2.23. External Nitrogen Cycle
2.23.1. Overview
In addition to the relatively rapid cycling of nitrogen within the plant – litter – soil organic matter system, CLM also represents several processes which couple the internal nitrogen cycle to external sources and sinks. Inputs of new mineral nitrogen are from atmospheric deposition and biological nitrogen fixation. Losses of mineral nitrogen are due to nitrification, denitrification, leaching, and losses in fire. While the short-term dynamics of nitrogen limitation depend on the behavior of the internal nitrogen cycle, establishment of total ecosystem nitrogen stocks depends on the balance between sources and sinks in the external nitrogen cycle (Thomas et al. 2015).
CLM represents inorganic N transformations based on the Century N-gas model; this includes separate NH4+ and NO3- pools, as well as environmentally controlled nitrification and denitrification rates that is described below.
2.23.2. Atmospheric Nitrogen Deposition
CLM uses a single variable to represent the total deposition of mineral nitrogen onto the land surface, combining wet and dry deposition of NOy and NHx as a single flux (\({NF}_{ndep\_sminn}\), gN m-2 s-1). This flux is intended to represent total reactive nitrogen deposited to the land surface which originates from the following natural and anthropogenic sources (Galloway et al. 2004): formation of NOx during lightning, NOxand NH3 emission from wildfire, NOx emission from natural soils, NH3 emission from natural soils, vegetation, and wild animals, NOx and NH3 emission during fossil fuel combustion (both thermal and fuel NOx production), NOx and NH3 emission from other industrial processes, NOx and NH3 emission from fire associated with deforestation, NOx and NH3 emission from agricultural burning, NOx emission from agricultural soils, NH3 emission from agricultural crops, NH3 emission from agricultural animal waste, and NH3 emission from human waste and waste water. The deposition flux is provided as a spatially and temporally varying dataset (see section 2.2.3.1 for a description of the default input dataset).
The nitrogen deposition flux is assumed to enter the NH4+ pool, and is vertically distributed throughout the soil profile. Although N deposition inputs include both oxidized and reduced forms, CLM5.0 and CLM6.0 only read in total N deposition. This approach is held over from CLM4.0, which only represented a single mineral nitrogen pool, however, real pathways for wet and dry nitrogen deposition can be more complex than currently represented in CLM, including release from melting snowpack and direct foliar uptake of deposited NOy (Tye et al. 2005; Vallano and Sparks, 2007).
As of CLM5.0, in off line (uncoupled) simulations monthly estimates of N deposition are provided, In coupled simulations, N depositions fluxes are passed to the land model at the frequency of the time step (every half hour) through the coupler.
2.23.3. Biological Nitrogen Fixation
The fixation of new reactive nitrogen from atmospheric N2 by soil microorganisms is an important component of both preindustrial and modern-day nitrogen budgets, but a mechanistic understanding of global-scale controls on biological nitrogen fixation (BNF) is still only poorly developed (Cleveland et al. 1999; Galloway et al. 2004). CLM5 introduced a new representation of biological nitrogen fixation (BNF) that includes both symbiotic and free-living (asymbiotic) components. The symbiotic component is calculated using the Fixation and Uptake of Nitrogen (FUN) model (chapter 2.19) to calculate the carbon cost of nitrogen fixation and the amount of nitrogen acquired through symbiotic fixation. This nitrogen is immediately available to plants. One drawback to this approach is that under elevated CO2, when plant productivity increases, FUN predicts increased rates of symbiotic nitrogen fixation, which may not be realistic (Wieder et al. 2019; Kou-Giesbrecht et al. 2025). Future work should address this issue.
The free-living component is calculated using an empirical relationship following Cleveland et al. (1999) who suggested using either evapotranspiration rate or net primary productivity to predicts rates of BNF for natural vegetation. CLM5.0 adopted the evapotranspiration approach to calculate asymbiotic, or free-living, N fixation. This function has been modified from the Cleveland et al. (1999) estimates to provide lower estimate of free-living nitrogen fixation in CLM (\({CF}_{ann\_ET}\), mm yr-1). This moves away from the NPP approach used in CLM4.0 and 4.5 and avoids unrealistically increasing freeliving rates of N fixation under global change scenarios (Wieder et al. 2015). The expression used is:
Where \({NF}_{nfix,sminn}\) (gN m-2 s-1) is the rate of free-living nitrogen fixation, calculated on a per second basis. As with atmospheric N deposition, free-living N inputs are added directly to the soil NH4+ pool.
2.23.4. Nitrification and Denitrification Losses of Nitrogen
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). 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).
CLM includes a detailed representation of nitrification and denitrification based on the Century N model (Parton et al. 1996, 2001; del Grosso et al. 2000). In this approach, nitrification of NH4+ to NO3- is a function of temperature, moisture, and pH:
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), 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. Although new surface datasets in CLM6.0 provide gridded estimates for soil pH, this information is not currently being used in the model. Instead, a fixed pH value of 6.5 is used in the pH function of Parton et al. (1996).
