What's the first step of the Nitrogen Cycle?
Nitrogen cycle
The nitrogen cycle is the biogeochemical cycle by which nitrogen is converted into multiple chemical forms as it circulates among atmosphere, 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 atmosphere 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.
Orchid mycorrhiza
Nitrogen transport is an equally important and influential process that often occurs through mycorrhizal associations. Nitrogen is significantly easier to obtain than phosphorus and far more abundant, but mycorrhizal interactions still provide a significant benefit in the allocation of nitrogen. Bioavailable nitrogen as nitrate and ammonium are absorbed from the soil media into the extraradical mycelium of the mycorrhizal fungi and assimilated into amino acids. In some cases amino acids and other nitrogenous organic compounds may be present in the surrounding soil. If so organic nitrogen uptake also takes place through amino acid permeases and peptide transporters. Once incorporated into the fungi as amino acids, there are a few different proposed mechanisms with which the nitrogen is transferred to the host plant. These pathways of nitrogen transfer are thought to be exclusively biotrophic, a significant amount of nitrogen may also be transferred necrotorphically but through a significantly different process. In the first pathway the amino acids are transferred to the extraradical mycelium where the amino acids are broken down by the catabolic stage of the urea cycle. The primary amino acid synthesized and intra-fungally transferred is arginine, which is catabolized into ammonium. The ammonium is then shunted into the interfacial space between the peloton and the surrounding plant membrane,and transported into the plant cell via ammonium transporters and incorporated into the plant.
Nitrogen cycle
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 (NH) 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.
Denitrification
Denitrification is a microbially facilitated process where nitrate (NO) is reduced and ultimately produces molecular nitrogen (N) through a series of intermediate gaseous nitrogen oxide products. Facultative anaerobic bacteria perform denitrification as a type of respiration that reduces oxidized forms of nitrogen in response to the oxidation of an electron donor such as organic matter. The preferred nitrogen electron acceptors in order of most to least thermodynamically favorable include nitrate (NO), nitrite (NO), nitric oxide (NO), nitrous oxide (NO) finally resulting in the production of dinitrogen (N) completing the nitrogen cycle. Denitrifying microbes require a very low oxygen concentration of less than 10%, as well as organic C for energy. Since denitrification can remove NO, reducing its leaching to groundwater, it can be strategically used to treat sewage or animal residues of high nitrogen content. Denitrification can leak NO, which is an ozone-depleting substance and a greenhouse gas that can have a considerable influence on global warming.
Nutrient cycle
In 1926 Vernadsky coined the term biogeochemistry as a sub-discipline of geochemistry. However, the term nutrient cycle pre-dates biogeochemistry in a pamphlet on silviculture in 1899: "These demands by no means pass over the fact that at places where sufficient quantities of humus are available and where, in case of continuous decomposition of litter, a stable, nutrient humus is present, considerable quantities of nutrients are also available from the biogenic "nutrient cycle" for the standing timber. In 1898 there is a reference to the nitrogen cycle in relation to nitrogen fixing microorganisms. Other uses and variations on the terminology relating to the process of nutrient cycling appear throughout history:Water is also a nutrient. In this context, some authors also refer to precipitation recycling, which "is the contribution of evaporation within a region to precipitation in that same region." These variations on the theme of nutrient cycling continue to be used and all refer to processes that are part of the global biogeochemical cycles. However, authors tend to refer to natural, organic, ecological, or bio-recycling in reference to the work of nature, such as it is used in organic farming or ecological agricultural systems.
Nitrogen cycle
Nitrogen is present in the environment in a wide variety of chemical forms including organic nitrogen, ammonium (NH), nitrite (NO), nitrate (NO), nitrous oxide (NO), nitric oxide (NO) or inorganic nitrogen gas (N). 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 as new. The diagram {besides} alongside shows how these processes fit together to form the nitrogen cycle.
Lithotroph
Biogeochemical cycling of elements is an essential component of lithotrophs within microbial environments. For example, in the carbon cycle, there are certain bacteria classified as photolithoautotrophs that generate organic carbon from atmospheric carbon dioxide. Certain chemolithoautotrophic bacteria can also produce organic carbon, some even in the absence of light. Similar to plants, these microbes provide a usable form of energy for organisms to consume. On the contrary, there are lithotrophs that have the ability to ferment, implying their ability to convert organic carbon into another usable form. Another example is the cycling of nitrogen. Many lithotrophic bacteria play a role in reducing inorganic nitrogen (nitrogen gas) to organic nitrogen (ammonium) in a process called nitrogen fixation. Likewise, there are many lithotrophic bacteria that also convert ammonium into nitrogen gas in a process called denitrification. Carbon and nitrogen are important nutrients, essential for metabolic processes, and can sometimes be the limiting factor that affects organismal growth and development. Thus, lithotrophs are key players in both providing and removing these important resource.
Nitrogen cycle
In this biological process, nitrite and ammonia are converted directly into molecular nitrogen (N) gas. This process makes up a major proportion of nitrogen conversion in the oceans. The balanced formula for this "anammox" chemical reaction is: NH + NO → N + 2HO (Δ"G"° = ).
Human impact on the nitrogen cycle
Approximately 78% of earth's atmosphere is N gas (N), which is an inert compound and biologically unavailable to most organisms. In order to be utilized in most biological processes, N must be converted to reactive N (Nr), which includes inorganic reduced forms (NH and NH), inorganic oxidized forms (NO, NO, HNO, NO, and NO), and organic compounds (urea, amines, and proteins). N has a strong triple bond, and so a significant amount of energy (226 kcal mol) is required to convert N to Nr. Prior to industrial processes, the only sources of such energy were solar radiation and electrical discharges. Utilizing a large amount of metabolic energy and the enzyme nitrogenase, some bacteria and cyanobacteria convert atmospheric N to NH, a process known as biological nitrogen fixation (BNF). The anthropogenic analogue to BNF is the Haber-Bosch process, in which H is reacted with atmospheric N at high temperatures and pressures to produce NH. Lastly, N is converted to NO by energy from lightning, which is negligible in current temperate ecosystems, or by fossil fuel combustion.
Nitrogen generator
The swing adsorption process in each of the two adsorbers consists of two stages running for a few minutes. At the adsorption stage oxygen, HO and CO molecules diffuse into the pore structure of the adsorbent whilst the nitrogen molecules are allowed to travel through the adsorber–adsorbent-containing vessel. At the regeneration stage the adsorbed components are released from the adsorbent vented into the atmosphere. The process is then multiplely repeated.
Nitrogen
Nitrogen may be usefully compared to its horizontal neighbours carbon and oxygen as well as its vertical neighbours in the pnictogen column (phosphorus, arsenic, antimony, and bismuth). Although each period 2 element from lithium to nitrogen shows some similarities to the period 3 element in the next group from magnesium to sulfur (known as the diagonal relationships), their degree drops off quite abruptly past the boron–silicon pair, so that the similarities of nitrogen to sulfur are mostly limited to sulfur nitride ring compounds when both elements are the only ones present. Nitrogen resembles oxygen far more than it does carbon with its high electronegativity and concomitant capability for hydrogen bonding and the ability to form coordination complexes by donating its lone pairs of electrons. It does not share carbon's proclivity for catenation, with the longest chain of nitrogen yet discovered being composed of only eight nitrogen atoms (PhN=N–N(Ph)–N=N–N(Ph)–N=NPh). One property nitrogen does share with both its horizontal neighbours is its preferentially forming multiple bonds, typically with carbon, nitrogen, or oxygen atoms, through p–p interactions; thus, for example, nitrogen occurs as diatomic molecules and thus has very much lower melting (−210 °C) and boiling points (−196 °C) than the rest of its group, as the N molecules are only held together by weak van der Waals interactions and there are very few electrons available to create significant instantaneous dipoles. This is not possible for its vertical neighbours; thus, the nitrogen oxides, nitrites, nitrates, nitro-, nitroso-, azo-, and diazo-compounds, azides, cyanates, thiocyanates, and imino-derivatives find no echo with phosphorus, arsenic, antimony, or bismuth. By the same token, however, the complexity of the phosphorus oxoacids finds no echo with nitrogen.
Nitrification
The second step (oxidation of nitrite into nitrate) is done (mainly) by bacteria of the genus "Nitrobacter" and "Nitrospira". Both steps are producing energy to be coupled to ATP synthesis. Nitrifying organisms are chemoautotrophs, and use carbon dioxide as their carbon source for growth. Some AOB possess the enzyme, urease, which catalyzes the conversion of the urea molecule to two ammonia molecules and one carbon dioxide molecule. "Nitrosomonas europaea", as well as populations of soil-dwelling AOB, have been shown to assimilate the carbon dioxide released by the reaction to make biomass via the Calvin Cycle, and harvest energy by oxidizing ammonia (the other product of urease) to nitrite. This feature may explain enhanced growth of AOB in the presence of urea in acidic environments.
