Denitrification

Denitrification can optionally be simulated (see switch Denitrification). In the simplified approach, the denitrification i.e. the conversion of soluble nitrate in the soil to gaseous nitrogen leaving the soil, N_NO3→Denit, is calculated as:

                           (6.37)

where d_pot is a parameter and f(T), f(θ) and f(N_NO3Cons) are response functions for soil temperature, soil moisture and nitrate concentration in the soil. A coefficient, d_dist(Δz), adjusts the potential denitrification rate for each soil layer. The variation of d_dist(Δz) with depth is determined by the switch Denit depth distribution Either the denitrification rate can be given as a table (“Table”), it can be distributed evenly in the soil profile (“Constant”), it can decrease linearly from the top layer (“Linear”) or finally it can decrease exponentially from the top layer (“Exponential”). The parameters used in these calculations are d_z and d_exp.

The switch Denit temp response determines the temperature response, f(T), described in the section Common abiotic functions.

The soil moisture response function, f(θ), looks different depending soil moisture content:

1.  θ  = θ_s

2.  θ_s - θ  < pθ_Dp

 

 

3.  θ_s - θ  > pθ_Dp
                                                     (6.38)

 

where pθ_DRange and p_θDp are parameters and the variables, θ_s and θ, are the soil moisture content at saturation and the actual soil moisture content respectively, described in the section “Soil Water Processes”.

The response function for nitrate concentration in the soil, f(N_NO3Cons), is calculated as:
                                   (6.39)

 

where d_Nhalfsat is a parameter. See viewing function Denitrification Nitrate Response.

If denitrifying microbes are calculated explicitly the denitrification rate is a function of the amount of denitrifying microbials, N_micrDN, and their activity, M_activity. The whole denitrification process consists of a chain of reactions where nitrogen in the form of nitrate is converted by microbial activity into nitrous gases. In this section processes concerning nitrogen in the forms of NO₃, NO₂, NO, N₂O and N₂ formed under anaerobic conditions are described. The following section, Gas , deals with the diffusion of the nitrous gases NO, N₂O and N₂ from the anaerobic fractions of the soil to the aerobic fractions and subsequently the transport through the soil profile into the atmosphere. The amount of nitrogen as nitrate (NO₂) and nitrous gases is not included in the overall nitrogen balance of the soil profile due to the low concentrations in these pools. A schematic image of nitrogen in the different anaerobic nitrogen pools, i.e. N_NO3, N_AnNO2, N_AnNO, N_AnN2O and N_AnN2, and the fluxes between these pools is given in Figure 5.0.3.

 

Figure 5.0.3. Denitrification chain when microbes are simulated explicitly.

The concentrations of anaerobic NO₃, NO₂, NO and N₂O are used in several calculations. For NO₃ the concentration, N_NO3Conc, is calculated by dividing the amount of nitrate, N_NO3, by the soil water content for each layer. In the other cases the concentration is calculated by:

                                                                                         (6.40)

 

where θ(z) is the soil water content and f_Anvol is the volumetric anaerobic fraction of each soil layer. This equation is used to calculate N_AnNOConc and N_AnN2OConc by exchanging N_AnNO2 to N_AnNO and N_AnN2O respectively.

Denitrifying microbes consume nitrogen from all anaerobic nitrogen pools except for N₂. This consumption results in growth and respiration of the microbes, i.e. out flux of nitrogen from the anaerobic nitrogen pools. The losses of nitrogen from the anaerobic nitrogen pools due to microbial growth is calculated as:

             (6.41)

where d_growthNO3 is a growth parameter and f(C_DO,dnCons) and f(N_NxOyConc) are response functions for dissolved organics and nitrogen concentration respectively. This equation can be used analogously to calculate N_NO2→micrDN, N_NO→micrDN and N_N2O→micrDN by exchanging d_growthNO3 to d_growthNO2, d_growthNO and d_growthN2O. For N_N2O→micrDN eq. (6.41) is further modified by multiplying the equation with an inhibition response function for the nitrate content, f(N_NO3Concinhib), calculated as:

                                                                     (6.42)

 

 

where d_inhihrate is the denitrification inhibition half rate.

The response function for dissolved organics concentration, f(C_DO,dnCons), is calculated as:

                                                                     (6.43)

 

 

where d_hrateDOC is the half rate for dissolved organic carbon and θ is the soil moisture content.

The response function for nitrogen concentration is calculated as:

                                                                      (6.44)

 

 

where d_hrateNxOy is the half rate for nitrogen concentration. N_NxOyConc is the nitrogen concentration, N_AnNO3Conc, N_AnNO2Conc, N_AnNOConc or N_AnN2OConc for N_NO3→micrDN, N_NO2→micrDN, N_NO→micrDN and N_N2O→micrDN respectively.

Each of the nitrogen pools looses nitrogen through microbial maintenance and growth respiration. The respiration loss in one pool will form an input to the next nitrogen pool in the denitrification chain, i.e. the production of N₂, N₂O, NO or NO₂ (see Figure 5.0.3). These fluxes are calculated as:

                         

             (6.45)

                           

where the index rg stands for growth respiration and rm stands for maintenance respiration. Note that the fluxes are either limited by the rate as estimated from the microbial activity or from the amount of gas available in the anaerobic storage.

The total denitrification rate is the sum of the production of N₂, N₂O and NO, i.e.:

                     (6.46)

The growth respiration for N₂O, NO, NO₂ and NO₃ is calculated as:

                                                           (6.47)

where d_effNO3 is an efficiency parameter. The same equation is used to calculate growth respiration for N₂O, NO and NO₂ by exchanging N_NO3→micrDN to N_{AnNO2→micrDN}, N_{AnNO→micrDN} and N_{AnN2O→micrDN}, and d_effNO3 to d_effNO2, d_effNO and d_effN2O respectively.

The maintenance respiration for N₂O, NO, NO₂ and NO₃ is calculated as:

                                                                                             (6.48)

 

 

where d_rcNO3 is a respiration coefficient and N_AnTot is the total nitrogen content in the N₂O, NO, NO₂ and NO₃ pools. The same equation is used to calculate growth respiration for N₂O, NO and NO₂ by exchanging N_NO3 to N_AnN2O, N_AnNO and N_AnNO2 and d_rcNO3 to d_rcN2O, d_rcNO and d_rcNO2 respectively.

The total biomass of the denitrifiers, N_micrDN, is dependent of their growth and their death rates.

                                           (6.49)

 

 

Microbial growth, M_growth,DN, is the sum of all the flows from the anaerobic nitrogen pools to the microbial pool as calculated by eq. (6.41). The death rate, M_death,DN is calculated as:

                                                                     (6.50)

where d_denitrdie is the death rate coefficient.

Microbial activity, M_activity, is calculated as:

                                    (6.51)

where d_actratecoef is the activity rate coefficient, and f(pH) and f(N_AnTot) are response functions for soil pH and total nitrogen content in the anaerobic nitrogen pools respectively. The switch Denit temp response determines the temperature response, f(T), described in the section Common abiotic functions.

The response function for soil pH is calculated as:

                                                                            (6.52)

 

 

where d_pHhrate is the pH half rate and d_pHshape is a shape coefficient. See viewing function Denitrification pH Response.

The response function for total nitrogen content in the anaerobic nitrogen pools is calculated as:

                                                                               (6.53)

 

 

where d_hrateNxOy is a half rate coefficient.