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The nitrogen cycle, irreducible interdependence, and the origin of life

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The nitrogen cycle, irreducible interdependence, and the origin of life

http://reasonandscience.catsboard.com/t1562-the-nitrogen-cycle-irreducible-interdependence-and-the-origin-of-life

The nitrogen cycle, incorporating a broad spectrum of unconsciously cooperating species, operates in a coordinated assembly-line manner that is extraordinary and impressive. 3
The biogeochemistry of nitrogen is almost entirely dependent on reduction-oxidation (redox) reactions primarily mediated by microorganisms, and to a lesser extent on long-term recycling through the geosphere. Nitrogen, the fifth most abundant element in our solar system, is essential for the synthesis of nucleic acids and proteins—the two most important polymers of life. The Nitrogen cycle has robust natural feedbacks and controls the nitrogen cycle, and restore balance through microbial processes. . Indeed, the nitrogen requirements for life are enormous; depending on the life form, for every 100 atoms of carbon incorporated into cells, between 2 and
20 atoms of nitrogen follow,     9

Important processes in the nitrogen cycle include

fixation,
ammonification,
nitrification,
denitrification

Without cyanobacteria, and micro-organisms that fix nitrogen - not enough fixed nitrogen is available.
Without fixed nitrogen, no DNA, no amino-acids, no protein can be synthesized.
Without DNA, no amino-acids, protein, or cyanobacteria are possible ( Ligthning storms are irregularly distributed, and the amount of nitrogen fixed is relatively small, and not enough to originate or sustain life )
It is an interdependent system. It cannot have evolved in small steps. All must exist at once.

Furthermore, most, if not all of following 13 enzyme complexes and apo-proteins are used by Bacteria and required for the reactions that permit the Nitrogen cycle:

nas nitrate reductase cytoplasmic, prokaryote-assimilatory 
euk-nr nitrate reductase cytoplasmic, eukaryote-assimilatory 
narG nitrate reductase membrane bound-dissimilatory 
napA nitrate reductase periplasmic-dissimilatory 
nir nitrite reductase, various kinds 
nrf nitrite reductase associated with 
napA norB nitric oxide reductase 
nosZ nitrous oxide reductase 
nif nitrogenase, various kinds 
amo ammonium monooxygenase 
hao hydroxylamine oxidoreductase 
nxr nitrite oxidoreductase 
hh hydrazine hydrolase

If we consider that to make Nitrogenase enzymes alone, 20 genes are required, it becomes clear, what formidable challenge that constitutes towards naturalistic proposals of origins. 






Nitrogen is present in the environment in a wide variety of chemical forms including

organic nitrogen,
ammonium (NH+4),
nitrite (NO−2),
nitrate (NO−3),
nitrous oxide (N2O),
nitric oxide (NO)

or  inorganic nitrogen

gas (N2).

Nitrogen is a basic element in all living things. Yet the chemical bonds of nitrogen gas are so strong that it is not usable until it is “fixed” into a form plants can use. Researchers have identified five major stages, each requiring different organisms with specialized proteins. 7

Biological Nitrogen Fixation. Nitrogen gas (N2) must first be changed into ammonia (NH3). A diversity of bacteria have the proteins necessary to do this. If one bacterial species is not present, another one can pick up the slack. This redundancy, or backup system, is marvelously designed.
Since oxygen hinders this chemical process, fixation needs to take place in an oxygen-less chamber. Plants provide bacteria with little chambers (nodules) in their roots.
A special protein (leghaemoglobin) then carries oxygen away so it will not interfere. Amazingly, the plant and bacteria cooperatively manufacture different parts of this protein. After the plant has fixed enough nitrogen, it communicates to the bacteria and they both stop production.
Nitrification. Ammonia needs to be changed into nitrite (NO2–) and then nitrate (NO3–). This requires a different suite of bacteria and some fungi. In some cases, bacteria can only change ammonia into nitrite, so they “hand it off” to other bacteria to finish the job. This form of nitrogen readily dissolves in water to be transported and used by organisms far away.
Denitrification. A different group of microbes change nitrate back into nitrogen gas (N2) or nitrous oxide (N2O). Without this process, nitrates could accumulate in water or soil, seriously harming the health of the ecosystem.
Assimilation. Nitrates were made in step 2 because plants can easily absorb that chemical. Later it must be changed back to ammonia to make other compounds needed for life, such as amino acids.
Excretion and Decay. A huge clean-up crew of diverse organisms breaks down waste products and recycles the nitrogen.
Just like a factory assembly line, all the workers must be in the right places, at the right time, with the right tools to make the product.1 Systems like the nitrogen cycle appear to be irreducibly complex. For them to work, all the components had to be in place at the same time


Nitrogen is a part of vital organic compounds in microorganisms, such as amino acids, proteins, and DNA. The gaseous form of nitrogen (N2), makes up 78% of the troposphere. One might think this means we always have plenty of nitrogen available, but that's, not the case. Nitrogen in the gaseous form cannot be absorbed and used as a nutrient by plants and animals; it must first be converted by nitrifying bacteria so that it can enter food chains as a part of the nitrogen cycle. During the conversion of nitrogen, cyanobacteria will first convert nitrogen into ammonia and ammonium, during the nitrogen fixation process. Plants can use ammonia as a nitrogen source. After ammonium fixation, the ammonia and ammonium that is formed will be transferred further, during the nitrification process. Aerobic bacteria use oxygen to convert these compounds. Nitrosomonas bacteria first convert nitrogen gas to nitrite (NO2-) and subsequently, Nitrobacter converts nitrite to nitrate (NO3-), a plant nutrient. Plants absorb ammonium and nitrate during the assimilation process, after which they are converted into nitrogen-containing organic molecules, such as amino acids and DNA. Animals cannot absorb nitrates directly. They receive their nutrient supplies by consuming plants or plant-consuming animals. When nitrogen nutrients have served their purpose in plants and animals, specialized decomposing bacteria will start a process called ammonification, to convert them back into ammonia and water-soluble ammonium salts. After the nutrients are converted back into ammonia, anaerobic bacteria will convert them back into nitrogen gas, during a process called denitrification. Finally, nitrogen is released into the atmosphere again. The whole process starts over after release.

The nitrogen cycle, incorporating a broad spectrum of unconsciously cooperating species, operates in a coordinated assembly-line manner that is extraordinary and impressive. 3 Nitrogen is a part of vital organic compounds in microorganisms, such as amino acids, proteins, and DNA. The gaseous form of nitrogen (N2), makes up 78% of the troposphere. One might think this means we always have plenty of nitrogen available, but unfortunately, it does not work that way. Nitrogen in the gaseous form cannot be absorbed and used as a nutrient by plants and animals; it must first be converted by nitrifying bacteria so that it can enter food chains as a part of the nitrogen cycle.
Could the oxygen and nitrogen cycle be explained by naturalistic means? The reason for the abundance of oxygen in the atmosphere is the presence of a very large number of organisms which produce oxygen as a byproduct of their metabolism. Cyanobacteria or blue-green algae became the first microbes to produce oxygen by photosynthesis. They are one of the oldest bacteria that live on earth, said to exist perhaps as long as 3.5 billion years. And their capabilities are nothing more than astounding. No cyanobacteria, no oxygen, no higher life forms. These cyanobacteria have incredibly sophisticated enzyme proteins and metabolic pathways, like the electron transport chains, ATP synthase motors, circadian clock, the photosynthetic light reactions, carbon concentration mechanism, and transcriptional regulation, they produce bound nitrogen through nitrogenase, a highly sophisticated mechanism to bind nitrogen, used as a nutrient for plant and animal growth.

The Nitrogen cycle is a lot more complex than the carbon cycle. Nitrogen is a very important element. It makes up almost 80% of our atmosphere, and it is an important component of proteins and DNA, both of which are the building blocks of animals and plants. Therefore without nitrogen, we would lose one of the most important elements on this planet, along with oxygen, hydrogen, and carbon. There are a number of stages to the nitrogen cycle, which involve breaking down and building up nitrogen and it’s various compounds.There is no real starting point for the nitrogen cycle. It is an endless cycle. Potential gaps in the system cannot be reasonably bypassed by inorganic nature alone. It must have a degree of specificity that in all probability could not have been produced by chance. A given function or step in the system may be found in several different unrelated organisms. The removal of any one of the individual biological steps will resort to the loss of function of the system. The data suggest that the nitrogen cycle may be irreducibly interdependent based on the above criteria. No proposed neo-Darwinian mechanisms can explain the origin of such a system.The ultimate source of nitrogen for the biosynthesis of amino acids is atmospheric nitrogen (N2), a nearly inert gas. Its needed by all living things to build proteins and nucleic acids.

This is one of the hardest chemical bonds of all to break. So, how can nitrogen be brought out of its tremendous reserves in the atmosphere and into a state where it can be used by living things? To be metabolically useful, atmospheric nitrogen must be reduced. It must be converted to a useful form. Without "fixed" nitrogen, plants, and therefore animals, could not exist as we know them. This process, known as nitrogen fixation, occurs through lightening, but most in certain types of bacteria, namely cyanobacteria. Even though nitrogen is one of the most prominent chemical elements in living systems, N2 is almost unreactive (and very stable) because of its triple bond (N≡N). This bond is extremely difficult to break because the three chemical bonds need to be separated and bonded to different compounds. Nitrogenase is the only family of enzymes capable of breaking this bond (i.e., it carries out nitrogen fixation). Nitrogenase is a very complex enzyme system. Nitrogenase genes are distributed throughout the prokaryotic kingdom, including representatives of the Archaea as well as the Eubacteria and Cyanobacteria.With assistance from an energy source (ATP) and a powerful and specific complementary reducing agent (ferredoxin), nitrogen molecules are bound and cleaved with surgical precision.

In this way, a ‘molecular sledgehammer’ is applied to the NN bond, and a single nitrogen molecule yields two molecules of ammonia. The ammonia then ascends the ‘food chain’, and is used as amino groups in protein synthesis for plants and animals. This is a very tiny mechanism but multiplied on a large scale it is of critical importance in allowing plant growth and food production on our planet to continue. ‘Nature is really good at it (nitrogen-splitting), so good in fact that we've had difficulty in copying chemically the essence of what bacteria do so well.’ If one merely substitutes the name of God for the word 'nature', the real picture emerges.These proteins use a collection of metal ions as the electron carriers that are responsible for the reduction of N2 to NH3. All organisms can then use this reduced nitrogen (NH3) to make amino acids. In humans, reduced nitrogen enters the physiological system in dietary sources containing amino acids. One thing is certain—that matter obeying existing laws of chemistry could not have created, on its own, such a masterpiece of chemical engineering.Without cyanobacteria - no fixed nitrogen is available.Without fixed nitrogen, no DNA, no amino-acids, no protein can be synthesized. Without DNA, no amino-acids, protein, or cyanobacteria are possible. So that's an interdependent system.

Beside cyanobacteria, some kinds of microbes found within the roots of legume plants, capable of converting nitrogen gas into molecules that other species can use. Nitrogen fixation, as the process is called, involves breaking the powerful chemical bonds that hold nitrogen atoms in pairs in the atmosphere and using the resulting single nitrogen atoms to help create molecules such as ammonia, which is a building block of many complex organic molecules, such as proteins, DNA and RNA. Stüeken developed a model of abiotic nitrogen processes that could have played a role in early Earth. The results showed that such abiotic processes alone could not explain the nitrogen levels seen in the Isua rocks. 

Nitrogen is a part of vital organic compounds in microorganisms, such as amino acids, proteins, and DNA. During the conversion of nitrogen, cyanobacteria will first convert nitrogen from the atmosphere into ammonia and ammonium through nitrogenase, during the nitrogen fixation process. After ammonium fixation, the ammonia and ammonium that is formed convert it through further reduction to nitrite and nitrate into their cellular material, and on dying, decompose and make nitrogen available to the soil,  which serves plants for nutrition, after which they are converted into nitrogen-containing organic molecules, such as amino acids and DNA. Animals cannot absorb nitrates directly. They receive their nutrient supplies by consuming plants or plant-consuming animals.

So, resuming:  Without cyanobacteria - no fixed nitrogen is available. Without fixed nitrogen, no DNA, no amino-acids, no protein can be synthesized. Without DNA, no amino-acids, protein, or cyanobacteria are possible. So there you have an interdependent cycle, with no beginning. But, wait: there is more: cyanobacteria are facultative anaerobes - meaning that they can respire either aerobically or anaerobically. The complexity of two respiratory cycles is very high: the Krebs cycle alone requiring about 12 enzymes, and the anaerobic requiring somewhat fewer, say 8.  So in order for the cyanobacteria to survive, about 40 enzymes are already involved - none of which can be made without fixed nitrogen. So here we have a chicken-egg problem par excellence, which came first..... ??

Lighting is another source, but since it's supposed that Photosynthesis had not evolved at the stage of a common ancestor, there was a reduced atmosphere without oxygen. Today, large amounts of nitrate are made when oxygen and nitrogen combine during lightning storms, but this could not happen in the early oxygen-deficient atmosphere.... The scarcity of ammonia and nitrate posed a major problem to life. If there was a reduced atmosphere ( which btw. there is no scientific evidence for, rather the opposite is the case ) then there would be no ozone layer, and the ultraviolet radiation would penetrate the atmosphere and would destroy the amino acids as soon as they were formed. If the Cyanobacteria, however, would overcome that problem ( its supposed the bacterias in the early earth lived in the water, but that would draw other unsurmountable problems ), and evolve photosynthesis, they would have to evolve at the same time protective enzymes that prevented them oxygen to damage their DNA through hydroxyl radicals. So what evolutionary advantage would there be they to do this?

