## 2.22.5. Nitrification and Denitrification Losses of Nitrogen[¶](#nitrification-and-denitrification-losses-of-nitrogen "Permalink to this headline")
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Nitrification is an autotrophic process that converts less mobile ammonium ions into nitrate, that can more easily be lost from soil systems by leaching or denitrification. The process catalyzed by ammonia oxidizing archaea and bacteria that convert ammonium (NH4+) into nitrite, which is subsequently oxidized into nitrate (NO3\-). Conditions favoring nitrification include high NH4+ concentrations, well aerated soils, a neutral pH and warmer temperatures.

Under aerobic conditions in the soil oxygen is the preferred electron acceptor supporting the metabolism of heterotrophs, but anaerobic conditions favor the activity of soil heterotrophs which use nitrate as an electron acceptor (e.g. _Pseudomonas_ and _Clostridium_) supporting respiration. This process, known as denitrification, results in the transformation of nitrate to gaseous N2, with smaller associated production of NOx and N2O. It is typically assumed that nitrogen fixation and denitrification were approximately balanced in the preindustrial biosphere ( [Galloway et al. 2004](https://escomp.github.io/ctsm-docs/versions/master/html/tech_note/References/CLM50_Tech_Note_References.html#gallowayetal2004)). It is likely that denitrification can occur within anaerobic microsites within an otherwise aerobic soil environment, leading to large global denitrification fluxes even when fluxes per unit area are rather low ([Galloway et al. 2004](https://escomp.github.io/ctsm-docs/versions/master/html/tech_note/References/CLM50_Tech_Note_References.html#gallowayetal2004)).

CLM includes a detailed representation of nitrification and denitrification based on the Century N model ([Parton et al. 1996](https://escomp.github.io/ctsm-docs/versions/master/html/tech_note/References/CLM50_Tech_Note_References.html#partonetal1996), [2001](https://escomp.github.io/ctsm-docs/versions/master/html/tech_note/References/CLM50_Tech_Note_References.html#partonetal2001); [del Grosso et al. 2000](https://escomp.github.io/ctsm-docs/versions/master/html/tech_note/References/CLM50_Tech_Note_References.html#delgrossoetal2000)). In this approach, nitrification of NH4+ to NO3\- is a function of temperature, moisture, and pH:

(2.22.2)[¶](#equation-22-2 "Permalink to this equation")\\\[f\_{nitr,p} =\\left\[NH\_{4} \\right\]k\_{nitr} f\\left(T\\right)f\\left(H\_{2} O\\right)f\\left(pH\\right)\\\]

where \\({f}\_{nitr,p}\\) is the potential nitrification rate (prior to competition for NH4+ by plant uptake and N immobilization), \\({k}\_{nitr}\\) is the maximum nitrification rate (10 % day\\(\\mathrm{-}\\)1, ([Parton et al. 2001](https://escomp.github.io/ctsm-docs/versions/master/html/tech_note/References/CLM50_Tech_Note_References.html#partonetal2001)), and _f(T)_ and _f(H)_2O) are rate modifiers for temperature and moisture content. CLM uses the same rate modifiers as are used in the decomposition routine. _f(pH)_ is a rate modifier for pH; however, because CLM does not calculate pH, instead a fixed pH value of 6.5 is used in the pH function of [Parton et al. (1996)](https://escomp.github.io/ctsm-docs/versions/master/html/tech_note/References/CLM50_Tech_Note_References.html#partonetal1996).

