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BIOGEOCHEMISTRY OF NITROGEN. I. Introduction II. N-cycle, and the Biochemistry of N III. Global N Patterns/Budget (Galloway et al. 1995) IV. Patterns of N at the HBEF V. Inputs, Effects and Management of Anthropogenic N in the Northeast. I. INTRODUCTION.

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biogeochemistry of nitrogen

I. Introduction

II. N-cycle, and the Biochemistry of N

III. Global N Patterns/Budget (Galloway et al. 1995)

IV. Patterns of N at the HBEF

V. Inputs, Effects and Management of Anthropogenic N in the Northeast

i introduction

Nitrogen is a difficult element to study. Nitrogen has many different species, phases and oxidation states.

Nitrogen is an interesting element because some pools (N2, Org N) are large and generally unavailable.

  • N is an important element because:
  • It is a macronutrient (protein);
  • At elevated concentrations, it may cause adverse environmental effects (NH3, NH4+, NO2-, NO3-).
ii n cycle and the biochemistry of n
  • N Utilization
  • 1. Assimilatory - used for biosynthetic reactions (amino acid production), not directly used in energy metabolism - All living organisms require N.
  • Dissimilatory processes - Nitrogen is taken up in a particular form (oxidized or reduced), for specialized reactions involving ATP production and excretion of a N product. Dissimilatory N is not incorporated into the physical or biochemical structure of an organism - Only a few specialized organisms can utilize dissimilatory processes.

N Assimilation

Nitrogen in biomass largely occurs as the reduced oxidation state (-III), so this is the energetically favored form of N. However, NO3- is generally preferred by plants. This may be due to greater mobility of NO3-. Energy must be expended by plants or microbes to extract NH4+ from soil sediments. Also competition of NH4+ with other cations on enzymes.

Plants/microorganisms can commonly assimilate NH4+, NO3- in water or soil. Organic N is rarely used as an N source. Some coniferous trees have been shown to assimilate dissolved organic N.

n cycle and the biochemistry of n cont
N-cycle, and the Biochemistry of N (cont.)

If N is taken in as NH4+, it is directly used by organisms in biosynthesis.

If N is assimilated as NO3-, it must be reduced within the cell.

Two enzymes are involved:

1. Nitrate reductase - contains molybdenum

NO3- + NADH + H+ = NO2- + H2O + NAD+

2. Nitrite reductase

NO2- + 3NADH + 5H+ = NH4+ + 2H2O + 3NAD+

Some organisms have the unique characteristic to assimilate molecular N - nitrogen fixation.

This process requires the enzyme, nitrogenase, which is a complex protein containing iron, molybdenum and inorganic S as part of its structure.

The process is extremely energy-intensive, as you might expect, to break a triple bond.

N  N

n cycle and the biochemistry of n cont5
N-cycle, and the Biochemistry of N (cont.)

Only a few species of microorganisms can fix nitrogen. These include free-living organisms (asymbotic, e.g. Clostribium, Azobacter, Azospirillum, and Anabena) and organisms in symbiotic relationships with roots (e.g. Rhizobium, Frankia).

N2 + 10H+ + 8e- + nATP + nH2O = 2NH4+ + H2 + nADP + nH2PO4-

where: n = 12 - 20 (exact number uncertain)

Ammonium assimilation occurs by two enzymatic routes:

1. Glutamine synthetase



CH2 + NH4++ATP = CH2 + ADP + H2O



glutamate glutamine

n cycle and the biochemistry of n cont6
N-cycle, and the Biochemistry of N (cont.)

2. Glutamate dehydrogenase



CH2 + NADH + H+ + NH4+ = CH2 + NAD + H2O

C = O CHNH3+


-ketoglutarate glutamate

n cycle and the biochemistry of n cont7
N-cycle, and the Biochemistry of N (cont.)

In addition, Glutamate synthase is used in plants and microorganisms to convert amido-nitrogen of glutamine back to glutamate for amino acid systems.

Glutamate synthase



CH2 + NADH + H+ + CH2 = 2 CH2 + NAD+



-ketoglutarate glutamine glutamate

n cycle and the biochemistry of n cont8
N-cycle, and the Biochemistry of N (cont.)


Mineralization is the decomposition of organic matter to inorganic matter. This is accomplished by heterotrophic microbes. The release of N is generally thought to be a by-product of the use of soil organic C as an energy source.

R - NH2 = NH3 + H2O = NH4+ + OH-

Mineralization of organic matter is critical to the supply of nutrients to vegetation in terrestrial environments (see Table).

Mineralization is directly related to the nitrogen content of soil and the availability of organic carbon. Vegetation with high C/N in litter generally shows low rates of mineralization in soil.


