DOE BER Research Programs Browser

Bioenergy Research Centers (4)

GLBRC Great Lakes Bioenergy Research Center

GLBRC is a cross-disciplinary research center developing sustainable biofuels and bioproducts from dedicated energy crops grown on marginal, nonagricultural lands. Research spans three crosscutting themes: sustainable bioenergy cropping systems, sustainable biomass conversion, and sustainable field-to-product optimization.

Lead institution: University of Wisconsin-Madison

Partners:

Michigan State University Doe Joint Genome Institute Pacific Northwest National Laboratory

Location: Madison, Wisconsin

Funding: DOE BER / Genomic Science Program (2023-2028) - $375 million (across three funding phases since 2007)

Established: 2007

Principal investigators:

Timothy Donohue

Director

University of Wisconsin-Madison

Federica Brandizzi

Science Director

Michigan State University

Links:

Main Doe Page Data Portal Atlas

NMDC umbrella study: nmdc:sty-11-y1kdd163

Scientific questions:

How can we develop sustainable bioenergy cropping systems on marginal lands?
What are the mechanisms of lignocellulose deconstruction?
How do we optimize conversion of biomass to fuels and chemicals?
What microorganisms and enzymes can efficiently convert plant biomass?
How do we balance productivity with ecosystem sustainability?

Keywords:

Bioenergy Biofuels Lignocellulose Switchgrass Poplar Energy Sorghum Miscanthus Microbial Conversion Sustainability Marginal Lands Cellulosic Biomass

Data types:

Genomics Transcriptomics Metabolomics Proteomics Field Trial Data Satellite Imagery Crop Yield Data Soil Microbiome Data Enzyme Activity Data

Modalities:

Field Experiments Greenhouse Studies Laboratory Fermentation Remote Sensing Long Term Ecological Research High Throughput Screening

Studies 9

nmdc:sty-11-e4yb9z58 - Seasonal activities of the phyllosphere microbiome of perennial crops (Ashley Shade)

Genome-centric approach to identify ecologically important leaf microbiome members on switchgrass and miscanthus, quantifying activities over two growing seasons. Classes represented by MAGs (Actinomycetia, Alpha- and Gamma-Proteobacteria, Bacteroidota) are active in late season with stress-associated pathways and biosynthetic pathways for terpenes and non-ribosomal peptides.

Organism: switchgrass phyllosphere metagenome

Data modalities:

Metagenomics Metatranscriptomics

Primary reference: doi:10.1038/s41467-023-36515-y - Seasonal activities of the phyllosphere microbiome of perennial crops

nmdc:sty-11-wbc14h22 - Switchgrass cropping systems on marginal lands (Maren Friesen)

Understanding how rhizosphere microbiome influences soil nitrogen transformations under low- and high-N conditions across five locations in the Great Lakes Region.

Organism: Panicum virgatum

Data modalities:

Amplicon 16s

Samples: 2971

BioProjects: PRJNA733109, PRJNA733505, PRJNA733764

HIGH Sorghum Phyllosphere Microbiome (Ashley Shade)

Functional and genomic diversity of the sorghum phyllosphere microbiome. Collection of 47 bacteria isolated from aerial root mucilage of energy sorghum plus metagenome and metatranscriptome data from phyllosphere communities.

Organism: Sorghum bicolor

Data modalities:

Metagenomics Metatranscriptomics Amplicon 16s

Keywords:

Sorghum Rhizosphere Plant Microbe Interactions Bioenergy

BioProjects: PRJNA862978, PRJNA844896

BRC Dataset IDs: Gs0157305, PRJNA862978, PRJNA844896, 503249

Primary reference: doi:10.1038/s41467-024-50463-1 - Disentangling plant- and environment-mediated drivers of active rhizosphere bacterial community dynamics during short-term drought

HIGH Switchgrass Root and Soil Microbiome (Lukas P. Bell-Dereske)

Variation in root and soil microbiome over space and time in switchgrass. Bacterial and fungal community characterization from GLBRC Marginal Lands Experiment via 16S and ITS amplicon sequencing.

Organism: Panicum virgatum

Data modalities:

Amplicon 16s Amplicon Its

Keywords:

Switchgrass Rhizosphere Soil Microbiome Marginal Lands Bacterial Fungal Interactions

BioProjects: PRJNA733764, PRJNA799201

BRC Dataset IDs: PRJNA733764, PRJNA799201, zenodo.7307179, 10.17605/OSF.IO/5VW9C

Primary reference: doi:10.1186/s40793-023-00504-x - Regional biogeography versus intra-annual dynamics of the root and soil microbiome

MEDIUM Transgenic Switchgrass Microbiome Effects (Greg Bonito)

Effects of genetic modification of the shikimate pathway (QsuB transgenic) on switchgrass-associated microbiomes in different plant compartments. 16S and ITS rDNA sequencing of roots, leaves, and soil.

Organism: Panicum virgatum

Data modalities:

Amplicon 16s Amplicon Its

Keywords:

Switchgrass Lignin Plant Microbe Interactions Metabolic Engineering

BioProjects: PRJNA1002602, PRJNA1002603

BRC Dataset IDs: PRJNA1002602, PRJNA1002603

Primary reference: doi:10.1128/spectrum.01546-24 - Genetic modification of the shikimate pathway to reduce lignin content in switchgrass ( Panicum virgatum L.) significantly impacts plant microbiomes

MEDIUM Terpene Effects on Sorghum Microbiome (Greg Bonito)

Examining the effects of terpene addition on the microbial community in Sorghum belowground compartments via amplicon sequencing.

Organism: Sorghum bicolor

Data modalities:

Amplicon 16s

Keywords:

Sorghum Rhizosphere Plant Microbe Interactions Terpenes

Samples: 228

BioProjects: PRJNA933671

BRC Dataset IDs: PRJNA933671

Primary reference: doi:10.1128/spectrum.01332-23 - Terpenes modulate bacterial and fungal growth and sorghum rhizobiome communities

HIGH KBS MCSE Long-term Cropping Experiment Metagenomes (Jennifer M. Jones)

Metagenomics from Kellogg Biological Station Long Term Ecological Research Main Cropping System Experiment (KBS MCSE). Testing how drought affects microbial allocation to stress tolerance across different cropping systems.

Organism: soil metagenome

Data modalities:

Metagenomics

Keywords:

Soil Microbiome Drought Carbon Use Efficiency Long Term Ecological Research

Samples: 106

BioProjects: PRJNA1156252

BRC Dataset IDs: PRJNA1156252, knb-lter-kbs.238.1

Primary reference: doi:10.1016/j.soilbio.2025.109787 - Drought increases microbial allocation to stress tolerance but with few tradeoffs among community-level traits

MEDIUM Soil Pore Space Decomposition Microbiome (Gian Maria Niccolò Benucci)

Exploring interactions between plant detritus decomposition and micro-scale characteristics of soil physical micro-environments. Soil metagenome sequencing of leaf litter decomposition in soil microcosms.

Organism: soil metagenome

Data modalities:

Metagenomics

Keywords:

Soil Microbiome Decomposition Carbon Cycling

Samples: 872

BioProjects: PRJNA938072

BRC Dataset IDs: PRJNA938072

Primary reference: doi:10.3389/fmicb.2023.1172862 - The microbiome structure of decomposing plant leaves in soil depends on plant species, soil pore sizes, and soil moisture content

LOW Bioreactor Fermentation Microbiomes (Daniel R. Noguera)

Metagenome-assembled genomes from anaerobic bioreactor microbial communities fermenting dairy coproducts (UltraFiltered Milk Permeate and Cottage cheese Acid Whey). Characterization of carboxylate platform fermentation systems.

Organism: bioreactor metagenome

Data modalities:

Metagenomics

Keywords:

Microbial Conversion Biofuels

BioProjects: PRJNA1159295, PRJNA1040840, PRJNA768492

BRC Dataset IDs: PRJNA1159295, PRJNA1040840, PRJNA768492

Primary reference: doi:10.3389/fbioe.2023.1173656 - A metagenome-level analysis of a microbial community fermenting ultra-filtered milk permeate

Key Publications 8

doi:10.1007/s12155-015-9660-8 The DOE Bioenergy Research Centers: History, Operations, and Scientific Output

The four BRCs have produced over 1,800 peer-reviewed publications since 2007
Cross-center collaborations have enabled genome-to-field integration approaches

doi:10.1038/s41586-020-03127-1 Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass

High-quality genome assembly of 732 switchgrass genotypes reveals extensive genomic evidence of climate adaptation across 10 common gardens spanning 1,800 km latitude
Gene flow accelerated climate adaptation during postglacial colonization through introgression between divergent ecotypes
Polyploidy enhanced adaptive potential through fractionation of duplicated gene functions between upland and lowland ecotypes
Collaboration across all four DOE Bioenergy Research Centers

doi:10.1094/PBIOMES-07-20-0051-R Seasonal dynamics of core fungi and bacterial networks in the switchgrass phyllosphere

Strong temporal patterns in epiphytic microbial composition across growing season
Fungi-bacteria network associations were much more common than bacteria-bacteria associations
Identified core fungal taxa persistent throughout the growing season

doi:10.3390/agronomy13051294 Genome-Resolved Metagenomics of Nitrogen Transformations in the Switchgrass Rhizosphere Microbiome on Marginal Lands

Resolved 29 metagenome-assembled genomes from switchgrass rhizosphere on marginal lands
Rhizosphere microbiome may provide associative nitrogen fixation via novel diazotroph Janthinobacterium
Taxa from Verrucomicrobia, Acidobacteria, and Planctomycetes dominate nitrogen cycling in switchgrass rhizosphere

doi:10.1038/s42003-023-05290-3 Anti-fungal bioactive terpenoids in the bioenergy crop switchgrass may contribute to ecotype-specific microbiome composition

Switchgrass produces bioactive terpenoids with antifungal properties
Ecotype-specific terpenoid profiles may shape distinct microbiome compositions

doi:10.1111/gcbb.13094 A 30% reduction in switchgrass rhizome reserves did not decrease biomass yield

Switchgrass can tolerate significant rhizome reserve reduction without yield loss
Findings support potential for late-season harvest management

doi:10.1111/nph.70313 Local adaptation in switchgrass rust pathosystem

Evidence for local adaptation in switchgrass-rust pathogen interactions

doi:10.1111/gcbb.70051 Agricultural management legacy effects on switchgrass growth

Prior agricultural management practices have lasting effects on switchgrass establishment and growth

Datasets 2

Switchgrass Reference Genome

High-quality reference genome assembly for switchgrass (Panicum virgatum), the preeminent American perennial C4 bioenergy crop for cellulosic ethanol. Genome assembly based on 732 resequenced genotypes grown across 10 common gardens spanning 1,800 km of latitude.

Repository: JGI Phytozome

URL: https://phytozome.jgi.doe.gov/

Data type: genomics

Reference: doi:10.1038/s41586-020-03127-1 - Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass

KBS Lux Arbor Reserve Switchgrass Flux Data

Eddy covariance flux tower data from switchgrass plots at the Lux Arbor Reserve. Measures carbon, water, and energy exchanges between switchgrass ecosystem and atmosphere.

Repository: Ameriflux

DOI: 10.17190/AMF/1644212

Data type: environmental sensor data

Outputs: Publications: >1800 peer-reviewed papers | Patent applications: 286 | Startups: 5

JBEI Joint BioEnergy Institute

JBEI is dedicated to developing advanced biofuels—liquid fuels derived from solar energy stored in plant biomass—that can replace gasoline, diesel, and jet fuels. JBEI takes an interdisciplinary approach combining expertise in synthetic biology, plant biology, and chemical engineering.

Lead institution: Lawrence Berkeley National Laboratory

Partners:

Sandia National Laboratories Lawrence Livermore National Laboratory University Of California, Berkeley University Of California, Davis Iowa State University Carnegie Institution For Science

Location: Emeryville, California

Funding: DOE BER / Genomic Science Program (2023-2028)

Established: 2007

Principal investigators:

Jay D. Keasling

CEO

Lawrence Berkeley National Laboratory / UC Berkeley

Blake A. Simmons

Chief Science and Technology Officer

Lawrence Berkeley National Laboratory

Henrik Vibe Scheller

VP of Feedstocks

Lawrence Berkeley National Laboratory

Links:

Main Doe Page Github

NMDC umbrella study: nmdc:sty-11-ggfd7z76

Scientific questions:

How can we engineer plants for improved biomass production?
What ionic liquid pretreatments optimize biomass deconstruction?
How do we engineer microbes for efficient biofuel production?
What metabolic pathways can produce drop-in biofuels?
How can synthetic biology accelerate biofuel development?

Keywords:

Biofuels Synthetic Biology Ionic Liquids Metabolic Engineering Plant Cell Walls Lignin Valorization Terpenes Fatty Acids Microbial Chassis

Data types:

Genomics Transcriptomics Metabolomics Proteomics Synthetic Biology Constructs Enzyme Kinetics

Modalities:

High Throughput Screening Robotic Automation Mass Spectrometry Nmr Spectroscopy Computational Modeling

Studies 1

nmdc:sty-11-n7mtj961 - Impact of modulating bioenergy traits on the sorghum microbiome under drought conditions (Henrik Vibe Scheller)

16S amplicon sequences from the rhizosphere of sorghum under well-watered and drought-stressed conditions in Davis, California.

