Nitrogen transformations in wet soils are markedly different from those in drained, aerated soils. These differences affect the prevalent soil microorganisms and microbial activities and the turnover, availabilility, and losses of N.

1. MASTER’S SEMINAR ON
NITROGEN TRANSFORMATIONS IN WET SOILS
Seminar Incharge Presented By

2. INTRODUCTION
• Nitrogen is one of the most important primary
nutrient non- metal elements which require large
quantity for the plant growth and nutrition
• No other element essential for life takes as many
forms in soil as nitrogen (N),and transformations
among these forms are mostly mediated by microbes.
• It occurs in the atmosphere, lithosphere, and
hydrosphere. The soil accounts for only a small
amount of lithospheric nitrogen, and of this soil
nitrogen, a very minute amount is directly available to
plants.
• Nitrogen takes nine different chemical forms in soil
corresponding to different oxidative states.
• Biological N2 fixation,whereby N2 is transformed to
organic N dominant natural process by which N enters
soil biological pools.

3. NITROGEN TRANSFORMATIONS
• Nitrogen transformations in wet soils are markedly different from those in drained, aerated soils.
• These differences affect the prevalent soil microorganisms and microbial activities and the turnover,
availabilility, and losses of N.
• The forms of N present in wet soils are generally similar to those in aerated soils; but the relative
magnitude of the N forms, particularly nitrate (NO3)and ammonium (NH4
+), and N transformation are
markedly affected by the oxidation status of soil.
• Nitrate is the dominant form of inorganic N in drained, aerated soils; whereas NH4
+ is the dominant and
stable form of inorganic N that accumulates in wet soils.
• The main N transformation processes in submerged soils—as in aerated soils—are mineralization,
immobilization, nitrification, denitrification, ammonia (NH3) volatilization, and biological N2 fixation.
• Soil submergence modifies these processes, and a unique feature of submerged soils is the simultaneous
formation and loss of NO3−, occurring within the adjoining aerobic and anaerobic soil zones.
• Submerged soils as compared with aerated soils are favorable environments for loss of N by nitrification–
denitrification, NH3 volatilization, and for addition of N via biological N2 fixation (BNF).

4. WET SOILS
• Wet soils are soils that are saturated with water for a
sufficiently long time in a year to give the soil the
following distinctive gley horizons resulting from
oxidation-reduction processes:
i. A partially oxidized ‘A’ horizon high in organic matter
ii. A mottled zone in which oxidation and reduction
alternates
iii. A permanently reduced zone which is bluish green in
colour
• They occur in a range of ecosystems including rice
(Oryza sativa L.) fields, wetlands, estuaries, and
floodplains.

5. PROPERTIES OF WET SOILS
• Depletion of oxygen
A unique feature of wet soils, affecting N transformations, is
the depletion of oxygen (O2) throughout most of the root zone.
• Development of aerobic and anaerobic layer
The greater potential consumption of O2 as compared to the
available supply through the flood water results in two
distinctly different layers being formed in wet soil: an oxidized
or aerobic layer where O2 is present and a reduced or
anaerobic layer in which no free O2 is present.
• Change in soil biology
When oxygen in the soil is depleted, aerobic organisms die or
become dormant. They are replaced by two types of
organisms surviving without oxygen called facultative and
obligate anaerobes

6. • Soil depends on oxygen from plants
Some plants like rice are adapted to grow in wet soils and have
porous structures in their stems and roots called aerenchyma
tissues. These tissues provides a passage for the flow of gas
into the plants through leaves and then down to the roots.
• Oxidation-reduction potential
The most striking and easiest-to-measure change occurring in
a soil as a result of submergence is the decrease in oxidation-
reduction or redox potential. Aerated soils have characteristic
redox potentials in the range +400 to +700 millivolts;
waterlogged soils exhibit potentials as low as -250 to -300
millivolts.