NH2 urease C = O + 2H2O + 2H+ = 2NH4+ + H2CO3



Percentage of the annual requirement of nutrients for growth in the Northern Hardwoods Forest at Hubbard Brook, New Hampshire, that could be supplied by various sources of available nutrients*

*Calculated using Eqs. 6.2 and 6.3. Reabsorption data are from Ryan and Bormann (1982). Data for N, K, Ca, and Mg are from Likens and Bormann (1995) and for P from Yanai (1992).

n cycle and the biochemistry of n cont10
N-cycle, and the Biochemistry of N (cont.)

Nitrogen Dissimilation

Nitrification - the oxidation of NH4+

NH4+ + 2O2 = NO3- + H2O + 2H+

Two different species of lithotrophic organisms are responsible for this reaction.


ammonia oxidase NH4+ + 3/2 O2 = NO2- + 2H+ + H2O

This oxidation/reduction sequence is not direct but includes an electron transport chain in which 1 mol of ATP is produced per mol of NH4+ oxidized.

This sequence is continued by the organism.


nitrite oxidase NO2- + ½O2 = NO3-

The electron produced from the oxidation of NO2- is also coupled with an electron transport cycle producing 1 mol of ATP.

n cycle and the biochemistry of n cont12
N-cycle, and the Biochemistry of N (cont.)

Nitrification can also be accomplished by heterotrophic bacteria.

Nitrification is an important process because many factors influence it and because it converts nitrogen from an immobile form (NH4+) to a mobile form (NO3-).

Because the organisms which mediate nitrification reactions are specific populations, they are easily disrupted.

  • 1. Lithotrophic organisms use inorganic C (CO2) to produce organic C through the Calvin cycle. This process is very energy intensive so these organisms have slow growth rates.
  • 2. Nitrifiers, require well-oxygenated conditions.
  • 3. Very sensitive to toxicants, trace metals.
  • Sensitive to pH (< 6?).
  • N2O and NO are released via nitrification.
n cycle and the biochemistry of n cont13
N-cycle, and the Biochemistry of N (cont.)


Denitrification is the process by which N is used as the terminal electron acceptor in a reduction reaction.

This may be conducted by species: Pseudomonas, Bacillus, Vibrio and Thiobacillus.

Because organisms favor O2 reduction due to energetics, denitrification only proceeds under anaerobic conditions.

Organisms produce 2 mol ATP per mol NO3- reduced.

The process proceeds through an electron transport chain. The reductant is generally organic matter, generally sugars or simple compounds (methanol used in waste water treatment). Reduced sulfur compounds can also be used (sulfur, sulfide). These electrons are transferred to the electron transport chain where the reduction occurs.

In this process, NO3- is first reduced to NO2-.

NO3- + NADH + H+ = NO2- + NAD+ + H2O

Through this process, ATP is produced.

n cycle and the biochemistry of n cont15
N-cycle, and the Biochemistry of N (cont.)

Subsequent reactions may occur:

NO2- + 2H+ + e- = NO + H2O

NO2- + 3H+ + 2e- = ½N2O + 3/2 H2O

NO2- + 4H+ + 3e- = ½N2 + 2H2O

NO + 2H+ + 2e- = ½N2 + H2O

½N2O + H+ + e- = ½N2 + ½H2O

The overall reaction to N2 is

C6H12O6 + 24/5 NO3- + 24/5 H+ = 6CO2 + 12/5 N2 + 42/5 H2O

The "leaky pipe" hypothesis suggests that trace gases, N2O and NO, are by-products of nitrification and denitrification.

n cycle and the biochemistry of n cont18
N-cycle, and the Biochemistry of N (cont.)

Mechanisms of N Immobilization

1. Plant assimilation

2. Microbial (thought to predominate)

bacteria C5H7O2N fungal higher C:N

Critical C:N  20-25

Above, microbial growth is N limited Little N leaching

Below, microbial growth is C limited N leaching occurs

3. Nitrification, distribution of NH4+, NO3-

Abiotic immobilization

Cation exchange X- - Na+ + NH4+ = X- - NH4+ + Na+

No significant mechanism for abiotic immobilization of NO3- (anion exchange weak).

n cycle and the biochemistry of n cont19
N-cycle, and the Biochemistry of N (cont.)


NH4+ participates in an acid-base reaction.

NH4+ = NH3 + H+ ; pKa = 9.1

NH3 also has the ability to volatilize.

NH3 aq = NH3 g

As a result, NH3 can volatilize, but the reaction is only quantitatively important under high pH conditions.

Forest soils are generally acidic, so NH3 volatilization is an insignificant process.

