Metagenome-assembled genomes from soil samples in control and warming plots in Blodgett Forest, CA (2014-2021)

Karaoz, Ulas; L. Brodie, Eoin; Torn, Margaret; J. Eloy Alves, Ricardo

doi:10.15485/2588706

Title: Metagenome-assembled genomes from soil samples in control and warming plots in Blodgett Forest, CA (2014-2021)

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Abstract

The pathways of carbon transport and loss through and from soils—soil organic matter (SOM) depolymerization to dissolved organic carbon and mineralization to carbon dioxide (CO2)—are fundamentally driven by microbial activity, which is strongly regulated by environmental conditions. As part of LBNL (Lawrence Berkeley National Laboratory) TES (Terrestrial Ecosystem Science) Belowground Biogeochemistry Science Focus Area (SFA), we have established a novel whole-soil long-term warming experiment at the University of California (UC) Blodgett Forest Research Station (Sierra Nevada) in 2014, where we study the role of biogeochemical, microbial and geochemical process interactions in SOM decomposition and stabilization.Here, we present metagenome-assembled genomes (MAGs) for the bacterial and archaeal community from soil depth profiles collected from 2014 to 2021 from three paired control and warming plots. We collected soil samples across a range of depth profiles (spanning surface to 90 cm deep) from three paired control and warming plots from a temperate mixed forest in Northern California. Each paired plot had been subjected to experimental warming since June 2014 to simulate a predicted climate change scenario for northern California. 101 soil metagenomes were sequenced at JGI (Joint Genome Institute) and UCSF (University of California San Francisco) Center for Advanced Technology and can be foundmore »« less

Authors:

;

Lawrence Berkeley National Laboratory

Publication Date:: Tue Dec 31 23:00:00 EST 2024

DOE Contract Number:: AC02-05CH11231

Research Org.:: Belowground Biogeochemistry Scientific Focus Area

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

Subject:: 54 ENVIRONMENTAL SCIENCES; 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

OSTI Identifier:: 2588706

DOI:: https://doi.org/10.15485/2588706

Citation Formats


                    Karaoz, Ulas, L. Brodie, Eoin, Torn, Margaret, and J. Eloy Alves, Ricardo. Metagenome-assembled genomes from soil samples in control and warming plots in Blodgett Forest, CA (2014-2021).  United States: N. p., 2024. 
        Web.  doi:10.15485/2588706.

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                    Karaoz, Ulas, L. Brodie, Eoin, Torn, Margaret, & J. Eloy Alves, Ricardo. Metagenome-assembled genomes from soil samples in control and warming plots in Blodgett Forest, CA (2014-2021).  United States.  doi:https://doi.org/10.15485/2588706

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                    Karaoz, Ulas, L. Brodie, Eoin, Torn, Margaret, and J. Eloy Alves, Ricardo. 2024.  
"Metagenome-assembled genomes from soil samples in control and warming plots in Blodgett Forest, CA (2014-2021)".  United States.  doi:https://doi.org/10.15485/2588706.  https://www.osti.gov/servlets/purl/2588706. Pub date:Tue Dec 31 23:00:00 EST 2024

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@article{osti_2588706,

  title        = {Metagenome-assembled genomes from soil samples in control and warming plots in Blodgett Forest, CA (2014-2021)},

  author       = {Karaoz, Ulas and L. Brodie, Eoin and Torn, Margaret and J. Eloy Alves, Ricardo},

  abstractNote = {The pathways of carbon transport and loss through and from soils—soil organic matter (SOM) depolymerization to dissolved organic carbon and mineralization to carbon dioxide (CO2)—are fundamentally driven by microbial activity, which is strongly regulated by environmental conditions. As part of LBNL (Lawrence Berkeley National Laboratory) TES (Terrestrial Ecosystem Science) Belowground Biogeochemistry Science Focus Area (SFA), we have established a novel whole-soil long-term warming experiment at the University of California (UC) Blodgett Forest Research Station (Sierra Nevada) in 2014, where we study the role of biogeochemical, microbial and geochemical process interactions in SOM decomposition and stabilization.Here, we present metagenome-assembled genomes (MAGs) for the bacterial and archaeal community from soil depth profiles collected from 2014 to 2021 from three paired control and warming plots. We collected soil samples across a range of depth profiles (spanning surface to 90 cm deep) from three paired control and warming plots from a temperate mixed forest in Northern California. Each paired plot had been subjected to experimental warming since June 2014 to simulate a predicted climate change scenario for northern California. 101 soil metagenomes were sequenced at JGI (Joint Genome Institute) and UCSF (University of California San Francisco) Center for Advanced Technology and can be found under the JGI (Joint Genome Institute) GOLD (Genomes Online Database) Sequencing project Gs0151586 and NCBI (National Center for Biotechnology Information) Projects PRJNA1225762 and PRJEB39497. Metagenomes were assembled using JGI (Joint Genome Institute) Metagenome Workflow (10.1128/mSystems.00804-20). For each metagenome, the assembled contigs were binned into genomes using 3 binning algorithms (cocacola, metabat, and maxbin) and the resulting bins were consolidated using dastool. The consolidated bins from all metagenomes were pooled, filtered by completeness (>50%) and contamination (<25%), and dereplicated at 99% ANI (average nucleotide identity) using dRep (https://github.com/MrOlm/drep).The dataset includes a zip file of 2321 MAG (Metagenome Assembled Genome) fasta files, the accession numbers for the underlying metagenomes, and a csv file with MAG (Metagenome Assembled Genome) quality metrics and taxonomic classification (GTDB -Genome Taxonomy Database-RS220). 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. A sample metadata file (samples.csv) that contains site information has also been included.},

  doi          = {10.15485/2588706},

  journal      = {},

  number       = ,

  volume       = ,

  place        = {United States},

  year         = {Tue Dec 31 23:00:00 EST 2024},

  month        = {Tue Dec 31 23:00:00 EST 2024}

}

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DOI: https://doi.org/10.15485/2588706

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