global-trawling-CO2

Code and data for refinement of the benthic trawling CO₂ emissions estimate originally presented in Sala et al., 2021. Protecting the global ocean for biodiversity, food and climate. Nature 592, 397–402. These calculations appear in the preprint Atmospheric carbon emissions from benthic trawling depend on water depth and ocean circulation, which has been submitted to EarthArXiv pending publication elsewhere. Calculations and data pertaining to other animal-mediated ocean carbon fluxes, including an analysis of the possible climate impacts from new benthic trawling in the emerging Arctic and support for a separate review (in prep) of zoogeochemical carbon fluxes in the ocean, are in this repository.

Raw, unmodified data and files

• The files in data/global_trawling/raw/sala_et_al_2021 are from Sala et al., 2021. Protecting the global ocean for biodiversity, food and climate. Nature 592, 397–402. Data files were retrieved from https://doi.org/10.25349/D9N89M on June 6, 2022. Resolution of the CO2 flux dataset (in co2_efflux.tif is 1 km². Resolution of both of the other two trawling-related datasets (bottom_trawling_Ia.tif and carbon_ranking.tif is 50 km².)

• The files in data/global_trawling/raw/FMI_world_EEZ_boundaries_v11 represent version 11 of the Flanders Marine Institute's global exclusive economic zone (EEZ) dataset. Data files were retrieved from https://www.vliz.be/en/imis?dasid=6316&doiid=386 on August 4, 2022.

• The GeoTIFF in data/global_trawling/raw/SRTM30_PLUS_v8 is version 8 of the SRTM30 digital elevation model, a 1-km resolution global DEM that includes ocean bathymetry. Retrieved from https://nextcloud.eatlas.org.au/apps/sharealias/a/world_e-atlas-ucsd_srtm30-plus_v8-tif on August 5, 2022. The SRTM30 DEM is described here: https://eatlas.org.au/data/uuid/80301676-97fb-4bdf-b06c-e961e5c0cb0b

• The dataset (.mat format) in data/global_trawling/raw/UCSD_Argo_MLD_climatology is the April 2022 version of the UCSD monthly mixed layer depth climatology, derived from Argo float profiles. Retrieved from http://mixedlayer.ucsd.edu/data/Argo_mixedlayers_monthlyclim_04142022.mat on August 19, 2022. The dataset is described here: http://mixedlayer.ucsd.edu

• The files "fseq_OCIM2_48L.mat" and "fseq_OCIM2_48L.nc" in data/global_trawling/raw/siegel_et_al_2021_v2 are from Siegel et al., 2021. Assessing the sequestration time scales of some ocean-based carbon dioxide reduction strategies. Environ. Res. Lett. 16 104003. The files contain the same data in MATLAB and NetCDF formats and were retrieved from https://doi.org/10.6084/m9.figshare.15228690.v2 on June 6, 2022. Per the published paper, model resolution is 2 degrees with 48 vertical levels. Update: These files are not stored on GitHub due to size. User replicating this analysis will have to download the datasets from the figshare link and then move the files to the correct location.

• The file "plot_sequestration_fraction.m" in data/global_trawling/raw/siegel_et_al_2021_v2 is the original, unmodified MATLAB script that Siegel et al. provided along with the data files containing the sequestration fractions. A modified version of this file, global_trawling/gen_fracs_to_constrain_trawlCO2.m, was used to pull out the necessary benthic sequestration fractions for the analysis using the three R scripts in global_trawling.

Scripts

Shell scripts for AWS provisioning

• The shell scripts still live here.

