68
S. Ambreetha et al.
2.1.3 Nitrification
The aerenchymatous tissue present in rice crop allows diffusion of oxygen into rice
roots and soil which favors nitrification in aerobic niche. Thus the rice roots are
exposed to mixture of NH 4
+ –NO 3
− . The anoxic environment in paddy encourages
microbial reduction of available NO 3
− making their availability low. The unceasing
supply of NO 3
− is warranted by oxic conditions prevailing in rhizosphere by their
oxygen supply. This chemolithotrophic nitrification involves two steps involving
ammonia oxidation to nitrite, and nitrite oxidation to nitrate [17] which is performed
by ammonia oxidizing bacteria or archaea (AOB/AOA) [55] and nitrite oxidizing
bacteria (NOB) [21] respectively. The activity shoots up upon the addition of N
fertilizer and AOB population like Nitrosomonas, Nitrosococcus which engrosses in
biological nitrification than AOA, however rice rhizosphere encompasses both AOA
and AOB. AOB communities are in turn decided by several factors including soil
temperature, pH, availability of ammonium and oxygen. With increase in N fertilization, the relative abundance of Nitrosomonas was found to be higher than that
of Nitrospira. The reason could be due to increased pore water NH 4
+ - N concentration upon N fertilization. Nitrite oxidation is carried out by genera belonging to
Nitrobacter and Nitrococcus. Recent nitrification research revealed certain common
microorganisms taking up role of both the process belonging to the genera Nitrospira
and termed as commamox [20, 97]. Commamox are contributors of nitrification in
paddy soil even at low ammonia niche than AOA and AOB characterized by higher
amoA gene abundance [60]. Anoxic condition prevailing enables the reduction of
NO 3
− thereby limiting their availability. However the oxygen leakage from the rice
roots enables the continuous supply of NO 3
− .
2.1.4 Denitrification
The major nitrogen removal mechanism characterized by respiratory transformation
of inorganic N (oxides of nitrogen) to gaseous forms such as nitric oxide, nitrous
oxide and N 2 [74, 89]. This process occurs just below the oxidized zone where nitrification occurs and accounts for more than 40% of N fertilizer loss [120, 122]. This
is considered as major contributor for nitrogen loss from applied nitrogenous fertilizers and source for greenhouse gases. When the redox potential decreases after 10–
14 days of water logging, denitrifier activity becomes higher. Nitrate ion conversion
to di-nitrogen gas has been studied in detail by [72], and elucidated their extreme
instability. This gives rise to potential denitrification activity in paddy ecosystem.
This reaction involves the reduction of nitrite to nitric oxide catalyzed by key enzyme
nitrite reductase [15]. In general, N fertilization coupled with flooded condition stimulates denitrifying bacteria, which denitrifies the nitrate in anaerobic soil. Facultative
and heterotrophic anaerobes use NO 3
− as terminal acceptor involving them redox
reaction between organic carbon and oxides of N. Organic carbon serves as electron
donor for the process and their availability plays a prime role. It was further supported
S. Ambreetha et al.
2.1.3 Nitrification
The aerenchymatous tissue present in rice crop allows diffusion of oxygen into rice
roots and soil which favors nitrification in aerobic niche. Thus the rice roots are
exposed to mixture of NH 4
+ –NO 3
− . The anoxic environment in paddy encourages
microbial reduction of available NO 3
− making their availability low. The unceasing
supply of NO 3
− is warranted by oxic conditions prevailing in rhizosphere by their
oxygen supply. This chemolithotrophic nitrification involves two steps involving
ammonia oxidation to nitrite, and nitrite oxidation to nitrate [17] which is performed
by ammonia oxidizing bacteria or archaea (AOB/AOA) [55] and nitrite oxidizing
bacteria (NOB) [21] respectively. The activity shoots up upon the addition of N
fertilizer and AOB population like Nitrosomonas, Nitrosococcus which engrosses in
biological nitrification than AOA, however rice rhizosphere encompasses both AOA
and AOB. AOB communities are in turn decided by several factors including soil
temperature, pH, availability of ammonium and oxygen. With increase in N fertilization, the relative abundance of Nitrosomonas was found to be higher than that
of Nitrospira. The reason could be due to increased pore water NH 4
+ - N concentration upon N fertilization. Nitrite oxidation is carried out by genera belonging to
Nitrobacter and Nitrococcus. Recent nitrification research revealed certain common
microorganisms taking up role of both the process belonging to the genera Nitrospira
and termed as commamox [20, 97]. Commamox are contributors of nitrification in
paddy soil even at low ammonia niche than AOA and AOB characterized by higher
amoA gene abundance [60]. Anoxic condition prevailing enables the reduction of
NO 3
− thereby limiting their availability. However the oxygen leakage from the rice
roots enables the continuous supply of NO 3
− .
2.1.4 Denitrification
The major nitrogen removal mechanism characterized by respiratory transformation
of inorganic N (oxides of nitrogen) to gaseous forms such as nitric oxide, nitrous
oxide and N 2 [74, 89]. This process occurs just below the oxidized zone where nitrification occurs and accounts for more than 40% of N fertilizer loss [120, 122]. This
is considered as major contributor for nitrogen loss from applied nitrogenous fertilizers and source for greenhouse gases. When the redox potential decreases after 10–
14 days of water logging, denitrifier activity becomes higher. Nitrate ion conversion
to di-nitrogen gas has been studied in detail by [72], and elucidated their extreme
instability. This gives rise to potential denitrification activity in paddy ecosystem.
This reaction involves the reduction of nitrite to nitric oxide catalyzed by key enzyme
nitrite reductase [15]. In general, N fertilization coupled with flooded condition stimulates denitrifying bacteria, which denitrifies the nitrate in anaerobic soil. Facultative
and heterotrophic anaerobes use NO 3
− as terminal acceptor involving them redox
reaction between organic carbon and oxides of N. Organic carbon serves as electron
donor for the process and their availability plays a prime role. It was further supported