Carbon fixation
In the second step, called the Calvin cycle, the actual fixation of carbon dioxide is carried out. This process consumes ATP and NADPH. The Calvin cycle in plants accounts for the preponderance of carbon fixation on land. In algae and cyanobacteria, it accounts for the preponderance of carbon fixation in the oceans. The Calvin cycle converts carbon dioxide into sugar, as triose phosphate (TP), which is glyceraldehyde 3-phosphate (GAP) together with dihydroxyacetone phosphate (DHAP):
An alternative perspective accounts for NADPH (source of e) and ATP:
Human impact on the nitrogen cycle
Human impact on the nitrogen cycle is diverse. Agricultural and industrial nitrogen (N) inputs to the environment currently exceed inputs from natural N fixation. As a consequence of anthropogenic inputs, the global nitrogen cycle (Fig. 1) has been significantly altered over the past century. Global atmospheric nitrous oxide (NO) mole fractions have increased from a pre-industrial value of ~270 nmol/mol to ~319 nmol/mol in 2005. Human activities account for over one-third of NO emissions, most of which are due to the agricultural sector. This article is intended to give a brief review of the history of anthropogenic N inputs, and reported impacts of nitrogen inputs on selected terrestrial and aquatic ecosystems.
Nitrogen
Nitrogen bonds to almost all the elements in the periodic table except the first three noble gases, helium, neon, and argon, and some of the very short-lived elements after bismuth, creating an immense variety of binary compounds with varying properties and applications. Many binary compounds are known: with the exception of the nitrogen hydrides, oxides, and fluorides, these are typically called nitrides. Many stoichiometric phases are usually present for most elements (e.g. MnN, MnN, MnN, MnN, MnN, and MnN for 9.2 < "x" < 25.3). They may be classified as "salt-like" (mostly ionic), covalent, "diamond-like", and metallic (or interstitial), although this classification has limitations generally stemming from the continuity of bonding types instead of the discrete and separate types that it implies. They are normally prepared by directly reacting a metal with nitrogen or ammonia (sometimes after heating), or by thermal decomposition of metal amides:
Many variants on these processes are possible.The most ionic of these nitrides are those of the alkali metals and alkaline earth metals, LiN (Na, K, Rb, and Cs do not form stable nitrides for steric reasons) and MN (M = Be, Mg, Ca, Sr, Ba). These can formally be thought of as salts of the N anion, although charge separation is not actually complete even for these highly electropositive elements. However, the alkali metal azides NaN and KN, featuring the linear anion, are well-known, as are Sr(N) and Ba(N). Azides of the B-subgroup metals (those in groups 11 through 16) are much less ionic, have more complicated structures, and detonate readily when shocked.
Many covalent binary nitrides are known. Examples include cyanogen ((CN)), triphosphorus pentanitride (PN), disulfur dinitride (SN), and tetrasulfur tetranitride (SN). The essentially covalent silicon nitride (SiN) and germanium nitride (GeN) are also known: silicon nitride in particular would make a promising ceramic if not for the difficulty of working with and sintering it. In particular, the group 13 nitrides, most of which are promising semiconductors, are isoelectronic with graphite, diamond, and silicon carbide and have similar structures: their bonding changes from covalent to partially ionic to metallic as the group is descended. In particular, since the B–N unit is isoelectronic to C–C, and carbon is essentially intermediate in size between boron and nitrogen, much of organic chemistry finds an echo in boron–nitrogen chemistry, such as in borazine ("inorganic benzene"). Nevertheless, the analogy is not exact due to the ease of nucleophilic attack at boron due to its deficiency in electrons, which is not possible in a wholly carbon-containing ring.
Cyclic nucleotide
The atom numbering convention is used to identify the carbons and nitrogens within a cyclic nucleotide. In the pentose, the carbon closest to the carbonyl group is labeled C-1. When a pentose is connected to a nitrogenous base, carbon atom numbering is distinguished with a prime (') notation, which differentiates these carbons from the atom numbering of the nitrogenous base.
Nitrobacter
The two-step conversion of ammonia to nitrate observed in bacteria species such as "Nitrobacter" is puzzling to researchers. Complete nitrification, the conversion of ammonia to nitrate in a single step, has an energy yield (∆G°′) of −349 kJ mol NH, while the energy yields for the ammonia-oxidation and nitrite-oxidation steps of the observed two-step reaction are −275 kJ mol NH, and −74 kJ mol NO, respectively. These values indicate that it would be energetically favourable for an organism to carry out complete nitrification from ammonia to nitrate, rather than conduct only one of the two steps. The evolutionary motivation for a decoupled, two-step nitrification reaction is an area of ongoing research. In 2015, it was discovered that the genus "Nitrospira" possesses all the enzymes required for carrying out complete nitrification in one step, suggesting that this reaction does occur. This discovery raises questions about evolutionary capability of "Nitrobacter" to conduct only nitrite-oxidation.
Microbiology of oxygen minimum zones
Denitrification is the reduction of nitrate and nitrite to the gaseous form of nitrogen, including the greenhouse gas nitrous oxide, that is released back into the atmosphere. Denitrification closes the nitrogen cycle by reducing the nitrogen available in organic matter fixed by phytoplankton at the surface ocean. OMZs are known for the role in the global nitrogen cycle, where the different chemical species of nitrogen and different microbes play its part. Under these anoxic conditions, nitrate is reduced to gaseous nitrogen or nitrite and ammonia in a process called dissimilatory nitrate reduction by the protein nitrate reductase. The ammonia and nitrite produced are further reduced by anaerobic ammonia-oxidizing bacteria (anammox) using an enzyme called hydrazine oxidoreductase. Genomic studies conducted in these ecosystems reveal a growing abundance of the genes encoding for the proteins responsible for the dissimilatory nitrate reduction and anammox at the core of these OMZs. Such studies also provide information to map out the nitrogen cycle in the water column and provide with missing links and unexplored pathways. Denitrification from OMZs leads to a significant loss of inorganic nitrogen from the oceans and thus limiting growth/productivity in many regions around the world.
Nitrogen
Nitrogen trichloride (NCl) is a dense, volatile, and explosive liquid whose physical properties are similar to those of carbon tetrachloride, although one difference is that NCl is easily hydrolysed by water while CCl is not. It was first synthesised in 1811 by Pierre Louis Dulong, who lost three fingers and an eye to its explosive tendencies. As a dilute gas it is less dangerous and is thus used industrially to bleach and sterilise flour. Nitrogen tribromide (NBr), first prepared in 1975, is a deep red, temperature-sensitive, volatile solid that is explosive even at −100 °C. Nitrogen triiodide (NI) is still more unstable and was only prepared in 1990. Its adduct with ammonia, which was known earlier, is very shock-sensitive: it can be set off by the touch of a feather, shifting air currents, or even alpha particles. For this reason, small amounts of nitrogen triiodide are sometimes synthesised as a demonstration to high school chemistry students or as an act of "chemical magic". Chlorine azide (ClN) and bromine azide (BrN) are extremely sensitive and explosive.
Citric acid cycle
Several of the components and reactions of the citric acid cycle were established in the 1930s by the research of Albert Szent-Györgyi, who received the Nobel Prize in Physiology or Medicine in 1937 specifically for his discoveries pertaining to fumaric acid, a key component of the cycle. He was able to make this discovery successful with the help of pigeon breast muscle. Because this tissue maintains its oxidative capacity well after breaking down in the "Latapie" mill and releasing in aqueous solutions breast muscle of the pigeon was very well qualified for the study of oxidative reactions. The citric acid cycle itself was finally identified in 1937 by Hans Adolf Krebs and William Arthur Johnson while at the University of Sheffield, for which the former received the Nobel Prize for Physiology or Medicine in 1953, and for whom the cycle is sometimes named (Krebs cycle).
Nitrogenase
As with many assays for enzyme activity, it is possible to estimate nitrogenase activity by measuring the rate of conversion of the substrate (N) to the product (NH). Since NH is involved in other reactions in the cell, it is often desirable to label the substrate with N to provide accounting or "mass balance" of the added substrate. A more common assay, the acetylene reduction assay or ARA, estimates the activity of nitrogenase by taking advantage of the ability of the enzyme to reduce acetylene gas to ethylene gas. These gases are easily quantified using gas chromatography. Though first used in a laboratory setting to measure nitrogenase activity in extracts of "Clostridium pasteurianum" cells, ARA has been applied to a wide range of test systems, including field studies where other techniques are difficult to deploy. For example, ARA was used successfully to demonstrate that bacteria associated with rice roots undergo seasonal and diurnal rhythms in nitrogenase activity, which were apparently controlled by the plant.
Nitrogen cycle
Plants can absorb nitrate or ammonium from the soil via 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.
Microorganism
The nitrogen cycle in soils depends on the fixation of atmospheric nitrogen. This is achieved by a number of diazotrophs. One way this can occur is in the nodules in the roots of legumes that contain symbiotic bacteria of the genera "Rhizobium", "Mesorhizobium", "Sinorhizobium", "Bradyrhizobium", and "Azorhizobium".
