Nitrogen Mineralization:
A microbial mediated process
Stephanie Yarwood
Assistant Professor
Soil Microbial Ecology
Outline
 Nitrogen mineralization in the context of
nitrogen cycling
 How C:N ratios work
 The microbes involved
Soil Nitrogen Cycling
We rely on pools of
ammonium and nitrate in
the soil that can be taken up
by plant roots, but these
pools are relatively small.
Plants
NH4+
Soil
NO3-
Distribution of Soil N
Nitrogen form
Nitrogen gas (N2)
Ammonium (NH4+)
Nitrate (NO3-)
Plant N
Organic N
Content
(g-N / m2)
230
2.2
4.4
25
880
Relative fraction
(%)
20.1
0.2
0.4
2.2
77.1
Soil Nitrogen Cycling
Organic N must be
decomposed to release
ammonium that can be
taken up by the plant.
Soil Organic Matter
Containing Organic N
Plants
NH4+
NO3-
Forms of Organic N
Chitin
Amino
sugar N
Nucleic
acid
DNA
Acid
Insoluble N
Micardis
Protein
Unknown N
Urea
Labile N
Soil Nitrogen Cycling
Compounds like protein are
broken down by soil
microbes
Protein
Microbes
Plants
NH4+
NO3-
Ammonification of Protein
Protein
Soil Enzymes
Produced by
Microbes
Protease
NH4+
Peptidase
Peptide
Amino Acid
Deamination
Soil Nitrogen Cycling
• Organic N is added to the
soil by plant and
microbes.
• Nitrogen is continually
recycled.
Organic N
Microbes
Plants
NH4+
NO3-
Bacterial Nitrogen Mineralization
• Soil bacteria
• Most are a single cell
• Like all organisms they
need nitrogen to build
cell material
• A single teaspoon of
soil can contain
1,000,000,000 bacteria
Bacterial Nitrogen Utilization
Organic N molecule
H
The bacterium will ingest:
5—Carbon atoms
2—Nitrogen atoms
H N
H
Model bacterial cell
C
H
C
O
H N
H
H C
C H
O
H
C
O
Bacterial Nitrogen Utilization
CO2
Used to
generate energy
C
Used to build
microbial biomass
• Carbon has two fates
• Some amount of C
always has to go to make
energy
• Carbon only goes to build
biomass if the bacterium
is repairing its cell or
growing
Bacterial Nitrogen Utilization
• Nitrogen is only used to
build biomass
• A bacterial cell needs 4 C
atoms for every 1 N atom
• A biomass C:N ratio = 4
N
Used to build
microbial biomass
Bacterial Nitrogen Utilization
CO2
Used to
generate energy
(68)
C
Used to build
microbial biomass
(32)
• For every one hundred
units of carbon
• 68—C is used for
energy and released at
CO2
• 32—C is used to build
biomass
• 32/4 = The bacterium
(100) needs 8—N
N (8)
Bacterial Nitrogen Utilization
Organic N molecule
H
The bacterium will ingest:
5—Carbon atoms
2—Nitrogen atoms
H N
H
C
H
C
O
H N
H
H C
C H
O
H
Or
100—Carbon atoms
40—Nitrogen atoms
Model bacterial cell
C
O
Bacterial Nitrogen Utilization
CO2
Used to
generate energy
(68)
Nitrogen Mineralization
C (100)
+
NH4 (32)
Used to build
microbial biomass
(32)
N (8)
Other Soil Microbial Biomass
 Fungi are mostly multicellular
and are composed of filaments
called hyphae

There are 1,000,000 fungi in a
teaspoon of soil
 Protozoa are single celled
organisms that graze on
bacteria
 Nematodes are multicellular
animals that include grazers
and predators
Bacteria vs. Fungi
• Fungi use C more efficiently
• They require less N per unit
biomass
• Therefore the composition of
soil microbial biomass can
change N demand
• Will a population of all bacteria
or all fungi mineralize more N
under the same conditions?
Used to
generate energy
(56)
C (100)
+
NH4 (35)
Nitrogen Mineralization
CO2
Used to build
microbial biomass
(48)
N (5)
Fungi to Bacteria Ratio
Fungal:bacterial ratio
0.40
0.30
0.20
0.10
0.00
Net NH4+ Production/Consumption
 Mineralization (production)
 Carbon is limiting
NH4+ consumption
 C:N ratio is low
 Imobilization (consumption)
C:N = 20
 Nitrogen is limiting
 C:N ratio is high
NH4+ production
Calculating production and consumption
 Community composition
 1/3 bacteria
 2/3 fungi