7. MINERALIZATION AND IMMOBILIZATION
• In aerated soils NO3- is the inorganic form and all of the nitrogen reactions that follow the decomposition
of organic matter proceed towards the production of NO3-. Thus, organic form of nitrogen undergoes
mineralization to NH4+, oxidation of NH4+ to NO2- and oxidation of NO2- to NO3-.
In aerobic soils:
Organic form of Nitrogen NH3+ NO2- NO3-
But in an anaerobic soil the absence of O2 inhibits the activity of Nitrosomonas microorganisms that
oxidises NH4+ and therefore, nitrogen mineralization stops at the NH4+ form.
In wet soils:
Organic form of Nitrogen NH4+ Stops at this point
• Mineralization, or more specifically ammonification- the conversion of soil organic N to ammonium-
supplies plant- available N in wet agricultural soils.
• This breakdown of organic N in wet soils is characterized by anaerobic decomposition, which involves
different microorganisms and end products than aerobic decomposition.
• Ammonium accumulates in anaerobic decomposition due to the absence of O2, which is required for
conversion of NH4
+ to NO3
−.
Mineralization
Ammonification
Microbial oxidation Microbial oxidation
Mineralization

8. • Microbial decomposition of organic matter in aerated soil is accomplished by a wide range of
microorganisms. Respiration by these organisms is associated with high energy release, and the
decomposition of substrates progresses rapidly with evolution of CO2. As cell synthesis proceeds, there is
a heavy demand for mineral nutrients, particularly N.
• Decomposition in the bulk volume of a submerged soil, on the other hand, depends on a relatively
restricted bacterial micro flora. These anaerobes operate at a lower energy level and are less efficient
than aerobes as a consequence of incomplete decomposition of carbohydrates and synthesis of fewer
microbial cells per unit of organic C degraded.
• The processes of both decomposition and cell synthesis are consequently slower under anaerobic than
aerobic conditions.
• In aerobic soil the main end products of decomposition are CO2,NO3
−, SO4
2−, water, and resistant residues.
The main end products of anaerobic decomposition are CO2, CH4, organic acids, NH4
+, H2S, and resistant
residues.
• The breakdown of SOM and plant residues is typically slower in wet soils than aerobic soil . Hence, a
lower gross N mineralization rate would be expected in wet soils as compared with aerobic soils.
• Gross N immobilization is characteristically lower in submerged soils because of the low metabolic
requirement of anaerobic microorganisms for N. The net effect of the lower gross mineralization and
lower gross immobilization is often a higher net N mineralization in submerged than aerobic soils,
leading to higher rates of inorganic N release in submerged soil.
• Because of the low N requirement of anaerobic metabolism, the net release of inorganic N from
decomposing plant residue would expectedly occur at a higher C/N in submerged rather than aerobic
soil.

9. NITRIFICATION- DENITRIFICATION
• Nitrification is the biological conversion of NH4
+ to NO3
- which requires free O2. It is a two step
process. Bacteria known as Nitrosomonas convert NH4
+ to NO2
-. Next, bacteria called
Nitrobacter finish the conversion of NO2
- to NO3
-. The reactions are generally coupled and
proceed rapidly to the NO3
- form; hence NO2
- levels at any given time are usually low.
• In wet soils it is restricted only in the oxidized zones which include the water column, a small
layer of surface soil, and soil in the root zone of aquatic plants.
• The magnitude of nitrification is regulated by the availability of O2, which determines the
fraction of the total soil volume occupied by aerobic zones, and NH4
+ concentration in these
aerobic zones.
• Ammonium in aerobic zones originates from formation by ammonification within the aerobic
zone, inputs of external N including fertilizer, and diffusion of NH4
+ from adjacent anaerobic
soil zones.
• Nitrate formed by nitrification is stable within an aerobic zone, but it can be readily reduced in
adjacent anaerobic soil zones.
• Oxygen availability is typically the factor most limiting nitrification in submerged agricultural
soils.

10. • Nitrate does not accumulate in the anaerobic zone because of the high demand for NO3
− to serve
as an electron acceptor in the absence of O2.
• Denitrification is the dissimilatory reduction of NO3
−, whereby NO3
− serves as a terminal
electron acceptor and is reduced to gaseous end products of nitrous oxide (N2O) and nitrogen
gas(N2).
• Denitrification is mediated by heterotrophic microorganisms; and its rate is regulated by NO3
−
concentration and available C, which serves as an energy source or electron donor.
• The supply of NO3
− originating from the aerobic zones is typically the factor limiting
denitrification in submerged soils.
• In submerged soils, the demand for NO3
− to serve as an electron acceptor is typically much
greater than the demand for NO3
− as an N source for microbes and plants.
• Assimilatory reduction of NO3
− where NO3
− is used as a nutrient source and incorporated into
cell biomass is consequently not a significant process.
• Anaerobic soil conditions promote the accumulation of NH4
+, which serves as the primary
inorganic N source for microbes and plants.
• Assimilatory reduction of NO3
− would only be expected when NH4
+ levels are low and NO3
−
levels are high.