Citric acid cycle
The name of this metabolic pathway is derived from the citric acid (a type of tricarboxylic acid, often called citrate, as the ionized form predominates at biological pH) that is consumed and then regenerated by this sequence of reactions to complete the cycle. The cycle consumes acetate (in the form of acetyl-CoA) and water, reduces NAD to NADH, and produces carbon dioxide as a waste byproduct. The NADH generated by the citric acid cycle is fed into the oxidative phosphorylation (electron transport) pathway. The net result of these two closely linked pathways is the oxidation of nutrients to produce usable chemical energy in the form of ATP.
Carbon monoxide dehydrogenase
The CODH catalytic site, referred to as the C-cluster, is a [3Fe-4S] cluster bonded to a Ni-Fe moiety. Two basic amino acids (Lys587 and His 113 in "M.thermoacetica") reside in proximity to the C-cluster and facilitate acid-base chemistry required for enzyme activity. Based on IR spectra suggesting the presence of an Ni-CO complex, the proposed first step in the oxidative catalysis of CO to CO involves the binding of CO to Ni and corresponding complexing of Fe to a water molecule. The binding of CO molecule causes a shift in the coordination of the Ni atom from a square-planar to square pyramidal geometry. Dobbek et al. further propose that movement of the Nickel atom’s cysteine ligand brings the CO into close proximity to the hydroxyl group, and facilitate a base-catalyzed, nucleophillic attack by the iron-bound hydroxy group. A carboxy bridge between the Ni and Fe atom has been proposed as an intermediate. A decarboxylation leads to the release of CO and the reduction of the cluster. Although the resulting intermediate oxidation state of the Ni and the degree to which electrons are distributed throughout the Ni-[3Fe-4S] cluster is subject of some debate, the electrons in the reduced C-cluster are transferred to nearby B and D [4Fe-4S] clusters, returning the Ni-[3Fe-4S] C-cluster to an oxidized state and reducing the single electron carrier ferredoxin.
Nitrogen
A nitrogen atom has seven electrons. In the ground state, they are arranged in the electron configuration 1s2s2p2p2p. It therefore has five valence electrons in the 2s and 2p orbitals, three of which (the p-electrons) are unpaired. It has one of the highest electronegativities among the elements (3.04 on the Pauling scale), exceeded only by chlorine (3.16), oxygen (3.44), and fluorine (3.98). Following periodic trends, its single-bond covalent radius of 71 pm is smaller than those of boron (84 pm) and carbon (76 pm), while it is larger than those of oxygen (66 pm) and fluorine (57 pm). The nitride anion, N, is much larger at 146 pm, similar to that of the oxide (O: 140 pm) and fluoride (F: 133 pm) anions. The first three ionisation energies of nitrogen are 1.402, 2.856, and 4.577 MJ·mol, and the sum of the fourth and fifth is 16.920 MJ·mol. Due to these very high figures, nitrogen has no simple cationic chemistry.
Nitrite oxidoreductase
Nitrite oxidoreductase (NOR or NXR) is an enzyme involved in nitrification. It is the last step in the process of aerobic ammonia oxidation, which is carried out by two groups of nitrifying bacteria: ammonia oxidizers such as "Nitrosospira", "Nitrosomonas" and "Nitrosococcus" convert ammonia to nitrite, while nitrite oxidizers such as "Nitrobacter" and "Nitrospira" oxidize nitrite to nitrate.
Carbon cycle
The carbon cycle is the biogeochemical cycle by which carbon is exchanged among the biosphere, pedosphere, geosphere, hydrosphere, and atmosphere of the Earth. Carbon is the main component of biological compounds as well as a major component of many minerals such as limestone. Along with the nitrogen cycle and the water cycle, the carbon cycle comprises a sequence of events that are key to make Earth capable of sustaining life. It describes the movement of carbon as it is recycled and reused throughout the biosphere, as well as long-term processes of carbon sequestration to and release from carbon sinks.
Nitrobacter
Nitrification is a crucial component of the nitrogen cycle, especially in the oceans. The production of nitrate (NO) by oxidation of nitrite (NO) by nitrification the process that produces the inorganic nitrogen that supplies much of the demand by marine oxygenic, photosynthetic organisms such as phytoplankton, particularly in areas of upwelling. For this reason, nitrification supplies much of the nitrogen that fuels planktonic primary production in the world's oceans. Nitrification is estimated to be the source of half of the nitrate consumed by phytoplankton globally. Phytoplankton are major contributors to oceanic production, and are therefore important for the biological pump which exports carbon and other particulate organic matter from the surface waters of the world's oceans. The process of nitrification is crucial for separating recycled production from production leading to export. Biologically metabolized nitrogen returns to the inorganic dissolved nitrogen pool in the form of ammonia. Microbe-mediated nitrification converts that ammonia into nitrate, which can subsequently be taken up by phytoplankton and recycled.
Nutrient cycle
A nutrient cycle (or ecological recycling) is the movement and exchange of organic and inorganic matter back into the production of matter. Energy flow is a unidirectional and noncyclic pathway, whereas the movement of mineral nutrients is cyclic. Mineral cycles include the carbon cycle, sulfur cycle, nitrogen cycle, water cycle, phosphorus cycle, oxygen cycle, among others that continually recycle along with other mineral nutrients into productive ecological nutrition.
Microbial metabolism
Denitrification is the utilization of nitrate () as a terminal electron acceptor. It is a widespread process that is used by many members of the Proteobacteria. Many facultative anaerobes use denitrification because nitrate, like oxygen, has a high reduction potential. Many denitrifying bacteria can also use ferric iron () and some organic electron acceptors. Denitrification involves the stepwise reduction of nitrate to nitrite (), nitric oxide (NO), nitrous oxide (), and dinitrogen () by the enzymes nitrate reductase, nitrite reductase, nitric oxide reductase, and nitrous oxide reductase, respectively. Protons are transported across the membrane by the initial NADH reductase, quinones, and nitrous oxide reductase to produce the electrochemical gradient critical for respiration. Some organisms (e.g. "E. coli") only produce nitrate reductase and therefore can accomplish only the first reduction leading to the accumulation of nitrite. Others (e.g. "Paracoccus denitrificans" or "Pseudomonas stutzeri") reduce nitrate completely. Complete denitrification is an environmentally significant process because some intermediates of denitrification (nitric oxide and nitrous oxide) are important greenhouse gases that react with sunlight and ozone to produce nitric acid, a component of acid rain. Denitrification is also important in biological wastewater treatment where it is used to reduce the amount of nitrogen released into the environment thereby reducing eutrophication. Denitrification can be determined via a nitrate reductase test.
Nitrospira moscoviensis
"Nitrospira moscoviensis" grows in temperatures from 33 to 40 °C and pH 7.6-8.0 with an optimal nitrite concentration of 0.35 nM. "Nitrospira moscoviensis" plays a key role in the two-step Nitrogen Cycle process. The first step of Nitrification requires an ammonia-oxidizing bacterium (AOB) or ammonia-oxidizing archaeon (AOA) followed by a nitrite-oxidizing bacterium (NOB). The unique capability of "N. moscoviensis" to cleave urea into ammonia and carbon dioxide allows for a symbiotic relationship with ammonia-oxidizing microorganisms (AOM) that lack this urease-production ability also known as negative AOM. A correlation in environment preferences between "Nitrospira" species with "nxrB" gene encoding the β-subunit of nitro-oxidoreductase and AOM species with "amoA" gene further confirmed this relationship. "N. moscoviensis" provides ammonia via hydrolysis of urea to these ammonia-oxidizing microorganisms which in turn produce nitrite, the primary energy source of "N. moscoviensis". The relationship between ureolytic nitrite-oxidizing bacteria and negative AOM is called reciprocal feeding. Thus far, "Nitrospira" species have been recognized in natural environments as the primary vehicle for nitrite oxidation including soils, activated-sludge, ocean and fresh water, hot springs, and water treatment plants.
Lichens and nitrogen cycling
The nitrogen cycle is one of the Earth’s biogeochemical cycle that involves the conversion of nitrogen into different chemical forms. The main processes of the nitrogen cycle are the fixation, ammonification, nitrification, and denitrification. As one of the macronutrients, nitrogen plays an important role in plant growth. Both nitrogen-fixing lichens and non-nitrogen fixing lichens absorb the nitrogen as the one of the nutrient. Different environments have different factors that contributes or affect the nitrogen cycle. For example, in the subarctic heath, increase in temperature can cause N2 fixation to increase or decrease based on season while overall climate warming indirectly caused the vegetation change which in turn affected of the N2 fixation process.
Nitrogen cycle
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 to produce a sustainable fish harvest. Harvesting fish from regenerated nitrogen areas will lead to a decrease in nitrogen and therefore a decrease in primary production. This will have a negative effect on the system. However, if fish are harvested from areas of new nitrogen the nitrogen will be replenished.