The potential denitrification rate is co-limited by NO-3 concentration and C consumption rates, and occurs only in the anoxic fraction of soils:
where \({f}_{denitr,p}\) is the potential denitrification rate and f(decomp) and f([NO3- ]) are the carbon- and nitrate- limited denitrification rate functions, respectively, (del Grosso et al. 2000). 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), the calculation of anoxic fraction \({frac}_{anox}\) uses this information following the anoxic microsite formulation of Arah and Vinten (1995).
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). 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). A constant fraction (6 * 10\({}^{-4}\), Li et al. 2000) 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) approach:
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:
and \({f}_{WFPS}\) is a function of the water filled pore space WFPS:
2.23.5. Leaching Losses of Nitrogen
Soil mineral nitrogen remaining after plant uptake, immobilization, and denitrification is subject to loss as a dissolved component of hydrologic outflow from the soil column (leaching). This leaching loss (\({NF}_{leached}\), gN m-2 s-1) depends on the concentration of dissolved mineral (inorganic) nitrogen in soil water solution (DIN, gN kgH2O), and the rate of hydrologic discharge from the soil column to streamflow (\({Q}_{dis}\), kgH2O m-2 s-1, section 2.7.5), as
DIN is calculated assuming that a constant fraction (sf, proportion) of the remaining soil mineral N pool is in soluble form, and that this entire fraction is dissolved in the total soil water. For the Century- based formulation in CLM5.0, the leaching acts only on the NO3- pool (which is assumed to be 100% soluble), while the NH4+ pool is assumed to be 100% adsorbed onto mineral surfaces and unaffected by leaching. DIN is then given as
where \({WS}_{tot\_soil}\) (kgH2O m-2) is the total mass of soil water content integrated over the column. The total mineral nitrogen leaching flux is limited on each time step to not exceed the soluble fraction of \({NS}_{sminn}\)
2.23.6. Alternative way of evaluating the Leaching Losses of Nitrogen
Leaching losses of \({NO}_{3}^{-}\) are notably low in CLM because of low rates of nitrification and high plant N uptake (Houlton et al. 2015, Nevison et al. 2022). Future work should address these biases.
Towards this end, the previous leaching mechanism is not designed for describing the vertical transport of \({NO}_{3}^{-}\) in soil, an alternative way to evaluate the vertical convective, diffusive, and dispersive of dissolved \({NO}_{3}^{-}\) in soil is provided in (Luo et al. 2025). This is option is not active by default in CLM6.0, but can be activated by the user. To obtain the vertical profile of soil mineral N after vertical movement of each timestep, the vertical transport equation is summarized in (2.23.11).
where \(NS_{sminn} (gN m^{-3})\) is the soil \({NO}_{3}^{-}\) concentration in each layer, \(J (gN m^{-2} s^{-1})\) is the different vertical transport terms (\(J_{convective}, J_{diffusive}, J_{dispersive}\)) between two soil layers, and \(S\) is the sources or sinks fluxes. Different transport terms are explained below
where \(q_{out} (mH_{2}Os^{-1})\) is the darcy flow of water, \(\theta (m^3H_{2}O m^{-3}soil)\) is the soil water content.
where \(\partial SN_{sminn}/ \partial z\) is the concentration gradient, \(D_{aq}\) is the nitrate aqueous diffusion coefficient which is taken as \(1.7*10^{-9} m^{2}s^{-1}\), and \(\phi (m^3m^{-3})\) is soil porosity.
where \(D_{dis}\) is the dispersion coefficient, which equal to \(L_{dis} q_{out} \theta ^{-1}\), for simplicity reasons, \(L_{dis}\) is taken as 0.1 meter.
Finally, the classical convective-diffusion algorithm described in (Patankar.2018) is used to discrete and solve the \({NO}_{3}^{-}\) vertical transport (2.23.11) in soils. The advantage of this leaching mechanism is the soil \({NO}_{3}^{-}\) is able to move vertically (both upward or downward) with soil water movement, the mass of \({NO}_{3}^{-}\) reaches bedrock layer is finally taken as the \(NF_{leached}\).
2.23.7. Losses of Nitrogen Due to Fire
The final pathway for nitrogen loss is through combustion, also known as pyrodenitrification. Detailed equations are provided, together with the effects of fire on the carbon budget, in Chapter 2.25. It is assumed in CLM-CN that losses of N due to fire are restricted to vegetation and litter pools (including coarse woody debris). Loss rates of N are determined by the fraction of biomass lost to combustion, assuming that most of the nitrogen in the burned biomass is lost to the atmosphere (Schlesinger, 1997; Smith et al. 2005). It is assumed that soil organic matter pools of carbon and nitrogen are not directly affected by fire (Neff et al. 2005).