To avoid their DNA getting wrecked by a hydroxyl radical that naturally occurs in the production of oxygen, the cyanobacteria would have had to evolve protective enzymes. But how could natural selection have led the cyanobacteria to evolve these enzymes if the need for them didn’t even exist yet?  The explanations are fantasious at best.  But even if let's say that enough nitrogen would be available at the primordial earth, that far from explains the information encoded in Fifteen nitrogen fixation or nitrogen fixation-related genes, including the structural genes for nitrogenase,nifHDK, which are clustered together as follows:nifB-fdxN-nifS-nifU-nifH-nifD- nifK-nifE-nifN-nifX-orf2-nifW-hesA-hesB-fdxH.These genes are organized in at least six transcriptional units:nifB-fdxN-nifS-nifU, nifHDK, nifEN,nifX-orf2, nifW-hesA-hesB, and fdxH.......  2
Atmospheric nitrogen fixation could not have been part of a bootstrap mechanism by which life originated because its product, nitrate, is not directly biologically useful. In addition, an abiotic mechanism to convert nitrate to biologically useful forms like ammonia is unavailable to bridge the gap between the products of atmospheric and biological fixation. There are no shared enzymes between biological nitrogen fixation and assimilation, even though their end product — ammonia — is the same. As a conse- quence, one cannot be explained as a relatively simple adaptation of the other to a different task.

Most arguments for evolution of the nitrogen cycle allow for the existence of life before a complete nitrogen cycle existed, but some source of nitrogen in the right form is required for life to exist. This is a major problem.
Nitrogen cycle
Nitrogen is a part of vital organic compounds in microorganisms, such as amino acids, proteins, and DNA. The gaseous form of nitrogen (N2), makes up 78% of the troposphere. One might think this means we always have plenty of nitrogen available, but that's, not the case. Nitrogen in the gaseous form cannot be absorbed and used as a nutrient by plants and animals; it must first be converted by nitrifying bacteria so that it can enter food chains as a part of the nitrogen cycle. During the conversion of nitrogen, cyanobacteria will first convert nitrogen into ammonia and ammonium, during the nitrogen fixation process. Plants can use ammonia as a nitrogen source. After ammonium fixation, the ammonia and ammonium that is formed will be transferred further, during the nitrification process. Aerobic bacteria use oxygen to convert these compounds. Nitrosomonas bacteria first convert nitrogen gas to nitrite (NO2-) and subsequently, Nitrobacter converts nitrite to nitrate (NO3-), a plant nutrient. Plants absorb ammonium and nitrate during the assimilation process, after which they are converted into nitrogen-containing organic molecules, such as amino acids and DNA. Animals cannot absorb nitrates directly. They receive their nutrient supplies by consuming plants or plant-consuming animals. When nitrogen nutrients have served their purpose in plants and animals, specialized decomposing bacteria will start a process called ammonification, to convert them back into ammonia and water-soluble ammonium salts. After the nutrients are converted back into ammonia, anaerobic bacteria will convert them back into nitrogen gas, during a process called denitrification. Finally, nitrogen is released into the atmosphere again. The whole process starts over after release.

Nitrogen as a limiting factor

Although the nitrogen conversion processes often occur and large quantities of plant nutrients are produced, nitrogen is often a limiting factor for plant growth. Water flowing across the soil causes this error. Nitrogen nutrients are water-soluble and as a result, they have easily drained away, so that they are no longer available for plants.

The annamox reaction
In 1999 researchers at the Gist-Brocades in Delft, The Netherlands, discovered a new reaction to be added to the nitrogen cycle; the so-called anammox reaction. This is now found to occur in the Black Sea, as well. The reaction implies conversion of nitrite and ammonium to pure nitrogen gas (N2), which then escapes to the atmosphere. The reaction mechanism is triggered by a newly discovered bacterium, called Brocadia anammoxidans. This appears to be a compartmentalized bacterium; within the cell membrane, two compartments can be found which are also surrounded by a membrane, a very rare phenomenon. Intermediate products of the reaction included hydroxylamine, and toxic hydrazine compounds. The bacterial membranes were found to consists of badly permeable membranes, which are thought to function as a barrier for hydrazines produced within the cell. This discovery has major consequences, as it alters the entire contribution of oceans to the nitrogen balance. 

The nitrogen cycle, incorporating a broad spectrum of unconsciously cooperating species, operates in a coordinated assembly-line manner that is extraordinary and impressive. 3

A relatively small, but not insignificant, amount of nitrogen is fixed by lightning passing through the atmosphere.

The function of the N cycle is to regulate concentrations of various nitrogen-containing molecules in the environment in such a way that life can thrive. 5 For those accustomed to thinking of the N cycle primarily in terms of nitrogen fixation for production of amino acids and other nitrogen-containing molecules, this may seem counterintuitive. However, when viewed from a global perspective this is precisely what the N cycle  achieves. In nature it works to keep reactive oxides of nitrogen, as well as chemically active reduced nitrogen compounds, particularly ammonia, at levels which allow life to exist while at the same time ensuring availability of reduced nitrogen when it is required for growth. In essence, the N cycle functions to ensure that the vast majority of nitrogen atoms are in the form of the inert gas N , while most of the remaining nitrogen is found in living things or their waste products. The cycle acts as a vital buffer to changes in nitrogen-containing molecules in the environment, while at the same time ensuring availability of reduced nitrogen for biological purposes. Some variation among different biomes on Earth is evident and some deviation from the current relative abundances of nitrogen in various chemical states may have occurred in the past, but life requires limits to the concentrations of various forms of nitrogen in the environment. It is the biological N cycle that prevents these limits from being exceeded under most circumstances. Because the ecological function of the N cycle is known, it meets Behe’s first requirement, that the function be known. Figure 1 gives a typical depiction of the N cycle.



This paper will examine two issues:
1. Whether some parts of the cycle are indispensable. By this we mean a part is necessary for the cycle to operate and lacking that step, the N cycle would not achieve its overall function.
2. Whether some reasonable step-by-small-step unguided natural process could be expected to produce the N cycle as we find it. In other words, can parts of the cycle be bridged by known inorganic processes in such a way that the cycle could be assembled incrementally as biological mechanisms accrued until the cycle became essentially a completely biological rather than abiotic process? Or are there necessary steps that are not practically bridgeable by inorganic processes?

In short, are the various stages of the nitrogen cycle indispensable to its function and do they represent functions that nature acting alone could not reasonably be expected to bridge? 

FIVE STAGES OF THE NITROGEN CYCLE
The nitrogen cycle, sometimes said to be a web, consists of five stages: 
The first stage, Nitrogen Fixation, is the process by which atmospheric nitrogen is reduced to ammonia. This stage is particularly important and is made up of multiple sub-stages. The second stage, Nitrification, first converts ammonia to nitrite and then to nitrate. Another stage, Denitrification, changes nitrate back to either atmospheric dinitrogen or nitrous oxide, another gas. The fourth stage, Assimilation, converts nitrates back to nitrites and finally to ammonia. This ammonia is used to produce amino acids via amination and these amino acids are used to produce biological compounds such as proteins, or serve as substrates for production of other nitrogen-containing molecules including nucleic acids. The final stage in the cycle is Decay or ammonification (also known as mineralization), in which nitrogen from wastes and decaying organic nitrogenous residues are converted back to ammonia and then recycled. This process is usually slow, with most nitrogenous wastes remaining in soil as larger organic molecules (amino acids, for example, as well as protein fragments) which are slowly converted to ammonia. These amino acids and protein residues may even be directly absorbed by plants.

Each stage in the nitrogen cycle involves specialized enzymes housed in widely diverse organisms. The nitrogen cycle, incorporating a broad spectrum of unconsciously cooperating species, operates in a coordinated assembly-line manner that is extraordinary and impressive. Whether it contains steps that are both indispensable and unbridgeable will be examined in the following sections.

NITROGEN FIXATION — OVERVIEW

Conversion of nitrogen into nitrates and nitrites through atmospheric, industrial and biological processes is called as nitrogen fixation. Atmospheric nitrogen must be processed, or "fixed", in a usable form to be taken up by plants. Some nitrogen is fixed by lightning strikes, but most fixation is done by free-living or symbiotic bacteria. These bacteria have the nitrogenase enzyme that combines gaseous nitrogen with hydrogen to produce ammonia, which is converted by the bacteria into other organic compounds. Most biological nitrogen fixation occurs by the activity of Mo-nitrogenase, found in a wide variety of bacteria and some Archaea. Mo-nitrogenase is a complex two-component enzyme that has multiple metal-containing prosthetic groups

Nitrogen fixation occurs in one of three different ways, two of them natural: 

1) Atmospheric (Lightning) Fixation
2) Biological Fixation, and 
3) Industrial Fixation (Haber Process) 

In this paper, biological and atmospheric nitrogen fixation will be discussed, but industrial fixation will only be mentioned where it contributes to understanding the impact of unbalancing the natural nitrogen cycle.
Biological nitrogen fixation could be the subject of an entire design argument by itself, but for the purposes of this discussion, the most important consideration is the final product: ammonia (NH ). Within cells, this reactive chemical must be handled with some degree of finesse if it is to react with the appropriate substrate and form an amino acid. It is these amino acid molecules which serve as nitrogen donors during synthesis of other nitrogen-containing organic molecules, like more complex amino acids and the nitrogen-containing bases of nucleotides.

ATMOSPHERIC NITROGEN FIXATION
A relatively small, but not insignificant, amount of nitrogen is fixed by lightning passing through the atmosphere. Other phenomena, including thermal shock from meteorites striking the atmosphere, may have a similar effect. Thermal shock splits atmospheric dinitrogen molecules (N ), allowing the separated atoms to combine with oxygen, producing highly reactive nitrogen oxides which ultimately combine with water to form nitric acid (HNO ). Nitric acid is converted to nitrate in soils. Nitrates derived from atmospheric fixation mix with nitrates of biological origin and are assimilated by microbes or plants or returned to the atmosphere as dinitrogen via denitrification.

DOES ATMOSPHERIC NITROGEN FIXATION BRIDGE BIOLOGICAL FIXATION?
Because nitrates can be produced in the absence of biological nitrogen fixation, it might be tempting to suggest that this biological step in the nitrogen cycle is dispensable. In real life this is not the case because of three factors: 

1) Nitrates from atmospheric fixation must be reduced to ammonia if they are to be biologically useful. 
2) Electric storms and other causes of atmospheric fixation are more common in some places than others so nitrate produced by this means is irregularly distributed. 
3) The amount of nitrogen fixed by thermal shock is comparatively small, so this method cannot be considered either consistent or sufficient in itself to sustain life as it is now.

One author has estimated (perhaps generously) that atmospheric nitrogen fixation produces as much as 10% of the total nitrogen fixed in nature. Another reference suggests that lightning fixes an estimated 3 to 5 Tg8 annually, while annual bacterial fixation accounts for 90 to 130 Tg. Thus 10 % appears to be at the high end of estimates and the real percentage could very well be lower. A complicating factor is the contribution of agriculture, particularly intensive cultivation of legumes and rice, which has, over the past century, significantly increased biological nitrogen fixation on the continents. In the past, the contribution of atmospheric nitrogen fixation to total nitrogen fixation may have been higher as a percentage of the total, but the actual amount of nitrogen fixed in this way would be expected to remain relatively constant.

Atmospheric nitrogen fixation could not have been part of a bootstrap mechanism by which life originated because of its product, nitrate, is not directly biologically useful. In addition, an abiotic mechanism to convert nitrate to biologically useful forms like ammonia is unavailable to bridge the gap between the products of atmospheric and biological fixation. There are no shared enzymes between biological nitrogen fixation and assimilation, even though their end product — ammonia — is the same. As a consequence, one cannot be explained as a relatively simple adaptation of the other to a different task.

In organisms living today, biological nitrogen fixation requires photosynthesis or chemosynthesis to provide both energy and carbon backbones for amination to produce amino acids. Of particular significance, both photosynthesis and chemosynthesis require nitrogen-containing proteins; thus, in these organisms, a chicken-or-egg conundrum exists which atmospheric nitrogen fixation does not solve (Figure 2).



The nitrogen cycle requiers atmospheric nitrogen, an energy source (typically photosynthesis), and enzymatic facilitation. Photosynthesis also provides carbon skeletons for amino acids which are aminated using nitrogen fixed in the nitrogen cycle. These amino acids serve in turn as building blocks of the enzymes and other proteins involved in both photosynthesis and the nitrogen cycle. In addition, amino acids provide the nitrogen found in nucleotides which are central to energy metabolism and serve as the building blocks of both DNA and RNA. Ultimately, protein enzymes mediate the manufacture of all biological macromolecules. Thus, all the vital processes found in living things are interdependently linked via the nitrogen cycle.

