Data and scripts associated with a manuscript investigating dissolved organic matter and microbial community linkages across seven globally distributed rivers

Danczak, Robert E.; Goldman, Amy E.; Borton, Mikayla A.; Chu, Rosalie; Toyoda, Jason G.; Garayburu-Caruso, Vanessa A.; Graham, Emily B.; Morad, Joseph W.; Renteria, Lupita; Wells, Jacqueline R.; Arnon, Shai; Brooks, Scott; Bar-Zeev, Edo; Jones, Michael; Jones, Nikki; Lewandowski, Jorg; Meile, Christof; Muller, Birgit M.; Powers-McCormack, Beck; Schalles, John; Schulz, Hanna; Ward, Adam; Stegen, James C.

doi:10.15485/2319037

Title: Data and scripts associated with a manuscript investigating dissolved organic matter and microbial community linkages across seven globally distributed rivers

Dataset
Other Related Research

Abstract

This data package is associated with the publication “Meta-metabolome ecology reveals that geochemistry and microbial functional potential are linked to organic matter development across seven rivers” submitted to Science of the Total Environment. This data package includes the data necessary to replicate the analyses presented within the manuscript to investigate dissolved organic matter (DOM) development across broad spatial distances and within divergent biomes. Specifically, we included the Fourier transform ion cyclotron mass spectrometry (FTICR-MS) data, geochemistry data, annotated metagenomic data, and results from ecological null modeling analyses in this data package. Additionally, we included the scripts necessary to generate the figures from the manuscript.Complete metagenomic data associated with this data package can be found at the National Center for Biotechnology (NCBI) under Bioproject PRJNA946291.This dataset consists of (1) four folders; (2) a file-level metadata (flmd) file; (3) a data dictionary (dd) file; (4) a factor sheet describing samples; and (5) a readme. The FTICR Data folder contains (1) the processed Fourier transform ion cyclotron mass spectrometry (FTICR-MS) data; (2) a transformation-weighted characteristics dendrogram generated from the FTICR-MS data; and (3) the script used to generate all FTICR-MS related figures. The Geochemical Data folder contains (1) the single geochemistry data filemore »« less

Authors:

;

; Morad, Joseph W.;

;

; Jones, Michael; Jones, Nikki;

;

; Muller, Birgit M.;

;

Pacific Northwest National Laboratory; Pacific Northwest National Laboratory
Pacific Northwest National Laboratory
Colorado State University
New Jersey Department of Environmental Protection
Ben-Gurion University of the Negev
Oak Ridge National Laboratory
Ben-Gurion University of the Negev, Zuckerberg Institute for Water Research
Leibniz Institute of Freshwater Ecology and Inland Fisheries
The University of Georgia
Creighton University
Oregon State University

Publication Date:: Mon Feb 19 23:00:00 EST 2024

Research Org.:: Environmental System Science Data Infrastructure for a Virtual Ecosystem

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

Subject:: 54 ENVIRONMENTAL SCIENCES; Biogeochemistry; Bioinformatics; Calcium; Chloride; DOC; Dissolved organic carbon; EARTH SCIENCE > TERRESTRIAL HYDROSPHERE > WATER QUALITY/WATER CHEMISTRY > WATER CHARACTERISTICS > CONDUCTIVITY; EARTH SCIENCE > TERRESTRIAL HYDROSPHERE > WATER QUALITY/WATER CHEMISTRY > WATER CHARACTERISTICS > pH; ESS-DIVE CSV File Formatting Guidelines Reporting Format; ESS-DIVE File Level Metadata Reporting Format; Environmental Metabolomics; FTICR-MS; Fluoride; Fourier-transform ion cyclotron resonance; Freshwater; Iron; Magnesium; Mass spectrometry; Metagenomic coverage; Microbiology; NPOC; Nitrate; Nitrite; Non-purgeable organic carbon; Organic matter; Phosphorus; Potassium; River; River corridor; Sodium; SpC; Specific conductivity; Stream; Sulfate; TN; Total dissolved nitrogen; WHONDRS; Watershed

OSTI Identifier:: 2319037

DOI:: https://doi.org/10.15485/2319037

Citation Formats


                    Danczak, Robert E., Goldman, Amy E., Borton, Mikayla A., Chu, Rosalie, Toyoda, Jason G., Garayburu-Caruso, Vanessa A., Graham, Emily B., Morad, Joseph W., Renteria, Lupita, Wells, Jacqueline R., Arnon, Shai, Brooks, Scott, Bar-Zeev, Edo, Jones, Michael, Jones, Nikki, Lewandowski, Jorg, Meile, Christof, Muller, Birgit M., Powers-McCormack, Beck, Schalles, John, Schulz, Hanna, Ward, Adam, and Stegen, James C. Data and scripts associated with a manuscript investigating dissolved organic matter and microbial community linkages across seven globally distributed rivers.  United States: N. p., 2024. 
        Web.  doi:10.15485/2319037.

