DOI: 10.5061/dryad.gf1vhhmw3
title: Data from: Sensitive response of atmospheric oxidative capacity to the uncertainty in the emissions of nitric oxide (NO) from soils in Amazonia

description: Soils are a major source of nitrogen oxides, which in the atmosphere help
 govern its oxidative capacity. Thus the response of soil nitric oxide (NO)
 emissions to forcings such as warming or forest loss has a meaningful
 impact on global atmospheric chemistry. We find that the soil emission
 rate of NO in Amazonia from a common inventory is biased low by at least
 an order of magnitude in comparison to tower-based observations.
 Accounting for this regional bias decreases the modeled global methane
 lifetime by 1.4% to 2.6%. In comparison, a fully deforested Amazonia,
 representing a 37% decrease in global emissions of isoprene, decreases
 methane lifetime by at most 4.6%, highlighting the sensitive response of
 oxidation rates to changes in emissions of NO compared to those of
 terpenes. Our results demonstrate that improving our understanding of soil
 NO emissions will yield a more accurate representation of atmospheric
 oxidative capacity.
description: Flux Data from Tapajos National Forest: Mixing
 ratios of NO, nitrogen dioxide (NO<sub>2</sub>), and
 O<sub>3</sub> were measured at the Tapajos National Forest
 from January to August of 2015. Ambient air in excess of instrument
 requirements was drawn in at 4-6 liters per minute (lpm) through inlets
 located at eight heights off of the tall tower (0.91, 3.05, 10.42, 19.57,
 28.71, 39.41, 53.04, 62.24 m above the ground). The NO chemiluminescence
 analyzer drew ~2 lpm and the O<sub>3</sub> analyzer drew ~1
 lpm. Excess flow was pulled by a bypass pump to maintain constant pressure
 measured by a pressure controller. The inlets were sampled in sequence for
 4 minutes each. NO and NO<sub>2</sub> were measured by an
 EcoPhysics CLD-780TR analyzer equipped with an external
 NO<sub>2</sub> photolysis cell using a Hamamatsu LED with peak
 wavelength at 365 nm (Pollack et al., 2010). The photolysis cell was
 toggled on and off at 60 s intervals to provide both NO and NO +
 NO<sub>2</sub> measurement at each sample height. All
 instruments were housed in an air conditioned shed near the base of the
 tower. Instrument background signal was measured by periodically adding
 O<sub>3</sub> generated by a Hg-vapor lamp to the sample
 stream to convert NO to NO<sub>2</sub> before the sample
 entered the detector. Instrument gain and NO<sub>2</sub>
 conversion efficiency were determined by routinely adding a small flow of
 NO or NO<sub>2</sub> standard to the sample inlet.
 Climate model simulation output: We performed
 six sets of coupled biosphere-atmospheric chemistry simulations using the
 CESM2-CAM-Chem global model (Danabasoglu et al., 2020; Emmons et al.,
 2010) with active biogeochemistry at ~1° spatial resolution. Three
 separate sets were initialized with forests in Amazonia in a state that is
 representative of the early 1980s. The other three were initialized with
 Amazonia that was effectively devoid of trees by changing the plant
 functional type to a grassland over the region (from 16°S to 8°N and from
 48°W to 78°W), as illustrated in <strong>Figure S1</strong>.
 Leaf area is calculated prognostically, as are other carbon fluxes and
 pools, however, atmospheric CO<sub>2</sub> concentrations are
 specified based on observed concentrations for each year. The removal of
 trees in the model changes physical fluxes of energy and water, as well as
 carbon and chemical species (e.g. isoprene). The model calculated total
 leaf area index is about 6.5 m<sup>2</sup>
 m<sup>-2</sup> in the forested scenarios and about 1.8
 m<sup>2</sup> m<sup>-2</sup> in the deforested
 scenario, wherein the emission rates of biogenic terpenes including
 isoprene and monoterpenes are negligible. For each of the forested and
 deforested Amazonia scenarios we calculated three sets of simulations
 representing different soil NO conditions: (i) baseline soil NO emission
 rate based on the work of <em>Yienger and Levy</em> (1995),
 and factors of (ii) 10´ that rate, and (ii) 20´ of that rate. All
 simulation scenarios span from 2001 to 2005, except for the forested
 baseline soil NO scenario which spans from 1980 to 2015. All aspects of
 the model except for plant type and soil NO fluxes within the Amazon vary
 transiently across years based on observed quantities, including
 greenhouse gas concentrations, sea surface temperatures, and land cover
 change outside the Amazon basin (“FCfireHIST” compset in CESM2).
description: # Data from: Sensitive response of atmospheric oxidative capacity to the
 uncertainty in the emissions of nitric oxide (NO) from soils in Amazonia
 There are two data types
 included in this dataset. 1\. Flux data from Tapajos National Forest 2\.