In addition, during assimilation the reducing power may be provided by photorespiration; thus a link exists between photosynthesis and both assimilation and nitrogen fixation.
How nitrates could have been abiotically modified to form biologically useful compounds is unclear. Even if the energy needed for nitrogen fixation or assimilation did not come from photosynthesis or chemosynthesis, some energy source is still required. In addition, enzymes that mediate the necessary reactions are also required. It may be possible to build a bypass around photosynthesis, but it is not clear that this would provide a more plausibly evolved pathway. No matter what the mechanism, complex protein catalysts appear to be required and production of these requires the ultimate products of nitrogen fixation — amino acids and nucleotides. A further impediment to biological usefulness of atmospheric nitrogen fixation stems from the fact that nitrates form by reacting with oxygen. Nitrogen can exist in positive oxidation states between 1 and 510 (Figure 1). In general, nitrogen oxides are unstable and break down to form nitric oxide (NO) or nitrogen dioxide (NO ). Both of these oxides of nitrogen are highly reactive free radicals. NO constitutes the brown photochemical smog found in some cities, which serves as a catalyst in producing the potent oxidizer ozone (O ). Ozone oxidizes organic molecules and, if present in the low concentrations sufficient to destroy abiotically formed organic molecules, would hamper accumulation of the organic soup thought to be necessary for the “natural” origin of life. Therefore, the formation of nitrate as a result of atmospheric nitrogen fixation notwithstanding, life itself appears unlikely to have originated in an oxidizing atmosphere and lightning-induced nitrate production seems improbable as a source of biologically useful nitrogen during alleged evolution of nitrogen fixation systems. 

In an oxidizing atmosphere, life — if it already existed — must have possessed systems to deal with damage caused by toxic byproducts of atmospheric nitrogen fixation, but life is unlikely to have emerged in the first place due to the impact of some of these byproducts.

This may partly explain why, despite significant evidence to the contrary, naturalistic “origin of life” scenarios commonly hinge on reducing primordial atmospheres. Proposed atmospheres commonly contain gases such as ammonia, methane, hydrogen, and water vapor. Research involving atmospheres consisting of various combinations of these gases, but always lacking oxygen, has been shown, when supplied with sufficient energy, to produce a variety of organic molecules including amino acids. Thus, under reducing conditions, early life could freely acquire amino acids without resorting to biological nitrogen fixation. The problem is that, while this scenario might explain why amino acids serve as nitrogen donors in anabolic biochemical pathways, it still does not explain evolution of the nitrogen cycle itself; at best it renders one step in the cycle superfluous while necessitating evolution of other steps to cycle nitrogen out of organic molecules and back into the atmosphere. In any case, the problems of biochemical evolution and the spontaneous generation of life have been so much discussed that there is no need to repeat them.

Most arguments for evolution of the nitrogen cycle allow for the existence of life before a complete nitrogen cycle existed, but some source of nitrogen in the right form is required for life to exist. This is a major problem. If a reducing atmosphere provides the nitrogen-containing building blocks of life, then biological nitrogen fixation becomes unnecessary raising the question of — at least before the switch from a reducing to an oxidizing atmosphere — what selective pressure would “cause” it to evolve. On the other hand, if nitrate is produced via thermal shock in an oxidizing atmosphere, then some unknown abiotic mechanism must have reduced the nitrate to a biologically useful form before the origin of mechanisms of assimilation. In addition, any reduced organic molecules must be protected in some way from O and other free radicals produced as a byproduct of atmospheric fixation. In either scenario, production of life and evolution of biological nitrogen fixation present conundrums that the neo-Darwinian mechanism does not reasonably resolve.

While any number of scenarios may be suggested to overcome these issues, none actually solves the problems using strictly Darwinian principles. Take the following scenario for example: life evolves in a reducing atmosphere which subsequently changes to an oxidizing atmosphere. Under these new circumstances, bacteria among the few organisms that survived the change evolve the ability to use nitrogen in nitrate thus evolving assimilation before biological nitrogen fixation. Life is sustained by atmospheric fixation until biological nitrogen fixation evolves. Problems with this scenario include: 

1) It assumes that assimilation is evolvable and had evolved enough before it was vital to sustain some bacteria that also had the ability to survive an oxidizing atmosphere; 
2) it assumes atmospheric fixation at levels sufficient to sustain life, but not so rapid that nitrate accumulated to the point that it caused problems; 
3) evidence is lacking for a reducing atmosphere; 
4) the concurrent need to develop a means of aminating carbon skeletons to produce amino acids; 
5) the concurrent need to deal with radicals produced as part of the process; 
6) availability of energy resources and reducing power sufficient to allow assimilation to work. 

The most troubling assumption is that any organism adapted to living in a reducing environment could survive the transition to an oxidizing environment. Ultimately scenarios of this kind simply split a single big problem into two big problems for Darwinism to explain; they do not reduce the problem to small steps that unguided nature might reasonably be expected to take via the neo-Darwinian process. In addition, they do not explain biological nitrogen fixation, but instead, invoke a different biological means of obtaining nitrogen without addressing the point of nitrogen fixation.

BIOLOGICAL NITROGEN FIXATION: NITROGEN MADE AVAILABLE IN MANY HABITATS
Biological nitrogen fixation is the main natural method by which nitrogen is made available to living organisms. In natural systems over 90 percent of fixed nitrogen comes from biological activity. The ability to fix nitrogen is restricted to certain microbes. Bacteria (including cyanobacteria) that reduce nitrogen to ammonia (NH ) span a selection of widely disparate genera and lifestyles, examples of which include:

Azotobacter (aerobic),
Klebsiella (facultatively anaerobic),
Rhodo-spirillum (photosynthetic, anaerobic),
Clostridium (free-living/anaerobic),
Nostoc (free-living or symbiotic cyanobacterium),
Frankia (actinomycete, symbiotic with Alnus, alder trees),
Anabaena (photosynthetic cyanobacterium, symbiotic with Azolla, water fern; reported as common in rice paddies)
Rhizobium (symbiotic with legumes)

The latter four genera form symbiotic relationships with several genera of plants, although some species may also be free-living. While several other examples are known, the best understood of such mutualistic relationship is that of Rhizobium strains and species in relationship with different legume species.
Anaerobic nitrogen-fixing bacteria are found in the guts of some herbivores including sea urchins and termites. The contribution of these bacteria to the nitrogen needs of their host may be negligible in some cases, but significant in others. Cyanobacteria may form symbiotic relationships (in lichens, for example), but it is as free-living organisms in aquatic and marine environments that they are especially important. Trichodesmium is one such marine nitrogen-fixing cyanobacterium.

The diversity of nitrogen-fixing bacteria ensures that nitrogen is made available to occupants of many different habitats. In addition, it illustrates the argument that the nitrogen cycle is not so much about individual species, but about steps in an eco-chemical pathway. A step may be necessary and unbridgeable, but an individual species that mediates the step may not be necessary at a given time as the machinery required to accomplish the step — the enzymes involved — may be found in other species, some apparently distantly if at all related. Redundancy is important as a back-up when circumstances preclude the presence or sufficient abundance of individual species that have the same abilities. Ecological systems are replete with redundancies.

BIOLOGICAL NITROGEN FIXATION — NITROGENASE
All known nitrogen-fixing bacteria produce nitrogenase, which is composed of two different protein complexes whose amino acids contain nitrogen. The existence of these protein complexes requires the very reactions they catalyze. When two different nitrogenase subunits from unrelated species are combined, they most often form “active hybrids” with nitrogenase activity. Consequently, nitrogenases from even very distinct species appear comparable, although some differences have been noted. This degree of similarity suggests a similar origin even though, as already noted, nitrogen-fixing bacteria occupy a range of very different habitats. Under these circumstances, convergent evolution appears unlikely to have produced similar protein complexes capable of interchanging parts. Lateral gene transfer may represent the most promising evolutionary explanation of the distribution of nitrogenase across species.

Nitrogenase expression is reversibly regulated by what is called the “ammonia switch-off.” In addition, nitrogenase expression may be re-pressed via a complex cascade of events when oxygen levels are high. While nitrogenase complexes in different species appear comparable, genetic regulation of nitrogenase expression differs widely in different organisms. In addition, strategies for shielding nitrogenase from oxygen vary among organisms.
Interactions between host plants and Rhizobium bacteria in root nodules are particularly intimate and elegant. When concentrations of nitrogen compounds are elevated in the shoots of host-plants, nitrogenase activity is lowered. Evidently, when no more fixed nitrogen is needed there is a means of communication between the host plant’s shoots and bacteroids, misshapen Rhizobium cells in root nodules. This is another example of interspecific cooperation, which in this case is believed to involve an amino acid as the inhibitor of nitrogenase. Down-regulation of nitrogenase is necessary due to its high energy demands and the reactive nature of its product, ammonia. Under normal conditions, free ammonia is essentially absent as it is immediately used to produce the amino acid glutamate and is thus sequestered in a glutamate pool.

Significantly, in all known cases oxygen acts as a poison to the nitrogenase enzyme. If nitrogen fixation had evolved in a reducing atmosphere, this may make some sense, but a reducing atmosphere should eliminate the need for nitrogen fixation as nitrogen would be freely available via abiotically produced amino acids and as ammonia. Thus, selective pressure for developing nitrogen fixation is difficult to conceive, especially given its high energy demands. As a consequence, the sensitivity of nitrogenase to oxygen presents a conundrum; in a reducing atmosphere, nitrogen fixation should not evolve, while in an oxidizing environment nitrogenase does not work.

Invoking a neutral atmosphere to circumvent this problem does not solve it and presents the worst of both options. On the one hand, neutral atmospheres are not known to produce nitrogen-containing molecules essential for life and on the other hand, oxygen may still be present in concentrations sufficient to poison nitrogenase. Under these circumstances, nitrogen fixation would need to evolve for life to exist before life could exist, a veritable evolutionary “Catch 22.” In addition, some mechanism for isolating nitrogenase would still need to evolve to protect it from the relatively low levels of oxygen present in such an atmosphere. A simpler and more direct path would be to evolve a nitrogenase that is not as sensitive to oxygen. Clearly, the sensitivity of nitrogenase to oxygen is not well explained by invoking its evolution in a reducing atmosphere or in a neutral one. This suggests that there may be a necessary design constraint that is worth looking for in nitrogenase, as that may be the true explanation of its sensitivity to oxygen.

All organisms that fix nitrogen use some mechanism to ensure anaerobic conditions. A notable example of this is leghaemoglobin, which occurs in legume root nodules and has a greater affinity for oxygen than mammalian hemoglobin. Leghaemoglobin is cooperatively manufactured, with legume genes determining the globin portion of the molecule, while the porphyrin ring comes from Rhizobium. However, the central iron ion in the porphyrin ring comes from the plant. Clearly, production of leghemoglobin requires exact coordination between both species. Cooperative synthesis, such as this, challenges Darwinian explanations and is another possible example of a system with irreducible - like characteristics spread across multiple species.

Most biological fixation is accomplished by symbiotic bacteria and photosynthetic nitrogen-fixing cyanobacteria. Nitrogen fixation in free-living non-photosynthetic soil bacteria is considered to be relatively low as a result of limited access to energy resources. Consequently, populations of such bacteria are also low. However, they may be more numerous and productive close to roots, a zone designated as the “rhizosphere,” where they may access photosynthetically produced nutrient exudates. Nevertheless, in the words of Moat & Foster: “Although free-living organisms, in general, appear less efficient in their ability to fix nitrogen, their number, variety, and ubiquitous distribution suggest that they are of major ecological importance.”

BIOLOGICAL NITROGEN FIXATION AND PHOTOSYNTHESIS
Biological nitrogen fixation requires hydrogen and large amounts of energy from ATP. nitrogenase-catalyzed reduction of N involves this complex protein machine directly transferring electrons to N2 in a stepwise fashion. , the conversion of N to ammonia is exergonic. Among other things, the need for energy stems from the cost of providing hydrogen and electrons to the reaction, and that energy is derived from ATP which is either directly or indirectly produced by photosynthesis or, rarely, chemosynthesis. The photosynthetic capacity of plants may be a limiting factor in nitrogen fixation. It is estimated that as much as 20% of ATP produced in photosynthesis may be used for nitrogen fixation. In legumes, fixing 1 mg of nitrogen require 4 mg of fixed carbon from the host plant. Clearly, there is a necessary relationship between photosynthesis or chemo-synthesis to supply energy for biological nitrogen fixation with its large energy requirement. In addition, ATP, contains a nitrogenous base, with its nitrogen traceable directly back to the nitrogen cycle.

Symbiotic rhizobia have direct access to chemical energy from the host plants photosynthesis, but free-living bacteria depend upon such energy either provided by their own photosynthetic processes (cyanobacteria) or if non-photosynthetic, from respiration or fermentation of photosynthetically derived reduced organic molecules absorbed from soil, mostly in the rhizosphere. Thus, relationships in the nitrogen cycle appear complex and obligatory, even for free-living species.

IS BIOLOGICAL NITROGEN FIXATION INDISPENSABLE AND UNBRIDGEABLE?
Unquestionably, biological nitrogen fixation is no simple process and a design argument could be made based on this single step in the nitrogen cycle. It is unlikely to have been produced via a step-by-step Darwinian process because nitrogenase itself is immensely complex, requires auxiliary complex mechanisms to maintain low oxygen tension, and also needs reduced carbon backbones as substrates for amination to store ammonia as glutamine. In addition, regulatory mechanisms are needed to coordinate the entire energetically expensive activity and its chemically reactive product, ammonia.