BioProjects: PRJNA1205755

Key Publications 2

doi:10.1038/nature04607 Designed divergent evolution of enzyme function

doi:10.1038/s41586-019-0978-9 Complete biosynthesis of cannabinoids and their unnatural analogues in yeast

Datasets 1

JBEI ICE (Inventory of Composable Elements)

Registry of standard biological parts for synthetic biology

URL: https://github.com/jbei

Data type: synthetic biology parts

Outputs: Publications: 685 (first 10 years) | Patent applications: 169 | Patents: 28 | Startups: 6

CABBI Center for Advanced Bioenergy and Bioproducts Innovation

CABBI develops fuels and products by integrating feedstock development, conversion science, and sustainability research. Using a "plants as factories" approach, CABBI researchers engineer crops to accumulate lipids and specialty chemicals while developing novel conversion technologies.

Lead institution: University of Illinois Urbana-Champaign

Partners:

Princeton University University Of California, Berkeley University Of Florida Iowa State University Colorado State University Hudsonalpha Institute For Biotechnology Lawrence Berkeley National Laboratory Brookhaven National Laboratory

Location: Urbana, Illinois

Funding: DOE BER / Genomic Science Program (2023-2028)

Established: 2017

Principal investigators:

Evan H. DeLucia

Director Emeritus

University of Illinois Urbana-Champaign

Andrew Leakey

Director

University of Illinois Urbana-Champaign

Links:

Main Doe Page Github Data Hub

NMDC umbrella study: nmdc:sty-11-3cmn1g53

Scientific questions:

How can we engineer crops to produce oils and specialty chemicals?
What are sustainable approaches to bioenergy crop production?
How do we optimize lipid accumulation in vegetative tissues?
What conversion technologies maximize bioproduct yields?
How do land use changes affect carbon and ecosystem services?

Keywords:

Lipid Accumulation Sugarcane Miscanthus Sorghum Bioproducts Sustainability Life Cycle Assessment Oil Crops Metabolic Engineering

Data types:

Genomics Transcriptomics Metabolomics Field Trial Data Life Cycle Assessment Data Economic Modeling Data

Modalities:

Field Experiments Greenhouse Studies Metabolic Flux Analysis Techno Economic Analysis Ecosystem Modeling

Studies 6

HIGH nmdc:sty-11-vh2hty57 - The Impact of Stand Age and Fertilization on the Soil Microbiome of Miscanthus × giganteus (Adina Howe)

Investigation of effects of stand age and N fertilizer rates on microbial community structure in Miscanthus × giganteus replicated chronosequence trial.

Organism: Miscanthus × giganteus

Data modalities:

Amplicon 16s

Samples: 648

BioProjects: PRJNA601860

HIGH Native Miscanthus Rhizosphere and Endophytic Microbiome (Angela Kent)

Survey of the native Miscanthus rhizosphere and endophytic microbiome in Taiwan, with particular attention to the diazotrophic community across strong biogeographical and ecological gradients in Miscanthus sinensis and M. floridulus.

Organism: Miscanthus sinensis, Miscanthus floridulus

Data modalities:

Amplicon 16s

Samples: 466

BioProjects: PRJNA561781

MEDIUM Soil Microbiome of Miscanthus × giganteus at LAMPS Study Site (Adina Howe)

SSU rRNA RNA library of soil microbiome at LAMPS. Complements DNA-based study examining total vs metabolically active microbial communities under nitrogen fertilization.

Organism: Miscanthus × giganteus

Data modalities:

Amplicon 16s

Samples: 271

BioProjects: PRJNA745191

HIGH Sorghum Rhizosphere Nitrification Study (Wendy Yang)

Intra- and inter-annual variability of nitrification in the rhizosphere of field-grown bioenergy sorghum, examining biological nitrification inhibition (BNI) potential and soil microbial communities across fertilizer treatments.

Organism: Sorghum bicolor

Data modalities:

Amplicon 16s

Samples: 288

BioProjects: PRJNA741261

HIGH Sugarcane and Oilcane Microbiome Differences (Adina Howe)

Study of bacterial and fungal microbiome structure and potential functions in leaves, stems, roots, rhizospheres, and bulk soils of sugarcane and metabolically engineered oilcane grown in greenhouses.

Data modalities:

Amplicon 16s Amplicon Its

Samples: 200

BioProjects: PRJNA892137

MEDIUM Plant-Nitrifier Interactions in Topsoil and Subsoil (Wendy Yang)

Investigation of soil microorganisms along 1 meter soil profiles in Miscanthus × giganteus, examining distinct mechanisms driving plant-nitrifier interactions at different depths.

Organism: Miscanthus × giganteus

Data modalities:

Amplicon 16s

Samples: 103

BioProjects: PRJNA1080623

Key Publications 1

doi:10.1094/PBIOMES-05-21-0033-MR Frontiers and Opportunities in Bioenergy Crop Microbiome Research Networks

Datasets 1

BEPAM Model Code and CABBI Simulation Results

Biofuel and Environmental Policy Analysis Model for assessing returns to land and greenhouse gas savings from energy crops.

Repository: Illinois Data Bank

DOI: 10.13012/B2IDB-5598609_V1

Data type: economic modeling

CBI Center for Bioenergy Innovation

CBI focuses on accelerating the domestication of bioenergy-relevant non-model plants and microbes to enable high-impact innovation across the sustainable aviation fuel supply chain. The center develops high-yielding, process-advantaged feedstock plants using advanced genetic technologies.

Lead institution: Oak Ridge National Laboratory

Partners:

University Of Tennessee Georgia Institute Of Technology National Renewable Energy Laboratory Dartmouth College University Of Georgia

Location: Oak Ridge, Tennessee

Funding: DOE BER / Genomic Science Program (2023-2028)

Established: 2017

Predecessor: BioEnergy Science Center (BESC, 2007-2017)

Principal investigators:

Gerald A. Tuskan

Director

Oak Ridge National Laboratory

Links:

Main Ornl Page Doe Page Publications Highlights

NMDC umbrella study: nmdc:sty-11-cssvjy19

Scientific questions:

How do we accelerate domestication of perennial bioenergy crops?
What genetic factors control biomass recalcitrance?
How can we engineer microbes for efficient biomass conversion?
What processes enable sustainable aviation fuel production?
How do plant-microbe interactions affect feedstock quality?

Keywords:

Poplar Switchgrass Sustainable Aviation Fuel Lignin Biomass Recalcitrance Genomic Selection Perennial Crops Populus Microbial Conversion

Data types:

Genomics Transcriptomics Metabolomics Proteomics Phenotypic Data Gwas Data

Modalities:

Genome Wide Association Field Trials Common Garden Experiments High Throughput Phenotyping Fermentation Studies

Studies 3

HIGH nmdc:sty-11-kfvmk798 - Chronic drought differentially alters the belowground microbiome of Populus trichocarpa (Melissa Cregger)

Assessment of archaeal/bacterial and fungal communities within root endosphere, rhizosphere, and bulk soil of P. trichocarpa genotypes under drought in Boardman, OR.

Organism: Populus trichocarpa

Data modalities:

Amplicon 16s Amplicon Its

Samples: 384

BioProjects: PRJNA784967

HIGH Poplar Rhizosphere Microbiota Assembly Dynamics (Aurelie Deveau)

Characterization of fungal and bacterial community assembly from root to shoot axis in poplar (P. tremula x tremuloides) over 30 days of growth, tracking changes in rhizosphere, root and shoot by DNA metabarcoding alongside metabolomics.

Organism: Populus tremula x tremuloides

Data modalities:

Amplicon 16s Amplicon Its Metabolomics

Samples: 505

BioProjects: PRJNA1017804

MEDIUM Clostridium thermocellum Strain Collection (Daniel Olson)

Whole genome resequencing data for hundreds of Clostridium thermocellum strains engineered for increased ethanol production and tolerance, with mutation and lineage metadata.

Key Publications 1

doi:10.1002/bbb.2148 Economic impact of yield and composition variation in bioenergy crops: Populus trichocarpa

Datasets 1

Populus GWAS Dataset

Over 28 million SNPs from approximately 882 resequenced poplar genotypes, linking DNA variations to plant characteristics.

Data type: genomics/GWAS

Size: ~17 terabytes raw data

Genomic Science SFAs (11)

ENIGMA ENIGMA: Ecosystems and Networks Integrated with Genes and Molecular Assemblies

ENIGMA emphasizes achieving a multiscale, causal, and predictive understanding of microbial biology and the reciprocal impact of microbial communities on their ecosystems. Focus on processes affecting denitrification and metal reduction in contaminated subsurface environments.

Lead institution: Lawrence Berkeley National Laboratory

Funding: DOE BER / Genomic Science Program

Principal investigators:

Paul D. Adams

Project Manager

Lawrence Berkeley National Laboratory

Adam P. Arkin

Technical Co-manager

Lawrence Berkeley National Laboratory

Links:

Main Doe Page Kbase

KBase Collection: ENIGMA

Scientific questions:

What mechanisms drive subcellular, cellular, and intercellular networks?
How do microbial networks drive macroscopic biogeochemical processes?
What controls denitrification and metal reduction in subsurface?
How do microbial communities respond to contamination?

Keywords:

Microbial Ecosystems Denitrification Metal Reduction Uranium Nitrate Subsurface Microbiology Systems Biology Metagenomics

Data types:

Metagenomics Transcriptomics Proteomics Metabolomics Structural Biology Environmental Sensor Data

Modalities:

High Throughput Sequencing Mass Spectrometry Imaging Synchrotron Methods Computational Modeling

Phenotype assays:

Rbtseq Fitness Stress Tolerance Anaerobic Growth Substrate Utilization Growth Curves Coculture Interactions

Field Sites 1

Oak Ridge Reservation (ORR) (East Tennessee)

Bear Creek aquifer with complex contaminant gradients

Contaminants:

Nitrates Uranium Volatile Organic Carbon Species

Isolate Collections 1

ENIGMA Subsurface Isolates 261 isolates

Bacterial and archaeal isolates from Oak Ridge Reservation subsurface environments including contaminated groundwater and sediments. Characterized for stress tolerance and denitrification/metal reduction capabilities.

Organism types:

Bacteria Archaea

Genomes sequenced: 261

Source environments:

Oak Ridge Subsurface Contaminated Groundwater Aquifer Sediments

Isolation methods: Aerobic plating, Anaerobic enrichment

Genome catalog: View genomes

Reference: doi:10.1128/msystems.00537-21 - Ecogenomics of Groundwater Phages Suggests Niche Differentiation Linked to Specific Environmental Tolerance

Studies 3

HIGH Oak Ridge Groundwater 100-Well Survey Metagenomes (Jizhong Zhou)

Comprehensive metagenomic survey of groundwater microbial communities from 100 wells at the Oak Ridge Field Research Center. Examines community assembly processes under environmental stress from contamination gradients.

Organism: groundwater metagenome

Data modalities:

Metagenomics

BioProjects: PRJNA1001011

Primary reference: doi:10.1038/s41564-023-01573-x - Environmental stress mediates groundwater microbial community assembly

MEDIUM Oak Ridge Sediment and Groundwater Metagenomes (Lauren M. Lui)

26 subsurface sediment and 9 groundwater metagenomes from the Oak Ridge Reservation studying subsurface microbiome from centimeter to field scale.

Organism: groundwater metagenome

Data modalities:

Metagenomics

BioProjects: PRJNA1001011

Primary reference: doi:10.1128/mra.00014-25 - Sediment and groundwater metagenomes from subsurface microbial communities from the Oak Ridge National Laboratory Oak Ridge Reservation, Oak Ridge, Tennessee, USA

MEDIUM ENIGMA Groundwater Archaeal Diversity (Jillian F. Banfield)

Genome-resolved metagenomic analysis of archaeal diversity in subsurface environments. Identified two new phyla (DPANN superphylum) from aquifer adjacent to Colorado River.

Organism: groundwater metagenome

Data modalities:

Metagenomics

BioProjects: PRJNA268032

Analyses & KBase Narratives 2

ENIGMA public isolates from Kothari et al 2020

261 ENIGMA isolate genomes from Oak Ridge subsurface with GTDB taxonomy assignments. Includes sequencing reads, assemblies, and annotations processed via KBase workflows.

Type: Kbase Narrative

Genomes: 261

Output types:

Genomics

Reference: doi:10.1128/msystems.00537-21 - Ecogenomics of Groundwater Phages Suggests Niche Differentiation Linked to Specific Environmental Tolerance

Data from Kothari et al 2020

Supporting data narrative for ENIGMA isolate phenotyping study

Type: Kbase Narrative

Key Publications 2

doi:10.1038/s41564-023-01573-x Environmental stress mediates groundwater microbial community assembly

Stochastic assembly processes are critical (>60% on average) in shaping groundwater community structure, but decrease in importance as environmental stress increases.
Selection processes leading to dissimilar communities increased with stresses, primarily related to pH, cobalt and molybdenum.

doi:10.2172/1963932 Ecosystems and Networks Integrated with Genes and Molecular Assemblies: Integrating Metabolomics into Environmental Systems Biology

Datasets 1

ENIGMA Environmental Data

Multi-omics data from Oak Ridge Reservation subsurface

Repository: KBase

Data type: metagenomics/environmental

m-CAFEs m-CAFEs: Microbial Community Analysis and Functional Evaluation in Soils

m-CAFEs develops and deploys unique laboratory capabilities to capture key aspects of grass rhizosphere communities and identify causal mechanisms governing microbial interactions within the rhizosphere. Uses advanced fabricated ecosystems with gene editing technologies for interrogating gene and microbial functions in situ.