Step 1


 Yield coefficient
 32% for bacteria
 44% for fungi

 C:N ratio
 4 for bacteria
 10 for fungi

Step 2

For 100 g substrate C→60 g CO2-C + 40 g
microbial biomass C
Step 3


Y.C. = (1/3) 0.32 + (2/3) 0.44 = 0.4
C:N = (1/3) 4 + (2/3) 10 = 8
Microbial biomass N = 40 g of microbial
biomass C/ C:N ratio of 8 = 5 g N
Step 4

Critical C:N = 100 g of substrate C / 5 g
substrate N = 20
Implications of C:N ratio
Plants
• If C:N is high what
process is occurring?
Organic N
Microbes
NH4+
NO3-
Implications of C:N ratio
Plants
• If C:N is high,
immobilization
Organic N
Microbes
NH4+
NO3-
Implications of C:N ratio
Plants
• If C:N is low,
mineralization
Organic N
Microbes
NH4+
NO3-
The C:N of Inputs
• Average C:N
• Cow Manure = 15
• Corn stalks = 65
• Wheat straw = 130
• Soil organic matter C:N = ~10
The C:N of Inputs
 Inputs are a mix of many different inputs
Low C:N
High C:N
Protein
Cellulose
Chitin
Lignin
Input Decomposition
Schmidt et al. 2011
Fate of NH4+
NH4+ is a critical control point
Plants

Volatilization of NH3

Plant uptake

Microbial assimilation

Held on cation exchange sites in soil

Fixed in interlayer of illite clays

Stabilized in soil organic matter

Nitrification (conversion to NO3-)
Organic N
Microbes
NH4+
NO3-
Nitrification
-3
NH3
-1
NH2OH
Ammonia oxidation
Nitrosomonas europea
+3
NO2-
+5
NO3-
Nitrite oxidation
Nitrobacter winigradsky
Nitrifying Bacteria
Ammonia oxidizers
Nitrite oxidizers

Nitrogen conversion is linked to
energy generation (they use N not
C)

Nitrogen conversion is linked to
energy generation (they use N
not C)

All are aerobic

All are aerobic

Obligate autotrophs: Fix C from CO2,
therefore they are not limited by
C:N ratio

Usually autotrophs, but under
some conditions heterotrophic
and so incorporate C

Examples

Examples

Nitrosomonas

Nitrobacter

Nitrosococcus

Nitrospina

Nitrosospira

Nitrococcus
Factors Affecting Nitrification
Nitrifiers present?
NO
YES
Aerobic conditions?
NO
YES
NH4+ availability
LOW
HIGH
Temperature, pH, nutrients,
inhibitors, etc.
YES
NITRIFICATION
PROBABLE
NO
NITRIFICATION
IMPROBABLE
Nitrogen uptake by Plants and Microbes
Rates of NH4+ and NO3uptake from the soil pools
by plants and microbial
biomass during 24 h periods
in annual grassland in early
spring (February) and in
late spring (April), 1985.
700
mg of N / m2 / day
600
500
400
300
200
100
0
Plant
Microbe
Plant
Ammonia
Early Spring
Microbes
Nitrate
Plant
Microbe
Plant
Ammonia
Microbes
Nitrate
Late Spring
Adapted from Jackson et al 1989
Summary
 The rate of mineralization depends on
 The C:N of inputs
 The composition of the microbial community
 Ammonia has many fates including nitrification
 Plant available N is the amount of N leftover from
microbial processes
 Microbes always win 
Measuring
+
NH4 :
Net vs. Gross
Net rate:
How much did the pool
size increase?
Gross rates:
How much NH4+
was produced?
NH4+
Gross vs. Net Rates
Soil A
Soil B
5
Organic N
1
4
50
NH4+
Organic N
1
NH4+
49
Net production of NH4+ may not adequately
describe the dynamics of N transformations
Ammonia versus Ammonium
 NH3 + H2O
NH4+ + OH-
 NH3 = gas (volatilization)
 NH4+ = aqueous
 pH < 6 NH4+ dominates
 pH > 8 NH3 dominates
Ammonia Assimilation



GDH

NAHPH

High NH4+
GS-GOGAT

ATP used

Low NH4+
Transaminases
Ammonia Oxidation
Step 1: Ammonia monooxygenase
 Endergonic
NH3 + O2 + 2H+ 2e-  NH2OH + H2O
Step 2: Hydroxylamine oxidoreductase
 Exergonic
NH2OH + H2O  NO2- + 5H+ + 4e-
 NO and N2O may be produced
 Net production of 2H+ per NH4+ oxidized
Nitrite Oxidation
Nitrite oxidoreductase (nitrite dehydrogenase)
 Exergonic, inhibited by chlorate
NO2- + H2O  NO3- + 2H+ +2e-
 About 1/3 the energy as ammonia oxidation
Archaeal Ammonia Oxidizers
 First reported in 2005
 Found in marine,
freshwater and soil
 Found to predominate in
some soils
Könneke et al. 2005
Leininger et al. 2006