Of equal importance to asking if biological nitrogen fixation could be produced in some gradual manner is the question of whether known natural abiotic processes — like atmospheric nitrogen fixation — could bridge or by-pass this step in the cycle. The answer in the case of atmospheric fixation is that the product — nitrate — is not directly useful and the chemical intermediates in nitrate production are destructive to organic molecules as is nitrate itself when in the form of nitric acid. Assimilation of nitrate requires a separate photosynthesis-dependent mechanism, at least in plants, which would be unlikely to develop in the absence of nitrogen-containing proteins.

A more promising inorganic workaround might be ammonia released by volcanoes, but volcanoes today do not release ammonia in large quantities. Even if they did, a secondary problem results from the fact that ammonia is readily subject to photolysis. The high solubility of ammonia in water may protect some ammonia from being broken down by light, but significant quantities of ammonia in water would raise the pH impacting water chemistry in a way that presents challenges for life. Whatever the abiotic source of ammonia, whether from volcanoes, a reducing atmosphere or some other source, none serves as a probable natural bridge over biological nitrogen fixation as, when nature provides nitrogen for free in the form of ammonia or amino acids, selective pressure for an energy-hungry metabolic process like nitrogen fixation seems unlikely.

NITRIFICATION
Nitrification is an essential process in the nitrogen cycle of soils, natural waters, and wastewater treatment systems. 6   It is responsible for the biological conversion of ammonium to nitrate. While both of these compounds are suitable for plant use as nutrients, they behave quite differently in soil systems, and have quite different sources and fates in the marine environment. Ammonium is produced as a waste product from cellular and organismal metabolism, a breakdown product of organic material. It is the preferred nitrogen source for many plants and algae. Nitrate is not only a nutrient, but the substrate for the bacterial process of denitrification, by which nitrate is reduced to dinitrogen gas, N2. Most plants cannot use dinitrogen gas as a nitrogen source, so denitrification represents a loss term for fixed nitrogen in the ecosystem. Nitrification itself does not directly affect the nitrogen budget, but by linking organic matter decomposition to denitrification, it completes the N cycle.

The significance of nitrification can be summarized in the following list:

(1) transformation of ammonium to nitrate, with implications for the availability of N for plants and algae,
(2) production of substrate for denitrification,
(3) production of nitrous oxide in aquatic and terrestrial ecosystems,
(4) consumption of oxygen in sediments,
(5) acidification of the environment.

Some ammonia produced in nitrogen fixation, as well as in ammonification, is directly taken up by plants through their roots, or from root-nodules, and assimilated, but large quantities of ammonia are also converted to nitrite and nitrate, a process generally known as nitrification. Many plants appear to preferentially take up nitrogen as nitrate (NO -). However, under conditions that are unfavorable for nitrification (low pH, anaerobic soils, etc), plants use ammonia. Use of ammonia as a primary source of nitrogen tends to lower soil pH. But even under unfavorable conditions, nitrification still occurs at a relatively slower rate. Aquatic plants absorb ammonia through their leaves.
Organisms (largely bacteria) that convert ammonia to nitrites and nitrates are referred to as nitrifiers. They are found in a variety of environments — soils, seawater, brackish waters, rivers, lakes, and wastewater treatment ponds, etc. Along with some other genera, Nitrosomonas converts ammonia to nitrite (NO -). In general, organisms that only oxidize to nitrite are referred to as ammonia oxidizers. Nitrite itself is quickly oxidized so little of it is available to be absorbed by plants. Since nitrite is toxic, its rapid conversion to nitrate detoxifies while benefiting both organisms that absorb nitrates and bacteria that reap energy in the process. Nitrobacter, along with several other genera, oxidizes nitrite to nitrate. All nitrifiers are aerobic and most are chemoautotrophic, the energy derived from nitrification is used to fix carbon. A few nitrifiers are heterotrophic. For example, in forest litter, it is not bacteria, but saprophytic fungi, which do most of the nitrifying.

Nitrification is a two-step process. The first step uses the enzyme ammonia monoxygenase. In this initial nitrification reaction, 66 kcal of energy is liberated per mole of ammonia oxidized. Under oxygen-limited conditions, the product is NO (nitrous oxide) instead of nitrite. The second step liberates 18 kcal per mole of nitrite oxidized. Why is nitrification essential to the nitrogen cycle when plants and bacteria are able to use ammonia directly? Indeed, even nitrate must be reduced back to ammonia before it becomes biologically accessible. That some organisms even have the enzyme system that enables them to use nitrate when the simpler alternative to use ammonia directly is available, says much about the evident importance of the more roundabout route through nitrate.

As chemoautotrophs, nitrifiers fix carbon and make it available for respiration. However, the process is not very efficient. A more reasonable answer is suggested in defining the function of the nitrogen cycle as it was earlier in this paper: “to regulate concentrations of various nitrogen-containing molecules in the environment in such a way that life can thrive.” 

For three reasons, conversion of ammonia to nitrate is an essential part of the cycle’s function of regulating various nitrogen-containing molecules:

1. It prevents accumulation of ammonia to toxic levels
2. It provides a biologically available, but relatively chemically inert reservoir of nitrogen that can be utilized without requiring the complex and energetically expensive mechanisms used in biological nitrogen fixation
3. The solubility of nitrate in water allows it to be relatively mobile, thus distributing biologically available nitrogen to organisms that do not have the ability to fix their own nitrogen.

Nitrification is thus an essential step in recycling nitrogen back to the atmosphere and plays a vital role in the global function of the nitrogen cycle in regulating nitrogen-containing molecules in the environment. It is worth noting that this understanding of the role and necessity of nitrification is driven by a design-oriented view of the nitrogen cycle and not a reductionistic view of nature.

IS NITRIFICATION INDISPENSABLE AND UNBRIDGEABLE?
How might a process like nitrification come about by Darwinian selection or be naturally bridged? In a reducing environment in which nitrogen fixation is not necessary, the reverse process might appear to be unnecessary as well. However, this seems unlikely; nitrogen incorporated into organisms would still need to be recycled when excreted as a waste product or following death. But this might be accomplished by pathways in which nitrogen could be released from amino acids. For example, if nitrogen from amino acids was recycled back into ammonia, as occurs with deamination of glutamate by glutamate dehydrogenase, this would prevent infinite accumulation of amino acids. Whatever the mechanism, in a reducing environment it seems unlikely that “nitrification” would have evolved to be anything like the oxidative process of nitrification seen today.

An oxidizing atmosphere presents an interesting situation. Ammonia in the presence of oxygen burns readily, producing nitrogen oxides and water. In addition, at even relatively low concentrations, ammonia is toxic to life. In the absence of enzymes in living things and at low concentrations, ammonia does not spontaneously oxidize to nitrogen oxides and water at a significant rate. In an oxidizing atmosphere, without nitrification, ammonia would be expected to accumulate in the environment until one of two (possibly both) things happened:

1. An equilibrium between organic ammonia production and inorganic ammonia degradation was reached, potentially resulting in ammonia concentrations incompatible with life.
2. Catastrophic oxidation set off by lightning or some other spark occurred.

The latter scenario is improbable given the solubility of ammonia in water. More reasonably, ammonia would be expected to accumulate in bodies of water turning them basic. This assumes that photolysis of ammonia in the atmosphere does not break down ammonia fast enough to preclude its accumulation. In our present world, neither of these scenarios occurs because nitrification limits accumulation of ammonia, but allows for a ready supply of nitrogen to organisms in the relatively inert form of nitrate. To get around problems resulting from the absence of nitrification, ammonia might be recycled into living material as it is in forests until some other limiting nutrient prevented further growth. As organisms died and the other limiting nutrient was recycled, biomass might be expected to accumulate until some conflagration burns all the accumulated nitrogen-containing biomass, returning the nitrogen to the atmosphere as nitrogen oxides. Nitric oxide (NO) and nitrogen dioxide (NO ) are both highly reactive gases dangerous to life. Thus it would be expected that biomass would accumulate past some tipping point and, at least on a local scale, destroy life. Nitrification prevents this kind of scenario by shuttling nitrogen in excess ammonia to a relatively benign molecule (nitrate) that can still be used by plants or, alternatively, continue on into denitrification where it is returned to the atmosphere as safe and inert N2.

1. http://www.astrobio.net/news-exclusive/nitrogen-ancient-rocks-sign-early-life/
2. http://www.ps-19.org/Crea06EcoSys/index.html
3. http://www.grisda.org/origins/60006.pdf
4. http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/N/NitrogenCycle.html
5. http://www.grisda.org/origins/60006.pdf
6. https://www.princeton.edu/nitrogen/publications/pdfs/Ward_2015_Nitrification.pdf
7. https://answersingenesis.org/biology/plants/seeing-the-forest-amid-the-trees/
8. https://en.wikipedia.org/wiki/Nitrogen_cycle
9. http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.465.3125&rep=rep1&type=pdf



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DENITRIFICATION
Denitrification is a microbial respiratory process by which nitrate is reduced to atmospheric dinitrogen gas (N ) or nitrous oxide (N O). Without this process, nitrates would accumulate in high concentrations, as has been seen in recent years with the overuse of nitrogenous fertilizers. On a global scale, in the absence of denitrification and sufficiently rapid assimilation by plants and microbes, nitrates would accrue in and acidify bodies of water while the concentration of atmospheric nitrogen would decline.  As it is, under normal conditions on Earth, nitrogen is often limiting in the biosphere as a result of low levels of nitrogen fixation along with denitrification. Organisms in soils require oxygen, but if soils are waterlogged for protracted periods (greater than 36 hours) and water fills spaces between soil particles usually occupied by air, then oxygen will be excluded. At such times, certain microbes are able to obtain essential oxygen from nitrite and nitrate. The oxygen from nitrate serves as an alternative electron acceptor. 

The last two products, nitrous oxide and dinitrogen, are returned to the atmosphere. Factors influencing denitrification include the quantity of organic material available, waterlogging and oxygen deprivation, soil temperature, levels of soil nitrates and pH. For example, denitrification is higher during summer when water temperatures are highest. Under normal conditions, waterlogging induces denitrification, which occurs at a rate amenable to environmental wellbeing. But when there is a nitrate overload, the highest attainable rates of denitrification may not be able to keep pace with demand and thus, nitrates may be carried to the water table and into aquifers. The result is eutrification of surface waters in which organisms grow so rapidly that oxygen is depleted resulting in death of many organisms. Ultimately, this may lead to increased rates of denitrification if nitrate becomes the most abundant electron acceptor available. Thus, even when the system is perturbed, it may be designed to still work to rectify the perturbation.

IS DENITRIFICATION INDISPENSABLE AND UNBRIDGEABLE?
The necessity of denitrification is evident when the logic applied to nitrification is also applied to this step. While nitrates can be recycled into plant material, the heterogeneity of nature and lack of rapid transport mechanisms for nitrate ensure that concentrations would, at least locally, reach high levels. While nitrate is relatively immobile in the absence of water, it is water soluble and can be leached out into bodies of water where it may reach significant concentrations. Excess nitrates have the potential to cause environmental damage as evidenced by the consequences of over-use of industrially fixed nitrogen for agricultural purposes. Under current conditions, if denitrification was not part of the nitrogen cycle, even under the natural rates of nitrogen fixation and nitrification, nitrate levels could be expected to eventually become excessive.

Compared to other nitrogen oxides, nitrate is relatively stable and does not spontaneously degrade at an appreciable rate to O and N or NO In an oxidizing atmosphere, nitrates are produced via atmospheric fixation with lightning providing a significant portion of the energy driving the reaction.  If biological nitrification was occurring, accumulation would be significantly faster. Assimilation does not act as a realistic way of removing nitrate as it simply recycles it into plants. As long as biological nitrogen fixation feeds nitrogen from the atmosphere into the nitrogen cycle, a way of removing nitrogen is necessary.

In the absence of biological denitrification, nitrate would be expected to accumulate. This is exactly what occurs in the Atacama Desert in northern Chile, which is among the driest areas on Earth.51 Average annual rainfall is between 1 and 2 mm. In addition, when rain does fall, it drains away rapidly as there are no soils as such to become waterlogged. In this arid region, conditions necessary for denitrification rarely occur. It is thus not surprising that, as in several other deserts, nitrate has accumulated. But unlike other deserts, this is the only known place on Earth where nitrate has accumulated to the point that nitrate mining is commercially feasible.
While debate continues about the source of nitrate in the Atacama Desert, this is not relevant to the question of whether nitrate will accumulate in the absence of denitrification. It clearly does. It is, however, worth noting that measurements of oxygen isotope composition of this nitrate suggests that a significant proportion of it accumulated within the past 2,000,000 years as a result of atmospheric deposition resulting from photochemical fixation in the upper atmosphere. Thus, in the absence of de-nitrification, nitrate appears to accumulate as a result of abiotic processes. As mentioned previously, low levels of atmospheric nitrogen on Mars may be attributable in part to accumulation of nitrates in the Martian regolith, where a biological nitrogen cycle is not thought to exist.

