Metagenome-assembled genomes from topsoils collected during NEON campaign in East River, CO (06/14/2018-06/28/2018)
- Lawrence Berkeley National Laboratory
- University of Rhode Island - Kingston
- NASA Jet Propulsion Laboratory (JPL)
- Oregon State University
- Stanford University
- Massachusetts Institute of Technology
The Watershed Function Science Focus Area (WF SFA) at Lawrence Berkeley National Lab is working to build a mechanistic understanding of the distribution and dynamics of biogeochemical processes in mountainous watersheds and their response to perturbation. In June 2018, the NEON (National Ecological Observatory Network) Airborne Observatory Platform (AOP) performed a taskable airborne imaging campaign to collect visible to shortwave infrared (VSWIR) imaging spectroscopy and LiDAR data across 330 km2 in the Upper East River at Crested Butte, CO. We conducted a parallel ground sampling campaign to sample vegetation traits, as well as soil physical, chemical, and microbiological characteristics. We collected these samples from 438 sites across 12 locations spanning much of the elevation, topographic, and geologic variability across the study area. A subset of 250 samples were used for soil metagenomics which is presented here.In addition, at each site, vegetation samples were collected to measure species-specific leaf water content and leaf mass area, foliar elemental composition and foliar CN stable isotope ratios. Soil samples were collected to measure soil physical properties which include bulk density and soil texture analysis. A suite of soil chemical properties was measured from the samples collected at each site, including pH, organic matter, concentrations exchangeable cations, total elemental composition, and the concentrations of extractable N pools (e.g. total free amino acids, ammonium, nitrate, dissolved organic N, and total dissolved N). Additionally, we have measured soil microbial biomass CN stoichiometry.Here, we present 1982 metagenome-assembled genomes (MAGs) for the bacterial and archaeal community from topsoil collected from during NEON 2018 campaign. All metagenomes were sequenced at JGI (Joint Genome Institute) (GOLD Study ID: Gs0149986). Metagenomes were assembled using JGI Metagenome Workflow (10.1128/mSystems.00804-20). The dataset includes (1) zip files for 1982 MAG fasta files (neon_genomes1-5.tar.gz, split into 5 tarballs to keep tarballs under 0.5 GB), (2) neon_Gs0149986_samples_soilproperties_metagenomes.csv: the sample information together with the accession numbers for the underlying metagenomes and the associated soil physical and chemical measurements in NMDC (National Microbiome Data Collaborative) compliant format, (3) neon_Gs0149986.kml: location bounding box file for the sampled locations, (4) samples.csv: sample metadata file used to register Internationall Generic Sample Numbers (IGSNs), (5) flmd.csv: file level metadata file, and (6) dd.csv: data dictionary 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.
- Research Organization:
- Watershed Function SFA
- Sponsoring Organization:
- U.S. DOE > Office of Science > Biological and Environmental Research (BER)
- DOE Contract Number:
- AC02-05CH11231
- OSTI ID:
- 2587101
- Country of Publication:
- United States
- Language:
- English
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Related Subjects
EARTH SCIENCE > BIOSPHERE > OMICS > BUILDING BLOCKS > CONTIG:GCMD
EARTH SCIENCE > BIOSPHERE > OMICS > BUILDING BLOCKS > eDNA:GCMD
EARTH SCIENCE > BIOSPHERE > OMICS > METAGENOME > METAGENOME ASSEMBLED GENOMES (MAGs):GCMD
EARTH SCIENCE > BIOSPHERE > OMICS > MICROBIOME:GCMD
EARTH SCIENCE > BIOSPHERE > OMICS > OMICS METHODOLOGY > BIN/BINNING:GCMD
EARTH SCIENCE > LAND SURFACE > SOILS
EARTH SCIENCE > LAND SURFACE > SOILS > MICROFAUNA:GCMD
ESS-DIVE CSV File Formatting Guidelines Reporting Format
ESS-DIVE File Level Metadata Reporting Format
ESS-DIVE Sample ID and Metadata Reporting Format
NEON Campaign 2018