Ammonification

Nutrient cycling is an important process that ensures the harmonious functioning of the ecosystem. Nitrogen is amongst the most crucial nutrients for a living organism and hence, its cycling between the atmosphere and biosphere is essential. The nitrogen in the atmosphere is not bioavailable and is subject to important transformations− biological nitrogen fixation, assimilation, ammonification, nitrification and denitrification, being converted from one chemical form to the other. The process of ammonification is essential in making nitrogen available for growth of plants and animals, and is discussed at length in this article.

What is Ammonification?

Once nitrogen has been fixed into ammonia ($\mathrm{NH_3}$), it is assimilated by the plants as nitrogenous biomolecules (amino acids, proteins and nucleic acids). Once incorporated into the living bodies of the plants and animals, the molecules will eventually be subjected to the process of decomposition, which is essentially carried out by microorganisms known as decomposers. Decomposition leads to conversion of nitrogenous organic molecules (R-NH2) into $\mathrm{NH_3}$ or $\mathrm{NH_4^{+}}$. This is known as ammonification.

The process of ammonification can be simply represented as.

$\mathrm{(N_2\:\rightarrow\:NH_3) \rightarrow\:Assimilation\:of\:into\:organic\:matter\:\longrightarrow\:decomposition\:of\:organic\:matter\:NH_4^{+} }$

The organic forms of nitrogen found in the soil and other environments include.

• Amino acids $\mathrm{R-CH(NH_2)-COOH}$ − These amino acids are polymerized to proteins in the living systems.

• Nucleic acidswhich comprise of purines and pyrimidines which are nitrogenous bases that make up an entire living organism.

• Urea $\mathrm{(CO(NH_2)_2)}$ − present in animal excretions in the form of urine and even in faecal matter. It is used extensively used as a fertiliser in agricultural fields.

Thus, ammonification can be defined as the conversion of organic nitrogen into ammonia or ammonium ions by the action of decomposing microorganisms including bacteria and fungi.

Steps involved in the ammonification process

The steps involved in this process of mineralization to release ammonia include.

• Aminization (proteins converted to amino acids, amides and amines.

• Ammonification.

For example, in the ammonification of amino acids.

$\mathrm{R-CH(NH_2)-COOH\rightarrow\:H_2O\:\longrightarrow\:R-COOH+CO_2+NH_4^{+}}$

Another example is the hydrolysis and ammonification of urea.

$\mathrm{CO(NH_2)_2\:+\: H_2O\:\longrightarrow\:2NH_3\:+ \:CO_2 }$ $\mathrm{2NH_3\:+\:2H_2O\rightarrow\: 2NH_4^{+} + 2 OH^{-}}$

Function of ammonification

The nitrogen present in the atmosphere must be converted to ammonia and nitrates. These forms are then taken up by the plants and reach the animals via the food chain. Eventually, the living organism experiences death and decay. The consequent decomposition of the dead organic matter is crucial not only for the cleaning up of the earth's surface, but also because it is imperative in the release of the bound nitrogen. Ammonifying microorganisms help in this release of nitrogen as ammonium which can then be taken up by a new generation of living organisms. Alternatively, some ammonium is subjected to nitrification.

Hence, ammonification basically serves the purpose of recycling nitrogen, ensuring it stays within the biosphere.

Implications of the ammonification process

From the above points, one can understand the implications of the process of ammonification.

• Ammonification occurs as a part of decomposition reactions.

• Ammonification prevents the stockpiling of unavailable nitrogen in the soil.

• Plants require access to nitrogen, in the form of nitrates or ammonium and ammonification provides the necessary transformations.

• Ensures continuous cycling of a certain amount of fixed nitrogen as ammonium, for nitrogen assimilation and nitrification.

• Prevents the exhaustion of $\mathrm{NH_3}$ (as $\mathrm{NH_3}$ is used in assimilation and nitrification), in the absence of which nitrogen would eventually become unavailable to living organisms and ultimately lead to the collapse of the entire biosphere!.

What do bacteria do during ammonification

Ammonifying bacteria in the soil metabolise nitrogenous organic compounds into ammonium.

For example, in the case of amino acids, the soil bacteria perform the following steps.

$\mathrm{\:Amino\:acids\:\rightarrow\:lmino\:acids\:\rightarrow\: keto\: acids\:\longrightarrow\:NH_3\:or\:NH_4^{+}}$

Several bacterial enzymes are involved in this process, including lyases (aspartase, histidase, etc.) and hydrolases (asparaginase, glutaminase, amidase, urease and arginase).

The bacterial cell utilises the ammonium for its own metabolic processes and excess ammonium is excreted into the ambient soil, being made available for uptake by plants. Additionally, a certain amount of the released ammonium is subjected to the next step in the nitrogen cycle, namely, microbially-mediated nitrification.

Examples of ammonifying bacteria

A variety of soil bacteria mediate ammonification as the enzymes mentioned in the previous section are found across different microbial genera. Examples include− Bacillus ramosus, Bacillus vulgaris, Streptomyces, Pseudomonas spp., Clostridium spp., Proteus spp., Micrococcus spp., and Actinomycetes.

What are nitrifying bacteria?

