Green Soil for a Green Future

Updated: Jul 24, 2021

Irin Ann Paul and Yagnit Vadhel,

St. Xavier's College (Autonomous),

Mumbai, Maharashtra, India


The human population is continuously rising, and large portions of land are being used for agriculture. Because of this, soil fertility is declining day by day.

Humans are highly evolving in intelligence, and we always try to find solutions to our problems. The same goes with this one too. We discovered newer forms of chemical fertilizers to meet this ever-increasing need for food production. But the usage of chemical-based fertilizers has made the conditions worse. Chemical fertilizers are no doubt effective in enhancing the overall mineral content of the soil. But it comes at a cost - soil pollution. The use of such fertilizers can increase the nitrate and phosphate content in soil and groundwater.

Interesting fact: Although nearly 80% of our atmosphere is composed of nitrogen, it is relatively inert and not easily accessible to organisms

Nitrogen is considered one of the building blocks of life. Every organism is trying a hand at fixing nitrogen but in vain. Only certain species of bacteria can do this. Plants being intelligent, have managed to outmaneuver other organisms by developing a special bond with these bacteria, called symbiosis. Plants are often wiser than other living organisms, not just because of their reservoir of chemicals called phytochemicals (which are responsible directly or indirectly to their associations). They house chloroplasts, which are known as kitchens of all ecosystems in the entire world. The associations they form with other organisms are also indicative of their intelligence.


Our blog explains the mechanism that underlies the nitrogen fixation in the root nodules of leguminous plants by symbiotic bacteria. We also look at its applications in agricultural biotechnology to enhance crop production and reduce the requirement of chemical fertilizers for a greener and cleaner tomorrow.

Do you know what exactly is biological nitrogen fixation and the obvious mechanism that underlies it? If you are very high on curiosity, then this is just the place for you!

Biological nitrogen fixation involves biochemical and physicochemical changes in the nitrogen-fixing bacteria Rhizobium and the host plant. Hence a multidisciplinary approach to the study is necessary. Their relationship is fascinating and does not need one to dive into the ocean of science.

The relationship between leguminous plants and bacteria takes place as follows:-

Signal exchange in the Rhizosphere:- Initially, roots of the leguminous plants secrete certain phytochemicals, such as flavonoids and betaines, to interact with saprophytic rhizobia present in the root-soil interface. This interaction results in the activation of nod genes in the bacterium, which is highly species-specific. The Nod factors thus transcribed causes calcium spiking in epidermal root cells. Calcium spiking results in the curling of the epidermal root hairs, trapping the bacteria. Then the bacteria try to invade the root hair.

Root hair invasion:- Rhizobia secrete exopolysaccharides that activate the receptors on the root surface. The activation causes invagination of the plant cell wall in the curled root, allowing bacterial entry. The bacteria enter into the epidermis through an apoplastic pathway. The exact mechanism is yet to be understood. However, many now believe that polygalacturonase is responsible for the root cell wall degradation and subsequent initiation of root infection, forming an infection thread.

Bacteroid differentiation:- An infection thread formed by the rhizobia then reaches the inner plant cortex. Here, the bacteria are endocytosed by plant cells, forming symbiosomes. Rhizobia multiply along the symbiosome membrane. Symbiosomes then differentiate into nitrogen-fixing forms called bacteroids. Symbiosomes, when present in groups, leads to nodulation.

Nodule development and physiology:- A complex hormonal signaling that results in activation of cytokinin and the suppression of polar auxin transport to the root cortex initiates the formation of nodules. Nodules consist of centrally occupied infected and non-infected cells, surrounded by a mass of non-infected tissues that connect the root vascular system. There are many zones in the nodules. The most studied zone is the zone of nitrogen fixation consisting of nitrogen-fixing bacteria.

Interesting Fact : Nitrogenase:- the enzyme nitrogenase is a crucial enzyme in biological nitrogen fixation. The structure of nitrogenase is very complex. It is an organometallic base enzyme that comprises Fe and FeS along with Mo and several ATP binding sites. This enzyme, through ATP-mediated electronic transfer reaction, is responsible for the conversion of nitrogen to ammonia.

The give and take of nitrogen and carbon happen simultaneously in a symbiotic relationship, as the exchange of checks and cash in a bank.