Copy to clipboard


                    Danczak, Robert E., Goldman, Amy E., Borton, Mikayla A., Chu, Rosalie, Toyoda, Jason G., Garayburu-Caruso, Vanessa A., Graham, Emily B., Morad, Joseph W., Renteria, Lupita, Wells, Jacqueline R., Arnon, Shai, Brooks, Scott, Bar-Zeev, Edo, Jones, Michael, Jones, Nikki, Lewandowski, Jorg, Meile, Christof, Muller, Birgit M., Powers-McCormack, Beck, Schalles, John, Schulz, Hanna, Ward, Adam, & Stegen, James C. Data and scripts associated with a manuscript investigating dissolved organic matter and microbial community linkages across seven globally distributed rivers.  United States.  doi:https://doi.org/10.15485/2319037

Copy to clipboard


                    Danczak, Robert E., Goldman, Amy E., Borton, Mikayla A., Chu, Rosalie, Toyoda, Jason G., Garayburu-Caruso, Vanessa A., Graham, Emily B., Morad, Joseph W., Renteria, Lupita, Wells, Jacqueline R., Arnon, Shai, Brooks, Scott, Bar-Zeev, Edo, Jones, Michael, Jones, Nikki, Lewandowski, Jorg, Meile, Christof, Muller, Birgit M., Powers-McCormack, Beck, Schalles, John, Schulz, Hanna, Ward, Adam, and Stegen, James C. 2024.  
"Data and scripts associated with a manuscript investigating dissolved organic matter and microbial community linkages across seven globally distributed rivers".  United States.  doi:https://doi.org/10.15485/2319037.  https://www.osti.gov/servlets/purl/2319037. Pub date:Mon Feb 19 23:00:00 EST 2024

Copy to clipboard


                    
@article{osti_2319037,

  title        = {Data and scripts associated with a manuscript investigating dissolved organic matter and microbial community linkages across seven globally distributed rivers},

  author       = {Danczak, Robert E. and Goldman, Amy E. and Borton, Mikayla A. and Chu, Rosalie and Toyoda, Jason G. and Garayburu-Caruso, Vanessa A. and Graham, Emily B. and Morad, Joseph W. and Renteria, Lupita and Wells, Jacqueline R. and Arnon, Shai and Brooks, Scott and Bar-Zeev, Edo and Jones, Michael and Jones, Nikki and Lewandowski, Jorg and Meile, Christof and Muller, Birgit M. and Powers-McCormack, Beck and Schalles, John and Schulz, Hanna and Ward, Adam and Stegen, James C.},

  abstractNote = {This data package is associated with the publication “Meta-metabolome ecology reveals that geochemistry and microbial functional potential are linked to organic matter development across seven rivers” submitted to Science of the Total Environment. This data package includes the data necessary to replicate the analyses presented within the manuscript to investigate dissolved organic matter (DOM) development across broad spatial distances and within divergent biomes. Specifically, we included the Fourier transform ion cyclotron mass spectrometry (FTICR-MS) data, geochemistry data, annotated metagenomic data, and results from ecological null modeling analyses in this data package. Additionally, we included the scripts necessary to generate the figures from the manuscript.Complete metagenomic data associated with this data package can be found at the National Center for Biotechnology (NCBI) under Bioproject PRJNA946291.This dataset consists of (1) four folders; (2) a file-level metadata (flmd) file; (3) a data dictionary (dd) file; (4) a factor sheet describing samples; and (5) a readme. The FTICR Data folder contains (1) the processed Fourier transform ion cyclotron mass spectrometry (FTICR-MS) data; (2) a transformation-weighted characteristics dendrogram generated from the FTICR-MS data; and (3) the script used to generate all FTICR-MS related figures. The Geochemical Data folder contains (1) the single geochemistry data file and (2) the R script responsible for generating associated figures. The Metagenomic Data folder contains (1) annotation information across different levels; (2) carbohydrate active enzyme (CAZyme) information from the dbCAN database (Yin et al., 2012); (3) phylogenetic tree data (FASTAs, alignments, and tree file); and (4) the scripts necessary to analyze all of these data and generate figures. The Null Modeling Data folder contains (1) data generated during null modeling for each river and all rivers combined and (2) the R scripts necessary to process the data. All files are .csv, .pdf, .tsv, .tre, .faa, .afa, .tree, or .R.},

  doi          = {10.15485/2319037},

  journal      = {},

  number       = ,

  volume       = ,

  place        = {United States},

  year         = {Mon Feb 19 23:00:00 EST 2024},

  month        = {Mon Feb 19 23:00:00 EST 2024}

}

Copy to clipboard

Dataset:

