Denitrifying bacteria are a diverse group of bacteria that encompass many different phyla. This group of bacteria, together with denitrifying fungi and archaea, is capable of performing denitrification as part of the nitrogen cycle. Denitrification is performed by a variety of denitrifying bacteria that are widely distributed in soils and sediments and that use oxidized nitrogen compounds in absence of oxygen as a terminal electron acceptor. They metabolise nitrogenous compounds using various enzymes, turning nitrogen oxides back to nitrogen gas (N2) or nitrous oxide (N2O).
Diversity of denitrifying bacteria
There is a great diversity in biological traits. Denitrifying bacteria have been identified in over 50 genera with over 125 different species and are estimated to represent 10-15% of bacteria population in water, soil and sediment. Denitrifying include for example several species of Pseudomonas, Alcaligenes , Bacillus and others. The majority of denitrifying bacteria are facultative aerobic heterotrophs that switch from aerobic respiration to denitrification when oxygen as an available terminal electron acceptor (TEA) runs out. This forces the organism to use nitrate to be used as a TEA. Because the diversity of denitrifying bacteria is so large, this group can thrive in a wide range of habitats including some extreme environments such as environments that are highly saline and high in temperature. Aerobic denitrifiers can conduct an aerobic respiratory process in which nitrate is converted gradually to N2 (NO3− →NO2− → NO → N2O → N2 ), using nitrate reductase (Nar or Nap), nitrite reductase (Nir), nitric oxide reductase (Nor), and nitrous oxide reductase (Nos). Phylogenetic analysis revealed that aerobic denitrifiers mainly belong to α-, β- and γ-Proteobacteria.
Denitrification mechanism
Denitrifying bacteria use denitrification to generate ATP.
The most common denitrification process is outlined below, with the nitrogen oxides being converted back to gaseous nitrogen:
2 NO3− + 10 e− + 12 H+ → N2 + 6 H2O
The result is one molecule of nitrogen and six molecules of water. Denitrifying bacteria are a part of the N cycle, and consists of sending the N back into the atmosphere. The reaction above is the overall half reaction of the process of denitrification. The reaction can be further divided into different half reactions each requiring a specific enzyme. The transformation from nitrate to nitrite is performed by nitrate reductase (Nar)
NO3− + 2 H+ + 2 e− → NO2− + H2O
Nitrite reductase (Nir) then converts nitrite into nitric oxide
2 NO2− + 4 H+ + 2 e− → 2 NO + 2 H2O
Nitric oxide reductase (Nor) then converts nitric oxide into nitrous oxide
2 NO + 2 H+ + 2 e− → N2O + H2O
Nitrous oxide reductase (Nos) terminates the reaction by converting nitrous oxide into dinitrogen
N2O + 2 H+ + 2 e− → N2 + H2O
It is important to note that any of the products produced at any step can be exchanged with the soil environment.
Oxidation of methane and denitrification
Anaerobic oxidation of methane coupled to denitrification
Anaerobic denitrification coupled to methane oxidation was first observed in 2008, with the isolation of a methane-oxidizing bacterial strain found to oxidize methane independently. This process uses the excess electrons from methane oxidation to reduce nitrates, effectively removing both fixed nitrogen and methane from aquatic systems in habitats ranging from sediment to peat bogs to stratified water columns.
The process of anaerobic denitrification may contribute significantly to the global methane and nitrogen cycles, especially in light of the recent influx of both due to anthropogenic changes. The extent to which anthropogenic methane affects the atmosphere is known to be a significant driver of climate change, and considering it is multiple times more potent than carbon dioxide. Removing methane is widely considered to be beneficial to the environment, although the extent of the role that denitrification plays in the global flux of methane is not well understood. Anaerobic denitrification as a mechanism has been shown to be capable of removing the excess nitrate caused by fertilizer runoff, even in hypoxic conditions.