Environmental & Soil Microbiology


Written by MicroDok

Nitrogen cycle is defined as the biogeochemical cycle by which nitrogen is exchanged between the biosphere, lithosphere, atmosphere and hydrosphere components of the earth. It is the cycle that describes the transformations of nitrogen and nitrogen-containing compounds in nature. The amount of nitrogen in the atmosphere is about 78 %; and even though nitrogen is very abundant in the atmosphere, it is still largely inaccessible to many forms of life in this molecular state (N2). Nitrogen becomes available to primary producers such as plants in the ecosystem only when it is converted from the dinitrogen gas (N2) to ammonia (NH3). For nitrogen to be available to make nucleic acid molecules, proteins, amino acids, and other important biological compounds or molecules, it must first be converted into different chemical forms that can be used by living organisms in the ecosystem. And this is what happens in the nitrogen cycle.

Nitrogen (N2) is an important element that is essential for a handful of biological activities in the ecosystem. It is incorporated in proteins, and amino acids, and nitrogen is part of the nitrogenous bases that make up the nucleic acid molecules including deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) molecules. Nitrogen is also found in various forms in rocks, soils, sediments, living matter and in the ocean and seas. Most microbes and plants obtain their nitrogen from the soil and surrounding water while animals get their nitrogen from the food they eat. Nitrogen is important for the optimal growth and development of plants; and plants that lack this element show stunted growth and produce yellowish leaves. However, the lack of nitrogen in the soil can be tackled through proper application of fertilizers using organic and inorganic fertilizers. When the amount of fertilizers in the soil is too much, it could be washed off into other ecosystems such as into water ways or rivers where they cause eutrophication. In such scenarios, nitrogen increases the growth of algae and other aquatic vegetation, thus creating aesthetic problems and depletion of available dissolved oxygen (DO) when these plants die.

The organic forms of nitrogen include amino acids, DNA and proteins while the inorganic forms of nitrogen include nitrite, nitrate, ammonia and ammonium. It is the inorganic forms of nitrogen that plants and microbes can use for their various metabolic activities. Nitrogen enters the soil from various sources including through rainfall (natural atmospheric deposition of N2), through some special plants that are known as nitrogen fixers (e.g. leguminous plants, alfalfa plants and ceanothus plants), and through human activities such as the application of chemical or organic fertilizers to the soil during plantation. Once in the soil, the nitrogen will be transformed into inorganic forms such as ammonia and ammonium that can be utilized by different forms of life for growth and development. The major processes involved in the nitrogen cycle for the conversion of atmospheric molecular nitrogen into usable forms of nitrogen include nitrogen fixation, nitrification, denitrification, ammonification, and assimilation (Figure 1).

Figure 1: Nitrogen cycle.



Nitrogen fixation occurs when atmospheric gaseous nitrogen is converted to ammonia (NH3) and other forms that is usable by living organisms. The process of nitrogen fixation is carried out by nitrogen fixing bacteria (symbiotic bacteria) that have nitrogenase enzymes – which combines gaseous nitrogen with hydrogen to form NH3. Nitrogen fixing bacteria include both the Archaea and bacteria; and typical examples are bacteria in the genus Nostoc, Anabaena, Azotobacter, Pseudomonas, Rhizobium, Clostridium, Desulfovibrio, Methanococcus (Archaea), Alcaligenes and Azotobacter. Nitrogen fixing bacteria are able to use the free (molecular) nitrogen in the atmosphere to make nitrogenous compounds such as ammonia (NH3) through the process of nitrogen fixation.

Nitrification is the biological oxidation of ammonia with oxygen into nitrite. And this is usually followed by the oxidation of nitrites (NO2) to nitrates (NO3). Nitrification is usually carried out by a group of bacteria known as nitrifying bacteria. Bacteria in the genus Nitrosomonas, Nitrosococcus and Nitrobacter are typical examples of nitrifying bacteria. Nitrate is one of the nitrogenous compounds produced by nitrogen fixing bacteria through nitrogen fixation; and this compound is taken up by plants from the soil for growth. The compounds made from the plants such as proteins are in turn used by other organisms that cannot use nitrates directly.

