Biogeochemical cycle by which nitrogen is converted into various chemical forms
The nitrogen cycle is the biogeochemical cycle by which nitrogen is converted into multiple chemical forms as it circulates among atmospheric, terrestrial, and marine ecosystems. The conversion of nitrogen can be carried out through both biological and physical processes. Important processes in the nitrogen cycle include fixation, ammonification, nitrification, and denitrification. The majority of Earth's atmosphere (78%) is atmospheric nitrogen, making it the largest source of nitrogen. However, atmospheric nitrogen has limited availability for biological use, leading to a scarcity of usable nitrogen in many types of ecosystems.
The nitrogen cycle is of particular interest to ecologists because nitrogen availability can affect the rate of key ecosystem processes, including primary production and decomposition. Human activities such as fossil fuel combustion, use of artificial nitrogen fertilizers, and release of nitrogen in wastewater have dramatically altered the global nitrogen cycle. Human modification of the global nitrogen cycle can negatively affect the natural environment system and also human health.
Processes.
Nitrogen is present in the environment in a wide variety of chemical forms including organic nitrogen, ammonium (), nitrite (), nitrate (), nitrous oxide (), nitric oxide (NO) or inorganic nitrogen gas (). Organic nitrogen may be in the form of a living organism, humus or in the intermediate products of organic matter decomposition. The processes in the nitrogen cycle is to transform nitrogen from one form to another. Many of those processes are carried out by microbes, either in their effort to harvest energy or to accumulate nitrogen in a form needed for their growth. For example, the nitrogenous wastes in animal urine are broken down by nitrifying bacteria in the soil to be used by plants. The diagram alongside shows how these processes fit together to form the nitrogen cycle.
Nitrogen fixation.
The conversion of nitrogen gas () into nitrates and nitrites through atmospheric, industrial and biological processes is called nitrogen fixation. Atmospheric nitrogen must be processed, or "fixed", into a usable form to be taken up by plants. Between 5 and 10 billion kg per year are fixed by lightning strikes, but most fixation is done by free-living or symbiotic bacteria known as diazotrophs. These bacteria have the nitrogenase enzyme that combines gaseous nitrogen with hydrogen to produce ammonia, which is converted by the bacteria into other organic compounds. Most biological nitrogen fixation occurs by the activity of molybdenum (Mo)-nitrogenase, found in a wide variety of bacteria and some Archaea. Mo-nitrogenase is a complex two-component enzyme that has multiple metal-containing prosthetic groups. An example of free-living bacteria is "Azotobacter". Symbiotic nitrogen-fixing bacteria such as "Rhizobium" usually live in the root nodules of legumes (such as peas, alfalfa, and locust trees). Here they form a mutualistic relationship with the plant, producing ammonia in exchange for carbohydrates. Because of this relationship, legumes will often increase the nitrogen content of nitrogen-poor soils. A few non-legumes can also form such symbioses. Today, about 30% of the total fixed nitrogen is produced industrially using the Haber-Bosch process, which uses high temperatures and pressures to convert nitrogen gas and a hydrogen source (natural gas or petroleum) into ammonia.
Assimilation.
Plants can absorb nitrate or ammonium from the soil by their root hairs. If nitrate is absorbed, it is first reduced to nitrite ions and then ammonium ions for incorporation into amino acids, nucleic acids, and chlorophyll. In plants that have a symbiotic relationship with rhizobia, some nitrogen is assimilated in the form of ammonium ions directly from the nodules. It is now known that there is a more complex cycling of amino acids between "Rhizobia" bacteroids and plants. The plant provides amino acids to the bacteroids so ammonia assimilation is not required and the bacteroids pass amino acids (with the newly fixed nitrogen) back to the plant, thus forming an interdependent relationship. While many animals, fungi, and other heterotrophic organisms obtain nitrogen by ingestion of amino acids, nucleotides, and other small organic molecules, other heterotrophs (including many bacteria) are able to utilize inorganic compounds, such as ammonium as sole N sources. Utilization of various N sources is carefully regulated in all organisms.
