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Mechanism of biological nitrogen fixation

1. Mechanism of biological nitrogen fixation

Biological nitrogen fixation can be represented by the following equation, in which two

moles of ammonia are produced from one mole of nitrogen gas, at the expense of 16 moles of 

ATP and a supply of electrons and protons (hydrogen ions):

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

This reaction is performed exclusively by prokaryotes (the bacteria and relatedorganisms), using an enzyme complex termed nitrogenase. This enzyme consists of two proteins

- an iron protein and a molybdenum-iron protein, as shown below.

The reactions occur while N2 is bound to the nitrogenase enzyme complex. The Fe

 protein is first reduced by electrons donated by ferredoxin. Then the reduced Fe protein binds

ATP and reduces the molybdenum-iron protein, which donates electrons to N2, producing

HN=NH. In two further cycles of this process (each requiring electrons donated by ferredoxin)

HN=NH is reduced to H2 N-NH2, and this in turn is reduced to 2NH3.

Depending on the type of microorganism, the reduced ferredoxin which supplies

electrons for this process is generated by photosynthesis, respiration or fermentation.

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There is a remarkable degree of functional conservation between the nitrogenase proteinsof all nitrogen-fixing bacteria. The Fe protein and the Mo-Fe protein have been isolated from

many of these bacteria, and nitrogen fixation can be shown to occur in cell-free systems in a

laboratory when the Fe protein of one species is mixed with the Mo-Fe protein of another 

 bacterium, even if the species are very distantly related.

The nitrogen-fixing organisms

All the nitrogen-fixing organisms are prokaryotes (bacteria). Some of them liveindependently of other organisms - the so-called free-living nitrogen-fixing bacteria. Others live

in intimate symbiotic associations with plants or with other organisms (e.g. protozoa). Examples

are shown in the table below.

Examples of nitrogen-fixing bacteria (* denotes a photosynthetic bacterium)

Free living Symbiotic with plants

Aerobic

Anaerobic (see

Winogradsky column for 

details)

Legumes Other plants

 Azotobacter 

 Beijerinckia

 Klebsiella (some)

Cyanobacteria (some)*

Clostridium (some)

 Desulfovibrio

Purple sulphur bacteria*

Purple non-sulphur bacteria*

Green sulphur bacteria*

 Rhizobium Frankia

 Azospirillum

 

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A point of special interest is that the nitrogenase enzyme complex is highly sensitive to

oxygen. It is inactivated when exposed to oxygen, because this reacts with the iron component of 

the proteins. Although this is not a problem for anaerobic bacteria, it could be a major problem

for the aerobic species such as cyanobacteria (which generate oxygen during photosynthesis) and

the free-living aerobic bacteria of soils, such as  Azotobacter and  Beijerinckia. These organisms

have various methods to overcome the problem. For example,  Azotobacter  species have the

highest known rate of respiratory metabolism of any organism, so they might protect the enzyme

 by maintaining a very low level of oxygen in their cells.  Azotobacter  species also produce

copious amounts of extracellular polysaccharide (as do  Rhizobium species in culture - see

Exopolysaccharides). By maintaining water within the polysaccharide slime layer, these bacteria

can limit the diffusion rate of oxygen to the cells. In the symbiotic nitrogen-fixing organisms

such as  Rhizobium, the root nodules can contain oxygen-scavenging molecules such as

leghaemoglobin, which shows as a pink colour when the active nitrogen-fixing nodules of 

legume roots are cut open. Leghaemoglobin may regulate the supply of oxygen to the nodule

tissues in the same way as haemoglobin regulates the supply of oxygen to mammalian tissues.

Some of the cyanobacteria have yet another mechanism for protecting nitrogenase: nitrogen

fixation occurs in special cells (heterocysts) which possess only photosystem I (used to generate

ATP by light-mediated reactions) whereas the other cells have both photosystem I and

 photosystem II (which generates oxygen when light energy is used to split water to supply H 2 for 

synthesis of organic compounds).

2. Interaction between plant and microorganism to make nodulation

Legumes release compounds called flavonoids from their roots, which trigger the

 production of nod factors  by the bacteria. When the nod factor is sensed by the root, a number of 

 biochemical and morphological changes happen: cell division is triggered in the root to create the

nodule, and the root hair  growth is redirected to wind around the bacteria multiple times until it

fully encapsulates 1 or more bacteria. The bacteria encapsulated divide multiple times, forming a

microcolony. From this microcolony, the bacteria enter the developing nodule through a

structure called an infection thread, which grows through the root hair into the basal part of the

epidermis  cell, and onwards into the root cortex; they are then surrounded by a plant-derived

membrane and differentiate into bacteroids that fix nitrogen.

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 Nodulation is controlled by a variety of processes, both external (heat, acidic soils, drought,

nitrate) and internal (autoregulation of nodulation, ethylene). Autoregulation of nodulation

controls nodule numbers per plant through a systemic process involving the leaf. Leaf tissue

senses the early nodulation events in the root through an unknown chemical signal, then restricts

further nodule development in newly developing root tissue. The Leucine rich repeat (LRR)

receptor kinases (NARK in soybean (Glycine max); HAR1 in   Lotus japonicus, SUNN in

Medicago truncatula) are essential for autoregulation of nodulation (AON). Mutation leading to

loss of function in these AON receptor kinases leads to supernodulation or hypernodulation.

Often root growth abnormalities accompany the loss of AON receptor kinase activity, suggesting

that nodule growth and root development are functionally linked. I. Investigations into the

mechanisms of nodule formation showed that the ENOD40 gene, coding for a 12–13 amino acid

 protein [41], is up-regulated during nodule formation [3].

3. Scheme of sulphur cycle

Sulphur is one of the components that make up proteins and vitamins. Proteins consist of amino

acids that contain sulphur atoms. Sulphur is important for the functioning of proteins and

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enzymes in plants, and in animals that depend upon plants for sulphur. Plants absorb sulphur 

when it is dissolved in water. Animals consume these plants, so that they take up enough sulphur 

to maintain their health.

Most of the earth's sulphur is tied up in rocks and salts or buried deep in the ocean in

oceanic sediments. Sulphur can also be found in the atmosphere. It enters the atmosphere

through both natural and human sources. Natural recourses can be for instance volcanic

eruptions, bacterial processes, evaporation from water, or decaying organisms. When sulphur 

enters the atmosphere through human activity, this is mainly a consequence of industrial

 processes where sulphur dioxide (SO2) and hydrogen sulphide (H2S) gases are emitted on a wide

scale.

When sulphur dioxide enters the atmosphere it will react with oxygen to produce sulphur trioxide

gas (SO3), or with other chemicals in the atmosphere, to produce sulphur salts. Sulphur dioxide

may also react with water to produce sulphuric acid (H2SO4). Sulphuric acid may also be

 produced from demethylsulphide, which is emitted to the atmosphere by plankton species.

All these particles will settle back onto earth, or react with rain and fall back onto earth as acid 

deposition. The particles will than be absorbed by plants again and are released back into the

atmosphere, so that the sulphur cycle will start over again.