Data and scripts associated with the manuscript "Organic Molecules are Deterministically Assembled in River Sediments"

Stegen, James C.; Garayburu-Caruso, Vanessa A.; Danczak, Robert E.; Chu, Rosalie; Forbes, Brieanne; Goldman, Amy E.; McCall, Marcy L.; McKever, Sophia A.; Powers-McCormack, Beck; Renteria, Lupita; Toyoda, Jason G.

doi:10.15485/2367553

Title: Data and scripts associated with the manuscript "Organic Molecules are Deterministically Assembled in River Sediments"

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Abstract

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 endingmore »« less

Authors:

;

; McCall, Marcy L.; McKever, Sophia A.;

;

Pacific Northwest National Laboratory; Pacific Northwest National Laboratory
Pacific Northwest National Laboratory

Publication Date:: Mon May 20 04:00:00 UTC 2024

Research Org.:: 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 Org.:: U.S. DOE > Office of Science > Biological and Environmental Research (BER)

Subject:: 54 ENVIRONMENTAL SCIENCES; 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

OSTI Identifier:: 2367553

DOI:: https://doi.org/10.15485/2367553

Citation Formats


                    Stegen, James C., Garayburu-Caruso, Vanessa A., Danczak, Robert E., Chu, Rosalie, Forbes, Brieanne, Goldman, Amy E., McCall, Marcy L., McKever, Sophia A., Powers-McCormack, Beck, Renteria, Lupita, and Toyoda, Jason G. Data and scripts associated with the manuscript "Organic Molecules are Deterministically Assembled in River Sediments".  United States: N. p., 2024. 
        Web.  doi:10.15485/2367553.

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                    Stegen, James C., Garayburu-Caruso, Vanessa A., Danczak, Robert E., Chu, Rosalie, Forbes, Brieanne, Goldman, Amy E., McCall, Marcy L., McKever, Sophia A., Powers-McCormack, Beck, Renteria, Lupita, & Toyoda, Jason G. Data and scripts associated with the manuscript "Organic Molecules are Deterministically Assembled in River Sediments".  United States.  doi:https://doi.org/10.15485/2367553

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                    Stegen, James C., Garayburu-Caruso, Vanessa A., Danczak, Robert E., Chu, Rosalie, Forbes, Brieanne, Goldman, Amy E., McCall, Marcy L., McKever, Sophia A., Powers-McCormack, Beck, Renteria, Lupita, and Toyoda, Jason G. 2024.  
"Data and scripts associated with the manuscript "Organic Molecules are Deterministically Assembled in River Sediments"".  United States.  doi:https://doi.org/10.15485/2367553.  https://www.osti.gov/servlets/purl/2367553. Pub date:Mon May 20 04:00:00 UTC 2024

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@article{osti_2367553,

  title        = {Data and scripts associated with the manuscript "Organic Molecules are Deterministically Assembled in River Sediments"},

  author       = {Stegen, James C. and Garayburu-Caruso, Vanessa A. and Danczak, Robert E. and Chu, Rosalie and Forbes, Brieanne and Goldman, Amy E. and McCall, Marcy L. and McKever, Sophia A. and Powers-McCormack, Beck and Renteria, Lupita and Toyoda, Jason G.},

  abstractNote = {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".},

  doi          = {10.15485/2367553},

  journal      = {},

  number       = ,

  volume       = ,

  place        = {United States},

  year         = {Mon May 20 04:00:00 UTC 2024},

  month        = {Mon May 20 04:00:00 UTC 2024}

}

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DOI: https://doi.org/10.15485/2367553

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