Lecture 20: Soil Nitrogen and
Sulfur Cycling
Overview of Soil Nitrogen
Importance of Nitrogen to Plant
Growth
• Nitrogen is an essential component of amino
acids, the building blocks of proteins
– Enzymes, specialized proteins, control almost all
biological processes
– Also component of nucleic acids and chlorophyll
• Nitrogen addition stimulates plant growth
• Plant foliage contains 2.5 to 4.0% nitrogen
Chlorosis from N Deficiency
Effects of N on Vegetation
Deficiency
Deficiency
Oversupply
Forms of N in Soils
Oxidized
• Nitrate (NO3-): +5 oxidation state, dissolved
• Nitrite (NO2-): +3 oxidation state, dissolved
• Nitric oxide (NO): +2 oxidation state, gas
• Nitrous oxide (N2O): +1 oxidation state, gas
• Nitrogen (N2): 0 oxidation state, gas, 78% of
atmosphere, ultimate source of all N
• Hydroxylamine (NH2OH): -1 oxidation state, dissolved
Reduced
• Ammonium (NH4+): -3 oxidation state, dissolved
• Ammonia (NH3): -3 oxidation state, dissolved or gas
• Organic N (R-NH2): -3 oxidation state
Forms of N Taken Up by Plants
• Ammonium (NH4+): Plants take up directly, convert
into organic nitrogen (R-NH2)
– Ammonium uptake tends to reduce soil pH
• Nitrate (NO3-): Plants take up and reduce first to
nitrite, then to ammonium (through NH2OH)
– Nitrate uptake tends to raise soil pH
– Plants and fungi have specific enzymes to use NO3-
• Nitrite (NO2-): Some plants may use NO2- but it is
toxic in even moderate concentrations
• Amino acids and proteins (R-NH2): ready to use
Distribution of N on Earth
• 78% of atmosphere is N2(g)
– N2 molecule has strong triple bond (N≡N)
– Useless for life; must be fixed (bacteria or lightning)
• Reactive nitrogen: Any form of N available for life
– N bonded to H, O, or C
• Most of the reactive N on land is found in soils
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A horizons contain 0.02-0.5% N
O horizons in forests contain additional N
Soils contain 10-20 times as much N as vegetation
Soil OM contains approximately 5% N
Key Concepts in Soil Nitrogen
• Nitrogen exists in many forms in soil
– Organic nitrogen exists in a reduced form as amine
groups
– Inorganic nitrogen exists dominantly as
ammonium or nitrate
• Most of the N on Earth exists as N2 gas in the
atmosphere
– This must be fixed into “reactive N” for use by life
Soil N Transformations and
Cycling
Key Processes in Soil N Cycle
• Fixation
– N2 to R-NH2
• Ammonification
– R-NH2 to NH4+
• Nitrification
– NH4+ to NO3-
• Assimilation
– NH4+ or NO3- to R-NH2
• Denitrification
– NO3- to N2
Image From: US EPA
Nitrogen Fixation
Biological Nitrogen Fixation
• 2nd most important biochemical reaction on
Earth after photosynthesis!!!
• Converts the inert gas N2 to reactive nitrogen
– Source of N for almost all life
• N-fixation carried out by Rhizobium species,
actinobacteria, cyanobacteria, and methanogenic
archaea
– No eukaryotes (including all higher life) can fix N:
purely a microbial process
– Requires the nitrogenase enzyme, which includes
molybdenum (Mo) and iron (Fe) at key reactive sites
Nitrogenase: A Mo-Fe-metalloenzyme
that is the sole natural source of
usable nitrogen
Symbiotic Fixation by Legumes
• N fixation occurs in root nodules of legumes
• Primarily carried out by bacteria of the
Rhizobium and Bradyrhizobium genera
• Specific bacterial species will only “infect”
some plant species
– Some agricultural soils need to be inoculated or N
fixation will not occur in legumes
• Fixation inhibited if soil is too acidic or has
excess nitrogen
Root Nodules
• Root nodules provide food to N-fixing bacteria
and keep out oxygen, which blocks N-fixation
Legumes that Fix N
Clover
Soybean
Peanuts
Alfalfa
Nodule-Forming Nonlegumes
• Actinomycetes of the genus Frankia are the
dominant N-fixers in roots of nonlegumes
• These actinorhizal plants are less diverse then
the legumes
Frankia Root Nodules
Symbiotic Fixation Without Nodules
• Cyanobacteria inhabit cavities
in leaves of the floating fern
