Soil Nitrogen
Roles of nitrogen in plant (2.5 – 4% in foliage plants)
 An integrated part of essential plant compounds :- -amino acids→proteins, enzymes,
nuclei acid, Chlorophyll
 Essential for carbohydrate use in plants
 Stimulates growth and uptake of other nutrients
 Increases plumpness of grain, protein content of grains and succulence of leaf-crops
Deficiency symptoms
-Chlorosis-paling or yellowing of leaves
-Stunting, thin spindly stems
-Low protein content, high sugar content
-Easily translocated within the plant as it is mobile-yellowing and senescence starts in older
leaves
-Young foliage receives nitrogen from below
-Low shoot to root ratio
-Plants mature more quickly
Signs of luxury Nitrogen consumption-Oversupply
-Excessive vegetative growth cells enlarged but flower production suffers as there is excessive
foliage
-Delayed maturity
-More susceptible to disease (fungal) and insects and pests
-Poor crop quality-colour, flavour
-Low sugar and vitamin content
-Nitrate builds up in foliage
Forms taken up by plants
-Dissolved nitrates and ammonium ions
-Nitrates and ammonium roughly equal amounts is suitable for most crops
-Low molecular weight organic compounds like dissolved proteins and amino acids can also be
taken up by mineral plants-important in natural grasslands and forests
-Also affected by availabity of inorganic Nitrogen
Usu less than inorganic nitrogen taken up
The Nitrogen Cycle
 Atmosphere is the reservoir for N2 (N=N) which is extremely inert and therefore insoluble
by plants in that form (78%)
 Microbial nitrogen fixation and lighting however can avail enough energy to break the
triple bond in atmospheric nitrogen into forms that are not inert and utilisable plants
 Most nitrogen in terrestrial systems is found in the soil approximately 0.02-0.5% in A
horizons averaging 0.15% in soils cultivated
 Soils contains 10-20 times nitrogen than standing vegetation
 Most soil nitrogen is in organic molecules
 SOM typically contains approx 5% Nitrogen
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 Except in the case of recently fertilized fields inorganic nitrogen rarely exceeds 1-2% of
total Nitrogen in soil
Photocopy pg 546
The Nitrogen Cycle Diagram
 It is important to understand translocation and transformations of nitrogen as these are
associated with many environmental, agricultural and natural resource related problems
 The Nitrogen cycle shows the principal pools and forms of nitrogen and the processes by
which they interact
 Ammonium and nitrate are too critical inorganic forms of nitrogen in the nitrogen cycle
Process involving ammonium nitrogen are:-Immobilization by microorganism -Assimilation by plant uptake
-Fixation in clay inter-layers
-Volatization as NH3 gas
-Oxidation to nitrite and nitrate thru nitrification
Nitrate nitrogen is subject to the processes:
-Microbial immobilization -Plant uptake
-Leaching losses
-Volatization through the process of denitrification
Mineralization
 This is the enzymatic breakdown of large insoluble organic molecules into simpler and
smaller units with the eventual release of inorganic (or mineral) nutrients
 Soil nitrogen in organic form is protected from loss as it is insoluble but this makes it
unavailable for use by plants
 Organic nitrogen is present as R-NH2 (amine group) largely in proteins or as part of humic
compounds
