Nitrogen Cycle

 In soil

Overview
Nitrogen is a component of proteins and nucleic acids and so a supply of nitrogen is essential to all living
things. Nitrogen is available to living things in a variety of forms, the source used depending on the
species:
• Heterotrophs (such as animals) can only use organic nitrogen i.e. nitrogen already incorporated
into organic molecules
• Plants use the inorganic nitrogen-containing ions nitrate (NO3-) and ammonium (NH4+)
• Some bacteria are able to use atmospheric nitrogen (N2 gas) as a nitrogen supply
• Other bacteria are involved in the interconversion of the inorganic nitrogen ions; ammonium,
nitrite (NO2-) and nitrate
• Some bacteria and fungi decompose dead organisms converting organic nitrogen to inorganic
nitrogen in the process
The movement of nitrogen between different groups of organisms and between the different molecular
types is known as the nitrogen cycle.

The micro organisms and their roles:

A number of different groups of organism play important roles in the nitrogen cycle. These include:

Nitrogen-fixing bacteria:
These fix atmospheric nitrogen gas (N2) to ammonia (NH3) in a reduction reaction.
N2 + 3H2 ----> 2NH3
Some nitrogen-fixing bacteria are free-living in the soil e.g. Azotobacter
Some, e.g. Rhizobium, form a mutualistic (symbiotic) relationship with legumes (peas, beans, clover etc.
These are members of the Papilionaceae) in which the bacteria live in nodules on the plant's roots. The
bacteria provide the plant with fixed nitrogen, the plant provide the bacteria with carbohydrates. The
diagram below shows root nodules in a member of the Papilionaceae

Decomposers:
These are bacteria and fungi that decompose dead animals and plants and, in the process, convert their
organic nitrogen (that found in proteins and nucleic acids) into inorganic ammonium (NH4+)

Nitrifying Bacteria
These are bacteria that interconvert inorganic nitrogen molecules:
• Nitrosomonas converts ammonium (NH4+) into nitrites (NO2-)
• Nitrobacter converts nitrites (NO2-) into nitrates (NO3-)
Collectively these processes are known as nitrification.
Nitrification only occurs when the soil conditions are appropriate i.e. not waterlogged, too cold or too
acidic. If the soil conditions are not appropriate ammonium accumulates.

Denitrifying Bacteria
These are bacteria that convert nitrates (NO3-) to nitrites (NO2-) and then to nitrogen gas (N2).
These bacteria thus bring about the conversion of inorganic nitrogen into atmospheric nitrogen; a process
known as denitrification.
The denitrifying bacteria include:
• Pseudomonas
• Thiobacillus
These are anaerobic bacteria so denitrification only occurs under anaerobic conditions (e.g. when the soil
is waterlogged).

Physical fixation
Some physical processes also have a role in the cycle:
• Lightning: The high energy available from lightning is sufficient to fix atmospheric nitrogen to
nitrates
• The Haber-Bosch process: this is an entirely artificial process that is used in the manufacture of
ammonium for fertilizer - but since it contributes to the total fixation of atmospheric nitrogen it is
often included
• Leaching: The loss of nitrates from the soil as a result of heavy rain fall. Nitrates leach into
bodies of water (e.g. lakes) enriching them and making them more fertile. This process is known
as eutrophication.

Diagrams of the whole Nitrogen Cycle:

There are many different ways of representing the nitrogen cycle

(Straightforward diagram illustrating the key points)

 (Visual diagram)

(Fairly visual diagram)

 (Detailed diagram)

Harmful effects of nitrogen deposition

The consequences of human-caused nitrogen deposition are profound and influence many aspects of the
Earth system, including
• Ecosystems: Nitrogen additions to the soil can lead to changes that favor weeds over native
plants, which in turn reduce species diversity and changes ecosystems. Research shows that
nitrogen levels are linked with changes in grassland species, from mosses and lichens to grasses
and flowers.
• Precipitation: Nitrogen oxides react with water to form nitric acid, which along with sulfur
dioxide is a major component of acid rain. Acid rain can damage and kill aquatic life and
vegetation, as well as corrode buildings, bridges, and other structures.
• Air quality: High concentrations of nitrogen oxides in the lower atmosphere are a precursor to
troposphere ozone which is known to damage living tissues, including human lungs, and decrease
plant production.
• Water quality: Adding large amounts of nitrogen to rivers, lakes, and coastal systems results in
eutrophication, a condition that occurs in aquatic ecosystems when excessive nutrient
concentrations stimulate blooms of algae that deplete oxygen, killing fish and other organisms
and ruining water quality. Parts of the Gulf of Mexico, for example, are so inundated with excess
fertilizer that the water is clogged with algae, suffocating fish and other marine life.
• Carbon cycle: The impacts of nitrogen deposition on the global carbon cycle are uncertain, but it
is likely that some ecosystems have been fertilized by additional nitrogen, which may boost their
capture and storage of carbon. Sustained carbon sinks are unlikely, however, because soil
acidification, ozone pollution, and other negative effects eventually compromise nitrogen-
enhanced carbon uptake.
  In marine
Nitrogen (N) is an essential macronutrient the non-availability of which in suitable form or concentration
often limits biological production both in the terrestrial and marine environments. It is a polyvalent
element that occurs in oxidation states ranging from –3 to +5. Molecular nitrogen (N2), the dominant
constituent of our atmosphere, is the most abundant form of nitrogen on Earth.

