Nitrification

Abstract

The global nitrogen cycle is initiated by the fixation of atmospheric N 2 , by either natural or chemical processes, to bioavailable ammonium (NH 4 + ). Nitrification is the oxidative process that transforms this ammonium to nitrate, via a nitrite intermediate. Nitrification is performed solely by microorganisms: ammonia‐oxidising bacteria and archaea oxidise ammonia to nitrite, nitrite‐oxidising bacteria oxidise nitrite to nitrate and comammox bacteria oxidise ammonia to nitrate. Nitrifiers (and anammox) are distinguished from other microorganisms as they can grow solely from the oxidation of inorganic nitrogenous molecules and fix carbon dioxide as their sole carbon source, although many can also grow using alternative catabolic processes, by cross‐feeding, and/or by mixotrophy. Key enzymes to the nitrification process include ammonia monooxygenase, hydroxylamine dehydrogenase and nitrite oxidoreductase. A putative enzyme catalysing nitric oxide oxidation to nitrite is currently uncharacterised. Essential intermediates to nitrification include hydroxylamine, nitric oxide and nitrite. As well as performing a required component of the global nitrogen cycle, nitrifying microorganisms are also responsible for the loss of nitrogen‐based fertilisers in soil and play a critical role in emission of the potent greenhouse gas, nitrous oxide, as mediated by production and consumption of nitric oxide in their metabolism. Key Concepts Nitrification is an oxidative process that transforms reduced nitrogen, primarily ammonia, to nitrate. Fluxes in nitrogen transformations associated with nitrification activity have accelerated greatly over the past century owing to the production and application of inorganic ammonium‐based fertilisers. Microorganisms involved in nitrification are ubiquitously distributed in nature and found virtually everywhere that ammonia and oxygen are present. Nitrification is mediated by bacteria and archaea and is performed by either two (ammonia and nitrite oxidisers) or one (comammox) canonical functional group. Autotrophic pathways of ammonia‐ and nitrite‐oxidising bacteria are the Calvin cycle or reverse TCA cycle; ammonia‐oxidising archaea assimilate carbon dioxide via the 3‐hydroxypropionate/4‐hydroxybutyrate pathway. Key enzymes of nitrification are ammonia monooxygenase, hydroxylamine dehydrogenase, nitric oxide oxidase (putative) and nitrite oxidoreductase. Methanotrophic and heterotrophic microorganisms can carry out parts of nitrification but cannot grow from oxidising reduced nitrogen compounds. Mechanisms for the production of nitric oxide and nitrous oxide are distinct among nitrifying microorganisms. Comparative genome analysis and the use of differential inhibitors can assist in determining differences in physiology and niche preference among nitrifying microorganisms. There is substantial physiological diversity within individual functional groups (e.g. ammonia oxidisers) which results in niche differentiation both within and between taxonomic groups of nitrifiers.

Greenhouse gas fluxes of microbial‐induced calcite precipitation at varying urea‐to‐calcium concentrations

“…N 2 O fluxes are likely to occur in MICP due to the abundance of $$$ {{\mathrm{NH}}_4}^{+} $$$. N 2 O is a minor product of both nitrification and denitrification (Stein & Nicol, 2018). Ammonia oxidation in quartz sand was observed after 27 days of being in contact with treatment solution (Gat et al, 2016), and a later study indicated an increase in activity of nitrifying bacteria and/or archaea during MICP (Tsesarsky et al, 2016).…”

A Review of the Main Process-Based Approaches for Modeling N2O Emissions from Agricultural Soils

“…Organic nitrogen, contained in crop residues and manure, is decomposed and mineralized by the soil microbial communities, resulting in the production of ammonium (NH 4 + ) [5]. During nitrification, which is operated by nitrifying bacteria and involves the oxidation of ammonium to nitrate (NO 3 − ) by key enzymes (e.g., ammonia monooxygenase, hydroxylamine dehydrogenase, nitric oxide oxidase, nitrite oxidoreductase) [6], a small proportion of N is lost as N 2 O. In contrast, denitrification, conducted by denitrifying bacteria, involves the reduction of nitrate and nitrite to gaseous N 2 and N 2 O [7], respectively, by nitrate and nitrite reductases [8].…”

Emission factors for Vietnamese beef cattle manure sun-drying and the effects of drying on manure microbial community

“…Nitrous oxide can be produced through a nitrification-denitrification process that can occur on the abundant inorganic nitrogen in manure. Nitrification occurs aerobically; it converts ammonia into hydroxyl amine via ammonia monooxygenase, hydroxyl amine into nitrite via hydroxylamine oxidoreductase and nitrite into nitrate via nitrite oxidoreductase [ 11 ]. Nitrifiers produce N 2 O during the oxidation of hydroxylamine to nitrite.…”