Nitrogen Cycle

 

Nitrogen Cycle

Nitrogen Cycle is a biogeochemical process through which nitrogen is converted into many forms, consecutively passing from the atmosphere to the soil to organism and back into the atmosphere.  Even though Nitrogen gas makes up nearly 80% of the Earth's atmosphere, nitrogen is often the nutrient that limits primary production in many ecosystems since plants and animals are not able to use nitrogen gas in that form.  It involves several processes such as nitrogen fixation, nitrification, denitrification, Nitrogen assimilation and ammonification.

www.sciencefacts.net

Nitrogen fixation

For nitrogen to be available to make biologically important compounds, it must first be converted biologically available nitrogen through a process called nitrogen fixation. N2 gas is a very stable compound due to the strength of the triple bond between the nitrogen atoms, and it requires a large amount of energy to break this bond and requires eight electrons and at least sixteen ATP molecules. As a result, only very few group of prokaryotes are able to carry out this. Most nitrogen fixation is carried out by prokaryotes, some nitrogen is fixed abiotically by lightning or certain industrial processes.

Atmospheric fixation - this occurs spontaneously due to lightning. Only a small amount is fixed this way.

Industrial fixation - the Haber process is used to make nitrogen fertilizers. This is very energy inefficient.

Biological fixation - in which nitrogen gas is converted into inorganic nitrogen compounds, is mostly (60-90 percent) accomplished by certain bacteria and blue-green algae.

Nitrogen fixation is carried out by aerobic or anaerobic procaryotes. Under aerobic conditions a wide range of free-living bacteria such as Azotobacter, Azospirillum, etc carry out nitrogen fixation.  Under anaerobic conditions example for free-living nitrogen fixers are members of the genus Clostridium. Nitrogen fixation is also done by cyanobacteria such as Anabaena and Oscillatoria in aquatic environments.  Another category is symbiotic nitrogen fixers, bacteria that develop symbiotic associations with plants. Examples of such symbiotic nitrogen fixation are Rhizobium and Bradyrhizobium with legumes, Frankia association with many woody shrubs and Anabaena with Azolla. Most of the symbiotic associations are very specific and have complex mechanisms that help to maintain the symbiosis.  Root exudates from legume plants serve as a signal to attract certain species of Rhizobium to the roots, and series of events occurs to initiate uptake of the bacteria into the root and trigger the process of nitrogen fixation in the root nodules that form on the roots.

Although there is great physiological and phylogenetic diversity among the organisms that carry out nitrogen fixation, they all have a similar enzyme complex called nitrogenase that catalyzes the reduction of N₂ to NH₃. The nitrogen-fixation process involves a sequence of reduction reactions that require energy. Ammonia is produced which will be immediately incorporated into organic matter as an amine. This reductive process and this enzyme complex are extremely sensitive to O2 and must occur under anaerobic conditions even in aerobic microorganisms. Nitrogen-fixers have evolved different ways to protect their nitrogenase from oxygen. Some examples are Physical barriers such as that in heterocysts that provide a low-oxygen environment for the enzyme and serves as the site where all the nitrogen fixation occurs in some Cyanobacteria, O2 scavenging molecules such as Leghemoglobin in the root nodules of leguminous plants involved in symbiotic nitrogen fixation which maintains a free oxygen concentration low enough to allow nitrogenase to function and provides enough total oxygen concentration for aerobic respiration, high rates of metabolic activity that keeps oxygen concentration low enough for nitrogenase, etc.  Some photosynthetic nitrogen-fixers fix nitrogen only at night when their photosystems are dormant and are not producing oxygen.

Nitrates and ammonia resulting from nitrogen fixation are assimilated into the specific tissue compounds of algae and higher plants. Animals then ingest these algae and plants, converting them into their own body compounds.

Nitrification

Nitrification is a process carried out by nitrifying bacteria which transforms soil ammonia into nitrates (NO3−), which plants can use.

During nitrification ammonia is converted to nitrite and then to nitrate. Most nitrification occurs aerobically by prokaryotes. There are two distinct steps of nitrification that are carried out by distinct types of microorganisms.

The first step in nitrification is the oxidation of ammonia to nitrite, which is carried out by microbes known as ammonia-oxidizers. Aerobic ammonia oxidizers or ammonia-oxidizing bacteria (AOB) in soil and ammonia-oxidizing archaea (AOA) in oceans and soils are autotrophs, they fix carbon dioxide using ammonia as the energy source instead of light. 

NH₃+O₂+2e^-  ----> NH₂OH + H₂O

NH₂OH +   H₂O ----> NO₂^- + 5 H⁺ +4 e^-

Examples for AOA are Nitrosopumilus maritimus and Nitrososphaera viennensis and AOB are Nitrosomonas, Nitrosospira and Nitrosococcus. Aerobic ammonia oxidizers convert ammonia to nitrite via the intermediate hydroxylamine.  This process requires two different enzymes, ammonia monooxygenase and hydroxylamine oxidoreductase. The process generates a very small amount of energy and thus these are very slow growers.

