DOI: 10.5061/dryad.gmsbcc2n2
title: Nitrification and denitrification in the Community Land Model compared to observations at Hubbard Brook Forest

description: 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.
description: <b><i>Modifications to CLM5.0 at
 Hubbard Brook LTER</i></b>
 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 [<i>Lawrence et al.</i>, 2019].  Atmospheric
 CO<sub>2</sub> concentration (= 367 ppm), land use and N
 deposition (= 0.7 gN/m<sup>2</sup>/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.
   <i>1a)
 Increased nitrification (Parton)
 </i>
 We added an
 NH<sub>4</sub><sup>+</sup> mineralization-based
 term to the CLM5.0 formula for potential nitrification in accord with the
 <i>Parton et al.</i> [2001] equation, from which the formula
 is derived.   
 <i>2a) Increased nitrification
 (Zhang)</i> 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
 <i>(pH-4)</i><i>6</i>, 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   <i>1b and 2b) Reduced denitrification (Reduced Denit) </i> We reduced the [NO<sub>3</sub><sup>-</sup>]-limited and CO<sub>2</sub> 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).   <i>1c) Denitrification scaled to Nitrification (Denit=Nitrif/10) </i> We tested an alternative parameterization, building off modification 1a), to reduce the rate of denitrification.  In this alternative approach, we bypassed the <i>Del Grosso et al.</i> [2000] algorithm altogether and instead set potential denitrification equal to potential nitrification divided by 10.    <i>1bx) No N<sub>2</sub> fixation </i> We turned off N<sub>2</sub> 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 N<sub>2</sub> 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.   <i>3) Swap NO<sub>3</sub><sup>-</sup>  </i> The order of competition for mineral N between plants and soil microbes was switched such that they competed first for NO<sub>3</sub><sup>-</sup> and second for NH<sub>4</sub><sup>+</sup>.  This was a swap in the sense that the default CLM5.0 competition occurs in the opposite order, i.e., first for NH<sub>4</sub><sup>+</sup> then for NO<sub>3</sub><sup>-</sup>.  Aside from reversing that order, we made no other adjustments to the algorithms for potential nitrification and denitrification in modification 3.
description: # Nitrification and denitrification in the Community Land Model compared
 to observations at Hubbard Brook Forest Dataset DOI:
 [10.5061/dryad.gmsbcc2n2](10.5061/dryad.gmsbcc2n2) ## Description of the
 data and file structure All files for this dataset are available through
 Zenodo
 at [https://doi.org/10.5281/zenodo.4641366](https://doi.org/10.5281/zenodo.4641366)