11. • A characteristic of submerged soils with important implications for N cycling is the adjoining presence of
aerobic zones where nitrification occurs and anaerobiczones where denitrification occurs.
• The environments suitable for the growth of nitrifiers and denitrifiers are mutually exclusive, but the
transport of substrates and products between the aerobic and anaerobic zones couples nitrification and
denitrification.
• Nitrogen loss by coupled processes of simultaneous nitrification and denitrification is consequently a
unique feature of submerged soils
• The addition of fertilizer N, transport of NH4
+ from anaerobic to aerobic zones, and ammonification in
aerobic zones typically supply adequate NH4
+ for nitrifiers. High NH4
+ levels in aerobic zones suggest the
supply ofNH4
+ exceeds the rate at which NH4
+ is converted to NO3
−.
• The loss of N by coupled nitrification–denitrification is usually limited by the formation of NO3
− , and the
supply of NO3
− can consequently control the size and activityof denitrifiers.
• The loss of fertilizer N by nitrification–denitrification can be reduced by controlling nitrification, which
is typically the rate-limiting step in the process leading to N loss.
• The buildup of NO3
- can be reduced by more effective placement of fertilizer N into the anaerobic zone of
soil , amendment of fertilizer with a nitrification inhibitor, and use of controlled release fertilizer.
• The reduction in NO3
− accumulationwith nitrification inhibitors, while effective in controlling N loss by
nitrification–denitrification and leaching, can enhance NH3 volatilization as a result of enhanced buildup
of ammoniacal N in floodwater and surface soil.

12. Figure: A schematic diagram of the processes by which ammonium fertilizer can be lost from a waterlogged soil.
Ammonium nitrogen applied to the oxidized soil surface is nitrified and then leaches down into the reduced
subsurface layer, where it is denitrified and lost from the soil.

13. AMMONIA VOLATILIZATION
• Ammonia volatilization is a major process by which fertilizer N is lost from rice fields with submerged or
saturated soils.
• A substantial portion of the fertilizer N broadcast into the floodwater of rice fields or incorporated into
puddled soils before rice establishment can accumulate in the floodwater as ammoniacal N (NH4
+ + NH3)
within the week after N application.
• Urea, a common fertilizer for rice, is rapidly hydrolyzed within the week after application to submerged
soils. Ammoniacal N originating from the hydrolyzed urea accumulates in floodwater. High concentrations
of ammoniacal N together with high floodwater pH and temperature favor loss of added fertilizer N by
NH3 volatilization.
• The magnitude of NH3 loss from submerged soils is directly related to the content of aqueous NH3 or
partial pressure of ammonia (ρNH3) in water at the interface with the atmosphere.
• Aqueous NH3 as a fraction of total ammoniacal N is directly influenced by water pH and temperature.
Aqueous NH3 is negligible below pH 7.5, but it increases rapidly from pH 7.5 to 10. At pH 9.2 about 50% of
the ammoniacal N in water is present as NH3.
• Aqueous NH3, at a constant ammoniacal N concentration and pH, increases linearly with temperature,
resulting in nearly a fourfold increase with a change in temperature from 10 to 40°C .
• Water pH is, however, a more important factor influencing NH3 loss than temperature.

