Ultrahigh-resolution mass spectrometry data associated with the manuscript “A functional microbiome catalog crowdsourced from North American rivers"

Danczak, Robert E.; Borton, Mikayla A.; Wrighton, Kelly C.; Goldman, Amy E.; Powers-McCormack, Beck; Stegen, James C.

doi:10.15485/2439202

Title: Ultrahigh-resolution mass spectrometry data associated with the manuscript “A functional microbiome catalog crowdsourced from North American rivers"

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Abstract

This data package is associated with the publication “A functional microbiome catalog crowdsourced from North American rivers” submitted to Nature (Borton et al., 2024); (https://www.biorxiv.org/content/10.1101/2023.07.22.550117v1). Predicting elemental cycles and maintaining water quality under increasing anthropogenic influence requires understanding the spatial drivers of river microbiomes. However, the unifying microbial determinants governing river biogeochemistry are hindered by a lack of genome-resolved functional insights and sampling across multiple rivers. Here we employed a community science effort to accelerate the sampling of river microbiomes to create the Genome Resolved Open Watersheds database (GROWdb). GROWdb is a publicly available resource that paves the way for watershed predictive modeling and microbiome-based management practices. This resource profiled the identity, distribution, function, and expression of thousands of microbial genomes across rivers covering 90% of United States watersheds. We identified the most cosmopolitan microbiome members, while also revealing local drivers of strain endemism across ecological dimensions. We provide the first evidence that microbial functional trait expression followed the tenets of the River Continuum Concept, suggesting the structure and function of river microbiomes is predictable. The Fourier-transform ion cyclotron resonance mass spectrometry (FTICR-MS) data were one of many different data types used in establishing the ecological dimensions along which differentmore »« less

Authors:

;

Pacific Northwest National Laboratory (PNNL); Pacific Northwest National Laboratory (PNNL)
Colorado State University
Pacific Northwest National Laboratory (PNNL)

Publication Date:: Sun Dec 31 23:00:00 EST 2023

Research Org.:: Environmental System Science Data Infrastructure for a Virtual Ecosystem; River Corridor and Watershed Biogeochemistry SFA

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

Subject:: 54 ENVIRONMENTAL SCIENCES; Biogeochemistry; ESS-DIVE CSV File Formatting Guidelines Reporting Format; ESS-DIVE File Level Metadata Reporting Format; Environmental metabolomics; FTICR-MS; Fourier-transform ion cyclotron resonance; Freshwater; Mass spectrometry; Organic matter; River; River corridor; Stream; WHONDRS; Watershed

OSTI Identifier:: 2439202

DOI:: https://doi.org/10.15485/2439202

Citation Formats


                    Danczak, Robert E., Borton, Mikayla A., Wrighton, Kelly C., Goldman, Amy E., Powers-McCormack, Beck, and Stegen, James C. Ultrahigh-resolution mass spectrometry data associated with the manuscript “A functional microbiome catalog crowdsourced from North American rivers".  United States: N. p., 2023. 
        Web.  doi:10.15485/2439202.

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                    Danczak, Robert E., Borton, Mikayla A., Wrighton, Kelly C., Goldman, Amy E., Powers-McCormack, Beck, & Stegen, James C. Ultrahigh-resolution mass spectrometry data associated with the manuscript “A functional microbiome catalog crowdsourced from North American rivers".  United States.  doi:https://doi.org/10.15485/2439202

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                    Danczak, Robert E., Borton, Mikayla A., Wrighton, Kelly C., Goldman, Amy E., Powers-McCormack, Beck, and Stegen, James C. 2023.  
"Ultrahigh-resolution mass spectrometry data associated with the manuscript “A functional microbiome catalog crowdsourced from North American rivers"".  United States.  doi:https://doi.org/10.15485/2439202.  https://www.osti.gov/servlets/purl/2439202. Pub date:Sun Dec 31 23:00:00 EST 2023

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@article{osti_2439202,

  title        = {Ultrahigh-resolution mass spectrometry data associated with the manuscript “A functional microbiome catalog crowdsourced from North American rivers"},

  author       = {Danczak, Robert E. and Borton, Mikayla A. and Wrighton, Kelly C. and Goldman, Amy E. and Powers-McCormack, Beck and Stegen, James C.},

