https://doi.org/10.5061/dryad.gf1vhhmw3

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 (NO₂), and O₃ 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 O₃ 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 NO₂ were measured by an EcoPhysics CLD-780TR analyzer equipped with an external NO₂ 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 + NO₂ 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 O₃ generated by a Hg-vapor lamp to the sample stream to convert NO to NO₂ before the sample entered the detector. Instrument gain and NO₂ conversion efficiency were determined by routinely adding a small flow of NO or NO₂ 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 CO₂ 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 m² m^-2 in the forested scenarios and about 1.8 m² m^-2in 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.