species of nematodes plus an assortment of various mites and other microarthropods. Almost all of these countless soil organisms are not only beneficial, but essential to the life giving properties of soil.
The best way to promote these organisms and keep them thriving is to maintain crop residue on the soil surface and do as little tillage (disturbance) as possible. The work of these soil microorganisms is exceedingly complex.
Organic matter decomposition serves two functions for the microorganisms, providing energy for growth and suppling carbon for the formation of new cells. Even soils that have had the advantages of crop rotation, cover crops, ample feedings of manures or composts do not have immunity from mineral deficiencies and particularly deficiencies relative to trace elements. If the materials that are used to feed the soil are deficient in some mineral, the deficience will show up in the soil. These problems will show up in soil testing.