  abstractNote = {This data package is associated with the publication “A functional microbiome catalog crowdsourced from North American rivers” submitted to Nature (Borton et al., 2024); (https://www.biorxiv.org/content/10.1101/2023.07.22.550117v1). Predicting elemental cycles and maintaining water quality under increasing anthropogenic influence requires understanding the spatial drivers of river microbiomes. However, the unifying microbial determinants governing river biogeochemistry are hindered by a lack of genome-resolved functional insights and sampling across multiple rivers. Here we employed a community science effort to accelerate the sampling of river microbiomes to create the Genome Resolved Open Watersheds database (GROWdb). GROWdb is a publicly available resource that paves the way for watershed predictive modeling and microbiome-based management practices. This resource profiled the identity, distribution, function, and expression of thousands of microbial genomes across rivers covering 90% of United States watersheds. We identified the most cosmopolitan microbiome members, while also revealing local drivers of strain endemism across ecological dimensions. We provide the first evidence that microbial functional trait expression followed the tenets of the River Continuum Concept, suggesting the structure and function of river microbiomes is predictable. The Fourier-transform ion cyclotron resonance mass spectrometry (FTICR-MS) data were one of many different data types used in establishing the ecological dimensions along which different microbes were detected .This data package only contains the processed FTICR-MS data associated with this manuscript; all other data is accessible via Zenodo (https://zenodo.org/records/8173287), GitHub (https://github.com/jmikayla1991/Genome-Resolved-Open-Watersheds-database-GROWdb), KBase (https://doi.org/10.25982/109073.30/1895615), and NCBI via Bioproject PRJNA946291.This dataset consists of (1) a file-level metadata (flmd) file; (2) a data dictionary (dd) file; (3) a readme; (4) three Fourier-transform ion cyclotron resonance mass spectrometry (FTICR-MS) processed data files (a ‘data’ file containing peak-by-sample observations, a ‘mol’ file containing peak metadata, and a transformation profile containing transformation-by-sample observations). All files are .csv or .pdf.},

  doi          = {10.15485/2439202},

  journal      = {},

  number       = ,

  volume       = ,

  place        = {United States},

  year         = {Sun Dec 31 23:00:00 EST 2023},

  month        = {Sun Dec 31 23:00:00 EST 2023}

}

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DOI: https://doi.org/10.15485/2439202

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The Genome Resolved Open Watersheds database (GROWdb): A functional microbiome catalog crowdsourced from North American rivers

Dataset Borton, Mikayla ; Wrighton, Kelly

This repository contains data for version 1 of the Genome Resolved Open Watersheds database (GROWdb), along with data for the manuscript describing GROWdb.
A functional microbiome catalogue crowdsourced from North American rivers

Journal Article Borton, Mikayla A. ; McGivern, Bridget B. ; Willi, Kathryn R. ; ... - Nature (London)

Predicting elemental cycles and maintaining water quality under increasing anthropogenic influence requires knowledge of the spatial drivers of river microbiomes. However, understanding of the core microbial processes governing river biogeochemistry is hindered by a lack of genome-resolved functional insights and sampling across multiple rivers. Here we used a community science effort to accelerate the sampling, sequencing and genome-resolved analyses of river microbiomes to create the Genome Resolved Open Watersheds database (GROWdb). GROWdb profiles the identity, distribution, function and expression of microbial genomes across river surface waters covering 90% of United States watersheds. Specifically, GROWdb encompasses microbial lineages from 27 phyla,more »« less
A functional microbiome catalogue crowdsourced from North American rivers

Journal Article Borton, Mikayla A. ; McGivern, Bridget B. ; Willi, Kathryn R. ; ... - Nature (London)

Predicting elemental cycles and maintaining water quality under increasing anthropogenic influence requires knowledge of the spatial drivers of river microbiomes. However, understanding of the core microbial processes governing river biogeochemistry is hindered by a lack of genome-resolved functional insights and sampling across multiple rivers. Here we used a community science effort to accelerate the sampling, sequencing and genome-resolved analyses of river microbiomes to create the Genome Resolved Open Watersheds database (GROWdb). GROWdb profiles the identity, distribution, function and expression of microbial genomes across river surface waters covering 90% of United States watersheds. Specifically, GROWdb encompasses microbial lineages from 27 phyla,more »« less
A functional microbiome catalogue crowdsourced from North American rivers

Journal Article Borton, Mikayla A. ; McGivern, Bridget B. ; Willi, Kathryn R. ; ... - Nature (London)

Predicting elemental cycles and maintaining water quality under increasing anthropogenic influence requires knowledge of the spatial drivers of river microbiomes. However, understanding of the core microbial processes governing river biogeochemistry is hindered by a lack of genome-resolved functional insights and sampling across multiple rivers. Here we used a community science effort to accelerate the sampling, sequencing and genome-resolved analyses of river microbiomes to create the Genome Resolved Open Watersheds database (GROWdb). GROWdb profiles the identity, distribution, function and expression of microbial genomes across river surface waters covering 90% of United States watersheds. Specifically, GROWdb encompasses microbial lineages from 27 phyla,more »« less
A functional microbiome catalogue crowdsourced from North American rivers

Journal Article Borton, Mikayla A. ; McGivern, Bridget B. ; Willi, Kathryn R. ; ... - Nature (London)

Predicting elemental cycles and maintaining water quality under increasing anthropogenic influence requires knowledge of the spatial drivers of river microbiomes. However, understanding of the core microbial processes governing river biogeochemistry is hindered by a lack of genome-resolved functional insights and sampling across multiple rivers. Here we used a community science effort to accelerate the sampling, sequencing and genome-resolved analyses of river microbiomes to create the Genome Resolved Open Watersheds database (GROWdb). GROWdb profiles the identity, distribution, function and expression of microbial genomes across river surface waters covering 90% of United States watersheds. Specifically, GROWdb encompasses microbial lineages from 27 phyla,more »« less

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