The second step in nitrification is the oxidation of nitrite (NO₂^-) to nitrate (NO₃^-). This step is carried out by a group of bacteria known as nitrite-oxidizing Bacteria. Examples are bacteria of the genera Nitrospira, Nitrobacter, Nitrococcus and Nitrospina. Here also the energy generated is very small and thus growth yields are very low.

2NO₂^-  + O₂  ----> 2NO₃^-

For complete nitrification, both ammonia oxidation and nitrite oxidation must occur.

Ammonia-oxidizers and nitrite-oxidizers are ubiquitous in aerobic environments such as soils, estuaries, lakes, and open-ocean environments. In wastewater treatment facilities they play a crucial role by removing potentially harmful levels of ammonium and they also help to maintain healthy aquaria by facilitating the removal of potentially toxic ammonium excreted in fish urine.

Anammox or anaerobic ammonia oxidation - Anammox is carried out by prokaryotes belonging to the Planctomycetes phylum of Bacteria. The first described anammox bacterium was Brocadia anammoxidans. Anammox bacteria oxidize ammonia by using nitrite as the electron acceptor to produce gaseous nitrogen.

NH4^- +NO₂^-  ---->N₂ + 2H₂O

Anammox bacteria are found in low-oxygen zones of the ocean, coastal and estuarine sediments, mangroves and freshwater lakes. Anammox process is responsible for a significant loss of nitrogen in ocean while denitrification is responsible nitrogen loss in other areas.

Denitrification and Nitrate reduction

Denitrification is the process that converts nitrate to nitrogen gas returning it to the atmosphere, thus removing bioavailable nitrogen. Nitrogen gas is the ultimate end product of denitrification, but some other intermediate gaseous forms of nitrogen are also formed such as nitrous oxide and nitrite. Some of these gases, such as nitrous oxide (N₂O), are greenhouse gasses.  Nitrite (NO₂^-) is of environmental concern because it can contribute to the formation of carcinogenic nitrosamines.

NO₃^- ----> NO₂^- ---->NO + H₂O ----> NO₂

2 NO₃^- + 12 H⁺ + 10 e^- ---->N₂ + 6H₂O

Denitrification is an anaerobic process, occurring mostly in soils and sediments and anoxic zones in lakes and oceans. Some denitrifying bacteria include species in the genera Bacillus, Paracoccus, and Pseudomonas. Denitrifiers are chemoorganotrophs and thus need supply of organic carbon.  Pseudomonas denitrificans is an example.

Denitrification is important in that it removes fixed nitrogen (i.e., nitrate) from the ecosystem and returns it to the atmosphere as N₂. This is particularly important in agriculture because this results in loss of soil fertility.  Denitrification in wastewater treatment plays a very beneficial role by removing unwanted nitrates from the wastewater effluent.

Nitrate reduction is the process by which nitrate ions are reduced, two modes are the assimilatory nitrate reduction and the dissimilatory nitrate reduction.  Assimilatory nitrate reduction is utilized by a heterogeneous group of microbes including bacterial, fungal and algal species where nitrate ions are incorporated into organic matter.  The process involves several enzyme systems including nitrate and nitrite reductases to form ammonia which is incorporated into amino acids.  Dissimilatory nitrate reduction is also known as nitrate respiration and occurs in the absence of oxygen.  Here nitrate is converted to a variety of reduced products and organic matter is oxidized.

There are two types of dissimilatory nitrate reduction.  In the first type, facultatively anaerobic bacteria such as Alcaligenes, Escherichia, Bacillus, Nocardia, etc reduce nitrate to nitrite under anaerobic conditions and these nitrites will be excreted or sometimes this nitrite may get reduced to ammonium.  Since Nitrogen gas is not formed, no denitrification occurs here.  In the second type of dissimilatory nitrate reduction, Paracoccus denitrificans, Thiobacillus denitrificans, etc convert nitrate to nitrite to nitric oxide to nitrous oxide to nitrogen.  As a result, Nitrogen is released in to atmosphere.

NO₃^- ----> NO₂^-  ----> NO ----> N₂O ----> N₂

Nitrogen assimilation

Nitrogen assimilation occurs when inorganic nitrogen is used as a nutrient and incorporated into new microbial biomass. Ammonium ion can be directly incorporated without major energy costs. When nitrate is assimilated, it must be reduced with a significant energy expenditure and in this process nitrite may accumulate as a transient intermediate.

Ammonification

Nitrogen in the tissues of organisms is in the form of organic nitrogen and it get decomposed when it excretes waste or dies. Various fungi and prokaryotes decompose the tissue and release inorganic nitrogen back into the ecosystem as ammonia in a process known as ammonification. The ammonia then becomes available for uptake by plants and other microorganisms for growth.