2. A fermentative reduction where the energy production is
derived from the substrate phosphorylation and is not
directly coupled to nitrite reduction. In strict anaerobic
microorganisms, the DRNA seems to be essentially fermentative whereas in facultative aerobes, some of the
steps are respiratory and others fermentative.
In all facultative anaerobic prokaryotes that reduce
nitrate, the first step of nitrate reduction is not different
from that encountered in denitrifying bacteria. The dissimilatory nitrate reductase (Type A, Nar) of a non-denitrifying
strain of Escherichia coli has been studied in detail and its
properties are common to those of nitrate reductase type A of
denitrifying bacteria (cf. Sect. 14.3.5). In strict anaerobic
fermentative prokaryotes, nitrate would, in this case, allow
the reoxidation of NADH, H
+ produced during glycolysis.
The reduction of nitrite to ammonia comprises a single
step, although the involved enzymes are diverse. Two main
types of nitrite reductases were identified: a cytoplasmic
nitrite reductase working with NADH, H
+ (fermentative
pathway), and a nitrite reductase-formate dehydrogenase
(respiratory pathway).
14.3.4 Processes Leading to the Production
of Nitrate: Nitrification
Nitrification is the unique process that leads to the production of organic nitrate in the environment. This reaction is
performed in two steps: the oxidation of ammonium to
nitrite (or ammonium oxidation, AO) and the oxidation of
nitrite to nitrate (nitrite oxidation, NO) (cf. Sect. 3.3.2,
Fig. 3.18a, b):
2NH 4
þ
þ 3O 2 ! 2NO 2
À
þ 4H
þ
þ 2H 2 O
NO 2
À
þ ½ O 2 ! NO 3
À
During nitrification, ammonia or nitrite are used as reducing power in the respiratory chain. These oxidation reactions
lead to the establishment of a gradient of protons which
enables the formation of ATP used to synthesize organic
matter via CO 2 fixation (Calvin cycle), oxygen being the
final electron acceptor. The energetic efficiency is very low.
Each step of the nitrification reaction is carried out by a
different bacterial community. The first step of ammonium
oxidation is performed by ammonium oxidizing bacteria
or archaea (AOB, AOA). In the second reaction, the oxidation of nitrite, is performed by nitrite oxidizing bacteria
(NOB).
Most of the AOB and NOB are chemiolitho-autotrophic
bacteria, meaning that they use energy obtained by ammonium oxidation and fix CO 2 to synthesize their biomass.
Chemolitho-autotrophic nitrification dominates in most
ecosystems. However, some organisms can perform
heterotrophic nitrification. In forest ecosystems for example,
the contribution of heterotrophic nitrification, which is a
poorly understood mechanism, may constitute a significant
part of nitrification. Such data is lacking for marine
ecosystems. Compared to autotrophic nitrification, heterotrophic nitrification would increase with increasing C:N
ratio, i.e., when microorganisms are in competition for
nitrogen.
Concerning AO, the electrons from the oxidation of a
molecule of ammonium are transferred to the respiratory
chain to form ATP, generally during aerobic respiration.
Most of these micro-organisms are microaerophilic. AOB
generally are strict aerobic Beta or Gammaproteobacteria.
Most of the known AOB belong to the phylum of Betaproteobacteria: Nitrosospira and Nitrosomonas. Some marine AOB
belong to the phylum of Gammaproteobacteria, particularly
to the genus Nitrosococcus. A limited number of genera
are capable of oxidizing ammonium: Nitrosomonas, Nitrosococcus, Nitrosospira, Nitrosovibrio, and Nitrosolobus.
These bacteria are found in many environments, such as
soils, marine sediments, and lakes. In addition, a nitrifying
Archaea, “Candidatus Nitrosopumilis maritimus” belonging
to Crenarchaeota, has been isolated. In different marine
ecosystems, nitrifying Archaea seems more abundant than
nitrifying bacteria (Nicol and Schleper 2006).
Nitrite oxidizing nitrite bacteria (NOB) are also
chemiolitho-autotrophs, using the oxidation of nitrite to
nitrate to produce energy, oxygen being the final electron
acceptor. These bacteria belong to phylogenetic groups
which are relatively close to each other, affiliated to Alpha
and Gammaproteobacteria, in addition to the genus
Nitrospira. Four known genera oxidize nitrite: Nitrobacter,
Nitrospina, Nitrococcus, and Nitrospira (Fig. 14.27).
Two enzymes are involved in the oxidation of ammonium
to nitrite: ammonia monooxygenase (i.e., the membranebound enzyme AMO encoded by three genes: amoA,
amoB, and amoC, which are grouped under the same
operon), and hydroxylamine oxidoreductase (the periplasmic enzyme HAO, encoded by the genes hao, hcy, and cyc
which also encode for the associated cytochrome c554).
AMO can oxidize ammonium into hydroxylamine, which
is then oxidized to HAO (Fig. 14.30). The oxidation of nitrite
to nitrate is performed by a nitrite oxidoreductase bounded
to the cell membrane (Fig. 14.30).
In some Nitrosomonas species, the presence of nitrite
(NIR) and nitric oxide reductase (NOR), enzymes of the
denitrification, is surprising. It has been shown that under
low oxygen conditions, these enzymes are expressed and
allow to accumulate nitrous oxide. However, the exact
conditions of this expression are not clear at all. The inactivation of gene nirK in N. europea reduces the tolerance to
nitrite in aerobic cultures, indicating its potential role in
nitrite detoxification. Moreover, Nitrosomonas eutropha
14 Biogeochemical Cycles
573
derived from the substrate phosphorylation and is not
directly coupled to nitrite reduction. In strict anaerobic
microorganisms, the DRNA seems to be essentially fermentative whereas in facultative aerobes, some of the
steps are respiratory and others fermentative.