A Darwinian scenario may be conceivable for this step in the nitrogen cycle if certain assumptions are made. These include the existence of aerobic bacteria — a mechanism for accumulation of nitrate — and niches, like soils from which oxygen is occasionally excluded. In this scenario, some aerobic bacteria might have a weak ability to use nitrate instead of oxygen as an electron acceptor during respiration. Perhaps this could have been related to their ability to utilize nitrate as a nitrogen source and then reduce it to ammonia for amino acid production. Natural selection working on these bacteria, as they survived periods of oxygen starvation better than those that are completely dependant on oxygen, may ultimately have produced the denitrifying bacteria living today.

This scenario presents a number of problems. The first is the obvious appeal to unknowns. Were there bacteria in the past capable of utilizing nitrate as an electron acceptor during anaerobic respiration before there was a fully developed nitrogen cycle? No evidence supports this, and there is a commensurate lack of evidence for nitrate having accumulated significantly in the environment. The way in which organisms both assimilate nitrates (which will be discussed in the next section), and engage in nitrate respiration also suggests no linkage between the two processes. In these organisms, two significantly different nitrate reductases are produced. For example, in E. coli, the respiratory enzyme is particulate and sensitive to oxygen while the assimilatory enzyme is soluble and the two enzymes are induced and repressed by different substrates. Evidently, the processes of nitrate respiration and nitrate assimilation are biochemically distinct and do not exhibit the kind of convergence needed to support the theory that they share a related evolutionary history.

Evolving nitrogen-reducing systems in a reducing environment appear to be out of the question, given the lack of oxidized nitrogen in such environments. In an oxidizing environment, even in the absence of biological fixation or nitrification, nitrates are likely to be present. In fact, they would presumably be the sole source of nitrogen for organisms lacking the ability to perform steps other than assimilation and amination in the nitrogen cycle. Assuming this to be the case, the ultimate problem of recycling nitrogen to the atmosphere might be temporarily suppressed by accumulation of nitrogen in living organisms and their byproducts, but this does not negate the ultimate need to recycle nitrogen to the atmosphere, and may even exacerbate it once nitrogen as either ammonia or nitrate reached excessive levels. The question then becomes, does this biological sink provide sufficient time for the stepwise evolution of other components of the nitrogen cycle? Ultimately, denitrification appears to be an indispensable part of the nitrogen cycle and unlikely to have evolved in Darwinian fashion independent of the rest of the cycle.

ASSIMILATION
Although nitrogenase is widely distributed among prokaryotic lineages, most organisms cannot fix nitrogen but rather obtain their nitrogen directly as NH4+ (or organic nitrogen) from the environment, or from the reduction of NO3 – to NH4 + through assimilatory nitrate reduction. Both prokaryotes and eukaryotes are able to mediate this process. Ammonium is returned to the environment when organisms die, and its fate (and the variety of subsequent forms of nitrogen) depends on whether the local environment contains oxygen. In the presence of oxygen, NH4+ is sequentially oxidized to NO3– by specific groups of bacteria and archaea. In this pathway, known as nitrification, organisms containing the enzyme ammonium monooxygenase first oxidize NH4 + to hydroxylamine, which is subsequently oxidized to NO2 – by hydroxylamine oxidoreductase, and finally the NO2 – is oxidized to NO3 – by nitrite oxidoreductase. The electrons and protons derived during ammonium and nitrite oxidation are used by the microbes to fix inorganic carbon in the absence of light (i.e., chemoautotrophy). The greenhouse gas N2O is a byproduct in this process; indeed, nitrification from both marine and terrestrial environments is an important source of atmospheric N2O 2

Plants absorb nitrogen from the soil in the form of nitrate (NO3−) and ammonium (NH4+). In aerobic soils where nitrification can occur, nitrate is usually the predominant form of available nitrogen that is absorbed. However this need not always be the case as ammonia can predominate in grasslands and in flooded, anaerobic soils like rice paddies . Ammonium ions are absorbed by the plant via ammonia transporters. Nitrate is taken up by several nitrate transporters that use a proton gradient to power the transport. Nitrogen is transported from the root to the shoot via the xylem in the form of nitrate, dissolved ammonia and amino acids. Usually (but not always) most of the nitrate reduction is carried out in the shoots while the roots reduce only a small fraction of the absorbed nitrate to ammonia. Ammonia (both absorbed and synthesized) is incorporated into amino acids via the glutamine synthetase-glutamate synthase (GS-GOGAT) pathway. In the chloroplasts, glutamine synthetase incorporates this ammonia as the amide group of glutamine using glutamate as a substrate. Glutamate synthase (Fd-GOGAT and NADH-GOGAT) transfer the amide group onto an 2-oxoglutarate molecule producing two glutamates. Further transaminations are carried out make other amino acids (most commonly aspargine) from glutamine. While the enzyme glutamate dehydrogenase (GDH) does not play a direct role in the assimilation, it protects the mitochondrial functions during periods of high nitrogen metabolism and takes part in nitrogen remobilization. 1

Nitrate serves as a major crossroads in the nitrogen cycle. Nitrate is produced via biological nitrification and abiotic atmospheric nitrogen fixation. Once it is in the form of nitrate, nitrogen can either be returned to the atmosphere as N during denitrification, or it can be assimilated by plants and bacteria. While nitrate is readily absorbed by plants and bacteria, it is only as ammonia that it can be utilized. The process of nitrogen assimilation involves conversion of nitrate to ammonia and the incorporation of that ammonia into amino acids.

Nitrates enter plant cells via a “proton-nitrate symport.” Once in plant cells, nitrates are converted to nitrites by the enzyme, nitrate reductase. Highly toxic nitrite, a metabolite in the process, is rapidly sequestered in chloroplasts, thus protecting plants from harm. Inside plastids, nitrite is quickly converted to ammonia by another enzyme, nitrite reductase. Significantly, in at least some plants, the reducing power is provided by photorespiration which is dependent on the presence of oxygen. In most organisms, assimilation is repressed by the presence of ammonia and induced by nitrate or nitrite.

Microbial assimilation of ammonia to produce amino acids occurs first through the synthesis of glutamate, alanine, or aspartate. These then serve as nitrogen donors via transaminases to form other amino acids. Ammonia, for example, may be used to aminate glutamate to produce the amino acid glutamine, by means of the enzyme, glutamine synthetase (GS) plus ATP. GS is the principle means by which ammonia enters the metabolic processes of plants. Then, by means of a glutamate synthase, known as GOGAT (Glutamine 2-OxoGlurate AminoTransferase), one out of two glutamines produced is converted back to glutamate to pick up yet another ammonium molecule. Each turn of the GS-GOGAT cycle results in a profit of one glutamine. From glutamine, nitrogen is passed on by means of transaminases to other molecules to form different amino acids. The process can also go in reverse. Ammonia assimilation occurs in both roots and leaves via this method.59 Eventually, assimilated nitrogen is used to produce nucleotides and nucleic acids.

Assimilation is too complex to be considered in detail here. However, the importance of enzymes in transferring nitrogen to various molecules cannot be overstated. Note that nitrogen assimilatory enzymes contain nitrogen, the very element whose assimilation they facilitate. These processes are intimately tied to the actions of genes (whose nucleotides also contain nitrogen) which determine the structure of proteins. The actions of these genes are facilitated by several of the very enzymes, which they have, in fact, encoded. It is difficult to avoid the necessity of all of these entities being simultaneously present in order for the whole system to function.

Nitrate reductase contains cytochrome b557 and molybdenum cofactor
A pair of electrons is transferred from NADH via enzyme-associated sulfhydryl groups, FAD, cytochrome b557, and MoCo (an essential molybdenum-containing cofactor) to nitrate, reducing it to nitrite. The brackets [ ] denote the protein-bound prosthetic groups that constitute an e2 transport chain between NADH and nitrate. Nitrate reductases typically are cytosolic 220-kD dimeric proteins. The structure of the molybdenum cofactor (MoCo) is shown in Figure a, below.

The novel prosthetic groups of nitrate reductase and nitrite reductase. (a) The molybdenum cofactor of nitrate reductase. The fifth ligand for the Mo atom is the sulfur atom of a conserved cysteine residue in the nitrate reductase. The Mo cofactor is a pyranopterin ring system: To form a pterin, a pyrimidine ring (left) is fused with a piperazine ring (center, [a piperazine ring is a sixmembered ring, with two nitrogens directly opposite from one another]). Adding a pyran ring (right, [a pyran ring contains one oxygen and five carbon atoms]) to the pterin yields a pyranopterin. (b) Siroheme, an essential prosthetic group of nitrite reductase. Siroheme is novel among hemes in having eight carboxylate-containing side chains. These carboxylate groups may act as H1 donors during the reduction of NO2 2 to NH4 1.


The novel prosthetic groups of nitrate reductase and nitrite reductase 
(a) The molybdenum cofactor of nitrate reductase. The fifth ligand for the Mo atom is the sulfur atom of a conserved cysteine residue in the nitrate reductase. The Mo cofactor is a pyranopterin ring system: To form a pterin, a pyrimidine ring (left) is fused with a piperazine ring (center, [a piperazine ring is a sixmembered ring, with two nitrogens directly opposite from one another]). Adding a pyran ring (right, [a pyran ring contains one oxygen and five carbon atoms]) to the pterin yields a pyranopterin.
(b) Siroheme, an essential prosthetic group of nitrite reductase. Siroheme is novel among hemes in having eight carboxylate-containing side chains. These carboxylate groups may act as H1 donors during the reduction of NO2 2 to NH4+

Molybdenum cofactor is necessary for both nitrate reductase activity and the assembly of nitrate reductase subunits into the active dimeric holoenzyme form. Molybdenum cofactor is also an essential cofactor for a variety of enzymes that catalyze hydroxylase-type reactions, including xanthine dehydrogenase, aldehyde oxidase, and sulfite oxidase.

IS ASSIMILATION INDISPENSABLE AND UNBRIDGEABLE?
It has been generally thought that plants only take up nitrogen as ammonium or nitrate, but evidence is mounting that plants may also take in partially decomposed organic nitrogen in the form of amino acids, and possibly even more complex nitrogen-containing compounds. Some evidence suggests that plants may access organic nitrogen by means of mycorrhizae. Given that the highest proportion of soil nitrogen is organic, organic nitrogen absorption should not be surprising. Could assimilation be bridged by absorption of amino acids or other nitrogen-containing organic molecules? On the surface, such an idea looks plausible, and it is not surprising that scenarios have been built around this idea as a way to entirely bridge the nitrogen cycle. However, on closer examination, simply bridging assimilation and nitrogen fixation by appealing to a reducing atmosphere in which amino acids, nitrogenous bases and other nitrogen-containing molecules are freely available creates its own set of problems. The first and most obvious problem is that evidence favoring such a reducing atmosphere in the distant past is absent and that the existence of such an atmosphere might have existed seems incredible. However, the purpose of this paper is not to argue against a reducing atmosphere; as already mentioned, these arguments have been convincingly made elsewhere.61
A second issue arises from the assumption that nitrogen-containing organic molecules could cross primitive cell membranes. This presents a significant issue as presumably more than one or two simple molecular pumps would be needed to transport any freely-available nitrogen-containing molecules. Pumps would be necessary as, even given some sort of primordial soup, the concentrations of amino acids and other nitrogen-containing molecules would be expected to be higher inside cells than outside.

Energy for pumping an array of nitrogen-containing molecules across primitive cell membranes would presumably not be available from photo-synthesis as this requires the presence of the very amino acids that need to be pumped. Chemosynthesis, if it was hypothesized to have evolved before photosynthesis, would suffer from the same difficulty. It is not clear how any realistic energy source would circumvent this problem. In addition, proteins from which the pumps would be made are composed of amino acids. A scenario of this sort presents another chicken-or-egg dilemma. Organic membranes across which amino acids freely flow from areas of lower concentration to areas of higher concentration are unknown; membranes lacking protein pumps that concentrate amino acids on one side seem impossible. In addition, powering pumps is typically tied in some way to the use of nitrogen-containing nucleotides like ATP, which serve as the currency of energy metabolism within cells.

Accumulation of ammonia within cells presents a third issue. Energy to drive any kind of metabolism comes from the catabolism of molecules and ultimately from photosynthesis, or, less commonly, from chemo-synthesis. In modern organisms some portion of this energy is derived from catabolism of nitrogen-containing molecules. How the waste nitrogen is handled will be dealt with in the next section. If a system for pumping amino acids across cell membranes existed in primitive cells, it would require energy from some source. If that source happened to be the amino acids themselves, then a mechanism would be required to be simultaneously in place to deal with the waste ammonia. This ammonia could not be consumed as a source of ammonia for amination, as these organic molecules would not yet be available without further complex protein-dependent biochemical pathways. In any case, there seems to be little reason for cells to make amino acids if they were freely available. Presumably, waste ammonia would have to be pumped or diffuse out of the cells via some sort of protein channel. This presumes that a mechanism for getting energy from reduced organic molecules could serve as a source of energy in a reducing environment via either anaerobic respiration or fermentation.