Carbon flow to the nodule:- The reduced sugar assimilated by the plant as a result of photosynthesis is transferred to the bacteria to produce ATP. ATP is crucial to reduce dinitrogen to ammonia. It also helps in the functioning of enzyme nitrogenase. Due to recent advancements in biochemistry and various other fields, knowledge of the mechanism of carbon flow has broadened.

Bacteroid metabolism:- Metabolic process except nitrogen fixation and respiration diminish in bacteroids. The host plant provides certain amino acids and dicarboxylic acids to the bacteria, and bacteria return amino acids to the host with newly fixed nitrogen.

Diffusion of oxygen to the bacteroid:- The enzyme nitrogenase is very sensitive to oxygen and the combined half-life period is less than 10 minutes. However, the oxygen concentration decreases within a symbiosome due to the anatomical, physiological, and biochemical adaptations in roots and bacteroids. Thus a microaerobic environment is created in the symbiosome. This environment protects the enzyme nitrogenase from getting oxidized. One such adaptation is the formation of leghemoglobin, an oxygen-binding protein similar to hemoglobin and myoglobin. It is a protein whose structure has a significant role in protecting the enzyme nitrogenase from oxidation.

Genes control the characteristics of organisms. The same applies to this relationship also. They act as the basis on which symbiosis happens, even though between organisms of two kingdoms that are poles apart.

Genetic regulation in response to low oxygen in the bacteroid:- In low oxygen level within a symbiosome, a regulatory cascade regulates the genes necessary for assembly and maintenance of nitrogenase, feedback regulation of oxygen, and those that encode high-affinity terminal oxidase enzymes. The regulatory proteins include FixL and FixJ.

Not only Rhizobium shows a friendly approach towards plants. Another species of bacteria called Frankia also seems interested in building a relationship with a plant counterpart. And this has been exploited by some ‘big brains’ in the field of biotechnology.

Nitrogen fixation in non-leguminous plants by Frankia:- Frankia is a genus of actinobacteria present in the soil. It forms symbiotic associations with actinorhizal plants by fixing the atmospheric nitrogen and receiving reduced carbon in return. They are capable of fixing nitrogen under both symbiotic and free-living conditions. They are less dependent on the host plant than rhizobia, and as a result, metabolic activity is higher in symbioses.

Biotechnological solutions:- Engineered nitrogen fixation in plants of great agricultural importance is one of the goals of agricultural biotechnology to reduce the demand for chemical nitrogen fertilizers. Three ways to engineer nitrogen fixation in crop plants are; 1. By introducing nitrogen fixation enzymes into the plants, 2. Engineering an association of the crop plant with nitrogen-fixing bacteria, and 3. By developing strains of non-nodulating nitrogen-fixing bacteria to colonize the plant.

The ever-increasing human population and the rapid utilization of fossil fuels have led to the erosion of soil fertility. But it can now be enhanced by symbiotic relationships between nitrogen-fixers and bacteria. Due to advancements in genetic engineering and agro-biotechnology, the translation of genes for symbiotic nitrogen fixation is the need of the hour. It will reduce our dependence on chemical fertilizers and provide a cleaner and greener environment for tomorrow.


  1. Hopkins, W., & Hüner, N. (2009). Introduction to plant physiology (4th ed.). Hoboken, N.J.: John Wiley & Sons.

  2. Geddes, B., & Oresnik, I. (2016). The Mechanism of Symbiotic Nitrogen Fixation. Advances In Environmental Microbiology, 69-97. doi: 10.1007/978-3-319-28068-4_4

  3. Pawlowski, K., & Newton, W. (2008). Nitrogen-fixing actinorhizal symbioses. Dordrecht: Springer.

  4. Sulieman, S., & Tran, L. (2014). Symbiotic Nitrogen Fixation in Legume Nodules: Metabolism and Regulatory Mechanisms. International Journal Of Molecular Sciences, 15(11), 19389-19393. doi: 10.3390/ijms151119389

  5. Santi, C., Bogusz, D., & Franche, C. (2013). Biological nitrogen fixation in non-legume plants. Annals Of Botany, 111(5), 743-767. doi: 10.1093/aob/mct048

  6. Willey, J., Sherwood, L., Woolverton, C., & Prescott, L. Prescott's Microbiology (10th ed., pp. 676-680). McGraw-Hill Education.

  7. 1. Oldroyd G, Dixon R. 2014. Biotechnological solutions to the nitrogen problem. Current Opinion in Biotechnology 26:19-24.

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