Jan 7, 2026
Soil Health: Decomposition of Organic Materials and Nutrient Mineralization
Organic materials include crop residues, manures, and other organic amendments that are commonly added to the soil in a crop production system. It is the breakdown and microbial digestion process of organic materials that can contribute to stable soil organic matter (SOM). Thus, organic materials are not the same as SOM.
The decomposition of organic materials is a process that is carried out by naturally occurring soil microbes. Organic material decomposition is an important aspect of nutrient cycling, soil fertility, and soil health.
The naturally occurring soil microorganisms, that include bacteria, fungi, actinomycetes, protozoa, and soil fauna (organisms such as nematodes, mites, springtails, and earthworms) drive the biochemical transformations converting complex organic compounds in organic materials into smaller, simpler, plant-available forms (Paul 2015; Sylvia et al. 2005).
In the initial steps of decomposition, these organisms exude extracellular enzymes that break down the large complex polymers (i.e., cellulose, hemicellulose, lignin, proteins, and lipids) in organic materials. The rate of decomposition is strongly influenced by substrate chemistry decay (Jenkinson 1981; Brady and Weil 2017).
The residues that decompose most rapidly have low carbon-to-nitrogen (C:N) ratios (higher N concentration), such as legumes or many manures. The low C:N ratio materials decompose most rapidly because microorganisms have sufficient nitrogen (N) to support biomass growth and enzyme production (Palm et al. 2001; Magdoff and van Es 2021). The microbes work hard to break down the complex organic materials, and they provide a great service in the process, but what they are seeking is N.
Organic materials with high C:N rations, such as cereal grain straw and most harvested crop residues are usually slower to decompose due to slower microbial activity. This is the result of microbes scavenging for mineral N, ammonium NH4+ or nitrate NO3− to meet their metabolic demands (McGill and Cole 1981; Janzen and Kucey 1988).
When sufficient mineral N is lacking in the soil, the microbes will consume most of the available N and incorporate into their own bodies. This can cause short-term nitrogen immobilization (McGill and Cole 1981; Janzen and Kucey 1988). We often see that in the field with early crop growth immediately following a previous crop.
Mineralization refers to the conversion of organically bound nutrients into inorganic, plant-available forms. Nitrogen mineralization involves microbial depolymerization of organic N compounds (e.g., the breakdown into amino acids and proteins) followed by the release of ammonium (NH₄⁺) (Figure 1; Stevenson and Cole 1999).

Figure 1. The nitrogen cycle. Source: Stevenson, 1982.
Mineralization becomes dominant as the decomposition process continues. The NH₄⁺-N (N in the form of ammonium) that is produced in the first steps of mineralization is rapidly converted to NO₃⁻-N by specialized autotrophic bacteria (Nitrosomonas and Nitrobacter). These bacterial organisms are abundant in healthy soil and we commonly see clear evidence of that in our agricultural soils. This is critically important because NO₃⁻-N is the primary form of N taken up by most crop plants. (Chapman et al. 2013).
The balance between immobilization and mineralization is central to predicting nutrient availability during crop growth. Environmental factors such as temperature, moisture, aeration, and pH regulate the rate of all of these transformations (Brady and Weil 2017; Paul 2015).
Other essential plant nutrients follow similar mineralization pathways. For example, organic phosphorus (P) must be enzymatically cleaved by phosphatases to release inorganic orthophosphate (McGill and Cole 1981). Organic sulfur (S) compounds are transformed into sulfate (SO₄²⁻), commonly much slower than N due to their chemical composition and the activity of specific microbes (Stevenson and Cole 1999).
Micronutrients such as zinc (Zn), copper (Cu), and iron (Fe), are released and mineralized during ligand degradation or humus (a diverse group of large, complex organic compounds) transformation, ultimately mineralizing into plant-available ions that are soluble or exchangeable in the soil (Brady and Weil 2017).
Nutrient mineralization plays a critical role in maintaining soil health and productivity. The breakdown and conversion of organic materials is important in providing essential nutrients to crops and it also contributes to SOM formation, improved soil particle aggregation and better soil structure, improved internal water movement and drainage, and overall carbon sequestration (Follett et al. 2001).
Effective management of residues incorporated into the soil is an important feature in managing soil health. The decomposition of organic materials, as well as mineralization and immobilization processes, are indicative of healthy soil (Kaspar et al. 1990; White 1994).
References:
Brady, N.C., and R.R. Weil. 2017. The nature and properties of soils. 15th ed. Pearson, Upper Saddle River, NJ.
Chapman, S.J., J.A. Campbell, Q. Fraser, G.C. Puri, and R. Lilly. 2013. Nitrogen mineralization and nitrification in Scottish soils: Effects of organic matter, texture, and land use. Soil Use Manag. 29: 612–621.
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