In agricultural lands, application of fertilizer (manure) can result in high pH conditions and significant NH3volatilization.

n cycle and the biochemistry of n cont23
N-cycle, and the Biochemistry of N (cont.)

Stable Isotopes of N

Stable isotopes of N can provide insight into biogeochemistry.

1. Addition tracer experiments

2. Natural abundance observations

There are two stable isotopes of N:

air composition

15N = 0.0037

14N = 0.9963

15N/14N = 1/272

Nitrogen isotopes are reported in values of per mil relative to atmospheric air.

Delta notation

n cycle and the biochemistry of n cont24
N-cycle, and the Biochemistry of N (cont.)

Let's consider an example:

sample 15N = 0.00371

std 15N = 0.00370

Note that this example suggests that the sample is slightly enriched in 15N relative to the standard (+ sign).

A negative value would indicate that the sample is depleted relative to the standard.

In most terrestrial ecosystems, 15N values range from -10 to +15 %o. In absolute abundance, this represents a range of 0.3626 to 0.3718 atom % 15N.

Rule of thumb  Organisms prefer the light isotope (14N) over the heavy isotope (15N) in transformations (see figures).









Isotope Enrichment Effect on Ammonium


N mineralization


NH 4

 15N



NH 4


NO 3

n cycle and the biochemistry of n cont27
N-cycle, and the Biochemistry of N (cont.)

The 15N of a cumulative product is always lighter than the residual reactant. Consider denitrification. Say that this process fractionates by 5, 10, 20 %o from an initial NO3- of 0 %o. The first bit of product (N2) is lighter than the reactant by the fractionation factor. As the reaction proceeds to completion, the product becomes progressively heavier until, at the end, it reaches its initial composition. The reactant also becomes progressively heavier until it is used up.

  • Several factors influence the degree of fractionation:
  • Specific process.
  • Size of the pool. Large pools exhibit large fractionation, small pools exhibit little fractionation.
  • Temperature.
n cycle and the biochemistry of n cont29
N-cycle, and the Biochemistry of N (cont.)

N Fractionation

ProcessQualitative ChargeLiterature

N fixation small -3 to +1 %o


microbial small -1.6 to +1 (-0.52)%o

plant small -2.2 to +0.5 (-0.25)%o

Mineralization small -1 to +1 %o

Nitrification large -12 to -29 %o

Volatilization large > 20 %o

Sorption/desorption small 1 to 8 %o

Denitrification large -40 to 5 %o

n cycle and the biochemistry of n cont30
N-cycle, and the Biochemistry of N (cont.)
  • Observations in the Literature
  • Terrestrial Ecosystem Compartments
  • 1. Plants are slightly depleted.
  • Organic soils are enriched.
  • Mineral soils are more enriched.

The 15N of plants is similar to what they assimilate (little fractionation). Variations in plant 15N are due to:

  • rooting depth; deeper roots  more enriched
  • NO3- vs. NH4+ preference; NH4+  more enriched

Rates of N Cycling

In general, 15N increases in ecosystems with increased rates of N cycling due to fractionation associated with nitrification and NO3- loss.

This is sometimes quantified as an enrichment factor (15N leaf - 15N soil).

See observations from Walker Branch, TN and Hubbard Brook.

n cycle and the biochemistry of n cont36
N-cycle, and the Biochemistry of N (cont.)

Food Web Studies

Food web studies show an enrichment in 15N.

N isotope scientists like to say you are what you eat, plus 3 %o.

See figure.Use of 18O and 15N as a Tracer of Ecosystem N Retention

There are some drawbacks to using 15N as an ecosystem tracer due to its relatively narrow range. 18O associated with NO3- offers additional information as a tracer.

Durke et al. (1994) used 15N and 18O together to evaluate the retention of atmospheric NO3- to forests in Germany.

See tables.


Carbon and Nitrogen

Stable Isotopes in Oneida

Lake Food Web from Mitchell

et al. (1996)

n cycle and the biochemistry of n cont40
N-cycle, and the Biochemistry of N (cont.)

Table 1. Characteristics of sites studied.


n cycle and the biochemistry of n cont41
N-cycle, and the Biochemistry of N (cont.)

Site conditions, atmospheric inputs of nitrogen to the watersheds, and NO3- output characteristics of eight forest springs in the Fichtelgebirge (northeast Bavaria, Germany).

*Definitions: slightly declining, single trees affected by needle yellowing and crown thinning; strongly declining, all trees affected.

1Extrapolated from measurements of throughfall sampled between 15 April and 15 December 1992 with ten funnels per site.

2Volume-weighted mean of monthly measurements in 1991 and 1992.