Ammonification.
When a plant or animal dies or an animal expels waste, the initial form of nitrogen is organic. Bacteria or fungi convert the organic nitrogen within the remains back into ammonium (), a process called ammonification or mineralization. Enzymes involved are:
Nitrification.
The conversion of ammonium to nitrate is performed primarily by soil-living bacteria and other nitrifying bacteria. In the primary stage of nitrification, the oxidation of ammonium () is performed by bacteria such as the "Nitrosomonas" species, which converts ammonia to nitrites (). Other bacterial species such as "Nitrobacter", are responsible for the oxidation of the nitrites () into nitrates (). It is important for the ammonia () to be converted to nitrates or nitrites because ammonia gas is toxic to plants.
Due to their very high solubility and because soils are highly unable to retain anions, nitrates can enter groundwater. Elevated nitrate in groundwater is a concern for drinking water use because nitrate can interfere with blood-oxygen levels in infants and cause methemoglobinemia or blue-baby syndrome. Where groundwater recharges stream flow, nitrate-enriched groundwater can contribute to eutrophication, a process that leads to high algal population and growth, especially blue-green algal populations. While not directly toxic to fish life, like ammonia, nitrate can have indirect effects on fish if it contributes to this eutrophication. Nitrogen has contributed to severe eutrophication problems in some water bodies. Since 2006, the application of nitrogen fertilizer has been increasingly controlled in Britain and the United States. This is occurring along the same lines as control of phosphorus fertilizer, restriction of which is normally considered essential to the recovery of eutrophied waterbodies.
Denitrification.
Denitrification is the reduction of nitrates back into nitrogen gas (N2), completing the nitrogen cycle. This process is performed by bacterial species such as "Pseudomonas" and "Paracoccus", under anaerobic conditions. They use the nitrate as an electron acceptor in the place of oxygen during respiration. These facultatively (meaning optionally) anaerobic bacteria can also live in aerobic conditions. Denitrification happens in anaerobic conditions e.g. waterlogged soils. The denitrifying bacteria use nitrates in the soil to carry out respiration and consequently produce nitrogen gas, which is inert and unavailable to plants. Denitrification occurs in free-living microorganisms as well as obligate symbionts of anaerobic ciliates.
Dissimilatory nitrate reduction to ammonium.
Dissimilatory nitrate reduction to ammonium (DNRA), or nitrate/nitrite ammonification, is an anaerobic respiration process. Microbes which undertake DNRA oxidise organic matter and use nitrate as an electron acceptor, reducing it to nitrite, then ammonium (). Both denitrifying and nitrate ammonification bacteria will be competing for nitrate in the environment, although DNRA acts to conserve bioavailable nitrogen as soluble ammonium rather than producing dinitrogen gas.
Anaerobic ammonia oxidation.
The ANaerobic AMMonia OXidation process is also known as the ANAMMOX process, an abbreviation coined by joining the first syllables of each of these three words. This biological process is a redox comproportionation reaction, in which ammonia (the reducing agent giving electrons) and nitrite (the oxidizing agent accepting electrons) transfer three electrons and are converted into one molecule of diatomic nitrogen (N2) gas and two water molecules. This process makes up a major proportion of nitrogen conversion in the oceans. The stoichiometrically balanced formula for the ANAMMOX chemical reaction can be written as following, where an ammonium ion includes the ammonia molecule, its conjugated base: 
 (Δ"G"° = ).
This an exergonic process (here also an exothermic reaction) releasing energy, as indicated by the negative value of Δ"G"°, the difference in Gibbs free energy between the products of reaction and the reagents.
Other processes.
Though nitrogen fixation is the primary source of plant-available nitrogen in most ecosystems, in areas with nitrogen-rich bedrock, the breakdown of this rock also serves as a nitrogen source. Nitrate reduction is also part of the iron cycle, under anoxic conditions Fe(II) can donate an electron to and is oxidized to Fe(III) while is reduced to , and depending on the conditions and microbial species involved. The fecal plumes of cetaceans also act as a junction in the marine nitrogen cycle, concentrating nitrogen in the epipelagic zones of ocean environments before its dispersion through various marine layers, ultimately enhancing oceanic primary productivity.
