Frequently we see statements in the lay literature about chemical fertilizers killing soil microbes or, worse yet, statements indicating these management inputs "sterilize" the soil. Statements such as these should be viewed with much skepticism! Remember that as we learned in FAQ #1, the soil can contain tons of microbes. Short of incineration its hard to imagine a stress in a soil that would lead to complete extermination of the microbial populations. It is true that some inputs, e.g., anhydrous ammonia, cause reductions in microbial numbers in the immediate vicinity of the application. After all, ammonia is a toxic gas. However, it quickly equilibrates with the soil solution in the form of ammonium ions and the toxicity subsides. Certain pesticides have been shown to cause similar transient reductions in selected microbial population. But remember, in some cases the microbes simply view these chemicals as food and degrade them fairly quickly.
Organic fertilizers circumvent the criticisms leveled at "synthetic" fertilizers but it should not be forgotten that plants take up nitrogen in the form of ammonium (NH4+) or nitrate (NO3-) ions regardless of whether it was mineralized from an organic source or applied as in inorganic fertilizer like ammonium nitrate. An advantage of using organics, where practical, is that nutrients are liberated slowly as the microbes mineralize the organic materials. Thus there is low risk for fertilizer burn on plants and less risk for environmental problems due to runoff and leaching. Another potentially negative effect of long-term use of ammonia-based fertilizers is soil acidification due to ammonia oxidation by the nitrifying bacteria. Soil pH can drop below 5.0 after prolonged use of ammonia-based fertilizers and this can cause marked reductions in populations of bacteria and actinomycetes and simultaneous increases in the relative abundance of fungi. Such changes might favor the development of certain fungal plant pathogens. On the other hand, the potato scab disease is reduced by the low pH because the actinomycete which causes it is eliminated. These changes are easily reversed with applications of lime to the soil. Thus we see qualitative changes in the soil populations due to some management inputs but this is a long way from "sterilizing" or "killing" the soil.