By contrast, nitrogen can be found in the marine environment as nitrate, NO3- , with an oxidation state of
+V, nitrite, NO2- (+III), nitrous oxide, N2O (+I), molecular nitrogen, N2 (O), and ammonia, NH4+ (-III). In
addition, there are a myriad of organic compounds containing nitrogen, most often in the form of amino-
groups in the -III oxidation state
Assimilation
The assimilation of nitrate or ammonium into organic nitrogen by marine phytoplankton in order to
satisfy their nitrogen demand for growth is the process that quantitatively dominates the marine nitrogen
cycle. NH4+ is thought to be the preferred source of fixed nitrogen for phytoplankton, because its
assimilation does not involve a redox reaction and therefore requires little energy. It is therefore not
surprising that all phytoplankton can grow on NH4+ as the only nitrogen source. By contrast, the
assimilation of NO3- involves the reduction of nitrogen from an oxidation state of +V to -III, i.e., the
transfer of eight electrons, which requires the investment of a substantial amount of energy. Since NO3- in
the ocean is generally much more abundant that NH4+, most phytoplankton have the enzymes necessary to
undertake this reduction (nitrate reductase), with a few notable exceptions. The best studied organisms
lacking the ability to use NO3- as a nitrogen source are Prochlorococcus and certain strains of
Synechococcus. All phytoplankton that can use NO3- can also use NO2- as a source of nitrogen. This is
because NO2- is an intermediary product during the assimilation of NO3-. However, NO2- is usually only a
very minor source of nitrogen for phytoplankton, as its concentration is often an order of magnitude lower
than that of NO3- or NH4+.
Since most phytoplankton appear to have a relatively fixed cell quota for protein, lipids, carbohydrates,
and DNA/RNA, they tend to take up these different elements with a relatively fixed ratio, permitting us to
write the synthesis of organic matter by the coupled assimilation of CO2, NO-3, and PO3-4 as:

106CO2 + 16NO3 + HPO4 -2+ 78H2O + 18H+ →→ C106H175O42N16P + 150O2

And in the case when NH4+is used as nitrogen source:

106CO2 + 16NH4 ++ HPO4 -2+ 48H2O + 14OH- →→ C106H175O42N16P + 118O2

Nitrification
Most of the fixed organic nitrogen in the ocean is returned back to nitrate by remineralization processes.
This occurs in three distinct steps: ammonification, ammonium oxidation, and nitrite oxidation, where the
latter two processes in combination are often referred to as nitrification. Ammonification is the reverse
process of the NH+4 assimilation reaction i.e. the transformation of organic nitrogen to NH+4. Most of this
process is done by heterotrophic bacteria, which use the oxidation of organic carbon to CO2 as a source of
energy, but release the organic nitrogen then as NH+4 as they lack the ability to oxidize it to NH4+or NO3.
This latter step is undertaken by a specialized group of bacteria, which are using the oxidation of NH+4 to
NO-3 as a source of energy, i.e., they are chemo-autotrophic. The two steps of nitrification, the oxidation
of NH+4 to NO2, and the oxidation of NO2 to NO3 are most often done by two distinct groups of
organisms. The best known are Nitrosomonas spp, an ammonium oxidizer, and Nitrobacter spp, a nitrite
oxidizer. Nitrification requires the presence of O2 and tends to be inhibited by light, which has important
implications for the upper ocean nitrogen cycle; three distinct reactions remineralize organic nitrogen to
nitrate:
The heterotrophic process of ammonification, which is the return pathway of NH4:

