The nitrogen cycle transforms nitrogen into multiple chemical forms as it circulates through the atmosphere, soil, and living organisms. Nitrogen is a fundamental building block for life, forming the structure of amino acids and the nucleotide bases found in DNA and RNA. Although air is nearly 78% nitrogen gas, this form is unusable by most organisms, requiring complex conversions to create bioavailable compounds. Ammonia is often the first inorganic compound formed, serving as the essential entry point for nitrogen into biological systems.
Ammonia: The Initial Nitrogen Compound and Its Origins
Ammonia exists as un-ionized ammonia (\(\text{NH}_3\)) and the ionized form, ammonium (\(\text{NH}_4^+\)). These two forms are in constant chemical equilibrium, with the surrounding environment’s pH determining which one is dominant. In most near-neutral or acidic soil and water, hydrogen ions attach to the ammonia molecule, making ammonium (\(\text{NH}_4^+\)) the more prevalent and stable form.
The main natural source of ammonia and ammonium is ammonification. This occurs when decomposers, primarily specialized bacteria and fungi, break down dead organic matter, animal carcasses, and nitrogenous waste. The nitrogen locked within these organic compounds, such as proteins and nucleic acids, is released back into the environment as ammonium ions.
This release of ammonium makes nitrogen available for use by other organisms, marking its re-entry into the cycle. While nitrogen fixation also introduces ammonium by converting atmospheric nitrogen gas, ammonification represents the constant recycling of nitrogen from biological decay. The ammonium product is highly water-soluble, allowing it to dissolve easily into soil water or aquatic systems where it is accessible to plants and microbes.
The Conversion Pathway: Nitrification of Ammonia
Once ammonium is present in the soil or water, it is typically processed further in a two-step biological pathway called nitrification. This process is exclusively aerobic, requiring oxygen, and is carried out by specialized chemoautotrophic bacteria. These microbes obtain energy by oxidizing inorganic nitrogen compounds rather than consuming organic carbon.
The first step, nitritation, involves the oxidation of ammonium (\(\text{NH}_4^+\)) into nitrite (\(\text{NO}_2^-\)). Bacteria from the genus Nitrosomonas are responsible for this conversion. Nitrite is an intermediate compound that rarely accumulates in healthy, oxygenated ecosystems because it is rapidly acted upon by a different group of microorganisms.
The second step, nitratation, quickly converts the nitrite (\(\text{NO}_2^-\)) into nitrate (\(\text{NO}_3^-\)). This final conversion is performed by bacteria such as Nitrobacter and Nitrospira, completing nitrification. Nitrate is the most stable and easily absorbed form of nitrogen for the majority of plants. Because nitrate is negatively charged, it does not bind to soil particles, making it highly mobile. While this mobility aids plant uptake, it also means nitrate is easily washed out of the soil into groundwater through leaching.
Biological Uptake and Environmental Impact
The newly formed nitrate and the initial ammonium are the two primary forms of nitrogen that plants and microorganisms absorb, a process called assimilation. Although plants generally prefer nitrate due to its abundance in oxygenated soils, they can also directly take up ammonium ions. Once absorbed, the inorganic nitrogen is incorporated into organic molecules, such as amino acids and proteins, via a metabolic pathway that often involves the Glutamine Synthetase-Glutamate Synthase (GS-GOGAT) cycle.
While essential for life, ammonia can become a significant environmental concern, particularly in aquatic systems, due to its toxicity. The un-ionized form of ammonia (\(\text{NH}_3\)) is highly toxic to fish and other aquatic organisms because it easily passes across biological membranes, unlike the ionized ammonium form. The concentration of this toxic \(\text{NH}_3\) is strongly influenced by water chemistry.
Increases in water temperature and, more significantly, increases in pH cause the equilibrium to shift, resulting in a greater proportion of total nitrogen existing as hazardous un-ionized ammonia. For example, a rise in pH above 8.0 can lead to a sharp increase in ammonia toxicity, causing stress or death in aquatic life. Understanding this chemical balance is necessary for managing water quality in natural ecosystems and controlled environments like fish farms and aquariums.