Denitrification
Denitrification
Denitrification
U Skiba, Centre for Hydrology and Ecology, Penicuik, UK
ª 2008 Elsevier B.V. All rights reserved.
of ammonium to nitrite and nitrate (nitrification). This can be a real problem, but direct measurements have been
reaction usually occurs at low pH and may be facilitated achieved by several scientific groups who replaced the
by the presence of iron or amines and high levels of atmosphere of soil columns with helium and then directly
organic matter. The most important chemodenitrification measured the N2 resulting from denitrification.
reaction is the decomposition of HNO2 to form NO. The traditional methods to measure total denitrifica-
tion are by the acetylene block technique or by adding
3HNO2 ! 2NO þ HNO3 þ H2 O 15
N as a tracer. Acetylene at a partial pressure of 10 kPa
Soil pH is a controlling factor in chemodenitrification blocks the final step of denitrification, so that the total
and above pH 5, this process is insignificant. product of denitrification is N2O. The main problem of
this method is that it is not very easy to administer the
inhibitor evenly throughout soils. The most active deni-
Measurements of Denitrification trification zones in a soil are likely to be those into which
diffusion is limited and have effectively managed to
The main products of heterotrophic denitrification are exclude O2.
N2O and N2 and of nitrifier denitrification, they are NO In tracer experiments, nitrogen substrates are labeled
and N2O. Emissions of NO and N2O are measured rela- with 15N and added to soils or waters. The appearance of
tively easily. For terrestrial systems a small area of the soil this label in the denitrification products N2O and N2 can
surface is enclosed by a chamber (see Figure 1), or in the be measured by isotope-ratio mass spectrometry.
laboratory a small amount of soil is incubated in an air- There are several methods that are used to distinguish
tight vessel, in order to allow the gases emitted to increase between N2O production by autotrophic nitrifiers or het-
to measurable concentrations. N2O is a very stable gas and erotrophic denitrifiers. (1) Acetylene at a partial pressure
samples from the enclosures can be stored in syringes or of 10 Pa inhibits N2O production during chemoauto-
vials until analysis by gas chromatography, using an trophic nitrification, whereas a much higher partial
electron-capture detector. NO is a highly reactive gas, pressure of 10 kPa is required to inhibit the reduction of
with a half-life of less than 1 min and therefore can only N2O to N2 in heterotrophic denitrifiers. (2) The contri-
be measured directly from the enclosed chamber by bution of nitrifiers and denitrifiers to N2O can be studied
chemiluminescence. In aquatic systems, the concentration by differential labeling NH4 and NO3 with 15N and
of N2O/NO in the water columns or in the headspace monitoring the occurrence and disappearance of the 15N
above the water column is analyzed. label in the NH4, NO3, and N2O pools. (3) Inhibitors
The measurement of the final denitrification product which specifically inhibit autotrophic nitrification (nitra-
N2 is not so straightforward. Direct measurements can pyrin), denitrification (O2), or heterotrophic nitrification
only be made in an N2-free environment. This is difficult, (cycloheximide) have been used to distinguish between
as more than 80% of our atmosphere is N2. Contamination these processes. (4) The use of natural abundance isotope
ratios is a new approach, still in development. The frac-
tionation of isotopic ratios 14/15N and 16/18O is different
during nitrification and denitrification.
33
40
11
12
16
19
23
26
–8
1
3
4
5
6
7
9
–2
–50
and soluble carbon content are not limiting, the response to Days after spring fertilizer application in 2002
mineral N fertilizer application is very fast, resulting in
peaks of NO, N2O, or N2 emissions within hours of appli- (b) 160
Manure
cation. These emission peaks can be 100 times larger than 140
NH4NO3
background emissions, but are short-lived and usually last
NO3. Many studies have shown an increase in denitrifica- leading to the emission of N2O from the water.
tion rate when a labile carbon source was added to soils in Denitrification occurs predominately in the top few mm
the laboratory or in the field. The importance of labile of the sediments and rates of denitrification depend on the
organic matter was shown in studies on intact soil cores, concentrations of organic C and N. Largest denitrification
and subsequently on dissecting these into smaller and rates can be expected from the most polluted rivers and
smaller subcores. Between 25% and 85% of the denitri- lakes and estuaries followed by coastal shelves and lowest
fication activity could be attributed to a single decaying rates from the open oceans. The main sources of NO3 are
leaf or worm. This study and many other field studies drainage and runoff from agriculturally managed fields
have shown that denitrification is a very opportunistic and effluents from sewage farms and industries. For rivers,
behavior, leading to spatial and temporal hotspots of the denitrification rates were shown to be inversely related to
production of N2O and N2. channel size, which would regulate the residence time of
Generally, the rhizosphere, the soil layer rich in root the NO3.