3Modelled from volume-weighted mean NO3- concentration and seepage.

n cycle and the biochemistry of n cont42
N-cycle, and the Biochemistry of N (cont.)

Table 2. Nitrate in spring water

*This value (>100% recovery) could have been caused by errors in the input-output balance, or by temporal NO3-atm storage in the aquifer.

iii global n patterns budget

Across the Earth, N largely occurs as N2 in the atmosphere (78%) and in the ocean and in soil.

Nitrogen is divided into two broad classes:

1. Reactive - NOy = NOx (NO + NO2) + any oxidized N with a single atom of N

- NHx = NH4+ + NH3

- organic N

2. Unreactive - N2

- N2O

- organic N (soil)

See tables.

global n patterns budget cont
Global N Patterns/budget (cont.)

Table 1. Estimates of the active pools in the global nitrogen cycle.

million tonnes N

Air N2 3 900 000 000 N2O 1 400

Land Plants 15 000 Animals 200 of which people 10 Soil organic matter 150 000 of which microbial biomass 6 000

Sea Plants 300 Animals 200 In solution or suspension 1 200 000 of which NO3--N 570 000 of which NH4+-N 7 000 Dissolved N2 22 000 000

global n patterns budget cont45
Global N Patterns/budget (cont.)

Table 2. Production of combined nitrogen gases by land, sea and air.

global n patterns budget cont46
Global N Patterns/budget (cont.)

Table 3. Distribution of nitrogen (g m-2) between plant biomass and above-ground litter and plant uptake in difference bioclimate zones. Calculated from Baztlevich and Soderlund and Svenson.

global n patterns budget cont47
Global N Patterns/budget (cont.)

Preindustrial N budget

The transfer of reactive to unreactive N was balanced.

N2, N2O produced by denitrification in oceans and soil.

NH3 is released by volatilization.

NH4+ = NH3(aq) + H+ ; pKa = 9.3

NH3(aq) = NH3(g)

This process occurs only under high pH conditions.

NH3 is released by burning of plants.

NH3 is very reactive and has a short residence time in the atmosphere.

NH3 + H2O = NH4+ + OH-

global n patterns budget cont48
Global N Patterns/budget (cont.)
  • NO can be formed by
  • Oxidation of N2 by lightning;
  • Soil microbes;
  • Burning of biomass.
  • NO, NOx are very reactive and have a short residence time in the atmosphere.
  • In the preindustrial world, N inputs were largely retained where they were deposited.

Nitrogen is a tightly conserved element in terrestrial environments because it is the growth limiting nutrient.

global n patterns budget cont49
Global N Patterns/budget (cont.)

NH4+ - relatively immobile form of N

a. Strongly assimilated by biota due to energetics;

b. Abiotically retained on soil cation exchange sites.

NO3- - relatively mobile from of N

a. No significant mechanism of abiotic retention.

Nitrification is a key process regulating the mobility of N.

Riverine fluxes of N are thought to be 75 - 120 kg N/km2-yr and this is thought to largely occur as particulate organic N.

global n patterns budget cont52
Global N Patterns/budget (cont.)

Anthropogenic Sources

Human activity has had a profound effect on the N cycle.

Three processes largely contribute to this disturbance, through anthropogenic nitrogen fixation.

1. Energy production - under high temperature combustion processes, unreactive nitrogen is converted to reactive nitrogen by two processes.

a. Thermal NOx


N2 + O2 2NO

b. Fuel NOx - the oxidation of organic N in fuels

Natural gas - very low 0% Coal - up to 3%

Both thermal and fuel NOx can be significant, but fuel NOx is often the dominant source.

global n patterns budget cont53
Global N Patterns/budget (cont.)
  • Fertilizer-Most anthropogenic fertilizers are either NH3 or urea produced from NH3.This material is produced by the Haber process. 4N2 + 12H2 = 8NH3This is a very energy intensive process if natural gas is the energy source for H2, as it usually is. 3CH4 + 6H2O + 4N2 = 3CO2 + 8NH3
  • Production of legumes and other crops allows for the conversion of N2 to reactive N by increasing biological nitrogen fixation.Legumes include: Soybeans Ground nuts (peanuts) Pulses (lentils) Forage (alfalfa, clover)

Global Population and Reactive Nitrogen Trends

Natural N Fixation

Tg N yr-1

Human Population (billions)

From Galloway et al. 2002. In review.

global n patterns budget cont57
Global N Patterns/budget (cont.)

All three categories of anthropogenic nitrogen fixation have increased, but most significant is fertilizer consumption. The rate of fertilizer consumption is increasing particularly in Asia.

There are two critical questions in response to this change.

1. What is the fate of this fixed N; and

2. What are the effects of this increase in fixed N?