 Climate model simulation output ## Description of the data and file
 structure **1. Flux data from Tapajos National Forest** Data collected at
 Tapajos National Forest is presented in a space delimited text file that
 contains the following columns as well as a header row: year (yyyy) month
 (mo) day (dd) hour (hh) minute (mm) second (ss) mixing ratio of NO
 (NO_ppt) mixing ratio of NO2 (NO2_ppt) mixing ratio of Ozone (O3_ppb)
 height in the canopy of the observation (height_m) Mixing ratios of NO,
 nitrogen dioxide (NO<sub>2</sub>), and
 O<sub>3</sub> were measured at the Tapajos National Forest
 from January to August of 2015. Ambient air in excess of instrument
 requirements was drawn in at 4-6 liters per minute (lpm) through inlets
 located at eight heights off of the tall tower (0.91, 3.05, 10.42, 19.57,
 28.71, 39.41, 53.04, 62.24 m above the ground). The NO chemiluminescence
 analyzer drew ~2 lpm and the O<sub>3</sub> analyzer drew ~1
 lpm. Excess flow was pulled by a bypass pump to maintain constant pressure
 measured by a pressure controller. The inlets were sampled in sequence for
 4 minutes each. NO and NO<sub>2</sub> were measured by an
 EcoPhysics CLD-780TR analyzer equipped with an external
 NO<sub>2</sub> photolysis cell using a Hamamatsu LED with peak
 wavelength at 365 nm (Pollack et al., 2010). The photolysis cell was
 toggled on and off at 60 s intervals to provide both NO and NO +
 NO<sub>2</sub> measurement at each sample height. All
 instruments were housed in an air conditioned shed near the base of the
 tower. Instrument background signal was measured by periodically adding
 O<sub>3</sub> generated by a Hg-vapor lamp to the sample
 stream to convert NO to NO<sub>2</sub> before the sample
 entered the detector. Instrument gain and NO<sub>2</sub>
 conversion efficiency were determined by routinely adding a small flow of
 NO or NO<sub>2</sub> standard to the sample inlet. Missing
 data code: NaN **2. Climate model simulation output.** We present data
 from 6 experiments and 1 baseline run. All simulations have time varying
 forcing (aerosols, greenhouse gasses, human land use, sea surface
 temperatures) and prognostic atmospheric chemistry. We use a coupled
 biosphere-atmospheric chemistry model, CESM2-CAM-Chem global model
 (Danabasoglu et al., 2020; Emmons et al., 2010) with active
 biogeochemistry at ~1° spatial resolution. All simulation scenarios span
 from 2001 to 2005, except for the forested baseline soil NO scenario which
 spans from 1980 to 2015. All aspects of the model except for plant type
 and soil NO fluxes within the Amazon vary transiently across years based
 on observed quantities, including greenhouse gas concentrations, sea
 surface temperatures, and land cover change outside the Amazon basin
 (“FCfireHIST” compset in CESM2). Three separate sets were initialized with
 forests in Amazonia in a state that is representative of the early 1980s
 (constantAmazon). The other three (deforestAmazon) were initialized with
 Amazonia that was effectively devoid of trees by changing the plant
 functional type to a grassland over the region (from 16°S to 8°N and from
 48°W to 78°W), as illustrated in Fig. S1 of the related manuscript (Lee et
 al. linked manuscript). Leaf area is calculated prognostically, as are
 other carbon fluxes and pools, however, atmospheric CO<sub>2
 </sub>concentrations are specified based on observed concentrations
 for each year. The removal of trees in the model changes physical fluxes
 of energy and water, as well as carbon and chemical species (e.g.
 isoprene). The model calculated total leaf area index is about 6.5
 m<sup>2</sup> m<sup>-2</sup> in the forested
 scenarios and about 1.8 m<sup>2</sup>
 m<sup>-2</sup>in the deforested scenario, wherein the emission
 rates of biogenic terpenes including isoprene and monoterpenes are
 negligible. For each of the forested and deforested Amazonia scenarios we
 calculated three sets of simulations representing different soil NO
 conditions: (i) baseline soil NO emission rate based on the work of
 *Yienger and Levy* (1995), and factors of (ii) 10X that rate, and (ii) 20X
 of that rate. Experiment names: TransientAMIP_defaultPlants_CHEM2
 TransientAMIP_constantAmazon_10xNOsoil_CHEMFIRE
 TransientAMIP_deforestAmazon_10xNOsoil_CHEMFIRE
 TransientAMIP_constantAmazon_20xNOsoil_CHEMFIRE
 TransientAMIP_deforestAmazon_20xNOsoil_CHEMFIRE
 TransientAMIP_constantAmazon_CHEMFIRE
 TransientAMIP_deforestAmazon_CHEMFIRE Files are provided packaged into
 tarballs, with one file for land output and one file for atmospheric
 output for each simulation. The file format is netcdf and the metadata
 contains descriptions of the variable names and units. Within each tarball
 there is one netcdf file for each variable. ## Code/Software The CESM2
 climate model can be accessed
 [here](https://www.cesm.ucar.edu/models/cesm2).