Nucleophilic aromatic substitution
In this sequence the carbons are numbered clockwise from 1–6 starting with the 1 carbon at 12 o'clock, which is bonded to the chloride. Since the nitro group is an activator toward nucleophilic substitution, and a meta director, it allows the benzene carbon to which it is bonded to have a negative charge. In the Meisenheimer complex, the nonbonded electrons of the carbanion become bonded to the aromatic pi system which allows the ipso carbon to temporarily bond with the hydroxyl group (-OH). In order to return to a lower energy state, either the hydroxyl group leaves, or the chloride leaves. In solution both processes happen. A small percentage of the intermediate loses the chloride to become the product (2,4-dinitrophenol), while the rest return to the reactant. Since 2,4-dinitrophenol is in a lower energy state it will not return to form the reactant, so after some time has passed, the reaction reaches chemical equilibrium that favors the 2,4-dinitrophenol.
Nif gene
The "nif" genes are genes encoding enzymes involved in the fixation of atmospheric nitrogen into a form of nitrogen available to living organisms. The primary enzyme encoded by the "nif" genes is the nitrogenase complex which is in charge of converting atmospheric nitrogen (N) to other nitrogen forms such as ammonia which the organism can use for various purposes. Besides the nitrogenase enzyme, the "nif" genes also encode a number of regulatory proteins involved in nitrogen fixation. The "nif" genes are found in both free-living nitrogen-fixing bacteria and in symbiotic bacteria associated with various plants. The expression of the "nif" genes is induced as a response to low concentrations of fixed nitrogen and oxygen concentrations (the low oxygen concentrations are actively maintained in the root environment of host plants). The first Rhizobium genes for nitrogen fixation (nif) and for nodulation (nod) were cloned in the early 1980s by Gary Ruvkun and Sharon R. Long in Frederick M. Ausubel's laboratory.
Human impact on the nitrogen cycle
Human activities dominate the global and most regional N cycles. N inputs have shown negative consequences for both nutrient cycling and native species diversity in terrestrial and aquatic systems. In fact, due to long-term impacts on food webs, Nr inputs are widely considered the most critical pollution problem in marine systems. In both terrestrial and aquatic ecosystems, responses to N enrichment vary; however, a general re-occurring theme is the importance of thresholds (e.g., nitrogen saturation) in system nutrient retention capacity. In order to control the N cascade, there must be integration of scientific disciplines and further work on Nr storage and denitrification rates.
Nitrogen
Nitrogen compounds constantly interchange between the atmosphere and living organisms. Nitrogen must first be processed, or "fixed", into a plant-usable form, usually ammonia. Some nitrogen fixation is done by lightning strikes producing the nitrogen oxides, but most is done by diazotrophic bacteria through enzymes known as nitrogenases (although today industrial nitrogen fixation to ammonia is also significant). When the ammonia is taken up by plants, it is used to synthesise proteins. These plants are then digested by animals who use the nitrogen compounds to synthesise their own proteins and excrete nitrogen–bearing waste. Finally, these organisms die and decompose, undergoing bacterial and environmental oxidation and denitrification, returning free dinitrogen to the atmosphere. Industrial nitrogen fixation by the Haber process is mostly used as fertiliser, although excess nitrogen–bearing waste, when leached, leads to eutrophication of freshwater and the creation of marine dead zones, as nitrogen-driven bacterial growth depletes water oxygen to the point that all higher organisms die. Furthermore, nitrous oxide, which is produced during denitrification, attacks the atmospheric ozone layer.
Nutrient cycling in the Columbia River Basin
Anaerobic respiration, which occurs in the absence of highly oxidizing molecular oxygen, utilizes less-oxidized electron acceptors such as nitrate (NO). As a result, high levels of anaerobic respiration can result in denitrification. This process of denitrification removes nitrogen from the Columbia River Basin, by converting available nitrogen, important for primary production, from its usable dissolved forms (i.e. NO and NO) to its gaseous form (N).
Argininosuccinate lyase
Ammonia (NH) is a toxic substance for many aerobic organisms and must be excreted. Some aquatic organisms release the toxin right directly into their environment, while other ureotelic species must convert their toxic nitrogen waste into non-toxic components, like uric acid or urea, through a series of catalyzed steps better known as the urea cycle. ASL catalyzes the fourth step in the cycle, following the action of argininosuccinate synthetase (ASS) in the liver cytosol. While ASS catalyzes the formation of argininosuccinate from citrulline and aspartate, ASL breaks the newly formed argininosuccinate into L-arginine and fumarate. L-arginine continues through the urea cycle to form urea and ornithine, while fumarate can enter the citric acid cycle.
Nitrogen cycle
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.
Nitrososphaera gargensis
As a chemolithoautotroph, "Nitrososphaera gargensis" performs aerobic oxidation of ammonia to nitrite and breaks down cyanate for energy. "N. gargensis" also encompasses a flexible carbon metabolism, allowing for the uptake of organic material. Nitrification, the process of oxidizing ammonia to nitrate, is a significant step in the nitrogen cycle. Since nitrogen is limited in marine environments, the recent discovery of ammonia-oxidizing archaea proves to be an active source of study for researchers. "N. gargensis" possesses ammonia monooxygenase, which is the enzyme that enables the organism the ability to oxidize ammonia, or urea and potentially cyanate as other sources of ammonia.
Nitrogen cycle
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.
Nitrogen
Nitrogen is the lightest member of group 15 of the periodic table, often called the pnictogens. The name comes from the Greek πνίγειν "to choke", directly referencing nitrogen's asphyxiating properties. It is a common element in the universe, estimated at about seventh in total abundance in the Milky Way and the Solar System. At standard temperature and pressure, two atoms of the element bind to form dinitrogen, a colourless and odorless diatomic gas with the formula N. Dinitrogen forms about 78% of Earth's atmosphere, making it the most abundant uncombined element. Nitrogen occurs in all organisms, primarily in amino acids (and thus proteins), in the nucleic acids (DNA and RNA) and in the energy transfer molecule adenosine triphosphate. The human body contains about 3% nitrogen by mass, the fourth most abundant element in the body after oxygen, carbon, and hydrogen. The nitrogen cycle describes movement of the element from the air, into the biosphere and organic compounds, then back into the atmosphere.
Daniel Sigman
He studies the global cycles of biologically active elements, in particular, nitrogen and carbon, and he is active in the development of analytical techniques for studying nitrogen in the environment. He also investigates the history of these cycles in order to understand the causes of past changes in the atmospheric concentration of carbon dioxide, the role of this greenhouse gas in the waxing and waning of ice ages, and the ocean’s response to climate change.
Cattle urine patches
Nitrification and denitrification are two microbial processes that are part of the nitrogen cycle. While denitrification contributes to the bulk production of nitrous oxide, small amounts are also produced during nitrification. When specific environmental factors are met, both processes will occur more quickly and produce higher emissions of nitrous oxide. For example, soils with relatively high temperatures and water-filled pore spaces ranging from 60-80% are required for peak performances of both processes.
Bacterioplankton
The nitrogen cycle in the oceans is mediated by microorganisms, many of which are bacteria, performing multiple conversions such as: nitrogen fixation, denitrification, assimilation, and anaerobic ammonia oxidation (anammox). There are many different nitrogen metabolism strategies employed by bacterioplankton. Starting with molecular nitrogen in the atmosphere (N), which is fixed by diazatrophs such as trichodesmium into usable forms like ammonia (NH). This ammonia can then be assimilated into organic matter like amino and nucleic acids, by both photoautrophic and heterotrophic plankton, it can also be nitrified to NO for energy production by nitrifying bacteria. Finally the use of NO or NO as terminal electron acceptors reduces the nitrogen back into N which is then released back into the atmosphere thus closing the cycle. Another important process involved in the regeneration of atmospheric N is anammox. Anammox, a process in which ammonia is combined with nitrite in order to produce diatomic nitrogen and water, could account for 30-50% of production of N in the ocean.
Human impact on the nitrogen cycle
The above system responses to reactive nitrogen (Nr) inputs are almost all exclusively studied separately; however, research increasingly indicates that nitrogen loading problems are linked by multiple pathways transporting nutrients across system boundaries. This sequential transfer between ecosystems is termed the nitrogen cascade. (see illustration from United Nations Environment Programme). During the cascade, some systems accumulate Nr, which results in a time lag in the cascade and enhanced effects of Nr on the environment in which it accumulates. Ultimately, anthropogenic inputs of Nr are either accumulated or denitrified; however, little progress has been made in determining the relative importance of Nr accumulation and denitrification, which has been mainly due to a lack of integration among scientific disciplines.
Nannochloropsis and biofuels
Nitrogen is essential for algal growth. Within a cell, nitrogen is involved in synthesizing amino acids, nucleic acids, chlorophyll, and other nitrogen-containing organic compounds. In a study in which 30 different microalgal strains were screened, one "Nannochloropsis" strain was shown to obtain 60% lipid content after nitrogen deprivation, up from 30% under normal growth conditions. This strain was selected for further scale-up experiments in a photobioreactor under natural sunlight. Lipid productivity increased to 204 milligram per liter per day(mg/L/day) under nitrogen starvation conditions, almost twice as much as the 117 mg/L/day under sufficient nutrition conditions. Based on these results, a two-phase cultivation process, with a nutrient sufficient phase to rapidly increase number of cells prior to a nitrogen deprived phase to boost lipid content, was found to produce more than 90 kg of lipid per hectare per day in outdoor cultures. I, depending on sun light conditions.