 During mineralization of R-NH2 compounds the groups are hydrolysed and nitrogen is
released as ammonium which can be oxidised to nitrates
 This process is mediated (brought about) by enzymes produced mainly by microorganisms
 Enzymes are hydrolasses and deaminases and these break down the C-H and C-NH2
Equation
Mineralization
+ 2H2O
+ O2
+ ½O2
R-NH2 ⇌ OH- + R-OH + NH4+ ⇌ 4H++ energy +NO2- ⇌ energy + NO3-2H2O
-O2
-
½O2
Immobilization
-1.5 to 3.5% of organic N mineralizes annual
-Mineralized N –major part of N taken up by plants
-When OM content is known, the amount of N mineralized annually can be estimated as:
2
Where:
A = Amt of SOM in upper 15cm of soil in kg SOM per 100kg soil
ranges from close to 0% to over 75% in Histosols.-common values are 0.5 to 5%
B = Amt of soil per Ha to 15cm depth : ------ approx 2×106 Kg/Ha
C = Amt of nitrogen in S0M :--------- approx 5kg/100kg S0M
D = Amt of S0M to be mineralized in 1yr----- -depends on texture, climate, management
approx2% in fine textured soil and approx 3.5% in coarse texture soil
Higher values are typical of warm climates and lower ones in cool climates
Common values may be averaging 2.5kg S0M/100kg S0M
Immobilization
-Opposite of mineralization
-Conversion of inorganic nitrate and ammonium into organic forms
-Maybe biotic or abiotic
-Biotic-microbial assimilation when C/N residues are decomposed
-Abiotic chemical reactions with high C/N soil OM, important in forests
Ammonium fixation by clay minerals
 Ammonium is held on exchange sites attracted to negatively charged surfaces in plants
available
 In this form it is protected from leaching
 Also because of its size it can be held in the interlayer of 2:1 type clays especially
vermiculite in non exchangeable and slowly available
 Potassium is similar in size to ammonium and is held in a similar measure
 Highly weathered soils have less 2:1 clays, ammonium fixation is minor
NB approximately 50% of N in O and A is immobilized by ammonium fixation or organic matter
(humus) reactions
Ammonium Volatization
-Ammonia gas can be produced from the breakdown of organic materials, manure and fertilizers
(urea) or anhydrous ammonia
-Ammonia gas is in eqm with ammonium ions
NH4t + OH- ⇌ H2O + NH3 ↑
Dissolved ions
gas
Ammonification is the process that produces ammonia which is the first stage in mineralization of
proteins
 Broad groups of organisms are responsible for ammonification
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Equation
Equation
R-CH2-CH(COOH)-NH2
→
R-CH2-CH2(COOH) + NH3
 Ammonification takes place under a wide range of soil conditions
NH3 + H2O ⇌ NH4 + OH-
Volatization is favoured by: pH levels which favour the formation of NH3
NH3 producing amendments moves the reaction towards the formation of OH- which
favour the loss of ammonia gas
Colloids bind NH4+ and slow down loss of NH3 gas, sandy soils favour volatization
-
Surface placement of NH3 producing amendments (incorporation reduces losses by 2575%)
-
Drying of the soil favours loss as ammonium gas
-
In rice paddies ammonia loss can occur even under slightly acid conditions
-
Fertilizer applied at surface of fish ponds and rice paddies stimulates algal growth which
utilizes carbon dioxide reducing carbonic acid formation
-
pH increases during day time even upto 9 → the NH3 volatilises
-
NH3 in atm can be absorbed by plants through leaves
NITRIFICATION
This is the process whereby