In all facultative anaerobic prokaryotes that reduce
nitrate, the first step of nitrate reduction is not different
from that encountered in denitrifying bacteria. The dissimilatory nitrate reductase (Type A, Nar) of a non-denitrifying
strain of Escherichia coli has been studied in detail and its
properties are common to those of nitrate reductase type A of
denitrifying bacteria (cf. Sect. 14.3.5). In strict anaerobic
fermentative prokaryotes, nitrate would, in this case, allow
the reoxidation of NADH, H
+ produced during glycolysis.
The reduction of nitrite to ammonia comprises a single
step, although the involved enzymes are diverse. Two main
types of nitrite reductases were identified: a cytoplasmic
nitrite reductase working with NADH, H
+ (fermentative
pathway), and a nitrite reductase-formate dehydrogenase
(respiratory pathway).
14.3.4 Processes Leading to the Production
of Nitrate: Nitrification
Nitrification is the unique process that leads to the production of organic nitrate in the environment. This reaction is
performed in two steps: the oxidation of ammonium to
nitrite (or ammonium oxidation, AO) and the oxidation of
nitrite to nitrate (nitrite oxidation, NO) (cf. Sect. 3.3.2,
Fig. 3.18a, b):
2NH 4
þ
þ 3O 2 ! 2NO 2
À
þ 4H
þ
þ 2H 2 O
NO 2
À
þ ½ O 2 ! NO 3
À
During nitrification, ammonia or nitrite are used as reducing power in the respiratory chain. These oxidation reactions
lead to the establishment of a gradient of protons which
enables the formation of ATP used to synthesize organic
matter via CO 2 fixation (Calvin cycle), oxygen being the
final electron acceptor. The energetic efficiency is very low.
Each step of the nitrification reaction is carried out by a
different bacterial community. The first step of ammonium
oxidation is performed by ammonium oxidizing bacteria
or archaea (AOB, AOA). In the second reaction, the oxidation of nitrite, is performed by nitrite oxidizing bacteria
(NOB).
Most of the AOB and NOB are chemiolitho-autotrophic
bacteria, meaning that they use energy obtained by ammonium oxidation and fix CO 2 to synthesize their biomass.
Chemolitho-autotrophic nitrification dominates in most
ecosystems. However, some organisms can perform
heterotrophic nitrification. In forest ecosystems for example,
the contribution of heterotrophic nitrification, which is a
poorly understood mechanism, may constitute a significant
part of nitrification. Such data is lacking for marine
ecosystems. Compared to autotrophic nitrification, heterotrophic nitrification would increase with increasing C:N
ratio, i.e., when microorganisms are in competition for
nitrogen.
Concerning AO, the electrons from the oxidation of a
molecule of ammonium are transferred to the respiratory
chain to form ATP, generally during aerobic respiration.
Most of these micro-organisms are microaerophilic. AOB
generally are strict aerobic Beta or Gammaproteobacteria.
Most of the known AOB belong to the phylum of Betaproteobacteria: Nitrosospira and Nitrosomonas. Some marine AOB
belong to the phylum of Gammaproteobacteria, particularly
to the genus Nitrosococcus. A limited number of genera
are capable of oxidizing ammonium: Nitrosomonas, Nitrosococcus, Nitrosospira, Nitrosovibrio, and Nitrosolobus.
These bacteria are found in many environments, such as
soils, marine sediments, and lakes. In addition, a nitrifying
Archaea, “Candidatus Nitrosopumilis maritimus” belonging
to Crenarchaeota, has been isolated. In different marine
ecosystems, nitrifying Archaea seems more abundant than
nitrifying bacteria (Nicol and Schleper 2006).
Nitrite oxidizing nitrite bacteria (NOB) are also
chemiolitho-autotrophs, using the oxidation of nitrite to
nitrate to produce energy, oxygen being the final electron
acceptor. These bacteria belong to phylogenetic groups
which are relatively close to each other, affiliated to Alpha
and Gammaproteobacteria, in addition to the genus
Nitrospira. Four known genera oxidize nitrite: Nitrobacter,
Nitrospina, Nitrococcus, and Nitrospira (Fig. 14.27).
Two enzymes are involved in the oxidation of ammonium
to nitrite: ammonia monooxygenase (i.e., the membranebound enzyme AMO encoded by three genes: amoA,
amoB, and amoC, which are grouped under the same
operon), and hydroxylamine oxidoreductase (the periplasmic enzyme HAO, encoded by the genes hao, hcy, and cyc
which also encode for the associated cytochrome c554).
AMO can oxidize ammonium into hydroxylamine, which
is then oxidized to HAO (Fig. 14.30). The oxidation of nitrite
to nitrate is performed by a nitrite oxidoreductase bounded
to the cell membrane (Fig. 14.30).
In some Nitrosomonas species, the presence of nitrite
(NIR) and nitric oxide reductase (NOR), enzymes of the
denitrification, is surprising. It has been shown that under
low oxygen conditions, these enzymes are expressed and
allow to accumulate nitrous oxide. However, the exact
conditions of this expression are not clear at all. The inactivation of gene nirK in N. europea reduces the tolerance to
nitrite in aerobic cultures, indicating its potential role in
nitrite detoxification. Moreover, Nitrosomonas eutropha
14 Biogeochemical Cycles
573