The potential denitrification rate is co-limited by NO\-3 concentration and C consumption rates, and occurs only in the anoxic fraction of soils:

(2.22.3)[¶](#equation-22-3 "Permalink to this equation")\\\[f\_{denitr,p} =\\min \\left(f(decomp),f\\left(\\left\[NO\_{3} ^{-} \\right\]\\right)\\right)frac\_{anox}\\\]

where \\({f}\_{denitr,p}\\) is the potential denitrification rate and _f(decomp)_ and _f(\[NO_3\- _\])_ are the carbon- and nitrate- limited denitrification rate functions, respectively, ([del Grosso et al. 2000](https://escomp.github.io/ctsm-docs/versions/master/html/tech_note/References/CLM50_Tech_Note_References.html#delgrossoetal2000)). Because the modified CLM includes explicit treatment of soil biogeochemical vertical profiles, including diffusion of the trace gases O2 and CH4 ([Riley et al. 2011a](https://escomp.github.io/ctsm-docs/versions/master/html/tech_note/References/CLM50_Tech_Note_References.html#rileyetal2011a)), the calculation of anoxic fraction \\({frac}\_{anox}\\) uses this information following the anoxic microsite formulation of [Arah and Vinten (1995)](https://escomp.github.io/ctsm-docs/versions/master/html/tech_note/References/CLM50_Tech_Note_References.html#arahvinten1995).

(2.22.4)[¶](#equation-22-4 "Permalink to this equation")\\\[frac\_{anox} =\\exp \\left(-aR\_{\\psi }^{-\\alpha } V^{-\\beta } C^{\\gamma } \\left\[\\theta +\\chi \\varepsilon \\right\]^{\\delta } \\right)\\\]

where _a_, \\(\\alpha\\), \\(\\beta\\), \\(\\gamma\\), and \\(\\delta\\) are constants (equal to 1.5x10\-10, 1.26, 0.6, 0.6, and 0.85, respectively), \\({R}\_{\\psi}\\) is the radius of a typical pore space at moisture content \\(\\psi\\), _V_ is the O2 consumption rate, _C_ is the O2 concentration, \\(\\theta\\) is the water-filled pore space, \\(\\chi\\) is the ratio of diffusivity of oxygen in water to that in air, and \\(\\epsilon\\) is the air-filled pore space ([Arah and Vinten (1995)](https://escomp.github.io/ctsm-docs/versions/master/html/tech_note/References/CLM50_Tech_Note_References.html#arahvinten1995)). These parameters are all calculated separately at each layer to define a profile of anoxic porespace fraction in the soil.

The nitrification/denitrification models used here also predict fluxes of N2O via a “hole-in-the-pipe” approach ([Firestone and Davidson, 1989](https://escomp.github.io/ctsm-docs/versions/master/html/tech_note/References/CLM50_Tech_Note_References.html#firestonedavidson1989)). A constant fraction (6 \* 10\\({}^{-4}\\), [Li et al. 2000](https://escomp.github.io/ctsm-docs/versions/master/html/tech_note/References/CLM50_Tech_Note_References.html#lietal2000)) of the nitrification flux is assumed to be N2O, while the fraction of denitrification going to N2O, \\({P}\_{N2:N2O}\\), is variable, following the Century ([del Grosso et al. 2000](https://escomp.github.io/ctsm-docs/versions/master/html/tech_note/References/CLM50_Tech_Note_References.html#delgrossoetal2000)) approach:

(2.22.5)[¶](#equation-22-5 "Permalink to this equation")\\\[P\_{N\_{2} :N\_{2} O} =\\max \\left(0.16k\_{1} ,k\_{1} \\exp \\left(-0.8P\_{NO\_{3} :CO\_{2} } \\right)\\right)f\_{WFPS}\\\]

where \\({P}\_{NO3:CO2}\\) is the ratio of CO2 production in a given soil layer to the NO3\- concentration, \\({k}\_{1}\\) is a function of \\({d}\_{g}\\), the gas diffusivity through the soil matrix:

(2.22.6)[¶](#equation-22-6 "Permalink to this equation")\\\[k\_{1} =\\max \\left(1.7,38.4-350\*d\_{g} \\right)\\\]

and \\({f}\_{WFPS}\\) is a function of the water filled pore space _WFPS:_

(2.22.7)[¶](#equation-22-16 "Permalink to this equation")\\\[f\_{WFPS} =\\max \\left(0.1,0.015\\times WFPS-0.32\\right)\\\]