Ammonium ions are oxidised to nitrates and nitrites by microorganisms enzymatically
The process is mediated by autotrophs which obtain energy by oxidising ammonium ions
and not OM
It is a 2 stage process:
1. NH4+ + 1½ O2-nitrosomonas
NO2- + 2H+ + H2O + 275KJ Energy
nitrite
2. NO2- + ½O2
-nitrobacter
NO3- + 76 KJ Energy
nitrate




Nitrite is phytotoxic even in mg/kg concentrations in soil
Removal of nitrite is rapid as stage 2 follows immediateld after stage 1
Nitrification is an acidifying process
Green house gases like N2O, NO and NO2 may be produced if O2 is limiting or in short
supply
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Conditions favouring nitrification





Supply of NH4+ ions . Excess NH4+ is toxic to nitrobacter
Oxygen supply --- well drained soils. nitrifying bacteria are aerobes
Optimum moisture similar to that for plant growth (60%)
Temperatures in the range 20-30 oC.
Abundance of exchangeable Mg2+ and Ca2+ and optimum nutrient levels for plant growth
The nitrate leaching problem



NO3- is negatively charged and moves freely with drainage water
This is problematic - results in loss of plant nutrients and fertility declines
-there is co-leaching of Mg2+, Ca2+ and K+
-leads to soil acidification
- environmental pollution
Leaching is dependent on 2 factors:
-volume of water leaching through soil (soil texture, precipitation, evapotranspiration)
-concentration of nitrates in the drainage water
- the magnitude of the NO3- pool during leaching event ie
-synchrony between inputs and outputs where inputs are due to org N mineralization, Nfertilization and outputs are due to N-immobilization and plant uptake of NO3-N

Leaching: Forests vs cultivated lands
NO3-N in leachate
NO3-N lost by leaching
Forests: N
0.1 mg/L
1-2 kg N/Ha
Cultivated land
2-3 mg/L
25kg N/Ha
Management to reduce nitrate-N losses





Timing of N inputs to allow for synchrony between nitrate mineralization and uptake by
plants
Synchrony is best achieved with perennials and poorest in cultivated cropping systems left
bare of crops
Modest applications of N-ammendments timed to coincide with peak crop N needs
Planting N-demanding winter cover crops where winter rainfall is significant
Reversing nitrate leaching through agroforestry- acid soils by AEC can retain nitrate-N
deep in their subsoils:- deep rooted adroforestry trees can then bring this up to surface
soils as they drop their leaves.
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Denitrification- gaseous losses of N


A series of biochemical rxns convert nitrate to gaseous forms
Involves microorganisms:-
facultative anaerobic bacteria of the genera
-Pseudomonas
-micrococus
-bacillus
-achromobacter
heterotrophs ie obtain energy by breaking
down organic compounds
Thiobacillus denitrificans – obtains energy from oxidation of sulfur.
Eqn
2NO3-
2NO2-
2NO↑
N2O↑
N2↑
N species
Nitrate ions
nitrite ions
nitric oxide gas
nitrous oxide gas
dinitrogen gas
Oxdn stae
(+5)
(+3)
(+2)
(+1)
(0)
Oxygen released at each step forms CO2 or SO42- in the case of thiobacillus oxidising bacteria
Conditions favouring denitrification






Low oxygen levels (<10%) in soils
TO = 25 -35 oC is optimal
Can occur within the range 2 oC -50 oC
Inhibited by strong acid conditions (pH<5), under these conditions N2O formation is favoured.
Flactuating aeration prevalent under field conditions favours formation of a mixture of gases
N2O is favoured under acid conditions is when oxygen is not too limiting
Prevalent form of gas is dependent on pH, temp and O2 level
Magnitude of N losses




Variable dependent on soil conditions and management practices
Highest when soil is saturated
Highest in low-lying organic matter rich areas and over hot spots
5-10kg N/Ha/yr is typical but up to 30-60kgN/ ha/ yr in OM rich areas
Atmospheric Pollution




NO and N2O are reactive unlike dinitrogen gas and are therefore environmentally important
They form nitric acid a component of acid rain
N2O is active in ozone layer depletion (also produces fron car exhausts)
Reacts with volatile organic pollutants forming smog or ground level ozone
6

