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

NH4+ NO3

-

Plants

Soil Nitrogen Cycling

Soil

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.

Distribution of Soil N

Nitrogen form Content

(g-N / m2)

Relative fraction (%)

Nitrogen gas (N2)

Ammonium (NH4+)

Nitrate (NO3-)

Plant N

Organic N

230

2.2

4.4

25

880

20.1

0.2

0.4

2.2

77.1

Plants

Soil Organic Matter

Containing Organic N

Soil Nitrogen Cycling

NH4+ NO3

-

Organic N must be decomposed to release ammonium that can be taken up by the plant.

Forms of Organic N

Protein

Labile N

Unknown N

Acid

Insoluble N

Amino

sugar N

Nucleic

acid Chitin

Urea

DNA

Micardis

Plants

Protein

Soil Nitrogen Cycling

NH4+ NO3

-

Compounds like protein are broken down by soil microbes

Microbes

Ammonification of Protein

Protein

Peptide Amino Acid

Protease

Peptidase

NH4+

Deamination

Soil Enzymes Produced by Microbes

Plants

Organic N

Soil Nitrogen Cycling

NH4+ NO3

-

• Organic N is added to the soil by plant and microbes.

• Nitrogen is continually recycled.

Microbes

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

Model bacterial cell

Organic N molecule

C

N

O

H

H

C

N H

C C

H

H

H

C

O

O

H H

H

The bacterium will ingest: 5—Carbon atoms 2—Nitrogen atoms

Bacterial Nitrogen Utilization

C

Used to build

microbial biomass

Used to

generate energy

• 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

CO2

Bacterial Nitrogen Utilization

N

Used to build

microbial biomass

• 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

Bacterial Nitrogen Utilization

C (100)

Used to build

microbial biomass

(32)

Used to

generate energy

(68)

• 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

needs 8—N

CO2

N (8)

Bacterial Nitrogen Utilization

Model bacterial cell

Organic N molecule

C

N

O

H

H

C

N H

C C

H

H

H

C

O

O

H H

H

The bacterium will ingest: 5—Carbon atoms 2—Nitrogen atoms Or 100—Carbon atoms 40—Nitrogen atoms

Bacterial Nitrogen Utilization

C (100)

Used to build

microbial biomass

(32)

Used to

generate energy

(68)

CO2

N (8)

NH4+ (32)

Nitrogen Mineralization

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?

C (100)

Used to build

microbial biomass

(48)

Used to

generate energy

(56)

CO2

N (5)

NH4+ (35)

Nitrogen Mineralization

Fungi to Bacteria Ratio F

un

gal:

bac

teri

al r

atio

0.00

0.10

0.20

0.30

0.40

Net NH4+ Production/Consumption

Mineralization (production)

Carbon is limiting

C:N ratio is low

Imobilization (consumption)

Nitrogen is limiting

C:N ratio is high

C:N = 20

NH4+ production

NH4+ consumption

Calculating production and consumption

Community composition

1/3 bacteria

2/3 fungi

Yield coefficient

32% for bacteria

44% for fungi

C:N ratio

4 for bacteria

10 for fungi

Step 1 Y.C. = (1/3) 0.32 + (2/3) 0.44 = 0.4

C:N = (1/3) 4 + (2/3) 10 = 8

Step 2

For 100 g substrate C→60 g CO2-C + 40 g microbial biomass C

Step 3

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

Plants

Organic N

Implications of C:N ratio

NH4+ NO3

- Microbes

• If C:N is high what process is occurring?

Plants

Organic N

Implications of C:N ratio

NH4+ NO3

- Microbes

• If C:N is high, immobilization

Plants

Organic N

Implications of C:N ratio

NH4+ NO3

- Microbes

• If C:N is low, mineralization

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

Cellulose

Protein

Lignin

Chitin

Input Decomposition

Schmidt et al. 2011

Fate of NH4+

NH4+ is a critical control point

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-)

Plants

Organic N NH4+ NO3

- Microbes

Nitrification

NH3 NH2OH NO2

- NO3-

Ammonia oxidation Nitrite oxidation

Nitrosomonas europea Nitrobacter winigradsky

-3 -1 +3 +5

Nitrifying Bacteria Ammonia oxidizers

Nitrogen conversion is linked to energy generation (they use N not C)

All are aerobic

Obligate autotrophs: Fix C from CO2, therefore they are not limited by C:N ratio

Examples

Nitrosomonas

Nitrosococcus

Nitrosospira

Nitrite oxidizers

Nitrogen conversion is linked to energy generation (they use N not C)

All are aerobic

Usually autotrophs, but under some conditions heterotrophic and so incorporate C

Examples

Nitrobacter

Nitrospina

Nitrococcus

Factors Affecting Nitrification

NITRIFICATION

PROBABLE

NITRIFICATION

IMPROBABLE Nitrifiers present?

Aerobic conditions?

NH4+ availability

Temperature, pH, nutrients,

inhibitors, etc.

NO

YES

LOW

HIGH

YES

NO

NO

YES

Nitrogen uptake by Plants and Microbes

Adapted from Jackson et al 1989

0

100

200

300

400

500

600

700

Plant Microbe Plant Microbes Plant Microbe Plant Microbes

Ammonia Nitrate Ammonia Nitrate

EarlySpring LateSpring

Rates of NH4+ and NO3

- uptake 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.

mg o

f N

/ m

2 / d

ay

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

NH4+

Net rate:

How much did the pool

size increase?

Gross rates:

How much NH4+

was produced?

Gross vs. Net Rates

Organic N NH4+ 1 Organic N NH4

+ 1

5

4 49

50

Net production of NH4+ may not adequately

describe the dynamics of N transformations

Soil A Soil B

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