Biology of soil determines the fate of applied fertilizer

There is a growing awareness in agriculture of the use of biologicals as part of crop nutrient management systems. Biological products can serve as a bridge to build soil health, or they can simply serve as another recurring input cost like fertilizer. When considering how to approach crop nutrient management we need to understand that the soil microbiome (a community of microorganisms that live in the soil) is in control of how crop nutrients are processed in the soil. It doesn’t matter what the source of crop nutrients are: synthetic fertilizer, natural fertilizer, manure, etc., they are each processed or impacted by biological processes.

Let’s use urea as an example. When urea fertilizer is applied to the soil it is hydrolyzed by urease enzymes that are produced by plants and soil microorganisms such as: Proteus, Bacillus, Pseudomonas, Clostridium. Urease converts urea to ammonium, which plants can utilize immediately, but often the ammonium is further transformed into nitrite, then nitrate, by Nitrosomonas, Nitrosospira, and Nitrobacter bacteria before being taken up by plants. The fate of the fertilizer applied to the soil is determined by the biology of the soil. This process has been known and accepted by agronomists for over 100 years!

It is also known that, at best, only 65 percent of the nitrogen fertilizer applied to the soil is actually taken up by plants. The other 35 percent becomes part of soil organic matter, moves in runoff water, leaches down to groundwater, or volatizes into the air. A healthy, functioning soil is not at all “leaky” when it comes to supplying nitrogen to plants. The soil microbiome keeps the nitrogen cycle “tight” and makes nitrogen available to plants only when they need it.

Not only does the biology of the soil process the fertilizer we apply to the soil, but it also processes nitrogen from plant residues and the air itself to make nitrogen available to plants. An example of this is the North Dakota State University Nitrogen Calculator which includes an entry for “tillage type” where the selection of “long-term no-till” (at least five years of continuous no-till) will generate a 50 pound per acre per year nitrogen credit. At 45 to 60 cents per pound for actual nitrogen, that 50 pounds is worth $22.50 to $30 per acre each year for free!

By not tilling the soil and disrupting the world of the soil microbiome, those organisms are able to do their job of capturing nitrogen from the air while also cycling nitrogen from previous crop residues and make it available to the next crop. Applying microbes to the soil each year can certainly contribute to the overall nitrogen that will be available to the plants, but it is also another input cost each year, just like synthetic fertilizer. Tillage of the soil destroys the soil aggregates that house the soil microbiome and in doing so, we take away the capacity of those organisms to supply nitrogen to our crops efficiently and inexpensively.

There are many nitrogen-fixing (convert nitrogen from the air into ammonium for plants) organisms that live in the soil and in association with plant roots. The most widely known organisms are Rhizobia spp., that associate with legumes, but there are many other species that live in the soil that will associate with any plant. Azotobacter, Bacillus, Clostridium, and Klebsiella bacteria are examples of organisms that live independently in the soil that fix nitrogen from the air. Azospirillum bacteria live within the rhizosphere (zone of influence of living plant roots) of many species of grass and can also fix nitrogen from the air. It is no wonder that many of these organisms have been isolated from the soil, cultured, and made available as “biologicals” that can be applied to assist with supplying nitrogen to crops.

The irony of biologicals is that any of them that you can buy and apply to your soil most likely are already present, but in numbers that are not great enough to have a significant impact on supplying nutrients to your crops. This is because the majority of cropland soils in the U.S. include too much tillage and too little plant diversity to support a viable soil microbiome. It is true of soil microbiomes: If you build it, they will come. A healthy soil microbial community can supply a substantial amount of free nitrogen in cropping systems that involve little or no tillage and a diversity of plants.

Biologicals can certainly be an additional tool producers can use to increase the supply of nitrogen (or other plant nutrients) to their crops, but they also must count it as another input cost. By building soil health, producers can truly wean their soils off of a dependency on fertilizer, reduce input costs and become more profitable.

References

Franche, C., Lindström, K. & Elmerich, C. Nitrogen-fixing bacteria associated with leguminous and non-leguminous plants. Plant Soil 321, 35–59 (2009).

Wagner, S. C.. (2011) Biological Nitrogen Fixation. Nature Education Knowledge 3(10):15

Winogradsky, S. (1890). Sur la nitrification. Annales de l’Institut Pasteur, 4, 123–141.

Yi, B., Huang, W., Liebman, M. et al. Diversified cropping systems with limited carbon accrual but increased nitrogen supply. Nat Sustain 8, 152–161 (2025).

Jon Stika is a retired Natural Resources Conservation Service soil health instructor and current part-time professional at the North Dakota State University Dickinson Research Extension Center. He is also the author of “A Soil Owner’s Manual: How to Restore and Maintain Soil Health.”