DOI: 10.5281/zenodo.3266771
title: Changing carbon dioxide and water budgets from deforestation and habitat modification

description: <b>Description: </b>SAFE Intensive Carbon Plots, part of the Global Ecosystem Monitoring (GEM) network, see http://gem.tropicalforests.ox.ac.uk/<br>Total soil respiration is measured at 25 points per plot, in the middle of each subplot (16 points per plot in OP, in subplot corners), using 12 cm diameter PVC collars inserted into approximately 5 cm depth<br>Partitioned respiration is measured at four points per plot, a using a cluster of six collars (see below)<br>Disturbance experiment in the plot centre<br>All the methods and installation is described in detail in the GEM Intensive Carbon Plots manual, available at http://gem.tropicalforests.ox.ac.uk/files/rainfor-gemmanual.v3.0.pdf<br>The aim is to measure monthly, but in practice the measurement interval is almost always longer (problems with access, staffing and instruments)<br>EGM-4 infrared CO2 analyser and SRC-1 respiration chamber (PP Systems)<br>Chamber closure time is 124 seconds, CO2 concentration inside the chamber is recorded every 5 s. Flux is calculated from the linear change in concentration in the chamber headspace<br><br><br>Conversion from parts per million (ppm) of total gas volume per second per unit collar area to mega grams (1 Mg = 10^6 g) of carbon per hectare per month <br> <br>Idea gas law: pV=nRT --&gt; n=pV/(RT) <br>Mass-Mole: n=m/M --&gt; m=n*M <br>Combined: m=MpV/(RT) <br> <br>p (constant) 101,325 <br>R (constant) 8.314472 <br>T temperature in Kelvins --&gt; AirT_Use + 273.15 <br>V headspace volume <br>M_carbon 12.01 <br> <br>parts per million to absolute units 10^-6 <br>A collar area, m2 0.008825 <br>m2 to hectare 10^4 <br>grams to megagrams 10^-6 <br>seconds to months 2592000 <br> <br>Flux_MgCha-1month-1 = Slope_ppm_s-1 * M* p* V /(R*T) * 10^-6 / A * 10^4 * 10^-6 * 2592000 <br>Soil collar codes Partitioned respiration <br>C1 All soil respiration components: litter, roots, mycorrhiza, soil organic matter (SOM)<br>C2 Roots excluded (litter, mycorrhiza, SOM)<br>C3 Roots and mycorrhiza excluded (litter, SOM)<br>S1 Litter excluded (roots, mycorrhiza, SOM)<br>S2 Litter and roots excluded (mycorrhiza, SOM)<br>S3 Litter, roots and mycorrhiza excluded (only SOM)<br>D1 Double litter, roots, mycorrhiza, soil organic matter (SOM)<br>D2 Roots excluded (double litter, mycorrhiza, SOM)<br>D3 Roots and mycorrhiza excluded (double litter, SOM)<br>X Organic layer of the soil removed<br> <br>Disturbance The purpose of the disturbance experiment is to quantify how much disturbance the removal of the roots and mixing the soil causes, compared to just hammering in the deep collar<br>ND1 Roots severed, not removed and soil not mixed at the installation<br>ND2 ND1-ND5 are replicates, same treatmet<br>ND3 <br>ND4 <br>ND5 <br>D1 Roots removed, soil mixed at the installation<br>D2 D1-D5 are replicates<br>D3 <br>D4 <br>D5 <br> <b>Project: </b>This dataset was collected as part of the following SAFE research project: <b>Changing carbon dioxide and water budgets from deforestation and habitat modification</b><b>Funding: </b>These data were collected as part of research funded by: Sime Darby Foundation (Grant, SAFE Core data)European Research Council Advanced Investigator Grant, GEM-TRAIT (Grant, Grant number 321131)NERC Human-Modified Tropical Forests Programme: Biodiversity And Land-use Impacts on tropical ecosystem function (BALI) Project (Grant, NE/K016369/1)NERC standard grant: The multi-year impacts of the 2015/2016 El Niño on the carbon cycle of tropical forests worldwide (Grant, NE/P001092/1)HSBC Malaysia (Grant)The University of Zurich (Grant)This dataset is released under the CC-BY 4.0 licence, requiring that you cite the dataset in any outputs, but has the additional condition that you acknowledge the contribution of these funders in any outputs.