Nitrogen fixing bacteria in plants

How the process is carried out and evolution of nitrogenase.

There is 78 % of molecular nitrogen (N2) in the atmosphere which can be bound in compounds only by procaryotes. Eukaryotes cannot fix (that is make useful compounds of) atmospheric nitrogen and convert it into an ion, therefore they need symbiosis with prokaryotes as atmospheric nitrogen 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 triply bonded diatomic form, N≡N, to be used in other ways.

Biological nitrogen fixation is carried out by:

  • free-living soil bacteria (aerobic Azotobacter sp., anaerobic Clostridium sp.);
  • cyanobacteria (Nostoc sp., Calothrix sp.), both in water and on land;
  • plant associated bacteria (Rhizobium sp.) – this is what we’re concetrating on in this post;
  • epiphytic lichens in the tropics (Cyanobacterium sp. – which presents the algae part of the lichen, the other part is a fungus).
Image source: Pixabay

Plants acquire majority of their nitrogen from the soil via root system, in case of legumes (Fabaceae) and alder (Alnus sp.) a symbiosis has established with the heterotrophic bacterium Rhizobium. When bacteria penetrate the cell cortex of the plant’s root, some of the cortex cells become meristem and begin to divide. This way root nodules are formed and the bacteria live in parenchyma of the nodule. Rhizobium cells live in the central part of the nodule just behind the meristem.

As mentioned, this is a symbiotic relationship, because plants obtain nitrogen compounds from bacteria, in return, the plant supplies the bacteria with carbohydrates, proteins and sufficient, but not too much oxygen, so as not to interfere with the fixation process.

Rhizobium sp. is aerobic, as nitrogen fixation is a very energy consuming process and large amounts of energy could not be produced reasonably through anaerobic pathways. However, the enzyme system responsible for nitrogen fixation is very sensitive to the presence of oxygen, so it is necessary to create anaerobic conditions. These two facts lead to what is termed the “oxygen dilemma” of nitrogen fixing bacteria. This is solved in Rhizobium with two mechanisms:

  • the first is through fast and efficient aerobic metabolism, so very little oxygen is stockpiled;
  • the second is through oxygen scavenging chemicals, specifically leghemoglobin (plant proteins similar to human hemoglobins, with a high affinity for oxygen), a transport protein which helps to provide oxygen for respiration while keeping the free oxygen concentration low enough so as not to inhibit nitrogenase activity.

The walls of the nodule exclude oxygen, allowing these controls to be effective.

As pointed out, nitrogen fixation is a highly energy expensive process. The energy that the bacteria needs to activate nitrogenase, it acquires from the plant as the latter provides it with carbohydrates. This process is called biological nitrogen fixation and as mentioned before, it is all done by the enzyme nitrogenase:

N2 + 3H2 → 2NH3 

When a nitrogen fixating plant dies, the nitrogen is released, thus making it available to other plants and this helps to fertilize the soil.

Some of the plants which are in a symbiotic relationship with bacteria from the genus Rhizobium are: Colutea arborescens, plants from Laburnum genus, Spartium junceum, Alnus incana, plants from Astragalus, Genista, Medicago, Trifolium genus, Cytisus pseudoprocumbens, Lotus corniculatus,Lathyrus vernus, Vicia pisiformis, Vicia faba, etc. The listed plants are all indigenous to Central Europe, some of them are spread throughout the world – naturally or through a human factor.

How is all this useful? For starters, crop rotation. A series of different types of crops in the same area are sequenced with seasons. About every three to four years the same crop returns to its primary area and meanwhile the soil is planted by a nitrogen fixing plant, for instance, plants from Trifolium genus, to naturally enrich the soil with nitrogen compounds, making it available to other plans that grow on the same area afterwards.

A complex genetic history of the nitrogenase family has been explored. Also a hypothesized presence of nitrogenase in the last common ancestor of modern organisms has been determined, as well as the additional possibility that nitrogen fixation might have evolved later. Perhaps in methanogenic archaea, and was subsequently transferred into the bacterial domain. Specific genes are universal in nitrogen fixing organisms—typically found within highly conserved operons.

Nitrogen fixation is, as it has been dicovered, an ancient process that is crucial for extant life and it played a critical role during the early expansion of microbial life.


You can find further information about the process and evolution of nitrogen fixation in the following articles:


An image for a better view of the big picture:


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