Lead institution: Lawrence Berkeley National Laboratory

Partners:

University Of California, Berkeley North Carolina State University Boston University Sandia National Laboratories

Funding: DOE BER / Genomic Science Program

Principal investigators:

Trent R. Northen

Principal Investigator

Lawrence Berkeley National Laboratory

Links:

Main Doe Page

NMDC umbrella study: nmdc:sty-11-abkzcd11

Scientific questions:

What mechanisms govern microbial interactions in the rhizosphere?
How can we predict and manipulate rhizosphere communities?
What controls carbon cycling in plant-microbe-soil systems?
How do microbiomes respond to perturbations?

Keywords:

Rhizosphere Soil Microbiome Fabricated Ecosystems Crispr Phage Carbon Cycling Brachypodium Ecofab

Data types:

Metagenomics Transcriptomics Metabolomics Exometabolomics Imaging Data

Modalities:

Fabricated Ecosystems High Throughput Sequencing Crispr Gene Editing Live Cell Imaging

Phenotype assays:

Ecofab Phenotyping Exometabolomics Synthetic Community Plant Colonization Substrate Utilization Growth Curves Live Cell Imaging

Isolate Collections 2

m-CAFEs Rhizosphere Bacterial Collection

Bacterial isolates from Brachypodium and grass rhizospheres used for synthetic community studies in EcoFAB devices. Includes reduced complexity consortia (RCC) strains representing core rhizosphere microbiome.

Organism types:

Bacteria

Source environments:

Brachypodium Rhizosphere Grass Rhizosphere Angelo Coast Range Reserve Soil

Host organisms: Brachypodium distachyon, Avena barbata

Isolation methods: Aerobic plating, Dilution-to-extinction

m-CAFEs Phage Collection

Bacteriophages isolated from soil for phage-based genome editing and microbial community manipulation studies.

Organism types:

Phage

Source environments:

Soil Rhizosphere

Studies 8

nmdc:sty-11-zs2syx06 - Meadow Soil Metagenomes from the Angelo Coast Range Reserve (Jillian F. Banfield)

Assembled metagenomes for 60 soil samples across multiple soil plots from a meadow in the Angelo Coastal Range Reserve, CA, part of a climate change experiment.

nmdc:sty-11-ev70y104 - EcoFAB 2.0 Root Microbiome Ring Trial (Trent R. Northen)

Multi-laboratory ring trial using EcoFAB 2.0 devices with synthetic bacterial communities and Brachypodium distachyon to test reproducibility and standardization.

TARGET Brachypodium Core Root Microbiome Metabarcoding (Trent R. Northen)

16S rRNA amplicon sequencing defining core root microbiome of Brachypodium distachyon grown in four distinct soils. Identified overlooked taxa via metabarcoding vs culture.

Organism: Brachypodium distachyon

Data modalities:

Amplicon 16s

Samples: 71

BioProjects: PRJNA1120948

Primary reference: doi:10.1007/s10725-024-01221-2 - Bacterial metabarcoding reveals plant growth promoting members of the core Brachypodium distachyon root-associated microbiome overlooked by culture dependent techniques

TARGET Fine Scale Rhizosphere Spatial Heterogeneity (Trent R. Northen)

Fine scale sampling reveals spatial heterogeneity of rhizosphere microbiome in young Brachypodium plant roots using EcoFABs. Strong rhizosphere effect with Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria enrichment.

Organism: Brachypodium distachyon

Data modalities:

Amplicon 16s

Primary reference: doi:10.1038/s43705-023-00265-1 - Fine scale sampling reveals early differentiation of rhizosphere microbiome from bulk soil in young Brachypodium plant roots

TARGET Dynamic Root Exudate Chemistry and Microbial Assembly (Trent R. Northen)

Landmark study showing dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly. Avena barbata in natural soil.

Organism: Avena barbata

Data modalities:

Amplicon 16s Metabolomics Exometabolomics

Primary reference: doi:10.1038/s41564-018-0129-3 - Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly

TARGET Core Metabolome and Root Exudation Dynamics (Trent R. Northen)

Core metabolome and root exudation dynamics of three phylogenetically distinct plant species (Brachypodium, Avena, Microbotryum). Multi-omics dataset from EcoFABs.

Organism: Brachypodium distachyon

Data modalities:

Metabolomics Exometabolomics

Primary reference: doi:10.1038/s41467-023-37164-x - The core metabolome and root exudation dynamics of three phylogenetically distinct plant species

TARGET Reduced Complexity Consortia from Brachypodium Rhizosphere (Trent R. Northen)

Systematic framework to generate Reduced Complexity Consortia (RCC) representing Brachypodium rhizosphere microbiome for sustainable agriculture applications. Inoculum from Angelo Coast Range Reserve soil.

Organism: Brachypodium distachyon

Data modalities:

Amplicon 16s Metagenomics

Primary reference: doi:10.3389/fmicb.2024.1401794 - Developing stable, simplified, functional consortia from Brachypodium rhizosphere for microbial application in sustainable agriculture

TARGET Multilab EcoFAB Reproducibility Study (Trent R. Northen)

Multilab study demonstrating highly reproducible plant physiology and soil metabolite depletion patterns using EcoFAB standardized fabricated ecosystems across 4 labs.

Organism: Brachypodium distachyon

Data modalities:

Metabolomics Phenotypic Data

Primary reference: doi:10.1111/nph.15662 - Multilab EcoFAB study shows highly reproducible physiology and depletion of soil metabolites by a model grass

Key Publications 3

doi:10.1126/sciadv.adg7888 Reproducible growth of Brachypodium in EcoFAB 2.0 reveals that nitrogen form and starvation modulate root exudation

EcoFAB 2.0 enables highly reproducible plant-microbiome experiments across multiple laboratories
Nitrogen form and starvation significantly modulate root exudation patterns

doi:10.1038/s41564-018-0129-3 Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly

Root exudate chemistry dynamically changes over plant development
Microbial substrate preferences drive rhizosphere community assembly patterns

doi:10.1038/s41467-023-37164-x Core metabolome and root exudation dynamics of three phylogenetically distinct plant species

Identified core metabolome shared across phylogenetically distinct plant species

Technologies Developed 4

EcoFAB
Fabricated ecosystem serving as standardized reproducible platform for plant-microbiome research

ET-Seq
Environmental Transformation Sequencing for assessing DNA uptake in microbial communities

DART
DNA-editing All-in-one RNA-guided CRISPR-Cas Transposase system for locus-specific DNA insertion

EcoPOD
Meter-scale contained controlled ecosystems

Microbes Persist Microbes Persist: Systems Biology of the Soil Microbiome

The Microbes Persist SFA aims to understand how microbes shape soil carbon persistence. Using stable isotope-informed approaches, the team characterizes the "active" microbiome and virome, scaling from metagenomes to computational models integrating traits at system scale.

Lead institution: Lawrence Livermore National Laboratory

Partners:

University Of California, Berkeley University Of California, Davis University Of Minnesota Northern Arizona University Lawrence Berkeley National Laboratory Pacific Northwest National Laboratory

Funding: DOE BER / Genomic Science Program

Established: 2017

Principal investigators:

Jennifer Pett-Ridge

Principal Investigator

Lawrence Livermore National Laboratory

Links:

Doe Page Llnl Page Kbase

NMDC umbrella study: nmdc:sty-11-msexsy29

Scientific questions:

How do microbial cellular chemistry and ecophysiology shape soil C persistence?
What role do viruses play in soil carbon cycling?
How do moisture regimes affect microbial transformations?
What mechanisms regulate soil organic matter stabilization?

Keywords:

Soil Carbon Soil Microbiome Stable Isotopes Qsip Nanosims Soil Organic Matter Carbon Persistence Virome Moisture Regimes

Data types:

Metagenomics Metatranscriptomics Stable Isotope Data Imaging Data Radiocarbon Data

Modalities:

Stable Isotope Probing Imaging Radioisotope Approaches Multi Omics

Phenotype assays:

Qsip Activity Nanosims Activity Soil Incubation Respiration Growth Curves

Studies 5

nmdc:sty-11-076c9980 - Microbial Carbon Transformations in Wet Tropical Soils (Jennifer Pett-Ridge)

Lab enrichment of tropical soil microbial communities from Luquillo Experimental Forest, Puerto Rico, examining effects of redox fluctuation on microbial ecophysiology.

TARGET Rhizosphere Microbiome Dynamics with Genome-Informed Energy Budget Model (Jennifer Pett-Ridge)

Predictions of rhizosphere microbiome dynamics using genome-informed and trait-based energy budget model. Published in Nature Microbiology 2024.

Organism: Avena fatua

Data modalities:

Metagenomics Metatranscriptomics

Primary reference: doi:10.1038/s41564-023-01582-w - Predictions of rhizosphere microbiome dynamics with a genome-informed and trait-based energy budget model

TARGET Radiocarbon Analysis of Soil Microbial Biomass (Jennifer Pett-Ridge)

Novel method for radiocarbon analysis of soil microbial biomass via direct chloroform extraction. Enables measurement of microbial C turnover.

Data modalities:

Stable Isotope Data Radiocarbon Data

Primary reference: doi:10.1017/RDC.2023.80 - RADIOCARBON ANALYSIS OF SOIL MICROBIAL BIOMASS VIA DIRECT CHLOROFORM EXTRACTION

TARGET MISIP Data Standard for Stable Isotope Probing (Jennifer Pett-Ridge)

Data standard for reuse and reproducibility of stable isotope probing-derived nucleic acid sequences. Published in GigaScience 2024.

Primary reference: doi:10.1093/gigascience/giae071 - MISIP: a data standard for the reuse and reproducibility of any stable isotope probing-derived nucleic acid sequence and experiment

HIGH California Grassland qSIP Metagenomes (Jennifer Pett-Ridge)

Quantitative stable isotope probing with metagenomics linking microbial physiology and activity to soil moisture in Mediterranean-climate grassland ecosystems.

Organism: soil metagenome

Data modalities:

Metagenomics Stable Isotope Data

Samples: 332

BioProjects: PRJNA718849

Primary reference: doi:10.1128/msystems.00417-22 - Quantitative Stable-Isotope Probing (qSIP) with Metagenomics Links Microbial Physiology and Activity to Soil Moisture in Mediterranean-Climate Grassland Ecosystems

Key Publications 3

doi:10.1128/msystems.00417-22 Quantitative stable-isotope probing with metagenomics links microbial physiology and activity to soil moisture

First application of qSIP to all organisms in soil simultaneously
Bacterial growth occurred rapidly after wet-up with ~40% of taxa growing within one week

doi:10.1038/s41564-023-01582-w Predictions of rhizosphere microbiome dynamics using genome-informed and trait-based energy budget model

Genome-informed trait-based models can predict rhizosphere microbiome dynamics

doi:10.1073/pnas.2413032122 Codon bias, nucleotide selection, and genome size predict in situ bacterial growth rate and transcription in rewetted soil

Genomic traits including codon bias predict bacterial growth rates in soil

Datasets 1

Microbes Persist qSIP Metagenome Bins

Microbial genome bins and annotations from qSIP metagenomics

Repository: ggKbase

URL: https://ggkbase.berkeley.edu/wsip-metawrap-drep-bins/organisms

Soil Microbiome SFA Phenotypic Response of the Soil Microbiome to Environmental Perturbations

PNNL's Soil Microbiome SFA focuses on understanding how interactions among soil microbial community members lead to emergence of community functions. Research identifies molecular-level metabolic interactions governing decomposition and moisture effects on microbial phenotypes.

Lead institution: Pacific Northwest National Laboratory

Funding: DOE BER / Genomic Science Program

Principal investigators:

Kirsten Hofmockel

Principal Investigator

Pacific Northwest National Laboratory

Links:

Main Doe Page Data Hub Kbase

Scientific questions:

How do microbial interactions lead to emergent community functions?
What predictable reaction modules exist based on resource availability?
How does soil desiccation affect metabolic processes?
What controls carbon use efficiency in soils?

Keywords:

Soil Microbiome Metaphenome Decomposition Moisture Effects Carbon Use Efficiency Microbial Interactions Tall Wheatgrass

Data types:

Metagenomics Metabolomics Imaging Data Imaging Data

Modalities:

Imaging Metagenomics Laboratory Experiments

Phenotype assays:

Soil Incubation Respiration Exometabolomics Substrate Utilization

Field Sites 1

Tall Wheatgrass Irrigation Trial

Testing discoveries in bioenergy feedstock system

Studies 4

TARGET Hi-C Metagenome Sequencing of Soil Moisture Impacts on Phage-Host Interactions (Kirsten Hofmockel)

High-throughput chromosomal conformation capture (Hi-C) metagenome sequencing revealing soil moisture impacts on phage-host interactions. Published in Nature Comm 2023.

Data modalities:

Metagenomics

Primary reference: doi:10.1038/s41467-023-42967-z - Hi-C metagenome sequencing reveals soil phage–host interactions

TARGET Soil Microbiome Response to Depth, Irrigation and Plant Genotype (Kirsten Hofmockel)

Influence of soil depth, irrigation, and plant genotype on the soil microbiome, metaphenome, and carbon chemistry. Multi-omics study published in mBio 2023.