Global benthic trawling reanalysis

• The R and MATLAB scripts global_trawling/01_ConstrainCO2Flux_genSiegelMetaData.m, global_trawling/02_ConstrainCO2Flux_IO.R, global_trawling/03_ConstrainCO2Flux_coordMatch.R, global_trawling/04_ConstrainCO2Flux_genTrawlSeqFracs.m, global_trawling/05_ConstrainCO2Flux_adjFlux_extended.R, global_trawling/06_ConstrainCO2Flux_adjFlux_MLDvalidation.R, global_trawling/07_ConstrainCO2Flux_adjFlux_EEZs.R, and global_trawling/08_ConstrainCO2Flux_plots_and_tables.R are the workhorse scripts for the benthic trawling reanalysis. They should be run in order, with the note that some of the library() calls and setting of working directory are repetitive. The R scripts assume that the objects generated in the previous scripts are still in the R environment. global_trawling/09_ConstrainCO2Flux_getSAUdata.R is a helper script to retrieve Sea Around Us data using the SAU API. The rsearoundus package seems to have disappeared from CRAN but the functions in the helper script were copied from the source files still available on Aug. 25, 2022 at https://github.com/robsalasco/rseaaroundus

Outputs and derived data

• The files in data/global_trawling/derived/benthic_seqfractions contain the applicable sequestration fractions for the indicated year(s) plus necessary metadata, pulled from the original Siegel et al. model output using the scripts global_trawling/01_ConstrainCO2Flux_genSiegelMetaData.m and global_trawling/04_ConstrainCO2Flux_genTrawlSeqFracs.m. fseq_bottom.multyears.RData is an R data object containing the necessary fractions for years 1-200 in one-year increments, plus years 300-1000 in 100-year increments. This object was assembled from the series of seven .mat files beginning with fseq_bottom_multyears_1of7.mat, which were created and exported using global_trawling/04_ConstrainCO2Flux_genTrawlSeqFracs.m. trawlYears.csv is a list of the years represented in this 3-D array, corresponding to the 3rd dimension of the array. The other files contain self-explanatory metadata/model domain parameters for the Siegel et al. OCIM48 model.

• The files in data/global_trawling/derived/output represent the outputs. Specifically:

  • coord.matches.NonZero.RData is an R data object containing the indices (and corresponding coordinates) of the geographically closest data points in the Siegel et al. OCIM model output to the locations of the data points in the Sala et al. dataset which represent non-zero values of CO₂ flux. These matches were generated using 03_ConstrainCO2Flux_coordMatch.R.

  • Sala_et_al_trawlTiming_results.csv contains the "timing" output from the sediment disturbance model presented in the Sala et al. paper (remineralization of 1.47 Pg CO₂ in the "first" year after commencement of trawling, declining to a steady rate of 0.58 Pg CO₂ yr^-1 at year 10 and beyond); this .csv file captures the values in the object results that is produced beginning on line 119 in this script.

  • adjCO2efflux_global_PgCO2_yr.csv contains adjusted global estimates of CO₂ emissions to the atmosphere in a given year n following a one-time, 1.47 Pg remineralization of CO₂ from sediment to bottom water in year 0 (as assumed by Sala et al.). The file includes adjusted (using the Siegel et al. sequestration fractions) estimates for several bottom depth fractions, and well as some unadjusted estimates for the same depth fractions. adjCO2efflux_global_PgCO2_yr_byEEZ.csv contains year-by-year estimates broken down by exclusive economic zone (EEZ) of the countries responsible for most of the world's benthic trawling.

  • adjCO2efflux_global_PgCO2_cumulative.csv contains cumulative global emissions estimates of CO₂ to the atmosphere based on the pattern of trawling-related sediment disturbance posited by Sala et al. (remineralization of 1.47 Pg CO₂ in the "first" year after commencement of trawling, declining to a steady rate of 0.58 Pg CO₂ yr^-1 at year 10 and beyond). The file includes adjusted (using the Siegel et al. sequestration fractions) estimates for several bottom depth fractions, and well as some unadjusted estimates for the same depth fractions. adjCO2efflux_global_PgCO2_cumulative_byEEZ.csv contains cumulative emissions estimates (both adjusted and unadjusted) broken down by exclusive economic zone (EEZ) of the countries responsible for most of the world's benthic trawling.

  • The other files in this directory are useful data objects exported (and in few cases, then reimported) during the analysis. These include additional coordinate pairings (matches against the UCSD MLD climatology dataset for the MLD validation "gut check," and coordinates subdivided by EEZ) and a .csv file containing data and metadata, including bottom depths that had to be reimported into MATLAB for use in global_trawling/04_ConstrainCO2Flux_genTrawlSeqFracs.m.