Argininosuccinate synthase
Defects in ASS disrupt the third step of the urea cycle, preventing the liver from processing excess nitrogen into urea. As a result, nitrogen (in the form of ammonia) and other byproducts of the urea cycle (such as citrulline) build up in the bloodstream. Ammonia is toxic, particularly to the nervous system. An accumulation of ammonia during the first few days of life leads to poor feeding, vomiting, seizures, and the other signs and symptoms of type I citrullinemia.
Denitrifying bacteria
The result is one molecule of nitrogen and six molecules of water. Denitrifying bacteria are a part of the N cycle, and consists of sending the N back into the atmosphere. 
The reaction above is the overall half reaction of the process of denitrification. The reaction can be further divided into different half reactions each requiring a specific enzyme. The transformation from nitrate to nitrite is performed by nitrate reductase (Nar)
Vanadium nitrogenase
Vanadium nitrogenase is a key enzyme for nitrogen fixation found in nitrogen-fixing bacteria, and is used as an alternative to molybdenum nitrogenase when molybdenum is unavailable. Vanadium nitrogenases are an important biological use of vanadium, which is uncommonly used by life. An important component of the nitrogen cycle, vanadium nitrogenase converts nitrogen gas to ammonia, thereby making otherwise inaccessible nitrogen available to plants. Unlike molybdenum nitrogenase, vanadium nitrogenase can also reduce carbon monoxide to ethylene, ethane and propane but both enzymes can reduce protons to hydrogen gas and acetylene to ethylene. 
Vanadium nitrogenases are found in members of the bacterial genus "Azotobacter" as well as the species "Rhodopseudomonas palustris" and "Anabaena variabilis". Most of the functions of vanadium nitrogenase match those of the more common molybdenum nitrogenases and serve as an alternative pathway for nitrogen fixation in molybdenum deficient conditions. Like molybdenum nitrogenase, dihydrogen functions as a competitive inhibitor and carbon monoxide functions as a non-competitive inhibitor of nitrogen fixation. Vanadium nitrogenase has an αβΎ subunit structure while molybdenum nitrogenase has an αβ structure. Though the structural genes encoding vanadium nitrogenase show only about 15% conservation with molybdenum nitrogenases, the two nitrogenases share the same type of redox centers. At room temperature, vanadium nitrogenase is less efficient at fixing nitrogen than moldybdenum nitrogenases because it converts more H to H as a side reaction. However, at low temperatures vanadium nitrogenases have been found to be more active than the molybdenum type, and at temperatures as low as 5 °C its nitrogen-fixing activity is 10 times higher than that of molybdenum nitrogenase. Like molybdenum nitrogenase, vanadium nitrogenase is easily oxidized and is thus only active under anaerobic conditions. Various bacteria employ complex protection mechanisms to avoid oxygen.
Nitrogen cycle
Increasing levels of nitrogen deposition are shown to have a number of negative effects on both terrestrial and aquatic ecosystems. Nitrogen gases and aerosols can be directly toxic to certain plant species, affecting the aboveground physiology and growth of plants near large point sources of nitrogen pollution. Changes to plant species interactions may also occur, as accumulation of nitrogen compounds increase its availability in a given ecosystem, eventually changing the species composition, plant diversity, and nitrogen cycling. Ammonia and ammonium - two reduced forms of nitrogen - can be detrimental over time due to an increased toxicity toward sensitive species of plants, particularly those that are accustomed to using nitrate as their source of nitrogen, causing poor development of their roots and shoots. Increased nitrogen deposition also leads to soil acidification, which increases base cation leaching in the soil and amounts of aluminium and other potentially toxic metals, along with decreasing the amount of nitrification occurring and increasing plant-derived litter. Due to the ongoing changes caused by high nitrogen deposition, an environment's susceptibility to ecological stress and disturbance - such as pests and pathogens - may increase, thus making it less resilient to situations that otherwise would have little impact to its long-term vitality.
Period 2 element
Nitrogen occurs in all living organisms, and the nitrogen cycle describes movement of the element from air into the biosphere and organic compounds, then back into the atmosphere. Synthetically produced nitrates are key ingredients of industrial fertilizers, and also key pollutants in causing the eutrophication of water systems. Nitrogen is a constituent element of amino acids and thus of proteins, and of nucleic acids (DNA and RNA). It resides in the chemical structure of almost all neurotransmitters, and is a defining component of alkaloids, biological molecules produced by many organisms.
Denitrifying bacteria
Denitrifying bacteria are a diverse group of bacteria that encompass many different phyla. This group of bacteria, together with denitrifying fungi and archaea, is capable of performing denitrification as part of the nitrogen cycle. They metabolise nitrogenous compounds using various enzymes, turning nitrogen oxides back to nitrogen gas or nitrous oxide.
Spongivore
Scientist have discovered that sponges play an important role in the nitrogen cycle. There are low amounts of nitrogen found in the water around coral reefs and most of the nitrogen that is found it bound into particulate or dissolved organic matter. Before this dissolved organic matter is able to be used by other reef organisms it must undergo a series of microbial transformations. The nitrogen cycle that occurs in sponges are able to cycle the nitrogen back into the water column and can be used by other organisms, especially the cyanobacteria.The cyanobacteria then can then fix the atmospheric nitrogen and then the sponges can use it. Therefore, if there is a high amount of spongivores present in an environment, it can effect other aspects of the environment besides sponges.
Simultaneous nitrification–denitrification
The oxidation of the ammonium to nitrogen gas has been achieved with attached growth and suspended growth wastewater treatment processes. The most common bacteria responsible for the two step conversion are the autotrophic organisms, "Nitrosomonas" and "Nitrobacter", and many different heterotrophs. The former obtain energy from the oxidation of ammonia, obtain carbon from CO, and use oxygen as the electron acceptor. They are termed autotrophic because of their carbon source and termed aerobes because of their aerobic environment. The heterotrophic organisms are responsible for denitrification or the reduction of nitrate, NO, to nitrogen gas, N. They use carbon from complex organic compounds, prefer low to zero dissolved oxygen, and use nitrate as the electron acceptor.
Nitrogenase
The reduction of nitrogen to two molecules of ammonia is carried out at the FeMo-co of Component I after the sequential addition of proton and electron equivalents from Component II. Steady state, freeze quench, and stopped-flow kinetics measurements carried out in the 70’s and 80’s by Lowe, Thorneley, and others provided a kinetic basis for this process. The Lowe-Thorneley (LT) kinetic model (depicted in Figure 4) was developed from these experiments and documents the eight correlated proton and electron transfers required throughout the reaction. Each intermediate stage is depicted as E where n = 0-8, corresponding to the number of equivalents transferred. The transfer of four equivalents are required before the productive addition of N, although reaction of E with N is also possible. Notably, nitrogen reduction has been shown to require 8 equivalents of protons and electrons as opposed to the 6 equivalents predicted by the balanced chemical reaction.
Microbial metabolism
Electron and proton cycling are very complex but as a net result only one proton is translocated across the membrane per molecule of ammonia oxidized. Nitrite oxidation is much simpler, with nitrite being oxidized by the enzyme nitrite oxidoreductase coupled to proton translocation by a very short electron transport chain, again leading to very low growth rates for these organisms. Oxygen is required in both ammonia and nitrite oxidation, meaning that both nitrosifying and nitrite-oxidizing bacteria are aerobes. As in sulfur and iron oxidation, NADH for carbon dioxide fixation using the Calvin cycle is generated by reverse electron flow, thereby placing a further metabolic burden on an already energy-poor process.
Microbial ecology
Other microbes are decomposers, with the ability to recycle nutrients from other organisms' waste products. These microbes play a vital role in biogeochemical cycles. The nitrogen cycle, the phosphorus cycle, the sulphur cycle and the carbon cycle all depend on microorganisms in one way or another. For example, the nitrogen gas which makes up 78% of the earth's atmosphere is unavailable to most organisms, until it is converted to a biologically available form by the microbial process of nitrogen fixation.
Human impact on the nitrogen cycle
Most Nr applied to global agroecosystems cascades through the atmosphere and aquatic and terrestrial ecosystems until it is converted to N, primarily through denitrification. Although terrestrial denitrification produces gaseous intermediates (nitric oxide [NO] and nitrous oxide [NO]), the last step—microbial production of N— is critical because atmospheric N is a sink for Nr. Many studies have clearly demonstrated that managed buffer strips and wetlands can remove significant amounts of nitrate (NO) from agricultural systems through denitrification. Such management may help attenuate the undesirable cascading effects and eliminate environmental Nr accumulation.
Nitrogen fixation
Much research has been conducted on the discovery of catalysts for nitrogen fixation, often with the goal of reducing the energy required for this conversion. However, such research has thus far failed to even approach the efficiency and ease of the Haber process. Many compounds react with atmospheric nitrogen to give dinitrogen complexes. The first dinitrogen complex to be reported was Ru(NH)(N).