Data modalities:

Metagenomics Metabolomics Proteomics

Primary reference: doi:10.1128/mbio.01758-23 - Influence of soil depth, irrigation, and plant genotype on the soil microbiome, metaphenome, and carbon chemistry

TARGET Birch Effect Respiratory Response of Soil Microbiome (Kirsten Hofmockel)

Real-time and rapid respiratory response (90 seconds to 90 minutes) of the soil microbiome to moisture shifts. Published in Microorganisms 2023.

Data modalities:

Metabolomics

Primary reference: doi:10.3390/microorganisms11112630 - Real-Time and Rapid Respiratory Response of the Soil Microbiome to Moisture Shifts

TARGET Viral Contributions to Soil Carbon Dynamics (Kirsten Hofmockel)

Estimating the importance of viral contributions to soil carbon dynamics through metagenomics. Published in Global Change Biology 2024.

Data modalities:

Metagenomics

Primary reference: doi:10.1111/gcb.17524 - Estimating the Importance of Viral Contributions to Soil Carbon Dynamics

Key Publications 5

doi:10.1038/s41467-023-42967-z Hi-C Metagenome Sequencing Reveals Soil Moisture Impacts on Phage-Host Interactions

High-throughput chromosomal conformation capture reveals soil moisture controls phage-host dynamics

doi:10.1128/mbio.01758-23 Influence of soil depth, irrigation, and plant genotype on the soil microbiome and metaphenome

Soil depth and irrigation interact to shape microbiome composition and metabolic phenotypes

doi:10.1038/s41564-024-01686-x A global atlas of soil viruses reveals unexplored biodiversity and potential biogeochemical impacts

Global soil virome atlas reveals vast unexplored viral diversity with biogeochemical implications

doi:10.3390/microorganisms11112630 Real-time and rapid respiratory response of the soil microbiome to moisture shifts

Soil microbiome responds to moisture within 90 seconds to 90 minutes (Birch effect)

doi:10.1186/s40168-022-01427-4 Significant remodeling of the soil lipidome following extreme moisture and temperature shifts

Extreme weather events cause significant restructuring of soil lipid chemistry

Datasets 1

PNNL Soil Microbiome SFA Data

Repository: PNNL DataHub

URL: https://data.pnnl.gov/Soil_SFA

DOI: 10.25584/PRJ.SFA/1780765

InCoGenTEC InCoGenTEC

InCoGenTEC SFA at Sandia National Laboratories. Details to be populated.

Lead institution: Sandia National Laboratories

Funding: DOE BER / Genomic Science Program

Principal investigators:

Katie Mageeney

Principal Investigator

Sandia National Laboratories

Phenotype assays:

Phage Host Range Growth Curves

Isolate Collections 2

InCoGenTEC Bacterial Collection

Bacterial isolates maintained by InCoGenTEC SFA

Organism types:

Bacteria

InCoGenTEC Phage Collection

Bacteriophage isolates for phage-host studies

Organism types:

Phage

µBiospheres µBiospheres SFA

µBiospheres SFA at Lawrence Livermore National Laboratory. Details to be populated.

Lead institution: Lawrence Livermore National Laboratory

Funding: DOE BER / Genomic Science Program

Principal investigators:

Rhona Stuart

Principal Investigator

Lawrence Livermore National Laboratory

Phenotype assays:

Growth Curves

IMAGINE IMAGINE BioSecurity: Integrative Modeling and Genome-Scale Engineering for Biosystems Security

IMAGINE develops an integrative biocontainment platform to build, characterize, and predictively design biocontainment in microbial systems. The SFA integrates synthetic biology, computational modeling, and plant-soil microbiology for secure biosystems design.

Lead institution: National Renewable Energy Laboratory

Partners:

J. Craig Venter Institute University Of California, San Diego

Funding: DOE BER / Genomic Science Program

Links:

Doe Page

Scientific questions:

How do we achieve predictive control of engineered biosystems?
What biocontainment strategies maintain fitness and productivity?
How can genome-scale engineering enable secure deployment?
What tracking mechanisms ensure biosecurity?

Keywords:

Biocontainment Biosecurity Synthetic Biology Genome Engineering Microbial Chassis Combigem Dna Barcoding

Data types:

Genomics Fitness Data Containment Efficacy Data

Modalities:

High Throughput Screening Genome Scale Engineering High Throughput Sequencing

Key Publications 4

doi:10.1016/j.copbio.2021.05.004 Biotechnology for secure biocontainment designs in an emerging bioeconomy

Review of biocontainment strategies for safe deployment of engineered microbes

doi:10.1021/acssynbio.3c00175 Improved Combinatorial Assembly and Barcode Sequencing for Gene-Sized DNA Constructs

Improved methods for combinatorial DNA assembly enabling rapid biocontainment testing

doi:10.3389/fpls.2022.839446 Biocontainment of Genetically Engineered Algae

Biocontainment strategies developed for algal biofuel production systems

doi:10.1007/s00248-023-02305-2 Risk Assessment of Industrial Microbes Using a Terrestrial Mesocosm Platform

Mesocosm platform enables environmental risk assessment of engineered microbes

BFI Bacterial-Fungal Interactions and Their Role in Soil Functioning

The BFI SFA discovers fundamental principles underlying bacterial-fungal interactions to harness their biotechnological potential for steering soil ecosystem functions. Research uses novel bioinformatics and multiomics approaches to understand how bacteria and fungi sense, respond to, and co-evolve with one another.

Lead institution: Los Alamos National Laboratory

Funding: DOE BER / Genomic Science Program

Principal investigators:

Patrick Chain

Principal Investigator

Los Alamos National Laboratory

Links:

Doe Page Kbase Bfi Portal

Scientific questions:

What principles drive bacterial-fungal interactions in soil?
How do BFI affect carbon flux and nutrient cycling?
How can we steer ecosystem functions through BFI manipulation?
What molecular mechanisms mediate BFI?

Keywords:

Bacterial Fungal Interactions Endohyphal Bacteria Fungal Highways Siderophores Soil Microbiome Carbon Flux Nutrient Cycling Plant Productivity Co Evolution

Data types:

Metagenomics Transcriptomics Metabolomics Amplicon 16s Amplicon Its Imaging Data Fish Imaging Siderophore Data Endohyphal Microbiome Data Bacterial Fungal Interaction Data Fungal Highway Data

Modalities:

Multi Omics Imaging Computational Modeling Targeted Metagenomics Fungal Highway Columns Fish Microscopy Coculture Experiments Sequence Enrichment

Phenotype assays:

Bacterial Fungal Interaction Assay Fungal Highway Assay Endohyphal Screening Internalization Assay Siderophore Assay Coculture Interactions Exometabolomics Live Cell Imaging Growth Curves Competition Assays

Field Sites 3

Valles Caldera National Preserve (Jemez Mountains, New Mexico)

Montane grassland site at highest elevation in the BFI gradient. Part of elevation/precipitation transect studying bacterial-fungal interactions across environmental conditions.

Los Alamos National Laboratory (Los Alamos, New Mexico)

Mid-elevation piñon-juniper woodland site. Intermediate conditions in the BFI elevation/precipitation gradient for studying bacterial-fungal interactions.

Sevilleta LTER (Sevilleta National Wildlife Refuge, New Mexico)

Desert grassland site at lowest elevation in the BFI gradient. Represents marginal lands with arid conditions for studying bacterial-fungal interactions under water limitation.

Isolate Collections 2

BFI Bacterial Collection

Bacterial isolates used for bacterial-fungal interaction studies. Includes strains selected for their ability to interact with diverse fungal partners.

Organism types:

Bacteria

Source environments:

Soil Rhizosphere

Isolation methods: Aerobic plating

BFI Fungal Collection

Fungal isolates including soil fungi and model organisms used for bacterial-fungal interaction studies.

Organism types:

Fungi

Source environments:

Soil Rhizosphere

Isolation methods: Fungal plating, Hyphal tip isolation

Key Publications 3

doi:10.1016/j.funbio.2023.04.002 A centralized resource for bacterial-fungal interactions research

BFI Research Portal provides centralized database of reported bacterial-fungal interactions
Resource serves as foundation for computational predictions of novel interactions

doi:10.1038/s41467-024-48535-7 Enhanced surface colonisation and competition during bacterial adaptation to a fungus

Bacteria adapt to fungal presence through enhanced surface colonization strategies

doi:10.1038/s41467-023-37158-7 Metabolomics of bacterial-fungal pairwise interactions reveal conserved molecular mechanisms

Conserved metabolic mechanisms underlie diverse bacterial-fungal interactions

Datasets 4

BFI Research Portal Database

Curated database of literature-derived bacterial-fungal interaction records. Users can query bacterial or fungal taxa to identify known interaction partners. Includes interactive Krona visualizations and supports user submission of new interaction reports.

URL: https://sfa-bfi.edgebioinformatics.org/search

Fungal Highway Column Dataset

Data from 3D-printed fungal highway column experiments studying bacterial dispersal via fungal mycelia. Includes 16S/ITS amplicon data and metagenomes (150-250 bp paired-end, 10-20 Gb/sample) from soil, dung, and rhizosphere substrates.

Endohyphal Microbiome Database

Genomic and imaging data on microorganisms living within fungal hyphae, including Mollicutes-related endobacteria (MRE), viruses, cyanobacteria, algae, archaea, and plastids detected in fungal cells.

BFI Metabolomics Interaction Data

Exometabolomics data from bacterial-fungal co-cultures including siderophore profiles (ferrichrome, coprogen, novel analogues), iron/biotin availability measurements, and metabolite exchange dynamics.

PMI Plant-Microbe Interfaces

PMI reveals mechanistic bases underpinning selection of symbiotic plant-microbe partnerships and how environment structures the host plant's microbiome. Various Populus species (eastern cottonwood, black cottonwood, aspen) serve as model hosts for bioenergy research.

Lead institution: Oak Ridge National Laboratory

Funding: DOE BER / Genomic Science Program

Established: 2008

Principal investigators:

Mitchel Doktycz

Principal Investigator

Oak Ridge National Laboratory

Dale Pelletier

Bacterial Collection Lead

Oak Ridge National Laboratory

Melissa Cregger

Microbiome Ecology Lead

Oak Ridge National Laboratory

Links:

Main Ornl Page Doe Page Kbase

NMDC umbrella study: nmdc:sty-11-f1he1955

KBase Collection: PMI

Scientific questions:

How do plants select symbiotic microbial partners?
What environmental factors structure the plant microbiome?
How do microbial community composition and host genetics interact?
What metabolites mediate plant-microbe communication?

Keywords:

Plant Microbe Interactions Populus Poplar Rhizosphere Endophytes Mycorrhizae Bioenergy Crops

Data types:

Genomics Metagenomics Transcriptomics Metabolomics Isolate Collections

Modalities:

Bacterial Isolation Genome Sequencing Multi Omics Imaging

Phenotype assays:

Growth Curves Biolog Phenotyping Plant Colonization Coculture Interactions Synthetic Community Exometabolomics Live Cell Imaging

Isolate Collections 2

PMI Bacterial Collection 3500 isolates

Bacterial isolates from native, field, and greenhouse-grown Populus trees. Includes rhizosphere, endosphere, and phyllosphere isolates characterized by 16S rDNA sequencing with full genome sequences for many strains. Represents ~50% of the natural community based on phylogenetic analyses, with multiple representatives of all highly abundant genera.

Organism types:

Bacteria

Genomes sequenced: 750

Source environments:

Populus Rhizosphere Populus Root Endosphere Populus Phyllosphere

Host organisms: Populus trichocarpa, Populus deltoides

Isolation methods: Aerobic plating, Root homogenization

Culture collection: Browse/Request

Genome catalog: View genomes

Reference: doi:10.1128/mSystems.01306-20 - Cultivating the Bacterial Microbiota of Populus Roots

PMI Fungal Collection 3000 isolates

Fungal isolates representing diverse guilds including ectomycorrhizal (ECM), endophytic (END), pathogens, and saprotrophs. Identified key symbiotic taxa and established new models for plant-fungal symbiosis research.

Organism types:

Fungi

Genomes sequenced: 100

Source environments:

Populus Rhizosphere Populus Root Endosphere Forest Soil

Host organisms: Populus trichocarpa, Populus deltoides

Studies 6

nmdc:sty-11-1t150432 - Defining the functional diversity of the Populus root microbiome (Mitchel J. Doktycz)

Characterization and interpretation of plant-microbe interfaces using poplar and its microbial community in the context of favorable plant microbe interactions.

Primary reference: doi:10.1128/mSystems.00045-18 - Exploration of the Biosynthetic Potential of the Populus Microbiome

HIGH nmdc:sty-11-r2h77870 - Bio-Scales - Integrated Metagenomic, Metabolomic and Transcriptomic Survey of Populus (Mitchel J. Doktycz)

Bio-Scales pilot project (PIs: Doktycz, Schadt, Mayes, Muchero, Weston) understanding how plant traits modify the microbiome and how the coupled plant-soil-microbial system influences nitrogen transformation. Integrated dataset of 318 metagenomes, 98 transcriptomes, and 314 metabolomic profiles from 27 P. trichocarpa genotypes across Oregon field sites. Largest publicly available metagenomics repository on tree endosphere.

