Metagenome-assembled genomes from topsoils along a hillslope water gradient across early snowmelt to late summer in East River, CO

Creators: Preston Tasoff, Ulas Karaoz ORCID, Jillian F. Banfield, Eoin L. Brodie ORCID

Year: 2025

License: CC-BY 4.0

Location: The East River (ER) is a snow‐dominated, headwater basin of the Upper Colorado River Basin (UCRB) located in the western United States. The ER is the designated testbed of Lawrence Berkeley National Laboratory and SLAC Accelerator Laboratory's Watershed Function Scientific Focus Area (WFSFA). This portion of the ER watershed contains the project-defined boundaries of East River, Washington Gulch, Slate River, and Coal Creek, as described in the location metadata. Through WFSFA, observational networks have been established to measure stream discharge and precipitation chemistry. The ER is considered representative of many snow‐dominated headwaters of the Rocky Mountains. The study domain encompasses nearly 85 square km, a 1.4‐km vertical drop in elevation (4,120 to 2,760 m) and pristine alpine, subalpine, montane, and riparian ecosystems. The ER contains high‐energy mountain streams to low‐energy meandering floodplains and is eroding primarily into the Cretaceous, carbon‐rich, marine shale of the Mancos Formation. This data package contains geographic metadata for specific observation points throughout the watershed. Additional metadata on specific locations within the watershed are provided in the following related data package: Varadharajan C. et al. (2025) doi:10.15485/1660962

Temporal extent: 2023-06-01 to 2023-08-31

Bounding box: 38.820°N to 39.033°N, -107.120°W to -106.880°W

Publisher: ESS_DIVE

Tags: EARTH SCIENCE > LAND SURFACE > SOILS, CATEGORICAL:GCMD metagenomics, EARTH SCIENCE > BIOSPHERE > OMICS > METAGENOME > METAGENOME ASSEMBLED GENOMES (MAGs):GCMD, EARTH SCIENCE > BIOSPHERE > OMICS > OMICS METHODOLOGY > BIN/BINNING:GCMD, EARTH SCIENCE > BIOSPHERE > OMICS > MICROBIOME:GCMD, VARIABLE:NONE EARTH SCIENCE > BIOSPHERE > OMICS > METAGENOME > METAGENOME ASSEMBLED GENOMES (MAGs):GCMD, EARTH SCIENCE > BIOSPHERE > OMICS > BUILDING BLOCKS > CONTIG:GCMD, EARTH SCIENCE > BIOSPHERE > OMICS > BUILDING BLOCKS > eDNA:GCMD, ESS-DIVE File Level Metadata Reporting Format, ESS-DIVE CSV File Formatting Guidelines Reporting Format, ESS-DIVE Sample ID and Metadata Reporting Format, ESS-DIVE Location Metadata Reporting Format, Alpine & Subalpine Ecology, Forest Ecology, Genetics & Evolution, Hydrology & Watersheds, Snow & Ice, Water Quality, Geology & Tectonics, Soil Science, Geochemistry & Isotopes, Weather & Atmospheric Science, Mining & Mineral Resources, Gunnison Basin, Research Programs

Description

Drought is changing the American Mountain West at unprecedented rates with unknown consequences to soil microbiome composition and function. As a part of LBNL Watershed Science Focus Area (SFA), we investigated shifts in microbial community and transcriptional activity on a subalpine conifer-meadow transition zone throughout the summer of 2023 as soil dried down. This work took place in Crested Butte, CO on Snodgrass mountain, using a proxy for drought conditions. Here we present metagenome assembled genomes (MAGs) for the bacterial and archaeal community at 0-10cm from three sites along a hillslope water gradient across five timepoints from early snowmelt to late summer. 42 metagenomes were sequenced at Joint Genome Institute (JGI) and can be found under the JGI GOLD (Genomes Online Database) sequencing project Gs0166660. Metagenomes were assembled through an inhouse pipeline (see methods), binned using four autobinners (concoct, maxbin2, metabat2, and vamb) and consolidated using dastool. The consolidated bins from all metagenomes were pooled, filtered by completeness (>70%) and contamination (<10%), and dereplicated at 95% ANI using drep. This dataset (1) a zip file of 157 MAGs (as fasta files, Gs0166660_bins_tar.gz), (2) sample metadata file with sample IGSNs (International Generic Sample Numbers) (samples.csv), (3) bounding box coordinates for the sampled locations (Gs0166660.kml), (4) metagenome assembly and coassembly metadata file listing IMG/M (Integrated Microbial Genomes/Metagenomes) metagenome accessions linking samples to metagenomes (EastRiver_Drought_ESSDive_Metadata.csv), (5) location metadata file (locations.csv), (6) file-level metadata file (flmd.csv) and (7) data dictionary (dd.csv) file. 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.

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