Azolla in rice paddies
– Fix comparable quantities of N
as legumes
• Various N-fixing bacterial
species inhabit the rhizosphere
– Obtain food from root exudates
– Widespread, but rate of fixation
is far lower than nodule forming
species
Floating Azolla Fern
Nonsymbiotic N Fixation
• Many free-living N-fixing microorganisms are
present in soil
• Complex associations of heterotrophs fix N in
many mineral soils
– Obtain carbon from root exudates or decomposition
of soil OM
– N-fixation likely occurs inside soil aggregates where O2
concentrations are low
• Autotrophs such as cyanobacteria fix N in
wetlands and on soil surfaces
Microbiotic Crusts
Key Concepts in N Fixation
• N fixation converts N2 gas into organic N
– Only performed by bacteria and archaea, not
higher life
– Essential for life on earth
• Requires the Nitrogenase enzyme, substantial
energy input, and a low O2 environment
– Microbes require molybdenum and iron to make
Nitrogenase
Key Concepts in N Fixation
• N fixation in legumes occurs through symbiosis
between the plant and Rhizobium and related
bacterial species
– Occurs in root nodules, which plants design to protect
the bacteria and maintain low-O2 conditions
• Non-legumes also form symbiotic relationships
with N-fixes (actinobacteria like Frankia) in
nodules
• Cyanobacteria (both free-living and in symbiotic
relationships) also fix N
– Important in both aquatic and arid environments
Non-Redox Transformations of
Reduced N (NH4+, Organic N)
Mineralization and Immobilization
• Most N in soils is in soil organic matter
– Generally unavailable for higher plants
• Mineralization is the process of converting organic N
(R-NH2) into ammonium (NH4+ )
– Carried out mostly by microbial enzymes
– Also called Ammonification; carried out by ammonifiers
• Immobilization/Assimilation is the reverse process,
converting NH4+ into organic N
– Abiotic or biotic, plants, fungi, and microbes all are capable
of N immobilization
Ammonium Fixation by Clays
This is the other fixation in soil science!
• NH4+ ions attracted to clays and humus like
other cations
– Held in exchangeable form
• Important process preventing rapid leaching from soil
• 2:1 clays, especially vermiculite, may fix
ammonium
– NH4+ just the right size and charge
– Interlayer collapses around NH4+
– NH4+ becomes non-exchangeable
Ammonium Fixation by Vermiculite
Ca2+
Na+
Mg2+
+ NH4+
NH4+
NH4+
NH4+
NH4+
Ammonia (NH3) Volatilization
• NH3 gas can be produced by:
– Breakdown of OM and
manure
– Certain N fertilizers
– Processes that raise soil pH
• Ammonia may leave soils
through volatilization
• Ammonia is in equilibrium
with ammonium:
NH4+ = NH3(g) + H+
– More volatilization at high pH
– Compounds that produce
ammonia raise pH
Key Concepts in Non-Redox
Transformations of Reduced N
• Mineralization releases N in OM as
ammonium
– Ammonium retained by cation exchange
– Ammonium can be bound up (the other
“fixation”) in clay interlayers
– Ammonium can be volatilized to the air as
ammonia; this is favored at higher pH
• Ammonia can be re-absorbed by plants
• Ammonium can be re-incorporated into
organic compounds by plants and microbes
Soil Nitrogen Redox Cycling
Nitrification:
Microbial
Oxidation of
NH4+ to NO3• Bacteria oxidized NH4+ to nitrate (NO3-) to gain energy
• Occurs in two steps (both require oxygen):
– Nitrosomonas and related microbes: NH4+ + 3/2O2 = NO2- + 2H+ + H2O +
energy
– Nitrobacter and related microbes: NO2- + 1/2O2 = NO3- + energy
• Nitrate binds weakly to soil minerals and OM and is highly
susceptible to being lost by leaching
Denitrification and Leaching Losses
• Denitrification: Microbial reduction of NO3- to N2(g):
2NO3- → 2NO2- → 2NO(g)↑ → N2O(g)↑ → N2(g)↑
– Only occurs under low-O2 conditions (e.g., flooded soils,
wetlands, interior of peds)
– N2O(g), a greenhouse gas, may be lost through
volatilization before being reduced to N2
• Denitrification is a major process through which N is
lost from soil!