Nutrient cycling in the Columbia River Basin
Nutrient cycling in the Columbia River Basin involves the transport of nutrients through the system, as well as transformations from among dissolved, solid, and gaseous phases, depending on the element. The elements that constitute important nutrient cycles include macronutrients such as nitrogen (as ammonium, nitrite, and nitrate), silicate, phosphorus, and micronutrients, which are found in trace amounts, such as iron. Their cycling within a system is controlled by many biological, chemical, and physical processes.
Nitrogen
Nitrogen is a chemical element with symbol N and atomic number 7. It was first discovered and isolated by Scottish physician Daniel Rutherford in 1772. Although Carl Wilhelm Scheele and Henry Cavendish had independently done so at about the same time, Rutherford is generally accorded the credit because his work was published first. The name "nitrogène" was suggested by French chemist Jean-Antoine-Claude Chaptal in 1790, when it was found that nitrogen was present in nitric acid and nitrates. Antoine Lavoisier suggested instead the name azote, from the Greek άζωτικός "no life", as it is an asphyxiant gas; this name is instead used in many languages, such as French, Russian, and Turkish, and appears in the English names of some nitrogen compounds such as hydrazine, azides and azo compounds.
Urea cycle
The entire process converts two amino groups, one from NH and one from Aspartate, and a carbon atom from HCO, to the relatively nontoxic excretion product urea at the cost of four "high-energy" phosphate bonds (3 ATP hydrolyzed to 2 ADP and one AMP). The conversion from ammonia to urea happens in five main steps. The first is needed for ammonia to enter the cycle and the following four are all a part of the cycle itself. To enter the cycle, ammonia is converted to carbamoyl phosphate. The urea cycle consists of four enzymatic reactions: one mitochondrial and three cytosolic.
Soil food web
After constructing the first soil flow webs, researchers discovered that nutrients and energy flowed from lower resources to higher trophic levels through three main channels. The bacterial and fungal channels had the largest energy flow, while the herbivory channel, in which organisms directly consumed plant roots, was smaller. It is now widely recognized that bacteria and fungi are critical to the decomposition of carbon and nitrogen and play important roles in both the carbon cycle and nitrogen cycle.
Aerobic denitrification
Nitrogen, acting as an oxidant, is therefore reduced in a succession of four reactions performed by the enzymes nitrate, nitrite, nitric-oxide, and nitrous oxide reductases. The pathway ultimately yields reduced molecular nitrogen (N), as well as, when the reaction does not reach completion, the intermediate species nitrous oxide (NO). A simple denitrification reaction proceeds as:
Cytochrome c nitrite reductase
Cytochrome "c" nitrite reductase (ccNiR) () is a bacterial enzyme that catalyzes the six electron reduction of nitrite to ammonia; an important step in the biological nitrogen cycle. The enzyme catalyses the second step in the two step conversion of nitrate to ammonia, which allows certain bacteria to use nitrite as a terminal electron acceptor, rather than oxygen, during anaerobic conditions. During this process, ccNiR draws electrons from the quinol pool, which are ultimately provided by a dehydrogenase such as formate dehydrogenase or hydrogenase. These dehydrogenases are responsible for generating a proton motive force.
Staudinger synthesis
The first step is a nucleophilic attack by the imine nitrogen on the carbonyl carbon to generate a zwitterionic intermediate. Electron donating groups on the imine facilitate this step, while electron-withdrawing groups impede the attack. The second step is either an intramolecular nucleophilic ring closure or a conrotary electrocyclic ring closure. The second step is different from typical electrocyclic ring closures as predicted by the Woodward–Hoffmann rules. Under photochemical and microwave conditions the intermediate's 4π-electron system cannot undergo a disrotatory ring closure to form the β-lactam, possibly because the two double bonds are not coplanar. Some products of the Staudinger Synthesis differ from those predicted by the torquoelectronic model. In addition, the electronic structure of the transition state differs from that of other conrotary ring closures.
There is evidence from computational studies on model systems that in the gas phase the mechanism is concerted.
Nitrogen mustard
Nitrogen mustards (NMs) form cyclic aminium ions (aziridinium rings) by intramolecular displacement of the chloride by the amine nitrogen. This aziridinium group then alkylates DNA once it is attacked by the N-7 nucleophilic center on the guanine base. A second attack after the displacement of the second chlorine forms the second alkylation step that results in the formation of interstrand cross-links (ICLs) as it was shown in the early 1960s. At that time it was proposed that the ICLs were formed between N-7 atom of guanine residue in a 5’-d(GC) sequence. Later it was clearly demonstrated that NMs form a 1,3 ICL in the 5’-d(GNC) sequence.
Nitrogenase
Nitrogenase is an enzyme responsible for catalyzing nitrogen fixation, which is the reduction of nitrogen (N) to ammonia (NH) and a process vital to sustaining life on Earth. There are three types of nitrogenase found in various nitrogen-fixing bacteria: molybdenum (Mo) nitrogenase, vanadium (V) nitrogenase, and iron-only (Fe) nitrogenase. Molybdenum nitrogenase, which can be found in diazotrophs and legumes, is the nitrogenase that has been studied the most extensively and thus is the most well characterized. Figures 1-2 display the crystal structure and key catalytic components of molybdenum nitrogenase extracted from "Azotobacter vinelandii". Vanadium nitrogenase and iron-only nitrogenase can both be found in select species of Azotobacter as an alternative nitrogenase. Equations 1 and 2 show the balanced reactions of nitrogen fixation in molybdenum nitrogenase and vanadium nitrogenase respectively.
Aquarium
A well-balanced tank contains organisms that are able to metabolize the waste products of other aquarium residents. This process is known in the aquarium hobby as the nitrogen cycle. Bacteria known as nitrifiers (genus "Nitrosomonas") metabolize nitrogen waste. Nitrifying bacteria capture ammonia from the water and metabolize it to produce nitrite. Nitrite is toxic to fish in high concentrations. Another type of bacteria (genus "Nitrospira") converts nitrite into nitrate, a less toxic substance. ("Nitrobacter" bacteria were previously believed to fill this role. While biologically they could theoretically fill the same niche as "Nitrospira", it has recently been found that "Nitrobacter" are not present in detectable levels in established aquaria, while "Nitrospira" are plentiful.) However, commercial products sold as kits to "jump start" the nitrogen cycle often still contain "Nitrobacter".
Constructed wetland
Ammonia removal occurs in constructed wetlands – if they are designed to achieve biological nutrient removal – in a similar ways as in sewage treatment plants, except that no external, energy-intensive addition of air (oxygen) is needed. It is a two-step process, consisting of nitrification followed by denitrification. The nitrogen cycle is completed as follows: ammonia in the wastewater is converted to ammonium ions; the aerobic bacterium "Nitrosomonas" sp. oxidizes ammonium to nitrite; the bacterium "Nitrobacter" sp. then converts nitrite to nitrate. Under anaerobic conditions, nitrate is reduced to relatively harmless nitrogen gas that enters the atmosphere.
Nitrogen
Nitric oxide (NO) is the simplest stable molecule with an odd number of electrons. In mammals, including humans, it is an important cellular signaling molecule involved in many physiological and pathological processes. It is formed by catalytic oxidation of ammonia. It is a colourless paramagnetic gas that, being thermodynamically unstable, decomposes to nitrogen and oxygen gas at 1100–1200 °C. Its bonding is similar to that in nitrogen, but one extra electron is added to a "π"* antibonding orbital and thus the bond order has been reduced to approximately 2.5; hence dimerisation to O=N–N=O is unfavourable except below the boiling point (where the "cis" isomer is more stable) because it does not actually increase the total bond order and because the unpaired electron is delocalised across the NO molecule, granting it stability. There is also evidence for the asymmetric red dimer O=N–O=N when nitric oxide is condensed with polar molecules. It reacts with oxygen to give brown nitrogen dioxide and with halogens to give nitrosyl halides. It also reacts with transition metal compounds to give nitrosyl complexes, most of which are deeply coloured.
Adenosine triphosphate
In the mitochondrion, pyruvate is oxidized by the pyruvate dehydrogenase complex to the acetyl group, which is fully oxidized to carbon dioxide by the citric acid cycle (also known as the Krebs cycle). Every "turn" of the citric acid cycle produces two molecules of carbon dioxide, one equivalent of ATP guanosine triphosphate (GTP) through substrate-level phosphorylation catalyzed by succinyl-CoA synthetase, as succinyl- CoA is converted to Succinate, three equivalents of NADH, and one equivalent of FADH. NADH and FADH are recycled (to NAD and FAD, respectively), generating additional ATP by oxidative phosphorylation. The oxidation of NADH results in the synthesis of 2–3 equivalents of ATP, and the oxidation of one FADH yields between 1–2 equivalents of ATP. The majority of cellular ATP is generated by this process. Although the citric acid cycle itself does not involve molecular oxygen, it is an obligately aerobic process because O is used to recycle the NADH and FADH. In the absence of oxygen, the citric acid cycle ceases.
