6
Benthic Cycling of Oxygen, Nitrogen and Phosphorus
212
The ∆G
0
-values indicate the higher energy
yield for using oxygen rather than nitrate as the
terminal electron acceptor. In these equations, it is
assumed that organic matter with a C/N/P ratio of
106/16/1 is oxidized. Equation (6.1) requires that
ammonia released during oxic respiration is
quantitatively oxidized to nitrate. The process of
nitrification is, however, more complex than
described above and is known as a stepwise oxidation of nitrogen species by different microbes.
Those can be grouped into ammonia oxidizers,
generally with a genus name starting with the
prefix Nitroso- and nitrite oxidizers, starting with
the prefix Nitro-. Although ammonia and nitrite
oxidizing bacteria are physiologically depending
on each other and usually occur in close
proximity, they are phylogenetically two distinct
groups of bacteria, which are not closely related
(Bock and Wagner 2001). The oxidation of
ammonia to nitrite is also a two step process in
which hydroxylamine is formed as an intermediate
product (Eq. 6.3). The second step yields the
biogeochemically useful energy (Eq. 6.4):
2 NH 3 + O 2 → 2 NH 2 OH
(6.3)
NH 2 OH + O 2 → NO 2
-
+ H 2 O + H
+
(6.4)
In the following step nitrite is oxidized by
lithotrophs like N itrobacter or N itrococcus to
nitrate (Eq. 6.5):
NO 2
-
+ ½ O 2 → NO 3
-
(6.5)
In summary, nitrifying bacteria are considered
to be strictly aerobic and therefore depend on
adequate oxygen supply for their energy gain
(Painter 1970). Experimental results of Henriksen et
al. (1981) on control factors of nitrification rates in
shallow water sediments from Denmark revealed
that nitrification is strongly dependent on temperature, oxygen availability (oxygen penetration
depth), ammonia supply and the number of nitrifying
bacteria. These complex interactions are more
thoroughly discussed in comprehensive reviews on
nitrification in coastal marine environments by
Kaplan (1983) and Henriksen and Kemp (1988).
Denitrification starts when oxygen is almost
depleted (below the oxygen penetration depth) by
inducing an enzymatic system of nitrate reductase
and nitrite reductase by facultative aerobic bacteria, which can only use nitrogenous oxides if
oxygen is - nearly - absent. Measurements carried
out with a combined microsensor for O 2 and N 2 O
indicated that denitrification is restricted to a thin
anoxic layer below the oxic zone (Christensen et
al. 1989). Denitrification is the only biological process that produces free nitrogen. It removes fixed
nitrogen compounds and, therefore, exerts a
negative feedback on eutrophication making it a
crucial process for the preservation of life on
earth. For example, denitrification in rivers and
coastal environments reduces the supply of fixed
nitrogen from the continents by about 40%.
(Seitzinger 1988).
The reduction of nitrate to dinitrogen occurs
first as a reduction of nitrate to nitrite (Eq. 6.6)
and then a stepwise reduction to nitrogen oxide,
dinitrogen oxide (Eq. 6.7) and dinitrogen (Eq. 6.8):
NO 3
-
+ 2 H
+
+ 2 e
-
→ NO 2
-
+ H 2 O
(6.6)
2 NO 2
-
+ 6 H
+
+ 4 e
-
→ N 2 O + 3 H 2 O
(6.7)
N 2 O + 2 H
+
+ 2 e
-
→ N 2 + H 2 O
(6.8)
The last reduction step from nitrous oxide to
dinitrogen (Eq. 6.8) is not always completed so
that the final product of denitrification is not
necessarily dinitrogen. Nitrous oxide may therefore be produced or consumed during denitrification. A compilation of Seitzinger (1998) for coastal
marine environments shows, however, that in most
cases the net ratios between N 2 O:N 2 production
rates are usually very small (between 0.0002-0.06).
The total amount of dinitrogen produced obviously depends on the partial pressure of oxygen (higher
oxygen contents seem to be suitable for the production of N 2 O; Jørgensen et al. 1984), the pH,
and the presence of H 2 S.
The major prerequisite for denitrification is the
availability of nitrate (including nitrite). In marine
sediments the dominant sources of nitrate are the
production during nitrification and the supply
from overlying bottom water by means of bioturbation, bioirrigation, and diffusion (see Section
6.3.2). Furthermore, denitrification is strongly
dependent on temperature, but also on the oxygen
concentration and the availability of organic matter are limiting for the process (Middelburg et al.