Within certain biomes, for example, boreal forests, organic nitrogen is cycled rapidly through ammonia which is absorbed directly by plants. In the absence of denitrification, organic material accumulates and is ultimately recycled via fires or goes on to form peat. Taken as a whole, some areas in the biosphere can do this without upsetting the overall balance of the nitrogen cycle, but, as noted in the discussion of denitrification, on a global scale such a system appears to be catastrophic in the end. Ultimately, easier ways of getting nitrogen into organic molecules inside cells other than assimilation seem improbable, although they would be necessary in a reducing environment. Given that the current atmosphere is an oxidizing one, and this seems to have been the case in the ascertainable past as well,62 assimilation is clearly necessary under current conditions, and presumably historically as well.

Nitrogen Fixation 
In addition to N2 and NH3, nitrogen exists in many different forms, including both inorganic (e.g., ammonia, nitrate) and organic (e.g., amino and nucleic acids) forms. Thus, nitrogen undergoes many different transformations in the ecosystem, changing from one form to another as organisms use it for growth and, in some cases, energy. The major transformations of nitrogen are nitrogen fixation, nitrification, denitrification, anammox, and ammonification (Figure 1). The transformation of nitrogen into its many oxidation states is key to productivity in the biosphere and is highly dependent on the activities of a diverse assemblage of microorganisms, such as bacteria, archaea, and fungi.

N2 gas is a very stable compound due to the strength of the triple bond between the nitrogen atoms, and it requires a large amount of energy to break this bond. The whole process requires eight electrons and at least sixteen ATP molecules (Figure 2). As a result, only a select group of prokaryotes are able to carry out this energetically demanding process. Although most nitrogen fixation is carried out by prokaryotes, some nitrogen can be fixed abiotically by lightning or certain industrial processes, including the combustion of fossil fuels.

Although there is great physiological and phylogenetic diversity among the organisms that carry out nitrogen fixation, they all have a similar enzyme complex called nitrogenase that catalyzes the reduction of N2 to NH3 (ammonia), which can be used as a genetic marker to identify the potential for nitrogen fixation.




The process of converting N2 into biologically available nitrogen is called nitrogen fixation. N2 gas is a very stable compound due to the strength of the triple bond between the nitrogen atoms, and it requires a large amount of energy to break this bond. The whole process requires eight electrons and at least sixteen ATP molecules (Figure 2). As a result, only a select group of prokaryotes are able to carry out this energetically demanding process. Although most nitrogen fixation is carried out by prokaryotes, some nitrogen can be fixed abiotically by lightning or certain industrial processes, including the combustion of fossil fuels.

Nitrification
Nitrification is the process that converts ammonia to nitrite and then to nitrate and is another important step in the global nitrogen cycle. Most nitrification occurs aerobically and is carried out exclusively by prokaryotes. There are two distinct steps of nitrification that are carried out by distinct types of microorganisms. The first step is the oxidation of ammonia to nitrite, which is carried out by microbes known as ammonia-oxidizers. Aerobic ammonia oxidizers convert ammonia to nitrite via the intermediate hydroxylamine, a process that requires two different enzymes, ammonia monooxygenase

Energy generation in Nitrosomonas. Only two enzymes, ammonia monooxygenase (AMO) and hydroxylamine oxidoreductase (HAO) are involved in the oxidation of ammonia to nitrite.

hydroxylamine oxidoreductase

Nitrite can be further acted on by another nitrifying bacteria, Nitrobacter. This microbe oxidizes nitrite to nitrate using oxygen as the terminal electron acceptor. A proton gradient is established with resultant synthesis of ATP. Nitrobacter is often found in tandem with Nitrosomonas since the end product of Nitrosomonas metabolism is the energy substrate for Nitrobacter. This type of loose association is probably common in the environment and in this case benefits both organisms. Nitrobacter is provided with substrate and Nitrosomonas has its end product removed, which helps drive its metabolism.

and hydroxylamine oxidoreductase (Figure 4). The process generates a very small amount of energy relative to many other types of metabolism; as a result, nitrosofiers are notoriously very slow growers. Additionally, aerobic ammonia oxidizers are also autotrophs, fixing carbon dioxide to produce organic carbon, much like photosynthetic organisms, but using ammonia as the energy source instead of light.

Unlike nitrogen fixation that is carried out by many different kinds of microbes, ammonia oxidation is less broadly distributed among prokaryotes. Until recently, it was thought that all ammonia oxidation was carried out by only a few types of bacteria in the genera Nitrosomonas, Nitrosospira, and Nitrosococcus. However, in 2005 an archaeon was discovered that could also oxidize ammonia (Koenneke et al. 2005). Since their discovery, ammonia-oxidizing Archaea have often been found to outnumber the ammonia-oxidizing Bacteria in many habitats. In the past several years, ammonia-oxidizing Archaea have been found to be abundant in oceans, soils, and salt marshes, suggesting an important role in the nitrogen cycle for these newly-discovered organisms. Currently, only one ammonia-oxidizing archaeon has been grown in pure culture, Nitrosopumilus maritimus, so our understanding of their physiological diversity is limited.

The second step in nitrification is the oxidation of nitrite (NO2-) to nitrate (NO3-) (Figure 5). This step is carried out by a completely separate group of prokaryotes, known as nitrite-oxidizing Bacteria. Some of the genera involved in nitrite oxidation include Nitrospira, Nitrobacter, Nitrococcus, and Nitrospina. Similar to ammonia oxidizers, the energy generated from the oxidation of nitrite to nitrate is very small, and thus growth yields are very low. In fact, ammonia- and nitrite-oxidizers must oxidize many molecules of ammonia or nitrite in order to fix a single molecule of CO2. For complete nitrification, both ammonia oxidation and nitrite oxidation must occur.

Anammox
Traditionally, all nitrification was thought to be carried out under aerobic conditions, but recently a new type of ammonia oxidation occurring under anoxic conditions was discovered (Strous et al. 1999). Anammox (anaerobic ammonia oxidation) is carried out by prokaryotes belonging to the Planctomycetes phylum of Bacteria. The first described anammox bacterium was Brocadia anammoxidans. Anammox bacteria oxidize ammonia by using nitrite as the electron acceptor to produce gaseous nitrogen (Figure 6). Anammox bacteria were first discovered in anoxic bioreactors of wastewater treatment plants but have since been found in a variety of aquatic systems, including low-oxygen zones of the ocean, coastal and estuarine sediments, mangroves, and freshwater lakes. In some areas of the ocean, the anammox process is considered to be responsible for a significant loss of nitrogen (Kuypers et al. 2005). However, Ward et al. (2009) argue that denitrification rather than anammox is responsible for most nitrogen loss in other areas. Whether anammox or denitrification is responsible for most nitrogen loss in the ocean, it is clear that anammox represents an important process in the global nitrogen cycle.

Denitrification
Denitrification is the process that converts nitrate to nitrogen gas, thus removing bioavailable nitrogen and returning it to the atmosphere. Dinitrogen gas (N2) is the ultimate end product of denitrification, but other intermediate gaseous forms of nitrogen exist (Figure 7). Some of these gases, such as nitrous oxide (N2O), are considered greenhouse gasses, reacting with ozone and contributing to air pollution.

Unlike nitrification, denitrification is an anaerobic process, occurring mostly in soils and sediments and anoxic zones in lakes and oceans. Similar to nitrogen fixation, denitrification is carried out by a diverse group of prokaryotes, and there is recent evidence that some eukaryotes are also capable of denitrification (Risgaard-Petersen et al. 2006). Some denitrifying bacteria include species in the genera Bacillus, Paracoccus, and Pseudomonas. Denitrifiers are chemoorganotrophs and thus must also be supplied with some form of organic carbon.

Denitrification is important in that it removes fixed nitrogen (i.e., nitrate) from the ecosystem and returns it to the atmosphere in a biologically inert form (N2). This is particularly important in agriculture where the loss of nitrates in fertilizer is detrimental and costly. However, denitrification in wastewater treatment plays a very beneficial role by removing unwanted nitrates from the wastewater effluent, thereby reducing the chances that the water discharged from the treatment plants will cause undesirable consequences (e.g., algal blooms).

Ammonification
When an organism excretes waste or dies, the nitrogen in its tissues is in the form of organic nitrogen (e.g. amino acids, DNA). Various fungi and prokaryotes then decompose the tissue and release inorganic nitrogen back into the ecosystem as ammonia in the process known as ammonification. The ammonia then becomes available for uptake by plants and other microorganisms for growth.


http://www.ck12.org/book/CK-12-Earth-Science-For-High-School/r2/section/18.2/

Nitrogen is also a very important element, used as a nutrient for plant and animal growth. First, the nitrogen must be converted to a useful form. Without "fixed" nitrogen, plants, and therefore animals, could not exist as we know them.

http://ellemedit1234.wordpress.com/2013/09/09/the-nitrogen-cycle/

The Nitrogen cycle is a lot more complex than the carbon cycle. Nitrogen is a very important element. It makes up almost 80% of our atmosphere, and it is an important component of proteins and DNA, both of which are the building blocks of animals and plants. Therefore without nitrogen we would lose one of the most important elements on this planet, along with oxygen, hydrogen and carbon. There are a number of stages to the nitrogen cycle, which involve breaking down and building up nitrogen and it’s various compounds.

There is no real starting point for the nitrogen cycle. It is an endless cycle. However we need a place to start from, and that is in the atmosphere. Nitrogen is very abundant in the atmosphere. Now through different processes nitrogen is constantly being removed from the atmosphere, and it is also being replaced again with more nitrogen. We are going to start with the process that removes nitrogen from the atmosphere, which is called nitrogen fixation. This is when nitrogen gas is transformed into various nitrogen compounds, such as ammonia, ammonium or even nitrate and nitrite. There are 3 ways in which the nitrogen gas can be fixed. The first method is slightly rare, but involves lightning. When lightning passes through the atmosphere it fixes the nitrogen, forming ammonia. However the other two processes are much more important when considering the nitrogen cycle. Both of the other methods are caused by bacteria.

One method involves free-living nitrogen-fixing bacteria. These bacteria convert the nitrogen into ammonia. These bacteria will naturally produce ammonia, however it will be used up in the production of amino acids. The other method involves mutualistic nitrogen-fixing bacteria, which live in the roots of different plants, including peas. They live in small bubbles, called nodules in the roots. This will provide the plants of the roots in which they live with amino acids.



http://ellemedit1234.wordpress.com/2013/09/09/the-nitrogen-cycle/

http://chemistry.about.com/od/geochemistry/ss/nitrogencycle.htm


http://belligerentdesign-asyncritus.blogspot.com.br/2010/01/cyanobacteria-evolutions-ignored.html

I am, and have long been, impressed with the great cycles in nature.
We see, inter alia, the carbon dioxide cycle, the oxygen cycle, the rain cycle and the nitrogen cycle.
Of these four, the nitrogen cycle has been of the greatest interest to me, because of its colossal importance to the survival of agriculture in all its forms.

We are faced with a tremendous problem, because nitrogen is one of the least reactive gases known, excepting only the rare gases of group 8 in the periodic table, such as helium. It just doesn't combine with anything under ordinary conditions.

The problem arises, of course, because nitrogen is an essential constituent of proteins and other substances, all needed for life to survive. No nitrogen: no proteins, no enzymes, no life. (By the way, when I say 'essential' I mean that survival is impossible without it.)

So how does nitrogen become available to living organisms? How could it?

The Almighty, as usual, has the answer that works perfectly.

Nitrogen becomes available in 3 ways:

1 Lightning discharges, at 30,000 deg C, force the combination of nitrogen and oxygen, to produce nitrogen dioxide, which dissolves in rain water to form nitric and nitrous acids, which then combine with compounds in the soil to produce nitrates and nitrites - which are utilisable by plants. So that's number one.

2 In the root nodules of leguminous plants, the bacterium Rhizobium leguminosarum has a symbiotic relationship with the plant. It 'fixes' atmospheric nitrogen, making it available to the plant, and in return, the plant provides the bacterium with salts etc for its survival. Curiously, haemoglobin is formed in the nodules too. It's role is not yet known with certainty, but researchers agree that it must have a function there.

Which, of course, drips another drop of poison into the evolutionist's already bitter cup: what on earth is haemoglobin doing in such a place? How does evolutionary biochemistry account for its existence? Well, easy. It can't. So nuts to evolutionary biochemistry.

3 By far, the greatest contribution to nitrogen fixation comes from the cyanobacteria. These bacteria have 'evolved (ho ho!)' the ability to take nitrogen from the air, [I wonder how they figured that little trick out???] convert it into their cellular material, and on dying, decompose and make nitrogen available to the soil. Without them, life would surely perish.

Just as an aside, it wasn't until 1918 that Haber received a nobel prize for inventing the process which took nitrogen from the air to make ammonia, using catalysts and very high temperatures. That's how difficult it is to do industrially. Yet, here were these little bacteria doing it for the last n billion years. At ambient temperature, give or take diurnal variation!!! So who deserves that Nobel Prize?

So in the beginning, not only was lack of oxygen a gigantic problem, but the lack of nitrogen was no less so. In order for the anaerobic organisms, whatever they might have been, to generate oxygen in quantity, they simply HAD to have nitrogen in their tissues (as enzymes etc). With nitrogen as unreactive as it is, then how did they fix it? The advanced nitrogen fixers hadn't 'evolved' yet.