14. • Ammonia loss from fertilizer N applied to young rice increases linearly with wind speed and ρNH3
Ammonia loss can be reduced with rice establishment practices that reduce wind speed near the
floodwater surface.
• Young broadcast-seeded rice has been reported to have lower wind speed at 3 to 10 cm above floodwater
and lower associated NH3 loss from applied fertilizer N than young transplanted rice .
• The denser plant population and greater surface cover with broadcast seeded rice, which restricted gas
exchange at the floodwater–atmosphere interface, presumably accounted for the lower ammonia loss.
Methods to reduce N loss through volatilization
 Incorporating urea before transplanting rather than broadcasting into floodwater at 10 to 21 days after
transplanting often reduces NH3 loss.
 The loss of NH3 from basal incorporated urea is reportedly less when floodwater is first removed and urea
is broadcast and incorporated into saturated soil with no floodwater rather than broadcast and
incorporated with standing floodwater.
 NH3 loss can be reduced by reducing the ρNH3 in water at the water–atmosphere interface of saturated or
submerged soils. Films of organic compounds, algal scum, and azolla on the surface of floodwater have
been shown to reduce NH3 loss by restricting the transfer of ammonia from floodwater to the overlying
atmosphere.
 The application of fertilizer N immediately before rather than 14 days before permanent flooding reduces
NH3 loss during production of dry-seeded rice on non puddled soils .
 The buildup of ammoniacal N in floodwater can be reduced by more effective incorporation and
placement of fertilizer N into puddled soils, application of fertilizer N immediately before rather than after
permanent flooding in non puddled soils, controlled release fertilizers, and urease inhibitors.

15. BIOLOGICAL NITROGEN FIXATION
• Biological Nitrogen Fixation is a process by which molecular nitrogen in the air is converted
into ammonia (NH3) or related nitrogenous compounds in soil which is metabolized by most organisms.
• Wet soils are favorable environments for BNF because of their depletion of O2 and ready supply of C
substrate.
• Nitrogen inputs by BNF help sustain SNSC and maintain SOM, and the input of N by BNF has helped
sustain rice yields at low levels without fertilizer N for hundreds of years on wet soils.
• Long-term N balances for rice grown on submerged soils without fertilizer N typically indicate the
maintenance of total soil N content, as a result of BNF by associative and free-living microorganisms
• Nitrogen fixers—diazotrophs—in wet agricultural soils can be broadly grouped into indigenous and
exogenous systems.
• The indigenous (autochthonous) BNF system comprises cyanobacteria and phototrophic bacteria
inhabiting the floodwater and soil surface, and it comprises heterotrophic bacteria in the root zone and
free-living in the soil. These diazotrophs are typically widespread and native in lowland rice ecosystems.
• The exogenous (allochthonous) BNF system comprises diazotrophs such as N2–fixing cyanobacteria
living in symbiosis with Azolla spp. and heterotrophic and phototrophic rhizobia harboured on aquatic
legumes.The exogenous system is not ubiquitous in lowland rice ecosystems, and it must be applied or
inoculated.

16. • The diverse autotrophs and heterotrophs comprising the indigenous BNF system occur in soil and
floodwater during rice growth and between rice crops when the water regime is favorable.
• Estimates of indigenous BNF based on N balances are typically in the range of 15 to 50 kg N ha−1 crop−1
for lowland rice ecosystems with soil submergence.
• Associative BNF in the rice rhizosphere occurs mostly during the heading stage when soil inorganic N is
low. It depends on rice cultivar and environment and it is often estimated at <10 kg N ha−1 crop−1
although it could theoretically achieve a maximum of 40 kg N ha−1 crop−1.
• Estimates of BNF by free-living heterotrophic bacteria are typically <20 kg N ha−1 crop−1 .
• The application of straw enhances heterotrophic and photodependent BNF by an estimated 2 to 4 kg N
ha−1 Mg−1 of applied straw. The straw serves as a C substrate for heterotrophs, and it can create a more
favorable environment for BNF by reducing inorganic N through temporary immobilization.
• A widely studied exogenous BNF system in submerged rice soils is the symbiotic association of the
Anabaena azollae Strasburger with the freshwater fern Azolla spp. The cyanobacterium inhabits the leaf
cavity of azolla, which can grow rapidly in submerged soils before the rice crop and during the early
growth of rice.
• Estimates of BNF under field rather than experimental conditions suggest symbiotic BNF from the azolla–
cyanobacterium association can contribute 10 to 50 kg N ha−1 crop−1.

