118
L. Schorr et al.
dissimilatory denitrification process, a broad spectrum of bacteria, archaea and fungi
is involved whereby their energy gaining strategy depends on various external factors
such as climate, soil properties, and anthropogenic activities as TNF spreading [5].
So far, only partial sequences of the organisms, involved in the denitrification process
are obtainable. Many of the bacteria beyond these genome sequences, which reduce
nitrate in four steps over nitrite, nitric oxide and nitrous oxide to N 2 , are not yet
cultivable [4, 30].
The first reduction step from NO
−
3 to NO
−
2 is initiated by the nitrate reductase
(Nar) enzyme complex, a two-electron reduction process. The nitrate reductases are
molybdopterin enzymes and classified into three distinct types—respiratory (Nar),
periplasmic (Nap), and assimilatory nitrate reductase (Nas)—defined by their cellular
location, operon organization, and active site structure [78]. The molybdopterin
oxide reductase Nar is located in the cytoplasm, whereas the nitrate reductase (Nap,
NapAB) works in the periplasm [92]. At first nitrate must be transported into the cell
that Nar can reduce NO
−
3 to nitrite, that is afterwards transferred to the periplasm
where it is reduced to NO and N 2 O [46]. The nitric oxide reductases are key enzymes
in the denitrification process encoded by nirK and nirS genes, which promote the
reduction of nitrite to nitric oxide [9, 18, 126]. While the Nar genes regulate the
nitrate respiration, nirK and nirS, encoding the copper-containing nitrite reductase
genes, regulate the NO
−
2 to NO reduction, whereby the transcription of nirK activates
nirS. The nor genes encode the NO reductase and lead in an one-electron reduction
step to N 2 O. All these genes play periplasm located a crucial role in the denitrification
process.
2.1 Nitrifying, Denitrifying Bacteria and Their Regulative
About 10–15% of the bacterial population, found in each known environmental niche,
are able to nitrify and/or denitrify, but due to the difficulty in cultivating, most details
are not yet known [4, 12, 22, 30, 126]. Nitrification occurs under aerobic, denitrification predominantly under anaerobic conditions. Thus, combining both processes
in one single reactor is difficult to manage because of the different O 2 requirements.
However, both energy gaining processes depend on each other and can thus coexist
at reduced oxygen conditions. The regulation of denitrification starts by receiving
transcription input signals from a sensor molecule. The absence of oxygen thereby
equals an appropriate signal. Receiving such signal, a regulator protein binds to the
promotor region and activates transcription, whereby the operator strength of transcription is influenced by the number of binding sites in the promotor region where
contacts with the RNA polymerase are made [71].
Prerequisites for expression of denitrification genes are anaerobic conditions, the
presence of NO, and the regulating nitrate reductase operon that is activated by
the transcription regulator protein fumarate (Fnr), a one-component regulator of the
nitrate reductase (Fig. 2; [71]). Sensor and regulator domain are within a single
protein, the FNR/CRP protein, located in the promoter region of the denitrification
L. Schorr et al.
dissimilatory denitrification process, a broad spectrum of bacteria, archaea and fungi
is involved whereby their energy gaining strategy depends on various external factors
such as climate, soil properties, and anthropogenic activities as TNF spreading [5].
So far, only partial sequences of the organisms, involved in the denitrification process
are obtainable. Many of the bacteria beyond these genome sequences, which reduce
nitrate in four steps over nitrite, nitric oxide and nitrous oxide to N 2 , are not yet
cultivable [4, 30].
The first reduction step from NO
−
3 to NO
−
2 is initiated by the nitrate reductase
(Nar) enzyme complex, a two-electron reduction process. The nitrate reductases are
molybdopterin enzymes and classified into three distinct types—respiratory (Nar),
periplasmic (Nap), and assimilatory nitrate reductase (Nas)—defined by their cellular
location, operon organization, and active site structure [78]. The molybdopterin
oxide reductase Nar is located in the cytoplasm, whereas the nitrate reductase (Nap,
NapAB) works in the periplasm [92]. At first nitrate must be transported into the cell
that Nar can reduce NO
−
3 to nitrite, that is afterwards transferred to the periplasm
where it is reduced to NO and N 2 O [46]. The nitric oxide reductases are key enzymes
in the denitrification process encoded by nirK and nirS genes, which promote the
reduction of nitrite to nitric oxide [9, 18, 126]. While the Nar genes regulate the
nitrate respiration, nirK and nirS, encoding the copper-containing nitrite reductase
genes, regulate the NO
−
2 to NO reduction, whereby the transcription of nirK activates
nirS. The nor genes encode the NO reductase and lead in an one-electron reduction
step to N 2 O. All these genes play periplasm located a crucial role in the denitrification
process.
2.1 Nitrifying, Denitrifying Bacteria and Their Regulative
About 10–15% of the bacterial population, found in each known environmental niche,
are able to nitrify and/or denitrify, but due to the difficulty in cultivating, most details
are not yet known [4, 12, 22, 30, 126]. Nitrification occurs under aerobic, denitrification predominantly under anaerobic conditions. Thus, combining both processes
in one single reactor is difficult to manage because of the different O 2 requirements.
However, both energy gaining processes depend on each other and can thus coexist
at reduced oxygen conditions. The regulation of denitrification starts by receiving
transcription input signals from a sensor molecule. The absence of oxygen thereby
equals an appropriate signal. Receiving such signal, a regulator protein binds to the
promotor region and activates transcription, whereby the operator strength of transcription is influenced by the number of binding sites in the promotor region where
contacts with the RNA polymerase are made [71].
Prerequisites for expression of denitrification genes are anaerobic conditions, the
presence of NO, and the regulating nitrate reductase operon that is activated by
the transcription regulator protein fumarate (Fnr), a one-component regulator of the
nitrate reductase (Fig. 2; [71]). Sensor and regulator domain are within a single
protein, the FNR/CRP protein, located in the promoter region of the denitrification