Marine nitrogen cycle.
The nitrogen cycle is an important process in the ocean as well. While the overall cycle is similar, there are different players and modes of transfer for nitrogen in the ocean. Nitrogen enters the water through the precipitation, runoff, or as N2 from the atmosphere. Nitrogen cannot be utilized by phytoplankton as N2 so it must undergo nitrogen fixation which is performed predominately by cyanobacteria. Without supplies of fixed nitrogen entering the marine cycle, the fixed nitrogen would be used up in about 2000 years. Phytoplankton need nitrogen in biologically available forms for the initial synthesis of organic matter. Ammonia and urea are released into the water by excretion from plankton. Nitrogen sources are removed from the euphotic zone by the downward movement of the organic matter. This can occur from sinking of phytoplankton, vertical mixing, or sinking of waste of vertical migrators. The sinking results in ammonia being introduced at lower depths below the euphotic zone. Bacteria are able to convert ammonia to nitrite and nitrate but they are inhibited by light so this must occur below the euphotic zone. Ammonification or Mineralization is performed by bacteria to convert organic nitrogen to ammonia. Nitrification can then occur to convert the ammonium to nitrite and nitrate. Nitrate can be returned to the euphotic zone by vertical mixing and upwelling where it can be taken up by phytoplankton to continue the cycle. N2 can be returned to the atmosphere through denitrification.
Ammonium is thought to be the preferred source of fixed nitrogen for phytoplankton because its assimilation does not involve a redox reaction and therefore requires little energy. Nitrate requires a redox reaction for assimilation but is more abundant so most phytoplankton have adapted to have the enzymes necessary to undertake this reduction (nitrate reductase). There are a few notable and well-known exceptions that include most "Prochlorococcus" and some "Synechococcus" that can only take up nitrogen as ammonium.
The nutrients in the ocean are not uniformly distributed. Areas of upwelling provide supplies of nitrogen from below the euphotic zone. Coastal zones provide nitrogen from runoff and upwelling occurs readily along the coast. However, the rate at which nitrogen can be taken up by phytoplankton is decreased in oligotrophic waters year-round and temperate water in the summer resulting in lower primary production. The distribution of the different forms of nitrogen varies throughout the oceans as well.
Nitrate is depleted in near-surface water except in upwelling regions. Coastal upwelling regions usually have high nitrate and chlorophyll levels as a result of the increased production. However, there are regions of high surface nitrate but low chlorophyll that are referred to as HNLC (high nitrogen, low chlorophyll) regions. The best explanation for HNLC regions relates to iron scarcity in the ocean, which may play an important part in ocean dynamics and nutrient cycles. The input of iron varies by region and is delivered to the ocean by dust (from dust storms) and leached out of rocks. Iron is under consideration as the true limiting element to ecosystem productivity in the ocean.
Ammonium and nitrite show a maximum concentration at 50–80 m (lower end of the euphotic zone) with decreasing concentration below that depth. This distribution can be accounted for by the fact that nitrite and ammonium are intermediate species. They are both rapidly produced and consumed through the water column. The amount of ammonium in the ocean is about 3 orders of magnitude less than nitrate. Between ammonium, nitrite, and nitrate, nitrite has the fastest turnover rate. It can be produced during nitrate assimilation, nitrification, and denitrification; however, it is immediately consumed again.
New vs. regenerated nitrogen.
Nitrogen entering the euphotic zone is referred to as new nitrogen because it is newly arrived from outside the productive layer. The new nitrogen can come from below the euphotic zone or from outside sources. Outside sources are upwelling from deep water and nitrogen fixation. If the organic matter is eaten, respired, delivered to the water as ammonia, and re-incorporated into organic matter by phytoplankton it is considered recycled/regenerated production.
New production is an important component of the marine environment. One reason is that only continual input of new nitrogen can determine the total capacity of the ocean