Data and scripts associated with the manuscript "Organic Molecules are Deterministically Assembled in River Sediments"
- Pacific Northwest National Laboratory; Pacific Northwest National Laboratory
- Pacific Northwest National Laboratory
This data package is associated with the publication "Organic Molecules are Deterministically Assembled in River Sediments" submitted to Scientific Reports (Stegen et al., 2024). The study applies community ecology methods to dissolved organic matter (DOM) chemistry from variably inundated riverbed sediments to uncover principles governing DOM composition at a reach-scale. This data package documents the workflow used to process and generate the main findings in the manuscript. The R scripts reference the raw, unprocessed Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) data from another data package, available on ESS-DIVE at https://data.ess-dive.lbl.gov/view/doi:10.15485/1834208. The scripts then process the raw FTICR-MS data and generate the findings and figures presented in the associated manuscript. In brief, this study demonstrates that DOM assemblages in variably inundated sediments are primarily governed by deterministic variable selection, including sediment moisture effecting the degree of deterministic assembly. See the manuscript for more details pertaining to interpretation and implications of the findings. This data package is associated with the GitHub repository found at https://github.com/WHONDRS-Hub/ECA_2020_Sed.This data package is comprised of 6 scripts and 7 folders. The file-level metadata file (file ending in "flmd.csv") lists all files contained in this data package and descriptions for each. The data dictionary (file ending in "dd.csv) describes all tabular data columns and their respective definitions and units. The FTICR_Processing_Scripts produce the outputs found in the "Processed_Data" folder. The remaining scripts (located in the parent directory) produce the outputs found in the following four folders: (1) "MCD_Dendrograms", "MCD_Randomizations", "MCD_bNTI_Outcomes", and "OM_Null_Modeling". The fifth script additionally takes the three comma-separated values (CSV) files found in the parent directory as input ("VGC_texture.csv", "merged_weights.csv", and "ECA2_FTICR_BetaDisp.csv"). The outputs of each of the five scripts serve as the input to the following script, with the final outputs stored in the folder "OM_Null_Modeling".
- Research Organization:
- Environmental System Science Data Infrastructure for a Virtual Ecosystem; Early Career Research Program: Watershed Perturbation-Response Traits Derived Through Ecological Theory - Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS)
- Sponsoring Organization:
- U.S. DOE > Office of Science > Biological and Environmental Research (BER)
- OSTI ID:
- 2367553
- Country of Publication:
- United States
- Language:
- English
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Related Subjects
Biogeochemistry
DOC
Dissolved organic carbon
EARTH SCIENCE > TERRESTRIAL HYDROSPHERE > SURFACE WATER
ESS-DIVE CSV File Formatting Guidelines Reporting Format
ESS-DIVE File Level Metadata Reporting Format
Ephemeral
FTICR-MS
Fourier transform ion cyclotron resonance mass spectrometry
Grain size
Intermittent
Inundation
MCD
Mass spectrometry
Metabolite
Metabolomics
Moisture
Molecular characteristics dendrogram
NPOC
Non-perennial
Non-purgeable organic carbon
Null Modeling
Organic Matter
Parafluvial
River corridor
Sediment
Stream
TN
Total dissolved nitrogen
bNTI
beta Nearest Taxon Index