So yet another evolutionary brick wall stares us in the face.

http://www.grisda.org/origins/60006.pdf

Zuill, H.A. and Standish, T.G., Irreducible interdependence: an ic-like ecological property potentially illustrated by the nitrogen cycle, Origins 60:6–40, 2007;

http://www.grisda.org/origins/60006.pdf

the cycle acts as a vital buffer to changes in nitrogen-containing molecules in the environment, while at the same time ensuring availability of reduced nitrogen for biological purposes.

http://creation.mobi/biblical-ecology

Nitrogen is crucial for the existence of all life and is a building block of amino acids needed for protein synthesis, as well as nucleotides and their nucleic acids. The nitrogen cycle’s function is to keep its various molecular forms in balance so that life can persist. Through five stages, atmospheric nitrogen is converted into nitrogen compounds that plants require and can assimilate, and it is then recycled back into the atmosphere again. Many chemical steps are involved in various parts of ecosystems and specific enzymes are needed at the right times and places. The nitrogen cycle is dependent on the carbon cycle and requires microbes and other creatures to work in concert. In turn, plants provide nutrition to animals. Amazingly, in order for certain chemical reactions to continue, plants contribute specific chemicals while the biomatrix provides what plants lack in order to complete the required chemical reactions. Many diverse genera are involved and this redundancy is important as a system back up should a certain taxon not be present.

Behe’s concept of irreducible complexity in biological systems41 was enlarged and extended to ecosystems, giving rise to a term ‘irreducible interdependence’.40 Behe discussed this concept in the context of biochemical reactions in single organisms. Zuill and Standish used the term ‘ecochemical pathways’ to refer to the series of biochemical reactions across multiple species, where each step of the reaction is mediated by one or several species. An irreducibly interdependent system has the following characteristics in this testable model:

  Potential gaps in the system cannot be reasonably bypassed by inorganic nature alone.
  It must have a degree of specificity that in all probability could not have been produced by chance.
  A given function or step in the system may be found in several different unrelated organisms.
  The removal of any one of the individual biological steps will resort in the loss of function of the system.

The data suggest that the nitrogen cycle may be irreducibly interdependent based on the above criteria. No proposed neo-Darwinian mechanisms can explain the origin of such a system. Compounding matters, Zuill makes a strong case by suggesting that this biodiversity of multi-species interactions have always been required for biospheric regulation and had to have been built rapidly.42 Several of the above arguments are based on logical inferences, but many of these inferences can be further tested to determine if they meet interdependence criteria. This research could be extended to test other global cycles, and interaction between cycles, for irreducible interdependence.

1. https://en.wikipedia.org/wiki/Nitrogen_assimilation
2. http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.465.3125&rep=rep1&type=pdf



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1. http://en.wikipedia.org/wiki/Nitrogen_fixation

Nitrogen fixation is a process by which nitrogen (N2) in the atmosphere is converted into ammonia (NH3).[1] Atmospheric nitrogen or molecular nitrogen (N2) is relatively inert: it does not easily react with other chemicals to form new compounds. The fixation process frees up the nitrogen atoms from their diatomic form (N2) to be used in other ways.

Nitrogen fixation, natural and synthetic, is essential for all forms of life because nitrogen is required to biosynthesize basic building blocks of plants, animals and other life forms, e.g., nucleotides for DNA and RNA and amino acids for proteins.

Whilst the chemical abundance is uncertain it is ridiculous to think that the spontaneous formation of say amino acids could not happen outside the lab some 4 billion years ago. Without cyanobacteria - no fixed nitrogen is available.
Without fixed nitrogen, no DNA, no amino-acids, no protein can be synthesised.
Without DNA, no amino-acids,protein, or cyanobacteria are possible.
There are several other points here, in addition.
These bacteria also photosynthesise (a process requiring a large number of proteins, both in the execution of the reactions, and in the structure of the membranes of the chloroplasts). Let's say 30 for argument's sake.
They fix nitrogen - and so require that marvellous enzyme nitrogenase, which is really a combination of 2 separate enzymes, proteins to be precise.
None of these, as shown above, can be made without fixed nitrogen.
Nitrogen cannot be fixed without them. So which came first, the chicken or the egg//http://en.wikipedia.org/wiki/Amino_acid_synthesis

A fundamental problem for biological systems is to obtain nitrogen in an easily usable form. This problem is solved by certain microorganisms capable of reducing the inert N≡N molecule (nitrogen gas) to two molecules of ammonia in one of the most remarkable reactions in biochemistry. Ammonia is the source of nitrogen for all the amino acids.

To obtain nitrogen in usable form, you need nitrogen fixation :

http://en.wikipedia.org/wiki/Nitrogen_fixation

Nitrogen fixation, natural and synthetic, is essential for all forms of life because nitrogen is required to biosynthesize basic building blocks of plants, animals and other life forms, e.g., nucleotides for DNA and RNA and amino acids for proteins.

How can this occur :

1) Nitrogen fixation occurs naturally in the air by means of lightning. It forces the combination of nitrogen and oxygen, to produce nitrogen dioxide, which dissolves in rain water to form nitric and nitrous acids, which then combine with compounds in the soil to produce nitrates and nitrites - which are utilisable by plants

the causes of lightning are still not fully understood .

2)Free-Living Heterotrophs
Many heterotrophic bacteria live in the soil and fix significant levels of nitrogen without the direct interaction with other organisms. Examples of this type of nitrogen-fixing bacteria include species of Azotobacter, Bacillus, Clostridium, and Klebsiella.

Associative Nitrogen Fixation
Species of Azospirillum ( bacteria )are able to form close associations with several members of the Poaceae (grasses), including agronomically important cereal crops, such as rice, wheat, corn, oats, and barley.

Nitrogen Fixation
Many microorganisms fix nitrogen symbiotically by partnering with a host plant.

Legume Nodule Formation
The Rhizobium or Bradyrhizobium bacteria colonize the host plant’s root system and cause the roots to form nodules to house the bacteria

By far, the greatest contribution to nitrogen fixation comes from the cyanobacteria.

These bacteria have the ability to take nitrogen from the air, [I wonder how they figured that little trick out???] convert it into their cellular material, and on dying, decompose and make nitrogen available to the soil.

So in the beginning, not only was lack of oxygen a gigantic problem, but the lack of nitrogen was no less so. In order for the anaerobic organisms, whatever they might have been, to generate oxygen in quantity, they simply HAD to have nitrogen in their tissues (as enzymes etc). With nitrogen as unreactive as it is, then how did they fix it? The advanced nitrogen fixers hadn't 'evolved' yet.

http://www.nature.com/.../an-evolutionary-perspective-on...

The ultimate source of nitrogen for the biosynthesis of amino acids is atmospheric nitrogen (N2), a nearly inert gas. However, to be metabolically useful, atmospheric nitrogen must be reduced. This process, known as nitrogen fixation, occurs only in certain types of bacteria. Even though nitrogen is one of the most prominent chemical elements in living systems, N2 is almost unreactive (and very stable) because of its triple bond (N≡N). This bond is extremely difficult to break because the three chemical bonds need to be separated and bonded to different compounds. Nitrogenase is the only family of enzymes capable of breaking this bond (i.e., it carries out nitrogen fixation).

http://mbe.oxfordjournals.org/content/21/3/541.long

Still, the origin and extant distribution of nitrogen fixation has been perplexing from a phylogenetic perspective.

http://chemwiki.ucdavis.edu/.../Nitrogenase/Nitrogenase_1

Nitrogenase is a unique enzyme with a crucial function that is distinct to bacteria that utilize it, has unique structure and symmetry, and is sensitive to other compounds that inhibits its functioning. It is “an enzymatic complex which enables fixation of atmospheric nitrogen” . The unique structure of nitrogenase is almost completely known because of the extensive research that has been done on this enzyme. Nitrogenase can also bind to compounds other than nitrogen gas, which can inhibit and decrease its production of ammonia to the rest of the organism’s body. Without proper functioning, the bacteria that utilize nitrogenase would not be able to survive, and other organisms that depend on these bacteria would also die.

Nitrogenase is unique in its ability to fix nitrogen, so that it is more reactive and able to be applied in other reactions that help organisms grow and thrive. David Goodsell states, “Nitrogen is needed by all living things to build proteins and nucleic acids” [4]. However, nitrogen gas, N2, is an inert gas that is stabilized by its triple bond [5], and is difficult for living organisms to use as a source of nitrogen because the molecule’s stability. Nitrogenase is used to separate nitrogen gas, N2, and transforms it into ammonia, NH3 in the reaction:

N2 + 8H+ + 8e- + 16 ATP + 16H2O ----> 2NH3 + H2 + 16ADP + 16Pi

In the form of ammonia organisms have a useable source of nitrogen that is more reactive and can be used to create proteins and nucleic acids that are also necessary for the organism. According to the Peters and Szilagyi, “Three types of nitrogenase are known, called molybdenum (Mo) nitrogenase, vanadium (V) nitrogenase and iron-only (Fe) nitrogenase” and the molybdenum nitrogenase,crystal structure shown in Figure 2, is the one that has been studied the most of the three . The nitrogenase enzyme breaks up a diatomic nitrogen gas molecule using a large number of ATP and 8 electrons to create two ammonia molecules and hydrogen gas for each molecule of nitrogen gas . As a result, the bacteria that utilize this enzyme must expend much of their energy, in the form of ATP, so that they will constantly obtain a steady source of nitrogen. Without nitrogenase’s function of fixing nitrogen gas into ammonia, then organisms would not be able to thrive since they would not receive a source of nitrogen for other important reactions.

How could those regulatory machines evolve at precisely the right rate so as to drop into the right place at precisely the right time to effect proper assembly of the nitrogenase machinery?

Fine, L.W., Chemistry Decoded, Oxford University Press, London, pp. 320-330, 1976.

“Nature is really good at it (nitrogen-splitting), so good in fact that we’ve had difficulty in copying chemically the essence of what bacteria do so well”

http://en.wikipedia.org/wiki/Nitrogen_cycle

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

So there we have a classic chicken and egg problem........


Nitrogen becomes available in 4 ways:

1 Lightning discharges, at 30,000 deg C, force the combination of nitrogen and oxygen, to produce nitrogen dioxide, which dissolves in rain water to form nitric and nitrous acids, which then combine with compounds in the soil to produce nitrates and nitrites - which are utilisable by plants. So that's number one. Lightening can break the bond but they do not produce sufficient quantities of the biologically reactive nitrogen to be of any substantial use.

2 In the root nodules of leguminous plants, the bacterium Rhizobium leguminosarum has a symbiotic relationship with the plant. It 'fixes' atmospheric nitrogen, making it available to the plant, and in return, the plant provides the bacterium with salts etc for its survival. Curiously, haemoglobin is formed in the nodules too. It's role is not yet known with certainty, but researchers agree that it must have a function there.

Which, of course, drips another drop of poison into the evolutionist's already bitter cup: what on earth is haemoglobin doing in such a place? How does evolutionary biochemistry account for its existence? Well, easy. It can't. So nuts to evolutionary biochemistry.

3.the release of these compounds during organic matter decomposition

4. By far, the greatest contribution to nitrogen fixation comes from the cyanobacteria. These bacteria have 'evolved (ho ho!)' the ability to take nitrogen from the air, [I wonder how they figured that little trick out???] convert it into their cellular material, and on dying, decompose and make nitrogen available to the soil. Without them, life would surely perish.

So in the beginning, not only was lack of oxygen a gigantic problem, but the lack of nitrogen was no less so. In order for the anaerobic organisms, whatever they might have been, to generate oxygen in quantity, they simply HAD to have nitrogen in their tissues (as enzymes etc). With nitrogen as unreactive as it is, then how did they fix it? The advanced nitrogen fixers hadn't 'evolved' yet.

Through five stages, atmospheric nitrogen is converted into nitrogen compounds that plants require and can assimilate, and it is then recycled back into the atmosphere again.

The nitrogenase enzyme breaks up a diatomic nitrogen gas molecule using a large number of ATP and 8 electrons to create two ammonia molecules and hydrogen gas for each molecule of nitrogen gas . As a result, the bacteria that utilize this enzyme must expend much of their energy, in the form of ATP, so that they will constantly obtain a steady source of nitrogen. Without nitrogenase’s function of fixing nitrogen gas into ammonia, then organisms would not be able to thrive since they would not receive a source of nitrogen for other important reactions.

How could those regulatory machines evolve at precisely the right rate so as to drop into the right place at precisely the right time to effect proper assembly of the nitrogenase machinery?


http://creation.mobi/biblical-ecology

The nitrogen cycle is dependent on the carbon cycle and requires microbes and other creatures to work in concert.

An irreducibly interdependent system has the following characteristics in this testable model:

Potential gaps in the system cannot be reasonably bypassed by inorganic nature alone.
It must have a degree of specificity that in all probability could not have been produced by chance.
A given function or step in the system may be found in several different unrelated organisms.
The removal of any one of the individual biological steps will resort in the loss of function of the system.


