U.S. Department of EnergyOffice of Scientific and Technical Information
Metagenome-assembled genomes from Slate River floodplain sediments near Crested Butte, CO, USA (September 2019)
Abstract
Microorganisms play a key role in cycling nutrients and contaminants in the terrestrial environment depending on their genetic potential. Here we present metagenome-assembled genomes (MAGs) for the bacterial and archaeal community in floodplain sediment samples taken September 2019 at one locations (OBJ1) near the confluence of the Oh-Be-Joyful Creek and Slate River. The site is one of the field sites in focus for the SLAC National Accelerator Laboratory Groundwater Quality Science Focus Area (SFA) program. Sediment samples from a deep soil pit were collected from 50 to 150 cm depth below surface at discrete depths every 20 cm for microbial analyses. A total of 6 metagenomes were sequenced through the Joint Genome Institute (JGI) and can be found under Genomes Online Database (GOLD) sequencing project: Gs0142591. Metagenomes were assembled, binned, and refined using metawrap to generate MAGs (>50% complete and < 10% contamination based on checkM scores). This dataset includes a zip file of 2562 MAG fasta files and a csv file with quality, taxonomic classification (Genome Taxonomy Database Release RS220), and metagenome accessions for MAGs. This dataset also includes a file-level metadata (flmd.csv) file that lists each file contained in the dataset with associated metadata and a data dictionarymore »
- Authors:
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- Stanford Linear Accelerator Center - National Accelerator Laboratory
- Stanford University
- Publication Date:
- DOE Contract Number:
- AC02-05CH11231
- Research Org.:
- Groundwater Quality SFA
- Sponsoring Org.:
- U.S. DOE > Office of Science > Biological and Environmental Research (BER)
- Subject:
- 54 ENVIRONMENTAL SCIENCES; EARTH SCIENCE > BIOSPHERE > ECOLOGICAL DYNAMICS > SPECIES/POPULATION INTERACTIONS > MICROBIAL CHANGES; EARTH SCIENCE > BIOSPHERE > OMICS > BUILDING BLOCKS > CONTIG; EARTH SCIENCE > BIOSPHERE > OMICS > BUILDING BLOCKS > eDNA; EARTH SCIENCE > BIOSPHERE > OMICS > METAGENOME > METAGENOME ASSEMBLED GENOMES (MAGs); EARTH SCIENCE > BIOSPHERE > OMICS > MICROBIOME; EARTH SCIENCE > BIOSPHERE > OMICS > OMICS METHODOLOGY > BIN/BINNING; EARTH SCIENCE > LAND SURFACE > SOILS > MICROFAUNA; ESS-DIVE CSV File Formatting Guidelines Reporting Format; ESS-DIVE File Level Metadata Reporting Format
- OSTI Identifier:
- 2588875
- DOI:
- https://doi.org/10.15485/2588875
Citation Formats
Rasmussen, Anna, Tolar, Bradley, Bargar, John, Boye, Kristin, and Francis, Christopher. Metagenome-assembled genomes from Slate River floodplain sediments near Crested Butte, CO, USA (September 2019). United States: N. p., 2024.
Web. doi:10.15485/2588875.
Rasmussen, Anna, Tolar, Bradley, Bargar, John, Boye, Kristin, & Francis, Christopher. Metagenome-assembled genomes from Slate River floodplain sediments near Crested Butte, CO, USA (September 2019). United States. doi:https://doi.org/10.15485/2588875
Rasmussen, Anna, Tolar, Bradley, Bargar, John, Boye, Kristin, and Francis, Christopher. 2024.
"Metagenome-assembled genomes from Slate River floodplain sediments near Crested Butte, CO, USA (September 2019)". United States. doi:https://doi.org/10.15485/2588875. https://www.osti.gov/servlets/purl/2588875. Pub date:Tue Dec 31 23:00:00 EST 2024
@article{osti_2588875,
title = {Metagenome-assembled genomes from Slate River floodplain sediments near Crested Butte, CO, USA (September 2019)},
author = {Rasmussen, Anna and Tolar, Bradley and Bargar, John and Boye, Kristin and Francis, Christopher},
abstractNote = {Microorganisms play a key role in cycling nutrients and contaminants in the terrestrial environment depending on their genetic potential. Here we present metagenome-assembled genomes (MAGs) for the bacterial and archaeal community in floodplain sediment samples taken September 2019 at one locations (OBJ1) near the confluence of the Oh-Be-Joyful Creek and Slate River. The site is one of the field sites in focus for the SLAC National Accelerator Laboratory Groundwater Quality Science Focus Area (SFA) program. Sediment samples from a deep soil pit were collected from 50 to 150 cm depth below surface at discrete depths every 20 cm for microbial analyses. A total of 6 metagenomes were sequenced through the Joint Genome Institute (JGI) and can be found under Genomes Online Database (GOLD) sequencing project: Gs0142591. Metagenomes were assembled, binned, and refined using metawrap to generate MAGs (>50% complete and < 10% contamination based on checkM scores). This dataset includes a zip file of 2562 MAG fasta files and a csv file with quality, taxonomic classification (Genome Taxonomy Database Release RS220), and metagenome accessions for MAGs. This dataset also includes a file-level metadata (flmd.csv) file that lists each file contained in the dataset with associated metadata and a data dictionary (dd.csv) file that contains column/row headers used throughout the files along with a definition, units, and data type.Part of this work was performed at SLAC Accelerator Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-76SF00515.},
doi = {10.15485/2588875},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Tue Dec 31 23:00:00 EST 2024},
month = {Tue Dec 31 23:00:00 EST 2024}
}