View Dataset

DOI: https://doi.org/10.15485/2319037

Save / Share:

Export Metadata

Save to My Library

Similar records in DOE Data Explorer and OSTI.GOV collections:

Scripts and data associated with a manuscript linking soil and sediment elemental composition with dissolved organic matter chemistry across CONUS

Dataset Roebuck, Alan ; Forbes, Brieanne ; Rod, Kenton A ; ...

This data package provides scripts and geochemical data for a manuscript titled “Linkages between mineral element composition of soils and sediments with hyporheic zone dissolved organic matter chemistry across the contiguous United States” (preprint: doi: 10.22541/essoar.169447343.31694990/v1). This data is associated with the Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS, https://whondrs.pnnl.gov) and is an extension of the Summer 2019 Sampling campaign which crowdsourced samples from rivers and sediment across the continental United States. Data from this study can be found at https://data.ess-dive.lbl.gov/datasets/doi:10.15485/1603775 and https://data.ess-dive.lbl.gov/datasets/doi:10.15485/1729719. The main objective of this manuscript was to couple sediment water extractable dissolved organic mattermore »« less
Data and scripts associated with the manuscript "Organic Molecules are Deterministically Assembled in River Sediments"

Dataset Stegen, James C. ; Garayburu-Caruso, Vanessa A. ; Danczak, Robert E. ; ...

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 datamore »« less
Data and Scripts associated with a manuscript on ecosystem responses to wildfires in the Columbia River Basin

Dataset Shi, Mingjie ; Mcdowell, Nate G. ; Huang, Huilin ; ...

This data package is associated with the publication “Ecosystem leaf area, gross primary production, and evapotranspiration responses to wildfire in the Columbia River Basin” submitted to Biogeosciences (Shi et al., 2024; doi: 10.22541/au.171053013.30286044/v1). In this research, data products, leaf area index (LAI), gross primary production (GPP), and evapotranspiration (ET), from the Moderate Resolution Imaging Spectroradiometer (MODIS) are used to quantify the resistance and resilience of different ecosystem types in the Columbia River Basin (CRB). A machine learning algorithm, random forest (RF), was used to examine the impacts of precipitation, vapor pressure deficit (VPD), and burn severity from Monitoring Trends inmore »« less
Data and scripts associated with a manuscript investigating impacts of solid phase extraction on freshwater organic matter optical signatures and mass spectrometry pairing

Dataset Roebuck, Alan ; Forbes, Brieanne ; Garayburu-Caruso, Vanessa A. ; ...

This data package is associated with the publication “Investigating the impacts of solid phase extraction on dissolved organic matter optical signatures and the pairing with high-resolution mass spectrometry data in a freshwater system” submitted to “Limnology and Oceanography: Methods.” This data is an extension of the River Corridor and Watershed Biogeochemistry SFA’s Spatial Study 2021 (https://doi.org/10.15485/1898914). Other associated data and field metadata can be found at the link provided. The goal of this manuscript is to assess the impact of solid phase extraction (SPE) on the ability to pair ultra-high resolution mass spectrometry data collected from SPE extracts with opticalmore »« less
Data and scripts associated with a manuscript on residence time distribution simulation in two 10-kilometer long river sections

Dataset Bao, Jie ; Song, Xuehang ; Chen, Yunxiang ; ...

This data package is associated with the publication “On the Transferability of Residence Time Distributions in Two 10-km Long River Sections with Similar Hydromorphic Units” submitted to the Journal of Hydrology (Bao et al. 2024).Quantifying hydrologic exchange fluxes (HEFs) at the stream-groundwater interface, along with their residence time distributions (RTDs) in the subsurface, is crucial for managing water quality and ecosystem health in dynamic river corridors. However, directly simulating high-spatial resolution HEFs and RTDs can be a time-consuming process, particularly for watershed-scale modeling. Efficient surrogate models that link RTDs to hydromorphic units (HUs) may serve as alternatives for simulating RTDsmore »« less

Similar Records