Microbes are also a crucial component in biogeochemical cycling. These cycles consist of the paths elements take through the global system for proper functioning and persistence of life. If microbes did not exist, the critical carbon, nitrogen and phosphorous cycles would not be possible and life would cease. Life affects chemistry and chemistry affects life.

http://rstb.royalsocietypublishing.org/content/363/1504/2731.long

The atmosphere has apparently been oxygenated since the ‘Great Oxidation Event’ ca 2.4 Ga ago, but when the photosynthetic oxygen production began is debatable. However, geological and geochemical evidence from older sedimentary rocks indicates that oxygenic photosynthesis evolved well before this oxygenation event. Fluid-inclusion oils in ca 2.45 Ga sandstones contain hydrocarbon biomarkers evidently sourced from similarly ancient kerogen, preserved without subsequent contamination, and derived from organisms producing and requiring molecular oxygen. Mo and Re abundances and sulphur isotope systematics of slightly older (2.5 Ga) kerogenous shales record a transient pulse of atmospheric oxygen. As early as ca 2.7 Ga, stromatolites and biomarkers from evaporative lake sediments deficient in exogenous reducing power strongly imply that oxygen-producing cyanobacteria had already evolved. Even at ca 3.2 Ga, thick and widespread kerogenous shales are consistent with aerobic photoautrophic marine plankton, and U–Pb data from ca 3.8 Ga metasediments suggest that this metabolism could have arisen by the start of the geological record. Hence, the hypothesis that oxygenic photosynthesis evolved well before the atmosphere became permanently oxygenated seems well supported.

Nitrogen fixation in methanogens: the archaeal perspective.

http://www.ncbi.nlm.nih.gov/pubmed/11471757

http://www.horizonpress.com/cimb/v/v2/v2n404.pdf

The methanogenic Archaea bring a broadened perspective to the field of nitrogen fixation. Biochemical and genetic studies show that nitrogen fixation in Archaea is evolutionarily related to nitrogen fixation in Bacteria and operates by the same fundamental mechanism. How ?? At least six nif genes present in Bacteria (nif H, D, K, E, N and X) are also found in the diazotrophic methanogens. So what ?? Most nitrogenases in methanogens are probably of the molybdenum type. However, differences exist in gene organization and regulation. All six known nif genes of methanogens, plus two homologues of the bacterial nitrogen sensor-regulator glnB, occur in a single operon in Methanococcus maripaludis. nif gene transcription in methanogens is regulated by what appears to be a classical prokaryotic repression mechanism. At least one aspect of regulation, post-transcriptional ammonia switch-off, involves novel members of the glnB family. Phylogenetic analysis suggests that nitrogen fixation may have originated in a common ancestor of the Bacteria and the Archaea.

A separate analysis by parsimony gave essentially the same results as the distance matrix analysis. nifD and nifE
are evidently paralogous, that is, related via an ancient gene duplication. Consequently, nifD genes provide a root for the nifE tree and vice versa.



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Amino Acids and Nucleotide are part of the Nitrogen Cycle

Nitrogen and sulfur are important constituents of biological macromolecules. Nitrogen and sulfur atoms pass from compound to compound and between organisms and their environment in a series of reversible cycles. Although molecular nitrogen is abundant in the Earth's atmosphere, nitrogen is chemically unreactive as a gas. Only a few living species are able to incorporate it into organic molecules, a process called nitrogen fixation. Nitrogen fixation occurs in certain microorganisms and by some geophysical processes, such as lightning discharge. It is essential to the biosphere as a whole, for without it life could not exist on this planet. Only a small fraction of the nitrogenous compounds in today's organisms, however, is due to fresh products of nitrogen fixation from the atmosphere. Most organic nitrogen has been in circulation for some time, passing from one living organism to another. Thus present-day nitrogen-fixing reactions can be said to perform a "topping-up" function for the total nitrogen supply. Vertebrates receive virtually all of their nitrogen from their dietary intake of proteins and nucleic acids. In the body these macromolecules are broken down to amino acids and the components of nucleotides, and the nitrogen they contain is used to produce new proteins and nucleic acids-or utilized to make other molecules. About half of the 20 amino acids found in proteins are essential amino acids for vertebrates , which means that they cannot be synthesized from other ingredients of the diet. The others can be so synthesized, using a variety of raw materials, including intermediates of the citric acid cycle as described previously. The essential amino acids are made by plants and other organisms, usually by long and energetically expensive pathways that have been lost in the course of vertebrate evolution. The nucleotides needed to make RNA and DNA can be synthesized using specialized biosynthetic pathways. All of the nitrogens in the purine and pyrimidine bases (as well as some of the carbons) are derived from the plentiful amino acids glutamine, aspartic acid, and glycine, whereas the ribose and deoxyribose sugars are derived from glucose. There are no "essential nucleotides" that must be provided in the diet. Amino acids not used in biosynthesis can be oxidized to generate metabolic energy. Most of their carbon and hydrogen atoms eventually form COz or HzO, whereas their nitrogen atoms are shuttled through various forms and eventually appear as urea, which is excreted. Each amino acid is processed differently, and a whole constellation of enzymatic reactions exists for their catabolism. 

Sulfur is abundant on Earth in its most oxidized form, sulfate (SOaz-)T. o convert it to forms useful for life, sulfate must be reduced to sulfide (S2-), the oxidation state of sulfur required for the synthesis of essential biological molecules. These molecules include the amino acids methionine and cysteine, coenzyme A (see Figure 2-62), and the iron-sulfur centers essential for electron transport (see Figure 14-23). The process begins in bacteria, fungi, and plants, where a special group of enzymes use ATP and reducing power to create a sulfate assimilation pathway. Humans and other animals cannot reduce sulfate and must therefore acquire the sulfur they need for their metabolism in the food that they eat.

The Evolution and Future of Earth’s Nitrogen Cycle 1



1. http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.465.3125&rep=rep1&type=pdf



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When we think about the elements that are essential for life on Earth, we hardly ever consider molybdenum. The biological role of molybdenum can only be appreciated when put in perspective. Nitrogen is the fourth most abundant element in living organisms (only behind hydrogen, oxygen and carbon) and life on Earth depends on the nitrogen biogeochemical cycle to keep this element in forms that can be used by the organisms. Noteworthy, the “closing” of the nitrogen cycle, with the atmospheric dinitrogen fixation into ammoniu–(Figure 1.1, blue arrow), depends virtually entirely on the trace element molybdenum :



nitrogenase, a prokaryotic enzyme responsible for dinitrogen reduction to ammonium, requires one molybdenum atom in its active site† (Figure 1.3b; see Section 1.4.5 and ref.
55).



The few organisms possessing this enzyme are capable of producing their own reduced (“fixed”) nitrogen forms, using directly the atmospheric dinitrogen, the largest nitrogen source (biological nitrogen fixation is the main route by which nitrogen enters the biosphere). All other organisms, the vast majority of life on Earth, depend on the availability of ammonium and nitrate (from soils, oceans and other organisms).

With this wide perspective in mind, the molybdenum biological role certainly assumes another dimension. In fact, it was recently proposed that the lack of molybdenum, while hampering the existence of an efficient nitrogenase, could have been the limiting factor for life evolution and expansion on early Earth. However, the involvement of molybdenum in the nitrogen cycle is not restricted to the dinitrogen fixation, as the element is also essential for the reduction of nitrate to nitrite and for the oxidation of nitrite to nitrate (Figure 1.1, grey arrows), both processes being exclusively dependent (as far as is presently known) on the molybdenum- containing enzymes nitrate reductases (from both prokaryotic and eukaryotic sources) and nitrite oxidoreductases (from prokaryotes only). Noteworthy, molybdenum has also been suggested to be essential for nitrite reduction to nitric oxide for biological signalling purposes. Nitric oxide is a signalling molecule involved in several physiological processes, in both prokaryotes and eukaryotes, and nitrite is presently recognized as a nitric oxide source particularly relevant to cell signalling and survival under challenging conditions. Nitrite-dependent signalling pathways have been described in mammals, plants and also bacteria, and are carried out by proteins present in cells to carry out other functions, including several molybdoenzymes (which thus form a new class of “non-dedicated” nitric oxide-forming nitrite reductases): mammalian xanthine oxidoreductase, aldehyde oxidase, sulfite oxidase and mitochondrial amidoxime reducing component, plant nitrate reductase and bacterial aldehyde oxidoreductase and nitrate reductases. Molybdenum is also involved in the carbon cycle. The first example that comes to mind is provided by the formate dehydrogenases that are used by acetogens to fix carbon dioxide (reduce it) into formate and eventually form acetate; but molybdenum is also present in carbon monoxide dehydrogenases (catalyzing the oxidation of carbon monoxide to carbon dioxide), aldehyde oxidoreductases (catalyzing the interconversion between aldehydes and carboxylic acids) and in other formate dehydrogenases (that are involved in physiological pathways where formate is oxidized to carbon dioxide). The primitive carbon cycle would have also been dependent on molybdenum, as the metal (together with tungsten) would have been essential for the earliest, strictly anaerobic, organisms to handle aldehydes and carboxylic acids, catalyzing their interconversion

Molybdenum also plays several other “carbon-related” roles in modern higher organisms. The aldehyde oxidase of higher plants is responsible for the oxidation of abscisic aldehyde to abscisic acid (a plant hormone involved in development processes and in a variety of abiotic and biotic stress responses) and has been implicated in the biosynthesis of indole-3-acetic acid (an auxin phytohormone). The mammalian aldehyde oxidases have been suggested to participate in the formation of retinoic acid (a metabolite of retinol (vitamin A) that is involved in growth and development) and in the metabolism of xenobiotic compounds, where they would catalyze the hydroxylation of carbon centres of heterocyclic aromatic compounds and the oxidation of aldehydic groups The dependence of higher plants and animals on molybdenum is also observed in purine catabolism, where xanthine oxidoreductase is involved in the hydroxylation of hypoxanthine and xanthine into urate. Noteworthy, involvement of molybdenum in purine metabolism is common to virtually all forms of life and only a small number of organisms use other mechanisms to oxidize xanthine (e.g. some yeasts), thus confirming the essential role of molybdenum for life on Earth. Another important aspect of molybdenum in biology can be seen in sulfite- oxidizing enzymes, which are used by almost all forms of life in the catabolism of sulfur-containing amino acids and other sulfur-containing compounds, oxidizing sulfite to sulfate. Certainly, sulfite oxidase is one of the most striking examples of the human dependence on molybdenum. Sulfite (derived not only from the catabolism of sulfur-containing amino acids, but also from sulfur-containing xenobiotic compounds) is toxic and its controlled oxidation to sulfate is critical for survival. Underscoring this vital role, human sulfite oxidase deficiency results in severe neonatal neurological problems, including attenuated growth of the brain, mental retardation, seizures and early death.‡ Molybdenum-dependent sulfite-oxidizing enzymes are also important for some prokaryotes that are able to generate energy from the respiratory oxidation of inorganic sulfur compounds – hence, extending the role of molybdenum to the sulfur cycle.

Why do living organisms expend so much effort to use these metals in a (comparatively) small number of reactions? This effort (including synthesizing the protein machinery to scavenge the metals from the environment, producing and inserting the specialized cofactors and regulating the whole process) underscores how important both metals would have been, and still are to extant organisms, particularly in the case of molybdenum.

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The evolution of Earth’s biogeochemical nitrogen cycle

A better understanding of what constrained the evolution of life on Earth, therefore, demands a reconstruction of the biogeochemical nitrogen cycle over time; in particular its role as a limiting nutrient affecting biological evolution and ecology. Evolution of the nitrogen cycle may also have had significant effects on the continued habitability of the Earth. The partial pressure of nitrogen gas (N2) in the atmosphere controls the degree of pressure-broadening of greenhouse gas adsorption and thus surface temperature


Nitrogen is an essential nutrient for all life on Earth and it acts as a major control on biological productivity in the modern ocean.
Accurate reconstructions of the evolution of life over the course of the last four billion years therefore demand a better understanding of nitrogen bioavailability and speciation through time. The biogeochemical nitrogen cycle has evidently been closely tied to the redox state of the ocean and atmosphere. Multiple lines of evidence indicate that the Earth‟s surface has passed in a non-linear fashion from an anoxic state in the Hadean to an oxic state in the later Phanerozoic. It is therefore likely that the nitrogen cycle has changed markedly over time, with potentially severe implications for the productivity and evolution of the biosphere. Here we compile nitrogen isotope data from the literature and review our current understanding of the evolution of the nitrogen cycle, with particular emphasis on the Precambrian. Combined with recent work on redox conditions, trace metal availability, sulfur and iron cycling on the early Earth, we then use the nitrogen isotope record as a platform to test existing and new hypotheses about biogeochemical pathways that may have controlled nitrogen availability through time.

Among other things, we conclude that
(a) abiotic nitrogen sources were likely insufficient to sustain a large biosphere, thus favoring an early origin of biological N2 fixation,
(b) evidence of nitrate in the Neoarchean and Paleoproterozoic confirm current views of increasing surface oxygen levels at those times,
(c) abundant ferrous iron and sulfide in the midPrecambrian ocean may have affected the speciation and size of the fixed nitrogen reservoir, and
(d) nitrate availability alone was not a major driver of eukaryotic evolution.

https://research-repository.st-andrews.ac.uk/bitstream/handle/10023/11269/Stueeken_2016_ESR_BiogeochemNitrogenCycle_AM.pdf?sequence=1&isAllowed=y

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