Select against those organisms that might cause or encourage disease. Fine-tuning is needed. We don't even know which ones are most beneficial for different plant species, much less be able to pick them out of the crowd. The classic way of assessing bacterial species is to spread a soil dilution on a specific kind of medium. Then the plate is incubated at a certain temperature, which further limits the set of species that can grow.
Incubation occurs at a certain humidity, which further limits the species that can grow.
We realistically know nothing about soil bacterial species based on plate counts. There are a number of programs around the world trying to understand which bacterial species are most beneficial for which plants. None of those labs get the funding they deserve. Molecular approaches are the only way to understand the full set of bacterial, and fungal for that matter, species in soil. Forest soils have even more species, maybe upwards of 40,000 species per teaspoon.