Soil is a living, breathing ecosystem. Just as you and I breathe, soil too respires, and we measure that respiration rate as an indicator of microbial activity in soil. While there are large, non-microscopic organisms living in soil such as worms, insects and small mammals, none of them exist by the billions in just a handful of soil except the microbes.
There are many scientific classifications for microbes in soil, but from the farmer’s perspective only two categories are relevant. Good microbes (majority) and bad microbes (small minority). Good microbes enhance plant growth, and bad microbes cause disease in plants. Of course, things are never quite so clear-cut in nature. Some things can be good under some circumstances and bad under other circumstances. So keep in mind this is a simplification of what are, in reality, very complex interactions.
Our management practices should be refined to support the good (most of the time) microbes and suppress the ones known to cause diseases in crop plants. Diseases are not always caused directly by organisms. Sometimes the balance of the system gets thrown off and something ordinarily not a problem finds a new niche and can become problematic.
Weak plants may also be susceptible to organisms in the environment that normally would not have much impact on them. For instance, a nutrient deficiency might weaken a plant and lead to susceptibility. The good news is, of the thousands of microorganisms identified in soil thus far, only a handful of those really fall into the bad category. The good far outweigh the bad, and with a little thoughtful management, you can keep it that way.
In the case of good microbes, we can take this a step further and narrow our focus to the most crucial organisms within this group, which are those that provide the macro and micronutrients plants require for growth. The most limiting of these nutrients is typically phosphorus.
Nitrogen can play a close second in the nutrient race, but in most soils phosphorus is the most limiting nutrient, often occurring in quantities a thousand times lower than other minerals. One of the reasons for this is the high reactivity of phosphorus. It tends to bind to soil particles and complex with metals in the soil. This makes it unavailable to plants even if it is present in the soil.