Nitrogen assimilation

Nitrogen assimilation is the formation of organic nitrogen compounds like amino acids from inorganic nitrogen compounds present in the environment. Organisms like plants, fungi and certain bacteria that cannot fix nitrogen gas (N₂) depend on the ability to assimilate nitrate or ammonia for their needs. Other organisms, like animals, depend entirely on organic nitrogen from their food.

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. Plant roots themselves can affect the abundance of various forms of nitrogen by changing the pH and secreting organic compounds or oxygen. This influences microbial activities like the inter-conversion of various nitrogen species, the release of ammonia from organic matter in the soil and the fixation of nitrogen by non-nodule-forming bacteria.

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. While nearly all the ammonia in the root is usually incorporated into amino acids at the root itself, plants may transport significant amounts of ammonium ions in the xylem to be fixed in the shoots. This may help avoid the transport of organic compounds down to the roots just to carry the nitrogen back as amino acids.

Nitrate reduction is carried out in two steps. Nitrate is first reduced to nitrite (NO₂⁻) in the cytosol by nitrate reductase using NADH or NADPH. Nitrite is then reduced to ammonia in the chloroplasts (plastids in roots) by a ferredoxin dependent nitrite reductase. In photosynthesizing tissues, it uses an isoform of ferredoxin (Fd1) that is reduced by PSI while in the root it uses a form of ferredoxin (Fd3) that has a less negative midpoint potential and can be reduced easily by NADPH. In non photosynthesizing tissues, NADPH is generated by glycolysis and the pentose phosphate pathway.

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