Organism: Populus trichocarpa

Data modalities:

Metagenomics Transcriptomics Metabolomics

Samples: 318

BioProjects: PRJNA1034652

Primary reference: doi:10.1038/s41597-024-03069-7 - An integrated metagenomic, metabolomic and transcriptomic survey of Populus across genotypes and environments

HIGH Seasonality and Temporal Dynamics in Populus Microbiome (Melissa Cregger)

Amplicon sequencing characterizing bacterial/archaeal and fungal communities in leaf endosphere, root endosphere, and rhizosphere of two Populus species over time.

Organism: Populus trichocarpa

Data modalities:

Amplicon 16s Amplicon Its

Samples: 2359

BioProjects: PRJNA993999

Primary reference: doi:10.1128/msystems.00886-23 - Seasonality and longer-term development generate temporal dynamics in the Populus microbiome

MEDIUM Populus Holobiont Niche and Genotype Effects (Melissa Cregger)

Dissecting effects of plant niches and genotype on the Populus microbiome using 16S and ITS amplicon sequencing across multiple tissue types.

Organism: Populus deltoides

Data modalities:

Amplicon 16s Amplicon Its

Samples: 590

BioProjects: PRJNA385484, PRJNA384978

Primary reference: doi:10.1186/s40168-018-0413-8 - The Populus holobiont: dissecting the effects of plant niches and genotype on the microbiome

MEDIUM Cultivating Bacterial Microbiota of Populus Roots (Dale Pelletier)

Isolation and characterization of culturable bacteria from Populus roots with 16S sequencing for community analysis.

Organism: Populus trichocarpa

Data modalities:

Amplicon 16s Genomics

Samples: 552

BioProjects: PRJNA666202

Primary reference: doi:10.1128/mSystems.01306-20 - Cultivating the Bacterial Microbiota of Populus Roots

HIGH Climate-driven Divergence in Plant-Microbiome Interactions (Jason Holliday)

Range-wide survey examining how tree genotypes condition their soil microbiomes across the geographic distribution of Populus angustifolia. Demonstrates that warming-adapted microbiomes can transmit thermotolerance to axenic laboratory-grown plants. PMI Variovorax collection (n=190 strains) used for functional validation of microbially-mediated thermotolerance.

Organism: Populus angustifolia

Data modalities:

Amplicon 16s Amplicon Its

Samples: 539

BioProjects: PRJNA726831

Primary reference: doi:10.1038/s41467-021-24112-w - Climate-driven divergence in plant-microbiome interactions generates range-wide variation in bud break phenology

Analyses & KBase Narratives 2

Populus Microbiome Narrative

Genome collection of Populus-associated microbes showing rhizosphere diversity. Includes isolate genomes and annotations from PMI bacterial collection.

Type: Kbase Narrative

Output types:

Genomics

PMI Synthetic Community Metabolic Modeling

CommScores analysis for predicting pairwise interactions among PMI bacterial isolates. Developed in collaboration with the PMI SFA.

Type: Kbase Narrative

Output types:

Genomics

Reference: doi:10.1016/j.csbj.2021.03.034 - Formation, characterization and modeling of emergent synthetic microbial communities

Key Publications 10

doi:10.1038/s41597-024-03069-7 An integrated metagenomic, metabolomic and transcriptomic survey of Populus

Comprehensive multi-omics dataset of 318 metagenomes from 27 Populus genotypes

doi:10.1128/msystems.00886-23 Seasonality and temporal dynamics in the Populus microbiome

Strong seasonal patterns drive Populus-associated microbial community structure

doi:10.1186/s40168-018-0413-8 Effects of plant niches and genotype on the Populus microbiome

Plant tissue niche has stronger effect on microbiome than host genotype

doi:10.1016/j.csbj.2021.03.034 CommScores metabolic modeling for microbial community interactions

Genome-scale metabolic modeling enables prediction of microbial interactions

doi:10.1093/hr/uhad087 CRISPR/Cas9-based gene activation and base editing in Populus

Established CRISPR tools for Populus genetic engineering

doi:10.1038/s41467-021-24112-w Climate-driven divergence in plant-microbiome interactions generates range-wide variation in bud break phenology

Warming-adapted microbiomes can transmit thermotolerance to axenic laboratory-grown plants
Tree genotypes condition their soil microbiomes across geographic distribution

doi:10.1128/mSystems.00045-18 Exploration of the Biosynthetic Potential of the Populus Microbiome

Populus microbiome encodes diverse biosynthetic gene clusters for secondary metabolites

doi:10.1186/s12866-021-02370-4 Metaproteomics Reveals Insights into Microbial Structure, Interactions, and Dynamic Regulation in Defined Communities

Metaproteomics reveals dynamic regulation of microbial communities responding to environmental disturbance

doi:10.1111/nph.15182 Fungal Endophytes of Populus trichocarpa Alter Host Phenotype, Gene Expression, and Rhizobiome Composition

Mortierella elongata PMI93 promotes P. trichocarpa growth in a cultivar-independent manner

doi:10.1186/s13007-023-01022-0 A rapid assay for assessing bacterial effects on Arabidopsis thermotolerance

Variovorax strains from Populus roots confer thermotolerance to plants
Six Variovorax strains (CF313, YR634, GV004, GV035, YR752, OV084) significantly improve plant heat tolerance

Datasets 2

Populus trichocarpa GWAS Population

>1500 natural variants of P. trichocarpa resequenced and phenotyped for genome-wide association studies (GWAS) linking plant genotype to microbiome composition. Includes backcross pedigrees for QTL mapping and transgenic lines in multiple host backgrounds.

Populus deltoides Common Garden Collection

~350 natural variants of P. deltoides planted in common gardens for studying genotype-environment interactions and microbiome assembly.

SEED SEED: Secure Ecosystem Engineering and Design

SEED develops predictive understanding of how microorganisms establish, spread, and influence ecosystems critical to DOE missions. Combines expertise in microbiology, plant biology, ecology, genetic engineering, and computational sciences. Currently deploying biodesign tools in the plant growth-promoting bacteria Bacillus velezensis to improve Populus resistance to the pathogenic fungus Sphaerulina musiva.

Lead institution: Oak Ridge National Laboratory

Funding: DOE BER / Genomic Science Program

Principal investigators:

Paul Abraham

Laboratory Research Manager

Oak Ridge National Laboratory

Xiaohan Yang

Lead Scientist

Oak Ridge National Laboratory

Links:

Main Ornl Page Doe Page Team

Scientific questions:

What factors influence microbial invasion success?
How do introduced microbes establish and spread in ecosystems?
How can we engineer ecosystems for DOE missions?
What risks do engineered organisms pose to ecosystems?
How can we detect and quantify microbial activity in situ?

Keywords:

Ecosystem Engineering Biosystems Design Microbial Invasion Biodefense Biosecurity Fungal Pathogens Crispr Rhizosphere

Data types:

Genomics Transcriptomics Metabolomics Imaging Data

Studies 3

LOW Bacillus velezensis EB14 Biocontrol Agent Genome (Paul Abraham)

Genome sequencing of Bacillus velezensis EB14, a native endophytic bacterial strain isolated from Populus × jackii with biocontrol potential against Sphaerulina musiva, the causative pathogen of poplar stem canker. Contains gene clusters for antimicrobial compound biosynthesis including iturin A, subtulene A, and fengycin.

Organism: Bacillus velezensis

Data modalities:

Genomics

BioProjects: PRJNA681597

Primary reference: doi:10.1094/PHYTO-09-20-0433-A - Genome Sequence Resource of Bacillus velezensis EB14, a Native Endophytic Bacterial Strain with Biocontrol Potential Against the Poplar Stem Canker Causative Pathogen, Sphaerulina musiva

MEDIUM Populus-Laccaria Symbiosis Effector Discovery (Xiaohan Yang)

Investigation of plant-derived effector proteins mediating symbiosis between Populus and the ectomycorrhizal fungus Laccaria bicolor. Identifies PtLecRLK1 receptor and small secreted proteins regulating fungal colonization.

Organism: Populus trichocarpa

Data modalities:

Genomics Transcriptomics Metabolomics

Primary reference: doi:10.1093/hr/uhae232 - A small secreted protein serves as a plant-derived effector mediating symbiosis between Populus and Laccaria bicolor

LOW CRISPRi High-Throughput Screens in Non-Model Bacteria (Paul Abraham)

Development of workflow for rapid enhancement of transformation efficiency and genetic part characterization in non-model bacteria for genome-wide CRISPRi screens. Tools being deployed in Bacillus velezensis for rhizosphere studies.

Organism: Bacillus velezensis

Data modalities:

Genomics

Analyses & KBase Narratives 1

SEED Microbial Interaction Predictions

CommScores analysis for predicting pairwise interactions among SEED bacterial isolates including Bacillus velezensis. Uses same KBase apps as PMI SFA.

Type: Kbase Narrative

Output types:

Genomics

Key Publications 6

doi:10.1094/PHYTO-09-20-0433-A Genome Sequence Resource of Bacillus velezensis EB14, a Native Endophytic Bacterial Strain with Biocontrol Potential

B. velezensis EB14 contains gene clusters for antimicrobial compound biosynthesis
Produces iturin A, subtulene A, and fengycin cyclic lipopeptides

doi:10.1093/hr/uhae232 A small secreted protein serves as a plant-derived effector mediating symbiosis between Populus and Laccaria bicolor

Identified plant-derived effector proteins regulating plant-fungal symbiosis

doi:10.1093/hr/uhad087 CRISPR/Cas9-based gene activation and base editing in Populus

Developed CRISPR tools for gene activation and editing in Populus trees

doi:10.1016/j.copbio.2020.10.007 Plant Biosystems Design Research Roadmap 1.0

Established research roadmap for plant biosystems design and ecosystem engineering

doi:10.1093/plphys/kiad076 Expanding the Application of Anti-CRISPR Proteins in Plants for Tunable Genome Editing

Developed anti-CRISPR tools for tunable genome editing in plants

doi:10.1094/PHYTOFR-10-20-0023-R Isolation and Characterization of Bacillus velezensis EB14 and Its Interactions with the Endophytic Fungal Microbiome

B. velezensis EB14 shows strong antifungal activity against S. musiva

Datasets 1

Bacillus velezensis EB14 Complete Genome

Complete genome sequence of B. velezensis EB14 (4.0 Mb) sequenced using PacBio RS II. Contains predicted gene clusters for antimicrobial compound biosynthesis.

Repository: NCBI

URL: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA681597

Secure Biosystems Design Scientific Focus Area

This SFA engineers plant-benefiting microbes for safe and effective deployment in the rhizosphere as plant-promoting probiotics. Develops multilayered containment strategies including kill-switches and gene overlap for circuit stability. Leverages LLNL Soil Microbiome SFA expertise to test containment designs in soil and rhizosphere environments.

Lead institution: Lawrence Livermore National Laboratory

Partners:

University Of Maryland University Of Minnesota Columbia University University Of California, Berkeley

Funding: DOE BER / Genomic Science Program

Principal investigators:

Yongqin Jiao

Lead Principal Investigator

Lawrence Livermore National Laboratory

Co-investigators:

William Bentley

University of Maryland

Gregory Payne

University of Maryland

Jeffrey Gralnick

Jonathan Allen

Dan Park

Mimi Yung

Jennifer Chlebek

Links:

Llnl Page

Scientific questions:

How do we deploy beneficial microbes safely in the rhizosphere?
What biocontainment mechanisms are evolutionarily stable?
How can machine learning improve sequence design for containment?
What population coordination strategies enhance containment?
How do we prevent potential negative ecological consequences of GEM persistence?

Keywords:

Plant Growth Promoting Bacteria Rhizosphere Biocontainment Shewanella Machine Learning Synthetic Biology

Data types:

Genomics Transcriptomics Proteomics

Studies 1

LOW Multilayered Biocontainment for Rhizosphere Deployment (Yongqin Jiao)

Developing and testing multilayered containment strategies for engineered microbes including kill-switches stabilized through gene overlap (sequence entanglement).

Organism: Shewanella oneidensis

Data modalities:

Genomics Transcriptomics

Environmental System Science SFAs (8)

Watershed Function Science Focus Area

The Watershed Function SFA develops predictive understanding of how mountainous watersheds retain and release water, nutrients, carbon, and metals. Research focuses on interacting impacts of warming and drought on hydro-biogeochemical functioning.

Lead institution: Lawrence Berkeley National Laboratory

Funding: DOE BER / Environmental System Science (ESS)

Principal investigators:

Susan Hubbard

Lead Research Manager / ESD Director

Lawrence Berkeley National Laboratory

Links:

Doe Page Ideas Watersheds Czen

NMDC umbrella study: nmdc:sty-11-2zhqs261

Scientific questions:

How do droughts and early snowmelt impact water availability?
What controls biogeochemical cycling in mountain watersheds?
How do hydrological, ecological, and biogeochemical processes interact?
What are the consequences of climate change for headwater systems?

Keywords:

Watershed Hydrology Biogeochemistry Upper Colorado River Basin Snowmelt Drought Mountain Hydrology Modex

Data types:

Hydrological Data Biogeochemical Data Remote Sensing Environmental Sensor Data Hydrological Data

Modalities:

Field Sensors Stream Sampling Groundwater Monitoring Remote Sensing Ecosystem Modeling

Phenotype assays:

Soil Incubation Respiration

Field Sites 2

East River Watershed (Colorado)

Mountainous community testbed in Upper Colorado River Basin, representative of vulnerable headwater systems

Taylor River Watershed (Colorado)

Expansion site within Upper Colorado River Basin

Studies 2

HIGH East River Floodplain Metagenomes (Eoin Brodie)

Metagenome-assembled genomes from floodplain soils in the East River watershed. 248 draft quality genomes reconstructed at sub-species level from upper, middle, and lower reaches. Demonstrates floodplains as scaling motifs for watershed models.