Denitrification is the process of reducing nitrate and nitrite into gaseous nitrogen (N2). It is noteworthy that nitrate and nitrite are the oxidized forms of nitrogen that is made available for usage or consumption by a wide variety of living organisms. The process of denitrification is carried out by heterotrophic bacteria including Thiobacillus denitrificans and Paracoccus denitrificans and various species of Pseudomonas. Ammonification is the mineralization of organic nitrogenous compounds such as ammonia or ammonium (NH4+) into inorganic compounds. When a living organism excretes waste into the environment or dies, the nitrogen in its waste or body tissues is in the form of organic nitrogen such as proteins or amino acids. Various microbes including fungi and bacteria will decompose the waste product or tissue of the deceased organism and release inorganic nitrogen back into the ecosystem as ammonia (NH3) in the process known as ammonification. The ammonia then becomes available for uptake by plants and other microorganisms for growth and development. Nitrification together with ammonification forms a mineralization process – in which organic materials are completely decomposed with the release of available nitrogen. The nitrogen so released helps in replenishing the nitrogen cycle.

Mineralization is the process by which organic matter in the environment is broken down into inorganic matter. In assimilation, the nitrates (NO3) are assimilated by heterotrophic organisms (via consumption of plant tissues) that cannot absorb NO3 from the soil the same way that plants do through their root hairs. Nitrogen is eventually returned to the atmosphere by the activities of decomposers such as fungi that breakdown complex dead organic organisms and animal wastes. This process returns simple nitrogenous compounds to the soil where they can be used by plants to produce more nutrients. And nitrogen will continue to move back and forth between the soil, plants and animals; and complex compounds are eventually broken down to release free nitrogen into the atmosphere.


Ulrich A and Becker R (2006). Soil parent material is a key determinant of the bacterial community structure in arable soils. FEMS Microbiol Ecol, 56(3):430–443.

Sylvia D.M, Jeffry J.F, Peter G.H and David A.Z (1998). Principles and Applications of Soil Microbiology. Upper Saddle River: Prentice Hall, USA.

Talaro, Kathleen P (2005). Foundations in Microbiology. 5th McGraw-Hill Companies Inc., New York, USA.

Salyers A.A and Whitt D.D (2001). Microbiology: diversity, disease, and the environment. Fitzgerald Science Press Inc. Maryland, USA.

Sawyer C.N, McCarty P.L and Parkin G.F (2003). Chemistry for Environmental Engineering and Science (5th). McGraw-Hill Publishers, New York, USA.

Reisser W (editor): Algae and Symbiosis: Plants, Animals, Fungi, Viruses, Interactions Explored. Biopress, 1992.

Pepper I.L and Gerba C.P (2005). Environmental Microbiology: A Laboratory Manual. Second Edition. Elsevier Academic Press, New York, USA.

Pelczar M.J., Chan E.C.S. and Krieg N.R. (2003). Microbiology of Soil.  Microbiology, 5th Tata McGraw-Hill Publishing Company Limited, New Delhi, India.

Paul E.A (2007). Soil Microbiology, ecology and biochemistry. 3rd Oxford: Elsevier Publications, New York.

Paerl H.W. and Paul V.J. (2012). Climate change: links to global expansion of harmful cyanobacteria. Water Research, 46: 1349-63 (2012).

Mishra B.B, Nanda D.R and Dave S.R (2009). Environmental Microbiology. First edition. APH Publishing Corporation, Ansari Road, Darya Ganj, New Delhi, India.

Hargitai L (1993). The soil of organic matter content and humus quality in the maintenance of soil fertility and in environmental protection. Landscape and Urban Planning, 27(2–4):161–167.

Heimann M. and Reichstein M (2008). Terrestrial ecosystem carbon dynamics and climate feedbacks. Nature, 451:289‐

Filippelli G.M (2002). The Global Phosphorus Cycle. Reviews in Mineralogy and Geochemistry, 48:391 – 425.

Bernhard A (2010). The Nitrogen Cycle: Processes, Players, and Human Impact. Nature Education Knowledge, 2(2):12-23.

Baumgardner D.J (2012). Soil-related bacterial and fungal infections. J Am Board Fam Med, 25:734-744.

Ballantyne A.P, Alden C.B, Miller J.B, Tans P.P and White J.W.C (2012). Increase in observed net carbon dioxide uptake by land and oceans during the past 50 years. Nature, 488: 70-72.

Andersson L  and  Rydberg  L (1988). Trends in nutrient and oxygen conditions within the Kattegat: effects on local nutrient supply. Coast. Shelf Sci, 26:559–579.

About the author


Leave a Comment