1996a). There is also evidence that denitrification
may be reduced at high sulfate reduction rates,
because low sulfide concentrations completely
inhibit nitrification which in turn is necessary for
denitrification (Seitzinger 1988). Generally, most
suitable conditions for denitrification are obtained
Benthic Cycling of Oxygen, Nitrogen and Phosphorus
212
The ∆G
0
-values indicate the higher energy
yield for using oxygen rather than nitrate as the
terminal electron acceptor. In these equations, it is
assumed that organic matter with a C/N/P ratio of
106/16/1 is oxidized. Equation (6.1) requires that
ammonia released during oxic respiration is
quantitatively oxidized to nitrate. The process of
nitrification is, however, more complex than
described above and is known as a stepwise oxidation of nitrogen species by different microbes.
Those can be grouped into ammonia oxidizers,
generally with a genus name starting with the
prefix Nitroso- and nitrite oxidizers, starting with
the prefix Nitro-. Although ammonia and nitrite
oxidizing bacteria are physiologically depending
on each other and usually occur in close
proximity, they are phylogenetically two distinct
groups of bacteria, which are not closely related
(Bock and Wagner 2001). The oxidation of
ammonia to nitrite is also a two step process in
which hydroxylamine is formed as an intermediate
product (Eq. 6.3). The second step yields the
biogeochemically useful energy (Eq. 6.4):
2 NH 3 + O 2 → 2 NH 2 OH
(6.3)
NH 2 OH + O 2 → NO 2
-
+ H 2 O + H
+
(6.4)
In the following step nitrite is oxidized by
lithotrophs like N itrobacter or N itrococcus to
nitrate (Eq. 6.5):
NO 2
-
+ ½ O 2 → NO 3
-
(6.5)
In summary, nitrifying bacteria are considered
to be strictly aerobic and therefore depend on
adequate oxygen supply for their energy gain
(Painter 1970). Experimental results of Henriksen et
al. (1981) on control factors of nitrification rates in
shallow water sediments from Denmark revealed
that nitrification is strongly dependent on temperature, oxygen availability (oxygen penetration
depth), ammonia supply and the number of nitrifying
bacteria. These complex interactions are more
thoroughly discussed in comprehensive reviews on
nitrification in coastal marine environments by
Kaplan (1983) and Henriksen and Kemp (1988).
Denitrification starts when oxygen is almost
depleted (below the oxygen penetration depth) by
inducing an enzymatic system of nitrate reductase
and nitrite reductase by facultative aerobic bacteria, which can only use nitrogenous oxides if
oxygen is - nearly - absent. Measurements carried
out with a combined microsensor for O 2 and N 2 O
indicated that denitrification is restricted to a thin
anoxic layer below the oxic zone (Christensen et
al. 1989). Denitrification is the only biological process that produces free nitrogen. It removes fixed
nitrogen compounds and, therefore, exerts a
negative feedback on eutrophication making it a
crucial process for the preservation of life on
earth. For example, denitrification in rivers and
coastal environments reduces the supply of fixed
nitrogen from the continents by about 40%.
(Seitzinger 1988).
The reduction of nitrate to dinitrogen occurs
first as a reduction of nitrate to nitrite (Eq. 6.6)
and then a stepwise reduction to nitrogen oxide,
dinitrogen oxide (Eq. 6.7) and dinitrogen (Eq. 6.8):
NO 3
-
+ 2 H
+
+ 2 e
-
→ NO 2
-
+ H 2 O
(6.6)
2 NO 2
-
+ 6 H
+
+ 4 e
-
→ N 2 O + 3 H 2 O
(6.7)
N 2 O + 2 H
+
+ 2 e
-
→ N 2 + H 2 O
(6.8)
The last reduction step from nitrous oxide to
dinitrogen (Eq. 6.8) is not always completed so
that the final product of denitrification is not
necessarily dinitrogen. Nitrous oxide may therefore be produced or consumed during denitrification. A compilation of Seitzinger (1998) for coastal
marine environments shows, however, that in most
cases the net ratios between N 2 O:N 2 production
rates are usually very small (between 0.0002-0.06).
The total amount of dinitrogen produced obviously depends on the partial pressure of oxygen (higher
oxygen contents seem to be suitable for the production of N 2 O; Jørgensen et al. 1984), the pH,
and the presence of H 2 S.
The major prerequisite for denitrification is the
availability of nitrate (including nitrite). In marine
sediments the dominant sources of nitrate are the
production during nitrification and the supply
from overlying bottom water by means of bioturbation, bioirrigation, and diffusion (see Section
6.3.2). Furthermore, denitrification is strongly
dependent on temperature, but also on the oxygen
concentration and the availability of organic matter are limiting for the process (Middelburg et al.
1996a). There is also evidence that denitrification
may be reduced at high sulfate reduction rates,
because low sulfide concentrations completely
inhibit nitrification which in turn is necessary for
denitrification (Seitzinger 1988). Generally, most
suitable conditions for denitrification are obtained