Organism: soil metagenome

Data modalities:

Metagenomics

MEDIUM East River Virome and Microbial Dynamics (Simon Roux)

Virus diversity and activity driven by snowmelt and host dynamics in high-altitude watershed soil ecosystem. Part of the Watershed Function SFA microbiome studies.

Organism: soil metagenome

Data modalities:

Metagenomics Metatranscriptomics

Primary reference: doi:10.1186/s40168-023-01666-z - Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem

Key Publications 3

doi:10.2136/vzj2018.03.0061 The East River, Colorado, Watershed: A Mountainous Community Testbed for Improving Predictive Understanding of Multiscale Hydrological-Biogeochemical Dynamics

doi:10.1186/s40168-023-01666-z Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem

Snowmelt drives seasonal pulses in viral activity linked to host population dynamics

doi:10.1021/acs.est.4c01108 Seasonal Controls on Microbial Depolymerization and Oxidation of Organic Matter in Floodplain Soils

Floodplain microbiomes mediate biogeochemical changes at watershed scale

Datasets 2

East River Watershed Data

Repository: DOE Data Explorer

Watershed Function SFA ESS-DIVE Collection

Comprehensive data collection from East River watershed studies

Repository: ESS-DIVE

URL: https://data.ess-dive.lbl.gov/portals/watershed-function-sfa

Collaborators: >450 individuals from 30+ institutions, 7 countries

WaDE Watershed Dynamics and Evolution (WaDE) Science Focus Area

WaDE advances predictive understanding of how dominant processes controlling watershed hydro-biogeochemical function operate under different hydrologic regimes and vary along stream networks draining heterogeneous land covers. Organized around Dynamic Headwaters, Stream Corridor Processes, Network Function, and Virtual Watershed themes.

Lead institution: Oak Ridge National Laboratory

Partners:

Colorado School Of Mines Kansas State University Oregon State University University Of Colorado At Boulder University Of Florida Virginia Tech

Funding: DOE BER / Environmental System Science (ESS)

Links:

Main Doe Page Publications

Scientific questions:

How do dominant processes vary under different hydrologic regimes?
What controls hydro-biogeochemical function along stream networks?
How does land cover heterogeneity affect watershed function?
How do biogeochemical processes respond to variable saturation in non-perennial channels?

Keywords:

Watershed Dynamics Tennessee River Basin Stream Networks Land Cover Hydro Biogeochemistry Mercury

Data types:

Water Chemistry Environmental Sensor Data Biogeochemical Data Hydrological Data

Field Sites 1

Tennessee River Basin Watersheds

Three mid-order watersheds broadly representative of the Tennessee River Basin, studied successively over 9-year plan. Most intensively used freshwater resource region in contiguous US, supporting ~4.5 million people with >280,000 gallons/day/sq mi withdrawals.

Key Publications 2

doi:10.5194/bg-22-995-2025 Reviews and syntheses: Variable inundation across Earth's terrestrial ecosystems

Synthesizes research on water dynamics across ecosystem types

doi:10.1029/2023WR036706 The Fragility of Bedform-Induced Hyporheic Zones

Subsurface water exchange dynamics vary with bedform morphology

RC-SFA River Corridor Hydrobiogeochemistry Science Focus Area

The RC-SFA delivers predictive understanding of how perturbations impact watershed hydro-biogeochemistry across the hillslope-to-stream continuum. Focus on wildfire and stream drying as interacting perturbations with uncertain impacts.

Lead institution: Pacific Northwest National Laboratory

Funding: DOE BER / Environmental System Science (ESS) (FY 2025-2028)

Links:

Main Doe Page Ideas Watersheds Github Ess Dive

NMDC umbrella study: nmdc:sty-11-x4aawf73

KBase Collection: GROW

Scientific questions:

How do precipitation and temperature control hydrologic connectivity?
What are impacts of wildfires on watershed hydro-biogeochemistry?
How does stream drying affect biogeochemical processes?
What controls carbon and nutrient transport in river corridors?

Keywords:

River Corridors Yakima River Basin Wildfire Stream Drying Hydrologic Connectivity Whondrs

Data types:

Water Chemistry Environmental Sensor Data Biogeochemical Data Geospatial

Field Sites 1

Yakima River Basin (Washington State)

Single-basin testbed with varied environmental features

Studies 2

HIGH nmdc:sty-11-aygzgv51 - Riverbed Sediment Microbial Communities from the Columbia River (James Stegen)

Molecular-scale processes governing biogeochemical function of subsurface groundwater-surface water mixing zones (hyporheic zone). Columbia River samples from areas with varied vegetation density for studying biogeochemical hotspots.

Data modalities:

Metagenomics Metabolomics Proteomics

Primary reference: doi:10.1371/journal.pone.0228165 - Distinct temporal diversity profiles for nitrogen cycling genes in a hyporheic microbiome

HIGH Functional Microbiome Catalogue from North American Rivers (Kelly Wrighton)

Catalog of 2,000+ microbial genomes from ~100 rivers across North America. Over 1,000 metagenomes sequenced through JGI from WHONDRS water samples. Landmark study published in Nature 2024.

Data modalities:

Metagenomics Metatranscriptomics

Primary reference: doi:10.1038/s41586-024-08240-z - A functional microbiome catalogue crowdsourced from North American rivers

Analyses & KBase Narratives 3

GROWdb US River Systems - Samples

Sample metadata and links for GROWdb US river systems. Part of the Genome Resolved Open Watersheds (GROW) database built from WHONDRS worldwide river sampling campaign.

Type: Kbase Narrative

Samples: 178

Output types:

Metagenomics

GROWdb Metagenome Assembled Genomes (MAGs)

Metagenome-assembled genomes from WHONDRS river samples. Includes MAG assemblies, quality metrics, and GTDB taxonomy assignments.

Type: Kbase Narrative

Output types:

Metagenomics

GROWdb Metabolic Models

Genome-scale metabolic models built from GROW MAGs using KBase ModelSEED pipeline. Enables prediction of metabolic capabilities and community interactions.

Type: Kbase Narrative

Output types:

Metagenomics

Key Publications 6

doi:10.1038/s41586-024-08240-z A functional microbiome catalogue crowdsourced from North American rivers

Over 2,000 microbial genomes catalogued from ~100 rivers across North America
WHONDRS provides globally scalable framework for river microbiome research

doi:10.1029/2023WR036023 Sinuosity-Driven Hyporheic Exchange: Hydrodynamics and Biogeochemical Potentials

River sinuosity drives hyporheic exchange affecting biogeochemical processes

doi:10.3390/w16010171 Quantifying drivers of methane hydrobiogeochemistry in a tidal river floodplain system

Multiple drivers control methane cycling in tidal river floodplains

doi:10.1029/2023gl106220 Linkages between mineral element composition of soils and sediments with hyporheic zone dissolved organic matter chemistry

Soil mineral composition linked to hyporheic zone DOM chemistry across CONUS

doi:10.1016/j.soilbio.2024.109364 Thermodynamic control on the decomposition of organic matter across different electron acceptors

Thermodynamic constraints control organic matter decomposition pathways

doi:10.1021/acs.est.3c10826 Experimental open air burning of vegetation enhances organic matter chemical heterogeneity compared to laboratory burns

Wildfire-derived organic matter differs significantly from lab-burned material

Datasets 1

WHONDRS Community Data Packages

Community-contributed data packages from WHONDRS (Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems).

Repository: ESS-DIVE

Mercury SFA Biogeochemical Transformations at Critical Interfaces in a Mercury Perturbed Watershed

The Mercury SFA provides foundational insight on exchange and feedback processes at critical interfaces controlling mercury fate and transformation. Research elucidates mechanisms by which inorganic mercury transforms into methylmercury at the sediment-water interface.

Lead institution: Oak Ridge National Laboratory

Funding: DOE BER / Environmental System Science (ESS)

Established: 2010

Principal investigators:

Scott Brooks

Oak Ridge National Laboratory

Links:

Main Doe Page Data Page

Scientific questions:

What mechanisms control mercury transformation to methylmercury?
How do sediment-water interfaces mediate mercury cycling?
What microorganisms are responsible for mercury methylation?
How does mercury fate interact with carbon and nutrient cycling?

Keywords:

Mercury Methylmercury Biogeochemistry Sediment Water Interface Mercury Methylation Hgca Hgcb

Data types:

Water Chemistry Hydrological Data Genomics Mercury Speciation

Field Sites 1

East Fork Poplar Creek (Oak Ridge, Tennessee)

Mercury-contaminated stream system

Contamination source: Historical nuclear material research and production

Studies 2

HIGH East Fork Poplar Creek Sediment Metagenomes (Mircea Podar)

Metagenome-assembled genomes of novel prokaryotic species from mercury-contaminated East Fork Poplar Creek sediments. 28 MAGs reconstructed including Hg methylators.

Organism: sediment metagenome

Data modalities:

Metagenomics

BioProjects: PRJNA670906

Primary reference: doi:10.1128/MRA.00153-21 - Metagenome-Assembled Genome Sequences of Novel Prokaryotic Species from the Mercury-Contaminated East Fork Poplar Creek, Oak Ridge, Tennessee, USA

MEDIUM Archaeal Mercury Methylators in Freshwater Sediments (Dwayne Elias)

Study demonstrating robust mercury methylation across diverse methanogenic archaea in freshwater sediments from East Fork Poplar Creek.

Organism: sediment metagenome

Data modalities:

Metagenomics Amplicon 16s

Primary reference: doi:10.1128/mBio.02403-17 - Robust Mercury Methylation across Diverse Methanogenic Archaea

Key Publications 2

doi:10.1038/s42003-020-1047-5 Structure determination of the HgcAB complex using metagenome sequence data: Insight into the mechanism of mercury methylation

doi:10.1016/j.scitotenv.2019.07.001 Dissolved organic matter reduces the effectiveness of sorbents for mercury removal

Datasets 3

East Fork Poplar Creek Discharge Data

Multi-year discharge records at Kilometer 5.4

ORNL Compiled Mercury Methylator Database

Custom reference database of hgcA and hgcB genes from mercury-methylating microorganisms (301 hgcA, 239 hgcB sequences)

Repository: DOE Data Explorer

DOI: dataset/1569274

Hg-MATE-Db

Hg-cycling Microorganisms in Aquatic and Terrestrial Ecosystems Database for identifying mercury-cycling microbes

Repository: Smithsonian Institution

DOI: 10.25573/serc.13105370.v1

Wetland Hydro-biogeochemistry Science Focus Area

This SFA investigates wetland hydro-biogeochemistry at a riparian wetland at DOE's Savannah River Site. Research aims to understand and predict wetland ecosystem function and control on carbon, nutrient, and contaminant transformations and transport.

Lead institution: Argonne National Laboratory

Partners:

Savannah River National Laboratory University Of Georgia (Savannah River Ecology Laboratory) Bulgarian Academy Of Science Illinois Institute Of Technology

Funding: DOE BER / Environmental System Science (ESS)

Principal investigators:

Ken Kemner

Principal Investigator

Argonne National Laboratory

Co-investigators:

Edward O'Loughlin

Co-PI

Argonne National Laboratory

Pamela Weisenhorn

Argonne National Laboratory

Maxim Boyanov

Bulgarian Academy of Science

Dan Kaplan

Savannah River National Laboratory

John Seaman

Savannah River Ecology Laboratory, University of Georgia

Carlo Segre

Illinois Institute of Technology

Links:

Doe Page Anl Page

Scientific questions:

How do wetlands control elemental transformations and transport?
What processes regulate carbon and nutrient cycling in wetlands?
How do contaminants transform in wetland environments?
What role does hydrology play in wetland biogeochemistry?

Keywords:

Wetland Biogeochemistry Riparian Wetland Savannah River Site Carbon Cycling Nutrient Cycling Contaminant Transport

Field Sites 1

Savannah River Site Riparian Wetland (Aiken, South Carolina)

Riparian wetland representative of many in humid regions of the Southeast US

Floodplain Hydro-Biogeochemistry Science Focus Area

The Floodplain Hydro-Biogeochemistry SFA investigates how subsurface interfaces mediate molecular-scale biogeochemical processes and groundwater quality. Research focuses on microbial and geochemical responses to hydrological processes in floodplain systems.

Lead institution: SLAC National Accelerator Laboratory

Funding: DOE BER / Environmental System Science (ESS)

Principal investigators:

Scott Fendorf

Stanford University / SLAC

Links:

Main Ssrl Page Doe Page

Scientific questions:

How do subsurface interfaces mediate biogeochemical processes?
What controls groundwater quality in floodplain systems?
How do wet-dry cycles affect redox processes and carbon mobilization?
What mechanisms control colloid generation and transport?

Keywords:

Floodplain Subsurface Interfaces Groundwater Quality Redox Cycling Colloid Transport Capillary Fringe

Data types:

Groundwater Chemistry Biogeochemical Data Structural Biology Economic Modeling Data

Field Sites 2

Riverton Floodplain (Wyoming)

Crested Butte Floodplain (Colorado)

Alluvial aquifer underlying Slate River with fine-grained soil overlying cobble/gravel alluvium (3600 m² interface)

Key Publications 1

doi:10.1038/ngeo2940 Thermodynamically controlled preservation of organic carbon in floodplains

Wetland Function SFA Terrestrial Wetland Function and Resilience Science Focus Area

Develops mechanistic understanding of how climatic conditions affect terrestrial wetland ecosystem function, particularly carbon dynamics. Organized around three themes: fine-scale hydro-biogeochemical mechanisms controlling C cycling and GHG emissions, above/belowground processes and interactions, and model integration at fine and intermediate scales.