C106H175O42N16P + 118O2 →→ 106CO2 + 16NH4 ++ HPO4 -2+ 48H2O + 14OH-

And the two processes of aerobic nitrification, i.e., ammonium oxidation, and nitrite oxidation:

2 NH4 + 3O2 →→ 2NO2 +4H++2H2O

2NO2+ O2 →→ 2NO3
The vast majority of the oxidation of organic matter follows reaction involving oxygen as the terminal
electron acceptor. Higher organisms are strict aerobes, i.e., they cannot switch to another oxidant, and
therefore cannot live in the absence of free oxygen. In contrast, most bacteria are more flexible and can
use a wide range of other electron acceptors, including sulfate, manganese, and iron.
Denitrification
However, the first electron acceptor that is generally being used by bacteria in the ocean is NO3, resulting
in a process called denitrification. The preference of NO3over other electron acceptors is because of the
higher energy yield of denitrification in comparison to the use of the alternative oxidants. Using organic
matter with the stoichiometry, heterotrophic denitrification can be written as:

C106H175O42N16P + 104NO3→→ 106CO2 + 60N2 + H3PO4+ 138H2O

Another anaerobic process that removes bio-available nitrogen from the water is the anaerobic oxidation
of ammonium (Anammox), in which ammonium and nitrite are combined to form N2, thus

NO2+ NH4→→ 2N2+2H2O

In contrast to denitrification, the Anammox reaction is used as a source of energy, i.e., the Anammox
bacteria are chemo-autotrophic. This process, first uncovered in wastewater bioreactors, has been
demonstrated to occur in marine environments only very recently.

Nitrogen fixation
The most important source for fixed nitrogen in the ocean is biological N2 fixation, which refers to the
conversion of N2 into organic nitrogen. It is undertaken in the ocean primarily by photoautotrophic
organisms in order to obtain nitrogen in environments where fixed nitrogen is usually exhausted. The
most conspicuousand best studied N2 fixing organism (diazotroph) is Trichodesmium, although there are
many other organisms known to fix nitrogen, including uni-cellular bacteria, and cyanobacteria that live
endosymbiontically within marine diatoms.
References:
• http://images.google.com.pk/imgres?
imgurl=http://www.nicksnowden.net/images/Nutrient_Cycles/nitrogen_cycle_cartoon.gif&imgref
url=http://www.nicksnowden.net/Module_3_pages/nitrogen_cycle.htm&usg=__jihjItgx8ZMv0VJ
ku7MVlCq7tE8=&h=517&w=904&sz=72&hl=en&start=6&um=1&tbnid=UdrNX-
ORaMoW3M:&tbnh=84&tbnw=147&prev=/images%3Fq%3Dnitrogen%2Bcycle%2Bin%2Bsoil
%26hl%3Den%26sa%3DN%26um%3D1
• http://database.sunsite.ualberta.ca/pls/biod1/ditrl.display.detail?p_mno=135
• This straightforward diagram illustrating the key points (but not giving details of, for example,
nitrogen fixation) is from http://helios.bto.ed.ac.uk/bto/microbes/nitrogen.htm
• A very visual diagram, but lacking in some detail, taken from http://ferl.becta.org.uk/display.cfm?
resID=3598
• A fairly visual diagram but lacking in detail taken from
http://www.soils.agri.umn.edu/academics/classes/soil2125/doc/s9chap2.htm
• A detailed diagram shown in an unusual form, this is from http://www.alken-
murray.com/Nitrogen.html
• http://images.search.yahoo.com/images/view?back=http%3A%2F%2Fimages.search.yahoo.com
%2Fsearch%2Fimages%3Fp%3Dnitrogen%2Bcycle%2Bin%2Bmarine%26ei%3Dutf-8%26fr
%3Dsfp&w=350&h=299&imgurl=www.eoearth.org%2Fupload%2Fthumb%2F0%2F0b
%2FMarine_N_cycle.JPG%2F350px-Marine_N_cycle.JPG&rurl=http%3A%2F
%2Fwww.eoearth.org%2Farticle
%2FMarine_nitrogen_cycle&size=18k&name=350px+Marine+N+c...&p=nitrogen+cycle+in+ma
rine&oid=0b826e26ca50826a&fr2=&no=1&tt=56&sigr=11kv9ec1e&sigi=12datk73s&sigb=12n
66eoms
• www.geo.uu.nl/Research/Geochemistry/jack/NCycle.ppt -
• http://www.soest.hawaii.edu/oceanography/courses/OCN626/2009/Gruber_et_al._2008_N_Book.
pdf