Skip to main content

Nitrification and denitrification in the Community Land Model compared to observations at Hubbard Brook Forest

Cite this dataset

Nevison, Cynthia et al. (2021). Nitrification and denitrification in the Community Land Model compared to observations at Hubbard Brook Forest [Dataset]. Dryad.


Models of terrestrial system dynamics often include nitrogen (N) cycles to better represent N limitation of terrestrial carbon (C) uptake but simulating the fate of N in ecosystems has proven challenging. Here, key soil N fluxes and flux ratios from the Community Land Model version 5.0 (CLM5.0) are compared to an extensive set of observations from the Hubbard Brook Forest Long-Term Ecological Research (LTER) site in New Hampshire. Simulated fluxes include microbial immobilization and plant uptake, which compete with nitrification and denitrification, respectively, for available soil ammonium (NH4+) and nitrate (NO3-). In its default configuration, CLM5.0 predicts that both plant uptake and immobilization are strongly dominated by NH4+ over NO3-, and that the model ratio of nitrification:denitrification is approximately 1:1. In contrast, Hubbard Brook observations suggest that NO3- plays a more significant role in plant uptake and that nitrification could exceed denitrification by an order of magnitude. Modifications to the standard CLM5.0 at Hubbard Brook indicate that a simultaneous increase in the competitiveness of nitrifying microbes for NH4+ and reduction in the competitiveness of denitrifying bacteria for NO3- are needed to bring soil N flux ratios into better agreement with observations. Such adjustments, combined with evaluation against observations, may help improve confidence in present and future simulations of N limitation on the C cycle, although C fluxes such as gross primary productivity (GPP) and net primary productivity (NPP) are less sensitive to the model modifications than soil N fluxes.


Modifications to CLM5.0 at Hubbard Brook LTER

The Community Land Model version 5.0 (CLM5.0) was modified at a single grid cell corresponding to the Hubbard Brook Experimental Forest, a northern hardwood forest site in the White Mountain National Forest in New Hampshire USA (43°56´N, 71°45´W).  The purpose was to test alternative parameterizations for nitrification and denitrification in CLM5.0.  The CLM5.0 simulations use site-level present day meteorological (from GSWP3 v. 1) and N deposition inputs, created by extracting the single grid cell values from the global gridded forcing data for CLM5.0 [Lawrence et al., 2019].  Atmospheric CO2 concentration (= 367 ppm), land use and N deposition (= 0.7 gN/m2/yr) were fixed at year 2000 conditions throughout the simulations, while meteorological forcings were cycled over 1991-2010.  The plant functional type of the grid cell was prescribed as 100% broadleaf deciduous temperate forest.  Spin-up for each simulation was run in accelerated decomposition mode for 400 years, followed by a final spin-up for 200 years, of which the last 20 years were sampled for the results archived here.  The N fluxes varied interannually but displayed no obvious drift or trends over these 20 years.  

We tested a variety of new parameterizations, described in detail in the text, in which model nitrification and/or denitrification was revised based on observed empirical relationships.


1a) Increased nitrification (Parton)

We added an NH4+ mineralization-based term to the CLM5.0 formula for potential nitrification in accord with the Parton et al. [2001] equation, from which the formula is derived. 


2a) Increased nitrification (Zhang)

In an alternative approach to boosting nitrifier competitiveness, we implemented a parameterization in which we parameterized potential nitrification as a direct linear function of gross mineralization multiplied by a scalar computed as (pH-4)6, reflecting the empirical linear relationship found by Zhang et al. [2018].  Since CLM5.0 has a uniform default pH of 6.5, this scalar was effectively 0.42


1b and 2b) Reduced denitrification (Reduced Denit)

We reduced the [NO3-]-limited and CO2 respiration-limited equations for potential denitrification by a factor of 100 and 10, respectively.  We ran two reduced denitrification modifications: 1b) Reduced Denitrification with Parton nitrification scheme (from modification 1a) and 2b) Reduced Denitrification with Zhang nitrification scheme (from modification 2a).


1c) Denitrification scaled to Nitrification (Denit=Nitrif/10)

We tested an alternative parameterization, building off modification 1a), to reduce the rate of denitrification.  In this alternative approach, we bypassed the Del Grosso et al. [2000] algorithm altogether and instead set potential denitrification equal to potential nitrification divided by 10. 


1bx) No N2 fixation

We turned off N2 fixation (beginning from year 1 in the spin-up phase) due to concern that CLM adds an excessive amount of N to northern temperate ecosystems such as Hubbard Brook that lack symbiotic N2 fixers and where heterotrophic N fixation rates are low.   N deposition was left turned on in this experiment.  Modification 1bx was performed with the 1b) modifications (Parton increased nitrification and Reduced Denitrification adjustments) also turned on.


3) Swap NO3-  

The order of competition for mineral N between plants and soil microbes was switched such that they competed first for NO3- and second for NH4+.  This was a swap in the sense that the default CLM5.0 competition occurs in the opposite order, i.e., first for NH4+ then for NO3-.  Aside from reversing that order, we made no other adjustments to the algorithms for potential nitrification and denitrification in modification 3.


National Science Foundation, Award: 0919047: Division of Environmental Biology

National Science Foundation, Award: Cooperative Agreement No. 1852977