NO in the upper atm contributes to greenhouse effect (x 300 effect of CO2) absorbs infra red
radiation
Denitrification in flooded soils
-
Flooded soils are usu found as part of wetlands, rice paddies
They are characterized by alternating drying and wetting cycles
These conds favour alternating nitrification and denitrification
There is also concurrent nitrification (at soil-water inter surface) and denitrification (at
lower depths)
Mgmt -lossess of nitrogen can be dramatically reduced by :-deep placement of fertilizer
-eliminating nitrification by maintaining flooded soil conditions at all times-insufficient
O2
Beneficial effects of denitrification
Overland-flow waste water treatment
- waste water rich in carbon and nitrogen poses danger of eutrophication
-waster water is passed over specially designed water saturated soil systems
Artificial wetlands-used to purify water before it is discharged into water bodies
Biological Nitrogen Fixation
Approximately 139 000Mg fixed annually globally
Next to photosynthesis in importance
A few organisms are involved:- Bacteria of the genii rhizobia brady-rhizobia, actinomycetes and
cyanobacteria
Mechanism
-Dependent on nitrogenase enzyme - nitrogenase catalyses reduction of dinitrogen gas to
ammonia
-Ammonia gas combines with organic acid to form amino acids and then proteins
nitrogenase
+
-N2 + 8H + 6e-
Fe, Mo
2NH3 + H2
Small protein
that supplies
electrons
-Nitrogen reduction takes place on nitrogenase
-Nitrogenase is a complex of 2 proteins:
-Small protein contains iron
-Large protein contains molybdenum
-nitrogenase is destroyed by oxygen so
it needs to be protected from oxygen
-This is achieved by the leghaemoglobin
which binds oxygen from nitrogenase but
available for respiration of other parts
-Nitrogen fixing nodules are red in colour
which is a distinguishing mark
Large
protein
N2 from air goes in
Iron-sulfur clusters
Molybdenum-iron-sulfur clusters
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NH3 andH2
come out
Breaking the tripple bond in nitrogen requires a lot of energy
This is obtained by association with higher plants which supply the energy through
photosynthesis
 The larger protein converts atmospheric energy to ammonia using electrons provided by
the smaller protein
 M sights capture nitrogen while P sites receive electrons provided by small protein
 Reduction reaction is end product-inhibited. Ammonia accumulation inhibits N-fixation
 Too much nitrogen soil inhibits the formation of nodules. N fixation takes place in nodules
 N fixing organisms have a high rqmt of molybdenum, iron, phosphorous and sulphur
 These are either part of nitrogenase or required in its synthesis and use
Symbiotic fixation with legumes
Symbiosis mutually beneficial relationship
In agric soils microorganisms are Rhizhobium and brady Rhizobium
Rhozobium are fast growers and acid producers
Brady rhizobium are slow growers and do not produce acids
Organisms infect root hair and cortical cells thereby inducing formation of nodules
Host plants supplies carbohydrates for energy bacteria supply the host plant with reactive N
compounds
The relationship is usually specific
Genus
species/subgroup
host legume
Rhizobium
R.leguminosarum
via(vatch),pisum I(peas),Ilens(lentles) lathyrus(sweet peas)
bv trifolli
Trifollium sp
bv phaseoli
Phaseolus spp
R Meliloti
Melilotus,Medicago,Trigonella
R loti
lotus ,lupians,cicer
Brady
rhizobium
R.Fredii
B.japonicum
B. sp
Glycine (soy bean)
Glycine
Vigna (cowpeas) Arachis (peanut) cajanus (pigeon pea)
Pueraria
Quantity of N fixed
Dependent on soil and climatic conditions
10 -500kgN/Ha/yr for Non-symbiotic and symbiotic N fixation respectively
Effect on soil N
- may increase gradually
-peas and beans are poor fixers
- most N is removed with the harvest where grain or foliage is removed
- More additions of N into the soil happen with green manures or perennial legumes
Symbiotic Fixation with non-legume (with nodules)
-Some non-legumes nodulate and fix N (200 species and >12 genera)
-Their nodules are invaded by actiomycetes of the genus frankia
-important in disturbed lands that are extremely low in fertility as first colonisers
-important in areas undergoing succession eg established artificial wetlands forests
8
-Cyanobacteria also develop N-fixing symbiotic relationships with green plants
Symbiotic Fixation without nodules
-Cyanobacteria involved, important in rice paddies
-Association is with azolla floating fern
-anabaena cyanobacteria inhabit cavities in the the leaves of the floating fern
-spirilum and azotobacter bacteria live in the rrhizosphere of certain grasses and non-legumes
-exchange is for root exudates
- amt fixed is 5-30kgN/ha/yr
Non Symbiotic fixation
 Free living microorganisms involved
 Present in soil and water
 Not associated with plants- therefore free living and non-symbiotic
 These are heterotrophs- obtain energy from saprophytic decomposition of organic matter
-Occurs in anaerobic pockets of soils, inside aggregates
 Autotrophs- photosynthesizing bacteria and cyano-bacteria
Nitrogen deposition from Atm
 Forms acid rain
 Important in high rainfall areas
 Damaging to forests thru N saturation
 Forests are low N-systems and have no capacity to utilize all received nitrates leading to N
losses which is usually accompanied by leaching of bases leading to soil acidification.
 This disrupts tree growth and the forest soil ecosystem low biodiversity.
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