Nitrifying bacteria are chemolithotrophic bacteria, which perform the oxidation of $\mathrm{NH_3}$ or $\mathrm{NH_4^{+}}$ to nitrite ($\mathrm{NO_2^{-}}$) and ultimately nitrate ($\mathrm{NO_3^{-}}$ ), known as Nitrification (aka ammonium oxidation) . There is a substantial abundance of the nitrifying bacteria in the soil.

Nitrification is a two step process.

• The first step involves the oxidation of ammonium to nitrite.

  $\mathrm{\:2NH_4^{+}\:+\:3O_2\longrightarrow\:2NO_2^{-}\:+\:4H^{+}\:+2H_2O\:+\:energy\:}$

  This step is carried out by bacterial genera like Nitrosomonas, Nitrosospira, Nitrosococcus, etc. aka the Ammonia-oxidising bacteria (AOB).

• The subsequent step involves further oxidation of nitrite to nitrate.

  $\mathrm{\:2NO_4^{-}\:+\:O_2\longrightarrow\:2NO_3^{-}+\:energy\:}$

  This step is mediated by the bacteria like Nitrospira, Nitrobacter, Nitrococcus, Nitrotoga, etc., aka the nitrate-oxidising bacteria (NOB).

Difference between ammonification and nitrification

Ammonification	Nitrification
Organically bound nitrogen within dead matter is converted into ammonium	Transformation of $\mathrm{NH_3}$ to $\mathrm{NO_2^{-}}$ and $\mathrm{NO_3^{-}}$
Bacteria involved include− Bacillus, Streptomyces, Pseudomonas, Clostridium, Proteus, Micrococcus, etc.	Involves the AOB (Nitrosomonas, Nitrosospira, Nitrosococcus) and the NOB (Nitrospira, Nitrobacter, Nitrococcus, Nitrotoga)
End product is $\mathrm{NH_3\:or\:NH_4^{+}}$	End product is $\mathrm{NO_3^{-}}$

Nitrogen cycle with the help of a diagram

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Importance of the ammonification process

Ammonification ensures the continuous cycling of a certain amount of fixed nitrogen within the biosphere. Dead matter is an important repository of nitrogen. However, this organically-bound nitrogen is unavailable for uptake by plants and animals. To prevent such an essential nutrient from going to waste and accumulating in large amounts, the decomposition of organic matter and consequent ammonification of organic nitrogen is necessary. .

In the absence of ammonification, the nitrogen would return to the atmosphere via denitrification, and become unavailable to plants and animals. Ammonification also serves as a source of energy derivation by the microorganisms. Lastly, its end product (ammonia) serves as a substrate for the next step in the nitrogen cycle.

Conclusion

• Nitrogen cycle involves the nitrogen fixation, nitrogen assimilation, ammonification, nitrification, and denitrification.

• Ammonification is the conversion of organic nitrogenous compounds into ammonia or ammonium.

• It is carried out by certain bacteria and fungi known as ammonifiers, including bacteria like Streptomyces, Bacillus, Clostridium, Pseudomonas, etc.

• It ensures the continuous supply of bioavailable nitrogen in the biosphere and supplies ammonium as the substrate for nitrification.

• Nitrification is the conversion of ammonia into nitrite and nitrate.

• Nitrifying bacteria include the AOB which convert ammonium to nitrite and the NOB which further oxidise nitrite to nitrate.

FAQs

Q1. What are anammox bacteria?

Ans. Anammox bacteria mediate the ANaerobic Ammonium OXidation (ANAMMOX) process. In this reaction, $\mathrm{NO_2^{-}}$ is the electron acceptor and itself undergoes reduction as $\mathrm{NH_4^{+}}$ (electron donor) is oxidised to molecular $\mathrm{N_2}$. This anaerobic process couples the nitrification (i.e., $\mathrm{NH_4^{+}}$ oxidation) with denitrification ($\mathrm{NO_2^{-}}$ reduction to $\mathrm{N_2}$) in a single process.

Q2. Do all plants rely on $\mathrm{NH_4^{+}}$ for their nitrogen needs?

Ans. No. Although $\mathrm{NH_4^{+}}$ is readily available in the soil for uptake by plants, $\mathrm{NH_4^{+}}$/ NH3 is more suitable for plants that grow in acidic soils, as the ammonifying bacteria grow well in such pH. Moreover, nitrifying bacteria can’t tolerate acidity and are less active in such soils. However, for plants that grow in non-acidic conditions, $\mathrm{NO_3^{-}}$ is a more suitable form.

Q3. What is nitrate ammonification?

Ans. Respiratory ammonification, or dissimilatory nitrate reduction or nitrate ammonification, is the process by which $\mathrm{NO_3^{-}}$ is converted $\mathrm{NH_4^{+}}$. This reaction occurs under anaerobic conditions, wherein $\mathrm{NO_3^{-}}$ acts as electron acceptor instead of $\mathrm{O_2}$.

Q4. What are comammox bacteria?

Ans. COMAMMOX (COMplete AMMonia OXidation) is the transformation of $\mathrm{NH_4^{+}}$ to $\mathrm{NO_2^{-}}$ and subsequently into $\mathrm{NO_3^{-}}$ within a single organism, such as the comammox Nitrospira bacteria. This is in contrast to the conventional process of nitrification, where two different groups of bacteria viz. the AOB and the NOB are involved.