<b>Permits: </b>These data were collected under permit from the following authorities:Sabah Biodiversity Council (Research licence JKM/MBs.1000-2/2 JLD.6 (76))<b>XML metadata: </b>GEMINI compliant metadata for this dataset is available here<b>Files: </b>This dataset consists of 2 files: SAFE_SoilRespiration_Data_SAFEdatabase.xlsx, SAFE_soil_DATA.zip<b>SAFE_SoilRespiration_Data_SAFEdatabase.xlsx</b>This file contains dataset metadata and 1 data tables:<b>Carbon flux data</b> (described in worksheet data)Description: Carbon flux dataNumber of fields: 21Number of data rows: 20602Fields: <b>ForestType</b>: Old-growth, Logged or Oil palm (Field type: Categorical)<b>SAFEPlotName</b>: SAFE plot name (Field type: Location)<b>PlotName</b>: Plot name (Field type: ID)<b>ForestPlotsCode</b>: Plot code in the ForestPlots database (this should be used in publications, instead of plot name). OP plot is not in the ForestPlots database (ForestPlotsCode = NA) (Field type: ID)<b>Date</b>: Measurement date (dd/mm/yyyy) (Field type: Date)<b>Observers</b>: Observers (Field type: Comments)<b>Subplot</b>: Subplot number within each plot, 1-25 (in OP, because the total respiration collars are in subplot corners, no subplot numbers are used, but the collars are refered to as SR1 - SR16. Subplot numbers are used for the partitioned respiration) (Field type: ID)<b>MeasurementType</b>: Total, Partitioned or Disturbance (Field type: Categorical)<b>CollarType</b>: Total; Partitioned: C1, C2, C3, S1, S2, S3, D1, D2, D3, X; Disturbance: ND1, ND2, ND3, ND4, ND5, D1, D2, D3, D4, D5 (see metadata description for codes) (Field type: ID)<b>EGM_RecordNumber</b>: Record number in of the raw flux file. (Field type: ID)<b>SoilMoisture</b>: Volumetric soil moisture content (% of pore space) next to the collar. measured with Campbell Scientific Hydrosense sensor with 12 cm rods. (Field type: Numeric)<b>SoilT</b>: Soil temperature (°C) is measured with a handheld digital thermometer next to the collar, inserted into 10 cm depth (Field type: Numeric)<b>AirT</b>: Air temperature (°C) is measured with a handheld digital thermometer outside the chamber, at the chamber height, in a shaded spot (Field type: Numeric)<b>Slope</b>: Slope of the linear regression between time (seconds) from the chamber closure and CO2 concentration (parts per million, ppm) in the chamber headspace. (Field type: Numeric)<b>Remarks</b>: Any notes in the field or at data entry stage. 0 = no remarks. If the measurement is repeated in the field multiple times, the other flux estimates are sometimes written in the remarks (not consistent). 2x, 3x etc. indicate multiple repeats. (Field type: Comments)<b>CollarHeight</b>: Height from the top of the soil to the top of the collar, mm. This is used for calculating the total headspapce volume (chamber volume + collar volume above the soil surface). (Field type: Numeric)<b>HeadspaceVolume</b>: Total headspace volume, sum of the chamber volume (0.001229 m3) and collar volume (d=0.106 m, h=CollarHeight_mm/1000) (Field type: Numeric)<b>AirT_Use</b>: Gap filled air temperature data, missing air temperatures replaced with average temperature in logged (27.1), old-growth forest (26.2) and OP (28.7). This is needed for calculating the flux, but should not be used in response functions etc. (Field type: Numeric)<b>Flux</b>: Flux corverted from ppm s-1 to Mg carbon per hectare per month. See conversion below. (Field type: Numeric)<b>Quality** (see description below)</b>: 1 - good flux; 0 - missing data or bad measurement; 2 - outlier (Field type: Numeric)<b>Girdling_0_1</b>: In Tower Plot (SAF-05), subplots 14-25, all trees were girdled in late January - early February 2016. Post-girdling data = 1, if no girdling = 0. (Field type: Numeric)<b>SAFE_soil_DATA.zip</b>Description: Raw EGM files and a ReadMe doc explaining how to interpret <b>Date range: </b>2011-08-25 to 2018-07-17<b>Latitudinal extent: </b>4.5000 to 5.0700<b>Longitudinal extent: </b>116.7500 to 117.8200