U.S. Department of EnergyOffice of Scientific and Technical Information
Metagenome-assembled genomes from East River floodplain sediments near Crested Butte, CO, USA (June to September 2017)
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 in 2017 in June (flooded conditions) and September (drained conditions) at two locations (MCB1 and MCB3) in an active meander (Meander C) of the East River. Sediment cores were collected from 2 depths, a near-surface, generally unsaturated depth (15-40 centimeter (cm) depth below surface) and a deeper depth influenced by flooding with redoximorphic features (50-88 cm depth below surface). Sediments were homogenized from the ~10 cm cores for microbial analyses. A total of 24 metagenomes were sequenced through the Joint genome institute (JGI) corresponding to 8 samples sequenced in triplicate. These metagenomes can be found under Genomes Online Database (GOLD) sequencing project: Gs0151851. 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 405 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 listsmore »
- Authors:
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- Stanford Linear Accelerator Center - National Accelerator Laboratory
- University of Massachusetts - Amherst
- Universite de Lausanne
- Stanford University
- Publication Date:
- DOE Contract Number:
- AC02-05CH11231
- Research Org.:
- Watershed Function 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:
- 2997557
- DOI:
- https://doi.org/10.15485/2997557
Citation Formats
Rasmussen, Anna, Anderson, Cam, Keiluweit, Marco, Fendorf, Scott, Boye, Kristin, and Francis, Christopher. Metagenome-assembled genomes from East River floodplain sediments near Crested Butte, CO, USA (June to September 2017). United States: N. p., 2024.
Web. doi:10.15485/2997557.
Rasmussen, Anna, Anderson, Cam, Keiluweit, Marco, Fendorf, Scott, Boye, Kristin, & Francis, Christopher. Metagenome-assembled genomes from East River floodplain sediments near Crested Butte, CO, USA (June to September 2017). United States. doi:https://doi.org/10.15485/2997557
Rasmussen, Anna, Anderson, Cam, Keiluweit, Marco, Fendorf, Scott, Boye, Kristin, and Francis, Christopher. 2024.
"Metagenome-assembled genomes from East River floodplain sediments near Crested Butte, CO, USA (June to September 2017)". United States. doi:https://doi.org/10.15485/2997557. https://www.osti.gov/servlets/purl/2997557. Pub date:Tue Dec 31 23:00:00 EST 2024
@article{osti_2997557,
title = {Metagenome-assembled genomes from East River floodplain sediments near Crested Butte, CO, USA (June to September 2017)},
author = {Rasmussen, Anna and Anderson, Cam and Keiluweit, Marco and Fendorf, Scott 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 in 2017 in June (flooded conditions) and September (drained conditions) at two locations (MCB1 and MCB3) in an active meander (Meander C) of the East River. Sediment cores were collected from 2 depths, a near-surface, generally unsaturated depth (15-40 centimeter (cm) depth below surface) and a deeper depth influenced by flooding with redoximorphic features (50-88 cm depth below surface). Sediments were homogenized from the ~10 cm cores for microbial analyses. A total of 24 metagenomes were sequenced through the Joint genome institute (JGI) corresponding to 8 samples sequenced in triplicate. These metagenomes can be found under Genomes Online Database (GOLD) sequencing project: Gs0151851. 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 405 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.This work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231. 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 = {10.15485/2997557},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Tue Dec 31 23:00:00 EST 2024},
month = {Tue Dec 31 23:00:00 EST 2024}
}