17. ANAEROBIC AMMONIUM OXIDATION/ ANAMMOX
• Anaerobic ammonium oxidation (anammox), the process of oxidizing ammonium through the reduction of
nitrite, removes N permanently from aquatic ecosystems and returns it to the atmosphere as nitrogen gas
(N2), as does denitrification.
• The proposed reactions for this process are shown below:
5NH4
+ + 3NO3
− = 4N2 + 9H2O + 2H+
NH4
+ + NO2
− = N2 + 2H2O
• The majority of the soil profile in wetlands is anaerobic, resulting in accumulation of high levels of NH4
+. In
the absence of oxygen, it is thermodynamically possible that several other alternate electron acceptors can
potentially oxidize NH4
+–N
• However, this pathway assumes that some anaerobic bacteria are capable of using NH4
+–N as an electron
donor and derive energy through oxidation.
• The significance of these processes has been documented for wastewater lagoons and marine sediments. At
present, this reaction is not reported in submerged agricultural soils, and the significance of the reaction to
overall N loss remains a subject of speculation.
• The reaction is controlled by availability of NO2
− and competition by heterotrophs,which are dominant in
submerged soils.
• Under conditions of limiting available C, it is likely that some autotrophs might use NH4
+ as an energy
source and potentially oxidize it to N2 gas. Submerged soils, however, are typically not limited by C; and
when NO3
− and NO2
− are present in these systems, they will be used by heterotrophic denitrifiers.

18. AMMONIUM FIXATION
• Fixation of the ammonium ion (NH4
+) by clay minerals is an alternate way of building the nitrogen (N)
pool in soil to optimize N crop recovery and minimize losses.
• The accumulation of NH4+ and the anaerobic conditions following soil submergence are favorable for
the temporary fixation of NH4+ in soils with high amounts of expandable 2:1 clay minerals.
• A buildup of exchangeable NH4+ from mineralization following soil submergence could lead to a
concentration gradient favouring NH4+ diffusion into the interlayers of clay minerals.
• Soil submergence can increase NH4+ fixation through the reduction and dissolution of Fe3+ oxide
coatings on the surface of clay minerals thereby reducing obstacles for NH4+ movement in and out of
interlayers of the clay minerals.
• Soil submergence can also increase NH4+ fixation through the reduction of octahedral Fe3+, which
increases the negative charge of interlayers of the clay minerals.
• The temporary fixation of NH4+ could protect N from losses, while still enabling a timely release of the
NH4+ to plants.
• Nonexchangeable NH4+ can be an important source of N to rice on submerged soils rich in vermiculite.

19. LEACHING LOSSES
(A) NITRATE
• Nitrate present in the root zone of a soil which is submerged at the beginning of the
season is almost invariably lost by denitrification or by being leached out of the root
zone before the plants are large enough to utilize the nitrogen.
• The biological activity and the rate of percolation of water through the soil will
determine which of these mechanisms is most important.
• Nitrate produced in the surface oxidized layer of a waterlogged soil can easily move
downward by diffusion and percolation into the underlying reduced layer, where it is
rapidly denitrified.
• This process is one of the most important pathways of nitrogen loss in waterlogged
soil. Nitrate nitrogen can also be lost from a flooded field by runoff, but the nitrate
content of the flood water seldom exceeds a few parts per million.

20. (B) AMMONIUM NITROGEN
• Ammonium nitrogen is much less subject to leaching from the soil than nitrate because
of its adsorption on the cation-exchange complex.
• Nonetheless, loss of ammonium by leaching is more severe in waterlogged soil than in
well drained soil because:
1. Ammonium is not as likely to accumulate in a well drained soil as in a waterlogged
soil.
2. Reduction reactions in a waterlogged soil produce ferrous and manganous ions which
displace ammonium from the exchange complex to the soil solution where it is more
subject to removal.
3. The constant head of water on the soil surface results in greater downward
percolation of the soil solution in a waterlogged soil than occurs in a well drained soil.
• The addition of organic matter increased the amount of ammonium in the soil solution
instead of immobilizing the nitrogen. There is an increase in the leaching loss of
ammonium due to the addition of organic matter.

21. Figure: A schematic diagram of N transformations in wet soil

22. REFERENCES
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House Pvt. Ltd. New Delhi
• Buresh,R.J., Reddy, K.R. and Kessel, C.V. 2008. Nitrogen Transformations in Submerged Soils. Soil Sci. Soc.
Am. J. 11:401-427
• Biswas, T.D. and Mukherjee, S.K. 2017. Textbook of Soil Science. 2nd Edition, Mc Graw Hill Education.
• Patrick, H.W.M. And Mahapatra, I.C. 1983. Transformation and availability to rice of nitrogen in
waterlogged Soils. 323-339
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• www.researchgate.net
• www.sciencedirect.com
• soils.ifas.ufl.edu