Instruct: Given a question, retrieve relevant documents that answer the question.
Query: What's the first step of the 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,[1] 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.
Archaea carry out many steps in the nitrogen cycle. This includes both reactions that remove nitrogen from ecosystems (such as nitrate-based respiration and denitrification) as well as processes that introduce nitrogen (such as nitrate assimilation and nitrogen fixation).
Researchers recently discovered archaeal involvement in ammonia oxidation reactions. These reactions are particularly important in the oceans. The archaea also appear crucial for ammonia oxidation in soils. They produce nitrite, which other microbes then oxidize to nitrate. Plants and other organisms consume the latter.
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).
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.
A variety of nutrient cycles is important in the aquarium. Dissolved oxygen enters at the surface water-air interface through agitation or what would be observed as waves in a natural environment, and Carbon dioxide escapes into the air. The phosphate cycle is an important, although often overlooked, nutrient cycle. Sulfur, iron, and micronutrients enter the system as food and exit as waste. Appropriate handling of the nitrogen cycle, along with a balanced food supply and consideration of biological loading, is usually enough to keep these nutrient cycles in adequate equilibrium.
The "ARG1" gene provides instructions for making an enzyme called arginase, this enzyme controls the last steps of the urea cycle, which produces urea by extracting nitrogen from arginine. In people with arginase deficiency, arginase is missing, and arginine is not broken down properly. consequently, urea cannot be produced and excess nitrogen accumulates in the blood in the form of ammonia. Ammonia and arginine are thought to cause neurological problems and other symptoms of arginase deficiency.
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
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.
During the first half of the first cycle the internal compressor forces this air through a system of chemical filters known as a molecular sieve. This filter is made up of silicate granules called zeolite which attract (via adsorption) nitrogen molecules onto their surfaces more strongly than they attract oxygen molecules – this takes the nitrogen out of the air and concentrates the oxygen. When the desired purity is reached and the first cylinder reaches roughly 20 psi the oxygen and small amounts of other gases are released into the pressure equalizing reservoir. As the pressure in the first cylinder drops the nitrogen is desorbed, the valve is closed, and the gas is vented into the ambient air. Most of the oxygen produced is delivered to the patient; part is fed back into the sieves (at greatly reduced pressure) to flush away left over nitrogen, and prepare the zeolite for the next cycle. The atmosphere contains around 21% oxygen and 78% nitrogen; the 1% remainder is a mixture of other gases which pass through this process. A POC system is functionally a nitrogen scrubber capable of consistently producing medical-grade oxygen of up to 90%.
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.
Nitrogen cycling
Biological soil crust contributions to the nitrogen cycle varies by crust composition because only cyanobacteria and cyanolichens fix nitrogen. Nitrogen fixation requires energy from photosynthesis products, and thus increase with temperature given sufficient moisture. Nitrogen fixed by crusts has been shown to leak into surrounding substrate and can be taken up by plants, bacteria, and fungi. 
Nitrogen fixation has been recorded at rates of 0.7–100 kg/ha*year, from hot deserts in Australia to cold deserts. Estimates of total biological nitrogen fixation are ~ 49 Tg/year (27-99 Tg/year).
In the marine environment, nitrogen is often the limiting nutrient, so the nitrogen cycle in the ocean is of particular interest. The nitrification step of the cycle is of particular interest in the ocean because it creates nitrate, the primary form of nitrogen responsible for "new" production. Furthermore, as the ocean becomes enriched in anthropogenic CO, the resulting decrease in pH could lead to decreasing rates of nitrification. Nitrification could potentially become a "bottleneck" in the 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.[2][3]
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.
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.
Nitrogen has two stable isotopes: N and N. The first is much more common, making up 99.634% of natural nitrogen, and the second (which is slightly heavier) makes up the remaining 0.366%. This leads to an atomic weight of around 14.007 u. Both of these stable isotopes are produced in the CNO cycle in stars, but N is more common as its neutron capture is the rate-limiting step. N is one of the five stable odd–odd nuclides (a nuclide having an odd number of protons and neutrons); the other four are H, Li, B, and Ta.
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.
(DS-PSA, sometimes referred to as Dual Step PSA).
With this variation of PSA developed for use in Laboratory Nitrogen Generators generation of nitrogen gas is divided into two steps: in the first step, the compressed air is forced to pass through a carbon molecular sieve to produce nitrogen at a purity of approximately 98%; in the second step this nitrogen is forced to pass into a second carbon molecular sieve and the nitrogen gas reaches a final purity up to 99.999%. The purge gas from the second step is recycled and partially used as feed gas in the first step.
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.
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.
Nitrification is the biological oxidation of ammonia or ammonium to nitrite followed by the oxidation of the nitrite to nitrate. The transformation of ammonia to nitrite is usually the rate limiting step of nitrification. Nitrification is an important step in the nitrogen cycle in soil. Nitrification is an aerobic process performed by small groups of autotrophic bacteria and archaea. This process was discovered by the Russian microbiologist Sergei Winogradsky.
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.
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.
The nitrogen cycle is an important process in the ocean as well. While the overall cycle is similar, there are different players[18] 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.[19] Without supplies of fixed nitrogen entering the marine cycle, the fixed nitrogen would be used up in about 2000 years.[20] 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.[21] 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.[22] 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.
Type I citrullinemia is the most common form of the disorder, affecting about one in 57,000 births worldwide. Mutations in the "ASS" gene cause type I citrullinemia. The enzyme made by this gene, argininosuccinate synthetase (), is responsible for one step of the urea cycle. Mutations in the "ASS" gene reduce the activity of the enzyme, which disrupts the urea cycle and prevents the body from processing nitrogen effectively. Excess nitrogen, in the form of ammonia, and other byproducts of the urea cycle, accumulate in the bloodstream, leading to the characteristic features of type I citrullinemia.