How Do Soil Microbes Cycle Nitrogen? Each Step Explained
As an Amazon Associate we earn from qualifying purchases.
How do soil microbes cycle nitrogen? They change nitrogen from one chemical form to another, and each form determines whether a plant can use it. The University of Delaware Cooperative Extension states that “soil microorganisms, including bacteria and fungi, change the complex, unavailable forms of N into forms that are plant-available.” The South Dakota State University Extension page describes the wider cycle as a series of steps carried out by organisms. This article follows those steps in order, from organic residue to ammonium, nitrate and gas, and it notes where the two sources differ in detail.
Quick answer
- Microbes break down organic nitrogen in residues and amendments into ammonium, a process called mineralization or ammonification.
- Other microbes convert ammonium into nitrate, a step called nitrification that needs oxygen.
- Under waterlogged conditions, microbes can turn nitrate into nitrogen gas, which is lost to the air.
- Some microbes fix nitrogen gas from the air into forms plants can use, including bacteria that live in legume roots.
Why plants cannot use most nitrogen directly
Much of the nitrogen in soil is locked in organic material. The Delaware page explains that in crop residues, “the organic N in these materials is not plant-available and must be converted to ammonium by soil microbes.” This is the starting point for the cycle: material that looks like nitrogen to a gardener is not yet something a root can absorb.
The South Dakota page explains the same idea through the process name. It states that “During ammonification, organic forms of nitrogen are converted into ammonia (NH 4 + ).” It also adds that “Microbes are essential for the ammonification process to occur in the soil.” The two sentences agree that the first conversion is performed by microbes rather than by plants.
Step one: mineralization into ammonium
The Delaware page uses a different name for the same first step. It states that “This process is called mineralization, and the end product is ammonium.” The South Dakota page describes the chemistry underneath: “The nitrogen that is contained in the organic carbon is broken down and can be converted into inorganic carbon and nitrogen (mineralization).” Both sources treat mineralization as the breakdown of organic material into an inorganic nitrogen form.
The South Dakota page then lists what happens to ammonium next. It states that “Once ammonification occurs, the NH 4 + can be taken up by plants, used by bacteria (immobilization), or transformed into nitrate.” This sentence shows that ammonium has three possible fates, and only one of them makes nitrogen immediately available to a plant.
The page also describes a related point about carbon. It says that “Bacteria have an ideal carbon: nitrogen ratio.” The exact ratio is not given in the quoted text, so this article does not state a number. What the page does establish is that the balance of carbon and nitrogen in the soil affects what microbes do with nitrogen.
Step two: nitrification into nitrate
Ammonium is often converted to nitrate, and microbes perform that step. The Delaware page states that “Ammonium can also be converted to nitrate by soil microbes through a process called nitrification.” The South Dakota page defines the step as “the process which converts ammonia or ammonium (NH 4 + ) into nitrate (NO 3 – ).”
The South Dakota page names the organisms involved. It states that “This process most commonly involves Nitrosomonas bacteria species, which convert NH 3 or NH 4 to nitrite (NO 2 – ), and Nitrobacter converts NO 2 – into NO 3 -.” The process therefore has two bacterial stages, with nitrite as an intermediate.
Speed depends on conditions. The Delaware page states that “Nitrification typically occurs rapidly (within days) under natural conditions.” It adds that “Use of a urease or nitrification inhibitor can slow nitrification from days to weeks, but ultimately, nitrification will occur.” The page presents the inhibitor option as a way to slow the step, not to stop it.
Oxygen is required. The South Dakota page states that “The nitrification process only occurs in environments where oxygen is present.” This is the condition that links nitrification to soil drainage and structure, which is why the step tends to slow in soils without air.
Step three: denitrification and loss to air
When oxygen runs out, the cycle takes a different path. The South Dakota page states that “In anaerobic soils or water, the denitrification process can occur,” and it explains the microbial role: “Microbes use nitrogen as an electron source and convert nitrate to nitrogen gas.” The Delaware page describes the same loss in practical terms: “if a soil remains waterlogged for a long period of time and loses its oxygen, nitrate can be converted to a gas by microbes and lost to the atmosphere through a process called denitrification.”
This step is a loss, not a recycling step. Nitrogen that leaves as gas is no longer in the soil for plant roots to take up. For a gardener, the practical sign is waterlogging, which the Delaware page links directly to this pathway.
Fixing nitrogen from the air
Not all nitrogen enters the cycle through decomposition. The Delaware page explains that “While most plants and animals cannot use N2, there are a few specialized microbes that can convert this gas into a plant available form of N.” The South Dakota page defines the process: “The process of converting nitrogen gas in the atmosphere to organic forms of nitrogen in plant and microbes is nitrogen fixation.”
The fixing microbes take different forms. The Delaware page states that “These N fixing microbes can live freely in the soil or can colonize the roots of legumes, such as soybean, alfalfa, clovers, lima beans, and peas.” The South Dakota page adds that “There also are bacteria that can create beneficial relationships with plant roots that benefit both the microorganism and the living plants.” It also notes that the free-living fixers “can take nitrogen from the air and directly convert it to organic nitrogen, but the amount of nitrogen converted is usually small, 0 to 25 pounds per acre, per growing season.”
Why the sources give different detail
The Delaware page is written for agricultural production and frames the cycle around plant availability. The South Dakota page uses more chemical names and labels each step with its process name, including ammonification, nitrification and denitrification. Both pages describe the same sequence, so the difference is one of depth rather than disagreement.
How this connects to compost
Compost is an organic amendment, and the Delaware page says that the organic nitrogen in such materials “must be converted to ammonium by soil microbes” before plants can use it. For practical guidance on the material itself, see how to make garden compost quickly and how to know when compost is done.
How we chose these sources
The two sources were selected because they are both university extension pages, and they approach the cycle from different angles. The Delaware page is titled Nitrogen Cycling in Agriculture. The South Dakota page is titled The Nitrogen Biochemical Cycle in Soil. Both returned HTTP 200 when requested directly with curl on 2026-10-27, and every quotation in this article was copied from the fetched text.
What we could not verify
The sources describe the cycle in general terms and do not measure how fast each step runs in a particular garden soil. The South Dakota page gives a per-acre range for free-living fixers, but that figure is for field conditions, not for a garden bed.
What the sources do not say
- They do not give the carbon to nitrogen ratio that microbes need.
- They do not give the time any single step takes in a home garden.
- They do not explain how to measure soil nitrogen at home.
Frequently asked questions
What is mineralization in the nitrogen cycle?
The Delaware page states that “This process is called mineralization, and the end product is ammonium.” The South Dakota page describes it as the breakdown of organic nitrogen into an inorganic form.
What is nitrification?
The South Dakota page defines it as “the process which converts ammonia or ammonium (NH 4 + ) into nitrate (NO 3 – ).” The Delaware page adds that nitrification “typically occurs rapidly (within days) under natural conditions.”
What happens to nitrogen in waterlogged soil?
The Delaware page states that when “a soil remains waterlogged for a long period of time and loses its oxygen, nitrate can be converted to a gas by microbes and lost to the atmosphere.” The page describes this as denitrification, and it does not say how much nitrogen is lost in any given storm.
Can plants use nitrogen gas from the air?
Not directly. The Delaware page states that “most plants and animals cannot use N2,” but that specialized microbes can convert it into a plant-available form.
Do all soil bacteria fix nitrogen?
No. The Delaware page describes only “a few specialized microbes” that can convert nitrogen gas into a plant-available form, and the other steps in the cycle are carried out by a different set of microbes.