Lead institution: Argonne National Laboratory

Partners:

Lawrence Livermore National Laboratory Bulgarian Academy Of Sciences University Of Minnesota University Of Nevada U.s. Geological Survey

Funding: DOE BER / Environmental System Science (ESS)

Principal investigators:

Roser Matamala

Principal Investigator

Argonne National Laboratory

Links:

Doe Page

Scientific questions:

How do climatic conditions affect wetland ecosystem function?
What mechanisms control carbon cycling and GHG emissions in wetland soils?
How do above and belowground processes interact in wetlands?
How can we integrate mechanistic understanding into ESM land components?

Keywords:

Wetland Resilience Carbon Cycling Nutrient Cycling Environmental Change

Data types:

Biogeochemical Data Water Chemistry Environmental Sensor Data

Field Sites 3

Upper Colorado River Basin - East River (Colorado)

Headwater system within the Upper Colorado River Basin

Taylor River Watershed (Colorado)

Expansion site within UCRB

Cottonwood Lake Study Area (North Dakota)

Depressional wetland complex in the Prairie Pothole Region

BGC-Interfaces BioGeoChemistry at Interfaces Science Focus Area

Identifies and quantifies biogeochemical processes and underlying mechanisms controlling actinide mobility to reliably predict and control cycling and migration of actinides in the environment. Focus on plutonium (>2200 metric tons deposited globally) and neptunium behavior, including interactions with lanmodulin and similar compounds.

Lead institution: Lawrence Livermore National Laboratory

Funding: DOE BER / Environmental System Science (ESS)

Principal investigators:

Mavrik Zavarin

Principal Investigator

Lawrence Livermore National Laboratory

Annie B. Kersting

Former PI / Director of University Relations

Lawrence Livermore National Laboratory

Links:

Doe Page

Scientific questions:

What biogeochemical processes control actinide mobility?
How do actinides interact with biological systems?
What mechanisms control plutonium migration in subsurface environments?
What is the role of lanmodulin in actinide chemistry?

Keywords:

Actinides Biogeochemistry Interfaces Environmental Systems Uranium Colloid Transport Contaminant Transport

Data types:

Biogeochemical Data Stable Isotope Data

Field Sites 1

Savannah River Site - Pond B (South Carolina)

Field site for actinide biogeochemistry studies

User Facilities & Data Resources (5)

JGI DOE Joint Genome Institute

JGI provides integrated high-throughput sequencing, DNA design and synthesis, metabolomics, and computational analysis enabling systems-based scientific approaches. JGI sequences and analyzes genomes for DOE-relevant research in bioenergy, carbon cycling, and environmental microbiome science.

Lead institution: Lawrence Berkeley National Laboratory

Funding: DOE BER / Genomic Science Program

Links:

Main Phytozome

Services:

Genome Sequencing Metagenome Sequencing Dna Synthesis Metabolomics Computational Analysis Single-Cell Genomics

Capabilities 4

OPERATIONAL High-Throughput Sequencing

Short- and long-read sequencing platforms producing billions of reads for genomic assembly, resequencing, RNAseq annotation, and metagenomics. Total output in 2024 was 870 Tb.

Type: Sequencing

Throughput: 870 Tb annually

Instruments:

Illumina NovaSeq - Short-read sequencing producing paired-end 150bp reads
PacBio Revio - Long-read sequencing averaging 60-70 kbp reads

Applications:

Genome Assembly Metagenome Sequencing Rna-Seq Single-Cell Genomics

Data products:

Raw Sequence Reads Assembled Genomes Annotated Transcripts

OPERATIONAL DNA Synthesis Platform

DNA design and synthesis capabilities supporting researchers exploring conversion of sequence into functional assessments. Minimum request is 100 kb.

Type: Dna Synthesis

Applications:

Biosynthetic Pathway Refactoring Gene Synthesis Construct Assembly

Data products:

Synthesized Dna Constructs Verified Plasmids

OPERATIONAL Metabolomics Program

Functional annotation of genomes through metabolomics, providing improved understanding of the role of small molecules in diverse biological systems. Minimum 22 samples required.

Type: Metabolomics Ms

Applications:

Secondary Metabolite Identification Biosynthetic Gene Cluster Characterization Pathway Validation

Data products:

Metabolite Profiles Mass Spectra (Submitted To Massive)

OPERATIONAL AI-Centric Analysis

AI/ML-based computational analysis including protein family discovery, biosynthetic gene cluster prediction, and genome annotation. Doubled known protein families using AI clustering algorithms.

Type: Ai Ml Analysis

Applications:

Protein Family Discovery Bgc Prediction Metagenome Analysis

Flagship Genomes 6

Populus trichocarpa (Poplar / Black Cottonwood) - 2006
First tree genome sequenced

Panicum virgatum (Switchgrass)
Candidate biofuel feedstock used by all BRCs

Miscanthus
Perennial grass bioenergy feedstock

Brachypodium distachyon
Model grass

Setaria italica (Foxtail millet)
Model C4 grass

Panicum hallii
Diploid relative of switchgrass

EMSL Environmental Molecular Sciences Laboratory

EMSL provides advanced analytical capabilities for environmental and biological research, including mass spectrometry, NMR, electron microscopy, and high-performance computing.

Lead institution: Pacific Northwest National Laboratory

Funding: DOE BER

Links:

Main

Services:

Mass Spectrometry Nmr Spectroscopy Electron Microscopy High-Performance Computing Imaging Molecular Characterization

Capabilities 6

OPERATIONAL Metabolomics Mass Spectrometry Suite

Comprehensive metabolomics workflow with 24 instruments for unbiased metabolite and lipid measurement including GC-MS, Orbitrap, and FTICR-MS platforms. Includes a 21 Tesla FTICR (one of two in the world).

Type: Metabolomics Ms

Instruments:

GC-MS Instruments (4) - Gas chromatography-mass spectrometry
Orbitrap Mass Spectrometers (16) - Diverse Orbitrap instruments including hybrid quadrupole and Tribrid
FTICR Mass Spectrometers (4)
Triple Quadrupole MS (9) - For sensitive targeted quantification and metabolic flux measurements
Imaging Mass Spectrometers (4) - Dedicated to mass spectrometry imaging

Applications:

Untargeted Metabolomics Targeted Metabolite Quantification Lipidomics Metabolic Flux Analysis

Data products:

Metabolite Profiles Lipid Profiles Metabolite Identifications

OPERATIONAL NMR Spectroscopy

Robust solid- and liquid-state NMR capabilities for structural biology, metabolomics, natural products, and organic matter characterization. Non-destructive with minimal sample preparation.

Type: Nmr

Instruments:

Liquid-State NMR - For metabolomics and natural products
Solid-State NMR - For structural biology and materials

Applications:

Metabolomics Structural Biology Natural Products Organic Matter Characterization

Data products:

Nmr Spectra Molecular Structure Data

OPERATIONAL Cryogenic Electron Microscopy

Cryo-TEM suite including Krios G3i cryogenic TEM and Aquilos 2 cryo-FIB-SEM for de novo structure determination, high-resolution cellular imaging, and tomography. Supports samples from 50 kDa proteins to whole cells.

Type: Cryo Em

Instruments:

Krios G3i - Cryogenic transmission electron microscope for high-resolution imaging
Aquilos 2 Cryo-FIB-SEM - Sample preparation via lamella generation with ~10 nm resolution

Applications:

De Novo Protein Structure Determination Cellular Architecture Imaging Plant-Microbe Interaction Studies Biofilm Morphology Cryo-Electron Tomography

Data products:

3d Structures Tomographic Reconstructions Cellular Ultrastructure Images

OPERATIONAL Anaerobic Microbial Phenotyping Platform (AMP2)

World's largest autonomous-capable science system for anaerobic microbial experimentation. Commissioned December 2024 by DOE Secretary Chris Wright. 18 instruments housed in 1,800 sq ft across seven anaerobic pods connected by robotic track system. Enables complete design-build-test-learn cycles with minimal operator intervention. Generates AI/ML-ready datasets in publicly available databases hosted on EMSL Science Central. Built in partnership with Ginkgo Bioworks under $4.66M contract.

Type: Anaerobic Phenotyping

Instruments:

Anaerobic Chambers (7) - Interconnected pods maintaining anaerobic environment
Liquid Handlers - Automated sample preparation, dispensing, and cherry-picking
Cultivation Systems - Supports up to 14 deep well plates for microbial growth
Fluorescence/Absorbance Readers - Optical density, fluorescence, and luminescence measurements
Flow Cytometers - Cell counting and characterization
HPLC Systems - Liquid chromatography for metabolite analysis
Electroporator - Cell transformation capabilities

Applications:

Anaerobic Microbe Characterization Design-Build-Test-Learn Cycles For Microbial Phenotyping High-Throughput Screening Under Variable Conditions Genotype-Phenotype Mapping Biofuel And Biomaterial Development Chemical And Energy Production From Microbes

Data products:

Growth Curves Metabolite Profiles Flow Cytometry Data Ai/ml-Ready Phenotype Datasets

OPERATIONAL NanoSIMS Imaging

Nanoscale secondary ion mass spectrometry for subcellular-resolution chemical imaging and isotope ratio analysis in biological samples.

Type: Nanosims Imaging

Applications:

Subcellular Metabolic Imaging Isotope Probing Element Mapping

OPERATIONAL Molecular Observation Network (MONet)

Open science network building a continental-scale database of standardized molecular and microstructural soil data. Integrates FTICR-MS for organic matter composition, X-ray CT for 3D pore structure, and metagenomics via JGI partnership. Data available on Science Central without embargo. See nmdc_sfas_brcs:monet for full program details.

Type: Fticr Ms

Applications:

Continental-Scale Soil Characterization Soil Organic Matter Molecular Analysis Soil Carbon Cycling Research Earth System Model Integration

Data products:

Fticr-Ms Organic Matter Profiles X-Ray Ct Pore Network Metrics Metagenome Sequences And Annotations Soil Biogeochemistry Measurements

KBase DOE Systems Biology Knowledgebase

KBase is an open-source software and data platform enabling data sharing, integration, and analysis of microbes, plants, and their communities. Provides genomic, metabolic modeling, and multi-omics analysis capabilities.

Lead institutions:

Lawrence Berkeley National Laboratory Argonne National Laboratory Brookhaven National Laboratory Oak Ridge National Laboratory

Funding: DOE BER / Genomic Science Program

Links:

Main Documentation Doe Page

Capabilities 3

OPERATIONAL Genome Annotation Services

Functional annotation tools including RAST and KEGG-based annotation, plus DRAM for metabolic profiling. Machine learning classifiers predict growth phenotypes from functional annotations.

Type: Genome Annotation

Applications:

Genome Functional Annotation Mag Annotation Viral Genome Annotation (Dram-V) Phenotype Prediction

Data products:

Annotated Genomes Functional Summaries Kegg Mappings

OPERATIONAL Metabolic Modeling Pipeline

Suite of apps for genome-scale metabolic model reconstruction, analysis, and prediction. Uses OMEGGA for omics-enabled global gapfilling. Over 500 media formulations available. Recent improvements achieve 72% model accuracy.

Type: Metabolic Modeling

Applications:

Genome-Scale Model Reconstruction Flux Balance Analysis Growth Media Optimization Essential Gene Prediction Pathway Analysis

Data products:

Metabolic Models Fba Solutions Growth Predictions

OPERATIONAL Metagenome Analysis

Metagenome assembly, binning, and annotation workflows. Applied to build models for over 2,000 MAGs from the GROW (Genome Resolved Open Watersheds) project.

Type: Metagenome Analysis

Applications:

Metagenome Assembly Genome Binning Community Metabolic Modeling

Data products:

Assembled Metagenomes Mags Community Models

Reference data: Microbial genomes: >90,000 from RefSeq
Plant genomes: >50 from Phytozome
Biolog media: >300 formulations

Supported data types:

Reads Contigs Genomes Metabolic Models Growth Media Rna-Seq Expression Data Growth Phenotype Data Flux Balance Analysis Solutions

ESS-DIVE Environmental System Science Data Infrastructure for a Virtual Ecosystem

ESS-DIVE is DOE's data archive for Environmental System Science research data. Provides open access to datasets from DOE-funded environmental research including watershed, soil, and ecosystem studies.

Lead institution: Lawrence Berkeley National Laboratory

Funding: DOE BER / Environmental System Science

Links:

Main

NMDC National Microbiome Data Collaborative

NMDC is a pilot initiative to advance microbiome science by building community-driven standards and infrastructure for microbiome data sharing, integration, and analysis.

Lead institutions:

Lawrence Berkeley National Laboratory Los Alamos National Laboratory Pacific Northwest National Laboratory Oak Ridge National Laboratory

Funding: DOE BER

Links:

Main

Other Initiatives (2)

SABI Sorghum-Anthracnose-Biocontrol Interactions

BRaVE project investigating molecular interactions between sorghum (a bioenergy crop), its anthracnose-disease causative fungal pathogen Colletotrichum sublineola (Cs), and antifungal biocontrol bacteria to create disease-resilient bioenergy crops. Uses computational and experimental approaches to study plant-pathosystem interactions.