• NH4+ and NO3- can also be leached from soil
– NO3- leaching is greater because NH4+ is retained by cation
exchange
Multiple Intermediates Formed During
Denitrification
• Major source of N2O, a greenhouse gas
Nitrification-Denitrification in Wetlands
Key Concepts in N Redox Cycling in
Soils
• Changes in N oxidation state in soils are largely
controlled by microbes
• Nitrification is the oxidation of NH4+ to NO3through NO2– Requires aerobic conditions
• Denitrification is the reduction of NO3- to N2(g)
– N is lost from soil as N2 and N2O; does not reduce
back to NH4+
– N can also be lost by leaching, especially of NO3-
Soil Sulfur
Plants and Animals need Sulfur
Methionine
Cysteine
Thiamine
• Key component of amino acids methionine, cysteine,
and cystine
• Present in various vitamins
• Component of many enzymes
• Critical element in proteins
Sulfur in Plants
• Plant foliage contains
0.15 – 0.45% sulfur
– About one-tenth as much
S as N
• Plants deficient in sulfur
have growth problems
– Spindly stems and petioles
– Show signs of chlorosis
Corn with enough sulfur (left)
and a deficiency (right)
Sulfur in Soil Environments
Natural Sources of Sulfur
• Three sources of S in
natural soils:
– Organic matter
– Soil minerals
– S gasses in atmosphere
• In natural ecosystems
sulfur is recycled
– S deficiency rare
Sources of Sulfur for Plants
Forms of S in Soils
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Sulfate (SO42-): +6 oxidation state, dissolved or minerals
Sulfate esters (R-C-O-SO3): +6 oxidation state, organic
Sulfonates (R-C-SO3): +5 oxidation state, organic
Sulfite (SO32-): +4 oxidation state, dissolved
Sulfur dioxide (SO2): +4 oxidation state, gas
Sulfone (R-S(=O)2-R): +4 oxidation state, organic
Sulfoxide (R-SO-R): +2 oxidation state, organic
Sulfonium (R-S-R2): +1 oxidation state, organic
Elemental sulfur (S): 0 oxidation state, solid
Organic disulfide (R-SS-R): 0 oxidation state, amino acids (e.g., cystine)
Disulfide (S22-): -1 oxidation state, dissolved or solid
Thiols (R-SH): -1 oxidation state, amino acids (e.g., cysteine)
Sulfide (S2-): -2 oxidation state, dissolved or solid
Sulfur in Organic Matter
• In surface soils 90-98% of the S is contained in
organic matter
– C:N:S approximately 100:8:1
– Inorganic S more important when OM content is low
• The exact form(s) is unknown
• Three general forms are thought to dominate:
– Reduced S in sulfides, disulfides, thiols, thiophenes,
proteins, amino acids
– Intermediate redox states in sulfoxides and sulfonates
– Oxidized S in ester sulfates
Organic Sulfur Compounds
Ester Sulfate
C-Bonded S:
Sulfonate
C-Bonded S:
Sulfoxide
C-Bonded S: Thiol
(Cysteine)
• Ester sulfates generally make up less than half of
organic S
– More reduced species common
– Ester sulfates more common in well-aerated plowed soils
• Soil microorganisms breakdown (mineralize) these
compounds and release sulfate ions (SO42- )
Sulfur Associated with Soil Minerals
• Less common form of sulfur in most soils
• Sulfate minerals: Gypsum (CaSO4·2H2O)
– Found in subsurface horizons of arid and semiarid soils
• Sulfide minerals: Pyrite (FeS2) and Mackinawite (FeS)
– Found in coastal wetland soils and in mine tailings
– Produces acid sulfate soils (sulfuric acid) when oxidized
• Fe and Al Oxide/Kaolinite: Adsorbed SO42-
– Sulfate adsorbs to mineral surfaces via surface complexation
– Dominant form of sulfur in Oxisols
Sulfur Content of Soils: Mollisols
Gypsum or
sulfate in
calcium
carbonates
Sulfur Content of Soils: Spodosols
E Horizon
Adsorbed
to oxides
Sulfur Content of Soils: Oxisols
Adsorbed
to oxides
Key Concepts in Soil Sulfur
• Sulfur originates in a soil from atmospheric
deposition, soil minerals, and soil organic matter
• Sulfur occurs in both inorganic (sulfate) and
organic forms in soil
– Content and ratio between inorganic and organic vary
with depth; more organic in A horizon, less below
• A wide range of oxidation states occurs in OM
• Inorganic forms include sulfate minerals (e.g.,
Gypsum), sulfides (e.g., Mackinawite, Pyrite),
and sulfate adsorbed on iron and aluminum
oxides and kaolinite