5
are then degraded by heterotrophic organisms for C and energy while releasing the
inorganic N as ammonium in a process generally referred to as ammonification or
mineralization (Strock 2008).
Some microorganisms obtain energy by oxidizing reduced forms of N such as
ammonium (Gottschalk 2012). Nitrification was first discovered in the late 1800s by
the pioneering microbial ecologist, Sergey Winogradsky (Dworkin and Gutnick
2012). Nitrification is the sequential oxidation of ammonium to nitrate and has conventionally been ascribed to phylogenetically limited groups of aerobic chemolithotrophic bacteria referred to as ammonia oxidizers and nitrite oxidizers (Ward
2011). Relatively recently, it was discovered that some of the most important ammonia oxidizers in soils and the oceans are members of the Archaea rather than Bacteria
(Ward 2011). Most recently, bacteria that can carry out both steps of nitrification on
their own have been discovered (Nitrospira, a process termed comammox)
(Santoro 2016).
Reducing oxidized forms can be coupled to oxidation of other compounds
(Fig. 1.2). Canonical denitrification, the reduction of oxidized N compounds ultimately to N 2 O and N 2 in anaerobic respiration, occurs in diverse, largely heterotrophic bacteria, where it is coupled to the oxidation of organic compounds (Thamdrup
2012), but is also found in some Archaea (Offre et al. 2013) and chemoautotrophic
bacteria. N 2 O, a potent greenhouse gas, is an important intermediate or product of
at least two of the abovementioned pathways, ammonia oxidation and denitrification (Barnard et al. 2005). Another pathway utilized by some microbes is the dissimilatory reduction of nitrate to ammonia (DNRA) which can be linked to either
fermentative or respiratory pathways (Thamdrup 2012). A pathway of ammonia
oxidation which occurs in the absence of O 2 referred to as anaerobic ammonia oxidation or Anammox has also been discovered (Van De Graaf et al. 1995). Anammox
bacteria oxidize ammonia with nitrite as an oxidizing agent yielding N 2 as an endproduct (Offre et al. 2013). Denitrification and Anammox each return fixed N back
to the atmosphere N 2 pool.
The chemical form of N 2 , two atoms with a triple bond between them, is very
stable and difficult to reduce even though the reduction from N 2 to NH 3 is overall
thermodynamically favorable, but has a very high activation energy in the transition
state (Howard and Rees 1996; Newton 2015). N 2 fixation is achieved industrially
(with the Haber-Bosch process) with high pressure and temperature (Galloway et al.
2008), or biologically with the enzyme nitrogenase (Postgate 2012). These reactions are called chemical or biological N 2 fixation (BNF), respectively.
1.2 Terrestrial and Aquatic Environments
N 2 fixation has contrasting characteristics in terrestrial and aquatic environments.
N 2 fixation has long been studied in the terrestrial environment because of its importance in agriculture. Bacteria symbiotically associated with multicellular plants
such as legumes are major N 2 -fixers as well as the associative symbioses with com1.2 Terrestrial and Aquatic Environments
are then degraded by heterotrophic organisms for C and energy while releasing the
inorganic N as ammonium in a process generally referred to as ammonification or
mineralization (Strock 2008).
Some microorganisms obtain energy by oxidizing reduced forms of N such as
ammonium (Gottschalk 2012). Nitrification was first discovered in the late 1800s by
the pioneering microbial ecologist, Sergey Winogradsky (Dworkin and Gutnick
2012). Nitrification is the sequential oxidation of ammonium to nitrate and has conventionally been ascribed to phylogenetically limited groups of aerobic chemolithotrophic bacteria referred to as ammonia oxidizers and nitrite oxidizers (Ward
2011). Relatively recently, it was discovered that some of the most important ammonia oxidizers in soils and the oceans are members of the Archaea rather than Bacteria
(Ward 2011). Most recently, bacteria that can carry out both steps of nitrification on
their own have been discovered (Nitrospira, a process termed comammox)
(Santoro 2016).
Reducing oxidized forms can be coupled to oxidation of other compounds
(Fig. 1.2). Canonical denitrification, the reduction of oxidized N compounds ultimately to N 2 O and N 2 in anaerobic respiration, occurs in diverse, largely heterotrophic bacteria, where it is coupled to the oxidation of organic compounds (Thamdrup
2012), but is also found in some Archaea (Offre et al. 2013) and chemoautotrophic
bacteria. N 2 O, a potent greenhouse gas, is an important intermediate or product of
at least two of the abovementioned pathways, ammonia oxidation and denitrification (Barnard et al. 2005). Another pathway utilized by some microbes is the dissimilatory reduction of nitrate to ammonia (DNRA) which can be linked to either
fermentative or respiratory pathways (Thamdrup 2012). A pathway of ammonia
oxidation which occurs in the absence of O 2 referred to as anaerobic ammonia oxidation or Anammox has also been discovered (Van De Graaf et al. 1995). Anammox
bacteria oxidize ammonia with nitrite as an oxidizing agent yielding N 2 as an endproduct (Offre et al. 2013). Denitrification and Anammox each return fixed N back
to the atmosphere N 2 pool.
The chemical form of N 2 , two atoms with a triple bond between them, is very
stable and difficult to reduce even though the reduction from N 2 to NH 3 is overall
thermodynamically favorable, but has a very high activation energy in the transition
state (Howard and Rees 1996; Newton 2015). N 2 fixation is achieved industrially
(with the Haber-Bosch process) with high pressure and temperature (Galloway et al.
2008), or biologically with the enzyme nitrogenase (Postgate 2012). These reactions are called chemical or biological N 2 fixation (BNF), respectively.
1.2 Terrestrial and Aquatic Environments
N 2 fixation has contrasting characteristics in terrestrial and aquatic environments.
N 2 fixation has long been studied in the terrestrial environment because of its importance in agriculture. Bacteria symbiotically associated with multicellular plants
such as legumes are major N 2 -fixers as well as the associative symbioses with com1.2 Terrestrial and Aquatic Environments