exudates and therefore high microbial activity, provides Estuaries have a relatively high organic carbon content
an ideal environment of high C and low O2 concentra- compared to many other aquatic systems, due to high
tions for denitrification to take place. The dense root mat rates of sedimentation and upwelling. They can denitrify
of grasslands is particularly active and denitrification rates between 20% and 50% (and more in isolated cases) of the
are larger than those in arable soils or forests. NO3 added by the rivers and thus stop the export of
Mineralization of complex carbon compounds in soil terrestrial N pollution to open oceans. Denitrification
increase the pool of simple carbon compounds. The most appears to be independent of salinity over the range of
well-studied processes that stimulate the mineralization 1–13 parts per trillion (ppt), but directly dependent on
of organic carbon are plowing, freeze–thaw events, and nitrate concentration.
wetting of very dry soil (pulsing effect). Plowing aerates In the interior of oceans, away from the euphotic surface
the soil and thereby stimulates mineralization of organic layer and coastal shelves, nitrification and denitrification
carbon compounds in parts of the soil previously not rates are primarily dependent on the mineralization of
receiving the O2 concentrations required for mineraliza- nitrogen-rich organic matter originating from N2 fixing
tion to take place. Increased mineralization stimulated by organisms. The demand for anaerobic conditions is
freeze–thaw events or the pulsing effects are governed by required in the same way as for terrestrial systems.
the same principle. Extreme cold and extreme dry condi- Denitrification rates in benthic sediments are most sensitive
tions kill a large part of the microbial community and to concentrations of labile organic carbon at the sediment–
reduce the activity of the survivors. When conditions water interface and have been shown to increase with
become more tolerable, due to a thaw or rainfall, the nitrate concentrations. The major areas of low O2 are the
remaining microbial population become activated and thermocline of the Arabian Sea and the eastern tropical
feed off the nutrients supplied by the dead microbial South and North Pacific. Many regions of the world’s
biomass and any nutrients deposited in the soil during oceans do not denitrify or fix nitrogen.
periods of drought or freeze. These three events are Measurements of the isotopic ratios 14/15N and 16/18O of
usually accompanied by increased rates in soil respiration N2O originating from surface and from deep waters in the
and NO and N2O emissions. Increased NO, N2O, and subtropical North Pacific Ocean have revealed large differ-
CO2 emissions are observed for a few days only and fade ences. Surface water N2O was depleted in 15N and 18O
away when the supply of nutrient has diminished. compared to atmospheric and deep water N2O. This
Subsequent pulsing, freeze–thaw cycles produce smaller implies that nitrification, rather than denitrification, is prob-
emission peaks, due to less substrate stored, compared to ably the main source of surface water N2O in open oceans.
the first event. The dominant N gas emitted depends on
the soil properties and meteorological conditions, with Control of denitrification by pH and temperature
low aeration stimulating N2O/N2 emission, while high pH
aeration stimulating NO emission. Emissions can be very Until recently, the general view was that in soils, optimal
high and these very sporadic events can significantly denitrification rates occur at pH 7–8, that the ratio of deni-
contribute to the overall annual NO or N2O flux. trification products N2O/N2 decreases as the pH is raised,
and that N2O produced in acid soils is more likely a product
Control of denitrification in aquatic systems of heterotrophic nitrification rather than denitrification.
In aquatic environments, the requirements for denitrifica- However, new studies have shown that microorganisms can
tion are the same as in terrestrial systems: a nitrogen and denitrify in acid soils, can adapt to acid soil conditions, and
carbon source and low O2 concentrations. The major end that microbial pH optima are similar to the pH of soils. Also,
product of denitrification in aquatic systems is N2, but in aquatic systems, a high denitrification potential was
surface layers of the water columns are also often observed for acid mine sediments from several affected
enriched in N2O in relation to the atmosphere, thus streams ranging from pH 2.6 to 4.9 in Colorado, US.