Viral shunt
Viral shunt is a big component to the cycling of nitrogen in marine environments. Nitrogen gas from the atmosphere gets dissolved into surface of the water. Nitrogen fixing cyanobacteria, such as "Trichodesmium" and "Anabaena," convert the nitrogen gas (N) into ammonium (NH) for microbes to use. The process of converting nitrogen gas to ammonia (and related nitrogen compounds) is called nitrogen fixation.The process of uptake of ammonium by microbes to be used in protein synthesis is called nitrogen assimilation. The viral shunt causes mass death of heterotrophic bacteria. The decomposition of these microbes releases particulate organic nitrogen (PON) and dissolved organic nitrogen (DON), which either stay in the upper mixing layer or sink to the deeper parts of the ocean. In the deep ocean, PON and DON are converted back into ammonium by remineralisation. This ammonium can be used by deep ocean microbes, or undergo nitrification and be oxidized into nitrites and nitrates. The sequence of nitrification is as followed:
Carbohydrate catabolism
If oxygen is present, then following glycolysis, the two pyruvate molecules are brought into the mitochondrion itself to go through the Krebs cycle. In this cycle, the pyruvate molecules from glycolysis are further broken down to harness the remaining energy. Each pyruvate goes through a series of reactions that converts it to acetyl coenzyme A. From here, only the acetyl group participates in the Krebs cycle—in which it goes through a series of redox reactions, catalyzed by enzymes, to further harness the energy from the acetyl group. The energy from the acetyl group, in the form of electrons, is used to reduce NAD+ and FAD to NADH and FADH, respectively. NADH and FADH contain the stored energy harnessed from the initial glucose molecule and is used in the electron transport chain where the bulk of the ATP is produced.
Lichens and nitrogen cycling
Nitrogen, as a macronutrient and a biogeochemical cycle, also affects the ecology. Through the nitrogen cycle, it breaks down into the chemical form that allows plants to absorb as nutrients. There are certain regions in the world that most plants can not live due to harsh environments as well as lack of nutrients such as nitrogen. That means that at in some regions, the biogeochemical cycle (including nitrogen cycle and carbon cycle) is unlikely to run smoothly. Lichen is able to absorb nitrogen is multiple forms from soil, rock, and air, taking a part in carbon cycle at the same time. Even though the only small fraction of lichens have the ability to fix nitrogen, it helps the lichen to spread throughout the world and survive even in the harsh environment.
CNO cycle
The first proposed catalytic cycle for the conversion of hydrogen into helium was initially called the carbon–nitrogen cycle (CN-cycle), also referred to as the Bethe–Weizsäcker cycle in honor of the independent work of Carl von Weizsäcker in 1937-38 and Hans Bethe. Bethe's 1939 papers on the CN-cycle drew on three earlier papers written in collaboration with Robert Bacher and Milton Stanley Livingston and which came to be known informally as "Bethe's Bible." It was considered the standard work on nuclear physics for many years and was a significant factor in his being awarded the 1967 Nobel Prize in Physics. Bethe's original calculations suggested the CN-cycle was the Sun's primary source of energy. This conclusion arose from what is now-known as a mistaken belief: that the abundance of nitrogen in the sun is approximately 10%, when it is actually less than half a percent. The CN-cycle, named as it contains no stable isotope of oxygen involves the following cycle of transformations:  →  →  →  →  →  → . This cycle is now understood as being the first part of a larger process, the CNO-cycle, and the main reactions in this part of the cycle (CNO-I) are: 
where the carbon-12 nucleus used in the first reaction is regenerated in the last reaction. After the two positrons emitted annihilate with two ambient electrons producing an additional 2.04 MeV, the total energy released in one cycle is 26.73 MeV; it should be noted that in some texts, authors are erroneously including the positron annihilation energy in with the beta-decay Q-value and then neglecting the equal amount of energy released by annihilation, leading to possible confusion. All values are calculated with reference to the Atomic Mass Evaluation 2003.
Mitochondrial matrix
The first two steps of the urea cycle take place within the mitochondrial matrix of liver and kidney cells. In the first step ammonia is converted into carbamoyl phosphate through the investment of two ATP molecules. This step is facilitated by carbamoyl phosphate synthetase I. The second step facilitated by ornithine transcarbamylase converts carbamoyl phosphate and ornithine into citrulline. After these initial steps the urea cycle continues in the inner membrane space until ornithine once again enters the matrix through a transport channel to continue the first to steps within matrix.
Nitrogen
Nitrogen is one of the most important elements in organic chemistry. Many organic functional groups involve a carbon–nitrogen bond, such as amides (RCONR), amines (RN), imines (RC(=NR)R), imides (RCO)NR, azides (RN), azo compounds (RNR), cyanates and isocyanates (ROCN or RCNO), nitrates (RONO), nitriles and isonitriles (RCN or RNC), nitrites (RONO), nitro compounds (RNO), nitroso compounds (RNO), oximes (RCR=NOH), and pyridine derivatives. C–N bonds are strongly polarised towards nitrogen. In these compounds, nitrogen is usually trivalent (though it can be tetravalent in quaternary ammonium salts, RN), with a lone pair that can confer basicity on the compound by being coordinated to a proton. This may be offset by other factors: for example, amides are not basic because the lone pair is delocalised into a double bond (though they may act as acids at very low pH, being protonated at the oxygen), and pyrrole is not acidic because the lone pair is delocalised as part of an aromatic ring. The amount of nitrogen in a chemical substance can be determined by the Kjeldahl method. In particular, nitrogen is an essential component of nucleic acids, amino acids and thus proteins, and the energy-carrying molecule adenosine triphosphate and is thus vital to all life on Earth.
Nitrification
Nitrification is a process of nitrogen compound oxidation (effectively, loss of electrons from the nitrogen atom to the oxygen atoms), and is catalyzed step-wise by a series of enzymes.
OR
In Nitrosomonas europaea, the first step of oxidation (ammonia to hydroxylamine) is carried out by the enzyme ammonia monooxygenase (AMO).
Urea cycle
The urea cycle and the citric acid cycle are independent cycles but are linked. One of the nitrogens in the urea cycle is obtained from the transamination of oxaloacetate to aspartate. The fumarate that is produced in step three is also an intermediate in the citric acid cycle and is returned to that cycle.
Urea cycle
The urea cycle (also known as the ornithine cycle) is a cycle of biochemical reactions that produces urea ((NH)CO) from ammonia (NH). This cycle occurs in ureotelic organisms. The urea cycle converts highly toxic ammonia to urea for excretion. This cycle was the first metabolic cycle to be discovered (Hans Krebs and Kurt Henseleit, 1932), five years before the discovery of the TCA cycle. The urea cycle takes place primarily in the liver and, to a lesser extent, in the kidneys.
Aza-Diels–Alder reaction
The catalytic cycle starts with the reactions of the aromatic amine with formaldehyde to the imine and the reaction of the ketone with proline to the diene. The second step, an endo trig cyclisation, is driven to one of the two possible enantiomers (99% ee) because the imine nitrogen atom forms a hydrogen bond with the carboxylic acid group of proline on the Si face. Hydrolysis of the final complex releases the product and regenerates the catalyst.
Biochemistry
In aerobic cells with sufficient oxygen, as in most human cells, the pyruvate is further metabolized. It is irreversibly converted to acetyl-CoA, giving off one carbon atom as the waste product carbon dioxide, generating another reducing equivalent as NADH. The two molecules acetyl-CoA (from one molecule of glucose) then enter the citric acid cycle, producing two molecules of ATP, six more NADH molecules and two reduced (ubi)quinones (via FADH as enzyme-bound cofactor), and releasing the remaining carbon atoms as carbon dioxide. The produced NADH and quinol molecules then feed into the enzyme complexes of the respiratory chain, an electron transport system transferring the electrons ultimately to oxygen and conserving the released energy in the form of a proton gradient over a membrane (inner mitochondrial membrane in eukaryotes). Thus, oxygen is reduced to water and the original electron acceptors NAD and quinone are regenerated. This is why humans breathe in oxygen and breathe out carbon dioxide. The energy released from transferring the electrons from high-energy states in NADH and quinol is conserved first as proton gradient and converted to ATP via ATP synthase. This generates an additional "28" molecules of ATP (24 from the 8 NADH + 4 from the 2 quinols), totaling to 32 molecules of ATP conserved per degraded glucose (two from glycolysis + two from the citrate cycle). It is clear that using oxygen to completely oxidize glucose provides an organism with far more energy than any oxygen-independent metabolic feature, and this is thought to be the reason why complex life appeared only after Earth's atmosphere accumulated large amounts of oxygen.
Light-independent reactions
Photosynthesis occurs in two stages in a cell. In the first stage, light-dependent reactions capture the energy of light and use it to make the energy-storage and transport molecules ATP and NADPH. The Calvin cycle uses the energy from short-lived electronically excited carriers to convert carbon dioxide and water into organic compounds that can be used by the organism (and by animals that feed on it). This set of reactions is also called "carbon fixation". The key enzyme of the cycle is called RuBisCO. In the following biochemical equations, the chemical species (phosphates and carboxylic acids) exist in equilibria among their various ionized states as governed by the pH.
