Nitrogen Metabolism

  • The nitrogen cycle depicts the different ways in which nitrogen, an essential element for life, is used and converted by organisms for various purposes.
  • Much of the chemical conversions are performed by microbes as part of their metabolism, performing a valuable
  • service in the process for other organisms in providing them with an alternate chemical form of the element.

1 21

  • Nitrogen fixation describes the conversion of the relatively inert dinitrogen gas (N2) into ammonia (NH3).
  • A much more useable form of nitrogen for most life forms.
  • The process is performed by diazotrophs, a limited number of bacteria and archaea that can grow without an external source of fixed nitrogen because of their abilities.
  • Nitrogen fixation is an essential process for Earth’s organisms, since nitrogen is a required component of various organic molecules, such as amino acids and nucleotides.
  • Plants, animals, and other organisms rely on bacteria and archaea to provide nitrogen in a fixed form, since no eukaryote is known that can fix nitrogen.
  • Nitrogen fixation is an extremely energy and electron intensive process, in order to break the triple bond in N2 and reduce it to NH3.
  • It requires a particular enzyme known as nitrogenase, which is inactivated by O2.
  • Thus, nitrogen fixation must take place in an anaerobic environment.
  • Aerobic nitrogen-fixing organisms must devise special conditions or arrangements in order to protect their enzyme.
  • Nitrogen-fixing organisms can either exist independently or pair up with a plant host:
  1. Symbiotic nitrogen-fixing organisms: these bacteria partner up with a plant, to provide them with an environment appropriate for the functioning of their nitrogenase enzyme.
  • The bacteria live in the plant’s tissue, often in root nodules, fixing nitrogen and sharing the results. The plant provides both the location to fix nitrogen, as well as additional nutrients to support the energy-taxing process of nitrogen fixation.
  • It has been shown that the bacteria and the host exchange chemical recognition signals that facilitate the relationship.
  • One of the best known bacteria in this category is Rhizobium, which partners up with plants of the legume family (clover, soybeans, alfalfa, etc).
  1. Free-living nitrogen-fixing organisms: these organisms, both bacteria and archaea, fix nitrogen for their own use that ends up being shared when the organisms dies or is ingested.
  2. Free-living nitrogen-fixing organisms that grow anaerobically do not have to worry about special adaptations for their nitrogenase enzyme.
  • Aerobic organisms must make adaptations. Cyanobacteria, a multicellular bacterium, make specialized cells known as heterocysts in which nitrogen fixation occurs.
  • Since Cyanobacteria produce oxygen as part of their photosynthesis, an anoxygenic version occurs within the heterocyst, allowing the nitrogenase to remain active.
  • The heterocysts share the fixed nitrogen with surrounding cells, while the surrounding cells provide additional nutrients to the heterocysts.


  • Assimilation is a reductive process by which an inorganic form of nitrogen is reduced to organic nitrogen compounds such as amino acids and nucleotides.
  • This allowing for cellular growth and reproduction. Only the amount needed by the cell is reduced.
  • Ammonia assimilation occurs when the ammonia (NH3)/ammonium ion (NH4+) formed during nitrogen fixation is incorporated into cellular nitrogen.
  • Assimilative nitrate reduction is a reduction of nitrate to cellular nitrogen, in a multi-step process where nitrate is reduced to nitrite then ammonia and finally into organic nitrogen.


  • As mentioned above, nitrification is performed by chemolithotrophs using a reduced or partially reduced form of nitrogen as an electron donor to obtain energy.
  • ATP is gained by the process of oxidative phosphorylation, using a ETC, PMF, and ATP synthase.


  • Denitrification refers to the reduction of NO3- to gaseous nitrogen compounds, such as N2.
  • Denitrifying microbes perform anaerobic respiration, using NO3- as an alternate final electron acceptor to 02.
  • This is a type of dissimilatory nitrate reduction where the nitrate is being reduced during energy conservation.