Lead institution: Lawrence Berkeley National Laboratory

Funding: DOE BER / Biopreparedness Research Virtual Environment (BRaVE)

Initiative: BRaVE

Funding period: 2023-2026

DOE offices: BER, ASCR

Principal investigators:

Trent Northen

Principal Investigator

Lawrence Berkeley National Laboratory

Links:

Doe Page

Scientific questions:

What molecular mechanisms underlie sorghum-Colletotrichum pathogenic interactions?
How do biocontrol bacteria protect sorghum from anthracnose disease?
How can we engineer disease-resilient bioenergy crops?

Keywords:

Biosecurity Sorghum Fungal Pathogens Bioenergy Crops Plant Microbe Interactions Biodefense

Data types:

Metagenomics Transcriptomics Metabolomics

Phenotype assays:

Plant Colonization Bacterial Fungal Interaction Assay Growth Curves Competition Assays

Isolate Collections 2

Sorghum-Associated Bacterial Collection

Bacterial isolates with biocontrol activity against Colletotrichum sublineola, collected from sorghum rhizosphere and phyllosphere.

Organism types:

Bacteria

Source environments:

Sorghum Rhizosphere Sorghum Phyllosphere

Host organisms: Sorghum bicolor

Colletotrichum Pathogen Collection

Colletotrichum sublineola isolates causing anthracnose disease in sorghum.

Organism types:

Fungi

Source environments:

Infected Sorghum Tissue

MONet Molecular Observation Network

MONet (Molecular Observation Network) is an open science network developed by EMSL to build a continental-scale database of standardized molecular and microstructural soil data. The initiative aims to advance understanding and prediction of microbially and root-driven inputs in soil ecosystems and terrestrial aerosol processes. MONet collects thousands of soil samples across US ecoregions to develop a comprehensive FAIR database of molecular and microscale information on soil composition, structure, water characteristics, microbial communities, and biogenic emissions. Data is publicly available on EMSL Science Central without embargo. First capability launched February 2023 with the Soil Function soil core solicitation.

Lead institution: Pacific Northwest National Laboratory

Funding: DOE BER / Environmental Molecular Sciences Laboratory

Initiative: MONet

Established: 2023

Principal investigators:

John Bargar

Principal Investigator

Pacific Northwest National Laboratory

Emily B. Graham

Co-Investigator

Pacific Northwest National Laboratory

Odeta Qafoku

Co-Investigator

Pacific Northwest National Laboratory

Links:

Main Data Portal

Scientific questions:

How do molecular and microscale processes determine whether soil carbon enters the atmosphere or remains sequestered?
What drives microbially and root-driven carbon inputs in soil ecosystems?
How can molecular-scale soil data be integrated into Earth system models?

Keywords:

Soil Carbon Soil Microbiome Soil Organic Matter Metagenomics Carbon Cycling Decomposition

Data types:

Metabolomics Metagenomics Imaging Data Biogeochemical Data Soil Microbiome Data

Modalities:

Mass Spectrometry Metagenomics Imaging Field Experiments Laboratory Experiments

Field Sites 22

NEON Terrestrial Sites Network (Continental United States and territories)

MONet leverages NEON's 47 terrestrial field sites across 20 ecoclimatic domains spanning the continental United States, Alaska, Hawaii, and Puerto Rico. Sites represent diverse ecosystems including forests, grasslands, shrublands, and wetlands. Each domain has 1-3 terrestrial sites with standardized sampling protocols. MONet-NEON First Collection ran September 2023 to July 2024.

Harvard Forest (HARV) (Massachusetts)

NEON Domain 01 - Northeast temperate forest site with archived soil cores

Konza Prairie (KONZ) (Kansas)

NEON Domain 06 - Prairie grassland site in the Great Plains

Ordway-Swisher Biological Station (OSBS) (Florida)

NEON Domain 03 - Southeast longleaf pine and oak scrub ecosystem

W.K. Kellogg Biological Station (Hickory Corners, Michigan)

Michigan State University long-term ecological research site. Sarah Evans (MSU) is studying how agricultural management affects soil molecular properties, linking soil measurements to management decisions (tillage, cover crops, perennials) and ecosystem service outcomes. Summer 2024 campaign.

MSU Bioenergy Cropping Systems (Hickory Corners, Michigan)

Alexandra Kravchenko (MSU) sampling energy sorghum, switchgrass (perennial monoculture), restored prairie (perennial polyculture), and poplar (fast-growing woody species) to obtain high-resolution molecular, microbial, and structural soil data. Goal is understanding microscale interactions leading to soil carbon accrual under long-term bioenergy cropping systems. Spring 2025 campaign.

Eastern Cottonwood Bioenergy Plantation (Algoma, Mississippi)

Heidi Renninger (Mississippi State) studying soil carbon sequestration through eastern cottonwood short rotation woody crops for sustainable aviation fuel feedstocks. Quantifying carbon accrual rates and soil carbon processes in short rotation woody crop fields. Summer 2024 campaign.

ORNL Bioenergy Plant-Soil Site (Midland, Oregon)

Udaya Kalluri (ORNL) characterizing bioenergy plant-soil interactions and soil health under field conditions. Spring 2025 campaign.

WSU Potato Cropland Management (Mount Vernon, Washington)

Deirdre Griffin-LaHue (WSU) investigating four soil management systems along a disturbance gradient in potato-driven crop rotations. Evaluating practices to improve soil functions including water supply, drainage, residue breakdown, and nutrient cycling while addressing soil degradation from intensive tillage. Winter 2024 campaign.

Stanford Salinas Valley Vegetable Systems (Salinas, California)

Robert Jackson (Stanford) assessing cover-crop system effectiveness in reducing excess nitrogen fertilizer losses through leaching, runoff, and emissions in vegetable production systems. Winter 2024 campaign.

Umpqua National Forest Wildfire Sites (Umpqua National Forest, Oregon)

USDA Forest Service ecologist Devin McMahon collecting and comparing severely burned soils with soils in areas of little apparent fire impact. Sampling allows land managers to assess effects of severe wildfire and postfire management on soil physical, chemical, and biological properties. Soil analyses provide microbial community data to form baseline for discussing potential impacts of forest management. Summer 2024 campaign.

California Sage Scrub Fire Frequency Sites (Claremont, California)

Jason Keller (Claremont McKenna) sampling California sage scrub ecosystems experiencing nonnative invasion, urbanization, and changing fire frequency to analyze carbon/nitrogen shifts and microbial community changes. Winter 2024 campaign.

Rocky Mountain Snowpack Decline Sites (Crested Butte, Colorado)

Mariah Carbone (NAU) quantifying how declining snowpack and earlier snowmelt affect soil CO2 flux and plant-microbial processes across forest elevations. Winter 2024 campaign.

Blue River Drought Hydraulic Redistribution Site (Blue River, Oregon)

Alexander Takver (Oregon State) studying hydraulic redistribution affecting soil properties and carbon dynamics during drought conditions. Summer 2024 campaign.

Grinnell Glacier Climate Change Site (Grinnell Glacier, Glacier National Park, Montana)

Christine Foreman (Montana State) studying glacier retreat impacts on downstream ecosystems and microbial communities at this rapidly receding glacier. Summer 2024 campaign.

Unalaska Island Climate-Defense Site (Unalaska Island, Alaska)

Yu (Frank) Yang (University of Nevada, Reno) studying soil organic carbon dynamics under climate change at formerly used defense sites. Summer 2024 campaign.

Douglas-fir Forest Health Sites (Stabler, Washington)

James Lutz (Utah State) examining how belowground soil and microbial characteristics vary around large-diameter Douglas-fir trees at different life stages (healthy, declining, standing dead, decomposing logs). Winter 2024 campaign.

Smoot Hill Invasive Species Site (Smoot Hill, Eastern Washington)

Tanya Cheeke (WSU Tri-Cities) studying impacts of Ventenata dubia invasion on above- and below-ground communities in Palouse prairie ecosystem. Summer 2024 campaign.

Sevilleta National Wildlife Refuge (Sevilleta National Wildlife Refuge, New Mexico)

Rae DeVan (University of New Mexico) studying water availability and plant cycles affecting microbial activity in arid lands of the desert southwest. Summer 2024 campaign.

Jornada Experimental Range (Las Cruces, New Mexico)

Kalpana Kukreja (UT El Paso) investigating phosphorus acquisition through microbial distribution and organic acid production. Spring 2025 campaign.

Worcester Urban Soils Gradient (Worcester and Petersham, Massachusetts)

Matt Kaufman (Worcester State) examining urban soil properties across an urbanization gradient to understand anthropogenic impacts on soil composition. Spring 2025 campaign.

North Carolina Coastal Wetlands (Wilmington, North Carolina)

Lori Sutter (UNC Wilmington) comparing microbial and plant-driven ecosystem function across sites with varying salinity and tidal conditions in wetland and saline marshland. Spring 2025 campaign.

Studies 5

1000 Soils Pilot (Emily B. Graham)

Pilot study collecting standardized soil samples across US ecoregions to develop continental-scale molecular and microstructural soil database. Samples analyzed using FTICR-MS for organic matter composition, X-ray computed tomography for 3D pore structure, and metagenomics via JGI partnership. Includes geochemistry, texture, respiration, enzyme activities, and microbial biomass measurements.

Data modalities:

Metabolomics Metagenomics Imaging Data Biogeochemical Data

Keywords:

Soil Carbon Soil Organic Matter Carbon Cycling

Primary reference: doi:10.3389/fsoil.2023.1120425 - One thousand soils for molecular understanding of belowground carbon cycling

MONet-NEON First Collection (Sarah Leichty)

Advanced soil physical, chemical and biological characterization of soil cores from all ecoregions within the United States through partnership with National Ecological Observatory Network (NEON). Observational sampling September 2023 to July 2024.

Data modalities:

Metabolomics Metagenomics Biogeochemical Data

Keywords:

Soil Carbon Soil Microbiome

Source: Molecular Observation Network (MONet) – First Collection | NSF NEON
NEON project page describing the MONet-NEON collaboration, sampling timeline, sites involved, and data products generated.

MONet Soil Function Call (John Bargar)

First major MONet capability launched February 2023. Community soil core solicitation with standardized analysis workflows. JGI proposal 510110 for metagenome sequencing.

Data modalities:

Metabolomics Metagenomics Imaging Data

Keywords:

Soil Carbon Soil Organic Matter

Source: MONet Soil Function Call at EMSL DOE User Facility | JGI
JGI Genome Portal page with proposal details, metagenome sequencing projects, and links to released sequence data.

MONet Winter Soil Sampling 2024

Five selected projects: Douglas-fir forest function (Lutz, Utah State), potato cropland management (Griffin-LaHue, WSU), vegetable cropping nitrogen (Jackson, Stanford), snowpack decline effects (Carbone, NAU), sage scrub recovery (Keller, Claremont McKenna).

Data modalities:

Metagenomics Biogeochemical Data

Keywords:

Soil Carbon Carbon Cycling

Source: EMSL Selects Five Projects for MONet Winter Soil Sampling
EMSL news announcement listing the five selected projects, PIs, institutions, and research focus areas for the winter 2024 sampling campaign.

SOILS-AI Campaign (Sakthi Kumaran)

Soil Organic Indicators at Large Scale for Artificial Intelligence campaign targeting ten underrepresented soil orders to strengthen AI models for soil carbon dynamics. Applies pedotransfer functions to upscale measurements to continental scales.

Data modalities:

Metabolomics Metagenomics Imaging Data Biogeochemical Data

Keywords:

Soil Carbon Machine Learning Carbon Cycling

Source: SOILS-AI Campaign | EMSL
EMSL proposal call page describing the campaign goals, targeted soil orders, sampling protocols, and how to submit proposals.

Key Publications 2

doi:10.3389/fsoil.2023.1120425 One thousand soils for molecular understanding of belowground carbon cycling

MONet pilot collected standardized soil samples using molecular techniques including FTICR-MS and X-ray computed tomography to advance understanding of belowground carbon cycling.
Wildfire may result in oxidation of SOM and structural changes to soil pore networks that persist into deeper soils, with reduced soil respiration, microbial biomass, and enzyme activity.

doi:10.1029/2024GL113091 Scaling High-Resolution Soil Organic Matter Composition to Improve Predictions of Potential Soil Respiration Across the Continental United States

Machine learning can distill thousands of SOM formulas into tractable units for integration into soil respiration models.
In surface soils, SOM chemistry provides better estimates of potential soil respiration than soil physicochemistry alone; combining both yields the best prediction.

Datasets 1

1000 Soils Pilot Dataset

Comprehensive dataset from MONet 1000 Soils Pilot including geochemistry, texture, respiration, enzyme activities, FTICR-MS organic matter chemistry, microbial biomass C and N, water-extractable organic matter TOC/TDN, X-ray computed tomography metrics, metagenomes, and soil hydraulic properties. Interactive visualization at https://shinyproxy.emsl.pnnl.gov/app/1000soils

Repository: Zenodo

URL: https://zenodo.org/records/15328215

DOI: 10.5281/zenodo.15328215

Data type: multi-omics

Collaborators: Joint Genome Institute (sequencing and metagenome analysis), National Ecological Observatory Network (field sites and continuous sensing), National Microbiome Data Collaborative (microbiome metadata standards)