870 Ecological Processes | Denitrification
In contrast to the above, various reports have demon- estuaries with good light penetration, the diurnal pattern
strated that NO3 concentrations can be reduced most of benthic microalgal production and associated rise in O2
efficiently at higher pH in effluent treatment works. In concentration at the sediment surface, during the day
one study, denitrification of synthetic wastewater with a inhibits denitrification. Consequently, larger denitrifica-
high NO3 concentration was inhibited at pH values below tion rates can be observed at night. For rivers, however,
7, but complete denitrification occurred from pH 7.5 to 9.0. the opposite was observed. Denitrification rates were
The process of denitrification increases the pH of its higher during the day than night, in spite of maximum
surrounding environment, which can be beneficial for O2 concentrations during the day. It has been suggested
some aquatic systems. The buildup of high NO3 concen- that diurnal denitrification patterns are controlled by the
trations in a closed seawater aquarium was minimized by nitrification cycling driven by diurnal variations in water
installing a biological denitrification system. In addition, pH and temperature.
this system offers additional benefits by increasing the pH
and alkalinity of seawater and providing a reducing envir-
onment to balance the oxidizing disinfection environment
Models of Denitrification
in the aquarium.
The importance of denitrification as a source of atmo-
spheric N2O, a greenhouse gas, and also an effective
Temperature
removal process of harmful NO3 in aquatic systems has
All microbial activity, including denitrification, is influ-
stimulated many researchers into modeling denitrifica-
enced by changes in temperature. Activity is very slow
tion rates and its products. Modeling denitrification is
below 5 C, increases linearly to a maximum around
complicated, as two microbial processes with very con-
25–30 C and thereafter decreases to a minimum at
trasting requirements (nitrification and denitrification)
around 65 C, where growth stops due to enzyme dena-
have to be considered. The denitrifying population is
turation. There are exceptions and some bacteria have
always present and respiring, but will only denitrify
evolved to grow in extremely hot (>100 C) or cold
under very specific conditions. Denitrification is therefore
(–12 C) conditions. Temperature optima in a particular
a very transient process both in space and time.
soil appear to be the same for a range of microbial
For terrestrial systems, simple models calculate deni-
processes, including nitrification and denitrification, but
trification from few essential parameters, for example,
temperature optima differ for different soils. The tem-
NO3 and carbon content, soil texture, and drainage.
perature optima do not appear to be linked to climate.
More complex models describe the denitrification process
Strong seasonal and diurnal variations in N2O and NO
in detail, for example, the DNDC model (denitrification
fluxes are observed in all marine and terrestrial systems,
decomposition model).
but only when carbon and nitrogen supply and anaerobi-
In aquatic systems, denitrification has been calculated
city is not limiting. Under nonlimiting conditions, the
from diffusion of substrates and products to and from the
temperature coefficient of denitrification, Q 10, is mostly
active sites for estuaries. For rivers, N removal was cal-
reported around 2–4. Frequently, the temperature
culated from the physical properties of the stream,
response of denitrification and other microbial reactions
especially channel size. For marine sediments, a more
is expressed as an activation energy, which can be calcu-
complex model has been developed that couples the
lated from the plot of the natural logarithm of the flux
biogeochemical cycling of sedimentary carbon, nitrogen,
against the inverse absolute temperature. Usually, activa-
and oxygen with that in the water column models.
tion energies range from 50 to 100 kJ mol1, and again are
similar for a range of microbial processes.
See also: Ammonification; Biological Nitrogen Fixation;
Nitrification.
Diurnal patterns
Diurnal patterns of N2O and NO emissions from soils are
linked to diurnal oscillations of the soil temperature. Soil Further Reading
temperature diurnal oscillations dampen with increasing
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soil depth. Comparison of diurnal patterns of temperature from autotrophic ammonia-oxidizing bacteria. Applied Environmental
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emissions may be used to locate the depth of maximum Davidson EA (1991) Fluxes of nitrous oxide and nitric oxide from
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denitrification or nitrification activity. In a well-drained Microbial Production and Consumption of Greenhouse Gases:
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Gruber L and Sarmiento JL (2005) Global patterns of marine nitrogen
In aquatic systems, very different diurnal denitrifica- fixation and denitrification. Global Biogeochemical Cycles
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Ecosystems | Desert Streams 871
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Desert Streams
T K Harms, R A Sponseller, and N B Grimm, Arizona State University, Tempe, AZ, USA
ª 2008 Elsevier B.V. All rights reserved.