Lichens and nitrogen cycling
Earth's mantle contains non-atmospheric nitrogen in the form of rocks and in the soil. Weathering of the rocks and stone are normally caused by physical, chemical and biological processes. Plants cannot absorb nitrogen from rocks however, fungi can. Fungi within lichens can extract nutrients from mineral surfaces by secreting organic acids. The organic acids (e.g. phenolic acids) are important in solubilizing nutrients from inorganic substrates. A study was conducted to test rock phosphate solubilization by lichen-forming fungi. Bacteria that were attached to biotic or abiotic surfaces stimulate exopolysaccharide synthesis. While lichens have the ability to absorb nitrogen from rock, this only accounts for a small portion of the nitrogen cycle compared to the conversion of atmospheric nitrogen as it is more easily available.
Citric acid cycle
"Acetyl-CoA", on the other hand, derived from pyruvate oxidation, or from the beta-oxidation of fatty acids, is the only fuel to enter the citric acid cycle. With each turn of the cycle one molecule of "acetyl-CoA" is consumed for every molecule of "oxaloacetate" present in the mitochondrial matrix, and is never regenerated. It is the oxidation of the acetate portion of "acetyl-CoA" that produces CO and water, with the energy thus released captured in the form of ATP. The three steps of beta-oxidation resemble the steps that occur in the production of oxaloacetate from succinate in the TCA cycle. Acyl-CoA is oxidized to trans-Enoyl-CoA while FAD is reduced to FADH, which is similar to the oxidation of succinate to fumarate. Following, trans-Enoyl-CoA is hydrated across the double bond to beta-hydroxyacyl-CoA, just like fumarate is hydrated to malate. Lastly, beta-hydroxyacyl-CoA is oxidized to beta-ketoacyl-CoA while NAD+ is reduced to NADH, which follows the same process as the oxidation of malate to oxaloacetate.
Nutrient cycling in the Columbia River Basin
Nitrogen is added to rivers through many natural processes, such as the decomposition of leaf litter and organic matter. Nitrogen gas is the most abundant molecule in earth's atmosphere, comprising about 78 percent of the total composition of air, however not typically a large source of nitrogen to the river. This form of nitrogen, dinitrogen gas (N2), is inert and biologically unavailable to most living organisms. However, some bacteria and archaea can utilize nitrogen fixation to convert dinitrogen into ammonia or other compounds accessible to organisms.
Hydrothermal vent microbial communities
Refer to Nitrogen Cycle
Nitrifying bacteria
Nitrification in nature is a two-step oxidation process of ammonium (NH) or ammonia (NH) to nitrate (NO) catalyzed by two ubiquitous bacterial groups. The first reaction is oxidation of ammonium to nitrite by ammonia oxidizing bacteria (AOB) represented by the "Nitrosomonas" genus. The second reaction is oxidation of nitrite (NO) to nitrate by nitrite-oxidizing bacteria (NOB), represented by the "Nitrobacter" genus.
Ecosystem
When plant tissues are shed or are eaten, the nitrogen in those tissues becomes available to animals and microbes. Microbial decomposition releases nitrogen compounds from dead organic matter in the soil, where plants, fungi, and bacteria compete for it. Some soil bacteria use organic nitrogen-containing compounds as a source of carbon, and release ammonium ions into the soil. This process is known as nitrogen mineralization. Others convert ammonium to nitrite and nitrate ions, a process known as nitrification. Nitric oxide and nitrous oxide are also produced during nitrification. Under nitrogen-rich and oxygen-poor conditions, nitrates and nitrites are converted to nitrogen gas, a process known as denitrification.
Nitrogen cycle
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 (NH), a process called ammonification or mineralization. Enzymes involved are:
Malate synthase
The citric acid cycle (also known as the tricarboxylic acid cycle or the Krebs cycle) is used by aerobic organisms to produce energy via the oxidation of acetyl-CoA, which is derived from pyruvate (a product of glycolysis). The citric acid cycle accepts acetyl-CoA and metabolizes it to form carbon dioxide. A related cycle, called the glyoxylate cycle, is found in many bacteria and plants. In plants, the glyoxylate cycle takes place in glyoxysomes. In this cycle, isocitrate lyase and malate synthase skip over the decarboxylation steps of the citric acid cycle. In other words, malate synthase works together with isocitrate lyase in the glyoxylate cycle to bypass two oxidative steps of Krebs cycle and permit carbon incorporation from acetate or fatty acids in many microorganisms. Together, these two enzymes serve to produce succinate (which exits the cycle to be used for synthesis of sugars) and malate (which remains in the glyoxylate cycle). During this process, acetyl-CoA and water are used as substrates. As a result, the cell does not lose 2 molecules of carbon dioxide as it does in the Krebs cycle. The glyoxylate cycle, facilitated by malate synthase and isocitrate lyase, allows plants and bacteria to subsist on acetyl-CoA or other two carbon compounds. For example, "Euglena gracilis", a single-celled eukaryotic alga, consumes ethanol to form acetyl-CoA and subsequently, carbohydrates. Within germinating plants, the glyoxylate cycle allows the conversion of reserve lipids into carbohydrates within glyoxysomes.
Citric acid cycle
The citric acid cycle (CAC) – also known as the" TCA cycle (tricarboxylic acid cycle) " or the" Krebs cycle "– is a series of chemical reactions used by all aerobic organisms to release stored energy through the oxidation of acetyl-CoA derived from carbohydrates, fats, and proteins, into adenosine triphosphate (ATP) and carbon dioxide. In addition, the cycle provides precursors of certain amino acids, as well as the reducing agent NADH, that are used in numerous other reactions. Its central importance to many biochemical pathways suggests that it was one of the earliest established components of cellular metabolism and may have originated abiogenically. Even though it is branded as a 'cycle', it is not necessary for metabolites to follow only one specific route; at least three segments of the citric acid cycle have been recognized.
Nitrobacter vulgaris
Nitrobacter vulgaris is a rod-shaped, Gram-negative, and a chemoautotrophic bacterium. It plays an important role in the nitrogen cycle by oxidizing nitrite into nitrate in soil. It cannot tolerate highly alkaline (NH+) conditions.
Hydrothermal vent microbial communities
The study of the Nitrogen Cycle in hydrothermal vent microbial communities still requires more comprehensive research. However, isotope data suggests that microorganism influence dissolved inorganic nitrogen quantities and compositions and all pathways of the nitrogen cycle are likely to be found at hydrothermal vents. Biological nitrogen fixation is important to provide some of the biologically available nitrogen to the nitrogen cycle especially at unsedimented hydrothermal vents. Nitrogen fixation is done by many different microbes including methanogen in the orders "Methanomicrobiales", "Methanococcales", and "Methanobacteriales""." Thermophilic microbes have been found to be able to fix nitrogen at higher temperatures such as 92°C. Nitrogen fixation may be especially prevalent in microbial mats and particulate material where biologically available levels of nitrogen are low, due to high microbe density and anaerobic environment allows the function of nitrogenase, a nitrogen fixing enzyme. Evidence have also been detected of assimilation, nitrification, denitrification, anamox, mineralization and dissimilatory nitrate reduction to ammonium. For example, sulfur oxidizing bacteria like "Begiatoa" species, perform denitrification and reduces nitrate to oxidize HS. Nitrate assimilation is done by symbiotic species of "Riftia pachyptil"a tubeworm
Cattle urine patches
Denitrification is the process that produces the most nitrous oxide. Denitrification involves the reduction of nitrites and nitrates produced during nitrification into nitrous oxide by denitrifying bacteria. Nitrous oxide is subsequently reduced to dinitrogen, the key product of the nitrogen cycle. Nitrous oxide is merely a free obligatory intermediate and is not a major product. Different strains of denitrifying bacteria utilize unique pathways in order to perform denitrification. While these pathways differ from each other, the substrates and products of this process remain the same. Below are two proposed schemes carried out by common denitrifying bacteria:
Denitrifying bacteria
The process of denitrification can lower the fertility of soil as nitrogen, a growth-limiting factor, is removed from the soil and lost to the atmosphere. This loss of nitrogen to the atmosphere can eventually be regained via introduced nutrients, as part of the nitrogen cycle. Some nitrogen may also be fixated by species of nitrifying bacteria and the cyanobacteria. Another important environmental issue concerning denitrification is the fact that the process tends to produce large amounts of by-products. Examples of by-products are nitric oxide (NO) and nitrous oxide (NO). NO is an ozone depleting species and NO is a potent greenhouse gas which can contribute to global warming.
Nitrogen fixation
Cyanobacteria inhabit nearly all illuminated environments on Earth and play key roles in the carbon and nitrogen cycle of the biosphere. In general, cyanobacteria can use various inorganic and organic sources of combined nitrogen, like nitrate, nitrite, ammonium, urea, or some amino acids. Several cyanobacterial strains are also capable of diazotrophic growth, an ability that may have been present in their last common ancestor in the Archean eon. Nitrogen fixation by cyanobacteria in coral reefs can fix twice as much nitrogen as on land—around 1.8 kg of nitrogen is fixed per hectare per day (around 660 kg/ha/year). The colonial marine cyanobacterium "Trichodesmium" is thought to fix nitrogen on such a scale that it accounts for almost half of the nitrogen fixation in marine systems globally.