N Fertilization Dependent Bacterial and Archaeal …
69
by [108] that nitrification, provides substrate for denitrification and creates competition between nitrifiers and rice plants for NH 4
+ . Coupled reaction of nitrification and
denitrification is supported by oxic/anoxic interface which give rise NO 3
− as intermediate product. Nitrification activity upon the addition of N fertilizer has a partitioning
activity of NO 3
− between denitrification and dissimilatory nitrate reduction to ammonium (DNRA). DNRA is one among the important NO 3
− reduction processes, which
enables the conversion of loss prone NO 3
− into retainable NH
4+ [111]. The rate of
nitrification is one of the major factor governing the nitrogen use efficiency and N
losses through denitrification. Nitrification of NH 4
+ into NO 3
− , indeed serves as a
substrate for denitrification, when plant uptake of NH 4
+ is reduced [108].
The enzymes involved in the process include nitrate reductase, nitrite reductase,
nitric oxide reductase and nitrous oxide reductase [15]. Among them, nitrite reductase
is considered as key enzyme, nirK and nirS as functional genes, which is widely
used as a molecular marker for denitrifiers. nirK and nirS are structurally distinct
and functionally equivalent, copper and cytochrome cd1 containing nitrite reductase
respectively. Braker et al. and Yoshida et al. [9, 109] have elucidated the diversity and
quantity nirS and nirK. NirS diversity was found more in paddy system belonging
to Burkholderiales, Rhodocyclales and Rhodobacteriales, while nirK was related to
rhizobiales.
2.1.5 Anaerobic Ammonium Oxidation (anammox)
The anaerobic oxidation of ammonium along with nitrite is a significant transformation process affecting the global N budget. Anoxic condition usually harbors
enormous NH 4
+ , while the supply NO 2
− is the limited. The condition is driven by
two ways either by oxidation of NH 4
+ to NO 2
− by AOB or from NO 3
− reduction by
denitrifying bacteria. Welte et al. [104] have reported nitrite dependent and nitrite
independent anaerobic methane oxidation in paddy fields, where the activity was
higher in top 20 cm of the soil. Similar results were found by [118] with higher
anommox activity in top layers. In contrast, their activity was even found in deeper
layers of continuously flooded systems. Zhu et al. and Ding et al. [121, 25] have
reported NH 3 oxidation pathway coupled with ferric minerals in paddy soil for the
first time. It is commonly called as feammox, involving dissimilatory Fe reducing
microbes [85] whose activity is significantly higher in rhizosphere [93]. They recruit
different microbes yielding NO 2
− , NO 3
− and N 2 as terminal products. Denitrification and annamox reaction responsible for NO 3
_ reduction contribute to significant
losses of N, which are equilibrated by DNRA. DNRA occurs when nitrate in the soil
is limiting. They in turn enhances N retention transforming NO 3
− into soil retainable
NH 4
+ [111].
69
by [108] that nitrification, provides substrate for denitrification and creates competition between nitrifiers and rice plants for NH 4
+ . Coupled reaction of nitrification and
denitrification is supported by oxic/anoxic interface which give rise NO 3
− as intermediate product. Nitrification activity upon the addition of N fertilizer has a partitioning
activity of NO 3
− between denitrification and dissimilatory nitrate reduction to ammonium (DNRA). DNRA is one among the important NO 3
− reduction processes, which
enables the conversion of loss prone NO 3
− into retainable NH
4+ [111]. The rate of
nitrification is one of the major factor governing the nitrogen use efficiency and N
losses through denitrification. Nitrification of NH 4
+ into NO 3
− , indeed serves as a
substrate for denitrification, when plant uptake of NH 4
+ is reduced [108].
The enzymes involved in the process include nitrate reductase, nitrite reductase,
nitric oxide reductase and nitrous oxide reductase [15]. Among them, nitrite reductase
is considered as key enzyme, nirK and nirS as functional genes, which is widely
used as a molecular marker for denitrifiers. nirK and nirS are structurally distinct
and functionally equivalent, copper and cytochrome cd1 containing nitrite reductase
respectively. Braker et al. and Yoshida et al. [9, 109] have elucidated the diversity and
quantity nirS and nirK. NirS diversity was found more in paddy system belonging
to Burkholderiales, Rhodocyclales and Rhodobacteriales, while nirK was related to
rhizobiales.
2.1.5 Anaerobic Ammonium Oxidation (anammox)
The anaerobic oxidation of ammonium along with nitrite is a significant transformation process affecting the global N budget. Anoxic condition usually harbors
enormous NH 4
+ , while the supply NO 2
− is the limited. The condition is driven by
two ways either by oxidation of NH 4
+ to NO 2
− by AOB or from NO 3
− reduction by
denitrifying bacteria. Welte et al. [104] have reported nitrite dependent and nitrite
independent anaerobic methane oxidation in paddy fields, where the activity was
higher in top 20 cm of the soil. Similar results were found by [118] with higher
anommox activity in top layers. In contrast, their activity was even found in deeper
layers of continuously flooded systems. Zhu et al. and Ding et al. [121, 25] have
reported NH 3 oxidation pathway coupled with ferric minerals in paddy soil for the
first time. It is commonly called as feammox, involving dissimilatory Fe reducing
microbes [85] whose activity is significantly higher in rhizosphere [93]. They recruit
different microbes yielding NO 2
− , NO 3
− and N 2 as terminal products. Denitrification and annamox reaction responsible for NO 3
_ reduction contribute to significant
losses of N, which are equilibrated by DNRA. DNRA occurs when nitrate in the soil
is limiting. They in turn enhances N retention transforming NO 3
− into soil retainable
NH 4
+ [111].